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Conserved domains on  [gi|29789343|ref|NP_598677|]
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eukaryotic translation initiation factor 3 subunit B [Mus musculus]

Protein Classification

RRM_eIF3B and COG5354 domain-containing protein( domain architecture ID 13198628)

protein containing domains KLF9_13_N-like, RRM_eIF3B, and COG5354

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
COG5354 super family cl34988
Uncharacterized protein, contains Trp-Asp (WD) repeat [General function prediction only];
297-796 6.13e-100

Uncharacterized protein, contains Trp-Asp (WD) repeat [General function prediction only];


The actual alignment was detected with superfamily member COG5354:

Pssm-ID: 227657 [Multi-domain]  Cd Length: 561  Bit Score: 320.67  E-value: 6.13e-100
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343 297 VIFESGDRTSIFWNDVKD-PVSIEERARWTETYVRWSPKGTYLATFHQRGIALWGGDKFKQIQRFSHQGVQLIDFSPCER 375
Cdd:COG5354   5 FPLDYSAVISVFWNSQSEvIHTRFESENWPVAYVSESPLGTYLFSEHAAGVECWGGPSKAKLVRFRHPDVKYLDFSPNEK 84

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343 376 YLVTFS---------PLMDTQDDPQaIIIWDILTGHKKRGFHCESSAH--WPIFKWSHDGKFFARMTLDTLSIYE-TPSM 443
Cdd:COG5354  85 YLVTWSrepiiepeiEISPFTSKNN-VFVWDIASGMIVFSFNGISQPYlgWPVLKFSIDDKYVARVVGSSLYIHEiTDNI 163

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343 444 GLLDKKSLKISGIKDFSWSPGGN--IIAFWVPEDKDIPARVTLMQLPTRQEIRVRNLFNVVDCKLHWQKNGDYLCVKVDR 521
Cdd:COG5354 164 EEHPFKNLRPVGILDFSISPEGNhdELAYWTPEKLNKPAMVRILSIPKNSVLVTKNLFKVSGVQLKWQVLGKYLLVLVMT 243

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343 522 TPKG--TQGVVTNFEIFRMREKQVPVDVvEMKETIIAFAWEPNGSKFAVLHGEAPrISVSFYHVKSN------------- 586
Cdd:COG5354 244 HTKSnkSYFGESNLYLLRITERSIPVEK-DLKDPVHDFTWEPLSSRFAVISGYMP-ASVSVFDLRGNlrfyfpeqkrnti 321

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343 587 -----GKIELIKMFDKQQANTIFWSPQGQFVVLAGLRSMN-------GALAFVDTS----------DCTVMNI--AEHYM 642
Cdd:COG5354 322 ffsphERYILFAGFDNLQGNIEIFDPAGRFKVAGAFNGLNtsycdwsPDGQFYDTDttseklrvdnSIKLWDVygAKVFE 401

                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343 643 ASDVEWDPTGRYVVTSVSWWSHKVDNAYWLWTFQGRLLQKNNKDRFCQLLWRPRPPTLLSQDQIKQIKKDLKKYSKIFEQ 722
Cdd:COG5354 402 LTNITWDPSGQYVTTSSSCPKHKVEHGYKIFKIAGALYPEEARGGFKNFAWRPEPPSKLTIESAKKYVKPSRHRFVPFEK 481

                       490       500       510       520       530       540       550
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 29789343 723 KDRLSQSKASKELVERRRTMMEDFRQYRKMAQELyMKQKNERlelrgGVDTDELDSNVDDwEEETIEFFVTEEV 796
Cdd:COG5354 482 AVIMEADSANRSSAPRKKELVEQWPEYSDEDKIR-SLLKKLR-----AIEALKERMRSGE-ELEVIQVNKIETE 548
RRM_eIF3B cd12278
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit B ...
 173-253 9.90e-39

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit B (eIF-3B) and similar proteins; This subfamily corresponds to the RRM domain in eukaryotic translation initiation factor 3 (eIF-3), a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3B, also termed eIF-3 subunit 9, or Prt1 homolog, eIF-3-eta, eIF-3 p110, or eIF-3 p116, is the major scaffolding subunit of eIF-3. It interacts with eIF-3 subunits A, G, I, and J. eIF-3B contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is involved in the interaction with eIF-3J. The interaction between eIF-3B and eIF-3J is crucial for the eIF-3 recruitment to the 40 S ribosomal subunit. eIF-3B also binds directly to domain III of the internal ribosome-entry site (IRES) element of hepatitis-C virus (HCV) RNA through its N-terminal RRM, which may play a critical role in both cap-dependent and cap-independent translation. Additional research has shown that eIF-3B may function as an oncogene in glioma cells and can be served as a potential therapeutic target for anti-glioma therapy. This family also includes the yeast homolog of eIF-3 subunit B (eIF-3B, also termed PRT1 or eIF-3 p90) that interacts with the yeast homologs of eIF-3 subunits A(TIF32), G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In yeast, eIF-3B (PRT1) contains an N-terminal RRM that is directly involved in the interaction with eIF-3A (TIF32) and eIF-3J (HCR1). In contrast to its human homolog, yeast eIF-3B (PRT1) may have potential to bind its total RNA through its RRM domain.


:

Pssm-ID: 409720 [Multi-domain]  Cd Length: 84  Bit Score: 138.10  E-value: 9.90e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343 173 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFG--KIINDYYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHT 249
Cdd:cd12278   1 DSVVVVDGLPVVGEEKLEKLKKVLTKIFSKFGsgKIVGIYMPvDETGKTKGFAFVEYATPEEAKKAVKALNGYKLDKKHT 80


                ....
gi 29789343 250 FRVN 253
Cdd:cd12278  81 FAVN 84
PHA03169 super family cl27451
hypothetical protein; Provisional
 28-173 4.32e-08

hypothetical protein; Provisional


The actual alignment was detected with superfamily member PHA03169:

Pssm-ID: 223003 [Multi-domain]  Cd Length: 413  Bit Score: 56.13  E-value: 4.32e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343   28 SPPTDEAAGSGGSEVGQTEDAEEDAEAG-PEPEVRAKPAAQSEEETATSPAASPTPQSaERSPSQEPSAPGKAEAVGEQA 106
Cdd:PHA03169  91 GPSGSGSESVGSPTPSPSGSAEELASGLsPENTSGSSPESPASHSPPPSPPSHPGPHE-PAPPESHNPSPNQQPSSFLQP 169

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 29789343  107 RGHPSAgaeEEGgsDGSAAEAEPRALENGEADEPSFSDPEdfvDDVSEEEllGDVLKDRPQEADGID 173
Cdd:PHA03169 170 SHEDSP---EEP--EPPTSEPEPDSPGPPQSETPTSSPPP---QSPPDEP--GEPQSPTPQQAPSPN 226
 
Name Accession Description Interval E-value
COG5354 COG5354
Uncharacterized protein, contains Trp-Asp (WD) repeat [General function prediction only];
297-796 6.13e-100

Uncharacterized protein, contains Trp-Asp (WD) repeat [General function prediction only];


Pssm-ID: 227657 [Multi-domain]  Cd Length: 561  Bit Score: 320.67  E-value: 6.13e-100
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343 297 VIFESGDRTSIFWNDVKD-PVSIEERARWTETYVRWSPKGTYLATFHQRGIALWGGDKFKQIQRFSHQGVQLIDFSPCER 375
Cdd:COG5354   5 FPLDYSAVISVFWNSQSEvIHTRFESENWPVAYVSESPLGTYLFSEHAAGVECWGGPSKAKLVRFRHPDVKYLDFSPNEK 84

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343 376 YLVTFS---------PLMDTQDDPQaIIIWDILTGHKKRGFHCESSAH--WPIFKWSHDGKFFARMTLDTLSIYE-TPSM 443
Cdd:COG5354  85 YLVTWSrepiiepeiEISPFTSKNN-VFVWDIASGMIVFSFNGISQPYlgWPVLKFSIDDKYVARVVGSSLYIHEiTDNI 163

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343 444 GLLDKKSLKISGIKDFSWSPGGN--IIAFWVPEDKDIPARVTLMQLPTRQEIRVRNLFNVVDCKLHWQKNGDYLCVKVDR 521
Cdd:COG5354 164 EEHPFKNLRPVGILDFSISPEGNhdELAYWTPEKLNKPAMVRILSIPKNSVLVTKNLFKVSGVQLKWQVLGKYLLVLVMT 243

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343 522 TPKG--TQGVVTNFEIFRMREKQVPVDVvEMKETIIAFAWEPNGSKFAVLHGEAPrISVSFYHVKSN------------- 586
Cdd:COG5354 244 HTKSnkSYFGESNLYLLRITERSIPVEK-DLKDPVHDFTWEPLSSRFAVISGYMP-ASVSVFDLRGNlrfyfpeqkrnti 321

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343 587 -----GKIELIKMFDKQQANTIFWSPQGQFVVLAGLRSMN-------GALAFVDTS----------DCTVMNI--AEHYM 642
Cdd:COG5354 322 ffsphERYILFAGFDNLQGNIEIFDPAGRFKVAGAFNGLNtsycdwsPDGQFYDTDttseklrvdnSIKLWDVygAKVFE 401

                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343 643 ASDVEWDPTGRYVVTSVSWWSHKVDNAYWLWTFQGRLLQKNNKDRFCQLLWRPRPPTLLSQDQIKQIKKDLKKYSKIFEQ 722
Cdd:COG5354 402 LTNITWDPSGQYVTTSSSCPKHKVEHGYKIFKIAGALYPEEARGGFKNFAWRPEPPSKLTIESAKKYVKPSRHRFVPFEK 481

                       490       500       510       520       530       540       550
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 29789343 723 KDRLSQSKASKELVERRRTMMEDFRQYRKMAQELyMKQKNERlelrgGVDTDELDSNVDDwEEETIEFFVTEEV 796
Cdd:COG5354 482 AVIMEADSANRSSAPRKKELVEQWPEYSDEDKIR-SLLKKLR-----AIEALKERMRSGE-ELEVIQVNKIETE 548
eIF2A pfam08662
Eukaryotic translation initiation factor eIF2A; This is a family of eukaryotic translation ...
 496-691 4.75e-85

Eukaryotic translation initiation factor eIF2A; This is a family of eukaryotic translation initiation factors.


Pssm-ID: 462552 [Multi-domain]  Cd Length: 194  Bit Score: 268.37  E-value: 4.75e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343   496 RNLFNVVDCKLHWQKNGDYLCVKVD-RTPKGTQGVVTNFEIFRMREKQVPVDVVEMKET--IIAFAWEPNGSKFAVLHGE 572
Cdd:pfam08662   1 KSFFKADKVQLKWNKNGTYLLVLTDtDVDKTGKSYYGETNLYLIGETGGPDCVVELDKEgpIHDVAWSPNGKEFAVIYGY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343   573 APRIsVSFYHVKSNgkieLIKMFDKQQANTIFWSPQGQFVVLAGLRSMNGALAFVDTSDCTVMNIAEHYMASDVEWDPTG 652
Cdd:pfam08662  81 MPAK-VSFFDLKGN----VIHSFGEQPRNTIFWSPFGRLVLLAGFGNLAGDIEFWDVVNKKKIATAEASNATLCEWSPDG 155

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 29789343   653 RYVVTSVSWWSHKVDNAYWLWTFQGRLLQKNNKDRFCQL 691
Cdd:pfam08662 156 RYFLTATTAPRLRVDNGFKIWHYNGALVYKYDFDELYQV 194
RRM_eIF3B cd12278
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit B ...
 173-253 9.90e-39

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit B (eIF-3B) and similar proteins; This subfamily corresponds to the RRM domain in eukaryotic translation initiation factor 3 (eIF-3), a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3B, also termed eIF-3 subunit 9, or Prt1 homolog, eIF-3-eta, eIF-3 p110, or eIF-3 p116, is the major scaffolding subunit of eIF-3. It interacts with eIF-3 subunits A, G, I, and J. eIF-3B contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is involved in the interaction with eIF-3J. The interaction between eIF-3B and eIF-3J is crucial for the eIF-3 recruitment to the 40 S ribosomal subunit. eIF-3B also binds directly to domain III of the internal ribosome-entry site (IRES) element of hepatitis-C virus (HCV) RNA through its N-terminal RRM, which may play a critical role in both cap-dependent and cap-independent translation. Additional research has shown that eIF-3B may function as an oncogene in glioma cells and can be served as a potential therapeutic target for anti-glioma therapy. This family also includes the yeast homolog of eIF-3 subunit B (eIF-3B, also termed PRT1 or eIF-3 p90) that interacts with the yeast homologs of eIF-3 subunits A(TIF32), G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In yeast, eIF-3B (PRT1) contains an N-terminal RRM that is directly involved in the interaction with eIF-3A (TIF32) and eIF-3J (HCR1). In contrast to its human homolog, yeast eIF-3B (PRT1) may have potential to bind its total RNA through its RRM domain.


Pssm-ID: 409720 [Multi-domain]  Cd Length: 84  Bit Score: 138.10  E-value: 9.90e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343 173 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFG--KIINDYYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHT 249
Cdd:cd12278   1 DSVVVVDGLPVVGEEKLEKLKKVLTKIFSKFGsgKIVGIYMPvDETGKTKGFAFVEYATPEEAKKAVKALNGYKLDKKHT 80


                ....
gi 29789343 250 FRVN 253
Cdd:cd12278  81 FAVN 84
PHA03169 PHA03169
hypothetical protein; Provisional
 28-173 4.32e-08

hypothetical protein; Provisional


Pssm-ID: 223003 [Multi-domain]  Cd Length: 413  Bit Score: 56.13  E-value: 4.32e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343   28 SPPTDEAAGSGGSEVGQTEDAEEDAEAG-PEPEVRAKPAAQSEEETATSPAASPTPQSaERSPSQEPSAPGKAEAVGEQA 106
Cdd:PHA03169  91 GPSGSGSESVGSPTPSPSGSAEELASGLsPENTSGSSPESPASHSPPPSPPSHPGPHE-PAPPESHNPSPNQQPSSFLQP 169

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 29789343  107 RGHPSAgaeEEGgsDGSAAEAEPRALENGEADEPSFSDPEdfvDDVSEEEllGDVLKDRPQEADGID 173
Cdd:PHA03169 170 SHEDSP---EEP--EPPTSEPEPDSPGPPQSETPTSSPPP---QSPPDEP--GEPQSPTPQQAPSPN 226
RRM smart00360
RNA recognition motif;
196-248 5.98e-08

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 50.28  E-value: 5.98e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 29789343    196 IHKIFSKFGKIINDYYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQH 248
Cdd:smart00360  16 LRELFSKFGKVESVRLVrdKETGKSKGFAFVEFESEEDAEKALEALNGKELDGRP 70
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 176-245 1.52e-07

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 49.15  E-value: 1.52e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 29789343   176 IVVDNVPQvgpdrlEKLKNVIHKIFSKFGKIIN-DYYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLD 245
Cdd:pfam00076   1 LFVGNLPP------DTTEEDLKDLFSKFGPIKSiRLVRDETGRSKGFAFVEFEDEEDAEKAIEALNGKELG 65
RCSD pfam05177
RCSD region; Proteins contain this region include C.elegans UNC-89. This region is found ...
 45-129 1.10e-05

RCSD region; Proteins contain this region include C.elegans UNC-89. This region is found repeated in UNC-89 and shows conservation in prolines, lysines and glutamic acids. Proteins with RCSD are involved in muscle M-line assembly, but the function of this region RCSD is not clear.


Pssm-ID: 428350 [Multi-domain]  Cd Length: 101  Bit Score: 44.65  E-value: 1.10e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343    45 TEDAEEDAEAGPEPEVRAKPAAQSEEETATSPAASPTPQSAERSPSQE--PSAPGKAEAVGEQARGHPSAGAEEEGGSDg 122
Cdd:pfam05177  18 TEKQEEKGRAPEEAEHSPKAVGGSEEEKPKSPAKEEAVEAQASSPEAAngCGSPTEEKKAGEKVEEKKSSEVKEERAEN- 96


                  ....*..
gi 29789343   123 saAEAEP 129
Cdd:pfam05177  97 --EEDSP 101
KLF14_N cd21576
N-terminal domain of Kruppel-like factor 14; Kruppel-like factor 14 (KLF14; also known as ...
 22-114 8.28e-05

N-terminal domain of Kruppel-like factor 14; Kruppel-like factor 14 (KLF14; also known as Krueppel-like factor 14 or basic transcription element-binding protein 5/BTEB5) is a protein that in humans is encoded by the KLF14 gene. KLF14 regulates the transcription of various genes, including TGFbetaRII (the type II receptor for TGFbeta). KLF14 is expressed in many tissues, lacks introns, and is subject to parent-specific expression. It also appears to be a master regulator of gene expression in adipose tissue. KLF14 is associated with coronary artery disease, hypercholesterolemia, and type 2 diabetes. KLF9, KLF10, KLF11, KLF13, KLF14, and KLF16 share a conserved alpha-helical motif AA/VXXL that mediates their binding to Sin3A and their activities as transcriptional repressors. KLF14 belongs to a family of proteins, called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Members of the KLF family can act as activators or repressors of transcription depending on cell and promoter context. KLFs regulate various cellular functions, such as proliferation, differentiation, and apoptosis, as well as the development and homeostasis of several types of tissue. In addition to the C-terminal DNA-binding domain, each KLF also has a unique N-terminal activation/repression domain that confers specificity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the N-terminal domain of KLF14.


Pssm-ID: 409238 [Multi-domain]  Cd Length: 195  Bit Score: 44.43  E-value: 8.28e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343  22 QQPASESPPTDEA----AGS------GGSEVGQTEDAEE---DAEAGPEPEVRAKPAAQSEEETATSPAASPTPQSAERS 88
Cdd:cd21576  67 QVPAPSPGAGGAAphllAASvladlrGGAGEGSREDSGEaprASSGSSDPARGSSPTLGSEPAPASGEDAVSGPESSFGA 146

                        90       100
                ....*....|....*....|....*...
gi 29789343  89 P--SQEPSAPGKAEAVGEQARGHPSAGA 114
Cdd:cd21576 147 PaiPSAPAAPGAPAVSGEVPGGAPGAGP 174
COG5373 COG5373
Uncharacterized membrane protein [Function unknown];
33-110 7.90e-04

Uncharacterized membrane protein [Function unknown];


Pssm-ID: 444140 [Multi-domain]  Cd Length: 854  Bit Score: 43.07  E-value: 7.90e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 29789343  33 EAAGSGGSEVGQTEDAEEDAEAGPEPEVRAKPAAQSEEETATsPAASPTPQSAERSPSQEPSA-PGKAEAVGEQARGHP 110
Cdd:COG5373  38 AEAAEAASAPAEPEPEAAAAATAAAPEAAPAPVPEAPAAPPA-AAEAPAPAAAAPPAEAEPAAaPAAASSFEEWLGGNW 115
 
Name Accession Description Interval E-value
COG5354 COG5354
Uncharacterized protein, contains Trp-Asp (WD) repeat [General function prediction only];
297-796 6.13e-100

Uncharacterized protein, contains Trp-Asp (WD) repeat [General function prediction only];


Pssm-ID: 227657 [Multi-domain]  Cd Length: 561  Bit Score: 320.67  E-value: 6.13e-100
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343 297 VIFESGDRTSIFWNDVKD-PVSIEERARWTETYVRWSPKGTYLATFHQRGIALWGGDKFKQIQRFSHQGVQLIDFSPCER 375
Cdd:COG5354   5 FPLDYSAVISVFWNSQSEvIHTRFESENWPVAYVSESPLGTYLFSEHAAGVECWGGPSKAKLVRFRHPDVKYLDFSPNEK 84

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343 376 YLVTFS---------PLMDTQDDPQaIIIWDILTGHKKRGFHCESSAH--WPIFKWSHDGKFFARMTLDTLSIYE-TPSM 443
Cdd:COG5354  85 YLVTWSrepiiepeiEISPFTSKNN-VFVWDIASGMIVFSFNGISQPYlgWPVLKFSIDDKYVARVVGSSLYIHEiTDNI 163

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343 444 GLLDKKSLKISGIKDFSWSPGGN--IIAFWVPEDKDIPARVTLMQLPTRQEIRVRNLFNVVDCKLHWQKNGDYLCVKVDR 521
Cdd:COG5354 164 EEHPFKNLRPVGILDFSISPEGNhdELAYWTPEKLNKPAMVRILSIPKNSVLVTKNLFKVSGVQLKWQVLGKYLLVLVMT 243

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343 522 TPKG--TQGVVTNFEIFRMREKQVPVDVvEMKETIIAFAWEPNGSKFAVLHGEAPrISVSFYHVKSN------------- 586
Cdd:COG5354 244 HTKSnkSYFGESNLYLLRITERSIPVEK-DLKDPVHDFTWEPLSSRFAVISGYMP-ASVSVFDLRGNlrfyfpeqkrnti 321

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343 587 -----GKIELIKMFDKQQANTIFWSPQGQFVVLAGLRSMN-------GALAFVDTS----------DCTVMNI--AEHYM 642
Cdd:COG5354 322 ffsphERYILFAGFDNLQGNIEIFDPAGRFKVAGAFNGLNtsycdwsPDGQFYDTDttseklrvdnSIKLWDVygAKVFE 401

                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343 643 ASDVEWDPTGRYVVTSVSWWSHKVDNAYWLWTFQGRLLQKNNKDRFCQLLWRPRPPTLLSQDQIKQIKKDLKKYSKIFEQ 722
Cdd:COG5354 402 LTNITWDPSGQYVTTSSSCPKHKVEHGYKIFKIAGALYPEEARGGFKNFAWRPEPPSKLTIESAKKYVKPSRHRFVPFEK 481

                       490       500       510       520       530       540       550
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 29789343 723 KDRLSQSKASKELVERRRTMMEDFRQYRKMAQELyMKQKNERlelrgGVDTDELDSNVDDwEEETIEFFVTEEV 796
Cdd:COG5354 482 AVIMEADSANRSSAPRKKELVEQWPEYSDEDKIR-SLLKKLR-----AIEALKERMRSGE-ELEVIQVNKIETE 548
eIF2A pfam08662
Eukaryotic translation initiation factor eIF2A; This is a family of eukaryotic translation ...
 496-691 4.75e-85

Eukaryotic translation initiation factor eIF2A; This is a family of eukaryotic translation initiation factors.


Pssm-ID: 462552 [Multi-domain]  Cd Length: 194  Bit Score: 268.37  E-value: 4.75e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343   496 RNLFNVVDCKLHWQKNGDYLCVKVD-RTPKGTQGVVTNFEIFRMREKQVPVDVVEMKET--IIAFAWEPNGSKFAVLHGE 572
Cdd:pfam08662   1 KSFFKADKVQLKWNKNGTYLLVLTDtDVDKTGKSYYGETNLYLIGETGGPDCVVELDKEgpIHDVAWSPNGKEFAVIYGY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343   573 APRIsVSFYHVKSNgkieLIKMFDKQQANTIFWSPQGQFVVLAGLRSMNGALAFVDTSDCTVMNIAEHYMASDVEWDPTG 652
Cdd:pfam08662  81 MPAK-VSFFDLKGN----VIHSFGEQPRNTIFWSPFGRLVLLAGFGNLAGDIEFWDVVNKKKIATAEASNATLCEWSPDG 155

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 29789343   653 RYVVTSVSWWSHKVDNAYWLWTFQGRLLQKNNKDRFCQL 691
Cdd:pfam08662 156 RYFLTATTAPRLRVDNGFKIWHYNGALVYKYDFDELYQV 194
RRM_eIF3B cd12278
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit B ...
 173-253 9.90e-39

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit B (eIF-3B) and similar proteins; This subfamily corresponds to the RRM domain in eukaryotic translation initiation factor 3 (eIF-3), a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3B, also termed eIF-3 subunit 9, or Prt1 homolog, eIF-3-eta, eIF-3 p110, or eIF-3 p116, is the major scaffolding subunit of eIF-3. It interacts with eIF-3 subunits A, G, I, and J. eIF-3B contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is involved in the interaction with eIF-3J. The interaction between eIF-3B and eIF-3J is crucial for the eIF-3 recruitment to the 40 S ribosomal subunit. eIF-3B also binds directly to domain III of the internal ribosome-entry site (IRES) element of hepatitis-C virus (HCV) RNA through its N-terminal RRM, which may play a critical role in both cap-dependent and cap-independent translation. Additional research has shown that eIF-3B may function as an oncogene in glioma cells and can be served as a potential therapeutic target for anti-glioma therapy. This family also includes the yeast homolog of eIF-3 subunit B (eIF-3B, also termed PRT1 or eIF-3 p90) that interacts with the yeast homologs of eIF-3 subunits A(TIF32), G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In yeast, eIF-3B (PRT1) contains an N-terminal RRM that is directly involved in the interaction with eIF-3A (TIF32) and eIF-3J (HCR1). In contrast to its human homolog, yeast eIF-3B (PRT1) may have potential to bind its total RNA through its RRM domain.


Pssm-ID: 409720 [Multi-domain]  Cd Length: 84  Bit Score: 138.10  E-value: 9.90e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343 173 DSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFG--KIINDYYP-EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHT 249
Cdd:cd12278   1 DSVVVVDGLPVVGEEKLEKLKKVLTKIFSKFGsgKIVGIYMPvDETGKTKGFAFVEYATPEEAKKAVKALNGYKLDKKHT 80


                ....
gi 29789343 250 FRVN 253
Cdd:cd12278  81 FAVN 84
PHA03169 PHA03169
hypothetical protein; Provisional
 28-173 4.32e-08

hypothetical protein; Provisional


Pssm-ID: 223003 [Multi-domain]  Cd Length: 413  Bit Score: 56.13  E-value: 4.32e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343   28 SPPTDEAAGSGGSEVGQTEDAEEDAEAG-PEPEVRAKPAAQSEEETATSPAASPTPQSaERSPSQEPSAPGKAEAVGEQA 106
Cdd:PHA03169  91 GPSGSGSESVGSPTPSPSGSAEELASGLsPENTSGSSPESPASHSPPPSPPSHPGPHE-PAPPESHNPSPNQQPSSFLQP 169

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 29789343  107 RGHPSAgaeEEGgsDGSAAEAEPRALENGEADEPSFSDPEdfvDDVSEEEllGDVLKDRPQEADGID 173
Cdd:PHA03169 170 SHEDSP---EEP--EPPTSEPEPDSPGPPQSETPTSSPPP---QSPPDEP--GEPQSPTPQQAPSPN 226
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 176-253 4.59e-08

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 50.74  E-value: 4.59e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 29789343 176 IVVDNVPQvgpdrlEKLKNVIHKIFSKFGKIIN-DYYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKqHTFRVN 253
Cdd:cd00590   1 LFVGNLPP------DTTEEDLRELFSKFGEVVSvRIVRDRDGKSKGFAFVEFESPEDAEKALEALNGTELGG-RPLKVS 72
RRM smart00360
RNA recognition motif;
196-248 5.98e-08

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 50.28  E-value: 5.98e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 29789343    196 IHKIFSKFGKIINDYYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQH 248
Cdd:smart00360  16 LRELFSKFGKVESVRLVrdKETGKSKGFAFVEFESEEDAEKALEALNGKELDGRP 70
WD40 COG2319
WD40 repeat [General function prediction only];
301-495 7.32e-08

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 55.69  E-value: 7.32e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343 301 SGDRTSIFWndvkDPVSIEERARWTE-----TYVRWSPKGTYLAT-FHQRGIALWGGDKFKQIQRFS-HQG-VQLIDFSP 372
Cdd:COG2319 139 SADGTVRLW----DLATGKLLRTLTGhsgavTSVAFSPDGKLLASgSDDGTVRLWDLATGKLLRTLTgHTGaVRSVAFSP 214

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343 373 CERYLVTFSplmdtqdDPQAIIIWDILTGHKKRGFHCESSAHWPIfKWSHDGKFFARMTLD-TLSIYETPSMGLLDKKSL 451
Cdd:COG2319 215 DGKLLASGS-------ADGTVRLWDLATGKLLRTLTGHSGSVRSV-AFSPDGRLLASGSADgTVRLWDLATGELLRTLTG 286

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....
gi 29789343 452 KISGIKDFSWSPGGNIIAFwVPEDKdipaRVTLMQLPTRQEIRV 495
Cdd:COG2319 287 HSGGVNSVAFSPDGKLLAS-GSDDG----TVRLWDLATGKLLRT 325
WD40 COG2319
WD40 repeat [General function prediction only];
301-469 8.21e-08

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 55.30  E-value: 8.21e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343 301 SGDRTSIFWN-DVKDPVSIEERARWTETYVRWSPKGTYLATFHQRG-IALWGGDKFKQIQRFSHQ--GVQLIDFSPCERY 376
Cdd:COG2319 223 SADGTVRLWDlATGKLLRTLTGHSGSVRSVAFSPDGRLLASGSADGtVRLWDLATGELLRTLTGHsgGVNSVAFSPDGKL 302

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343 377 LVTFSplmdtqDDpQAIIIWDILTGHKKRGFHCESSAHWPIfKWSHDGKFFARMTLD-TLSIYETPSMGLLDKKSLKISG 455
Cdd:COG2319 303 LASGS------DD-GTVRLWDLATGKLLRTLTGHTGAVRSV-AFSPDGKTLASGSDDgTVRLWDLATGELLRTLTGHTGA 374

                       170
                ....*....|....
gi 29789343 456 IKDFSWSPGGNIIA 469
Cdd:COG2319 375 VTSVAFSPDGRTLA 388
PHA03169 PHA03169
hypothetical protein; Provisional
 24-145 8.24e-08

hypothetical protein; Provisional


Pssm-ID: 223003 [Multi-domain]  Cd Length: 413  Bit Score: 55.36  E-value: 8.24e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343   24 PASESPPTDEAAGSGGSEVGQTEDAEEDAEAGPEPEvrAKPAAQSEEETATSPAASPTPQSAERSPSQEP-SAPGKAEAV 102
Cdd:PHA03169 131 PASHSPPPSPPSHPGPHEPAPPESHNPSPNQQPSSF--LQPSHEDSPEEPEPPTSEPEPDSPGPPQSETPtSSPPPQSPP 208

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 29789343  103 GEQARGHPSAGAEEEGGSDGSAAEAEPRALENgEADEPSFSDP 145
Cdd:PHA03169 209 DEPGEPQSPTPQQAPSPNTQQAVEHEDEPTEP-EREGPPFPGH 250
WD40 COG2319
WD40 repeat [General function prediction only];
329-469 1.16e-07

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 54.92  E-value: 1.16e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343 329 VRWSPKGTYLATFHQ-RGIALWGGDKFKQIQRFSHQG--VQLIDFSPCERYLVTFSplmdtqDDpQAIIIWDILTGHKKR 405
Cdd:COG2319 210 VAFSPDGKLLASGSAdGTVRLWDLATGKLLRTLTGHSgsVRSVAFSPDGRLLASGS------AD-GTVRLWDLATGELLR 282

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 29789343 406 GFHCESSAHWPIfKWSHDGKFFARMTLD-TLSIYETPSMGLLDKKSLKISGIKDFSWSPGGNIIA 469
Cdd:COG2319 283 TLTGHSGGVNSV-AFSPDGKLLASGSDDgTVRLWDLATGKLLRTLTGHTGAVRSVAFSPDGKTLA 346
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 176-245 1.52e-07

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 49.15  E-value: 1.52e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 29789343   176 IVVDNVPQvgpdrlEKLKNVIHKIFSKFGKIIN-DYYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLD 245
Cdd:pfam00076   1 LFVGNLPP------DTTEEDLKDLFSKFGPIKSiRLVRDETGRSKGFAFVEFEDEEDAEKAIEALNGKELG 65
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 23-141 5.62e-07

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 53.45  E-value: 5.62e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343   23 QPASESPPTDEAAGSGGSEVGQTedAEEDAEAGPEPEVRAKPAAQSeeETATSPAASPTPQSAERSPSQEPSAPGKAEAV 102
Cdd:PRK07764 392 GAPAAAAPSAAAAAPAAAPAPAA--AAPAAAAAPAPAAAPQPAPAP--APAPAPPSPAGNAPAGGAPSPPPAAAPSAQPA 467

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 29789343  103 GEQARGHPSAGAEEEGGSDGSAAEAEPRALENGEADEPS 141
Cdd:PRK07764 468 PAPAAAPEPTAAPAPAPPAAPAPAAAPAAPAAPAAPAGA 506
WD40 COG2319
WD40 repeat [General function prediction only];
329-469 8.68e-07

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 52.22  E-value: 8.68e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343 329 VRWSPKGTYLATFHQ-RGIALWGGDKFKQIQRFS-HQG-VQLIDFSPCERYLVTFSplmdtqDDpQAIIIWDILTGHKKR 405
Cdd:COG2319 126 VAFSPDGKTLASGSAdGTVRLWDLATGKLLRTLTgHSGaVTSVAFSPDGKLLASGS------DD-GTVRLWDLATGKLLR 198

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 29789343 406 GFHCESSAHWPIfKWSHDGKFFARMTLD-TLSIYETPSMGLLDKKSLKISGIKDFSWSPGGNIIA 469
Cdd:COG2319 199 TLTGHTGAVRSV-AFSPDGKLLASGSADgTVRLWDLATGKLLRTLTGHSGSVRSVAFSPDGRLLA 262
PRK12495 PRK12495
hypothetical protein; Provisional
 22-174 1.55e-06

hypothetical protein; Provisional


Pssm-ID: 183558 [Multi-domain]  Cd Length: 226  Bit Score: 49.87  E-value: 1.55e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343   22 QQPASESpptDEAAGSGGSEVGQTEDAEEDAEAGPEPEvrAKPAAQSEEETATSPAASPTPQSAERSPSQEPsapgkaea 101
Cdd:PRK12495  65 QQPVTED---GAAGDDAGDGAEATAPSDAGSQASPDDD--AQPAAEAEAADQSAPPEASSTSATDEAATDPP-------- 131

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 29789343  102 VGEQARGHPSAGAEEEGGSDGSAAEAEPRALENGEADEPSFSDPEDFVDDVSEEELLGDVLKDRPQEADGIDS 174
Cdd:PRK12495 132 ATAAARDGPTPDPTAQPATPDERRSPRQRPPVSGEPPTPSTPDAHVAGTLQAARESLVETLARFARRAAATDD 204
PRK07003 PRK07003
DNA polymerase III subunit gamma/tau;
22-146 3.37e-06

DNA polymerase III subunit gamma/tau;


Pssm-ID: 235906 [Multi-domain]  Cd Length: 830  Bit Score: 50.62  E-value: 3.37e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343   22 QQPASESPPTDEAAGSGGSEVGQTEDAEEDAEAGPEPEVRAKPAAQSEEETATSPAASPTPQSAERSPSQEPSAPGKAEA 101
Cdd:PRK07003 412 PKAAAAAAATRAEAPPAAPAPPATADRGDDAADGDAPVPAKANARASADSRCDERDAQPPADSGSASAPASDAPPDAAFE 491

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 29789343  102 VGEQARGHPSAGAEEEGGSDGSAAEAEPRALENGEADEPSFSDPE 146
Cdd:PRK07003 492 PAPRAAAPSAATPAAVPDARAPAAASREDAPAAAAPPAPEARPPT 536
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 22-141 3.90e-06

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 50.37  E-value: 3.90e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343   22 QQPASESPPTDEAAGSGGSEVGQTED-----AEEDAEAGPEPE-VRAKPAAQSEEETATSPAASPTPQSAERSPSQEPSA 95
Cdd:PRK07764 627 PAPAGAAAAPAEASAAPAPGVAAPEHhpkhvAVPDASDGGDGWpAKAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPA 706

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 29789343   96 PGKAEAVGEQARGHPSAGAEEEGGSDGSAAEAEPRALENGEADEPS 141
Cdd:PRK07764 707 ATPPAGQADDPAAQPPQAAQGASAPSPAADDPVPLPPEPDDPPDPA 752
PRK13108 PRK13108
prolipoprotein diacylglyceryl transferase; Reviewed
 25-156 8.47e-06

prolipoprotein diacylglyceryl transferase; Reviewed


Pssm-ID: 237284 [Multi-domain]  Cd Length: 460  Bit Score: 49.21  E-value: 8.47e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343   25 ASESPPTDEAAGSGGSEVGQTEDAE------------------EDAEAGPEPEVRAKPAAQSEEETATSPAASPTPQSAE 86
Cdd:PRK13108 312 ASAVGPVGPGEPNQPDDVAEAVKAEvaevtdevaaesvvqvadRDGESTPAVEETSEADIEREQPGDLAGQAPAAHQVDA 391

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343   87 RSPSQEPSAPgKAEAVGEQARGHPSAgAEEEGGSDGSAAEAEPRAleNGEADEPSFSDPEDFVDDVSEEE 156
Cdd:PRK13108 392 EAASAAPEEP-AALASEAHDETEPEV-PEKAAPIPDPAKPDELAV--AGPGDDPAEPDGIRRQDDFSSRR 457
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 24-168 8.54e-06

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 49.60  E-value: 8.54e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343   24 PASESPPTDEAAGSGGSEVGQTEDAEEDAEAGPEPEVRAKPAAQSEEETATSPAASPTPQ----SAERSPSQ-------- 91
Cdd:PRK07764 661 DASDGGDGWPAKAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPAGQADDPAAQppqaAQGASAPSpaaddpvp 740

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343   92 ---EPSAPGKAEAVGEQARGHPSAGAEEEGGSDGSAA--EAEPRALEN--GEADEPSFSDPEDFVDDVSEEELLGDVLKD 164
Cdd:PRK07764 741 lppEPDDPPDPAGAPAQPPPPPAPAPAAAPAAAPPPSppSEEEEMAEDdaPSMDDEDRRDAEEVAMELLEEELGAKKIEE 820


                 ....
gi 29789343  165 RPQE 168
Cdd:PRK07764 821 FAAD 824
RCSD pfam05177
RCSD region; Proteins contain this region include C.elegans UNC-89. This region is found ...
 45-129 1.10e-05

RCSD region; Proteins contain this region include C.elegans UNC-89. This region is found repeated in UNC-89 and shows conservation in prolines, lysines and glutamic acids. Proteins with RCSD are involved in muscle M-line assembly, but the function of this region RCSD is not clear.


Pssm-ID: 428350 [Multi-domain]  Cd Length: 101  Bit Score: 44.65  E-value: 1.10e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343    45 TEDAEEDAEAGPEPEVRAKPAAQSEEETATSPAASPTPQSAERSPSQE--PSAPGKAEAVGEQARGHPSAGAEEEGGSDg 122
Cdd:pfam05177  18 TEKQEEKGRAPEEAEHSPKAVGGSEEEKPKSPAKEEAVEAQASSPEAAngCGSPTEEKKAGEKVEEKKSSEVKEERAEN- 96


                  ....*..
gi 29789343   123 saAEAEP 129
Cdd:pfam05177  97 --EEDSP 101
RRM_CSTF2_CSTF2T cd12671
RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), cleavage ...
 176-253 1.36e-05

RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), cleavage stimulation factor subunit 2 tau variant (CSTF2T) and similar proteins; This subgroup corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64.


Pssm-ID: 410072 [Multi-domain]  Cd Length: 85  Bit Score: 44.04  E-value: 1.36e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343 176 IVVDNVPQVGPDrlEKLKNvihkIFSKFGKIIND--YYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQhTFRVN 253
Cdd:cd12671   9 VFVGNIPYEATE--EQLKD----IFSEVGPVVSFrlVYDRETGKPKGYGFCEYQDQETALSAMRNLNGYELNGR-ALRVD 81
PRK13108 PRK13108
prolipoprotein diacylglyceryl transferase; Reviewed
 39-138 3.88e-05

prolipoprotein diacylglyceryl transferase; Reviewed


Pssm-ID: 237284 [Multi-domain]  Cd Length: 460  Bit Score: 46.90  E-value: 3.88e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343   39 GSEVGQTEDAEEDAEAGPEPEVRAKPAAQSEEETATSPAASPTP---QSAERSPSQEPSAPGKAEAVGEQARGHPSAGAE 115
Cdd:PRK13108 357 GESTPAVEETSEADIEREQPGDLAGQAPAAHQVDAEAASAAPEEpaaLASEAHDETEPEVPEKAAPIPDPAKPDELAVAG 436

                         90       100
                 ....*....|....*....|...
gi 29789343  116 EEGGSDGSAAEAEPRALENGEAD 138
Cdd:PRK13108 437 PGDDPAEPDGIRRQDDFSSRRRR 459
RRM2_PUF60 cd12371
RNA recognition motif 2 (RRM2) found in (U)-binding-splicing factor PUF60 and similar proteins; ...
 196-253 5.00e-05

RNA recognition motif 2 (RRM2) found in (U)-binding-splicing factor PUF60 and similar proteins; This subfamily corresponds to the RRM2 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition.


Pssm-ID: 409806 [Multi-domain]  Cd Length: 77  Bit Score: 42.27  E-value: 5.00e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343 196 IHKIFSKFGKIIN-DYYPE-EDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHtFRVN 253
Cdd:cd12371  17 IKSVFEAFGKIKScSLAPDpETGKHKGYGFIEYENPQSAQDAIASMNLFDLGGQY-LRVG 75
PRK13108 PRK13108
prolipoprotein diacylglyceryl transferase; Reviewed
 25-180 5.16e-05

prolipoprotein diacylglyceryl transferase; Reviewed


Pssm-ID: 237284 [Multi-domain]  Cd Length: 460  Bit Score: 46.51  E-value: 5.16e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343   25 ASESPPTDEAAG------SGGSEVGQTEDAEEDAEAGPEpEVRAKPAAQSEEETATSPAAS-PTPQSAERSPSQEP-SAP 96
Cdd:PRK13108 300 PAELAAAAVASAasavgpVGPGEPNQPDDVAEAVKAEVA-EVTDEVAAESVVQVADRDGEStPAVEETSEADIEREqPGD 378

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343   97 GKAEAVGEqarghPSAGAEEEGGSDGSAAEAEPRALENGEADEPSFSDPEDfvDDVSEEELLGDVLKDRPQEADGIDSVI 176
Cdd:PRK13108 379 LAGQAPAA-----HQVDAEAASAAPEEPAALASEAHDETEPEVPEKAAPIP--DPAKPDELAVAGPGDDPAEPDGIRRQD 451


                 ....
gi 29789343  177 VVDN 180
Cdd:PRK13108 452 DFSS 455
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
22-147 5.43e-05

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 46.79  E-value: 5.43e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343   22 QQPASESPPTDEAAGSGGSEVGQTEDAEEDAEAGPEPEVRAKPAAQ------SEEETATSPAASPTPQSAERSPSQEPSA 95
Cdd:PRK12323 392 PAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPARRSPAPEALAAARqasargPGGAPAPAPAPAAAPAAAARPAAAGPRP 471

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 29789343   96 PGkAEAVGEQARGHPSAGA----------EEEGGSDGSAA----EAEPRALENGEADEPSFSDPED 147
Cdd:PRK12323 472 VA-AAAAAAPARAAPAAAPapadddpppwEELPPEFASPApaqpDAAPAGWVAESIPDPATADPDD 536
rne PRK10811
ribonuclease E; Reviewed
 44-184 5.62e-05

ribonuclease E; Reviewed


Pssm-ID: 236766 [Multi-domain]  Cd Length: 1068  Bit Score: 46.96  E-value: 5.62e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343    44 QTEDAEEDAEAGPEPEVRAKPAAQSEEETATSPAASPTPQSAERSPSQEPSAPGKAEAVGEQARGHPSAGAEEEggSDGS 123
Cdd:PRK10811  854 QVEEQREAEEVQVQPVVAEVPVAAAVEPVVSAPVVEAVAEVVEEPVVVAEPQPEEVVVVETTHPEVIAAPVTEQ--PQVI 931

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 29789343   124 AAEAEPRALENGEADEPSfSDPEDFVDDVSEEELLGDVLKDRPQEADGIDSVIVVDNVPQV 184
Cdd:PRK10811  932 TESDVAVAQEVAEHAEPV-VEPQDETADIEEAAETAEVVVAEPEVVAQPAAPVVAEVAAEV 991
PRK12678 PRK12678
transcription termination factor Rho; Provisional
 33-171 5.68e-05

transcription termination factor Rho; Provisional


Pssm-ID: 237171 [Multi-domain]  Cd Length: 672  Bit Score: 46.82  E-value: 5.68e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343   33 EAAGSGGSEVGQTEDAEEDAEAGPEPEVRAkPAAQSEEETATSPAAsPTPQSAERSPSQEPSAPGKAEAVGEQARGHPSA 112
Cdd:PRK12678  56 KEARGGGAAAAAATPAAPAAAARRAARAAA-AARQAEQPAAEAAAA-KAEAAPAARAAAAAAAEAASAPEAAQARERRER 133

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 29789343  113 GAEEEGGSDGSAAEAE--PRALENGEADEPSFSDPEDFVDDVSEEEllgdvlkDRPQEADG 171
Cdd:PRK12678 134 GEAARRGAARKAGEGGeqPATEARADAAERTEEEERDERRRRGDRE-------DRQAEAER 187
RRM_CSTF2_RNA15_like cd12398
RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ...
 196-244 7.18e-05

RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins; This subfamily corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. The family also includes yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins. RNA15 is a core subunit of cleavage factor IA (CFIA), an essential transcriptional 3'-end processing factor from Saccharomyces cerevisiae. RNA recognition by CFIA is mediated by an N-terminal RRM, which is contained in the RNA15 subunit of the complex. The RRM of RNA15 has a strong preference for GU-rich RNAs, mediated by a binding pocket that is entirely conserved in both yeast and vertebrate RNA15 orthologs.


Pssm-ID: 409832 [Multi-domain]  Cd Length: 77  Bit Score: 41.73  E-value: 7.18e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 29789343 196 IHKIFSKFGKIIND--YYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKL 244
Cdd:cd12398  17 LKEIFSEVGPVVSFrlVTDRETGKPKGYGFCEFRDAETALSAVRNLNGYEL 67
KLF14_N cd21576
N-terminal domain of Kruppel-like factor 14; Kruppel-like factor 14 (KLF14; also known as ...
 22-114 8.28e-05

N-terminal domain of Kruppel-like factor 14; Kruppel-like factor 14 (KLF14; also known as Krueppel-like factor 14 or basic transcription element-binding protein 5/BTEB5) is a protein that in humans is encoded by the KLF14 gene. KLF14 regulates the transcription of various genes, including TGFbetaRII (the type II receptor for TGFbeta). KLF14 is expressed in many tissues, lacks introns, and is subject to parent-specific expression. It also appears to be a master regulator of gene expression in adipose tissue. KLF14 is associated with coronary artery disease, hypercholesterolemia, and type 2 diabetes. KLF9, KLF10, KLF11, KLF13, KLF14, and KLF16 share a conserved alpha-helical motif AA/VXXL that mediates their binding to Sin3A and their activities as transcriptional repressors. KLF14 belongs to a family of proteins, called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Members of the KLF family can act as activators or repressors of transcription depending on cell and promoter context. KLFs regulate various cellular functions, such as proliferation, differentiation, and apoptosis, as well as the development and homeostasis of several types of tissue. In addition to the C-terminal DNA-binding domain, each KLF also has a unique N-terminal activation/repression domain that confers specificity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the N-terminal domain of KLF14.


Pssm-ID: 409238 [Multi-domain]  Cd Length: 195  Bit Score: 44.43  E-value: 8.28e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343  22 QQPASESPPTDEA----AGS------GGSEVGQTEDAEE---DAEAGPEPEVRAKPAAQSEEETATSPAASPTPQSAERS 88
Cdd:cd21576  67 QVPAPSPGAGGAAphllAASvladlrGGAGEGSREDSGEaprASSGSSDPARGSSPTLGSEPAPASGEDAVSGPESSFGA 146

                        90       100
                ....*....|....*....|....*...
gi 29789343  89 P--SQEPSAPGKAEAVGEQARGHPSAGA 114
Cdd:cd21576 147 PaiPSAPAAPGAPAVSGEVPGGAPGAGP 174
RRM2_NsCP33_like cd21608
RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ...
 176-254 9.81e-05

RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and similar proteins; The family includes NsCP33, Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (CP31A) and mitochondrial glycine-rich RNA-binding protein 2 (AtGR-RBP2). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. AtGR-RBP2, also called AtRBG2, or glycine-rich protein 2 (AtGRP2), or mitochondrial RNA-binding protein 1a (At-mRBP1a), plays a role in RNA transcription or processing during stress. It binds RNAs and DNAs sequence with a preference to single-stranded nucleic acids. AtGR-RBP2 displays strong affinity to poly(U) sequence. It exerts cold and freezing tolerance, probably by exhibiting an RNA chaperone activity during the cold and freezing adaptation process. Some members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.


Pssm-ID: 410187 [Multi-domain]  Cd Length: 76  Bit Score: 41.39  E-value: 9.81e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343 176 IVVDNVP-QVGPDRLeklknviHKIFSKFG-----KIINDyypEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHt 249
Cdd:cd21608   2 LYVGNLSwDTTEDDL-------RDLFSEFGevesaKVITD---RETGRSRGFGFVTFSTAEAAEAAIDALNGKELDGRS- 70


                ....*
gi 29789343 250 FRVNL 254
Cdd:cd21608  71 IVVNE 75
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 26-147 1.10e-04

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 45.93  E-value: 1.10e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343    26 SESPPTDEAAGSGGSEVGQTEDAEEDAEAGPEPEVRAKP-----AAQSEEETATSPAASPTPQSAERSPSQEPSAPGK-- 98
Cdd:PHA03307  228 AADDAGASSSDSSSSESSGCGWGPENECPLPRPAPITLPtriweASGWNGPSSRPGPASSSSSPRERSPSPSPSSPGSgp 307

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 29789343    99 ----AEAVGEQARGHPSAGAEEEGGSDGSAAEAEPRALENGEAdePSFSDPED 147
Cdd:PHA03307  308 apssPRASSSSSSSRESSSSSTSSSSESSRGAAVSPGPSPSRS--PSPSRPPP 358
RRM3_RBM19_RRM2_MRD1 cd12316
RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition ...
 196-241 1.15e-04

RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409755 [Multi-domain]  Cd Length: 74  Bit Score: 41.17  E-value: 1.15e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 29789343 196 IHKIFSKFGKIINDYYP--EEDGKTKGYIFLEYASPAHAVDAVKNADG 241
Cdd:cd12316  16 LRELFEAFGKISEVHIPldKQTKRSKGFAFVLFVIPEDAVKAYQELDG 63
RRM_ist3_like cd12411
RNA recognition motif (RRM) found in ist3 family; This subfamily corresponds to the RRM of the ...
 199-252 1.54e-04

RNA recognition motif (RRM) found in ist3 family; This subfamily corresponds to the RRM of the ist3 family that includes fungal U2 small nuclear ribonucleoprotein (snRNP) component increased sodium tolerance protein 3 (ist3), X-linked 2 RNA-binding motif proteins (RBMX2) found in Metazoa and plants, and similar proteins. Gene IST3 encoding ist3, also termed U2 snRNP protein SNU17 (Snu17p), is a novel yeast Saccharomyces cerevisiae protein required for the first catalytic step of splicing and for progression of spliceosome assembly. It binds specifically to the U2 snRNP and is an intrinsic component of prespliceosomes and spliceosomes. Yeast ist3 contains an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In the yeast pre-mRNA retention and splicing complex, the atypical RRM of ist3 functions as a scaffold that organizes the other two constituents, Bud13p (bud site selection 13) and Pml1p (pre-mRNA leakage 1). Fission yeast Schizosaccharomyces pombe gene cwf29 encoding ist3, also termed cell cycle control protein cwf29, is an RNA-binding protein complexed with cdc5 protein 29. It also contains one RRM. The biological function of RBMX2 remains unclear. It shows high sequence similarity to yeast ist3 protein and harbors one RRM as well.


Pssm-ID: 409845 [Multi-domain]  Cd Length: 89  Bit Score: 41.04  E-value: 1.54e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 29789343 199 IFSKFGKIINDYYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQhTFRV 252
Cdd:cd12411  29 VFSQYGEIVDINLVrdKKTGKSKGFAFLAYEDQRSTILAVDNLNGIKLLGR-TIRV 83
PHA03169 PHA03169
hypothetical protein; Provisional
 26-192 1.79e-04

hypothetical protein; Provisional


Pssm-ID: 223003 [Multi-domain]  Cd Length: 413  Bit Score: 44.58  E-value: 1.79e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343   26 SESPPTDEAAGSGGSEVGQTEDAEEDAEAGPEPEVRAKPAAQSEEETAtSPAASPTPQ-----SAERSPSQEPSAPGKAE 100
Cdd:PHA03169 108 SGSAEELASGLSPENTSGSSPESPASHSPPPSPPSHPGPHEPAPPESH-NPSPNQQPSsflqpSHEDSPEEPEPPTSEPE 186

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343  101 AVGEQARGHPSAGAEEEGGsDGSAAEAEPRALENGEADEPSFSDPEDFVDDVSEEELLGDvlkdrPQEADGIDSVIVVDN 180
Cdd:PHA03169 187 PDSPGPPQSETPTSSPPPQ-SPPDEPGEPQSPTPQQAPSPNTQQAVEHEDEPTEPEREGP-----PFPGHRSHSYTVVGW 260

                        170
                 ....*....|..
gi 29789343  181 VPQVGPDRLEKL 192
Cdd:PHA03169 261 KPSTRPGGVPKL 272
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 33-146 1.86e-04

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 44.98  E-value: 1.86e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343   33 EAAGSGGSEVGQTEDAEEDAEAGPEPEVrAKPAAQSEEETATSPAASPTPQ-SAERSPSQEPSAPGKAEAVGEQARGHPS 111
Cdd:PRK07764 585 EAVVGPAPGAAGGEGPPAPASSGPPEEA-ARPAAPAAPAAPAAPAPAGAAAaPAEASAAPAPGVAAPEHHPKHVAVPDAS 663

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 29789343  112 AGAEEEGGSDGSAAEAEPRALENGEADEPSFSDPE 146
Cdd:PRK07764 664 DGGDGWPAKAGGAAPAAPPPAPAPAAPAAPAGAAP 698
PRK07003 PRK07003
DNA polymerase III subunit gamma/tau;
25-147 2.09e-04

DNA polymerase III subunit gamma/tau;


Pssm-ID: 235906 [Multi-domain]  Cd Length: 830  Bit Score: 44.84  E-value: 2.09e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343   25 ASESPPTDEAAGSGGSEVGQTEDAEEDAEAGPEPEVRAKPAAQSEEetATSPAASPTP-QSAERSPSQEPSAPGKAEAVg 103
Cdd:PRK07003 393 ASAVPAVTAVTGAAGAALAPKAAAAAAATRAEAPPAAPAPPATADR--GDDAADGDAPvPAKANARASADSRCDERDAQ- 469

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 29789343  104 EQARGHPSAGAEEEGGSDgSAAEAEPRALENGEADEPSFSDPED 147
Cdd:PRK07003 470 PPADSGSASAPASDAPPD-AAFEPAPRAAAPSAATPAAVPDARA 512
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 22-147 2.17e-04

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 45.16  E-value: 2.17e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343    22 QQPASESPPTDEAAGSGGSEVGQTEDAEeDAEAGPEPEVRAKPAAQSEEETATSPAASPTPQSAERSPSQEPSAPGKAEA 101
Cdd:PHA03307  782 RGAGSSPPVRAEAAFRRPGRLRRSGPAA-DAASRTASKRKSRSHTPDGGSESSGPARPPGAAARPPPARSSESSKSKPAA 860

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 29789343   102 VGEQARGHPSAGAEEEGGSDGSAAEAEPRALENGEADEPSFSDPED 147
Cdd:PHA03307  861 AGGRARGKNGRRRPRPPEPRARPGAAAPPKAAAAAPPAGAPAPRPR 906
RRM_RNPS1 cd12365
RNA recognition motif (RRM) found in RNA-binding protein with serine-rich domain 1 (RNPS1) and ...
 188-247 2.31e-04

RNA recognition motif (RRM) found in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins; This subfamily corresponds to the RRM of RNPS1 and its eukaryotic homologs. RNPS1, also termed RNA-binding protein prevalent during the S phase, or SR-related protein LDC2, was originally characterized as a general pre-mRNA splicing activator, which activates both constitutive and alternative splicing of pre-mRNA in vitro.It has been identified as a protein component of the splicing-dependent mRNP complex, or exon-exon junction complex (EJC), and is directly involved in mRNA surveillance. Furthermore, RNPS1 is a splicing regulator whose activator function is controlled in part by CK2 (casein kinase II) protein kinase phosphorylation. It can also function as a squamous-cell carcinoma antigen recognized by T cells-3 (SART3)-binding protein, and is involved in the regulation of mRNA splicing. RNPS1 contains an N-terminal serine-rich (S) domain, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and the C-terminal arginine/serine/proline-rich (RS/P) domain.


Pssm-ID: 409800 [Multi-domain]  Cd Length: 73  Bit Score: 40.23  E-value: 2.31e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 29789343 188 RLEKL-KNV----IHKIFSKFGKIINDYYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ 247
Cdd:cd12365   2 HVGKLtRNVtkdhLKEIFSVYGTVKNVDLPidREPNLPRGYAYVEFESPEDAEKAIKHMDGGQIDGQ 68
PRK07003 PRK07003
DNA polymerase III subunit gamma/tau;
34-140 3.29e-04

DNA polymerase III subunit gamma/tau;


Pssm-ID: 235906 [Multi-domain]  Cd Length: 830  Bit Score: 44.46  E-value: 3.29e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343   34 AAGSGGSEVGQTEDAEedAEAGPEPEVRAKPAAQSEEETATSP-----AASPTPQSAERSPSQEPSAPGKAEAVGEQARG 108
Cdd:PRK07003 361 AVTGGGAPGGGVPARV--AGAVPAPGARAAAAVGASAVPAVTAvtgaaGAALAPKAAAAAAATRAEAPPAAPAPPATADR 438

                         90       100       110
                 ....*....|....*....|....*....|..
gi 29789343  109 HPSAGAEEEGGSDGSAAEAEPRALENGEADEP 140
Cdd:PRK07003 439 GDDAADGDAPVPAKANARASADSRCDERDAQP 470
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 22-155 3.40e-04

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 44.39  E-value: 3.40e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343    22 QQPASESPPTDEAAGSGGSEV-GQTEDAEEDAEAGPEPEVRAKPAAQSEEETATSPAASP--------TPQSAERSPSQE 92
Cdd:PHA03307  111 PSSPDPPPPTPPPASPPPSPApDLSEMLRPVGSPGPPPAASPPAAGASPAAVASDAASSRqaalplssPEETARAPSSPP 190

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 29789343    93 PSAPGKAEAVGEQARGHP-----SAGAEEEGGSDGSAAEAEPRAlengEADEPSFSDPEDFVDDVSEE 155
Cdd:PHA03307  191 AEPPPSTPPAAASPRPPRrsspiSASASSPAPAPGRSAADDAGA----SSSDSSSSESSGCGWGPENE 254
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 23-187 4.98e-04

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 44.01  E-value: 4.98e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343    23 QPASESPPTDEAAGSGGSEVgqTEDAEEDAEAGPEPEVRAKPAAQSEEETATSPAASPTPQSAERSPSQEPS-APGKAEA 101
Cdd:PHA03307   60 AACDRFEPPTGPPPGPGTEA--PANESRSTPTWSLSTLAPASPAREGSPTPPGPSSPDPPPPTPPPASPPPSpAPDLSEM 137

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343   102 V----GEQARGHPSAGAEEEGGSDGSAAEAEPRALEN-----GEADEPSFSDPEDFVDDVSEEEllgdvLKDRPQEADGI 172
Cdd:PHA03307  138 LrpvgSPGPPPAASPPAAGASPAAVASDAASSRQAALplsspEETARAPSSPPAEPPPSTPPAA-----ASPRPPRRSSP 212

                         170
                  ....*....|....*
gi 29789343   173 DSVIVVDNVPQVGPD 187
Cdd:PHA03307  213 ISASASSPAPAPGRS 227
RRM_PPIE cd12347
RNA recognition motif (RRM) found in cyclophilin-33 (Cyp33) and similar proteins; This ...
 195-254 5.54e-04

RNA recognition motif (RRM) found in cyclophilin-33 (Cyp33) and similar proteins; This subfamily corresponds to the RRM of Cyp33, also termed peptidyl-prolyl cis-trans isomerase E (PPIase E), or cyclophilin E, or rotamase E. Cyp33 is a nuclear RNA-binding cyclophilin with an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal PPIase domain. Cyp33 possesses RNA-binding activity and preferentially binds to polyribonucleotide polyA and polyU, but hardly to polyG and polyC. It binds specifically to mRNA, which can stimulate its PPIase activity. Moreover, Cyp33 interacts with the third plant homeodomain (PHD3) zinc finger cassette of the mixed lineage leukemia (MLL) proto-oncoprotein and a poly-A RNA sequence through its RRM domain. It further mediates downregulation of the expression of MLL target genes HOXC8, HOXA9, CDKN1B, and C-MYC, in a proline isomerase-dependent manner. Cyp33 also possesses a PPIase activity that catalyzes cis-trans isomerization of the peptide bond preceding a proline, which has been implicated in the stimulation of folding and conformational changes in folded and unfolded proteins. The PPIase activity can be inhibited by the immunosuppressive drug cyclosporin A.


Pssm-ID: 409783 [Multi-domain]  Cd Length: 75  Bit Score: 39.13  E-value: 5.54e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 29789343 195 VIHKIFSKFGKIINDYYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQhTFRVNL 254
Cdd:cd12347  14 VLHAAFIPFGDIVDIQIPldYETEKHRGFAFVEFEEAEDAAAAIDNMNESELFGR-TIRVNL 74
motB PRK05996
MotB family protein;
29-135 5.58e-04

MotB family protein;


Pssm-ID: 235665 [Multi-domain]  Cd Length: 423  Bit Score: 43.15  E-value: 5.58e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343   29 PPTDEAAGSGGSEVGQTEDAEEdAEAGPEPEVRAKPAAQSEEETATSPAASPTPQSAERSPSQEPSAPGKAEAvgEQARG 108
Cdd:PRK05996 200 PPGQAREQAQGAKSATAAPATV-PQAAPLPQAQPKKAATEEELIADAKKAATGEPAANAAKAAKPEPMPDDQQ--KEAEQ 276

                         90       100
                 ....*....|....*....|....*...
gi 29789343  109 HPSAGAEEEGGSDGSAAEA-EPRALENG 135
Cdd:PRK05996 277 LQAAIAQAIGGVAGKLAEGvTVTPVEGG 304
RRM_SRSF2_SRSF8 cd12311
RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF2, SRSF8 and ...
 178-245 5.59e-04

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins; This subfamily corresponds to the RRM of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or splicing component, 35 kDa (splicing factor SC35 or SC-35), is a prototypical SR protein that plays important roles in the alternative splicing of pre-mRNA. It is also involved in transcription elongation by directly or indirectly mediating the recruitment of elongation factors to the C-terminal domain of polymerase II. SRSF2 is exclusively localized in the nucleus and is restricted to nuclear processes. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. The RRM is responsible for the specific recognition of 5'-SSNG-3' (S=C/G) RNA. In the regulation of alternative splicing events, it specifically binds to cis-regulatory elements on the pre-mRNA. The RS domain modulates SRSF2 activity through phosphorylation, directly contacts RNA, and promotes protein-protein interactions with the spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a novel mammalian SR splicing factor encoded by a PR264/SC35 functional retropseudogene. SRSF8 is localized in the nucleus and does not display the same activity as PR264/SC35. It functions as an essential splicing factor in complementing a HeLa cell S100 extract deficient in SR proteins. Like SRSF2, SRSF8 contains a single N-terminal RRM and a C-terminal RS domain.


Pssm-ID: 409751 [Multi-domain]  Cd Length: 73  Bit Score: 39.17  E-value: 5.59e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 29789343 178 VDNVP-QVGPDRLEKLknvihkiFSKFGKIINDYYPEE--DGKTKGYIFLEYASPAHAVDAVKNADGYKLD 245
Cdd:cd12311   3 VDNLTyRTTPDDLRRV-------FEKYGEVGDVYIPRDryTRESRGFAFVRFYDKRDAEDAIDAMDGAELD 66
eIF2A pfam08662
Eukaryotic translation initiation factor eIF2A; This is a family of eukaryotic translation ...
 304-381 6.98e-04

Eukaryotic translation initiation factor eIF2A; This is a family of eukaryotic translation initiation factors.


Pssm-ID: 462552 [Multi-domain]  Cd Length: 194  Bit Score: 41.49  E-value: 6.98e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343   304 RTSIFWNDVKDPVSIEERARWTetyVRWSPKGTY--LATFH--QRGIALWGGDKFKQIQRFSHQGVQLIDFSPCERYLVT 379
Cdd:pfam08662  84 KVSFFDLKGNVIHSFGEQPRNT---IFWSPFGRLvlLAGFGnlAGDIEFWDVVNKKKIATAEASNATLCEWSPDGRYFLT 160


                  ..
gi 29789343   380 FS 381
Cdd:pfam08662 161 AT 162
COG5373 COG5373
Uncharacterized membrane protein [Function unknown];
33-110 7.90e-04

Uncharacterized membrane protein [Function unknown];


Pssm-ID: 444140 [Multi-domain]  Cd Length: 854  Bit Score: 43.07  E-value: 7.90e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 29789343  33 EAAGSGGSEVGQTEDAEEDAEAGPEPEVRAKPAAQSEEETATsPAASPTPQSAERSPSQEPSA-PGKAEAVGEQARGHP 110
Cdd:COG5373  38 AEAAEAASAPAEPEPEAAAAATAAAPEAAPAPVPEAPAAPPA-AAEAPAPAAAAPPAEAEPAAaPAAASSFEEWLGGNW 115
kgd PRK12270
multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine ...
 22-115 9.52e-04

multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine pyrophosphate-binding subunit/dihydrolipoyllysine-residue succinyltransferase subunit;


Pssm-ID: 237030 [Multi-domain]  Cd Length: 1228  Bit Score: 42.96  E-value: 9.52e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343    22 QQPASESPPTDEAAGSGGSEVGQTEDAEEDAEAGPEPEVRAKPAAQSEEETATSPAASPTPQSAERSPSQEPSAPGKAEA 101
Cdd:PRK12270   36 YGPGSTAAPTAAAAAAAAAASAPAAAPAAKAPAAPAPAPPAAAAPAAPPKPAAAAAAAAAPAAPPAAAAAAAPAAAAVED 115

                          90
                  ....*....|....
gi 29789343   102 VGEQARGHPSAGAE 115
Cdd:PRK12270  116 EVTPLRGAAAAVAK 129
PHA03169 PHA03169
hypothetical protein; Provisional
 24-174 9.76e-04

hypothetical protein; Provisional


Pssm-ID: 223003 [Multi-domain]  Cd Length: 413  Bit Score: 42.27  E-value: 9.76e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343   24 PASESPPTDEAAGSGGSEVGQTEDAEEDAEAGPEPEVRAKPAAQSEEETATSPAASPTPQSAERSPSQEPSA-PGKAEAV 102
Cdd:PHA03169  51 PTTSGPQVRAVAEQGHRQTESDTETAEESRHGEKEERGQGGPSGSGSESVGSPTPSPSGSAEELASGLSPENtSGSSPES 130

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343  103 GEQARGHPSAGAEEEGGSDGSAAEAEPRALENGEA-DEPSFSD-------PEDFVDDVSEEELLGDVLKDRPQEADGIDS 174
Cdd:PHA03169 131 PASHSPPPSPPSHPGPHEPAPPESHNPSPNQQPSSfLQPSHEDspeepepPTSEPEPDSPGPPQSETPTSSPPPQSPPDE 210
DamX COG3266
Cell division protein DamX, binds to the septal ring, contains C-terminal SPOR domain [Cell ...
 22-99 9.94e-04

Cell division protein DamX, binds to the septal ring, contains C-terminal SPOR domain [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 442497 [Multi-domain]  Cd Length: 455  Bit Score: 42.53  E-value: 9.94e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 29789343  22 QQPASESPPTDEAAGSGGSEVGQTEDAEEDAEAGPEPEVRAKPAAQSEEETATSPAASPTPQSAERSPSQEPSAPGKA 99
Cdd:COG3266 260 QASSASAPATTSLGEQQEVSLPPAVAAQPAAAAAAQPSAVALPAAPAAAAAAAAPAEAAAPQPTAAKPVVTETAAPAA 337
PRK07003 PRK07003
DNA polymerase III subunit gamma/tau;
23-145 1.10e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 235906 [Multi-domain]  Cd Length: 830  Bit Score: 42.53  E-value: 1.10e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343   23 QPASESPPTDEAAGSGGSEVGQTEDAEEDAEAGPEPEVRAKPAAQSEEETAtsPAASPTPQSAERSP--SQEPSAPGKAE 100
Cdd:PRK07003 473 DSGSASAPASDAPPDAAFEPAPRAAAPSAATPAAVPDARAPAAASREDAPA--AAAPPAPEARPPTPaaAAPAARAGGAA 550

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 29789343  101 AVGEQARghpSAG---AEEEGGSDGSAAE--AEPRALENGEADEPSFSDP 145
Cdd:PRK07003 551 AALDVLR---NAGmrvSSDRGARAAAAAKpaAAPAAAPKPAAPRVAVQVP 597
FimV COG3170
Type IV pilus assembly protein FimV [Cell motility, Extracellular structures];
4-170 1.40e-03

Type IV pilus assembly protein FimV [Cell motility, Extracellular structures];


Pssm-ID: 442403 [Multi-domain]  Cd Length: 508  Bit Score: 42.09  E-value: 1.40e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343   4 AENVAVPEAAEERAEPARQQPASESPPTDEAAGSGGSEVG---QTEDAEEDAEAGPEPEVRAKPAAQSE----------- 69
Cdd:COG3170 225 AQSADWAAYRARLAAAVEPAPAAAAPAAPPAAAAAAGPVPaaaEDTLSPEVTAAAAAEEADALPEAAAElaerlaaleaq 304

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343  70 --------EETATSPAASPT-PQSAERSPSQEPSAPgkaEAVGEQARGHPsagAEEEGGSDGSAAEAEPRALENGEADEP 140
Cdd:COG3170 305 laelqrllALKNPAPAAAVSaPAAAAAAATVEAAAP---AAAAQPAAAAP---APALDNPLLLAGLLRRRKAEADEVDPV 378

                       170       180       190
                ....*....|....*....|....*....|.
gi 29789343 141 SFSD-PEDFVDDVSEEELLGDVLKDRPQEAD 170
Cdd:COG3170 379 AEADvYLAYGRDDQAEEILKEALASEPERLD 409
RRM_snRNP70 cd12236
RNA recognition motif (RRM) found in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and ...
 196-245 1.56e-03

RNA recognition motif (RRM) found in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins; This subfamily corresponds to the RRM of U1-70K, also termed snRNP70, a key component of the U1 snRNP complex, which is one of the key factors facilitating the splicing of pre-mRNA via interaction at the 5' splice site, and is involved in regulation of polyadenylation of some viral and cellular genes, enhancing or inhibiting efficient poly(A) site usage. U1-70K plays an essential role in targeting the U1 snRNP to the 5' splice site through protein-protein interactions with regulatory RNA-binding splicing factors, such as the RS protein ASF/SF2. Moreover, U1-70K protein can specifically bind to stem-loop I of the U1 small nuclear RNA (U1 snRNA) contained in the U1 snRNP complex. It also mediates the binding of U1C, another U1-specific protein, to the U1 snRNP complex. U1-70K contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region at the N-terminal half, and two serine/arginine-rich (SR) domains at the C-terminal half. The RRM is responsible for the binding of stem-loop I of U1 snRNA molecule. Additionally, the most prominent immunodominant region that can be recognized by auto-antibodies from autoimmune patients may be located within the RRM. The SR domains are involved in protein-protein interaction with SR proteins that mediate 5' splice site recognition. For instance, the first SR domain is necessary and sufficient for ASF/SF2 Binding. The family also includes Drosophila U1-70K that is an essential splicing factor required for viability in flies, but its SR domain is dispensable. The yeast U1-70k doesn't contain easily recognizable SR domains and shows low sequence similarity in the RRM region with other U1-70k proteins and therefore not included in this family. The RRM domain is dispensable for yeast U1-70K function.


Pssm-ID: 409682 [Multi-domain]  Cd Length: 91  Bit Score: 38.37  E-value: 1.56e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 29789343 196 IHKIFSKFGKI--INDYYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLD 245
Cdd:cd12236  18 LRREFEKYGPIkrVRLVRDKKTGKSRGYAFIEFEHERDMKAAYKHADGKKID 69
RRM_HP0827_like cd12399
RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; ...
 190-253 1.56e-03

RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827.


Pssm-ID: 409833 [Multi-domain]  Cd Length: 75  Bit Score: 37.88  E-value: 1.56e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 29789343 190 EKLKNVihkiFSKFGKIINDYYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQhTFRVN 253
Cdd:cd12399  13 EQLKSL----FGQFGAVFDVKLPmdRETKRPRGFGFVELQEEESAEKAIAKLDGTDFMGR-TIRVN 73
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 21-101 1.65e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 41.90  E-value: 1.65e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343   21 RQQPASESPPTDEAAGSGGSevgQTEDAEEDAEAGPEPEVRAKPAAQSEEETATSPAASPTPQSAersPSQEPSAPGKAE 100
Cdd:PRK07764 428 APQPAPAPAPAPAPPSPAGN---APAGGAPSPPPAAAPSAQPAPAPAAAPEPTAAPAPAPPAAPA---PAAAPAAPAAPA 501


                 .
gi 29789343  101 A 101
Cdd:PRK07764 502 A 502
RRM1_Crp79 cd21619
RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and ...
 196-244 1.79e-03

RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and similar proteins; Crp79, also called meiotic expression up-regulated protein 5 (Mug5), or polyadenylate-binding protein crp79, or PABP, or poly(A)-binding protein, is an auxiliary mRNA export factor that binds the poly(A) tail of mRNA and is involved in the export of mRNA from the nucleus to the cytoplasm. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410198 [Multi-domain]  Cd Length: 78  Bit Score: 37.89  E-value: 1.79e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 29789343 196 IHKIFSKFGKIINDYYPEED----GKTKGYIFLEYASPAHAVDAVKNADGYKL 244
Cdd:cd21619  18 LEKIFSRYGQVESVRRPPIHtdkaDRTTGFGFIKYTDAESAERAMQQADGILL 70
RRM3_RBM19 cd12567
RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and similar proteins; ...
 196-241 1.82e-03

RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and similar proteins; This subgroup corresponds to the RRM3 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409983 [Multi-domain]  Cd Length: 79  Bit Score: 37.76  E-value: 1.82e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 29789343 196 IHKIFSKFGKIINDYYPEED--GKTKGYIFLEYASPAHAVDAVKNADG 241
Cdd:cd12567  19 LEKLFSKYGPLSEVHFPIDSltKKPKGFAFVTYMIPEHAVKAYAELDG 66
KLF9_13_N-like cd21975
Kruppel-like factor (KLF) 9, KLF13, KLF14, KLF16, and similar proteins; Kruppel/Krueppel-like ...
 24-131 2.17e-03

Kruppel-like factor (KLF) 9, KLF13, KLF14, KLF16, and similar proteins; Kruppel/Krueppel-like transcription factors (KLFs) belong to a family of proteins, called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Members of the KLF family can act as activators or repressors of transcription depending on cell and promoter context. KLFs regulate various cellular functions, such as proliferation, differentiation, and apoptosis, as well as the development and homeostasis of several types of tissue. KLF9, KLF10, KLF11, KLF13, KLF14, and KLF16 share a conserved alpha-helical motif AA/VXXL that mediates their binding to Sin3A and their activities as transcriptional repressors. In addition to the C-terminal DNA-binding domain, each KLF also has a unique N-terminal activation/repression domain that confers specificity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the related N-terminal domains of KLF9, KLF13, KLF14, KLF16, and similar proteins.


Pssm-ID: 409240 [Multi-domain]  Cd Length: 163  Bit Score: 39.67  E-value: 2.17e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343  24 PASESPPTDEAAGSGGSEVGQTEDAEEDAEAGPEPEVRAKPAAQSEEETATSPAASPTPQSAERSPSQE---PSAPGKAE 100
Cdd:cd21975  49 PGPAWKPDGADSPGLVTAAPHLLAANVLAPLRGPSVEGSSLESGDADMGSDSDVAPASGAAASTSPESSsdaASSPSPLS 128

                        90       100       110
                ....*....|....*....|....*....|.
gi 29789343 101 AVGEQARGHPSAGAEEEGGSDGSAAEAEPRA 131
Cdd:cd21975 129 LLHPGEAGLEPERPRPRVRRGVRRRGVTPAA 159
RRM_RBMX_like cd12382
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y ...
 195-245 2.18e-03

RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins; This subfamily corresponds to the RRM domain of hnRNP G, also termed glycoprotein p43 or RBMX, an RNA-binding motif protein located on the X chromosome. It is expressed ubiquitously and has been implicated in the splicing control of several pre-mRNAs. Moreover, hnRNP G may function as a regulator of transcription for SREBP-1c and GnRH1. Research has shown that hnRNP G may also act as a tumor-suppressor since it upregulates the Txnip gene and promotes the fidelity of DNA end-joining activity. In addition, hnRNP G appears to play a critical role in proper neural development of zebrafish and frog embryos. The family also includes several paralogs of hnRNP G, such as hRBMY and hnRNP G-T (also termed RNA-binding motif protein, X-linked-like-2). Both, hRBMY and hnRNP G-T, are exclusively expressed in testis and critical for male fertility. Like hnRNP G, hRBMY and hnRNP G-T interact with factors implicated in the regulation of pre-mRNA splicing, such as hTra2-beta1 and T-STAR. Although members in this family share a high conserved N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), they appear to recognize different RNA targets. For instance, hRBMY interacts specifically with a stem-loop structure in which the loop is formed by the sequence CA/UCAA. In contrast, hnRNP G associates with single stranded RNA sequences containing a CCA/C motif. In addition to the RRM, hnRNP G contains a nascent transcripts targeting domain (NTD) in the middle region and a novel auxiliary RNA-binding domain (RBD) in its C-terminal region. The C-terminal RBD exhibits distinct RNA binding specificity, and would play a critical role in the regulation of alternative splicing by hnRNP G.


Pssm-ID: 409816 [Multi-domain]  Cd Length: 80  Bit Score: 37.77  E-value: 2.18e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 29789343 195 VIHKIFSKFGKI-----INDyypEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLD 245
Cdd:cd12382  17 ALEAVFGKYGRIvevllMKD---RETNKSRGFAFVTFESPADAKDAARDMNGKELD 69
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 48-145 2.31e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 41.51  E-value: 2.31e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343   48 AEEDAEAGPEPEVRAKPAAQSEEETATSPAASPTPQSAERSPSQEPSAPGKAEAVGEQARGHPSAGAEEEGGSDGSAAEA 127
Cdd:PRK07764 390 GAGAPAAAAPSAAAAAPAAAPAPAAAAPAAAAAPAPAAAPQPAPAPAPAPAPPSPAGNAPAGGAPSPPPAAAPSAQPAPA 469

                         90
                 ....*....|....*...
gi 29789343  128 EPRALENGEADEPSFSDP 145
Cdd:PRK07764 470 PAAAPEPTAAPAPAPPAA 487
RRM5_RBM19_like cd12318
RNA recognition motif 5 (RRM5) found in RNA-binding protein 19 (RBM19 or RBD-1) and similar ...
 198-245 2.42e-03

RNA recognition motif 5 (RRM5) found in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins; This subfamily corresponds to the RRM5 of RBM19 and RRM4 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409757 [Multi-domain]  Cd Length: 80  Bit Score: 37.59  E-value: 2.42e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 29789343 198 KIFSKFGK-----IINDYYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLD 245
Cdd:cd12318  19 KHFEKCGPirsvtIAKKKDPKGPLLSMGYGFVEFKSPEAAQKALKQLQGTVLD 71
CobT2 COG4547
Cobalamin biosynthesis cobaltochelatase CobT subunit [Coenzyme transport and metabolism]; ...
 39-157 2.43e-03

Cobalamin biosynthesis cobaltochelatase CobT subunit [Coenzyme transport and metabolism]; Cobalamin biosynthesis cobaltochelatase CobT subunit is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis


Pssm-ID: 443611 [Multi-domain]  Cd Length: 608  Bit Score: 41.32  E-value: 2.43e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343  39 GSEVGQTEDAEEDAEAGPEPEvrakpAAQSEEETATSPAASPTPQSAERSpsqEPSAPGKAEAVGEQARGHPSAGAEEEG 118
Cdd:COG4547 208 AEELGEDEDEEDEDDEDDSGE-----QEEDEEDGEDEDEESDEGAEAEDA---EASGDDAEEGESEAAEAESDEMAEEAE 279

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|.
gi 29789343 119 GSDGSAAEAEPRALENGEADEPSFS------------DPEDFVDdvsEEEL 157
Cdd:COG4547 280 GEDSEEPGEPWRPNAPPPDDPADPDykvfttafdevvAAEDLCD---PEEL 327
RRM1_SF2_plant_like cd12599
RNA recognition motif 1 (RRM1) found in plant pre-mRNA-splicing factor SF2 and similar ...
 196-254 2.52e-03

RNA recognition motif 1 (RRM1) found in plant pre-mRNA-splicing factor SF2 and similar proteins; This subgroup corresponds to the RRM1 of SF2, also termed SR1 protein, a plant serine/arginine (SR)-rich phosphoprotein similar to the mammalian splicing factor SF2/ASF. It promotes splice site switching in mammalian nuclear extracts. SF2 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal domain rich in proline, serine and lysine residues (PSK domain), a composition reminiscent of histones. This PSK domain harbors a putative phosphorylation site for the mitotic kinase cyclin/p34cdc2.


Pssm-ID: 410011 [Multi-domain]  Cd Length: 72  Bit Score: 37.42  E-value: 2.52e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 29789343 196 IHKIFSKFGKI--INDYYPEedgKTKGYIFLEYASPAHAVDAVKNADGYKLDKqHTFRVNL 254
Cdd:cd12599  16 VEDLFSKYGPVvsIDLKIPP---RPPAYAFVEFEDARDAEDAIRGRDGYDFDG-HRLRVEL 72
PRK12373 PRK12373
NADH-quinone oxidoreductase subunit E;
39-151 3.02e-03

NADH-quinone oxidoreductase subunit E;


Pssm-ID: 237082 [Multi-domain]  Cd Length: 400  Bit Score: 40.94  E-value: 3.02e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343   39 GSEVGQTEDAEEDAeAGPEPEVRAKPaaqseeetatsPAASPTPQSAERSPSQEPSAPGKAEAVGEQARGHPSAGAEEeG 118
Cdd:PRK12373 225 GTEVPLLAPWQGDA-APVPPSEAARP-----------KSADAETNAALKTPATAPKAAAKNAKAPEAQPVSGTAAAEP-A 291

                         90       100       110
                 ....*....|....*....|....*....|...
gi 29789343  119 GSDGSAAEAEPRALENGEADEPSFSDPEDFVDD 151
Cdd:PRK12373 292 PKEAAKAAAAAAKPALEDKPRPLGIARPGGADD 324
PHA03247 PHA03247
large tegument protein UL36; Provisional
 23-148 3.38e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 41.08  E-value: 3.38e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343    23 QPASESPPTDEAAGSggsevgQTEDAEEDAEAGPEPEVRAKPAAQSEEETATSPAASPTPQSAERSPSQEPSAPGKAEAV 102
Cdd:PHA03247 2902 PDQPERPPQPQAPPP------PQPQPQPPPPPQPQPPPPPPPRPQPPLAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVP 2975

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 29789343   103 GEQA-----------------RGHPSAGAEEEGGSDGSAAEAEPRA------------LENGEADEPSFSDPEDF 148
Cdd:PHA03247 2976 RFRVpqpapsreapasstpplTGHSLSRVSSWASSLALHEETDPPPvslkqtlwppddTEDSDADSLFDSDSERS 3050
DamX COG3266
Cell division protein DamX, binds to the septal ring, contains C-terminal SPOR domain [Cell ...
 22-107 3.56e-03

Cell division protein DamX, binds to the septal ring, contains C-terminal SPOR domain [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 442497 [Multi-domain]  Cd Length: 455  Bit Score: 40.60  E-value: 3.56e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343  22 QQPASESPPTDEAAGSggSEVGQTEDAEEDAEAGPEPEVRAKPAAQSEEETATSPAASPTPQSAERSPSQEPSAPGKAEA 101
Cdd:COG3266 280 LPPAVAAQPAAAAAAQ--PSAVALPAAPAAAAAAAAPAEAAAPQPTAAKPVVTETAAPAAPAPEAAAAAAAPAAPAVAKK 357


                ....*.
gi 29789343 102 VGEQAR 107
Cdd:COG3266 358 LAADEQ 363
PRK07003 PRK07003
DNA polymerase III subunit gamma/tau;
24-114 3.79e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 235906 [Multi-domain]  Cd Length: 830  Bit Score: 40.99  E-value: 3.79e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343   24 PASESPPTDEAAGSGGSEVGQTEDAEEDAEAGPEP-EVRAKPAAQSEEETATSPAASPTPQSAERSPSQEPSAPGKAEAV 102
Cdd:PRK07003 460 DSRCDERDAQPPADSGSASAPASDAPPDAAFEPAPrAAAPSAATPAAVPDARAPAAASREDAPAAAAPPAPEARPPTPAA 539

                         90
                 ....*....|..
gi 29789343  103 GEQARGHPSAGA 114
Cdd:PRK07003 540 AAPAARAGGAAA 551
RRM2_RBM28_like cd12414
RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
 190-245 4.38e-03

RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409848 [Multi-domain]  Cd Length: 76  Bit Score: 36.76  E-value: 4.38e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 29789343 190 EKLKnvihKIFSKFGKIINDYYPE-EDGKTKGYIFLEYASPAHAVDAVKNADGYKLD 245
Cdd:cd12414  14 DDLK----KLFSKFGKVLEVTIPKkPDGKLRGFAFVQFTNVADAAKAIKGMNGKKIK 66
RRM_RBM8 cd12324
RNA recognition motif (RRM) found in RNA-binding protein RBM8A, RBM8B nd similar proteins; ...
 196-244 4.86e-03

RNA recognition motif (RRM) found in RNA-binding protein RBM8A, RBM8B nd similar proteins; This subfamily corresponds to the RRM of RBM8, also termed binder of OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is one of the components of the exon-exon junction complex (EJC). It has two isoforms, RBM8A and RBM8B, both of which are identical except that RBM8B is 16 amino acids shorter at its N-terminus. RBM8, together with other EJC components (such as Magoh, Aly/REF, RNPS1, Srm160, and Upf3), plays critical roles in postsplicing processing, including nuclear export and cytoplasmic localization of the mRNA, and the nonsense-mediated mRNA decay (NMD) surveillance process. RBM8 binds to mRNA 20-24 nucleotides upstream of a spliced exon-exon junction. It is also involved in spliced mRNA nuclear export, and the process of nonsense-mediated decay of mRNAs with premature stop codons. RBM8 forms a specific heterodimer complex with the EJC protein Magoh which then associates with Aly/REF, RNPS1, DEK, and SRm160 on the spliced mRNA, and inhibits ATP turnover by eIF4AIII, thereby trapping the EJC core onto RNA. RBM8 contains an N-terminal putative bipartite nuclear localization signal, one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), in the central region, and a C-terminal serine-arginine rich region (SR domain) and glycine-arginine rich region (RG domain).


Pssm-ID: 409762 [Multi-domain]  Cd Length: 88  Bit Score: 36.82  E-value: 4.86e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 29789343 196 IHKIFSKFGKIINDY--YPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKL 244
Cdd:cd12324  23 IHDKFAEFGEIKNLHlnLDRRTGFVKGYALVEYETKKEAQAAIEGLNGKEL 73
PRK07735 PRK07735
NADH-quinone oxidoreductase subunit C;
45-156 5.26e-03

NADH-quinone oxidoreductase subunit C;


Pssm-ID: 236081 [Multi-domain]  Cd Length: 430  Bit Score: 39.96  E-value: 5.26e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343   45 TEDAEEDAEAGPEPEVRAKPAAQSEEETATSPAASPTPQSAERSPSQEpSAPGKAEAVGEQARGHPSAGAEEEGGSD--- 121
Cdd:PRK07735  86 TEEEKAKAKAKAAAAAKAKAAALAKQKREGTEEVTEEEKAAAKAKAAA-AAKAKAAALAKQKREGTEEVTEEEEETDkek 164

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 29789343  122 -----GSAAEAEPRALENGEADEPSFSDpedfvDDVSEEE 156
Cdd:PRK07735 165 akakaAAAAKAKAAALAKQKAAEAGEGT-----EEVTEEE 199
RRM2_MRD1 cd12566
RNA recognition motif 2 (RRM2) found in yeast multiple RNA-binding domain-containing protein 1 ...
 198-242 5.63e-03

RNA recognition motif 2 (RRM2) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM2 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409982 [Multi-domain]  Cd Length: 79  Bit Score: 36.63  E-value: 5.63e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 29789343 198 KIFSKFGKIINDYYP--EEDGKTKGYIFLEYASPAHAVDAVKNADGY 242
Cdd:cd12566  21 KLFSKFGEVSEVHVPidKKTKKSKGFAYVLFLDPEDAVQAYNELDGK 67
PRK11633 PRK11633
cell division protein DedD; Provisional
 23-102 5.73e-03

cell division protein DedD; Provisional


Pssm-ID: 236940 [Multi-domain]  Cd Length: 226  Bit Score: 39.22  E-value: 5.73e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343   23 QPASESPPTDEAAGSGGSEVG-----QTEDAEEDAEAGPEPEVRAKPAA------QSEEETATSPAASPTPQSAERSPSQ 91
Cdd:PRK11633  61 QALPTQPPEGAAEAVRAGDAAapsldPATVAPPNTPVEPEPAPVEPPKPkpvekpKPKPKPQQKVEAPPAPKPEPKPVVE 140

                         90
                 ....*....|..
gi 29789343   92 EPSAP-GKAEAV 102
Cdd:PRK11633 141 EKAAPtGKAYVV 152
RRM3_RAVER cd12390
RNA recognition motif 3 (RRM3) found in ribonucleoprotein PTB-binding raver-1, raver-2 and ...
 187-248 5.87e-03

RNA recognition motif 3 (RRM3) found in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins; This subfamily corresponds to the RRM3 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only.


Pssm-ID: 409824 [Multi-domain]  Cd Length: 91  Bit Score: 36.83  E-value: 5.87e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 29789343 187 DRLEK-LKNV--IHKIFSKFGKIINDYYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQH 248
Cdd:cd12390   8 DRLPKdFRDGseLRKLFSQVGKPTFCQLAMGNGVPRGFAFVEFASAEDAEEAQQLLNGHDLQGSP 72
motB PRK05996
MotB family protein;
45-139 6.13e-03

MotB family protein;


Pssm-ID: 235665 [Multi-domain]  Cd Length: 423  Bit Score: 39.68  E-value: 6.13e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343   45 TEDAEEDAEAGPEPEVRAKPAAQSEEETATSPAASPTPQSAERSPSQEPSAPGKAEAvGEQARGHPSAGAEEEGGSDGSA 124
Cdd:PRK05996 187 SKQVEVTTAGDLLPPGQAREQAQGAKSATAAPATVPQAAPLPQAQPKKAATEEELIA-DAKKAATGEPAANAAKAAKPEP 265

                         90
                 ....*....|....*
gi 29789343  125 AeAEPRALENGEADE 139
Cdd:PRK05996 266 M-PDDQQKEAEQLQA 279
PRK14951 PRK14951
DNA polymerase III subunits gamma and tau; Provisional
 52-140 6.54e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237865 [Multi-domain]  Cd Length: 618  Bit Score: 40.08  E-value: 6.54e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343   52 AEAGPEPEVRAKPAAQSEeetATSPAASPTPQSAERSPSQEPSAPGKAEAVGEQARGHPSAGAEEEGGSDGSAAEAEPRA 131
Cdd:PRK14951 368 AAAEAAAPAEKKTPARPE---AAAPAAAPVAQAAAAPAPAAAPAAAASAPAAPPAAAPPAPVAAPAAAAPAAAPAAAPAA 444


                 ....*....
gi 29789343  132 LENGEADEP 140
Cdd:PRK14951 445 VALAPAPPA 453
PRK12495 PRK12495
hypothetical protein; Provisional
 22-140 6.85e-03

hypothetical protein; Provisional


Pssm-ID: 183558 [Multi-domain]  Cd Length: 226  Bit Score: 39.08  E-value: 6.85e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343   22 QQPASESPPTDEAAgsgGSEVGQTEDAEE-DAEAGPEPEVRAKPaaqseEETATSPAASPTPqsaERSPSQEPSAPGKAE 100
Cdd:PRK12495 100 AQPAAEAEAADQSA---PPEASSTSATDEaATDPPATAAARDGP-----TPDPTAQPATPDE---RRSPRQRPPVSGEPP 168

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 29789343  101 AVGEQarghPSAGAEEEGGSDGSAAEAEPRALENGEA-DEP 140
Cdd:PRK12495 169 TPSTP----DAHVAGTLQAARESLVETLARFARRAAAtDDP 205
ZipA COG3115
Cell division protein ZipA, interacts with FtsZ [Cell cycle control, cell division, chromosome ...
 47-181 6.94e-03

Cell division protein ZipA, interacts with FtsZ [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 442349 [Multi-domain]  Cd Length: 298  Bit Score: 39.29  E-value: 6.94e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343  47 DAEEDAEAGPEPEVRAKPAAQSEEetatsPAASPTPQSAERSPSQEPSAPgkaeAVGEQARGHPSAGAEEEGGSDGSAAE 126
Cdd:COG3115  42 DVLLDDDGIGEVRVVAAEAPERVE-----PEASFDAEDEVREPDQEEVDP----LLDDEADIEAAPAEPVRWAGTAAAVE 112

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*
gi 29789343 127 AEPRAlENGEADEPSFSDPEDFVDDVSEEELLGDVLKDRPQEADGIDSVIVVDNV 181
Cdd:COG3115 113 PAPEQ-EAYEEAGPAGESAEQEDAPAEEPEAEAPAEEALAAELCAEPEEVIVLNV 166
RRM_AKAP17A cd12264
RNA recognition motif (RRM) found in A-kinase anchor protein 17A (AKAP-17A) and similar ...
 194-260 6.97e-03

RNA recognition motif (RRM) found in A-kinase anchor protein 17A (AKAP-17A) and similar proteins; This subfamily corresponds to the RRM domain of AKAP-17A, also termed 721P, or splicing factor, arginine/serine-rich 17A (SFRS17A). It was originally reported as the pseudoautosomal or X inactivation escape gene 7 (XE7) and as B-lymphocyte antigen precursor. It has been suggested that AKAP-17A is an alternative splicing factor and an SR-related splicing protein that interacts with the classical SR protein ASF/SF2 and the SR-related factor ZNF265. Additional studies have indicated that AKAP-17A is a dual-specific protein kinase A anchoring protein (AKAP) that can bind both type I and type II protein kinase A (PKA) with high affinity and co-localizes with the catalytic subunit of PKA in nuclear speckles as well as the splicing factor SC35 in splicing factor compartments. It is involved in regulation of pre-mRNA splicing possibly by docking a pool of PKA in splicing factor compartments. AKAP-17A contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409708 [Multi-domain]  Cd Length: 122  Bit Score: 37.25  E-value: 6.97e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343 194 NVIHKIFSKFGKI-------INDYYPEEDGKT------------KGYI-FLEYASPAHAVDAVKNAD-GYKLDKQHTFRV 252
Cdd:cd12264  29 NVLRKVFEKFGKIrnvdipmLDPYRKEMDGNGfdtfsfgghlhfEAYVqYEEYDGFVKAMDALRGMKlMYKGEDGKALAA 108


                ....*...
gi 29789343 253 NLFTDFDK 260
Cdd:cd12264 109 NIKVDFDK 116
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 24-140 7.15e-03

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 40.15  E-value: 7.15e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343    24 PASESPPTDEAAGSGGSEVGQT-EDAEEDAEAGPEPEVRAKPAA---QSEEETAT---SPAASP---TPQSAERSPSQEP 93
Cdd:PHA03307  130 PAPDLSEMLRPVGSPGPPPAASpPAAGASPAAVASDAASSRQAAlplSSPEETARapsSPPAEPppsTPPAAASPRPPRR 209

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 29789343    94 SAPGKAEAVGEQARGHPSAGAEEEGGSDGSAAEAEPRALENGEADEP 140
Cdd:PHA03307  210 SSPISASASSPAPAPGRSAADDAGASSSDSSSSESSGCGWGPENECP 256
PRK14950 PRK14950
DNA polymerase III subunits gamma and tau; Provisional
 52-203 8.26e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237864 [Multi-domain]  Cd Length: 585  Bit Score: 39.79  E-value: 8.26e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29789343   52 AEAGPEPEVRAKPAAQSEEETATSPAASPTPQSAERSPSQEPSAPGKAEAVGEQARghPSAGAEEEGGSDGSAAEAEPRA 131
Cdd:PRK14950 386 STRPKAAAAANIPPKEPVRETATPPPVPPRPVAPPVPHTPESAPKLTRAAIPVDEK--PKYTPPAPPKEEEKALIADGDV 463

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 29789343  132 LENGEADEPsfsdpeDFVDDVS-EEELLGDVLKDRPQEADGIDSVIVVDNVPQVGPDRLEKLKN--VIHKIFSKF 203
Cdd:PRK14950 464 LEQLEAIWK------QILRDVPpRSPAVQALLSSGVRPVSVEKNTLTLSFKSKFHKDKIEEPENrkITEELLSNF 532
RRM_SNP1_like cd21615
RNA recognition motif (RRM) found in Saccharomyces cerevisiae U1 small nuclear ...
 196-247 9.53e-03

RNA recognition motif (RRM) found in Saccharomyces cerevisiae U1 small nuclear ribonucleoprotein SNP1 and similar proteins; SNP1, also called U1 snRNP protein SNP1, or U1 small nuclear ribonucleoprotein 70 kDa homolog, or U1 70K, or U1 snRNP 70 kDa homolog, interacts with mRNA and is involved in nuclear mRNA splicing. It is a component of the spliceosome, where it is associated with snRNP U1 by binding stem loop I of U1 snRNA. Members in this family contain an N-terminal U1snRNP70 domain and an RNA recognition motif (RRM), also called RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410194 [Multi-domain]  Cd Length: 118  Bit Score: 36.91  E-value: 9.53e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 29789343 196 IHKIFSKFG-----KIINDyypEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQ 247
Cdd:cd21615  35 LQKKFSKFGeiekiRIVRD---KETGKSRGYAFIVFKSESDAKNAFKEGNGLRGLKI 88
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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