NCBI Conserved Domain Search

ninth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the ninth one.

Pssm-ID: 411840 Cd Length: 70 Bit Score: 131.26 E-value: 3.27e-36

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24655011  668 IVTEEVQIPPKYYNSIIGTGGKLISSIMEECGGVSIKFPNSDSKSDKVTIRGPKDDVEKAKVQLLELANE 737
Cdd:cd22412    1 IVEVEVEIPAKLHNSLIGAKGRLIRSIMEECGGVHIHFPPEGSGSDKVTIRGPKEDVEKAKKQLLELANE 70

eleventh type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the eleventh one.

Pssm-ID: 411842 Cd Length: 66 Bit Score: 128.96 E-value: 1.88e-35

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24655011  817 EGEVSVDPKHHKHFVAKRGFILHRISEECGGVMISFPRVGINSDKVTIKGAKDCIEAARQRIEEIV 882
Cdd:cd22414    1 EDEMTVDPKHHRHFVARRGQVLREIADEYGGVMVSFPRSGTQSDKVTLKGAKDCVEGAKKRILEIV 66

twelfth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the twelfth one.

Pssm-ID: 411843 [Multi-domain] Cd Length: 92 Bit Score: 129.73 E-value: 1.88e-35

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24655011  890 TIEVVIPQRHHRTIMGARGFKVQQVTFEFDVQIKFPDRDATEPVEGltnggsgengGENEGQEGEQEVEKEAEQEPVRQC 969
Cdd:cd22415    1 TIECVIPQKFHRTVMGAKGSRVQQITSEFDVQIKFPDRESNQPAPA----------ENGEGNGGEGVEGEAVDDNSPRKC 70

                         90       100
                 ....*....|....*....|..
gi 24655011  970 DVIRITGRIEKCEAAKQALLDL 991
Cdd:cd22415   71 DIIIITGKKENCEAAKEALLAL 92

thirteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the thirteenth one.

Pssm-ID: 411844 [Multi-domain] Cd Length: 78 Bit Score: 123.88 E-value: 1.40e-33

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 24655011  993 PIEEELSVPFDLHRTIIGPRGANVRQFMSKHDVHVELPPSELKSDVIKVCGTPARVAEAREALVKMIEDYEADRADRE 1070
Cdd:cd22416    1 PVTEEVNVPFDLHRFIIGQKGADVRKMMDEFDVNISIPPAELQSDIIKITGPPANVERAKAALLERVKELEAEKEDRE 78

tenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the tenth one.

Pssm-ID: 411841 [Multi-domain] Cd Length: 66 Bit Score: 116.59 E-value: 3.93e-31

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24655011  741 ASFTAEVRAKQQHHKFLIGKNGASIRKIRDATGARIIFPSNEDTDKEVITIIGKEESVKKAREQLE 806
Cdd:cd22413    1 NSFTVEIRAKPEYHRFLIGRGGANIRKIRDNTGARIIFPTARDEDQELITIIGTKEAVEKAKEELE 66

second type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the second one.

Pssm-ID: 411834 [Multi-domain] Cd Length: 75 Bit Score: 114.33 E-value: 3.82e-30

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 24655011  165 FSTQASRQVTVPREHFRVILGKGGQRLREIERVTATRINIPSQSDESEFITIAGTKEGIAQAEQEIRQLSAEQYK 239
Cdd:cd22406    1 LQTQASVTVNIPKEHHRFILGKKGKKLQELELKTATKIVIPRQEDNSDEIKITGTKEGIEKARHEIQLISDEQAK 75

seventh type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the seventh one.

Pssm-ID: 411838 Cd Length: 67 Bit Score: 113.91 E-value: 3.85e-30

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24655011  522 EKSKDVIIDRRLHRSIIGAKGEKIREVKDRYRQVTITIPTPQENTDIVKLRGPKEDVDKCHKDLLKL 588
Cdd:cd22410    1 EKTKDIIIEQRFHRTIIGQKGEKIREIRDKFPQVQITFPDPGSKSDVVTLRGPKDEVDKCYKYLKKL 67

fourteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fourteenth one.

Pssm-ID: 411845 [Multi-domain] Cd Length: 72 Bit Score: 113.46 E-value: 6.12e-30

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24655011 1074 FVLQVDVDTEFHSKLIGRHGAVINKLRADHDVIISLPKRDEPNDRIISITGYQANAEAARDAILEIVGDPE 1144
Cdd:cd22417    1 FTLTVEVDPKYHPKIIGRKGAVITKLRDDHDVNIQFPDKGDENDDEITITGYEKNAEAAKDAILKIVQELE 71

first type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the first one.

Pssm-ID: 411833 Cd Length: 69 Bit Score: 105.46 E-value: 3.85e-27

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24655011   95 THIVHVPCKERKSTESE-KFGEGESKRICQQITKETGAQIEIVSGKNQSLTFLIKGKQSELLDARRKIL 162
Cdd:cd22405    1 TQVFHVPLEERRYKESNqQFGEGEQAKICKDIMQKTGATIELSSAKDQSLTIMVTGKQSAVMKARREVL 69

fourth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fourth one.

Pssm-ID: 411836 [Multi-domain] Cd Length: 62 Bit Score: 103.40 E-value: 1.43e-26

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 24655011  315 TVSVEVAKPKHRYVIGPKGSTIAEILQLTGVSVEMPPNDSPSETITLRGPQVALGNALTVVY 376
Cdd:cd22408    1 TVSVEVPKSQHRFVIGPRGSTIQEILEETGCSVEVPPNDSDSETITLRGPADKLGAALTLVY 62

eighth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the eighth one.

Pssm-ID: 411839 [Multi-domain] Cd Length: 62 Bit Score: 100.74 E-value: 1.30e-25

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24655011  599 IEVPIFKQFHKFVIGKGGANIKKIRDETQTKIDLPAEGDTNEVIVITGKKENVLEAKERIQ 659
Cdd:cd22411    2 IKVPIFKQFHKNIIGKGGATIKKIREETNTRIDLPEENSDSDVITITGKKEDVEKARERIL 62

fifteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fifteenth one.

Pssm-ID: 411846 [Multi-domain] Cd Length: 69 Bit Score: 96.95 E-value: 3.14e-24

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24655011 1147 HREVIEIDKRIHPHLIGQRRRTIRKIIEDNKVNIKFSAD-DDNPNSIFISGKIEDVENVKELLFGMAED 1214
Cdd:cd22418    1 VTEEVEIDSRVHPRLIGARGKAIRKIMEDFKVDIRFPRSgDADPNLVTITGLEENVEECKDHLLNLEEE 69

fifth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fifth one.

Pssm-ID: 411837 [Multi-domain] Cd Length: 70 Bit Score: 92.26 E-value: 1.34e-22

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24655011  382 VKSVEINAAHWIHKYVIGRKGANMKQLEEDCPNVNVNCLE--DKIKLEGDPENVDRAVAYLSEIIKNYEE 449
Cdd:cd22409    1 VVVAEVSAPSWLHRFIIGKKGANIKKITQDLPKVHIEFTEgeDKIELEGPPEEVEVVREQLEAIVKELVA 70

third type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the third one.

Pssm-ID: 411835 [Multi-domain] Cd Length: 62 Bit Score: 86.49 E-value: 1.29e-20

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 24655011  243 DRITVPKVYHPFIVGPYSENLNKLQEETGARINVPPQQVQKDEIVISG 290
Cdd:cd22407    2 ERLDIPKVYHPFIAGPNNENVKELQEETGVRINIPPPSVNKDEIVVSG 49

sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the sixth one.

Pssm-ID: 411804 [Multi-domain] Cd Length: 68 Bit Score: 81.08 E-value: 1.07e-18

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 24655011  451 FTFEVMTVNPSYYKHIIGKAGANVNRLKDELKVNINIEERE-GQNNIRIEGPKEGVRQAQLELQEKID 517
Cdd:cd02394    1 MAFTTIEIDPKFHGHIIGKGGANIKRIREESGVSIRIPDDEaNSDEIRIEGSPEGVKKAKAEILELVD 68

sixth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the sixth one.

Pssm-ID: 411879 [Multi-domain] Cd Length: 69 Bit Score: 72.10 E-value: 1.85e-15

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24655011  169 ASRQVTVPREHFRVILGKGGQRLREIERVTATRINIPSQSDESEFITIAGTKEGIAQAEQEIRQLSAEQ 237
Cdd:cd22451    1 ASIDIDIPKEYHRAIIGKGGAVLRELEAETGCRIQVPKKDDPSGKIRITGARDGVEAATAKILNISDEE 69

K homology RNA-binding domain;

Pssm-ID: 197652 [Multi-domain] Cd Length: 68 Bit Score: 68.48 E-value: 2.94e-14

                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24655011     595 SSHIIEVPIFKQFHKFVIGKGGANIKKIRDETQTKIDLPAEGDTNEVIVITGKKENVLEAKERIQKI 661
Cdd:smart00322    1 DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSEERVVEITGPPENVEKAAELILEI 67

tenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the tenth one.

Pssm-ID: 411841 [Multi-domain] Cd Length: 66 Bit Score: 68.44 E-value: 3.09e-14

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 24655011  595 SSHIIEVPIFKQFHKFVIGKGGANIKKIRDETQTKIDLPAEGDTN-EVIVITGKKENVLEAKERI 658
Cdd:cd22413    1 NSFTVEIRAKPEYHRFLIGRGGANIRKIRDNTGARIIFPTARDEDqELITIIGTKEAVEKAKEEL 65

sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the sixth one.

Pssm-ID: 411804 [Multi-domain] Cd Length: 68 Bit Score: 68.37 E-value: 3.86e-14

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 24655011  600 EVPIFKQFHKFVIGKGGANIKKIRDETQTKIDLPAEGDTNEVIVITGKKENVLEAKERIQKI 661
Cdd:cd02394    5 TIEIDPKFHGHIIGKGGANIKRIREESGVSIRIPDDEANSDEIRIEGSPEGVKKAKAEILEL 66

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.

Pssm-ID: 459630 [Multi-domain] Cd Length: 65 Bit Score: 67.69 E-value: 6.40e-14

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 24655011    598 IIEVPIFKQFHKFVIGKGGANIKKIRDETQTKIDLPAEGD--TNEVIVITGKKENVLEAKERIQK 660
Cdd:pfam00013    1 TVEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSESegNERIVTITGTPEAVEAAKALIEE 65

second type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the second one.

Pssm-ID: 411834 [Multi-domain] Cd Length: 75 Bit Score: 66.57 E-value: 2.13e-13

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 24655011  599 IEVPIFKQFHKFVIGKGGANIKKIRDETQTKIDLPAEGDTNEVIVITGKKENVLEAKERIQKIQNELS 666
Cdd:cd22406    7 VTVNIPKEHHRFILGKKGKKLQELELKTATKIVIPRQEDNSDEIKITGTKEGIEKARHEIQLISDEQA 74

ninth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the ninth one.

Pssm-ID: 411840 Cd Length: 70 Bit Score: 65.78 E-value: 3.33e-13

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24655011  815 VTEGEVSVDPKHHKHFVAKRGFILHRISEECGGVMISFPRVGINSDKVTIKGAKDCIEAARQRIEEI 881
Cdd:cd22412    1 IVEVEVEIPAKLHNSLIGAKGRLIRSIMEECGGVHIHFPPEGSGSDKVTIRGPKEDVEKAKKQLLEL 67

sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the sixth one.

Pssm-ID: 411804 [Multi-domain] Cd Length: 68 Bit Score: 65.67 E-value: 3.44e-13

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24655011  668 IVTEEVQIPPKYYNSIIGTGGKLISSIMEECgGVSIKFPNSDSKSDKVTIRGPKDDVEKAKVQLLELAN 736
Cdd:cd02394    1 MAFTTIEIDPKFHGHIIGKGGANIKRIREES-GVSIRIPDDEANSDEIRIEGSPEGVKKAKAEILELVD 68

eleventh type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the eleventh one.

Pssm-ID: 411842 Cd Length: 66 Bit Score: 65.40 E-value: 3.90e-13

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24655011  671 EEVQIPPKYYNSIIGTGGKLISSIMEECGGVSIKFPNSDSKSDKVTIRGPKDDVEKAKVQLLEL 734
Cdd:cd22414    2 DEMTVDPKHHRHFVARRGQVLREIADEYGGVMVSFPRSGTQSDKVTLKGAKDCVEGAKKRILEI 65

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.

Pssm-ID: 459630 [Multi-domain] Cd Length: 65 Bit Score: 65.00 E-value: 4.92e-13

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 24655011    744 TAEVRAKQQHHKFLIGKNGASIRKIRDATGARIIFPSNEDTDKE-VITIIGKEESVKKAREQLEA 807
Cdd:pfam00013    1 TVEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSESEGNErIVTITGTPEAVEAAKALIEE 65

seventh type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the seventh one.

Pssm-ID: 411838 Cd Length: 67 Bit Score: 64.60 E-value: 6.60e-13

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 24655011  670 TEEVQIPPKYYNSIIGTGGKLISSIMEECGGVSIKFPNSDSKSDKVTIRGPKDDVEKAKVQLLEL 734
Cdd:cd22410    3 TKDIIIEQRFHRTIIGQKGEKIREIRDKFPQVQITFPDPGSKSDVVTLRGPKDEVDKCYKYLKKL 67

ninth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the ninth one.

Pssm-ID: 411840 Cd Length: 70 Bit Score: 62.70 E-value: 3.72e-12

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24655011  526 DVIIDRRLHRSIIGAKGEKIREVKDRYRQVTITIPTPQENTDIVKLRGPKEDVDKCHKDLLKLVKE 591
Cdd:cd22412    5 EVEIPAKLHNSLIGAKGRLIRSIMEECGGVHIHFPPEGSGSDKVTIRGPKEDVEKAKKQLLELANE 70

eighth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the eighth one.

Pssm-ID: 411839 [Multi-domain] Cd Length: 62 Bit Score: 62.61 E-value: 3.91e-12

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24655011  746 EVRAKQQHHKFLIGKNGASIRKIRDATGARIIFPsNEDTDKEVITIIGKEESVKKAREQLE 806
Cdd:cd22411    3 KVPIFKQFHKNIIGKGGATIKKIREETNTRIDLP-EENSDSDVITITGKKEDVEKARERIL 62

K homology RNA-binding domain;

Pssm-ID: 197652 [Multi-domain] Cd Length: 68 Bit Score: 62.70 E-value: 4.03e-12

                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 24655011     667 DIVTEEVQIPPKYYNSIIGTGGKLISSIMEECGgVSIKFPNSDSKSDKVTIRGPKDDVEKAKVQLLEL 734
Cdd:smart00322    1 DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETG-VKIDIPGPGSEERVVEITGPPENVEKAAELILEI 67

fifth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the fifth one.

Pssm-ID: 411878 Cd Length: 80 Bit Score: 62.68 E-value: 5.25e-12

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24655011  666 SDIVTEEVQIPPKYYNSIIGTGGKLISSIMEECGGVS--------IKFPNSDSKSDKVTIRGPKDDVEKAKVQLLELANE 737
Cdd:cd22450    1 EDEVTRTIKVDRKYHRTIIGPGGSTLRELISKAGGPTdrqeqarlVRFPNQNSESDEVVIRGPKKIVEKIIAEIEKIVEE 80

fourteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fourteenth one.

Pssm-ID: 411845 [Multi-domain] Cd Length: 72 Bit Score: 62.22 E-value: 6.29e-12

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24655011  599 IEVPIFKQFHKFVIGKGGANIKKIRDETQTKIDLPAEGDTNE-VIVITGKKENVLEAKERIQKIQNELSD 667
Cdd:cd22417    3 LTVEVDPKYHPKIIGRKGAVITKLRDDHDVNIQFPDKGDENDdEITITGYEKNAEAAKDAILKIVQELES 72

K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include an N-terminal extension and type I KH domains (e.g. hnRNP K) contain a C-terminal extension. Some KH-I superfamily members contain a divergent KH domain that lacks the RNA-binding GXXG motif. Some others have a mutated GXXG motif which may or may not have nucleic acid binding ability.

Pssm-ID: 411802 [Multi-domain] Cd Length: 63 Bit Score: 61.55 E-value: 8.22e-12

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 24655011  597 HIIEVPifKQFHKFVIGKGGANIKKIRDETQTKIDLPAEGDTNE--VIVITGKKENVLEAKERIQ 659
Cdd:cd00105    1 EEIEVP--SELVGLIIGKGGSTIKEIEEETGARIQIPKEGEGSGerVVTITGTPEAVEKAKELIE 63

third type I K homology (KH) RNA-binding domain found in protein bicaudal C homolog 1 (BICC1) and similar proteins; BICC1, also called Bic-C, is a mammalian homologue of Drosophila Bicaudal-C (dBic-C). BICC1 functions as an RNA-binding protein that represses the translation of selected mRNAs to control development. It regulates gene expression and modulates cell proliferation and apoptosis. BICC1 is a negative regulator of Wnt signaling. Increased levels of BICC1 may be associated with depression. Besides, BICC1 is a genetic determinant of osteoblastogenesis and bone mineral density. BICC1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411850 Cd Length: 67 Bit Score: 61.20 E-value: 1.22e-11

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 24655011  752 QHHKFLIGKNGASIRKIRDATGARIIFP--SNEDTDKEVITIIGKEESVKKAREQL 805
Cdd:cd22422   11 QHHLFMLGRNGSNIKHIMQRTGAQIHFPdpNNPPQRKSTVFISGSIDSVYLARQQL 66

third type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the third one.

Pssm-ID: 411835 [Multi-domain] Cd Length: 62 Bit Score: 59.91 E-value: 2.65e-11

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 24655011  600 EVPIFKQFHKFVIGKGGANIKKIRDETQTKIDLPAEGDTNEVIVITGKKENVLEAKERIQ 659
Cdd:cd22407    3 RLDIPKVYHPFIAGPNNENVKELQEETGVRINIPPPSVNKDEIVVSGEKEGVAQAVAKIK 62

third type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411876 Cd Length: 81 Bit Score: 60.62 E-value: 3.02e-11

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24655011  667 DIVTEEVQIPPKYYNSIIGTGGKLISSiMEECGGVSIKFPNSDSKS-----------DKVTIRGPKDDVEKAKVQLLEL 734
Cdd:cd22448    1 DETTLILKIPVQFHGSLIGQQGKYVNR-LQEKYGVKINFPRENSSSndtetkkpqapDEVTIRGGKKGVAEAKQELLEL 78

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.

Pssm-ID: 459630 [Multi-domain] Cd Length: 65 Bit Score: 59.60 E-value: 4.15e-11

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24655011    670 TEEVQIPPKYYNSIIGTGGKLISSIMEECgGVSIKFPNSDS--KSDKVTIRGPKDDVEKAKVQLLE 733
Cdd:pfam00013    1 TVEILVPSSLVGLIIGKGGSNIKEIREET-GAKIQIPPSESegNERIVTITGTPEAVEAAKALIEE 65

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.

Pssm-ID: 459630 [Multi-domain] Cd Length: 65 Bit Score: 58.83 E-value: 7.11e-11

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 24655011    170 SRQVTVPREHFRVILGKGGQRLREIERVTATRINIPSQSDE--SEFITIAGTKEGIAQAEQEIRQ 232
Cdd:pfam00013    1 TVEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSESEgnERIVTITGTPEAVEAAKALIEE 65

fourth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fourth one.

Pssm-ID: 411836 [Multi-domain] Cd Length: 62 Bit Score: 58.34 E-value: 1.03e-10

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 24655011  601 VPIFKQFHKFVIGKGGANIKKIRDETQTKIDLPAEGDTNEVIVITGKKENVLEAKERI 658
Cdd:cd22408    4 VEVPKSQHRFVIGPRGSTIQEILEETGCSVEVPPNDSDSETITLRGPADKLGAALTLV 61

K homology RNA-binding domain;

Pssm-ID: 197652 [Multi-domain] Cd Length: 68 Bit Score: 58.46 E-value: 1.29e-10

                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24655011     741 ASFTAEVRAKQQHHKFLIGKNGASIRKIRDATGARIIFPSNEDTDKeVITIIGKEESVKKAREQLEAII 809
Cdd:smart00322    1 DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSEER-VVEITGPPENVEKAAELILEIL 68

sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the sixth one.

Pssm-ID: 411804 [Multi-domain] Cd Length: 68 Bit Score: 57.97 E-value: 1.65e-10

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24655011 1148 REVIEIDKRIHPHLIGQRRRTIRKIIEDNKVNIKFSADDDNPNSIFISGKIEDVENVKELLFGMAE 1213
Cdd:cd02394    3 FTTIEIDPKFHGHIIGKGGANIKRIREESGVSIRIPDDEANSDEIRIEGSPEGVKKAKAEILELVD 68

fifth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the fifth one.

Pssm-ID: 411878 Cd Length: 80 Bit Score: 58.44 E-value: 1.85e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24655011  813 DEVTEgEVSVDPKHHKHFVAKRGFILHRISEECGGV--------MISFPRVGINSDKVTIKGAKDCIEAARQRIEEIVAD 884
Cdd:cd22450    2 DEVTR-TIKVDRKYHRTIIGPGGSTLRELISKAGGPtdrqeqarLVRFPNQNSESDEVVIRGPKKIVEKIIAEIEKIVEE 80

thirteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the thirteenth one.

Pssm-ID: 411844 [Multi-domain] Cd Length: 78 Bit Score: 57.63 E-value: 3.42e-10

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24655011  524 SKDVIIDRRLHRSIIGAKGEKIREVKDRYrQVTITIPTPQENTDIVKLRGPKEDVDKCHKDLLKLVKEIQE 594
Cdd:cd22416    3 TEEVNVPFDLHRFIIGQKGADVRKMMDEF-DVNISIPPAELQSDIIKITGPPANVERAKAALLERVKELEA 72

sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the sixth one.

Pssm-ID: 411804 [Multi-domain] Cd Length: 68 Bit Score: 57.20 E-value: 3.53e-10

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 24655011 1078 VDVDTEFHSKLIGRHGAVINKLRADHDVIISLPKRDEPNDRIIsITGYQANAEAARDAILEIV 1140
Cdd:cd02394    6 IEIDPKFHGHIIGKGGANIKRIREESGVSIRIPDDEANSDEIR-IEGSPEGVKKAKAEILELV 67

fourteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fourteenth one.

Pssm-ID: 411845 [Multi-domain] Cd Length: 72 Bit Score: 57.22 E-value: 3.70e-10

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 24655011  743 FTAEVRAKQQHHKFLIGKNGASIRKIRDATGARIIFPSNEDTDKEVITIIGKEESVKKAREQLEAIIKECDE 814
Cdd:cd22417    1 FTLTVEVDPKYHPKIIGRKGAVITKLRDDHDVNIQFPDKGDENDDEITITGYEKNAEAAKDAILKIVQELES 72

sixth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the sixth one.

Pssm-ID: 411879 [Multi-domain] Cd Length: 69 Bit Score: 56.69 E-value: 4.68e-10

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 24655011  597 HIIEVPIFKQFHKFVIGKGGANIKKIRDETQTKIDLPAEGDTNEVIVITGKKENVLEAKERIQKIQNE 664
Cdd:cd22451    1 ASIDIDIPKEYHRAIIGKGGAVLRELEAETGCRIQVPKKDDPSGKIRITGARDGVEAATAKILNISDE 68

fourteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fourteenth one.

Pssm-ID: 411845 [Multi-domain] Cd Length: 72 Bit Score: 56.83 E-value: 5.10e-10

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24655011  819 EVSVDPKHHKHFVAKRGFILHRISEEcGGVMISFPRVGI-NSDKVTIKGAKDCIEAARQRIEEIVADLE 886
Cdd:cd22417    4 TVEVDPKYHPKIIGRKGAVITKLRDD-HDVNIQFPDKGDeNDDEITITGYEKNAEAAKDAILKIVQELE 71

fourth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the fourth one.

Pssm-ID: 411877 [Multi-domain] Cd Length: 70 Bit Score: 56.51 E-value: 5.80e-10

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24655011  449 ENFTFEVMTVNPSYYKHIIGKAGANVNRLKDELKVNINIEEREGQNNIRIEGPKEGVRQAQLELQEKIDK 518
Cdd:cd22449    1 ENGYTVKFDVPAKYVPHIIGKKGANINKLREEYGVKIDFEDKTGEGNVEIKGSKKNVEEAKKRILSQIDE 70

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.

Pssm-ID: 459630 [Multi-domain] Cd Length: 65 Bit Score: 56.14 E-value: 6.60e-10

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 24655011   1075 VLQVDVDTEFHSKLIGRHGAVINKLRADHDVIISLPK-RDEPNDRIISITGYQANAEAARDAILE 1138
Cdd:pfam00013    1 TVEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPsESEGNERIVTITGTPEAVEAAKALIEE 65

K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include an N-terminal extension and type I KH domains (e.g. hnRNP K) contain a C-terminal extension. Some KH-I superfamily members contain a divergent KH domain that lacks the RNA-binding GXXG motif. Some others have a mutated GXXG motif which may or may not have nucleic acid binding ability.

Pssm-ID: 411802 [Multi-domain] Cd Length: 63 Bit Score: 56.15 E-value: 6.62e-10

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 24655011  751 QQHHKFLIGKNGASIRKIRDATGARIIFPSNEDTDKE-VITIIGKEESVKKAREQLE 806
Cdd:cd00105    7 SELVGLIIGKGGSTIKEIEEETGARIQIPKEGEGSGErVVTITGTPEAVEKAKELIE 63

second type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the second one.

Pssm-ID: 411834 [Multi-domain] Cd Length: 75 Bit Score: 55.78 E-value: 1.30e-09

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 24655011  744 TAEVRAKQQHHKFLIGKNGASIRKIRDATGARIIFPSNEDtDKEVITIIGKEESVKKAREQLEAIIKE 811
Cdd:cd22406    6 SVTVNIPKEHHRFILGKKGKKLQELELKTATKIVIPRQED-NSDEIKITGTKEGIEKARHEIQLISDE 72

fifteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fifteenth one.

Pssm-ID: 411846 [Multi-domain] Cd Length: 69 Bit Score: 55.35 E-value: 1.46e-09

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24655011  669 VTEEVQIPPKYYNSIIGTGGKLISSIMEECgGVSIKFPNSDSK-SDKVTIRGPKDDVEKAKVQLLELANE 737
Cdd:cd22418    1 VTEEVEIDSRVHPRLIGARGKAIRKIMEDF-KVDIRFPRSGDAdPNLVTITGLEENVEECKDHLLNLEEE 69

fifteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fifteenth one.

Pssm-ID: 411846 [Multi-domain] Cd Length: 69 Bit Score: 55.35 E-value: 1.67e-09

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24655011  524 SKDVIIDRRLHRSIIGAKGEKIREVKDRYRqVTITIPTPQ-ENTDIVKLRGPKEDVDKCHKDLLKLVKE 591
Cdd:cd22418    2 TEEVEIDSRVHPRLIGARGKAIRKIMEDFK-VDIRFPRSGdADPNLVTITGLEENVEECKDHLLNLEEE 69

type I K homology (KH) RNA-binding domain found in activating signal cointegrator 1 complex subunit 1 (ASCC1) and similar proteins; ASCC1, also called ASC-1 complex subunit p50, or Trip4 complex subunit p50, plays a role in DNA damage repair as component of the ASCC complex. It is part of the ASC-1 complex that enhances NF-kappa-B, SRF and AP1 transactivation. In cells responding to gastrin-activated paracrine signals, it is involved in the induction of SERPINB2 expression by gastrin. ASCC1 may also play a role in the development of neuromuscular junction.

Pssm-ID: 411847 [Multi-domain] Cd Length: 66 Bit Score: 54.89 E-value: 1.85e-09

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 24655011  598 IIEVPifKQFHKFVIGKGGANIKKIRDETQTKIDLPAEGDTNEvIVITGK-KENVLEAKERIQKI 661
Cdd:cd22419    4 SLDVP--SALFKFIIGKKGETKKRLESETKTQIRIPRQGKEGD-IVITGKdRSGVDSARTRIEVL 65

sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the sixth one.

Pssm-ID: 411804 [Multi-domain] Cd Length: 68 Bit Score: 54.88 E-value: 1.90e-09

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 24655011  753 HHKFLIGKNGASIRKIRDATGARIIFPSNEDTDKEVItIIGKEESVKKAREQLEAIIK 810
Cdd:cd02394   12 FHGHIIGKGGANIKRIREESGVSIRIPDDEANSDEIR-IEGSPEGVKKAKAEILELVD 68

fourth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fourth one.

Pssm-ID: 411836 [Multi-domain] Cd Length: 62 Bit Score: 54.48 E-value: 2.77e-09

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24655011  744 TAEVRAKQQHHKFLIGKNGASIRKIRDATGARIIFPSNeDTDKEVITIIGKEESVKKAREQ 804
Cdd:cd22408    1 TVSVEVPKSQHRFVIGPRGSTIQEILEETGCSVEVPPN-DSDSETITLRGPADKLGAALTL 60

seventh type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the seventh one.

Pssm-ID: 411880 [Multi-domain] Cd Length: 65 Bit Score: 54.25 E-value: 2.98e-09

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 24655011  608 HKFVIGKGGANIKKIRDETQTKIDLPAEGDTNEVIVITGKKENVLEAKERIQK 660
Cdd:cd22452   13 FGRIIGPGGSNINQIREKSGCFINVPKKNKESDVITLRGTKEGVEKAEEMIKK 65

third type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ribonucleoprotein K (hnRNP K) and similar proteins; hnRNP K, also called transformation up-regulated nuclear protein (TUNP), is a pre-mRNA binding protein that binds tenaciously to poly(C) sequences. It may be involved in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. It can also bind poly(C) single-stranded DNA. hnRNP K plays an important role in p53/TP53 response to DNA damage, acting at the level of both transcription activation and repression. hnRNP K contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411862 [Multi-domain] Cd Length: 74 Bit Score: 54.25 E-value: 3.73e-09

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24655011  168 QASRQVTVPREHFRVILGKGGQRLREIERVTATRINI--PSQSDESEFITIAGTKEGIAQAeQEIRQLSAEQYK 239
Cdd:cd22434    1 TTTTQVTIPKDLAGSIIGKGGQRIRQIRHESGASIKIdePLPGSEDRIITITGTQDQIQNA-QYLLQNSVKQYS 73

thirteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the thirteenth one.

Pssm-ID: 411844 [Multi-domain] Cd Length: 78 Bit Score: 54.16 E-value: 5.12e-09

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 24655011  599 IEVPIfkQFHKFVIGKGGANIKKIRDETQTKIDLPAEGDTNEVIVITGKKENVLEAK----ERIQKIQNELSD 667
Cdd:cd22416    6 VNVPF--DLHRFIIGQKGADVRKMMDEFDVNISIPPAELQSDIIKITGPPANVERAKaallERVKELEAEKED 76

K homology RNA-binding domain;

Pssm-ID: 197652 [Multi-domain] Cd Length: 68 Bit Score: 53.45 E-value: 6.40e-09

                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 24655011    1076 LQVDVDTEFHSKLIGRHGAVINKLRADHDVIISLPKRDEpNDRIISITGYQANAEAARDAILEIV 1140
Cdd:smart00322    5 IEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGS-EERVVEITGPPENVEKAAELILEIL 68

thirteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the thirteenth one.

Pssm-ID: 411844 [Multi-domain] Cd Length: 78 Bit Score: 53.77 E-value: 6.60e-09

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24655011  669 VTEEVQIPPKYYNSIIGTGGKLISSIMEECgGVSIKFPNSDSKSDKVTIRGPKDDVEKAKVQLLELANE 737
Cdd:cd22416    2 VTEEVNVPFDLHRFIIGQKGADVRKMMDEF-DVNISIPPAELQSDIIKITGPPANVERAKAALLERVKE 69

K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include an N-terminal extension and type I KH domains (e.g. hnRNP K) contain a C-terminal extension. Some KH-I superfamily members contain a divergent KH domain that lacks the RNA-binding GXXG motif. Some others have a mutated GXXG motif which may or may not have nucleic acid binding ability.

Pssm-ID: 411802 [Multi-domain] Cd Length: 63 Bit Score: 53.07 E-value: 7.07e-09

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 24655011  171 RQVTVPREHFRVILGKGGQRLREIERVTATRINIPSQSDESE--FITIAGTKEGIAQAEQEIR 231
Cdd:cd00105    1 EEIEVPSELVGLIIGKGGSTIKEIEEETGARIQIPKEGEGSGerVVTITGTPEAVEKAKELIE 63

fourteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fourteenth one.

Pssm-ID: 411845 [Multi-domain] Cd Length: 72 Bit Score: 53.36 E-value: 7.51e-09

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 24655011  456 MTVNPSYYKHIIGKAGANVNRLKDELKVNINIEER--EGQNNIRIEGPKEGVRQAQLELQEKIDKLEN 521
Cdd:cd22417    5 VEVDPKYHPKIIGRKGAVITKLRDDHDVNIQFPDKgdENDDEITITGYEKNAEAAKDAILKIVQELES 72

second type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411875 [Multi-domain] Cd Length: 80 Bit Score: 53.58 E-value: 7.66e-09

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 24655011  599 IEVPIFKQFHKFVIGKGGANIKKIRDETQTKIDLPAEGDTNEV----------IVITGKKENVLEAKERIQKI 661
Cdd:cd22447    6 LTVPIPASTRARIIGKKGANLKQIREKTGVRIDIPPRDADAAPadedddtmveVTITGDEFNVQHAKQRIEEI 78

fourth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fourth one.

Pssm-ID: 411836 [Multi-domain] Cd Length: 62 Bit Score: 52.94 E-value: 7.82e-09

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 24655011  998 LSVPFDLHRTIIGPRGANVRQFMSKHDVHVELPPSELKSDVIKVCGTPARVAEAREALV 1056
Cdd:cd22408    4 VEVPKSQHRFVIGPRGSTIQEILEETGCSVEVPPNDSDSETITLRGPADKLGAALTLVY 62

K homology RNA-binding domain;

Pssm-ID: 197652 [Multi-domain] Cd Length: 68 Bit Score: 53.45 E-value: 7.86e-09

                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24655011     993 PIEEELSVPFDLHRTIIGPRGANVRQFMSKHDVHVELPPSELKSDVIKVCGTPARVAEAREALVKMI 1059
Cdd:smart00322    2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSEERVVEITGPPENVEKAAELILEIL 68

sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the sixth one.

Pssm-ID: 411804 [Multi-domain] Cd Length: 68 Bit Score: 52.96 E-value: 1.07e-08

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 24655011  993 PIEEELSVPFDLHRTIIGPRGANVRQFMSKHDVHVELPPSELKSDVIKVCGTPARVAEAREALVKMIE 1060
Cdd:cd02394    1 MAFTTIEIDPKFHGHIIGKGGANIKRIREESGVSIRIPDDEANSDEIRIEGSPEGVKKAKAEILELVD 68

thirteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the thirteenth one.

Pssm-ID: 411844 [Multi-domain] Cd Length: 78 Bit Score: 53.00 E-value: 1.10e-08

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24655011 1077 QVDVDTEFHSKLIGRHGAVINKLRADHDVIISLPKRDEPNDrIISITGYQANAEAARDAILEIV 1140
Cdd:cd22416    5 EVNVPFDLHRFIIGQKGADVRKMMDEFDVNISIPPAELQSD-IIKITGPPANVERAKAALLERV 67

fifth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fifth one.

Pssm-ID: 411837 [Multi-domain] Cd Length: 70 Bit Score: 52.97 E-value: 1.22e-08

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24655011  744 TAEVRAKQQHHKFLIGKNGASIRKIR-DATGARIIFPSNEDTdkevITIIGKEESVKKAREQLEAIIKE 811
Cdd:cd22409    3 VAEVSAPSWLHRFIIGKKGANIKKITqDLPKVHIEFTEGEDK----IELEGPPEEVEVVREQLEAIVKE 67

fourteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fourteenth one.

Pssm-ID: 411845 [Multi-domain] Cd Length: 72 Bit Score: 52.21 E-value: 2.00e-08

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24655011  672 EVQIPPKYYNSIIGTGGKLISSIMEEcGGVSIKFPNSDS-KSDKVTIRGPKDDVEKAKVQLLELANE 737
Cdd:cd22417    4 TVEVDPKYHPKIIGRKGAVITKLRDD-HDVNIQFPDKGDeNDDEITITGYEKNAEAAKDAILKIVQE 69

fifth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fifth one.

Pssm-ID: 411837 [Multi-domain] Cd Length: 70 Bit Score: 52.20 E-value: 2.02e-08

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24655011  996 EELSVPFDLHRTIIGPRGANVRQFMSK-HDVHVELPPSElksDVIKVCGTPARVAEAREALVKMIEDYEA 1064
Cdd:cd22409    4 AEVSAPSWLHRFIIGKKGANIKKITQDlPKVHIEFTEGE---DKIELEGPPEEVEVVREQLEAIVKELVA 70

K homology RNA-binding domain;

Pssm-ID: 197652 [Multi-domain] Cd Length: 68 Bit Score: 51.91 E-value: 2.15e-08

                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 24655011     172 QVTVPREHFRVILGKGGQRLREIERVTATRINIPSQSDESEFITIAGTKEGIAQAEQEIRQL 233
Cdd:smart00322    6 EVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSEERVVEITGPPENVEKAAELILEI 67

eighth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the eighth one.

Pssm-ID: 411839 [Multi-domain] Cd Length: 62 Bit Score: 51.82 E-value: 2.33e-08

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 24655011 1076 LQVDVDTEFHSKLIGRHGAVINKLRADHDVIISLPKRDEpNDRIISITGYQANAEAARDAIL 1137
Cdd:cd22411    2 IKVPIFKQFHKNIIGKGGATIKKIREETNTRIDLPEENS-DSDVITITGKKEDVEKARERIL 62

tenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the tenth one.

Pssm-ID: 411841 [Multi-domain] Cd Length: 66 Bit Score: 51.88 E-value: 2.40e-08

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 24655011  173 VTVPREHFRVILGKGGQRLREIERVTATRINIPSQSDE-SEFITIAGTKEGIAQAEQEI 230
Cdd:cd22413    7 IRAKPEYHRFLIGRGGANIRKIRDNTGARIIFPTARDEdQELITIIGTKEAVEKAKEEL 65

first type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing protein (TDRKH) and similar proteins; TDRKH, also called tudor domain-containing protein 2 (TDRD2), is a mitochondria-anchored RNA-binding protein that is required for spermatogenesis and involved in piRNA biogenesis. It specifically recruits MIWI, but not MILI, to engage the piRNA pathway. TDRKH contains two K-homology (KH) RNA-binding domains and one tudor domain, which are involved in binding to RNA or single-strand DNA. The model corresponds to the first one.

Pssm-ID: 411856 [Multi-domain] Cd Length: 74 Bit Score: 51.95 E-value: 3.08e-08

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 24655011  598 IIEVPIFKQFHKFVIGKGGANIKKIRDETQTKIDLPAEGDTNE----VIVITGKKENVLEAKERIQKI 661
Cdd:cd22428    6 EIEMKVPREAVGLIIGRQGATIKQIQKETGARIDFKDEGSGGElperVLLIQGNPVQAQRAEEAIHQI 73

K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include an N-terminal extension and type I KH domains (e.g. hnRNP K) contain a C-terminal extension. Some KH-I superfamily members contain a divergent KH domain that lacks the RNA-binding GXXG motif. Some others have a mutated GXXG motif which may or may not have nucleic acid binding ability.

Pssm-ID: 411802 [Multi-domain] Cd Length: 63 Bit Score: 51.15 E-value: 3.32e-08

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 24655011 1076 LQVDVDTEFHSKLIGRHGAVINKLRADHDVIISLPKRDEPN-DRIISITGYQANAEAARDAIL 1137
Cdd:cd00105    1 EEIEVPSELVGLIIGKGGSTIKEIEEETGARIQIPKEGEGSgERVVTITGTPEAVEKAKELIE 63

third type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411876 Cd Length: 81 Bit Score: 51.76 E-value: 3.42e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24655011  521 NEKSKDVIIDRRLHRSIIGAKGEKIREVKDRYrQVTITIP-----------TPQENTDIVKLRGPKEDVDKCHKDLLKLV 589
Cdd:cd22448    1 DETTLILKIPVQFHGSLIGQQGKYVNRLQEKY-GVKINFPrensssndtetKKPQAPDEVTIRGGKKGVAEAKQELLELL 79

K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include an N-terminal extension and type I KH domains (e.g. hnRNP K) contain a C-terminal extension. Some KH-I superfamily members contain a divergent KH domain that lacks the RNA-binding GXXG motif. Some others have a mutated GXXG motif which may or may not have nucleic acid binding ability.

Pssm-ID: 411802 [Multi-domain] Cd Length: 63 Bit Score: 51.15 E-value: 3.52e-08

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 24655011  671 EEVQIPPKYYNSIIGTGGKLISSIMEECgGVSIKFP--NSDSKSDKVTIRGPKDDVEKAK 728
Cdd:cd00105    1 EEIEVPSELVGLIIGKGGSTIKEIEEET-GARIQIPkeGEGSGERVVTITGTPEAVEKAK 59

fourth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fourth one.

Pssm-ID: 411836 [Multi-domain] Cd Length: 62 Bit Score: 51.02 E-value: 3.93e-08

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 24655011  673 VQIPPKYYNSIIGTGGKLISSIMEECGgVSIKFPNSDSKSDKVTIRGPKDDVEKAK 728
Cdd:cd22408    4 VEVPKSQHRFVIGPRGSTIQEILEETG-CSVEVPPNDSDSETITLRGPADKLGAAL 58

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.

Pssm-ID: 459630 [Multi-domain] Cd Length: 65 Bit Score: 51.13 E-value: 4.52e-08

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 24655011    995 EEELSVPFDLHRTIIGPRGANVRQFMSKHDVHVELPPSE--LKSDVIKVCGTPARVAEAREALVK 1057
Cdd:pfam00013    1 TVEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSEseGNERIVTITGTPEAVEAAKALIEE 65

sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the sixth one.

Pssm-ID: 411804 [Multi-domain] Cd Length: 68 Bit Score: 51.03 E-value: 4.71e-08

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 24655011  523 KSKDVIIDRRLHRSIIGAKGEKIREVKDRYrQVTITIPTPQENTDIVKLRGPKEDVDKCHKDLLKLVK 590
Cdd:cd02394    2 AFTTIEIDPKFHGHIIGKGGANIKRIREES-GVSIRIPDDEANSDEIRIEGSPEGVKKAKAEILELVD 68

sixth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the sixth one.

Pssm-ID: 411879 [Multi-domain] Cd Length: 69 Bit Score: 50.92 E-value: 5.54e-08

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24655011  669 VTEEVQIPPKYYNSIIGTGGKLISSIMEECGgVSIKFPNSDSKSDKVTIRGPKDDVEKAKVQLLELANE 737
Cdd:cd22451    1 ASIDIDIPKEYHRAIIGKGGAVLRELEAETG-CRIQVPKKDDPSGKIRITGARDGVEAATAKILNISDE 68

fifteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fifteenth one.

Pssm-ID: 411846 [Multi-domain] Cd Length: 69 Bit Score: 50.73 E-value: 6.19e-08

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24655011  597 HIIEVPIFKQFHKFVIGKGGANIKKIRDETQTKIDLPAEGDTN-EVIVITGKKENVLEAKERIQKIQNE 664
Cdd:cd22418    1 VTEEVEIDSRVHPRLIGARGKAIRKIMEDFKVDIRFPRSGDADpNLVTITGLEENVEECKDHLLNLEEE 69

fourth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the fourth one.

Pssm-ID: 411877 [Multi-domain] Cd Length: 70 Bit Score: 50.73 E-value: 7.49e-08

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24655011  594 ESSHIIEVPIFKQFHKFVIGKGGANIKKIRDETQTKIDLPAEGDTNEViVITGKKENVLEAKERIQKIQNE 664
Cdd:cd22449    1 ENGYTVKFDVPAKYVPHIIGKKGANINKLREEYGVKIDFEDKTGEGNV-EIKGSKKNVEEAKKRILSQIDE 70

second type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411875 [Multi-domain] Cd Length: 80 Bit Score: 50.88 E-value: 8.49e-08

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24655011  756 FLIGKNGASIRKIRDATGARIIFP--------SNEDTDKEV-ITIIGKEESVKKAREQLEAIIK 810
Cdd:cd22447   17 RIIGKKGANLKQIREKTGVRIDIPprdadaapADEDDDTMVeVTITGDEFNVQHAKQRIEEIIS 80

seventh type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the seventh one.

Pssm-ID: 411880 [Multi-domain] Cd Length: 65 Bit Score: 50.01 E-value: 1.03e-07

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 24655011  743 FTAEVRAKQQHHKFLIGKNGASIRKIRDATGARIIFPSNeDTDKEVITIIGKEESVKKAREQLEA 807
Cdd:cd22452    2 FRGWIKVSPRYFGRIIGPGGSNINQIREKSGCFINVPKK-NKESDVITLRGTKEGVEKAEEMIKK 65

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.

Pssm-ID: 459630 [Multi-domain] Cd Length: 65 Bit Score: 49.97 E-value: 1.09e-07

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 24655011    315 TVSVEVAKPKHRYVIGPKGSTIAEILQLTGVSVEMPPNDSP--SETITLRGPQVALGNALTVVYQ 377
Cdd:pfam00013    1 TVEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSESEgnERIVTITGTPEAVEAAKALIEE 65

third type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the third one.

Pssm-ID: 411835 [Multi-domain] Cd Length: 62 Bit Score: 49.90 E-value: 1.16e-07

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 24655011  173 VTVPREHFRVILGKGGQRLREIERVTATRINIPSQSDESEFITIAGTKEGIAQAEQEIR 231
Cdd:cd22407    4 LDIPKVYHPFIAGPNNENVKELQEETGVRINIPPPSVNKDEIVVSGEKEGVAQAVAKIK 62

second type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the second one.

Pssm-ID: 411834 [Multi-domain] Cd Length: 75 Bit Score: 49.62 E-value: 1.82e-07

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 24655011  239 KKSSDRITVPKVYHPFIVGPYSENLNKLQEETGARINVPPQQVQKDEIVISG 290
Cdd:cd22406    3 TQASVTVNIPKEHHRFILGKKGKKLQELELKTATKIVIPRQEDNSDEIKITG 54

sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the sixth one.

Pssm-ID: 411804 [Multi-domain] Cd Length: 68 Bit Score: 49.49 E-value: 1.91e-07

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24655011  313 CSTVSVEVAKPKHRYVIGPKGSTIAEILQLTGVSVEMPPNDSPSETITLRGPQVALGNALTVVY 376
Cdd:cd02394    1 MAFTTIEIDPKFHGHIIGKGGANIKRIREESGVSIRIPDDEANSDEIRIEGSPEGVKKAKAEIL 64

eighth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the eighth one.

Pssm-ID: 411839 [Multi-domain] Cd Length: 62 Bit Score: 48.74 E-value: 2.31e-07

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 24655011  172 QVTVPREHFRVILGKGGQRLREIERVTATRINIPSQSDESEFITIAGTKEGIAQAEQEI 230
Cdd:cd22411    3 KVPIFKQFHKNIIGKGGATIKKIREETNTRIDLPEENSDSDVITITGKKEDVEKARERI 61

third type I K homology (KH) RNA-binding domain found in protein bicaudal C homolog 1 (BICC1) and similar proteins; BICC1, also called Bic-C, is a mammalian homologue of Drosophila Bicaudal-C (dBic-C). BICC1 functions as an RNA-binding protein that represses the translation of selected mRNAs to control development. It regulates gene expression and modulates cell proliferation and apoptosis. BICC1 is a negative regulator of Wnt signaling. Increased levels of BICC1 may be associated with depression. Besides, BICC1 is a genetic determinant of osteoblastogenesis and bone mineral density. BICC1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411850 Cd Length: 67 Bit Score: 48.49 E-value: 3.26e-07

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 24655011  603 IFKQFHKFVIGKGGANIKKIRDETQTKIDLPaegDTNE------VIVITGKKENVLEAKERI 658
Cdd:cd22422    8 IAPQHHLFMLGRNGSNIKHIMQRTGAQIHFP---DPNNppqrksTVFISGSIDSVYLARQQL 66

seventh type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the seventh one.

Pssm-ID: 411880 [Multi-domain] Cd Length: 65 Bit Score: 48.47 E-value: 3.76e-07

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 24655011  173 VTVPREHFRVILGKGGQRLREIERVTATRINIPSQSDESEFITIAGTKEGIAQAEQEI 230
Cdd:cd22452    6 IKVSPRYFGRIIGPGGSNINQIREKSGCFINVPKKNKESDVITLRGTKEGVEKAEEMI 63

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.

Pssm-ID: 459630 [Multi-domain] Cd Length: 65 Bit Score: 48.43 E-value: 3.98e-07

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24655011    454 EVMTVNPSYYKHIIGKAGANVNRLKDELKVNINI---EEREGQNNIRIEGPKEGVRQAQLELQE 514
Cdd:pfam00013    2 VEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIppsESEGNERIVTITGTPEAVEAAKALIEE 65

K homology RNA-binding domain;

Pssm-ID: 197652 [Multi-domain] Cd Length: 68 Bit Score: 48.45 E-value: 3.99e-07

                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24655011     454 EVMTVNPSYYKHIIGKAGANVNRLKDELKVNINIEEREGQNN-IRIEGPKEGVRQAQLELQEKI 516
Cdd:smart00322    5 IEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSEERvVEITGPPENVEKAAELILEIL 68

sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the sixth one.

Pssm-ID: 411804 [Multi-domain] Cd Length: 68 Bit Score: 48.34 E-value: 4.26e-07

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 24655011  169 ASRQVTVPREHFRVILGKGGQRLREIERVTATRINIPSQSDESEFITIAGTKEGIAQAEQEIRQL 233
Cdd:cd02394    2 AFTTIEIDPKFHGHIIGKGGANIKRIREESGVSIRIPDDEANSDEIRIEGSPEGVKKAKAEILEL 66

K homology RNA-binding domain;

Pssm-ID: 197652 [Multi-domain] Cd Length: 68 Bit Score: 48.45 E-value: 4.57e-07

                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|
gi 24655011     315 TVSVEVAKPKHRYVIGPKGSTIAEILQLTGVSVEMPPNDSPSETITLRGP 364
Cdd:smart00322    4 TIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSEERVVEITGP 53

sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the sixth one.

Pssm-ID: 411804 [Multi-domain] Cd Length: 68 Bit Score: 47.95 E-value: 5.08e-07

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24655011  381 SVKSVEINAAHwiHKYVIGRKGANMKQLEEDCpNVNVNCLE-----DKIKLEGDPENVDRAVAYLSEIIK 445
Cdd:cd02394    2 AFTTIEIDPKF--HGHIIGKGGANIKRIREES-GVSIRIPDdeansDEIRIEGSPEGVKKAKAEILELVD 68

fifth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the fifth one.

Pssm-ID: 411878 Cd Length: 80 Bit Score: 48.43 E-value: 5.60e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24655011  520 ENEKSKDVIIDRRLHRSIIGAKGEKIREV-------KDRYRQV-TITIPTPQENTDIVKLRGPKEDVDKCHKDLLKLVKE 591
Cdd:cd22450    1 EDEVTRTIKVDRKYHRTIIGPGGSTLRELiskaggpTDRQEQArLVRFPNQNSESDEVVIRGPKKIVEKIIAEIEKIVEE 80

fourth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the fourth one.

Pssm-ID: 411877 [Multi-domain] Cd Length: 70 Bit Score: 48.03 E-value: 5.86e-07

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24655011 1071 LRSFVLQVDVDTEFHSKLIGRHGAVINKLRADHDVIISLpkRDEPNDRIISITGYQANAEAARDAILEIV 1140
Cdd:cd22449    1 ENGYTVKFDVPAKYVPHIIGKKGANINKLREEYGVKIDF--EDKTGEGNVEIKGSKKNVEEAKKRILSQI 68

fifth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fifth one.

Pssm-ID: 411837 [Multi-domain] Cd Length: 70 Bit Score: 47.96 E-value: 6.16e-07

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 24655011  533 LHRSIIGAKGEKIREVKDRYRQVTITIPTPQentDIVKLRGPKEDVDKCHKDLLKLVKEIQE 594
Cdd:cd22409   12 LHRFIIGKKGANIKKITQDLPKVHIEFTEGE---DKIELEGPPEEVEVVREQLEAIVKELVA 70

type I K homology (KH) RNA-binding domain found in Mask family proteins; The Mask family includes Drosophila melanogaster ankyrin repeat and KH domain-containing protein Mask, and its mammalian homologues Mask1/ANKHD1 and Mask2/ANKRD17. Mask, also called multiple ankyrin repeat single KH domain-containing protein, is a large ankyrin repeat and KH domain-containing protein involved in Drosophila receptor tyrosine kinase signaling. It acts as a mediator of receptor tyrosine kinase (RTK) signaling and may act either downstream of MAPK or transduce signaling through a parallel branch of the RTK pathway. Mask is required for the development and organization of indirect flight muscle sarcomeres by regulating the formation of M line and H zone and the correct assembly of thick and thin filaments in the sarcomere. Mask1/ANKHD1, also called HIV-1 Vpr-binding ankyrin repeat protein, or multiple ankyrin repeats single KH domain, or Hmask, is highly expressed in various cancer tissues and is involved in cancer progression, including proliferation and invasion. Mask2/ANKRD17, also called ankyrin repeat protein 17, or gene trap ankyrin repeat protein (GTAR), or serologically defined breast cancer antigen NY-BR-16, is a ubiquitously expressed ankyrin factor essential for the vascular integrity during embryogenesis. It may be directly involved in the DNA replication process and play pivotal roles in cell cycle and DNA regulation. It is also involved in innate immune defense against bacteria and viruses.

Pssm-ID: 411832 [Multi-domain] Cd Length: 71 Bit Score: 47.98 E-value: 7.26e-07

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24655011  170 SRQVTVPREHFRVILGKGGQRLREIERVTATRINIPSQSDES--EFITIAGTKEGIAQAEQEIRQL 233
Cdd:cd22404    2 SKKVTVPNSAISRVIGRGGCNINAIREVSGAHIEIDKQKGEQgdRRITIKGSADATRQAAQLINAL 67

second type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411875 [Multi-domain] Cd Length: 80 Bit Score: 48.18 E-value: 7.37e-07

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24655011  166 STQASRQVTVPREHFRVILGKGGQRLREIERVTATRINIPSQSDESEF----------ITIAGTKEGIAQAEQEIRQ 232
Cdd:cd22447    1 SPKQNLTVPIPASTRARIIGKKGANLKQIREKTGVRIDIPPRDADAAPadedddtmveVTITGDEFNVQHAKQRIEE 77

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.

Pssm-ID: 459630 [Multi-domain] Cd Length: 65 Bit Score: 47.66 E-value: 7.83e-07

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 24655011    242 SDRITVPKVYHPFIVGPYSENLNKLQEETGARINVPPQQVQKDE--IVISG 290
Cdd:pfam00013    1 TVEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSESEGNEriVTITG 51

fifth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fifth one.

Pssm-ID: 411837 [Multi-domain] Cd Length: 70 Bit Score: 47.58 E-value: 7.95e-07

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 24655011  607 FHKFVIGKGGANIKKIRDET-QTKIDLPAEGDTnevIVITGKKENVLEAKERIQKIQNEL 665
Cdd:cd22409   12 LHRFIIGKKGANIKKITQDLpKVHIEFTEGEDK---IELEGPPEEVEVVREQLEAIVKEL 68

K homology RNA-binding domain;

Pssm-ID: 197652 [Multi-domain] Cd Length: 68 Bit Score: 47.68 E-value: 7.99e-07

                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24655011     521 NEKSKDVIIDRRLHRSIIGAKGEKIREVKDRYrQVTITIPTPQENTDIVKLRGPKEDVDKCHKDLLKLV 589
Cdd:smart00322    1 DPVTIEVLIPADKVGLIIGKGGSTIKKIEEET-GVKIDIPGPGSEERVVEITGPPENVEKAAELILEIL 68

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.

Pssm-ID: 459630 [Multi-domain] Cd Length: 65 Bit Score: 47.28 E-value: 8.55e-07

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 24655011   1149 EVIEIDKRIHPHLIGQRRRTIRKIIEDNKVNIKFSADDDNPNS--IFISGKIEDVENVKELL 1208
Cdd:pfam00013    2 VEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSESEGNEriVTITGTPEAVEAAKALI 63

fifth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the fifth one.

Pssm-ID: 411878 Cd Length: 80 Bit Score: 47.66 E-value: 9.69e-07

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 24655011  168 QASRQVTVPREHFRVILGKGGQRLREI---------ERVTATRINIPSQSDESEFITIAGTKEGIAQAEQEIRQLSAE 236
Cdd:cd22450    3 EVTRTIKVDRKYHRTIIGPGGSTLRELiskaggptdRQEQARLVRFPNQNSESDEVVIRGPKKIVEKIIAEIEKIVEE 80

fifteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fifteenth one.

Pssm-ID: 411846 [Multi-domain] Cd Length: 69 Bit Score: 47.26 E-value: 1.02e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 24655011  743 FTAEVRAKQQHHKFLIGKNGASIRKIRDATGARIIFPSNEDTDKEVITIIGKEESVKKAREQL 805
Cdd:cd22418    1 VTEEVEIDSRVHPRLIGARGKAIRKIMEDFKVDIRFPRSGDADPNLVTITGLEENVEECKDHL 63

third type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 and similar proteins; BTR1, also called Binding to ToMV RNA 1, is a negative regulator of tomato mosaic virus (ToMV) multiplication but has no effect on the multiplication of cucumber mosaic virus (CMV). BTR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411942 [Multi-domain] Cd Length: 71 Bit Score: 47.42 E-value: 1.05e-06

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24655011  170 SRQVTVPREHFRVILGKGGQRLREIERVTATRINIpsqSDESEFI--------TIAGTKEGIAQAEQEIRQ 232
Cdd:cd22514    2 SVTIGVPDEHIGAILGRGGRTINEIQQHSGARIKI---SDRGDFVsgtrnrkvTITGPQDAVQMAQYLLEQ 69

sixth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the sixth one.

Pssm-ID: 411879 [Multi-domain] Cd Length: 69 Bit Score: 47.06 E-value: 1.12e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 24655011 1078 VDVDTEFHSKLIGRHGAVINKLRADHDVIISLPKRDEPNDRiISITGYQANAEAARDAILEI 1139
Cdd:cd22451    5 IDIPKEYHRAIIGKGGAVLRELEAETGCRIQVPKKDDPSGK-IRITGARDGVEAATAKILNI 65

fourteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fourteenth one.

Pssm-ID: 411845 [Multi-domain] Cd Length: 72 Bit Score: 47.20 E-value: 1.18e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 24655011 1151 IEIDKRIHPHLIGQRRRTIRKIIEDNKVNIKF-SADDDNPNSIFISGKIEDVENVKELLFGMAEDYER 1217
Cdd:cd22417    5 VEVDPKYHPKIIGRKGAVITKLRDDHDVNIQFpDKGDENDDEITITGYEKNAEAAKDAILKIVQELES 72

ninth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the ninth one.

Pssm-ID: 411840 Cd Length: 70 Bit Score: 47.29 E-value: 1.20e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24655011 1149 EVIEIDKRIHPHLIGQRRRTIRKIIED-NKVNIKFSADDDNPNSIFISGKIEDVENVKELLFGMAED 1214
Cdd:cd22412    4 VEVEIPAKLHNSLIGAKGRLIRSIMEEcGGVHIHFPPEGSGSDKVTIRGPKEDVEKAKKQLLELANE 70

sixth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the sixth one.

Pssm-ID: 411879 [Multi-domain] Cd Length: 69 Bit Score: 47.06 E-value: 1.39e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 24655011  744 TAEVRAKQQHHKFLIGKNGASIRKIRDATGARIIFPsNEDTDKEVITIIGKEESVKKAREQLEAIIKE 811
Cdd:cd22451    2 SIDIDIPKEYHRAIIGKGGAVLRELEAETGCRIQVP-KKDDPSGKIRITGARDGVEAATAKILNISDE 68

third type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding proteins; The far upstream element-binding protein (FUBP) family includes FUBP1-3. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP proteins contain four K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411826 [Multi-domain] Cd Length: 67 Bit Score: 46.87 E-value: 1.40e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 24655011  599 IEVPIFKQFHKFVIGKGGANIKKIRDETQTKIDLPAEGDTNE--VIVITGKKENVLEAKERIQKI 661
Cdd:cd22398    2 MEVPVPRFAVGVVIGKGGEMIKKIQNETGARVQFKPDDGNSPdrICVITGPPDQVQHAARMIQEL 66

first type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the first one.

Pssm-ID: 411874 [Multi-domain] Cd Length: 86 Bit Score: 47.40 E-value: 1.47e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 24655011  756 FLIGKNGASIRKIRDATGARIIFP-------SNEDTDKEVITII--GKEESVKKAREQLEAIIKE 811
Cdd:cd22446   20 AIIGSRGKNLKSIQDKTGTKIQIPkrneegnYDEDDDDETVEISieGDAEGVELAKKEIEAIVKE 84

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.

Pssm-ID: 459630 [Multi-domain] Cd Length: 65 Bit Score: 46.89 E-value: 1.48e-06

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 24655011    527 VIIDRRLHRSIIGAKGEKIREVKDRYrQVTITIPTPQENT--DIVKLRGPKEDVDKCHKDLLK 587
Cdd:pfam00013    4 ILVPSSLVGLIIGKGGSNIKEIREET-GAKIQIPPSESEGneRIVTITGTPEAVEAAKALIEE 65

fourth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fourth one.

Pssm-ID: 411836 [Multi-domain] Cd Length: 62 Bit Score: 46.39 E-value: 1.71e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 24655011  524 SKDVIIDRRLHRSIIGAKGEKIREVKDRYrQVTITIPTPQENTDIVKLRGPKEDVDK 580
Cdd:cd22408    1 TVSVEVPKSQHRFVIGPRGSTIQEILEET-GCSVEVPPNDSDSETITLRGPADKLGA 56

K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include an N-terminal extension and type I KH domains (e.g. hnRNP K) contain a C-terminal extension. Some KH-I superfamily members contain a divergent KH domain that lacks the RNA-binding GXXG motif. Some others have a mutated GXXG motif which may or may not have nucleic acid binding ability.

Pssm-ID: 411802 [Multi-domain] Cd Length: 63 Bit Score: 46.14 E-value: 2.03e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 24655011  454 EVMTVNPSYYKHIIGKAGANVNRLKDELKVNINI---EEREGQNNIRIEGPKEGVRQAQLELQ 513
Cdd:cd00105    1 EEIEVPSELVGLIIGKGGSTIKEIEEETGARIQIpkeGEGSGERVVTITGTPEAVEKAKELIE 63

K homology RNA-binding domain;

Pssm-ID: 197652 [Multi-domain] Cd Length: 68 Bit Score: 46.52 E-value: 2.09e-06

                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24655011    1145 TLHREVIEIDKRIHPHLIGQRRRTIRKIIEDNKVNIKFSADDDNPNSIFISGKIEDVENVKELL 1208
Cdd:smart00322    1 DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSEERVVEITGPPENVEKAAELI 64

seventh type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the seventh one.

Pssm-ID: 411880 [Multi-domain] Cd Length: 65 Bit Score: 46.16 E-value: 2.52e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24655011 1078 VDVDTEFHSKLIGRHGAVINKLRADHDVIISLPKRDEPNDrIISITGYQANAEAARDAILE 1138
Cdd:cd22452    6 IKVSPRYFGRIIGPGGSNINQIREKSGCFINVPKKNKESD-VITLRGTKEGVEKAEEMIKK 65

tenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the tenth one.

Pssm-ID: 411841 [Multi-domain] Cd Length: 66 Bit Score: 46.10 E-value: 2.54e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24655011  667 DIVTEEVQIPPKYYNSIIGTGGKLISSIMEECGgVSIKFPNS-DSKSDKVTIRGPKDDVEKAKVQL 731
Cdd:cd22413    1 NSFTVEIRAKPEYHRFLIGRGGANIRKIRDNTG-ARIIFPTArDEDQELITIIGTKEAVEKAKEEL 65

K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include an N-terminal extension and type I KH domains (e.g. hnRNP K) contain a C-terminal extension. Some KH-I superfamily members contain a divergent KH domain that lacks the RNA-binding GXXG motif. Some others have a mutated GXXG motif which may or may not have nucleic acid binding ability.

Pssm-ID: 411802 [Multi-domain] Cd Length: 63 Bit Score: 46.14 E-value: 2.63e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 24655011 1149 EVIEIDKRIHPHLIGQRRRTIRKIIEDNKVNIKFSADDDNPNS--IFISGKIEDVENVKELL 1208
Cdd:cd00105    1 EEIEVPSELVGLIIGKGGSTIKEIEEETGARIQIPKEGEGSGErvVTITGTPEAVEKAKELI 62

type I K homology (KH) RNA-binding domain found in activating signal cointegrator 1 complex subunit 1 (ASCC1) and similar proteins; ASCC1, also called ASC-1 complex subunit p50, or Trip4 complex subunit p50, plays a role in DNA damage repair as component of the ASCC complex. It is part of the ASC-1 complex that enhances NF-kappa-B, SRF and AP1 transactivation. In cells responding to gastrin-activated paracrine signals, it is involved in the induction of SERPINB2 expression by gastrin. ASCC1 may also play a role in the development of neuromuscular junction.

Pssm-ID: 411847 [Multi-domain] Cd Length: 66 Bit Score: 46.03 E-value: 2.72e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 24655011  175 VPREHFRVILGKGGQRLREIERVTATRINIPSQSDESEfITIAGT-KEGIAQAEQEIRQL 233
Cdd:cd22419    7 VPSALFKFIIGKKGETKKRLESETKTQIRIPRQGKEGD-IVITGKdRSGVDSARTRIEVL 65

ninth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the ninth one.

Pssm-ID: 411840 Cd Length: 70 Bit Score: 46.13 E-value: 2.99e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24655011  994 IEEELSVPFDLHRTIIGPRGANVRQFMSKHD-VHVELPPSELKSDVIKVCGTPARVAEAREALVKMIED 1061
Cdd:cd22412    2 VEVEVEIPAKLHNSLIGAKGRLIRSIMEECGgVHIHFPPEGSGSDKVTIRGPKEDVEKAKKQLLELANE 70

thirteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the thirteenth one.

Pssm-ID: 411844 [Multi-domain] Cd Length: 78 Bit Score: 46.07 E-value: 3.67e-06

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24655011  454 EVMTVNPSYYKHIIGKAGANVNRLKDELKVNINIEEREGQNN-IRIEGPKEGVRQAQLELQEKIDKLENEK 523
Cdd:cd22416    4 EEVNVPFDLHRFIIGQKGADVRKMMDEFDVNISIPPAELQSDiIKITGPPANVERAKAALLERVKELEAEK 74

fifteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fifteenth one.

Pssm-ID: 411846 [Multi-domain] Cd Length: 69 Bit Score: 45.72 E-value: 3.79e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24655011  994 IEEELSVPFDLHRTIIGPRGANVRQFMSKHDVHVELPPSELK-SDVIKVCGTPARVAEAREALVKMIED 1061
Cdd:cd22418    1 VTEEVEIDSRVHPRLIGARGKAIRKIMEDFKVDIRFPRSGDAdPNLVTITGLEENVEECKDHLLNLEEE 69

K homology RNA-binding domain;

Pssm-ID: 197652 [Multi-domain] Cd Length: 68 Bit Score: 45.75 E-value: 3.84e-06

                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24655011     819 EVSVDPKHHKHFVAKRGFILHRISEECGgVMISFPRVGINSDKVTIKGAKDCIEAARQRIEEIV 882
Cdd:smart00322    6 EVLIPADKVGLIIGKGGSTIKKIEEETG-VKIDIPGPGSEERVVEITGPPENVEKAAELILEIL 68

third type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411876 Cd Length: 81 Bit Score: 45.98 E-value: 4.25e-06

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 24655011  452 TFEVMTVNPSYYKHIIGKAGANVNRLKDELKVNINIEEREGQNN------------IRIEGPKEGVRQAQLELQEKID 517
Cdd:cd22448    3 TTLILKIPVQFHGSLIGQQGKYVNRLQEKYGVKINFPRENSSSNdtetkkpqapdeVTIRGGKKGVAEAKQELLELLE 80

fifth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fifth one.

Pssm-ID: 411837 [Multi-domain] Cd Length: 70 Bit Score: 45.65 E-value: 4.25e-06

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24655011  668 IVTEEVQIPPKYYNSIIGTGGKLISSIMEECGGVSIKFPNsdsKSDKVTIRGPKDDVEKAKVQLLELANE 737
Cdd:cd22409    1 VVVAEVSAPSWLHRFIIGKKGANIKKITQDLPKVHIEFTE---GEDKIELEGPPEEVEVVREQLEAIVKE 67

seventh type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the seventh one.

Pssm-ID: 411880 [Multi-domain] Cd Length: 65 Bit Score: 45.39 E-value: 4.77e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 24655011  673 VQIPPKYYNSIIGTGGKLISSIMEEcGGVSIKFPNSDSKSDKVTIRGPKDDVEKA 727
Cdd:cd22452    6 IKVSPRYFGRIIGPGGSNINQIREK-SGCFINVPKKNKESDVITLRGTKEGVEKA 59

sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the sixth one.

Pssm-ID: 411804 [Multi-domain] Cd Length: 68 Bit Score: 45.25 E-value: 4.89e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24655011  816 TEGEVSVDPKHHKHFVAKRGFILHRISEECgGVMISFPRVGINSDKVTIKGAKDCIEAARQRIEEIV 882
Cdd:cd02394    2 AFTTIEIDPKFHGHIIGKGGANIKRIREES-GVSIRIPDDEANSDEIRIEGSPEGVKKAKAEILELV 67

fourth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the fourth one.

Pssm-ID: 411877 [Multi-domain] Cd Length: 70 Bit Score: 45.34 E-value: 5.01e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 24655011  670 TEEVQIPPKYYNSIIGTGGKLISSIMEECgGVSIKFpNSDSKSDKVTIRGPKDDVEKAKVQLLELANE 737
Cdd:cd22449    5 TVKFDVPAKYVPHIIGKKGANINKLREEY-GVKIDF-EDKTGEGNVEIKGSKKNVEEAKKRILSQIDE 70

fourteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fourteenth one.

Pssm-ID: 411845 [Multi-domain] Cd Length: 72 Bit Score: 45.28 E-value: 5.05e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24655011  526 DVIIDRRLHRSIIGAKGEKIREVKDRYrQVTITIPTP-QENTDIVKLRGPKEDVDKCHKDLLKLVKE 591
Cdd:cd22417    4 TVEVDPKYHPKIIGRKGAVITKLRDDH-DVNIQFPDKgDENDDEITITGYEKNAEAAKDAILKIVQE 69

fifth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fifth one.

Pssm-ID: 411837 [Multi-domain] Cd Length: 70 Bit Score: 45.26 E-value: 6.23e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 24655011 1157 IHPHLIGQRRRTIRKIIEDN-KVNIKFSADDDnpnSIFISGKIEDVENVKELLFGMAEDYER 1217
Cdd:cd22409   12 LHRFIIGKKGANIKKITQDLpKVHIEFTEGED---KIELEGPPEEVEVVREQLEAIVKELVA 70

third type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ribonucleoprotein K (hnRNP K) and similar proteins; hnRNP K, also called transformation up-regulated nuclear protein (TUNP), is a pre-mRNA binding protein that binds tenaciously to poly(C) sequences. It may be involved in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. It can also bind poly(C) single-stranded DNA. hnRNP K plays an important role in p53/TP53 response to DNA damage, acting at the level of both transcription activation and repression. hnRNP K contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411862 [Multi-domain] Cd Length: 74 Bit Score: 45.39 E-value: 6.28e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 24655011  611 VIGKGGANIKKIRDET--QTKIDLPAEGDTNEVIVITGKKENVLEAKERIQK 660
Cdd:cd22434   16 IIGKGGQRIRQIRHESgaSIKIDEPLPGSEDRIITITGTQDQIQNAQYLLQN 67

first type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing protein (TDRKH) and similar proteins; TDRKH, also called tudor domain-containing protein 2 (TDRD2), is a mitochondria-anchored RNA-binding protein that is required for spermatogenesis and involved in piRNA biogenesis. It specifically recruits MIWI, but not MILI, to engage the piRNA pathway. TDRKH contains two K-homology (KH) RNA-binding domains and one tudor domain, which are involved in binding to RNA or single-strand DNA. The model corresponds to the first one.

Pssm-ID: 411856 [Multi-domain] Cd Length: 74 Bit Score: 45.02 E-value: 6.66e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24655011  746 EVRAKQQHHKFLIGKNGASIRKIRDATGARIIFP---SNEDTDKEVITIIGKEESVKKAREQLEAII 809
Cdd:cd22428    8 EMKVPREAVGLIIGRQGATIKQIQKETGARIDFKdegSGGELPERVLLIQGNPVQAQRAEEAIHQII 74

second type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 mRNA-binding protein (IGF2BP) family; The IGF2BP family includes three members: IGF2BP1/IMP-1/ CRD-BP/ VICKZ1, IGF2BP2/IMP-2/ VICKZ2, and IGF2BP3/IMP-3/VICKZ3, which are RNA-binding factors that recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). They function by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. IGF2BP proteins contain four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the second one.

Pssm-ID: 411829 [Multi-domain] Cd Length: 72 Bit Score: 44.91 E-value: 6.81e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 24655011  183 ILGKGGQRLREIERVTATRINIPSQSDESEF-----ITIAGTKEGIAQAEQEI 230
Cdd:cd22401   14 LIGKDGRNIKKIMEDTNTKITISSLQDLTSYnpertITIKGSLEAMSEAESLI 66

K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include an N-terminal extension and type I KH domains (e.g. hnRNP K) contain a C-terminal extension. Some KH-I superfamily members contain a divergent KH domain that lacks the RNA-binding GXXG motif. Some others have a mutated GXXG motif which may or may not have nucleic acid binding ability.

Pssm-ID: 411802 [Multi-domain] Cd Length: 63 Bit Score: 44.60 E-value: 7.07e-06

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 24655011  996 EELSVPFDLHRTIIGPRGANVRQFMSKHDVHVELPPSELKSD--VIKVCGTPARVAEAREAL 1055
Cdd:cd00105    1 EEIEVPSELVGLIIGKGGSTIKEIEEETGARIQIPKEGEGSGerVVTITGTPEAVEKAKELI 62

polynucleotide phosphorylase/polyadenylase; Provisional

Pssm-ID: 236995 [Multi-domain] Cd Length: 693 Bit Score: 50.43 E-value: 7.09e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 24655011   611 VIGKGGANIKKIRDETQTKIDLpaeGDTNEVIVITGKKENVLEAKERIQKIQNE 664
Cdd:PRK11824  568 VIGPGGKTIREITEETGAKIDI---EDDGTVKIAATDGEAAEAAKERIEGITAE 618

second type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ribonucleoprotein K (hnRNP K) and similar proteins; hnRNP K, also called transformation up-regulated nuclear protein (TUNP), is a pre-mRNA binding protein that binds tenaciously to poly(C) sequences. It may be involved in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. It can also bind poly(C) single-stranded DNA. hnRNP K plays an important role in p53/TP53 response to DNA damage, acting at the level of both transcription activation and repression. hnRNP K contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411861 [Multi-domain] Cd Length: 70 Bit Score: 44.94 E-value: 8.19e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 24655011  611 VIGKGGANIKKIRDETQTKIDL---PAEGDTNEVIVITGKKENVLEAKERI 658
Cdd:cd22433   16 IIGRAGFKIKELREKTGATIKVyseCCPRSTDRVVQIGGKPDKVVECIREI 66

second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein PEPPER and similar proteins; The family includes a group of plant RNA-binding KH domain-containing proteins, such as PEPPER, flowering locus K homology domain protein (FLK), RNA-binding KH domain-containing protein RCF3 and KH domain-containing protein HEN4. PEPPER regulates vegetative and gynoecium development. It acts as a positive regulator of the central floral repressor FLOWERING LOCUS C. In concert with HUA2, PEPPER antagonizes FLK by positively regulating FLC probably at transcriptional and post-transcriptional levels, and thus acts as a negative regulator of flowering. FLK, also called flowering locus KH domain protein, regulates positively flowering by repressing FLC expression and post-transcriptional modification. PEPPER and FLK contain three K-homology (KH) RNA-binding domains. RCF3, also called protein ENHANCED STRESS RESPONSE 1 (ESR1), or protein HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5), or protein REGULATOR OF CBF GENE EXPRESSION 3, or protein SHINY 1 (SHI1), acts as negative regulator of osmotic stress-induced gene expression. It is involved in the regulation of thermotolerance responses under heat stress. It functions as an upstream regulator of heat stress transcription factor (HSF) genes. HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. RCF3 and HEN4 contain five KH RNA-binding domains. The model corresponds to the KH2 domain of PEPPER and FLK, as well as KH2 and KH4 domains of RCF3 and HEN4.

Pssm-ID: 411888 [Multi-domain] Cd Length: 73 Bit Score: 44.92 E-value: 8.37e-06

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 24655011  611 VIGKGGANIKKIRDETQTKIDLPAEGD-------TNEVIVITGKKENVLEAKERI 658
Cdd:cd22460   14 LIGKGGAIIKQIREESGASVRILPEEElppcaspDDRVVQISGEAQAVKKALELV 68

fourteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fourteenth one.

Pssm-ID: 411845 [Multi-domain] Cd Length: 72 Bit Score: 44.89 E-value: 8.82e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24655011  890 TIEVVIPQRHHRTIMGARGFKVQQVTFEFDVQIKFPDRDATEPvegltnggsgenggenegqegeqevekeaeqepvrqc 969
Cdd:cd22417    2 TLTVEVDPKYHPKIIGRKGAVITKLRDDHDVNIQFPDKGDEND------------------------------------- 44

                         90       100
                 ....*....|....*....|...
gi 24655011  970 DVIRITGRIEKCEAAKQALLDLI 992
Cdd:cd22417   45 DEITITGYEKNAEAAKDAILKIV 67

third type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ventral antigen (Nova); The family includes two related neuronal RNA-binding proteins, Nova-1 and Nova-2. Nova-1, also called onconeural ventral antigen 1, or paraneoplastic Ri antigen, or ventral neuron-specific protein 1, may regulate RNA splicing or metabolism in a specific subset of developing neurons. It interacts with RNA containing repeats of the YCAY sequence. It is a brain-enriched splicing factor regulating neuronal alternative splicing. Nova-1 is involved in neurological disorders and carcinogenesis. Nova-2, also called astrocytic NOVA1-like RNA-binding protein, is a neuronal RNA-binding protein expressed in a broader central nervous system (CNS) distribution than Nova-1. It functions in neuronal RNA metabolism. NOVA family proteins contain three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411807 [Multi-domain] Cd Length: 71 Bit Score: 44.49 E-value: 1.11e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24655011  172 QVTVPREHFRVILGKGGQRLREIERVTATRINIpsqSDESEFI--------TIAGTKEGIAQAEQEIRQ 232
Cdd:cd09031    4 ELEVPENLVGAILGKGGKTLVEIQELTGARIQI---SKKGEFVpgtrnrkvTITGTPAAVQAAQYLIEQ 69

seventh type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the seventh one.

Pssm-ID: 411880 [Multi-domain] Cd Length: 65 Bit Score: 44.23 E-value: 1.21e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 24655011  458 VNPSYYKHIIGKAGANVNRLKDELKVNINIEEREGQNN-IRIEGPKEGVRQAQLELQE 514
Cdd:cd22452    8 VSPRYFGRIIGPGGSNINQIREKSGCFINVPKKNKESDvITLRGTKEGVEKAEEMIKK 65

first type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding proteins; The far upstream element-binding protein (FUBP) family includes FUBP1-3. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP proteins contain four K-homology (KH) RNA-binding domains. The model corresponds to the first one.

Pssm-ID: 411824 [Multi-domain] Cd Length: 68 Bit Score: 44.17 E-value: 1.23e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 24655011  610 FVIGKGGANIKKIRDETQTKIDLPAE--GDTNEVIVITGKKENVLEAKERIQKI 661
Cdd:cd22396   14 LIIGRGGEQINRLQAESGAKIQIAPDsgGLPERPCTLTGTPDAIETAKRLIDQI 67

type I K homology (KH) RNA-binding domain found in Drosophila melanogaster eukaryotic translation initiation factor 4E-binding protein Mextli and similar proteins; Mextli is a novel eukaryotic translation initiation factor 4E-binding protein that promotes translation in Drosophila melanogaster.

Pssm-ID: 411882 [Multi-domain] Cd Length: 71 Bit Score: 44.23 E-value: 1.26e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 24655011  611 VIGKGGANIKKIRDETQTKI--DLPAEGDTNEVIVITGKKENVLEAKERI 658
Cdd:cd22454   18 VIGKGGETIKRIEALTDTVItfERVNGGSPNREVQITGSPDNVAAAKRLI 67

third type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding proteins (PCBPs); The PCBP family, also known as hnRNP E family, comprises four members, PCBP1-4, which are RNA-binding proteins that interact in a sequence-specific manner with single-stranded poly(C) sequences. They are mainly involved in various posttranscriptional regulations, including mRNA stabilization or translational activation/silencing. Besides, PCBPs may share iron chaperone activity. PCBPs contain three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411867 [Multi-domain] Cd Length: 68 Bit Score: 44.14 E-value: 1.41e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 24655011  168 QASRQVTVPREHFRVILGKGGQRLREIERVTATRINIPSQSDES--EFITIAGTKEGIAQAEQEIRQL 233
Cdd:cd22439    1 QTTQEITIPNDLIGCIIGKGGTKINEIRQLSGATIKIANSEDGSteRSVTITGTPEAVSLAQYLINAR 68

second type I K homology (KH) RNA-binding domain found in the family of MEX-3 RNA-binding proteins; The MEX-3 protein family includes four members, MEX3A/RKHD4, MEX3B/RKHD3/RNF195, MEX3C/ RKHD2/RNF194, and MEX3D/RKHD1/RNF193/TINO. They are homologous of Caenorhabditis elegans MEX-3 protein, a translational regulator that specifies the posterior blastomere identity in the early embryo and contributes to the maintenance of the germline totipotency. Mex-3 proteins are RNA-binding phosphoproteins involved in post-transcriptional regulatory mechanisms. They are characterized by containing two K-homology (KH) RNA-binding domains and a C-terminal RING finger. They bind RNA through their KH domains and shuttle between the nucleus and the cytoplasm via the CRM1-dependent export pathway. The model corresponds to the second KH domain.

Pssm-ID: 411852 [Multi-domain] Cd Length: 72 Bit Score: 43.86 E-value: 1.82e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 24655011  611 VIGKGGANIKKIRDETQTKIDLPAEgDTNEVIVITGKKENVLEAKERIQK 660
Cdd:cd22424   18 VVGPKGATIKRIQQQTHTYIVTPSR-DKEPVFEVTGMPENVERAREEIEA 66

third type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411876 Cd Length: 81 Bit Score: 44.05 E-value: 1.88e-05

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24655011  594 ESSHIIEVPIfkQFHKFVIGKGGANIKKIRDETQTKIDLPAEGDTN-----------EVIVITGKKENVLEAKERI 658
Cdd:cd22448    2 ETTLILKIPV--QFHGSLIGQQGKYVNRLQEKYGVKINFPRENSSSndtetkkpqapDEVTIRGGKKGVAEAKQEL 75

type I K homology (KH) RNA-binding domain found in polyribonucleotide nucleotidyltransferase (PNPase) and similar proteins; PNPase, also called polynucleotide phosphorylase, is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. It catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction. It is also involved, along with RNase II, in tRNA processing. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. The model corresponds to the KH domain.

Pssm-ID: 411803 [Multi-domain] Cd Length: 70 Bit Score: 43.62 E-value: 1.91e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 24655011  611 VIGKGGANIKKIRDETQTKIDLpaeGDTNEVIVITGKKENVLEAKERIQKIQNE 664
Cdd:cd02393   18 VIGPGGKTIRAIIEETGAKIDI---EDDGTVTIFATDKESAEAAKAMIEDIVAE 68

tenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the tenth one.

Pssm-ID: 411841 [Multi-domain] Cd Length: 66 Bit Score: 43.40 E-value: 2.12e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 24655011  450 NFTFEVMTVNPSYYKHIIGKAGANVNRLKDELKVNINI--EEREGQNNIRIEGPKEGVRQAQLEL 512
Cdd:cd22413    1 NSFTVEIRAKPEYHRFLIGRGGANIRKIRDNTGARIIFptARDEDQELITIIGTKEAVEKAKEEL 65

K homology RNA-binding domain;

Pssm-ID: 197652 [Multi-domain] Cd Length: 68 Bit Score: 43.44 E-value: 2.55e-05

                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|..
gi 24655011     239 KKSSDRITVPKVYHPFIVGPYSENLNKLQEETGARINVPPQQVQKDEIVISG 290
Cdd:smart00322    1 DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSEERVVEITG 52

third type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411876 Cd Length: 81 Bit Score: 43.67 E-value: 2.62e-05

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 24655011  744 TAEVRAKQQHHKFLIGKNGASIRKIRDATGARIIFPSNEDTDKEV----------ITIIGKEESVKKAREQL 805
Cdd:cd22448    4 TLILKIPVQFHGSLIGQQGKYVNRLQEKYGVKINFPRENSSSNDTetkkpqapdeVTIRGGKKGVAEAKQEL 75

second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein PEPPER and similar proteins; The family includes a group of plant RNA-binding KH domain-containing proteins, such as PEPPER, flowering locus K homology domain protein (FLK), RNA-binding KH domain-containing protein RCF3 and KH domain-containing protein HEN4. PEPPER regulates vegetative and gynoecium development. It acts as a positive regulator of the central floral repressor FLOWERING LOCUS C. In concert with HUA2, PEPPER antagonizes FLK by positively regulating FLC probably at transcriptional and post-transcriptional levels, and thus acts as a negative regulator of flowering. FLK, also called flowering locus KH domain protein, regulates positively flowering by repressing FLC expression and post-transcriptional modification. PEPPER and FLK contain three K-homology (KH) RNA-binding domains. RCF3, also called protein ENHANCED STRESS RESPONSE 1 (ESR1), or protein HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5), or protein REGULATOR OF CBF GENE EXPRESSION 3, or protein SHINY 1 (SHI1), acts as negative regulator of osmotic stress-induced gene expression. It is involved in the regulation of thermotolerance responses under heat stress. It functions as an upstream regulator of heat stress transcription factor (HSF) genes. HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. RCF3 and HEN4 contain five KH RNA-binding domains. The model corresponds to the KH2 domain of PEPPER and FLK, as well as KH2 and KH4 domains of RCF3 and HEN4.

Pssm-ID: 411888 [Multi-domain] Cd Length: 73 Bit Score: 43.38 E-value: 2.74e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 24655011  757 LIGKNGASIRKIRDATGARI-IFPSNE-----DTDKEVITIIGKEESVKKAreqLEAI 808
Cdd:cd22460   14 LIGKGGAIIKQIREESGASVrILPEEElppcaSPDDRVVQISGEAQAVKKA---LELV 68

fourth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fourth one.

Pssm-ID: 411836 [Multi-domain] Cd Length: 62 Bit Score: 42.93 E-value: 3.35e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 24655011 1150 VIEIDKRIHPHLIGQRRRTIRKIIEDNKVNIKFSADDDNPNSIFISGKIEDVENVKEL 1207
Cdd:cd22408    3 SVEVPKSQHRFVIGPRGSTIQEILEETGCSVEVPPNDSDSETITLRGPADKLGAALTL 60

second type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 mRNA-binding protein (IGF2BP) family; The IGF2BP family includes three members: IGF2BP1/IMP-1/ CRD-BP/ VICKZ1, IGF2BP2/IMP-2/ VICKZ2, and IGF2BP3/IMP-3/VICKZ3, which are RNA-binding factors that recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). They function by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. IGF2BP proteins contain four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the second one.

Pssm-ID: 411829 [Multi-domain] Cd Length: 72 Bit Score: 42.98 E-value: 3.68e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 24655011  757 LIGKNGASIRKIRDATGARIIFPSNED----TDKEVITIIGKEESVKKAREQLEAIIKE 811
Cdd:cd22401   14 LIGKDGRNIKKIMEDTNTKITISSLQDltsyNPERTITIKGSLEAMSEAESLISEKLRE 72

eleventh type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the eleventh one.

Pssm-ID: 411842 Cd Length: 66 Bit Score: 42.68 E-value: 3.77e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24655011  526 DVIIDRRLHRSIIGAKGEKIREVKDRYRQVTITIPTPQENTDIVKLRGPKEDVDKCHKDLLKLV 589
Cdd:cd22414    3 EMTVDPKHHRHFVARRGQVLREIADEYGGVMVSFPRSGTQSDKVTLKGAKDCVEGAKKRILEIV 66

twelfth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the twelfth one.

Pssm-ID: 411843 [Multi-domain] Cd Length: 92 Bit Score: 43.44 E-value: 3.78e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24655011  997 ELSVPFDLHRTIIGPRGANVRQFMSKHDVHVELPPSElksdvikvcgtPARVAEAREALVKMIEDYEADRADrelrsfvl 1076
Cdd:cd22415    3 ECVIPQKFHRTVMGAKGSRVQQITSEFDVQIKFPDRE-----------SNQPAPAENGEGNGGEGVEGEAVD-------- 63

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 24655011 1077 qvDVDTEfhskligrhgavinklradhdviislpKRDepndrIISITGYQANAEAARDAILE 1138
Cdd:cd22415   64 --DNSPR---------------------------KCD-----IIIITGKKENCEAAKEALLA 91

type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe meiotically up-regulated gene 60 protein (MUG60) and similar proteins; MUG60 is a KH domain-containing protein that has a role in meiosis. The family also contains Saccharomyces cerevisiae KH domain-containing protein YLL032C.

Pssm-ID: 411881 [Multi-domain] Cd Length: 72 Bit Score: 43.12 E-value: 3.87e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 24655011  675 IPPKYYNSIIGTGGKLISSIMEECgGVSIKFPNS-----DSKSDKVTIRGPKDDVE 725
Cdd:cd22453    8 VPEKYHKRIIGKGGQNIQRIMKKY-NVFIKFSNAndradNYYPDNVVIRTPAKNAA 62

thirteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the thirteenth one.

Pssm-ID: 411844 [Multi-domain] Cd Length: 78 Bit Score: 42.99 E-value: 3.88e-05

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24655011  744 TAEVRAKQQHHKFLIGKNGASIRKIRDATGARIIFPSNEDTDkEVITIIGKEESVKKAREQLEAIIKECDE 814
Cdd:cd22416    3 TEEVNVPFDLHRFIIGQKGADVRKMMDEFDVNISIPPAELQS-DIIKITGPPANVERAKAALLERVKELEA 72

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.

Pssm-ID: 459630 [Multi-domain] Cd Length: 65 Bit Score: 42.65 E-value: 3.92e-05

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24655011    819 EVSVDPKHHKHFVAKRGFILHRISEECGgVMISFPR--VGINSDKVTIKGAKDCIEAARQRIEE 880
Cdd:pfam00013    3 EILVPSSLVGLIIGKGGSNIKEIREETG-AKIQIPPseSEGNERIVTITGTPEAVEAAKALIEE 65

tenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the tenth one.

Pssm-ID: 411841 [Multi-domain] Cd Length: 66 Bit Score: 42.63 E-value: 4.25e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 24655011 1158 HPHLIGQRRRTIRKIIEDNKVNIKF-SADDDNPNSIFISGKIEDVENVKELL 1208
Cdd:cd22413   14 HRFLIGRGGANIRKIRDNTGARIIFpTARDEDQELITIIGTKEAVEKAKEEL 65

seventh type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the seventh one.

Pssm-ID: 411880 [Multi-domain] Cd Length: 65 Bit Score: 42.69 E-value: 4.47e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 24655011  318 VEVAKPKHRYVIGPKGSTIAEILQLTGVSVEMPPNDSPSETITLRGPQVALGNAL 372
Cdd:cd22452    6 IKVSPRYFGRIIGPGGSNINQIREKSGCFINVPKKNKESDVITLRGTKEGVEKAE 60

tenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the tenth one.

Pssm-ID: 411841 [Multi-domain] Cd Length: 66 Bit Score: 42.63 E-value: 4.69e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24655011 1073 SFVLQVDVDTEFHSKLIGRHGAVINKLRADHDVIISLPKRDEPNDRIISITGYQANAEAARDAI 1136
Cdd:cd22413    2 SFTVEIRAKPEYHRFLIGRGGANIRKIRDNTGARIIFPTARDEDQELITIIGTKEAVEKAKEEL 65

second type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 mRNA-binding protein (IGF2BP) family; The IGF2BP family includes three members: IGF2BP1/IMP-1/ CRD-BP/ VICKZ1, IGF2BP2/IMP-2/ VICKZ2, and IGF2BP3/IMP-3/VICKZ3, which are RNA-binding factors that recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). They function by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. IGF2BP proteins contain four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the second one.

Pssm-ID: 411829 [Multi-domain] Cd Length: 72 Bit Score: 42.60 E-value: 4.79e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 24655011  611 VIGKGGANIKKIRDETQTKI-----DLPAEGDTNEVIVITGKKENVLEAKERIQK 660
Cdd:cd22401   14 LIGKDGRNIKKIMEDTNTKItisslQDLTSYNPERTITIKGSLEAMSEAESLISE 68

eighth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the eighth one.

Pssm-ID: 411839 [Multi-domain] Cd Length: 62 Bit Score: 42.19 E-value: 5.09e-05

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 24655011  315 TVSVEVAKPKHRYVIGPKGSTIAEILQLTGVSVEMPPNDSPSETITLRG 363
Cdd:cd22411    1 SIKVPIFKQFHKNIIGKGGATIKKIREETNTRIDLPEENSDSDVITITG 49

type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe meiotically up-regulated gene 60 protein (MUG60) and similar proteins; MUG60 is a KH domain-containing protein that has a role in meiosis. The family also contains Saccharomyces cerevisiae KH domain-containing protein YLL032C.

Pssm-ID: 411881 [Multi-domain] Cd Length: 72 Bit Score: 42.35 E-value: 5.50e-05

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24655011  993 PIEEELSVPFDLHRTIIGPRGANVRQFMSKHDVHVELPPSELKSDVIK----VCGTPARVAEAREALVKMI 1059
Cdd:cd22453    1 PAEISFYVPEKYHKRIIGKGGQNIQRIMKKYNVFIKFSNANDRADNYYpdnvVIRTPAKNAANLISVKSDI 71

seventh type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the seventh one.

Pssm-ID: 411838 Cd Length: 67 Bit Score: 42.26 E-value: 5.57e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24655011  383 KSVEINAAHWIHKYVIGRKGANMKQLEEDCPNVNVNCLE-----DKIKLEGDPENVDRAVAYLSEI 443
Cdd:cd22410    2 KTKDIIIEQRFHRTIIGQKGEKIREIRDKFPQVQITFPDpgsksDVVTLRGPKDEVDKCYKYLKKL 67

first type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ventral antigen (Nova); The family includes two related neuronal RNA-binding proteins, Nova-1 and Nova-2. Nova-1, also called onconeural ventral antigen 1, or paraneoplastic Ri antigen, or ventral neuron-specific protein 1, may regulate RNA splicing or metabolism in a specific subset of developing neurons. It interacts with RNA containing repeats of the YCAY sequence. It is a brain-enriched splicing factor regulating neuronal alternative splicing. Nova-1 is involved in neurological disorders and carcinogenesis. Nova-2, also called astrocytic NOVA1-like RNA-binding protein, is a neuronal RNA-binding protein expressed in a broader central nervous system (CNS) distribution than Nova-1. It functions in neuronal RNA metabolism. NOVA family proteins contain three K-homology (KH) RNA-binding domains. The model corresponds to the first one.

Pssm-ID: 411863 [Multi-domain] Cd Length: 73 Bit Score: 42.52 E-value: 6.30e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 24655011  611 VIGKGGANIKKIRDETQTKIDLPAEGD----TNE-VIVITGKKENVLEAKERI 658
Cdd:cd22435   16 IIGKGGQTIAQLQKETGARIKLSKNNDfypgTTErVCLIQGEVEAVNAVLDFI 68

first type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing protein (TDRKH) and similar proteins; TDRKH, also called tudor domain-containing protein 2 (TDRD2), is a mitochondria-anchored RNA-binding protein that is required for spermatogenesis and involved in piRNA biogenesis. It specifically recruits MIWI, but not MILI, to engage the piRNA pathway. TDRKH contains two K-homology (KH) RNA-binding domains and one tudor domain, which are involved in binding to RNA or single-strand DNA. The model corresponds to the first one.

Pssm-ID: 411856 [Multi-domain] Cd Length: 74 Bit Score: 42.32 E-value: 6.60e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24655011  172 QVTVPREHFRVILGKGGQRLREIERVTATRINIPSQSDESEF----ITIAGTKEGIAQAEQEIRQL 233
Cdd:cd22428    8 EMKVPREAVGLIIGRQGATIKQIQKETGARIDFKDEGSGGELpervLLIQGNPVQAQRAEEAIHQI 73

K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include an N-terminal extension and type I KH domains (e.g. hnRNP K) contain a C-terminal extension. Some KH-I superfamily members contain a divergent KH domain that lacks the RNA-binding GXXG motif. Some others have a mutated GXXG motif which may or may not have nucleic acid binding ability.

Pssm-ID: 411802 [Multi-domain] Cd Length: 63 Bit Score: 41.90 E-value: 6.63e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 24655011  243 DRITVPKVYHPFIVGPYSENLNKLQEETGARINVPPQQVQKDE--IVISG 290
Cdd:cd00105    1 EEIEVPSELVGLIIGKGGSTIKEIEEETGARIQIPKEGEGSGErvVTITG 50

type I K homology (KH) RNA-binding domain found in DEAD box protein 43 (DDX43), DEAD box protein 53 (DDX53) and similar proteins; DDX43 (also called cancer/testis antigen 13, or DEAD box protein HAGE, or helical antigen) displays tumor-specific expression. Diseases associated with DDX43 include rheumatoid lung disease. DDX53 (also called cancer-associated gene protein, or cancer/testis antigen 26, or DEAD box protein CAGE) shows high expression level in various tumors and is involved in anti-cancer drug resistance. Both DDX46 and DDX53 are members of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation.

Pssm-ID: 411858 [Multi-domain] Cd Length: 66 Bit Score: 41.89 E-value: 6.89e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 24655011  611 VIGKGGANIKKIRDETQTKIDLPAEGDTNEVIvITGKKENVLEAKERIQKI 661
Cdd:cd22430   14 VIGRGGSKIRELEESTGSKIKIIKGGQEAEVK-IFGSDEAQQKAKELIDEL 63

sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the sixth one.

Pssm-ID: 411804 [Multi-domain] Cd Length: 68 Bit Score: 42.17 E-value: 7.12e-05

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 24655011  245 ITVPKVYHPFIVGPYSENLNKLQEETGARINVPPQQVQKDEIVISG 290
Cdd:cd02394    6 IEIDPKFHGHIIGKGGANIKRIREESGVSIRIPDDEANSDEIRIEG 51

twelfth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the twelfth one.

Pssm-ID: 411843 [Multi-domain] Cd Length: 92 Bit Score: 42.67 E-value: 7.56e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24655011  670 TEEVQIPPKYYNSIIGTGGKLISSIMEECgGVSIKFPNSDS----------------------------KSDKVTIRGPK 721
Cdd:cd22415    1 TIECVIPQKFHRTVMGAKGSRVQQITSEF-DVQIKFPDRESnqpapaengegnggegvegeavddnsprKCDIIIITGKK 79

                         90
                 ....*....|...
gi 24655011  722 DDVEKAKVQLLEL 734
Cdd:cd22415   80 ENCEAAKEALLAL 92

second type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the second one.

Pssm-ID: 411834 [Multi-domain] Cd Length: 75 Bit Score: 42.30 E-value: 7.75e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24655011  672 EVQIPPKYYNSIIGTGGKLISSImEECGGVSIKFPNSDSKSDKVTIRGPKDDVEKAKVQLLELANER 738
Cdd:cd22406    8 TVNIPKEHHRFILGKKGKKLQEL-ELKTATKIVIPRQEDNSDEIKITGTKEGIEKARHEIQLISDEQ 73

third type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the third one.

Pssm-ID: 411835 [Multi-domain] Cd Length: 62 Bit Score: 41.81 E-value: 8.05e-05

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 24655011  996 EELSVPFDLHRTIIGPRGANVRQFMSKHDVHVELPPSELKSDVIKVCGTPARVAEAREAL 1055
Cdd:cd22407    2 ERLDIPKVYHPFIAGPNNENVKELQEETGVRINIPPPSVNKDEIVVSGEKEGVAQAVAKI 61

second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 and similar proteins; BTR1, also called Binding to ToMV RNA 1, is a negative regulator of tomato mosaic virus (ToMV) multiplication but has no effect on the multiplication of cucumber mosaic virus (CMV). BTR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411865 [Multi-domain] Cd Length: 69 Bit Score: 41.82 E-value: 8.20e-05

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 24655011  611 VIGKGGANIKKIRDETQTKI-----DLPAEGDTNEVIVITGKKENVLEA 654
Cdd:cd22437   13 IIGKGGSTIKELREDSNANIkispkDQLLPGSSERIVTITGSFDQVVKA 61

second type I K homology (KH) RNA-binding domain found in protein bicaudal C homolog 1 (BICC1) and similar proteins; BICC1, also called Bic-C, is a mammalian homologue of Drosophila Bicaudal-C (dBic-C). BICC1 functions as an RNA-binding protein that represses the translation of selected mRNAs to control development. It regulates gene expression and modulates cell proliferation and apoptosis. BICC1 is a negative regulator of Wnt signaling. Increased levels of BICC1 may be associated with depression. Besides, BICC1 is a genetic determinant of osteoblastogenesis and bone mineral density. BICC1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411849 Cd Length: 70 Bit Score: 41.94 E-value: 8.68e-05

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 24655011  608 HKFVIGKGGANIKKIRDETQTKIDLP-----AEGDTNEVIVITGKKENVLEAKERI 658
Cdd:cd22421   14 HSHVIGKGGNNIKKVMEDTGCHIHFPdsnrtSQAEKSNQVSIAGQPAGVESARAQI 69

first type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the first one.

Pssm-ID: 411874 [Multi-domain] Cd Length: 86 Bit Score: 42.39 E-value: 8.95e-05

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24655011  599 IEVPIFKQfhKFVIGKGGANIKKIRDETQTKIDLPAEGDTNEV----------IVITGKKENVLEAKERIQKIQNE 664
Cdd:cd22446   11 ISVPSSVR--GAIIGSRGKNLKSIQDKTGTKIQIPKRNEEGNYdeddddetveISIEGDAEGVELAKKEIEAIVKE 84

thirteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the thirteenth one.

Pssm-ID: 411844 [Multi-domain] Cd Length: 78 Bit Score: 41.83 E-value: 9.95e-05

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24655011  172 QVTVPREHFRVILGKGGQRLREIERVTATRINIPSQSDESEFITIAGTKEGIAQA----EQEIRQLSAEQ 237
Cdd:cd22416    5 EVNVPFDLHRFIIGQKGADVRKMMDEFDVNISIPPAELQSDIIKITGPPANVERAkaalLERVKELEAEK 74

second type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the second one.

Pssm-ID: 411834 [Multi-domain] Cd Length: 75 Bit Score: 41.91 E-value: 1.06e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 24655011  314 STVSVEVAKPKHRYVIGPKGSTIAEILQLTGVSVEMPPNDSPSETITLRGPQ 365
Cdd:cd22406    5 ASVTVNIPKEHHRFILGKKGKKLQELELKTATKIVIPRQEDNSDEIKITGTK 56

type I K homology (KH) RNA-binding domain found in mitochondrial A-kinase anchor protein 1 (AKAP1) and similar proteins; AKAP1, also called A-kinase anchor protein 149 kDa, or AKAP 149, or dual specificity A-kinase-anchoring protein 1, or D-AKAP-1, or protein kinase A-anchoring protein 1 (PRKA1), or spermatid A-kinase anchor protein 84, or S-AKAP84, is a novel developmentally regulated A kinase anchor protein of male germ cells. It binds to type I and II regulatory subunits of protein kinase A and anchors them to the cytoplasmic face of the mitochondrial outer membrane.

Pssm-ID: 411823 [Multi-domain] Cd Length: 68 Bit Score: 41.35 E-value: 1.11e-04

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 24655011  756 FLIGKNGASIRKIRDATGARI-IFPSNEDTDKEVITIIGKEESVKKA 801
Cdd:cd22395   13 RLIGKQGRNVKQLKQKSGAKIyIKPHPYTQNFQICSIEGTQQQIDKA 59

K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include an N-terminal extension and type I KH domains (e.g. hnRNP K) contain a C-terminal extension. Some KH-I superfamily members contain a divergent KH domain that lacks the RNA-binding GXXG motif. Some others have a mutated GXXG motif which may or may not have nucleic acid binding ability.

Pssm-ID: 411802 [Multi-domain] Cd Length: 63 Bit Score: 41.52 E-value: 1.12e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 24655011  316 VSVEVAKPKHRYVIGPKGSTIAEILQLTGVSVEMPPND--SPSETITLRGPQ 365
Cdd:cd00105    1 EEIEVPSELVGLIIGKGGSTIKEIEEETGARIQIPKEGegSGERVVTITGTP 52

thirteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the thirteenth one.

Pssm-ID: 411844 [Multi-domain] Cd Length: 78 Bit Score: 41.83 E-value: 1.15e-04

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24655011  384 SVEINAAHWIHKYVIGRKGANMKQLEEDCpNVNV-----NCLEDKIKLEGDPENVDRAVAYLSEIIKNYEE 449
Cdd:cd22416    3 TEEVNVPFDLHRFIIGQKGADVRKMMDEF-DVNIsippaELQSDIIKITGPPANVERAKAALLERVKELEA 72

K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include an N-terminal extension and type I KH domains (e.g. hnRNP K) contain a C-terminal extension. Some KH-I superfamily members contain a divergent KH domain that lacks the RNA-binding GXXG motif. Some others have a mutated GXXG motif which may or may not have nucleic acid binding ability.

Pssm-ID: 411802 [Multi-domain] Cd Length: 63 Bit Score: 41.13 E-value: 1.16e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 24655011  819 EVSVDPKHHKHFVAKRGFILHRISEECGgVMISFPRVGINSD--KVTIKGAKDCIEAARQRIE 879
Cdd:cd00105    2 EIEVPSELVGLIIGKGGSTIKEIEEETG-ARIQIPKEGEGSGerVVTITGTPEAVEKAKELIE 63

first type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding proteins; The far upstream element-binding protein (FUBP) family includes FUBP1-3. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP proteins contain four K-homology (KH) RNA-binding domains. The model corresponds to the first one.

Pssm-ID: 411824 [Multi-domain] Cd Length: 68 Bit Score: 41.47 E-value: 1.19e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 24655011  756 FLIGKNGASIRKIRDATGARIIFPSNEDTDKE-VITIIGKEESVKKAREQLEAII 809
Cdd:cd22396   14 LIIGRGGEQINRLQAESGAKIQIAPDSGGLPErPCTLTGTPDAIETAKRLIDQIV 68

fourth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the fourth one.

Pssm-ID: 411877 [Multi-domain] Cd Length: 70 Bit Score: 41.49 E-value: 1.19e-04

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24655011  742 SFTAEVRAKQQHHKFLIGKNGASIRKIRDATGARIIFpsnEDTDKEV-ITIIGKEESVKKAREQLEAIIKE 811
Cdd:cd22449    3 GYTVKFDVPAKYVPHIIGKKGANINKLREEYGVKIDF---EDKTGEGnVEIKGSKKNVEEAKKRILSQIDE 70

third type I K homology (KH) RNA-binding domain found in protein bicaudal C homolog 1 (BICC1) and similar proteins; BICC1, also called Bic-C, is a mammalian homologue of Drosophila Bicaudal-C (dBic-C). BICC1 functions as an RNA-binding protein that represses the translation of selected mRNAs to control development. It regulates gene expression and modulates cell proliferation and apoptosis. BICC1 is a negative regulator of Wnt signaling. Increased levels of BICC1 may be associated with depression. Besides, BICC1 is a genetic determinant of osteoblastogenesis and bone mineral density. BICC1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411850 Cd Length: 67 Bit Score: 41.17 E-value: 1.25e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24655011  669 VTEEVQIPPKYYNSIIGTGGKLISSIMEECGgVSIKFPNSDSKSDK---VTIRGPKDDVEKAKVQLL 732
Cdd:cd22422    2 VSMQLEIAPQHHLFMLGRNGSNIKHIMQRTG-AQIHFPDPNNPPQRkstVFISGSIDSVYLARQQLM 67

first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein PEPPER and similar proteins; The family includes a group of plant RNA-binding KH domain-containing proteins, such as PEPPER, flowering locus K homology domain protein (FLK), RNA-binding KH domain-containing protein RCF3 and KH domain-containing protein HEN4. PEPPER regulates vegetative and gynoecium development. It acts as a positive regulator of the central floral repressor FLOWERING LOCUS C. In concert with HUA2, PEPPER antagonizes FLK by positively regulating FLC probably at transcriptional and post-transcriptional levels, and thus acts as a negative regulator of flowering. FLK, also called flowering locus KH domain protein, regulates positively flowering by repressing FLC expression and post-transcriptional modification. PEPPER and FLK contain three K-homology (KH) RNA-binding domains. RCF3, also called protein ENHANCED STRESS RESPONSE 1 (ESR1), or protein HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5), or protein REGULATOR OF CBF GENE EXPRESSION 3, or protein SHINY 1 (SHI1), acts as negative regulator of osmotic stress-induced gene expression. It is involved in the regulation of thermotolerance responses under heat stress. It functions as an upstream regulator of heat stress transcription factor (HSF) genes. HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. RCF3 and HEN4 contain five KH RNA-binding domains. The model corresponds to the KH1 domain of PEPPER and FLK, as well as KH1 and KH3 domains of RCF3 and HEN4.

Pssm-ID: 411887 [Multi-domain] Cd Length: 69 Bit Score: 41.44 E-value: 1.32e-04

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 24655011  758 IGKNGASIRKIRDATGARI-IFPSNEDTDKEVITIIGKEE 796
Cdd:cd22459   17 IGKGGEIIKQLRQETGARIkVEDGVPGTEERVITISSSEA 56

arCOG04150 universal archaeal KH domain protein; This family of proteins is universal among the 41 archaeal genomes analyzed, and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.

Pssm-ID: 274711 [Multi-domain] Cd Length: 172 Bit Score: 44.09 E-value: 1.35e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24655011    672 EVQIPPKYYNSIIGTGGKLISSIMEECGgVSIKFpnsDSKSDKVTIRGPKDD-------------------VEKAkvqlL 732
Cdd:TIGR03665    1 YVKIPKDRIGVLIGKGGETKKEIEERTG-VKLDI---DSETGEVKIEPEDEDplavmkarevvkaigrgfsPEKA----L 72

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24655011    733 ELANERQ------LASFTAEVRAKQQHHKFLIGKNGASIRKIRDATGARIIFpsnedTDKEViTIIGKEESVKKAREQLE 806
Cdd:TIGR03665   73 KLLDDDYmlevidLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISV-----YGKTV-GIIGDPEQVQIAREAIE 146


                   ....
gi 24655011    807 AIIK 810
Cdd:TIGR03665  147 MLIE 150

thirteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the thirteenth one.

Pssm-ID: 411844 [Multi-domain] Cd Length: 78 Bit Score: 41.45 E-value: 1.40e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 24655011  315 TVSVEVAKPKHRYVIGPKGSTIAEILQLTGVSVEMPPNDSPSETITLRGP 364
Cdd:cd22416    3 TEEVNVPFDLHRFIIGQKGADVRKMMDEFDVNISIPPAELQSDIIKITGP 52

fourth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fourth one.

Pssm-ID: 411836 [Multi-domain] Cd Length: 62 Bit Score: 41.00 E-value: 1.45e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24655011  170 SRQVTVPREHFRVILGKGGQRLREIERVTATRINIPSQSDESEFITIAGTKEGIAQAEQEI 230
Cdd:cd22408    1 TVSVEVPKSQHRFVIGPRGSTIQEILEETGCSVEVPPNDSDSETITLRGPADKLGAALTLV 61

sixth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the sixth one.

Pssm-ID: 411879 [Multi-domain] Cd Length: 69 Bit Score: 41.29 E-value: 1.47e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 24655011  315 TVSVEVAKPKHRYVIGPKGSTIAEILQLTGVSVEMPPNDSPSETITLRGPQ 365
Cdd:cd22451    2 SIDIDIPKEYHRAIIGKGGAVLRELEAETGCRIQVPKKDDPSGKIRITGAR 52

second type I K homology (KH) RNA-binding domain found in protein bicaudal C homolog 1 (BICC1) and similar proteins; BICC1, also called Bic-C, is a mammalian homologue of Drosophila Bicaudal-C (dBic-C). BICC1 functions as an RNA-binding protein that represses the translation of selected mRNAs to control development. It regulates gene expression and modulates cell proliferation and apoptosis. BICC1 is a negative regulator of Wnt signaling. Increased levels of BICC1 may be associated with depression. Besides, BICC1 is a genetic determinant of osteoblastogenesis and bone mineral density. BICC1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411849 Cd Length: 70 Bit Score: 41.17 E-value: 1.58e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 24655011  669 VTEEVQIPPKYYNSIIGTGGKLISSIMEECGgVSIKFPNSD-----SKSDKVTIRGPKDDVEKAKVQL 731
Cdd:cd22421    3 VTLKMDVSHTDHSHVIGKGGNNIKKVMEDTG-CHIHFPDSNrtsqaEKSNQVSIAGQPAGVESARAQI 69

second type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the second one.

Pssm-ID: 411834 [Multi-domain] Cd Length: 75 Bit Score: 41.14 E-value: 1.60e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 24655011  527 VIIDRRLHRSIIGAKGEKIREVKdryrQVT---ITIPTPQENTDIVKLRGPKEDVDKCHKDLLKLVKE 591
Cdd:cd22406    9 VNIPKEHHRFILGKKGKKLQELE----LKTatkIVIPRQEDNSDEIKITGTKEGIEKARHEIQLISDE 72

eighth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the eighth one.

Pssm-ID: 411839 [Multi-domain] Cd Length: 62 Bit Score: 40.65 E-value: 1.69e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24655011 1148 REVIEIDKRIHPHLIGQRRRTIRKIIEDNKVNIKFSADDDNPNSIFISGKIEDVENVKELL 1208
Cdd:cd22411    1 SIKVPIFKQFHKNIIGKGGATIKKIREETNTRIDLPEENSDSDVITITGKKEDVEKARERI 61

K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include an N-terminal extension and type I KH domains (e.g. hnRNP K) contain a C-terminal extension. Some KH-I superfamily members contain a divergent KH domain that lacks the RNA-binding GXXG motif. Some others have a mutated GXXG motif which may or may not have nucleic acid binding ability.

Pssm-ID: 411802 [Multi-domain] Cd Length: 63 Bit Score: 40.74 E-value: 1.72e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 24655011  527 VIIDRRLHRSIIGAKGEKIREVKDRYR-QVTITIPTPQENTDIVKLRGPKEDVDKCHK 583
Cdd:cd00105    3 IEVPSELVGLIIGKGGSTIKEIEEETGaRIQIPKEGEGSGERVVTITGTPEAVEKAKE 60

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.

Pssm-ID: 459630 [Multi-domain] Cd Length: 65 Bit Score: 40.73 E-value: 1.75e-04

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 24655011    384 SVEINAAHWIHKYVIGRKGANMKQLEEDC------PNVNVNCLEDKIKLEGDPENVDRAVAYLSE 442
Cdd:pfam00013    1 TVEILVPSSLVGLIIGKGGSNIKEIREETgakiqiPPSESEGNERIVTITGTPEAVEAAKALIEE 65

third type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the third one.

Pssm-ID: 411835 [Multi-domain] Cd Length: 62 Bit Score: 40.65 E-value: 1.77e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 24655011  670 TEEVQIPPKYYNSIIGTGGKLISSIMEEcGGVSIKFPNSDSKSDKVTIRGPKDDVEKAK 728
Cdd:cd22407    1 TERLDIPKVYHPFIAGPNNENVKELQEE-TGVRINIPPPSVNKDEIVVSGEKEGVAQAV 58

ninth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the ninth one.

Pssm-ID: 411840 Cd Length: 70 Bit Score: 41.13 E-value: 1.86e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 24655011  316 VSVEVAKPKHRYVIGPKGSTIAEIL-QLTGVSVEMPPNDSPSETITLRGP 364
Cdd:cd22412    4 VEVEIPAKLHNSLIGAKGRLIRSIMeECGGVHIHFPPEGSGSDKVTIRGP 53

type I K homology (KH) RNA-binding domain found in activating signal cointegrator 1 complex subunit 1 (ASCC1) and similar proteins; ASCC1, also called ASC-1 complex subunit p50, or Trip4 complex subunit p50, plays a role in DNA damage repair as component of the ASCC complex. It is part of the ASC-1 complex that enhances NF-kappa-B, SRF and AP1 transactivation. In cells responding to gastrin-activated paracrine signals, it is involved in the induction of SERPINB2 expression by gastrin. ASCC1 may also play a role in the development of neuromuscular junction.

Pssm-ID: 411847 [Multi-domain] Cd Length: 66 Bit Score: 40.64 E-value: 1.96e-04

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 24655011  244 RITVPKVYHPFIVGPYSENLNKLQEETGARINVPPQQvQKDEIVISG 290
Cdd:cd22419    4 SLDVPSALFKFIIGKKGETKKRLESETKTQIRIPRQG-KEGDIVITG 49

third type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the third one.

Pssm-ID: 411835 [Multi-domain] Cd Length: 62 Bit Score: 40.65 E-value: 1.97e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 24655011  753 HHKFLIGKNGASIRKIRDATGARI-IFPSneDTDKEVITIIGKEESVKKAREQLE 806
Cdd:cd22407   10 YHPFIAGPNNENVKELQEETGVRInIPPP--SVNKDEIVVSGEKEGVAQAVAKIK 62

first type I K homology (KH) RNA-binding domain found in the family of MEX-3 RNA-binding proteins; The MEX-3 protein family includes four members, MEX3A/RKHD4, MEX3B/RKHD3/RNF195, MEX3C/ RKHD2/RNF194, and MEX3D/RKHD1/RNF193/TINO. They are homologous of Caenorhabditis elegans MEX-3 protein, a translational regulator that specifies the posterior blastomere identity in the early embryo and contributes to the maintenance of the germline totipotency. Mex-3 proteins are RNA-binding phosphoproteins involved in post-transcriptional regulatory mechanisms. They are characterized by containing two K-homology (KH) RNA-binding domains and a C-terminal RING finger. They bind RNA through their KH domains and shuttle between the nucleus and the cytoplasm via the CRM1-dependent export pathway. The model corresponds to the first KH domain.

Pssm-ID: 411851 Cd Length: 73 Bit Score: 40.93 E-value: 2.03e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 24655011  611 VIGKGGANIKKIRDETQTKIDLPAEGDtNEVIVITGKKENVLEAKERIQKIQNELSDI 668
Cdd:cd22423   16 IVGRQGCKIKALRAKTNTYIKTPVRGE-EPVFVVTGRKEDVAMAKREILSAAEHFSMI 72

third type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411876 Cd Length: 81 Bit Score: 41.36 E-value: 2.09e-04

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24655011  168 QASRQVTVPREHFRVILGKGGQRLREIERVTATRINIPSQSDES-----------EFITIAGTKEGIAQAEQEIRQL 233
Cdd:cd22448    2 ETTLILKIPVQFHGSLIGQQGKYVNRLQEKYGVKINFPRENSSSndtetkkpqapDEVTIRGGKKGVAEAKQELLEL 78

seventh type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the seventh one.

Pssm-ID: 411838 Cd Length: 67 Bit Score: 40.72 E-value: 2.10e-04

                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 24655011  890 TIEVVIPQRHHRTIMGARGFKVQQVTFEF-DVQIKFPD 926
Cdd:cd22410    3 TKDIIIEQRFHRTIIGQKGEKIREIRDKFpQVQITFPD 40

second type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ventral antigen (Nova); The family includes two related neuronal RNA-binding proteins, Nova-1 and Nova-2. Nova-1, also called onconeural ventral antigen 1, or paraneoplastic Ri antigen, or ventral neuron-specific protein 1, may regulate RNA splicing or metabolism in a specific subset of developing neurons. It interacts with RNA containing repeats of the YCAY sequence. It is a brain-enriched splicing factor regulating neuronal alternative splicing. Nova-1 is involved in neurological disorders and carcinogenesis. Nova-2, also called astrocytic NOVA1-like RNA-binding protein, is a neuronal RNA-binding protein expressed in a broader central nervous system (CNS) distribution than Nova-1. It functions in neuronal RNA metabolism. NOVA family proteins contain three K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411864 [Multi-domain] Cd Length: 70 Bit Score: 40.68 E-value: 2.22e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 24655011  610 FVIGKGGANIKKIRDETQTKIDL---PAEGDTNE-VIVITGKKENVLEAKERI-QKI 661
Cdd:cd22436   14 MIIGKGGATIKAIMEQSGARVQIsqkPESINLQErVVTVTGEPEANRKAVSLIlQKI 70

first type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding proteins (PCBPs); The PCBP family, also known as hnRNP E family, comprises four members, PCBP1-4, which are RNA-binding proteins that interact in a sequence-specific manner with single-stranded poly(C) sequences. They are mainly involved in various posttranscriptional regulations, including mRNA stabilization or translational activation/silencing. Besides, PCBPs may share iron chaperone activity. PCBPs contain three K-homology (KH) RNA-binding domains. The model corresponds to the first one.

Pssm-ID: 411866 [Multi-domain] Cd Length: 67 Bit Score: 40.70 E-value: 2.27e-04

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 24655011  611 VIGKGGANIKKIRDETQTKIDLPAEGDTNEVIVITGKKENVLEAKERI 658
Cdd:cd22438   13 IIGKKGETIKKFREESGARINISDGSCPERIVTVTGTTDAVFKAFELI 60

first type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding proteins; The far upstream element-binding protein (FUBP) family includes FUBP1-3. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP proteins contain four K-homology (KH) RNA-binding domains. The model corresponds to the first one.

Pssm-ID: 411824 [Multi-domain] Cd Length: 68 Bit Score: 40.70 E-value: 2.41e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24655011  669 VTEEVQIPPKYYNSIIGTGGKLISSIMEECGGVSIKFPNSDSKSDK-VTIRGPKDDVEKAK 728
Cdd:cd22396    1 VTEEYKVPDKMVGLIIGRGGEQINRLQAESGAKIQIAPDSGGLPERpCTLTGTPDAIETAK 61

thirteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the thirteenth one.

Pssm-ID: 411844 [Multi-domain] Cd Length: 78 Bit Score: 40.68 E-value: 2.65e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24655011 1158 HPHLIGQRRRTIRKIIEDNKVNIKFSADDDNPNSIFISGKIEDVENVKELLFGMAEDYERD 1218
Cdd:cd22416   13 HRFIIGQKGADVRKMMDEFDVNISIPPAELQSDIIKITGPPANVERAKAALLERVKELEAE 73

fourth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fourth one.

Pssm-ID: 411836 [Multi-domain] Cd Length: 62 Bit Score: 40.23 E-value: 2.82e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 24655011 1076 LQVDVDTEFHSKLIGRHGAVINKLRADHDVIISLPKRDEPNDRIIsITGYQANAEAARDAIL 1137
Cdd:cd22408    2 VSVEVPKSQHRFVIGPRGSTIQEILEETGCSVEVPPNDSDSETIT-LRGPADKLGAALTLVY 62

second type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing protein (TDRKH) and similar proteins; TDRKH, also called tudor domain-containing protein 2 (TDRD2), is a mitochondria-anchored RNA-binding protein that is required for spermatogenesis and involved in piRNA biogenesis. It specifically recruits MIWI, but not MILI, to engage the piRNA pathway. TDRKH contains two K-homology (KH) RNA-binding domains and one tudor domain, which are involved in binding to RNA or single-strand DNA. The model corresponds to the second one.

Pssm-ID: 411857 [Multi-domain] Cd Length: 82 Bit Score: 40.78 E-value: 3.07e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24655011  168 QASRQVTVPREHFRVILGKGGQRLREIERVTATRINIPSQSD----ESEFITIAGTKEGIAQAEQEI 230
Cdd:cd22429    1 IITEELHVPQRAVGRIIGRGGETIRSICRTSGAKVKCDRESDdtldLVRLITITGTKKEVDAAKSLI 67

fourth type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 mRNA-binding protein (IGF2BP) family; The IGF2BP family includes three members: IGF2BP1/IMP-1/CRD-BP/VICKZ1, IGF2BP2/IMP-2/VICKZ2, and IGF2BP3/IMP-3/VICKZ3, which are RNA-binding factors that recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). They function by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. IGF2BP proteins contain four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the fourth one.

Pssm-ID: 411831 [Multi-domain] Cd Length: 66 Bit Score: 39.92 E-value: 3.60e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24655011  172 QVTVPREHFRVILGKGGQRLREIERVTATRINIPSQSDESE----FITIAGTKEGIAQAEQEIR 231
Cdd:cd22403    3 EIRVPSSMVGRIIGKGGQNVRELQRLTGAIIKLPRDQTPDEgdevPVEIIGNFYATQSAQRRIR 66

sixth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the sixth one.

Pssm-ID: 411879 [Multi-domain] Cd Length: 69 Bit Score: 40.13 E-value: 3.69e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24655011  997 ELSVPFDLHRTIIGPRGANVRQFMSKHDVHVELPPSELKSDVIKVCGTPARVAEAREALVKMIE 1060
Cdd:cd22451    4 DIDIPKEYHRAIIGKGGAVLRELEAETGCRIQVPKKDDPSGKIRITGARDGVEAATAKILNISD 67

Uncharacterized membrane protein YbjL, putative transporter [General function prediction only];

Pssm-ID: 442224 [Multi-domain] Cd Length: 543 Bit Score: 44.73 E-value: 3.73e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24655011 1022 KHDVHVELPPSEL---KSDVIKVCGTPARVAEAREALVKMIEDYEADRADRELRSFVLQvdvDTEFHSKLIG------RH 1092
Cdd:COG2985  236 RRGGEIIVPTPDTvlqEGDIVLVVGTREALEAAEALLGEEVDDSELLDSDLDVRRIVVT---NKEVAGKTLGelnlrnRF 312

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 24655011 1093 GAVINKL-RADHDVIISLPKRDEPNDRiISITGyqanAEAARDAILEIVGDPEtlhREVIEID 1154
Cdd:COG2985  313 GVVITRVrRGGVELPATPDTVLQLGDR-LTVVG----PKEDVERVAKLLGNSE---RKLSETD 367

type I K homology (KH) RNA-binding domain found in polyribonucleotide nucleotidyltransferase (PNPase) and similar proteins; PNPase, also called polynucleotide phosphorylase, is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. It catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction. It is also involved, along with RNase II, in tRNA processing. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. The model corresponds to the KH domain.

Pssm-ID: 411803 [Multi-domain] Cd Length: 70 Bit Score: 40.15 E-value: 4.08e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24655011  172 QVTVPREHFRVILGKGGQRLREIERVTATRINIpsqsDESEFITIAGT-KEGIAQAEQEIRQLSAE 236
Cdd:cd02393    7 TIKIPPDKIGDVIGPGGKTIRAIIEETGAKIDI----EDDGTVTIFATdKESAEAAKAMIEDIVAE 68

fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana KH domain-containing protein HEN4 and similar protein; HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. HEN4 contains five K-homology (KH) RNA-binding domains. The model corresponds to the KH5 domain of HEN4.

Pssm-ID: 411890 [Multi-domain] Cd Length: 66 Bit Score: 39.93 E-value: 4.39e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 24655011  756 FLIGKNGASIRKIRDATGARI-IFPSNEDTDKEVITIIGKEESVKKAREQLEAII 809
Cdd:cd22462   12 SVIGRGGSNINQIREISGAKVeVLKPDSATGERIVLISGTPDQARHAQNLIEAFI 66

second type I K homology (KH) RNA-binding domain found in protein bicaudal C homolog 1 (BICC1) and similar proteins; BICC1, also called Bic-C, is a mammalian homologue of Drosophila Bicaudal-C (dBic-C). BICC1 functions as an RNA-binding protein that represses the translation of selected mRNAs to control development. It regulates gene expression and modulates cell proliferation and apoptosis. BICC1 is a negative regulator of Wnt signaling. Increased levels of BICC1 may be associated with depression. Besides, BICC1 is a genetic determinant of osteoblastogenesis and bone mineral density. BICC1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411849 Cd Length: 70 Bit Score: 40.02 E-value: 4.43e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 24655011  998 LSVPFDLHRTIIGPRGANVRQFMSKHDVHVELPPSEL-----KSDVIKVCGTPARVAEAR 1052
Cdd:cd22421    7 MDVSHTDHSHVIGKGGNNIKKVMEDTGCHIHFPDSNRtsqaeKSNQVSIAGQPAGVESAR 66

fourteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fourteenth one.

Pssm-ID: 411845 [Multi-domain] Cd Length: 72 Bit Score: 39.88 E-value: 5.07e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 24655011  315 TVSVEVAKPKHRYVIGPKGSTIAEILQLTGVSVEMPPNDSPSE-TITLRGPQ 365
Cdd:cd22417    2 TLTVEVDPKYHPKIIGRKGAVITKLRDDHDVNIQFPDKGDENDdEITITGYE 53

second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) and similar proteins; IGF2BP2, also called IGF2 mRNA-binding protein 2 (IMP-2), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 2, or VICKZ family member 2 (VICKZ2), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP2 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP3 in an RNA-dependent manner. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the second one.

Pssm-ID: 411922 Cd Length: 77 Bit Score: 40.01 E-value: 5.21e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 24655011  183 ILGKGGQRLREIERVTATRINIPSQSDESEF-----ITIAGTKEGIAQAEQEIRQLSAEQYK 239
Cdd:cd22494   14 LIGKEGRNLKKIEQDTGTKITISSLQDLTIYnpertITVKGSIEACSSAEVEIMKKLREAYE 75

third type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the third one.

Pssm-ID: 411835 [Multi-domain] Cd Length: 62 Bit Score: 39.50 E-value: 5.75e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 24655011  453 FEVMTVNPSYYKHIIGKAGANVNRLKDELKVNINI-EEREGQNNIRIEGPKEGVRQA 508
Cdd:cd22407    1 TERLDIPKVYHPFIAGPNNENVKELQEETGVRINIpPPSVNKDEIVVSGEKEGVAQA 57

third type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411876 Cd Length: 81 Bit Score: 39.82 E-value: 6.03e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24655011  813 DEVTEgEVSVDPKHHKHFVAKRGFILHRIsEECGGVMISFPRVGINS-----------DKVTIKGAKDCIEAARQRIEEI 881
Cdd:cd22448    1 DETTL-ILKIPVQFHGSLIGQQGKYVNRL-QEKYGVKINFPRENSSSndtetkkpqapDEVTIRGGKKGVAEAKQELLEL 78


                 .
gi 24655011  882 V 882
Cdd:cd22448   79 L 79

K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include an N-terminal extension and type I KH domains (e.g. hnRNP K) contain a C-terminal extension. Some KH-I superfamily members contain a divergent KH domain that lacks the RNA-binding GXXG motif. Some others have a mutated GXXG motif which may or may not have nucleic acid binding ability.

Pssm-ID: 411802 [Multi-domain] Cd Length: 63 Bit Score: 39.20 E-value: 6.06e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 24655011  385 VEINAAHWIHKYVIGRKGANMKQLEEDC------PNVNVNCLEDKIKLEGDPENVDRAVAYL 440
Cdd:cd00105    1 EEIEVPSELVGLIIGKGGSTIKEIEEETgariqiPKEGEGSGERVVTITGTPEAVEKAKELI 62

fifteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fifteenth one.

Pssm-ID: 411846 [Multi-domain] Cd Length: 69 Bit Score: 39.56 E-value: 6.23e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24655011  890 TIEVVIPQRHHRTIMGARGFKVQQVTFEFDVQIKFPDRDATEPvegltnggsgenggenegqegeqevekeaeqepvrqc 969
Cdd:cd22418    2 TEEVEIDSRVHPRLIGARGKAIRKIMEDFKVDIRFPRSGDADP------------------------------------- 44

                         90       100
                 ....*....|....*....|....*...
gi 24655011  970 DVIRITGRIEKCEAAKQALLDLipiEEE 997
Cdd:cd22418   45 NLVTITGLEENVEECKDHLLNL---EEE 69

tenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the tenth one.

Pssm-ID: 411841 [Multi-domain] Cd Length: 66 Bit Score: 39.17 E-value: 6.27e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 24655011  819 EVSVDPKHHKHFVAKRGFILHRISEECgGVMISFPRVG-INSDKVTIKGAKDCIEAARQRIE 879
Cdd:cd22413    6 EIRAKPEYHRFLIGRGGANIRKIRDNT-GARIIFPTARdEDQELITIIGTKEAVEKAKEELE 66

eighth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the eighth one.

Pssm-ID: 411839 [Multi-domain] Cd Length: 62 Bit Score: 39.11 E-value: 6.37e-04

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 24655011  245 ITVPKVYHPFIVGPYSENLNKLQEETGARINVPPQQVQKDEIVISG 290
Cdd:cd22411    4 VPIFKQFHKNIIGKGGATIKKIREETNTRIDLPEENSDSDVITITG 49

third type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411876 Cd Length: 81 Bit Score: 39.82 E-value: 6.84e-04

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24655011 1075 VLQVDVDTEFHSKLIGRHGAVINKLRADHDVIISLPKRDEPNDR----------IISITGYQANAEAARDAILEIV 1140
Cdd:cd22448    4 TLILKIPVQFHGSLIGQQGKYVNRLQEKYGVKINFPRENSSSNDtetkkpqapdEVTIRGGKKGVAEAKQELLELL 79

type I K homology (KH) RNA-binding domain found in Mask family proteins; The Mask family includes Drosophila melanogaster ankyrin repeat and KH domain-containing protein Mask, and its mammalian homologues Mask1/ANKHD1 and Mask2/ANKRD17. Mask, also called multiple ankyrin repeat single KH domain-containing protein, is a large ankyrin repeat and KH domain-containing protein involved in Drosophila receptor tyrosine kinase signaling. It acts as a mediator of receptor tyrosine kinase (RTK) signaling and may act either downstream of MAPK or transduce signaling through a parallel branch of the RTK pathway. Mask is required for the development and organization of indirect flight muscle sarcomeres by regulating the formation of M line and H zone and the correct assembly of thick and thin filaments in the sarcomere. Mask1/ANKHD1, also called HIV-1 Vpr-binding ankyrin repeat protein, or multiple ankyrin repeats single KH domain, or Hmask, is highly expressed in various cancer tissues and is involved in cancer progression, including proliferation and invasion. Mask2/ANKRD17, also called ankyrin repeat protein 17, or gene trap ankyrin repeat protein (GTAR), or serologically defined breast cancer antigen NY-BR-16, is a ubiquitously expressed ankyrin factor essential for the vascular integrity during embryogenesis. It may be directly involved in the DNA replication process and play pivotal roles in cell cycle and DNA regulation. It is also involved in innate immune defense against bacteria and viruses.

Pssm-ID: 411832 [Multi-domain] Cd Length: 71 Bit Score: 39.50 E-value: 6.89e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24655011  455 VMTVNPSYYKHIIGKAGANVNRLKDELKVNINIEEREGQN---NIRIEGPKEGVRQAQLELQEKID 517
Cdd:cd22404    4 KVTVPNSAISRVIGRGGCNINAIREVSGAHIEIDKQKGEQgdrRITIKGSADATRQAAQLINALIK 69

third type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding proteins (PCBPs); The PCBP family, also known as hnRNP E family, comprises four members, PCBP1-4, which are RNA-binding proteins that interact in a sequence-specific manner with single-stranded poly(C) sequences. They are mainly involved in various posttranscriptional regulations, including mRNA stabilization or translational activation/silencing. Besides, PCBPs may share iron chaperone activity. PCBPs contain three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411867 [Multi-domain] Cd Length: 68 Bit Score: 39.14 E-value: 7.58e-04

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 24655011  757 LIGKNGASIRKIRDATGARI-IFPSNEDTDKEVITIIGKEESVKKA 801
Cdd:cd22439   16 IIGKGGTKINEIRQLSGATIkIANSEDGSTERSVTITGTPEAVSLA 61

third type I K homology (KH) RNA-binding domain found in protein bicaudal C homolog 1 (BICC1) and similar proteins; BICC1, also called Bic-C, is a mammalian homologue of Drosophila Bicaudal-C (dBic-C). BICC1 functions as an RNA-binding protein that represses the translation of selected mRNAs to control development. It regulates gene expression and modulates cell proliferation and apoptosis. BICC1 is a negative regulator of Wnt signaling. Increased levels of BICC1 may be associated with depression. Besides, BICC1 is a genetic determinant of osteoblastogenesis and bone mineral density. BICC1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411850 Cd Length: 67 Bit Score: 39.24 E-value: 7.72e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24655011  170 SRQVTVPREHFRVILGKGGQRLREIERVTATRINIPSQSDESE---FITIAGTKEGIAQAEQEI 230
Cdd:cd22422    3 SMQLEIAPQHHLFMLGRNGSNIKHIMQRTGAQIHFPDPNNPPQrksTVFISGSIDSVYLARQQL 66

eighth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the eighth one.

Pssm-ID: 411839 [Multi-domain] Cd Length: 62 Bit Score: 39.11 E-value: 7.83e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 24655011  995 EEELSVPFDLHRTIIGPRGANVRQFMSKHDVHVELPPSELKSDVIKVCGTPARVAEARE 1053
Cdd:cd22411    1 SIKVPIFKQFHKNIIGKGGATIKKIREETNTRIDLPEENSDSDVITITGKKEDVEKARE 59

eighth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the eighth one.

Pssm-ID: 411839 [Multi-domain] Cd Length: 62 Bit Score: 39.11 E-value: 7.83e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24655011  819 EVSVDPKHHKHFVAKRGFILHRISEECGgVMISFPRVGINSDKVTIKGAKDCIEAARQRIE 879
Cdd:cd22411    3 KVPIFKQFHKNIIGKGGATIKKIREETN-TRIDLPEENSDSDVITITGKKEDVEKARERIL 62

second type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding proteins (PCBPs); The PCBP family, also known as hnRNP E family, comprises four members, PCBP1-4, which are RNA-binding proteins that interact in a sequence-specific manner with single-stranded poly(C) sequences. They are mainly involved in various posttranscriptional regulations, including mRNA stabilization or translational activation/silencing. Besides, PCBPs may share iron chaperone activity. PCBPs contain three K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411806 [Multi-domain] Cd Length: 72 Bit Score: 39.18 E-value: 7.86e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 24655011  757 LIGKNGASIRKIRDATGARIIFPSN---EDTDKeVITIIGKEESVKKAREQLEAIIKE 811
Cdd:cd02396   16 LIGKGGSKIKEIRESTGASVQVASEmlpNSTER-AVTISGSPEAITKCVEQICCVMLE 72

third type I K homology (KH) RNA-binding domain found in protein bicaudal C homolog 1 (BICC1) and similar proteins; BICC1, also called Bic-C, is a mammalian homologue of Drosophila Bicaudal-C (dBic-C). BICC1 functions as an RNA-binding protein that represses the translation of selected mRNAs to control development. It regulates gene expression and modulates cell proliferation and apoptosis. BICC1 is a negative regulator of Wnt signaling. Increased levels of BICC1 may be associated with depression. Besides, BICC1 is a genetic determinant of osteoblastogenesis and bone mineral density. BICC1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411850 Cd Length: 67 Bit Score: 39.24 E-value: 7.88e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 24655011  315 TVSVEVAKPKHRYVIGPKGSTIAEILQLTGVSVEMP-PNDSPSE--TITLRGP 364
Cdd:cd22422    3 SMQLEIAPQHHLFMLGRNGSNIKHIMQRTGAQIHFPdPNNPPQRksTVFISGS 55

seventh type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the seventh one.

Pssm-ID: 411838 Cd Length: 67 Bit Score: 39.18 E-value: 7.90e-04

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 24655011 1004 LHRTIIGPRGANVRQFMSKH-DVHVELPPSELKSDVIKVCGTPARVAEAREALVKM 1058
Cdd:cd22410   12 FHRTIIGQKGEKIREIRDKFpQVQITFPDPGSKSDVVTLRGPKDEVDKCYKYLKKL 67

sixth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the sixth one.

Pssm-ID: 411879 [Multi-domain] Cd Length: 69 Bit Score: 38.98 E-value: 8.18e-04

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 24655011  242 SDRITVPKVYHPFIVGPYSENLNKLQEETGARINVPPQQVQKDEIVISG 290
Cdd:cd22451    2 SIDIDIPKEYHRAIIGKGGAVLRELEAETGCRIQVPKKDDPSGKIRITG 50

fourteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fourteenth one.

Pssm-ID: 411845 [Multi-domain] Cd Length: 72 Bit Score: 39.11 E-value: 8.21e-04

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 24655011  245 ITVPKVYHPFIVGPYSENLNKLQEETGARINVPPQQVQ-KDEIVISG 290
Cdd:cd22417    5 VEVDPKYHPKIIGRKGAVITKLRDDHDVNIQFPDKGDEnDDEITITG 51

second type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ventral antigen (Nova); The family includes two related neuronal RNA-binding proteins, Nova-1 and Nova-2. Nova-1, also called onconeural ventral antigen 1, or paraneoplastic Ri antigen, or ventral neuron-specific protein 1, may regulate RNA splicing or metabolism in a specific subset of developing neurons. It interacts with RNA containing repeats of the YCAY sequence. It is a brain-enriched splicing factor regulating neuronal alternative splicing. Nova-1 is involved in neurological disorders and carcinogenesis. Nova-2, also called astrocytic NOVA1-like RNA-binding protein, is a neuronal RNA-binding protein expressed in a broader central nervous system (CNS) distribution than Nova-1. It functions in neuronal RNA metabolism. NOVA family proteins contain three K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411864 [Multi-domain] Cd Length: 70 Bit Score: 39.14 E-value: 8.36e-04

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 24655011  756 FLIGKNGASIRKIRDATGARIIF---PSNEDTDKEVITIIGKEESVKKA 801
Cdd:cd22436   14 MIIGKGGATIKAIMEQSGARVQIsqkPESINLQERVVTVTGEPEANRKA 62

type I K homology (KH) RNA-binding domain found in Drosophila melanogaster eukaryotic translation initiation factor 4E-binding protein Mextli and similar proteins; Mextli is a novel eukaryotic translation initiation factor 4E-binding protein that promotes translation in Drosophila melanogaster.

Pssm-ID: 411882 [Multi-domain] Cd Length: 71 Bit Score: 38.84 E-value: 9.49e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 24655011  669 VTEEVQIPPKYYNSIIGTGGKLISSIMEECGGVsIKF--PNSDSKSDKVTIRGPKDDVEKAKVQLLEL 734
Cdd:cd22454    4 TTIEVVIPNADVGKVIGKGGETIKRIEALTDTV-ITFerVNGGSPNREVQITGSPDNVAAAKRLIEDT 70

second type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411875 [Multi-domain] Cd Length: 80 Bit Score: 39.32 E-value: 9.75e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 24655011  314 STVSVEVAKPKHRYVIGPKGSTIAEILQLTGVSVEMPP--NDSPSET--------ITLRGPQVALGNA 371
Cdd:cd22447    4 QNLTVPIPASTRARIIGKKGANLKQIREKTGVRIDIPPrdADAAPADedddtmveVTITGDEFNVQHA 71

type I K homology (KH) RNA-binding domain found in activating signal cointegrator 1 complex subunit 1 (ASCC1) and similar proteins; ASCC1, also called ASC-1 complex subunit p50, or Trip4 complex subunit p50, plays a role in DNA damage repair as component of the ASCC complex. It is part of the ASC-1 complex that enhances NF-kappa-B, SRF and AP1 transactivation. In cells responding to gastrin-activated paracrine signals, it is involved in the induction of SERPINB2 expression by gastrin. ASCC1 may also play a role in the development of neuromuscular junction.

Pssm-ID: 411847 [Multi-domain] Cd Length: 66 Bit Score: 38.71 E-value: 1.01e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 24655011  461 SYYKHIIGKAGANVNRLKDELKVNINIEEREGQNNIRIEGP-KEGVRQAQLELQ 513
Cdd:cd22419   10 ALFKFIIGKKGETKKRLESETKTQIRIPRQGKEGDIVITGKdRSGVDSARTRIE 63

eighth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the eighth one.

Pssm-ID: 411839 [Multi-domain] Cd Length: 62 Bit Score: 38.72 E-value: 1.03e-03

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 24655011  462 YYKHIIGKAGANVNRLKDELKVNINIEEREGQNN-IRIEGPKEGVRQAQ 509
Cdd:cd22411   10 FHKNIIGKGGATIKKIREETNTRIDLPEENSDSDvITITGKKEDVEKAR 58

type I K homology (KH) RNA-binding domain found in Drosophila melanogaster eukaryotic translation initiation factor 4E-binding protein Mextli and similar proteins; Mextli is a novel eukaryotic translation initiation factor 4E-binding protein that promotes translation in Drosophila melanogaster.

Pssm-ID: 411882 [Multi-domain] Cd Length: 71 Bit Score: 38.84 E-value: 1.04e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24655011  172 QVTVPREHFRVILGKGGQRLREIERVTATRINI-PSQSDESE-FITIAGTKEGIAQAEQEIRQL 233
Cdd:cd22454    7 EVVIPNADVGKVIGKGGETIKRIEALTDTVITFeRVNGGSPNrEVQITGSPDNVAAAKRLIEDT 70

thirteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the thirteenth one.

Pssm-ID: 411844 [Multi-domain] Cd Length: 78 Bit Score: 39.14 E-value: 1.14e-03

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 24655011  245 ITVPKVYHPFIVGPYSENLNKLQEETGARINVPPQQVQKDEIVISG 290
Cdd:cd22416    6 VNVPFDLHRFIIGQKGADVRKMMDEFDVNISIPPAELQSDIIKITG 51

type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae meiotic recombination 1 protein (MER1) and similar proteins; MER1 is required for chromosome pairing and genetic recombination. It may function to bring the axial elements of the synaptonemal complex corresponding to homologous chromosomes together by initiating recombination. MER1 might be responsible for regulating the MER2 gene and/or gene product.

Pssm-ID: 411886 [Multi-domain] Cd Length: 65 Bit Score: 38.58 E-value: 1.14e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 24655011  743 FTAEVRAKQQHHKFLIGKNGASIRKIRDATGARI-IFPSNEDTDKeVITIIGKEESVKKAREQLE 806
Cdd:cd22458    1 VTWEIKLPQALCGRLIGAKGKNIKALSEKSGASIrLIPISNSSQQ-TIHLSGTDKQIALAISSIE 64

type I K homology (KH) RNA-binding domain found in polyribonucleotide nucleotidyltransferase (PNPase) and similar proteins; PNPase, also called polynucleotide phosphorylase, is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. It catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction. It is also involved, along with RNase II, in tRNA processing. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. The model corresponds to the KH domain.

Pssm-ID: 411803 [Multi-domain] Cd Length: 70 Bit Score: 38.61 E-value: 1.18e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 24655011  757 LIGKNGASIRKIRDATGARIifpsneDTDKE-VITIIGK-EESVKKAREQLEAIIKE 811
Cdd:cd02393   18 VIGPGGKTIRAIIEETGAKI------DIEDDgTVTIFATdKESAEAAKAMIEDIVAE 68

seventh type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the seventh one.

Pssm-ID: 411880 [Multi-domain] Cd Length: 65 Bit Score: 38.46 E-value: 1.35e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 24655011  993 PIEEELSVPFDLHRTIIGPRGANVRQFMSKHDVHVELPPSELKSDVIKVCGTPARVAEAREALVK 1057
Cdd:cd22452    1 DFRGWIKVSPRYFGRIIGPGGSNINQIREKSGCFINVPKKNKESDVITLRGTKEGVEKAEEMIKK 65

fifth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fifth one.

Pssm-ID: 411837 [Multi-domain] Cd Length: 70 Bit Score: 38.33 E-value: 1.55e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 24655011  827 HKHFVAKRGFILHRISEECGGVMISFPRvgiNSDKVTIKGAKDCIEAARQRIEEIVADLEA 887
Cdd:cd22409   13 HRFIIGKKGANIKKITQDLPKVHIEFTE---GEDKIELEGPPEEVEVVREQLEAIVKELVA 70

twelfth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the twelfth one.

Pssm-ID: 411843 [Multi-domain] Cd Length: 92 Bit Score: 39.20 E-value: 1.56e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24655011  599 IEVPIFKQFHKFVIGKGGANIKKI------------RDETQTKIDLPAEGDTNE----------------VIVITGKKEN 650
Cdd:cd22415    2 IECVIPQKFHRTVMGAKGSRVQQItsefdvqikfpdRESNQPAPAENGEGNGGEgvegeavddnsprkcdIIIITGKKEN 81


                 ....*.
gi 24655011  651 VLEAKE 656
Cdd:cd22415   82 CEAAKE 87

K homology RNA-binding domain;

Pssm-ID: 197652 [Multi-domain] Cd Length: 68 Bit Score: 38.05 E-value: 1.64e-03

                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 24655011     381 SVKSVEINAAHWIHKYVIGRKGANMKQLEEDCpNVNVN-----CLEDKIKLEGDPENVDRAVAYLSEII 444
Cdd:smart00322    1 DPVTIEVLIPADKVGLIIGKGGSTIKKIEEET-GVKIDipgpgSEERVVEITGPPENVEKAAELILEIL 68

first type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding proteins (PCBPs); The PCBP family, also known as hnRNP E family, comprises four members, PCBP1-4, which are RNA-binding proteins that interact in a sequence-specific manner with single-stranded poly(C) sequences. They are mainly involved in various posttranscriptional regulations, including mRNA stabilization or translational activation/silencing. Besides, PCBPs may share iron chaperone activity. PCBPs contain three K-homology (KH) RNA-binding domains. The model corresponds to the first one.

Pssm-ID: 411866 [Multi-domain] Cd Length: 67 Bit Score: 38.01 E-value: 1.98e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 24655011  757 LIGKNGASIRKIRDATGARIIFpSNEDTDKEVITIIGKEESVKKAreqLEAIIKECDEV 815
Cdd:cd22438   13 IIGKKGETIKKFREESGARINI-SDGSCPERIVTVTGTTDAVFKA---FELICRKLEED 67

third type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding proteins; The far upstream element-binding protein (FUBP) family includes FUBP1-3. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP proteins contain four K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411826 [Multi-domain] Cd Length: 67 Bit Score: 38.01 E-value: 2.07e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 24655011  758 IGKNGASIRKIRDATGARIIFPSNEDTDKEVI-TIIGKEESVKKAREQLEAII 809
Cdd:cd22398   15 IGKGGEMIKKIQNETGARVQFKPDDGNSPDRIcVITGPPDQVQHAARMIQELI 67

first type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 mRNA-binding protein (IGF2BP) family; The IGF2BP family includes three members: IGF2BP1/IMP-1/ CRD-BP/ VICKZ1, IGF2BP2/IMP-2/ VICKZ2, and IGF2BP3/IMP-3/VICKZ3, which are RNA-binding factors that recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). They function by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. IGF2BP proteins contain four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the first one.

Pssm-ID: 411828 [Multi-domain] Cd Length: 68 Bit Score: 38.02 E-value: 2.11e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 24655011  611 VIGKGGANIKKIRDETQTKIDL---PAEGDTNEVIVITGKKENVLEAKERIQKI 661
Cdd:cd22400   14 IIGKGGATIRQITQQTGARIDIhrkENAGAAEKAITIYGTPEGCSSACKQILEI 67

tenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the tenth one.

Pssm-ID: 411841 [Multi-domain] Cd Length: 66 Bit Score: 38.01 E-value: 2.12e-03

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 24655011  245 ITVPKVYHPFIVGPYSENLNKLQEETGARINVPPQQVQKDEIV 287
Cdd:cd22413    7 IRAKPEYHRFLIGRGGANIRKIRDNTGARIIFPTARDEDQELI 49

third type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the third one.

Pssm-ID: 411876 Cd Length: 81 Bit Score: 38.28 E-value: 2.52e-03

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24655011  996 EELSVPFDLHRTIIGPRGANVRQFMSKHDVHVELP-----------PSELKSDVIKVCGTPARVAEAREALVKMIE 1060
Cdd:cd22448    5 LILKIPVQFHGSLIGQQGKYVNRLQEKYGVKINFPrensssndtetKKPQAPDEVTIRGGKKGVAEAKQELLELLE 80

eleventh type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the eleventh one.

Pssm-ID: 411842 Cd Length: 66 Bit Score: 37.67 E-value: 2.56e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24655011 1078 VDVDTEFHSKLIGRHGAVINKLRADHD-VIISLPKRDEPNDRIiSITGYQANAEAARDAILEIV 1140
Cdd:cd22414    4 MTVDPKHHRHFVARRGQVLREIADEYGgVMVSFPRSGTQSDKV-TLKGAKDCVEGAKKRILEIV 66

first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein PEPPER and similar proteins; The family includes a group of plant RNA-binding KH domain-containing proteins, such as PEPPER, flowering locus K homology domain protein (FLK), RNA-binding KH domain-containing protein RCF3 and KH domain-containing protein HEN4. PEPPER regulates vegetative and gynoecium development. It acts as a positive regulator of the central floral repressor FLOWERING LOCUS C. In concert with HUA2, PEPPER antagonizes FLK by positively regulating FLC probably at transcriptional and post-transcriptional levels, and thus acts as a negative regulator of flowering. FLK, also called flowering locus KH domain protein, regulates positively flowering by repressing FLC expression and post-transcriptional modification. PEPPER and FLK contain three K-homology (KH) RNA-binding domains. RCF3, also called protein ENHANCED STRESS RESPONSE 1 (ESR1), or protein HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5), or protein REGULATOR OF CBF GENE EXPRESSION 3, or protein SHINY 1 (SHI1), acts as negative regulator of osmotic stress-induced gene expression. It is involved in the regulation of thermotolerance responses under heat stress. It functions as an upstream regulator of heat stress transcription factor (HSF) genes. HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. RCF3 and HEN4 contain five KH RNA-binding domains. The model corresponds to the KH1 domain of PEPPER and FLK, as well as KH1 and KH3 domains of RCF3 and HEN4.

Pssm-ID: 411887 [Multi-domain] Cd Length: 69 Bit Score: 37.59 E-value: 2.62e-03

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 24655011  611 VIGKGGANIKKIRDETQTKIDL--PAEGDTNEVIVITGKKE 649
Cdd:cd22459   16 VIGKGGEIIKQLRQETGARIKVedGVPGTEERVITISSSEA 56

fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein RCF3 and similar protein; RCF3, also called protein ENHANCED STRESS RESPONSE 1 (ESR1), or protein HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5), or protein REGULATOR OF CBF GENE EXPRESSION 3, or protein SHINY 1 (SHI1), acts as negative regulator of osmotic stress-induced gene expression. It is involved in the regulation of thermotolerance responses under heat stress. It functions as an upstream regulator of heat stress transcription factor (HSF) genes. HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. RCF3 contains five K-homology (KH) RNA-binding domains. The model corresponds to the KH5 domain of RCF3.

Pssm-ID: 411891 [Multi-domain] Cd Length: 71 Bit Score: 37.41 E-value: 3.17e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 24655011  757 LIGKNGASIRKIRDATGARIIF---PSNEDTDKEVITIIGKEESVKKAREQLEAII 809
Cdd:cd22463   16 IIGKSGNTIKQISERSGAFVAIvqdRYPLEETQKILRISGTEEQLKRAQSLVEGLI 71

seventh type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the seventh one.

Pssm-ID: 411838 Cd Length: 67 Bit Score: 37.25 E-value: 3.23e-03

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 24655011  325 HRYVIGPKGSTIAEIL-QLTGVSVEMPPNDSPSETITLRGP 364
Cdd:cd22410   13 HRTIIGQKGEKIREIRdKFPQVQITFPDPGSKSDVVTLRGP 53

seventh type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the seventh one.

Pssm-ID: 411880 [Multi-domain] Cd Length: 65 Bit Score: 37.30 E-value: 3.25e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 24655011  532 RLHRSIIGAKGEKIREVKDRYrQVTITIPTPQENTDIVKLRGPKEDVDKCHKDLLK 587
Cdd:cd22452   11 RYFGRIIGPGGSNINQIREKS-GCFINVPKKNKESDVITLRGTKEGVEKAEEMIKK 65

twelfth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the twelfth one.

Pssm-ID: 411843 [Multi-domain] Cd Length: 92 Bit Score: 38.05 E-value: 3.25e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24655011  526 DVIIDRRLHRSIIGAKGEKIREVKDRYrQVTITIPTPQEN----------------------------TDIVKLRGPKED 577
Cdd:cd22415    3 ECVIPQKFHRTVMGAKGSRVQQITSEF-DVQIKFPDRESNqpapaengegnggegvegeavddnsprkCDIIIITGKKEN 81

                         90
                 ....*....|.
gi 24655011  578 VDKCHKDLLKL 588
Cdd:cd22415   82 CEAAKEALLAL 92

second type I K homology (KH) RNA-binding domain found in protein bicaudal C homolog 1 (BICC1) and similar proteins; BICC1, also called Bic-C, is a mammalian homologue of Drosophila Bicaudal-C (dBic-C). BICC1 functions as an RNA-binding protein that represses the translation of selected mRNAs to control development. It regulates gene expression and modulates cell proliferation and apoptosis. BICC1 is a negative regulator of Wnt signaling. Increased levels of BICC1 may be associated with depression. Besides, BICC1 is a genetic determinant of osteoblastogenesis and bone mineral density. BICC1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411849 Cd Length: 70 Bit Score: 37.32 E-value: 3.35e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 24655011  754 HKFLIGKNGASIRKIRDATGARIIFP-SNEDTDKE---VITIIGKEESVKKAREQL 805
Cdd:cd22421   14 HSHVIGKGGNNIKKVMEDTGCHIHFPdSNRTSQAEksnQVSIAGQPAGVESARAQI 69

type I K homology (KH) RNA-binding domain found in ankyrin repeat domain-containing protein 17 (ANKRD17) and similar proteins; ANKRD17, also called ankyrin repeat protein 17, or gene trap ankyrin repeat protein (GTAR), or serologically defined breast cancer antigen NY-BR-16, is a ubiquitously expressed ankyrin factor essential for the vascular integrity during embryogenesis. It may be directly involved in the DNA replication process and play pivotal roles in cell cycle and DNA regulation. It is also involved in innate immune defense against bacteria and viruses.

Pssm-ID: 411930 [Multi-domain] Cd Length: 71 Bit Score: 37.43 E-value: 3.42e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 24655011  757 LIGKNGASIRKIRDATGARIIFPSNED-TDKEVITIIGKEESVKKAREQLEAIIKE 811
Cdd:cd22502   15 VIGRGGCNINAIREFTGAHIDIDKQKDkTGDRIITIRGGTESTRQATQLINALIKD 70

fourth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fourth one.

Pssm-ID: 411836 [Multi-domain] Cd Length: 62 Bit Score: 37.15 E-value: 3.61e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 24655011  820 VSVDPKHHKHFVAKRGFILHRISEECgGVMISFPRVGINSDKVTIKGAKDCIEAARQRIE 879
Cdd:cd22408    4 VEVPKSQHRFVIGPRGSTIQEILEET-GCSVEVPPNDSDSETITLRGPADKLGAALTLVY 62

putative RNA-processing protein; Provisional

Pssm-ID: 237494 [Multi-domain] Cd Length: 180 Bit Score: 39.85 E-value: 3.71e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24655011   598 IIEVPIFKQFHKFVIGKGGANIKKIRDETQTKIDLpaEGDTNEVIVITGKKEN---VLEAKERIQKI----QNE-----L 665
Cdd:PRK13763    4 MEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEI--DSETGEVIIEPTDGEDplaVLKARDIVKAIgrgfSPEkalrlL 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24655011   666 SDIVTEEVQIPPKYYNS----------IIGTGGKlISSIMEECGGVSIkfpnsdSKSDK-VTIRGPKDDVEKAK 728
Cdd:PRK13763   82 DDDYVLEVIDLSDYGDSpnalrrikgrIIGEGGK-TRRIIEELTGVDI------SVYGKtVAIIGDPEQVEIAR 148

type I K homology (KH) RNA-binding domain found in activating signal cointegrator 1 complex subunit 1 (ASCC1) and similar proteins; ASCC1, also called ASC-1 complex subunit p50, or Trip4 complex subunit p50, plays a role in DNA damage repair as component of the ASCC complex. It is part of the ASC-1 complex that enhances NF-kappa-B, SRF and AP1 transactivation. In cells responding to gastrin-activated paracrine signals, it is involved in the induction of SERPINB2 expression by gastrin. ASCC1 may also play a role in the development of neuromuscular junction.

Pssm-ID: 411847 [Multi-domain] Cd Length: 66 Bit Score: 37.17 E-value: 3.94e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 24655011  754 HKFLIGKNGASIRKIRDATGARIIFPSNEDTDKevITIIGKEES-VKKAREQLEAII 809
Cdd:cd22419   12 FKFIIGKKGETKKRLESETKTQIRIPRQGKEGD--IVITGKDRSgVDSARTRIEVLV 66

tenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the tenth one.

Pssm-ID: 411841 [Multi-domain] Cd Length: 66 Bit Score: 37.24 E-value: 3.99e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 24655011  995 EEELSVPFDLHRTIIGPRGANVRQFMSKHDVHVELPPSELK-SDVIKVCGTPARVAEAREAL 1055
Cdd:cd22413    4 TVEIRAKPEYHRFLIGRGGANIRKIRDNTGARIIFPTARDEdQELITIIGTKEAVEKAKEEL 65

first type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding protein Rnc1 and similar proteins; Rnc1, also called RNA-binding protein that suppresses calcineurin deletion 1, is an RNA-binding protein that acts as an important regulator of the posttranscriptional expression of the MAPK phosphatase Pmp1 in fission yeast. It binds and stabilizes pmp1 mRNA and hence acts as a negative regulator of pmk1 signaling. Overexpression of Rnc1 suppresses the Cl(-) sensitivity of calcineurin deletion. The nuclear export of Rnc1 requires mRNA-binding ability and the mRNA export factor Rae1. Rnc1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.

Pssm-ID: 411883 Cd Length: 70 Bit Score: 37.27 E-value: 4.02e-03

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 24655011  757 LIGKNGASIRKIRDATGARIIF----PSNEDtdkEVITIIGKEESVKKA 801
Cdd:cd22455   15 IIGKGGENIARLRATTGVKAGVskvvPGVHD---RVLTVSGPLEGVAKA 60

first type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 2 (FUBP2) and similar proteins; FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP2 contains four K-homology (KH) RNA-binding domains. The model corresponds to the first one.

Pssm-ID: 411907 [Multi-domain] Cd Length: 71 Bit Score: 37.23 E-value: 4.42e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24655011  669 VTEEVQIPPKYYNSIIGTGGKLISSIMEECGGVSIKFPNSDSKSDK-VTIRGPKDDVEKAKVQLLEL 734
Cdd:cd22479    1 MTEEYRVPDGMVGLIIGRGGEQINKIQQDSGCKVQISPDSGGLPERsVSLTGSPEAVQKAKMMLDDI 67

fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein RCF3 and similar protein; RCF3, also called protein ENHANCED STRESS RESPONSE 1 (ESR1), or protein HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5), or protein REGULATOR OF CBF GENE EXPRESSION 3, or protein SHINY 1 (SHI1), acts as negative regulator of osmotic stress-induced gene expression. It is involved in the regulation of thermotolerance responses under heat stress. It functions as an upstream regulator of heat stress transcription factor (HSF) genes. HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. RCF3 contains five K-homology (KH) RNA-binding domains. The model corresponds to the KH5 domain of RCF3.

Pssm-ID: 411891 [Multi-domain] Cd Length: 71 Bit Score: 37.03 E-value: 4.84e-03

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24655011  596 SHIIEVPIFKQFHKFVIGKGGANIKKIRDETQTKI----DLPAEGDTNEVIVITGKKENVLEAKERIQKI 661
Cdd:cd22463    1 RSKIEFQIPEAVVGLIIGKSGNTIKQISERSGAFVaivqDRYPLEETQKILRISGTEEQLKRAQSLVEGL 70

fifth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the fifth one.

Pssm-ID: 411878 Cd Length: 80 Bit Score: 37.26 E-value: 4.87e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 24655011  315 TVSVEVAKPKHRYVIGPKGSTIAEILQLTGVS---------VEMPPNDSPSETITLRGPQ 365
Cdd:cd22450    5 TRTIKVDRKYHRTIIGPGGSTLRELISKAGGPtdrqeqarlVRFPNQNSESDEVVIRGPK 64

type I K homology (KH) RNA-binding domain found in ankyrin repeat domain-containing protein 17 (ANKRD17) and similar proteins; ANKRD17, also called ankyrin repeat protein 17, or gene trap ankyrin repeat protein (GTAR), or serologically defined breast cancer antigen NY-BR-16, is a ubiquitously expressed ankyrin factor essential for the vascular integrity during embryogenesis. It may be directly involved in the DNA replication process and play pivotal roles in cell cycle and DNA regulation. It is also involved in innate immune defense against bacteria and viruses.

Pssm-ID: 411930 [Multi-domain] Cd Length: 71 Bit Score: 37.04 E-value: 5.02e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24655011  170 SRQVTVPREHFRVILGKGGQRLREIERVTATRINIPSQSDES--EFITIAGTKEGIAQAEQEIRQL 233
Cdd:cd22502    2 SKKVSVPSTVISRVIGRGGCNINAIREFTGAHIDIDKQKDKTgdRIITIRGGTESTRQATQLINAL 67

first type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the first one.

Pssm-ID: 411874 [Multi-domain] Cd Length: 86 Bit Score: 37.39 E-value: 5.14e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 24655011  183 ILGKGGQRLREIERVTATRINIPSQS----------DESEFITIAGTKEGIAQAEQEIRQLSAEQ 237
Cdd:cd22446   21 IIGSRGKNLKSIQDKTGTKIQIPKRNeegnydedddDETVEISIEGDAEGVELAKKEIEAIVKER 85

first type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding protein Rnc1 and similar proteins; Rnc1, also called RNA-binding protein that suppresses calcineurin deletion 1, is an RNA-binding protein that acts as an important regulator of the posttranscriptional expression of the MAPK phosphatase Pmp1 in fission yeast. It binds and stabilizes pmp1 mRNA and hence acts as a negative regulator of pmk1 signaling. Overexpression of Rnc1 suppresses the Cl(-) sensitivity of calcineurin deletion. The nuclear export of Rnc1 requires mRNA-binding ability and the mRNA export factor Rae1. Rnc1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.

Pssm-ID: 411883 Cd Length: 70 Bit Score: 36.89 E-value: 5.84e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 24655011  611 VIGKGGANIKKIRDETQTKIDL--PAEGDTNEVIVITGKKENVLEAKERIQKIQNE 664
Cdd:cd22455   15 IIGKGGENIARLRATTGVKAGVskVVPGVHDRVLTVSGPLEGVAKAFGLIARTLNE 70

second type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ribonucleoprotein K (hnRNP K) and similar proteins; hnRNP K, also called transformation up-regulated nuclear protein (TUNP), is a pre-mRNA binding protein that binds tenaciously to poly(C) sequences. It may be involved in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. It can also bind poly(C) single-stranded DNA. hnRNP K plays an important role in p53/TP53 response to DNA damage, acting at the level of both transcription activation and repression. hnRNP K contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.

Pssm-ID: 411861 [Multi-domain] Cd Length: 70 Bit Score: 36.85 E-value: 5.95e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24655011  533 LHRS----IIGAKGEKIREVKDRYrQVTITI---PTPQENTDIVKLRGPKEDVDKCHKDLLKLV 589
Cdd:cd22433    8 VHQSqagcIIGRAGFKIKELREKT-GATIKVyseCCPRSTDRVVQIGGKPDKVVECIREILELL 70

first type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 mRNA-binding protein (IGF2BP) family; The IGF2BP family includes three members: IGF2BP1/IMP-1/ CRD-BP/ VICKZ1, IGF2BP2/IMP-2/ VICKZ2, and IGF2BP3/IMP-3/VICKZ3, which are RNA-binding factors that recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). They function by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. IGF2BP proteins contain four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the first one.

Pssm-ID: 411828 [Multi-domain] Cd Length: 68 Bit Score: 36.48 E-value: 6.34e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 24655011  758 IGKNGASIRKIRDATGARIIFPSNED---TDKeVITIIGKEESVKKAREQL 805
Cdd:cd22400   15 IGKGGATIRQITQQTGARIDIHRKENagaAEK-AITIYGTPEGCSSACKQI 64

polynucleotide phosphorylase/polyadenylase; Provisional

Pssm-ID: 236995 [Multi-domain] Cd Length: 693 Bit Score: 40.80 E-value: 6.42e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24655011   757 LIGKNGASIRKIRDATGARI-IfpsnEDTDKevITIIGK-EESVKKAREQLEAIIKecdEVTEGEV 820
Cdd:PRK11824  568 VIGPGGKTIREITEETGAKIdI----EDDGT--VKIAATdGEAAEAAKERIEGITA---EPEVGEI 624

second type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the second one.

Pssm-ID: 411834 [Multi-domain] Cd Length: 75 Bit Score: 36.90 E-value: 6.61e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24655011  461 SYYKHIIGKAGANVNRLKDELKVNINI-EEREGQNNIRIEGPKEGVRQAQLELQekidKLENEKSK 525
Cdd:cd22406   14 EHHRFILGKKGKKLQELELKTATKIVIpRQEDNSDEIKITGTKEGIEKARHEIQ----LISDEQAK 75

ninth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the ninth one.

Pssm-ID: 411840 Cd Length: 70 Bit Score: 36.50 E-value: 6.77e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 24655011  599 IEVPIFKQFHKFVIGKGGANIKKIRDET-QTKIDLPAEGDTNEVIVITGKKENVLEAKERIQKIQNE 664
Cdd:cd22412    4 VEVEIPAKLHNSLIGAKGRLIRSIMEECgGVHIHFPPEGSGSDKVTIRGPKEDVEKAKKQLLELANE 70

second type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the second one.

Pssm-ID: 411834 [Multi-domain] Cd Length: 75 Bit Score: 36.52 E-value: 7.01e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24655011  819 EVSVDPKHHKHFVAKRGFILHRIsEECGGVMISFPRVGINSDKVTIKGAKDCIEAARQRIEEIVAD 884
Cdd:cd22406    8 TVNIPKEHHRFILGKKGKKLQEL-ELKTATKIVIPRQEDNSDEIKITGTKEGIEKARHEIQLISDE 72

seventh type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the seventh one.

Pssm-ID: 411838 Cd Length: 67 Bit Score: 36.48 E-value: 7.02e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 24655011  744 TAEVRAKQQHHKFLIGKNGASIRKIRDA-TGARIIFPsNEDTDKEVITIIGKEESVKKAREQLEAI 808
Cdd:cd22410    3 TKDIIIEQRFHRTIIGQKGEKIREIRDKfPQVQITFP-DPGSKSDVVTLRGPKDEVDKCYKYLKKL 67

sixth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the sixth one.

Pssm-ID: 411879 [Multi-domain] Cd Length: 69 Bit Score: 36.28 E-value: 7.41e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 24655011  819 EVSVDPKHHKHFVAKRGFILHRISEECGgVMISFPRVGINSDKVTIKGAKDCIEAARQRIEEIVA 883
Cdd:cd22451    4 DIDIPKEYHRAIIGKGGAVLRELEAETG-CRIQVPKKDDPSGKIRITGARDGVEAATAKILNISD 67

second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) and similar proteins; IGF2BP3, also called IGF2 mRNA-binding protein 3 (IMP-3), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 3, or VICKZ family member 3 (VICKZ3), or KH domain-containing protein overexpressed in cancer, or KOC, is primarily found in the nucleolus, where it can bind to the 5' UTR of the insulin-like growth factor II leader 3 mRNA and may repress translation of insulin-like growth factor II during late development. It acts as an RNA-binding factor that may recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It also modulates the rate and location at which target transcripts encounter the translational apparatus and shields them from endonuclease attacks or microRNA-mediated degradation. IGF2BP3 binds to the 3'-UTR of CD44 mRNA and stabilizes it, hence promotes cell adhesion and invadopodia formation in cancer cells. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP3 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP2 in an RNA-dependent manner. IGF2BP3 contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the second one.

Pssm-ID: 411923 Cd Length: 77 Bit Score: 36.56 E-value: 7.44e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 24655011  183 ILGKGGQRLREIERVTATRINIPSQSDESEF-----ITIAGTKEGIAQAEQEIRQLSAEQYK 239
Cdd:cd22495   14 LIGKEGRNLKKIEQDTDTKITISPLQDLTLYnpertITVKGSIETCAKAEEEIMKKIRESYE 75

type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe meiotically up-regulated gene 60 protein (MUG60) and similar proteins; MUG60 is a KH domain-containing protein that has a role in meiosis. The family also contains Saccharomyces cerevisiae KH domain-containing protein YLL032C.

Pssm-ID: 411881 [Multi-domain] Cd Length: 72 Bit Score: 36.58 E-value: 8.00e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 24655011  606 QFHKFVIGKGGANIKKIRDETQTKI------DLPAEGDTNEVIVIT--GKKENVLEAKERIQ 659
Cdd:cd22453   11 KYHKRIIGKGGQNIQRIMKKYNVFIkfsnanDRADNYYPDNVVIRTpaKNAANLISVKSDIM 72

eighth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the eighth one.

Pssm-ID: 411839 [Multi-domain] Cd Length: 62 Bit Score: 36.03 E-value: 8.07e-03

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 24655011  394 HKYVIGRKGANMKQLEE------DCPNVNVNclEDKIKLEGDPENVDRAVA 438
Cdd:cd22411   11 HKNIIGKGGATIKKIREetntriDLPEENSD--SDVITITGKKEDVEKARE 59

first type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding proteins; The far upstream element-binding protein (FUBP) family includes FUBP1-3. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP proteins contain four K-homology (KH) RNA-binding domains. The model corresponds to the first one.

Pssm-ID: 411824 [Multi-domain] Cd Length: 68 Bit Score: 36.08 E-value: 8.14e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 24655011  175 VPREHFRVILGKGGQRLREIERVTATRINIPSQSDESEF--ITIAGTKEGIAQAEQEIRQ 232
Cdd:cd22396    7 VPDKMVGLIIGRGGEQINRLQAESGAKIQIAPDSGGLPErpCTLTGTPDAIETAKRLIDQ 66

first type I K homology (KH) RNA-binding domain found in the family of MEX-3 RNA-binding proteins; The MEX-3 protein family includes four members, MEX3A/RKHD4, MEX3B/RKHD3/RNF195, MEX3C/ RKHD2/RNF194, and MEX3D/RKHD1/RNF193/TINO. They are homologous of Caenorhabditis elegans MEX-3 protein, a translational regulator that specifies the posterior blastomere identity in the early embryo and contributes to the maintenance of the germline totipotency. Mex-3 proteins are RNA-binding phosphoproteins involved in post-transcriptional regulatory mechanisms. They are characterized by containing two K-homology (KH) RNA-binding domains and a C-terminal RING finger. They bind RNA through their KH domains and shuttle between the nucleus and the cytoplasm via the CRM1-dependent export pathway. The model corresponds to the first KH domain.

Pssm-ID: 411851 Cd Length: 73 Bit Score: 36.31 E-value: 8.17e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 24655011  173 VTVP-REHFRVILGKGGQRLREIERVTATRINIPSQSDESEFItIAGTKEGIAQAEQEIRQLS 234
Cdd:cd22423    5 VPVPsSEHVAEIVGRQGCKIKALRAKTNTYIKTPVRGEEPVFV-VTGRKEDVAMAKREILSAA 66

type I K homology (KH) RNA-binding domain found in ankyrin repeat and KH domain-containing protein 1 (ANKHD1) and similar proteins; ANKHD1, also called HIV-1 Vpr-binding ankyrin repeat protein, or multiple ankyrin repeats single KH domain, or Hmask, is highly expressed in various cancer tissues and is involved in cancer progression, including proliferation and invasion. It acts as a scaffolding protein that may be associated with the abnormal phenotype of leukemia cells. It may play might have a role in MM cell proliferation and cell cycle progression by regulating expression of p21. It also regulates cell cycle progression and proliferation in multiple myeloma cells. ANKHD1 is a component of Hippo signaling pathway. It functions as a positive regulator of YAP1 and promotes cell growth and cell cycle progression through Cyclin A upregulation in prostate cancer cells.

Pssm-ID: 411931 Cd Length: 83 Bit Score: 36.65 E-value: 8.39e-03

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 24655011  170 SRQVTVPREHFRVILGKGGQRLREIERVTATRINIPSQSDES--EFITIAGTKEGIAQAEQEIRQLSAEQYKKSSDRI 245
Cdd:cd22503    2 SKKLSVPASVVSRIMGRGGCNITAIQDVTGAHIDVDKQKDKNgeRMITIRGGTESTRYAVQLINALIQDPAKELEDLI 79

seventh type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the seventh one.

Pssm-ID: 411880 [Multi-domain] Cd Length: 65 Bit Score: 36.14 E-value: 9.22e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 24655011  817 EGEVSVDPKHHKHFVAKRGFILHRISEEcGGVMISFPRVGINSDKVTIKGAKDCIEAARQRIEE 880
Cdd:cd22452    3 RGWIKVSPRYFGRIIGPGGSNINQIREK-SGCFINVPKKNKESDVITLRGTKEGVEKAEEMIKK 65

Uncharacterized conserved protein [Function unknown];

Pssm-ID: 227495 [Multi-domain] Cd Length: 657 Bit Score: 40.35 E-value: 9.34e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24655011  583 KDLLKLVKEIQ---ESSHIIEVPifkQFHKFVIGKGGANIKKIRDETQTKIDLPAEGDTNEVIVITGKKENvLEAKERIQ 659
Cdd:COG5166  366 KTALRIAKLASkyvQGKTQFGVE---DNEDFLRGKKNGKATRIMKGVSCSELSSIVSSTGSIVETNGIGEK-MSFSKKLS 441

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 24655011  660 KIQNELsdIVTEEVQIPPKYYNSIIGTGGKLISSIMEECgGVSIKFPNS-----DSKSDKVTIRGPKDDV 724
Cdd:COG5166  442 IPPTEF--PAEIAFIIMESGHEMIIGTGGIEIQENMVKH-AVDIAFKNFykfgqSQWHDNVLIEAPRKNQ 508

seventh type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the seventh one.

Pssm-ID: 411880 [Multi-domain] Cd Length: 65 Bit Score: 36.14 E-value: 9.59e-03

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 24655011  245 ITVPKVYHPFIVGPYSENLNKLQEETGARINVPPQQVQKDEIVISG 290
Cdd:cd22452    6 IKVSPRYFGRIIGPGGSNINQIREKSGCFINVPKKNKESDVITLRG 51

second type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the second one.

Pssm-ID: 411834 [Multi-domain] Cd Length: 75 Bit Score: 36.13 E-value: 9.79e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 24655011  997 ELSVPFDLHRTIIGPRGANVRQFMSKHDVHVELPPSELKSDVIKVCGTPARVAEAREALVKMIED 1061
Cdd:cd22406    8 TVNIPKEHHRFILGKKGKKLQELELKTATKIVIPRQEDNSDEIKITGTKEGIEKARHEIQLISDE 72