NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|114187921|gb|EAU29621|]
View 

conserved hypothetical protein [Aspergillus terreus NIH2624]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
RNA12 pfam10443
RNA12 protein; This family includes RNA12 from S. cerevisiae. That protein contains an RRM ...
 362-780 0e+00

RNA12 protein; This family includes RNA12 from S. cerevisiae. That protein contains an RRM domain. This region is C-terminal to that and includes a P-loop motif suggesting this region binds to NTP. The RNA12 proteins is involved in pre-rRNA maturation.


:

Pssm-ID: 371055  Cd Length: 429  Bit Score: 734.11  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114187921   362 RQGDISQLQSWLTENAETFIVIQGPRGSGKRELVMNQALAPYKYKVVIDCKQIQDARGDTAKIARAASQVGYRPVFSWMN 441
Cdd:pfam10443    1 RKEKIEQLQEWLLENVNTFIVVQGPRGSGKRELVMDRVLKDRKNVLVIDCDQLQKARGDAGFISTAASQVGYFPVFSWMN 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114187921   442 SISSFVDLAAQGMIGTKAGFSETLDAQLSNIWQNTATALKQITLENRRKSDKDASLTDEEYLEAHPEQRPVVIIDNFLHN 521
Cdd:pfam10443   81 SISSLIDLAAQGLTGQKAGFSETKEAQLRNILQTTATALKDIALEEYKKEDKDANLKEEDYLEAHPEAKPVVVIDNFLHK 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114187921   522 ASEDNVVYEKITEWAAGLTTGNIAHVIFLTTDVSFAKPLSKALPNAVFRTISLGDCSLDVARRFVLSHLA------GESK 595
Cdd:pfam10443  161 AEENGFVYKKLAEWAASLVQNNIAHVIFLTEDVSYSKPLSKALPNQVFKTISLGDASPDVARKYVLSQLDedtrkeENSS 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114187921   596 GEDQQAEKR-----GDLAGLDSCIEILGGRVTDLEFMAHRIEAGETPEAAVNRIIEQSASEILKMFILD-GGASSTAWTH 669
Cdd:pfam10443  241 DEQNTDDKAataneKDLKELDSCIEPLGGRMTDLQAFARRIKSGESPSEAVNDIIEQSASEILKMFLLDsGDASDLPWTP 320

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114187921   670 EQAWHLIKTLakAKHGSIPYNQVLLSDLFKENGEATLRALEQAELISIVSTNGCPEAVKPGKPVYRTVFKRLTENKTLSS 749
Cdd:pfam10443  321 EQAWYLIKLL--SKNGSIPYNELLLSPLFKGSGETALRALEQAELISVTRDNGRPSTIRPGKPVYRAAFKRLLNDKVLSS 398

                          410       420       430
                   ....*....|....*....|....*....|.
gi 114187921   750 RLDLEILSQLIAKENKSIGKHEEELRLLGGL 780
Cdd:pfam10443  399 RLDLEYLTALIAKENKKIKKYEEELRLLGKL 429
RRM_SF super family cl17169
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 177-275 1.16e-27

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).


The actual alignment was detected with superfamily member cd12433:

Pssm-ID: 473069 [Multi-domain]  Cd Length: 86  Bit Score: 107.35  E-value: 1.16e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114187921  177 RIPSQRLKVEFHPASadgaadiLTTETLYSLFRSYGKLRDIEKQPADSkvSPHYAFVEFTRPRYAVMAKNCMHGFTCSEs 256
Cdd:cd12433     1 RYPSRTIRVEFEGPE-------LSQEELYSLFRPYGRINDITPPPPDS--LPRYATVTFRRIRGAIAAKNCLHGYVVNE- 70

                          90
                  ....*....|....*....
gi 114187921  257 qgggkFGTRVKIKYERKIK 275
Cdd:cd12433    71 -----GGTRLRIQYEPKLR 84
DEAD-like_helicase_N super family cl28899
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
 966-1038 2.60e-07

N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase superfamily is a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. The N-terminal domain contains the ATP-binding region.


The actual alignment was detected with superfamily member cd17934:

Pssm-ID: 475120 [Multi-domain]  Cd Length: 121  Bit Score: 50.31  E-value: 2.60e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 114187921  966 FVIFNEASFFRDPDLFHGLGQLRedvRVLLVGDHKQLSPPVF----TPAGEAAWSKSAFERLIEK-GYYQTLLNISYR 1038
Cdd:cd17934    47 VVIIDEASQITEPELLIALIRAK---KVVLVGDPKQLPPVVQedhaALLGLSFILSLLLLFRLLLpGSPKVMLDTQYR 121
 
Name Accession Description Interval E-value
RNA12 pfam10443
RNA12 protein; This family includes RNA12 from S. cerevisiae. That protein contains an RRM ...
 362-780 0e+00

RNA12 protein; This family includes RNA12 from S. cerevisiae. That protein contains an RRM domain. This region is C-terminal to that and includes a P-loop motif suggesting this region binds to NTP. The RNA12 proteins is involved in pre-rRNA maturation.


Pssm-ID: 371055  Cd Length: 429  Bit Score: 734.11  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114187921   362 RQGDISQLQSWLTENAETFIVIQGPRGSGKRELVMNQALAPYKYKVVIDCKQIQDARGDTAKIARAASQVGYRPVFSWMN 441
Cdd:pfam10443    1 RKEKIEQLQEWLLENVNTFIVVQGPRGSGKRELVMDRVLKDRKNVLVIDCDQLQKARGDAGFISTAASQVGYFPVFSWMN 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114187921   442 SISSFVDLAAQGMIGTKAGFSETLDAQLSNIWQNTATALKQITLENRRKSDKDASLTDEEYLEAHPEQRPVVIIDNFLHN 521
Cdd:pfam10443   81 SISSLIDLAAQGLTGQKAGFSETKEAQLRNILQTTATALKDIALEEYKKEDKDANLKEEDYLEAHPEAKPVVVIDNFLHK 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114187921   522 ASEDNVVYEKITEWAAGLTTGNIAHVIFLTTDVSFAKPLSKALPNAVFRTISLGDCSLDVARRFVLSHLA------GESK 595
Cdd:pfam10443  161 AEENGFVYKKLAEWAASLVQNNIAHVIFLTEDVSYSKPLSKALPNQVFKTISLGDASPDVARKYVLSQLDedtrkeENSS 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114187921   596 GEDQQAEKR-----GDLAGLDSCIEILGGRVTDLEFMAHRIEAGETPEAAVNRIIEQSASEILKMFILD-GGASSTAWTH 669
Cdd:pfam10443  241 DEQNTDDKAataneKDLKELDSCIEPLGGRMTDLQAFARRIKSGESPSEAVNDIIEQSASEILKMFLLDsGDASDLPWTP 320

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114187921   670 EQAWHLIKTLakAKHGSIPYNQVLLSDLFKENGEATLRALEQAELISIVSTNGCPEAVKPGKPVYRTVFKRLTENKTLSS 749
Cdd:pfam10443  321 EQAWYLIKLL--SKNGSIPYNELLLSPLFKGSGETALRALEQAELISVTRDNGRPSTIRPGKPVYRAAFKRLLNDKVLSS 398

                          410       420       430
                   ....*....|....*....|....*....|.
gi 114187921   750 RLDLEILSQLIAKENKSIGKHEEELRLLGGL 780
Cdd:pfam10443  399 RLDLEYLTALIAKENKKIKKYEEELRLLGKL 429
RRM_Yme2p_like cd12433
RNA recognition motif (RRM) found in yeast mitochondrial escape protein 2 (Yme2p) and similar ...
 177-275 1.16e-27

RNA recognition motif (RRM) found in yeast mitochondrial escape protein 2 (Yme2p) and similar proteins; This subfamily corresponds to the RRM of Yme2p, also termed protein RNA12, an inner mitochondrial membrane protein that plays a critical role in mitochondrial DNA transactions. It may serve as a mediator of nucleoid structure and number in mitochondria of the yeast Saccharomyces cerevisiae. Yme2p contains an exonuclease domain, an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal domain.


Pssm-ID: 409867 [Multi-domain]  Cd Length: 86  Bit Score: 107.35  E-value: 1.16e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114187921  177 RIPSQRLKVEFHPASadgaadiLTTETLYSLFRSYGKLRDIEKQPADSkvSPHYAFVEFTRPRYAVMAKNCMHGFTCSEs 256
Cdd:cd12433     1 RYPSRTIRVEFEGPE-------LSQEELYSLFRPYGRINDITPPPPDS--LPRYATVTFRRIRGAIAAKNCLHGYVVNE- 70

                          90
                  ....*....|....*....
gi 114187921  257 qgggkFGTRVKIKYERKIK 275
Cdd:cd12433    71 -----GGTRLRIQYEPKLR 84
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
415-1091 1.33e-14

Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 78.63  E-value: 1.33e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114187921  415 QDARGDTAKIARAASQVGYRPVFSWMNSISSFVDLAAQGMIGTKAGFSETLDAQLSNIWQNTATALKQITLENRRKSDKD 494
Cdd:COG1112    37 LLLAAALLLLALALALLLLALRALELLDLLAALALLLLLLLLDAELLLLALRALLLLLAAELLLLLLLLLLLAALLLALA 116

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114187921  495 ASLTDEEYLEAHPEQRPVVIIDNFLHNASEDNVVYEKITEWAAGLTTGNIAHVIFLTTDVSFAKPLSKALPNAVFRTISL 574
Cdd:COG1112   117 ALLLALALLLLALALLALLALLLAELLDLLAALAALAALLAALLLLLLLLAALLLLDLRLLALLELLLAAALALALLALL 196

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114187921  575 GDCSLDVARRFVLSHLAGESKGEDQQAEKRGDLAGLDSCIEILGGRVTDLEFMAHRIEAGETPEAAVNRIIEQSASEILK 654
Cdd:COG1112   197 ALALEDELALLLLLLLLALLLLLALLLLLDALLLLLAALALLALALLLALLLLLLALLLLAALALLRAALRLDLLAALEL 276

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114187921  655 MFILDGGASSTAWTHEQAWHLIKTLAKAKHGSIPYNQVLLSDLFKENGEATLRALEQAELISIVSTNGCPEAVKPGKPVY 734
Cdd:COG1112   277 LAALSLALLALLAALALALLLLAALALLLALALAALLALLALLALLAARLAAALAALLLLLLLEELALLAALLLLLELAL 356

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114187921  735 RTVFKRLTENKTLSSRLDLEILSQLIAKENKSIGKHEEELRLLGGLPKQPYELRWRIQWLLDKVYKSQNKIRQYESESAV 814
Cdd:COG1112   357 LRLLAALLLALALLLLLALEELLLLALLRLLAEGLALLLLLLLAALLRLARALLLLALLLAAAAAALAALLLLALALLAA 436

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114187921  815 LQKLLRSLSLVGWLDPRHTVADSPLRYACWTKRSWSSSVAVKVSTSYTCDGQETLSQADtearlfadvhgfhddidkvva 894
Cdd:COG1112   437 LLALLLLLAAALAALLALLLLLLLALAALLLLLAAAAALLALALLESLLEELIEEHPEE--------------------- 495

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114187921  895 lINQNPSQYGQFLKGIQKIKDsgrldmnkdQLRLYNKQRRELIDRVMADVQVVVTLPFNVKEILRRNFNpQF--VIFNEA 972
Cdd:COG1112   496 -LEKLIAELREAARLRRALRR---------ELKKRRELRKLLWDALLELAPVVGMTPASVARLLPLGEG-SFdlVIIDEA 564

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114187921  973 SFFRDPDLfhgLGQLREDVRVLLVGDHKQLSPPVFTPAGEAAW----SKSAFERLIEK-GYYQTLLNISYRSYKDLYEPT 1047
Cdd:COG1112   565 SQATLAEA---LGALARAKRVVLVGDPKQLPPVVFGEEAEEVAeeglDESLLDRLLARlPERGVMLREHYRMHPEIIAFS 641

                         650       660       670       680
                  ....*....|....*....|....*....|....*....|....
gi 114187921 1048 SVAYYEGKVDTFRNQPSGDLNITANPLRVRLADKTCTLRGLSHF 1091
Cdd:COG1112   642 NRLFYDGKLVPLPSPKARRLADPDSPLVFIDVDGVYERRGGSRT 685
DEXXQc_Upf1-like cd17934
DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, ...
 966-1038 2.60e-07

DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, HELZ, Mov10L1, Aquarius, IGHMBP2 (SMUBP2), coronavirus Nsp13, and similar proteins. They belong to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438708 [Multi-domain]  Cd Length: 121  Bit Score: 50.31  E-value: 2.60e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 114187921  966 FVIFNEASFFRDPDLFHGLGQLRedvRVLLVGDHKQLSPPVF----TPAGEAAWSKSAFERLIEK-GYYQTLLNISYR 1038
Cdd:cd17934    47 VVIIDEASQITEPELLIALIRAK---KVVLVGDPKQLPPVVQedhaALLGLSFILSLLLLFRLLLpGSPKVMLDTQYR 121
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 199-252 8.67e-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: 47.23  E-value: 8.67e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 114187921   199 LTTETLYSLFRSYGKLRDIEKQPADSKVSPHYAFVEFTRPRYAVMAKNCMHGFT 252
Cdd:pfam00076   10 TTEEDLKDLFSKFGPIKSIRLVRDETGRSKGFAFVEFEDEEDAEKAIEALNGKE 63
RRM smart00360
RNA recognition motif;
200-251 2.67e-05

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 43.35  E-value: 2.67e-05
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|...
gi 114187921    200 TTETLYSLFRSYGKLRDIE-KQPADSKVSPHYAFVEFTRPRYAVMAKNCMHGF 251
Cdd:smart00360   12 TEEELRELFSKFGKVESVRlVRDKETGKSKGFAFVEFESEEDAEKALEALNGK 64
 
Name Accession Description Interval E-value
RNA12 pfam10443
RNA12 protein; This family includes RNA12 from S. cerevisiae. That protein contains an RRM ...
 362-780 0e+00

RNA12 protein; This family includes RNA12 from S. cerevisiae. That protein contains an RRM domain. This region is C-terminal to that and includes a P-loop motif suggesting this region binds to NTP. The RNA12 proteins is involved in pre-rRNA maturation.


Pssm-ID: 371055  Cd Length: 429  Bit Score: 734.11  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114187921   362 RQGDISQLQSWLTENAETFIVIQGPRGSGKRELVMNQALAPYKYKVVIDCKQIQDARGDTAKIARAASQVGYRPVFSWMN 441
Cdd:pfam10443    1 RKEKIEQLQEWLLENVNTFIVVQGPRGSGKRELVMDRVLKDRKNVLVIDCDQLQKARGDAGFISTAASQVGYFPVFSWMN 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114187921   442 SISSFVDLAAQGMIGTKAGFSETLDAQLSNIWQNTATALKQITLENRRKSDKDASLTDEEYLEAHPEQRPVVIIDNFLHN 521
Cdd:pfam10443   81 SISSLIDLAAQGLTGQKAGFSETKEAQLRNILQTTATALKDIALEEYKKEDKDANLKEEDYLEAHPEAKPVVVIDNFLHK 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114187921   522 ASEDNVVYEKITEWAAGLTTGNIAHVIFLTTDVSFAKPLSKALPNAVFRTISLGDCSLDVARRFVLSHLA------GESK 595
Cdd:pfam10443  161 AEENGFVYKKLAEWAASLVQNNIAHVIFLTEDVSYSKPLSKALPNQVFKTISLGDASPDVARKYVLSQLDedtrkeENSS 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114187921   596 GEDQQAEKR-----GDLAGLDSCIEILGGRVTDLEFMAHRIEAGETPEAAVNRIIEQSASEILKMFILD-GGASSTAWTH 669
Cdd:pfam10443  241 DEQNTDDKAataneKDLKELDSCIEPLGGRMTDLQAFARRIKSGESPSEAVNDIIEQSASEILKMFLLDsGDASDLPWTP 320

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114187921   670 EQAWHLIKTLakAKHGSIPYNQVLLSDLFKENGEATLRALEQAELISIVSTNGCPEAVKPGKPVYRTVFKRLTENKTLSS 749
Cdd:pfam10443  321 EQAWYLIKLL--SKNGSIPYNELLLSPLFKGSGETALRALEQAELISVTRDNGRPSTIRPGKPVYRAAFKRLLNDKVLSS 398

                          410       420       430
                   ....*....|....*....|....*....|.
gi 114187921   750 RLDLEILSQLIAKENKSIGKHEEELRLLGGL 780
Cdd:pfam10443  399 RLDLEYLTALIAKENKKIKKYEEELRLLGKL 429
RRM_Yme2p_like cd12433
RNA recognition motif (RRM) found in yeast mitochondrial escape protein 2 (Yme2p) and similar ...
 177-275 1.16e-27

RNA recognition motif (RRM) found in yeast mitochondrial escape protein 2 (Yme2p) and similar proteins; This subfamily corresponds to the RRM of Yme2p, also termed protein RNA12, an inner mitochondrial membrane protein that plays a critical role in mitochondrial DNA transactions. It may serve as a mediator of nucleoid structure and number in mitochondria of the yeast Saccharomyces cerevisiae. Yme2p contains an exonuclease domain, an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal domain.


Pssm-ID: 409867 [Multi-domain]  Cd Length: 86  Bit Score: 107.35  E-value: 1.16e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114187921  177 RIPSQRLKVEFHPASadgaadiLTTETLYSLFRSYGKLRDIEKQPADSkvSPHYAFVEFTRPRYAVMAKNCMHGFTCSEs 256
Cdd:cd12433     1 RYPSRTIRVEFEGPE-------LSQEELYSLFRPYGRINDITPPPPDS--LPRYATVTFRRIRGAIAAKNCLHGYVVNE- 70

                          90
                  ....*....|....*....
gi 114187921  257 qgggkFGTRVKIKYERKIK 275
Cdd:cd12433    71 -----GGTRLRIQYEPKLR 84
DNA2 COG1112
Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];
415-1091 1.33e-14

Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];


Pssm-ID: 440729 [Multi-domain]  Cd Length: 819  Bit Score: 78.63  E-value: 1.33e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114187921  415 QDARGDTAKIARAASQVGYRPVFSWMNSISSFVDLAAQGMIGTKAGFSETLDAQLSNIWQNTATALKQITLENRRKSDKD 494
Cdd:COG1112    37 LLLAAALLLLALALALLLLALRALELLDLLAALALLLLLLLLDAELLLLALRALLLLLAAELLLLLLLLLLLAALLLALA 116

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114187921  495 ASLTDEEYLEAHPEQRPVVIIDNFLHNASEDNVVYEKITEWAAGLTTGNIAHVIFLTTDVSFAKPLSKALPNAVFRTISL 574
Cdd:COG1112   117 ALLLALALLLLALALLALLALLLAELLDLLAALAALAALLAALLLLLLLLAALLLLDLRLLALLELLLAAALALALLALL 196

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114187921  575 GDCSLDVARRFVLSHLAGESKGEDQQAEKRGDLAGLDSCIEILGGRVTDLEFMAHRIEAGETPEAAVNRIIEQSASEILK 654
Cdd:COG1112   197 ALALEDELALLLLLLLLALLLLLALLLLLDALLLLLAALALLALALLLALLLLLLALLLLAALALLRAALRLDLLAALEL 276

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114187921  655 MFILDGGASSTAWTHEQAWHLIKTLAKAKHGSIPYNQVLLSDLFKENGEATLRALEQAELISIVSTNGCPEAVKPGKPVY 734
Cdd:COG1112   277 LAALSLALLALLAALALALLLLAALALLLALALAALLALLALLALLAARLAAALAALLLLLLLEELALLAALLLLLELAL 356

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114187921  735 RTVFKRLTENKTLSSRLDLEILSQLIAKENKSIGKHEEELRLLGGLPKQPYELRWRIQWLLDKVYKSQNKIRQYESESAV 814
Cdd:COG1112   357 LRLLAALLLALALLLLLALEELLLLALLRLLAEGLALLLLLLLAALLRLARALLLLALLLAAAAAALAALLLLALALLAA 436

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114187921  815 LQKLLRSLSLVGWLDPRHTVADSPLRYACWTKRSWSSSVAVKVSTSYTCDGQETLSQADtearlfadvhgfhddidkvva 894
Cdd:COG1112   437 LLALLLLLAAALAALLALLLLLLLALAALLLLLAAAAALLALALLESLLEELIEEHPEE--------------------- 495

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114187921  895 lINQNPSQYGQFLKGIQKIKDsgrldmnkdQLRLYNKQRRELIDRVMADVQVVVTLPFNVKEILRRNFNpQF--VIFNEA 972
Cdd:COG1112   496 -LEKLIAELREAARLRRALRR---------ELKKRRELRKLLWDALLELAPVVGMTPASVARLLPLGEG-SFdlVIIDEA 564

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114187921  973 SFFRDPDLfhgLGQLREDVRVLLVGDHKQLSPPVFTPAGEAAW----SKSAFERLIEK-GYYQTLLNISYRSYKDLYEPT 1047
Cdd:COG1112   565 SQATLAEA---LGALARAKRVVLVGDPKQLPPVVFGEEAEEVAeeglDESLLDRLLARlPERGVMLREHYRMHPEIIAFS 641

                         650       660       670       680
                  ....*....|....*....|....*....|....*....|....
gi 114187921 1048 SVAYYEGKVDTFRNQPSGDLNITANPLRVRLADKTCTLRGLSHF 1091
Cdd:COG1112   642 NRLFYDGKLVPLPSPKARRLADPDSPLVFIDVDGVYERRGGSRT 685
DEXXQc_Upf1-like cd17934
DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, ...
 966-1038 2.60e-07

DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, HELZ, Mov10L1, Aquarius, IGHMBP2 (SMUBP2), coronavirus Nsp13, and similar proteins. They belong to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438708 [Multi-domain]  Cd Length: 121  Bit Score: 50.31  E-value: 2.60e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 114187921  966 FVIFNEASFFRDPDLFHGLGQLRedvRVLLVGDHKQLSPPVF----TPAGEAAWSKSAFERLIEK-GYYQTLLNISYR 1038
Cdd:cd17934    47 VVIIDEASQITEPELLIALIRAK---KVVLVGDPKQLPPVVQedhaALLGLSFILSLLLLFRLLLpGSPKVMLDTQYR 121
DEXXQc_UPF1 cd18039
DEXXQ-box helicase domain of UPF1; UPF1 (also called RNA Helicase And ATPase, Regulator Of ...
 902-1038 5.61e-07

DEXXQ-box helicase domain of UPF1; UPF1 (also called RNA Helicase And ATPase, Regulator Of Nonsense Transcripts, or ATP-Dependent Helicase RENT1) is an RNA-dependent helicase and ATPase required for nonsense-mediated decay (NMD) of mRNAs containing premature stop codons. It is recruited to mRNAs upon translation termination and undergoes a cycle of phosphorylation and dephosphorylation; its phosphorylation appears to be a key step in NMD. It is recruited by release factors to stalled ribosomes together with the SMG1C protein kinase complex to form the transient SURF (SMG1-UPF1-eRF1-eRF3) complex. In EJC-dependent NMD, the SURF complex associates with the exon junction complex (EJC) located downstream from the termination codon through UPF2 and allows the formation of an UPF1-UPF2-UPF3 surveillance complex which is believed to activate NMD. Diseases associated with UPF1 include juvenile amyotrophic lateral sclerosis and epidermolysis bullosa, junctional, non-Herlitz type. UPF1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350797 [Multi-domain]  Cd Length: 234  Bit Score: 51.86  E-value: 5.61e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114187921  902 QYGQFLKgiQKIKDSGRLDmNKDQLRlYNKQRRELIDRVMADVQVVVTLPFNVKEILRRNFNPQFVIFNEASFFRDPD-- 979
Cdd:cd18039   103 EKLELLK--LLKLETGELS-SADEKR-YRKLKRKAERELLRNADVICCTCVGAGDPRLSKMKFRTVLIDEATQATEPEcl 178

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 114187921  980 --LFHGLGQlredvrVLLVGDHKQLSPPVFTP-AGEAAWSKSAFERLIEKGYYQTLLNISYR 1038
Cdd:cd18039   179 ipLVHGAKQ------VILVGDHCQLGPVVMCKkAAKAGLSQSLFERLVQLGIRPIRLQVQYR 234
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 199-252 5.68e-07

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: 48.05  E-value: 5.68e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 114187921  199 LTTETLYSLFRSYGKLRDIEKQPADSKVSPHYAFVEFTRPRYAVMAKNCMHGFT 252
Cdd:cd00590    10 TTEEDLRELFSKFGEVVSVRIVRDRDGKSKGFAFVEFESPEDAEKALEALNGTE 63
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 199-252 8.67e-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: 47.23  E-value: 8.67e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 114187921   199 LTTETLYSLFRSYGKLRDIEKQPADSKVSPHYAFVEFTRPRYAVMAKNCMHGFT 252
Cdd:pfam00076   10 TTEEDLKDLFSKFGPIKSIRLVRDETGRSKGFAFVEFEDEEDAEKAIEALNGKE 63
DEXXQc_SETX cd18042
DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in ...
 992-1038 8.98e-07

DEXXQ-box helicase domain of SETX; The RNA/DNA helicase senataxin (SETX) plays a role in transcription, neurogenesis, and antiviral response. SEXT is an R-loop-associated protein that is thought to function as an RNA/DNA helicase. R-loops consist of RNA/DNA hybrids, formed during transcription when nascent RNA hybridizes to the DNA template strand, displacing the non-template DNA strand. Mutations in SETX are linked to two neurodegenerative disorders: ataxia with oculomotor apraxia type 2 (AOA2) and amyotrophic lateral sclerosis type 4 (ALS4). S. cerevisiae homolog splicing endonuclease 1 (Sen1) is an exclusively nuclear protein, important for nucleolar organization. S. cerevisiae Sen1 and its ortholog, the Schizosaccharomyces pombe Sen1, share conserved domains and belong to the family I class of helicases. Both proteins translocate 5' to 3' and unwind both DNA and RNA duplexes and also RNA/DNA hybrids in vitro. SETX is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438712 [Multi-domain]  Cd Length: 218  Bit Score: 51.06  E-value: 8.98e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 114187921  992 RVLLVGDHKQLSPPVF-TPAGEAAWSKSAFERLIEKGYYQTLLNISYR 1038
Cdd:cd18042   171 RLILVGDPKQLPATVFsKVAQKLGYDRSLFERLQLAGYPVLMLTTQYR 218
RRM smart00360
RNA recognition motif;
200-251 2.67e-05

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 43.35  E-value: 2.67e-05
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|...
gi 114187921    200 TTETLYSLFRSYGKLRDIE-KQPADSKVSPHYAFVEFTRPRYAVMAKNCMHGF 251
Cdd:smart00360   12 TEEELRELFSKFGKVESVRlVRDKETGKSKGFAFVEFESEEDAEKALEALNGK 64
DEXXc_HELZ2-C cd18040
C-terminal DEXX-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known ...
 895-1038 3.33e-05

C-terminal DEXX-box helicase domain of HELZ2; Helicase with zinc finger 2 (HELZ2, also known as PPAR-alpha-interacting complex protein 285 or PRIC285 and PPAR-gamma DBD-interacting protein 1 or PDIP1) acts as a transcriptional coactivator for a number of nuclear receptors including PPARA, PPARG, THRA, THRB and RXRA. It belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350798 [Multi-domain]  Cd Length: 271  Bit Score: 47.13  E-value: 3.33e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114187921  895 LINQNPSQYGQFLKGIQ-KIKDSGRLDMNKDQ---LRLYNKQRRELIDRVmaDVqVVVTLPFNVKEILRRNFNPQFVIFN 970
Cdd:cd18040   129 RIRQPSNPHSQQIKAFEaRFERTQEKITEEDIktyKILIWEARFEELETV--DV-ILCTCSEAASQKMRTHANVKQCIVD 205

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 114187921  971 EASFFRDPDLFHGLGQLREDVRVLLVGDHKQLSPPVftpAGEAAWS----KSAFERLIEKGyyqTLLNISYR 1038
Cdd:cd18040   206 ECGMCTEPESLIPIVSAPRAEQVVLIGDHKQLRPVV---QNKEAQKlglgRSLFERYAEKA---CMLDTQYR 271
RRM_PPIE cd12347
RNA recognition motif (RRM) found in cyclophilin-33 (Cyp33) and similar proteins; This ...
 194-249 8.80e-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: 8.80e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 114187921  194 GAADILTTETLYSLFRSYGKLRDIEkQPADSKVSPH--YAFVEFTRPRYAVMAKNCMH 249
Cdd:cd12347     5 GLAEEVDEKVLHAAFIPFGDIVDIQ-IPLDYETEKHrgFAFVEFEEAEDAAAAIDNMN 61
DEXXQc_Helz-like cd18038
DEXXQ/H-box helicase domain of Helz-like helicase; This subfamily contains HELZ, Mov10L1, and ...
 946-1038 1.24e-03

DEXXQ/H-box helicase domain of Helz-like helicase; This subfamily contains HELZ, Mov10L1, and similar proteins. Helicase with zinc finger (HELZ) acts as a helicase that plays a role in RNA metabolism during development. Moloney leukemia virus 10-like protein 1 (Mov10L1) binds Piwi-interacting RNA (piRNA) precursors to initiate piRNA processing. All are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350796 [Multi-domain]  Cd Length: 229  Bit Score: 41.84  E-value: 1.24e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114187921  946 VVVTLpfNVKEILRRNFNPQ----FVIFNEASFFRDPDLFHGLGQLRED-VRVLLVGDHKQLSPPVFTP-AGEAAWSKSA 1019
Cdd:cd18038   123 VVCTL--MTAGRLVQAGVPNghftHIFIDEAGQATEPEALIPLSELASKnTQIVLAGDPKQLGPVVRSPlARKYGLGKSL 200

                          90       100
                  ....*....|....*....|....*....
gi 114187921 1020 FERLIEKGYYQ----------TLLNISYR 1038
Cdd:cd18038   201 LERLMERPLYYkdgeynpsyiTKLLKNYR 229
DEXXQc_DNA2 cd18041
DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses ...
 935-1038 3.59e-03

DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses different enzymatic activities, such as single-stranded DNA (ssDNA)-dependent ATPase, 5-3 helicase, and endonuclease activities, and is involved in DNA replication and DNA repair in the nucleus and mitochondrion. It is involved in Okazaki fragment processing by cleaving long flaps that escape FEN1: flaps that are longer than 27 nucleotides are coated by replication protein A complex (RPA), leading to recruit DNA2 which cleaves the flap until it is too short to bind RPA and becomes a substrate for FEN1. It is also involved in 5-end resection of DNA during double-strand break (DSB) repair; it is recruited by BLM and mediates the cleavage of 5-ssDNA, while the 3-ssDNA cleavage is prevented by the presence of RPA. DNA2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350799 [Multi-domain]  Cd Length: 203  Bit Score: 39.91  E-value: 3.59e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114187921  935 ELIDRVMADVQVVVT--LPFNVKEILRRNFNpqFVIFNEASFFRDPDLfhgLGQLREDVRVLLVGDHKQLSPPVFTP-AG 1011
Cdd:cd18041   101 EELESKYESVSVVATtcLGINHPIFRRRTFD--YCIVDEASQITLPIC---LGPLRLAKKFVLVGDHYQLPPLVKSReAR 175

                          90       100
                  ....*....|....*....|....*...
gi 114187921 1012 EAAWSKSAFERLIEKGYYQTL-LNISYR 1038
Cdd:cd18041   176 ELGMDESLFKRLSEAHPDAVVqLTIQYR 203
EEXXEc_NFX1 cd17936
EEXXE-box helicase domain of NFX1; Human NFX1 protein was identified as a protein that ...
 891-1032 3.99e-03

EEXXE-box helicase domain of NFX1; Human NFX1 protein was identified as a protein that represses class II MHC (major histocompatibility complex) gene expression. NFX1 binds a conserved cis-acting element, termed the X-box, in promoters of human class II MHC genes. The Cys-rich region contains several NFX1-type zinc finger domains. Frequently, a R3H domain is present in the C-terminus, and a RING finger domain and a PAM2 motif are present in the N-terminus. The lack of R3H and PAM2 motifs in the plant proteins indicates functional differences. Plant NFX1-like proteins are proposed to modulate growth and survival by coordinating reactive oxygen species, salicylic acid, further biotic stress and abscisic acid responses. A common feature of all members may be E3 ubiquitin ligase, due to the presence of a RING finger domain, as well as DNA binding. NFX1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350694 [Multi-domain]  Cd Length: 178  Bit Score: 39.45  E-value: 3.99e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114187921  891 KVVALINQNPSQYG---------------QFLKGIqkikdsgrLDMNKDQlrlynkqrrelIDRVMADVqVVVTLPFNVK 955
Cdd:cd17936    35 KLVRALLQNQDLSItgpilvvcytnhaldQFLEGL--------LDFGPTK-----------IVRLGARV-IGMTTTGAAK 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114187921  956 --EILRRnFNPQFVIFNEASFFRDPdlfHGLGQLREDVR-VLLVGDHKQLSPPVFTPAGEAAWSK---SAFERLIEKGY- 1028
Cdd:cd17936    95 yrELLQA-LGPKVVIVEEAAEVLEA---HILAALTPSTEhLILIGDHKQLRPKVNVYELTAKKYNldvSLFERLVKNGLp 170


                  ....
gi 114187921 1029 YQTL 1032
Cdd:cd17936   171 FVTL 174
RRM_RBM7_like cd12336
RNA recognition motif (RRM) found in RNA-binding protein 7 (RBM7) and similar proteins; This ...
 200-269 4.42e-03

RNA recognition motif (RRM) found in RNA-binding protein 7 (RBM7) and similar proteins; This subfamily corresponds to the RRM of RBM7, RBM11 and their eukaryotic homologous. RBM7 is an ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. It interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20, and may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM11 is a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. It is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. Both, RBM7 and RBM11, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization.


Pssm-ID: 409773 [Multi-domain]  Cd Length: 75  Bit Score: 36.90  E-value: 4.42e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 114187921  200 TTETLYSLFRSYGKLRDIeKQPADSKVSPH-YAFVEFTRPRYAVMAKNCMHGFTCsesqgggkFGTRVKIK 269
Cdd:cd12336    14 TEEILYELFLQAGPLEGV-KIPKDPNGKPKnFAFVTFKHEVSVPYAIQLLNGIRL--------FGREIRIK 75
DEXXQc_SMUBP2 cd18044
DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, ...
 992-1038 4.74e-03

DEXXQ-box helicase domain of SMUBP2; SMUBP2 (also called immunoglobulin mu-binding protein 2, or IGHMBP2) is a 5' to 3' helicase that unwinds RNA and DNA duplexes in an ATP-dependent reaction. It is a DNA-binding protein specific to 5'-phosphorylated single-stranded guanine-rich sequence (5'-GGGCT-3') related to the immunoglobulin mu chain switch region. The IGHMBP2 gene is responsible for Charcot-Marie-Tooth disease (CMT) type 2S and spinal muscular atrophy with respiratory distress type 1 (SMARD1). It is also thought to play a role in frontotemporal dementia (FTD) with amyotrophic lateral sclerosis (ALS) and major depressive disorder (MDD). SMUBP2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350802 [Multi-domain]  Cd Length: 191  Bit Score: 39.52  E-value: 4.74e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 114187921  992 RVLLVGDHKQLSPPVFTPAGEAA-WSKSAFERLIEKGYYQ--TLLNISYR 1038
Cdd:cd18044   142 RCILAGDHKQLPPTILSDKAARGgLGVTLFERLVNLYGESvvRMLTVQYR 191
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH