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Conserved domains on  [gi|1707477765|gb|TRZ13260|]
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hypothetical protein HGM15179_013851, partial [Zosterops borbonicus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CAS_CSE1 pfam03378
CAS/CSE protein, C-terminus; Mammalian cellular apoptosis susceptibility (CAS) proteins are ...
 486-907 0e+00

CAS/CSE protein, C-terminus; Mammalian cellular apoptosis susceptibility (CAS) proteins are homologous to the yeast chromosome-segregation protein, CSE1. This family aligns the C-terminal halves (approximately). CAS is involved in both cellular apoptosis and proliferation. Apoptosis is inhibited in CAS-depleted cells, while the expression of CAS correlates to the degree of cellular proliferation. Like CSE1, it is essential for the mitotic checkpoint in the cell cycle (CAS depletion blocks the cell in the G2 phase), and has been shown to be associated with the microtubule network and the mitotic spindle, as is the protein MEK, which is thought to regulate the intracellular localization (predominantly nuclear vs. predominantly cytosolic) of CAS. In the nucleus, CAS acts as a nuclear transport factor in the importin pathway. The importin pathway mediates the nuclear transport of several proteins that are necessary for mitosis and further progression. CAS is therefore thought to affect the cell cycle through its effect on the nuclear transport of these proteins. Since apoptosis also requires the nuclear import of several proteins (such as P53 and transcription factors), it has been suggested that CAS also enables apoptosis by facilitating the nuclear import of at least a subset of these essential proteins.


:

Pssm-ID: 367469  Cd Length: 435  Bit Score: 656.30  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  486 ERLFTMRGTNNATLITAAEMAPYVEVLLTNLFKALTLPGSSENEYIMKAIMRSFSLLQESIIPYIPSVITQLTQKLLAVS 565
Cdd:pfam03378    1 ERLLTLRDEQGQPIFTSADIAPFAKDLLTHLFAAIEKPGSQENEYLMKCIMRVLIVIQEAVLPVADVVLQHLTNILQEVS 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  566 KNPSKPHFNHYMFESICLSIRITCKANPEAVGSFEEALFMVFTEILQNDVQEFIPYVFQVMSLLLEMHKNE-IPTSYMAL 644
Cdd:pfam03378   81 KNPSNPRFNHYLFEAIGALIRFACKADPAAVSKFEEALFPPFQAILQEDVTEFMPYVFQLLAQLLEANPSGtLPDYYMAL 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  645 FPHLLQPVLWERTGNIPPLVRLLQAYLERGASTIasAAADKIPGLLGVFQKLIASKANDHQGFYLLNSIIEHMPPESVDQ 724
Cdd:pfam03378  161 FPPLLSPALWERRGNVPALVRLLSAFIPKASQEI--VANNKLEPVLGIFQKLIASKANDHQGFYLLESVIENFPPEVLEP 238

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  725 YRKQIFILLFQRLQNSKTTKFIKSFLVFINLYCVRYGALALQEIFDSIQPKMFGMVLEKIIIPEIQKVSGQVEKKICAVG 804
Cdd:pfam03378  239 YFKTIFSLLFQRLQNSKTEKFVKRFVIFYHLYSAKHGADFLIQLIDAIQPGVFGMIYLNVILPETQKLAGPLDRKLAAVS 318

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  805 ITKILTECPPMMDTeYTKLWIPLLQALIGLFELPEDDTIPDEEHFIDIEDTP--GYQTAFSQLAFAGKKEHDPVGQmVNN 882
Cdd:pfam03378  319 YTKLLCESPAFADR-YPKGWGFLLQSLLKLLELPPDPAAADEDDIIDEADVDdmGYGVGFTQLNTAGKKERDPFPD-IPD 396

                          410       420
                   ....*....|....*....|....*
gi 1707477765  883 PRIHLAQSLHKLSTACPGRVSNLVS 907
Cdd:pfam03378  397 VKQWVGQSLKEASQAHPGRISQIIS 421
Cse1 super family cl38282
Cse1; This domain is present in Cse1 nuclear export receptor proteins. Cse1 mediates the ...
 115-485 4.61e-177

Cse1; This domain is present in Cse1 nuclear export receptor proteins. Cse1 mediates the nuclear export of importin alpha. This domain contains HEAT repeats.


The actual alignment was detected with superfamily member pfam08506:

Pssm-ID: 430038 [Multi-domain]  Cd Length: 370  Bit Score: 534.58  E-value: 4.61e-177
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  115 LFKRYRHEFKSNELWTEIKLVLDAFALPLTNLFKATIELCSTHANDASALKVLFSSLILIAKLFYSLNFQDLPEFFEDNM 194
Cdd:pfam08506    1 IFKRWRPLFRSDELFLEIKLVLDKFAEPFLTLLQKVDELIEANKNNKASLKILFEVLLLLCKLFYDLNCQDIPEFFEDNM 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  195 ETWMTNFHSLLTLDNKLLQTDDEEEAGLLELLKSQICDNAALYAQKYDEEFQPYLPRFVTAIWNLLVTTGQEVKYDLLVS 274
Cdd:pfam08506   81 KEWMGIFHKYLSYDNPLLETDDDEEATVLEKLKASICELVQLYTLRYEEEFGPMVNDFIQAVWNLLVSTSPQPKYDILVS 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  275 NAIQFLASVCERPHYKHLFEDQNTLTSICEKVIVPNMEFRAADEEAFEDNSEEYIRRDLEGSDIDTRRRAACDLVRGLCK 354
Cdd:pfam08506  161 KALSFLTSVARRPKYAELFNNESVLKQIIEKVVLPNVTLRESDEELFEDDPIEYIRRDLEGSDSDTRRRAATDFLKELKE 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  355 FFEGPVTGIFSGYVNSMLQEYAKNPSVNWKHKDAAIYLVTSLASKAQTQKHGITQANELVNLTEFFVNHIQPDLKSAtVN 434
Cdd:pfam08506  241 KFEALVTNVVLEYIQRLLEKYSANPSLNWKAKDTAIYLFTSIAAKGAVTKSGVTSTNPLVDVVDFFQQQIAPDLMAN-VN 319

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1707477765  435 EFPVLKADGIKYIMIFRNQVPKEQLLVSIPLLINHLQAESIVVHTYAAHAL 485
Cdd:pfam08506  320 QHPILKADAIKYIYTFRNQLTKEQLIEIFPLLINFLQSSSYVVYTYAAITI 370
Staufen_C pfam16482
Staufen C-terminal domain; This is the C-terminal domain of Staufen proteins. It consists of ...
 1466-1575 6.43e-58

Staufen C-terminal domain; This is the C-terminal domain of Staufen proteins. It consists of an N-terminal Staufen-swapping motif (SSM) comprising two alpha helices, connected by a linker region to a dsRNA-binding-like domain ('RBD'). The 'RBD' has the fold of a functional dsRNA-binding domain, but lacks the residues required to bind RNA. This domain is responsible for dimerization, the SSM from one molecule interacts with the 'RBD' of another.


:

Pssm-ID: 465131  Cd Length: 110  Bit Score: 195.12  E-value: 6.43e-58
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765 1466 KATVTAMIARELLYGGTSPTAETILKSSNSSGHVPHGPlTRPSEQLDYLSNVQGIQVEYKDFPKNNKNEFVSLINCSSQP 1545
Cdd:pfam16482    2 KATVTAAIARELLYGGTSPTAEAILKNNGKTGAVPCGL-VQPSQQLEYLARVQGFQVEYSDFPRQNKNEFLSLLTLSSQP 80

                           90       100       110
                   ....*....|....*....|....*....|
gi 1707477765 1546 PLISHGIGKDVESCHDMAALNILKLLSELD 1575
Cdd:pfam16482   81 VQMTHGIGSSLEASHDQAALSALKQLSEQG 110
DSRM_STAU1_rpt4 cd19885
fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen ...
 1295-1373 4.72e-53

fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 1 (Staufen 1) and similar proteins; Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 1 contains five double-stranded RNA binding motifs (DSRMs). This model describes the fourth motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


:

Pssm-ID: 380714  Cd Length: 86  Bit Score: 180.28  E-value: 4.72e-53
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1707477765 1295 QTSPEYGQGMNPISRLAQIQQAKKEKEPEYMLITERGLPRRREFVMQVKVGVHTAEGMGTNKKVAKRNAAENMLEILGF 1373
Cdd:cd19885      1 QTSPEYGQGMNPISRLAQIQQAKKEKEPEYTLITERGLPRRREFVMQVKVGNQTAEGMGPNKKVAKRNAAEKMLELLGF 79
DSRM_STAU1_rpt2 cd19881
second double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen ...
 1101-1165 2.79e-44

second double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 1 (Staufen 1) and similar proteins; Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 1 contains five double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


:

Pssm-ID: 380710  Cd Length: 79  Bit Score: 155.04  E-value: 2.79e-44
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1707477765 1101 MKLGKKPMYKPIDPYTGMRSTYNYTMRG-GTYPPRYFYPF-PVGPLLYQVELSIGGQQFHGKGRTRQ 1165
Cdd:cd19881      1 MKLGKKPIYKPIDPYTGMRSAYNYNMRGnGAYPPRYFYPFpPVGPVLYQVELSIGGQQFHGKGRTRQ 67
DSRM_STAU1_rpt1 cd19879
first double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...
 1002-1067 1.13e-43

first double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 1 (Staufen 1) and similar proteins; Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 1 contains five double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


:

Pssm-ID: 380708  Cd Length: 66  Bit Score: 152.92  E-value: 1.13e-43
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1707477765 1002 KEKTPMCLVNELARFNKIQPEYKLLSEQGPAHSKVFTVQLTLGDQHWEAEGTSIKKAQHAAAAKAL 1067
Cdd:cd19879      1 KEKTPMCLVNELARFNKIQPEYKLLSEQGPAHSKVFTVQLTLGDQHWEAEGTSIKKAQHAAAAKAL 66
DSRM_STAU1_rpt3 cd19883
third double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...
 1202-1268 7.28e-41

third double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 1 (Staufen 1) and similar proteins; Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 1 contains five double-stranded RNA binding motifs (DSRMs). This model describes the third motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


:

Pssm-ID: 380712  Cd Length: 67  Bit Score: 144.77  E-value: 7.28e-41
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1707477765 1202 KSEISQVFEIALKRNLPVNFEVTKESGPPHMKSFVTKVSVGEFMGEGEGKSKKISKKNAAIAVLEEL 1268
Cdd:cd19883      1 KSEISQVFEIALKRNMPVNFEVTKETGPPHMKSFVTKVSVGEFAGEGEGKSKKISKKNAAIAVLEEL 67
 
Name Accession Description Interval E-value
CAS_CSE1 pfam03378
CAS/CSE protein, C-terminus; Mammalian cellular apoptosis susceptibility (CAS) proteins are ...
 486-907 0e+00

CAS/CSE protein, C-terminus; Mammalian cellular apoptosis susceptibility (CAS) proteins are homologous to the yeast chromosome-segregation protein, CSE1. This family aligns the C-terminal halves (approximately). CAS is involved in both cellular apoptosis and proliferation. Apoptosis is inhibited in CAS-depleted cells, while the expression of CAS correlates to the degree of cellular proliferation. Like CSE1, it is essential for the mitotic checkpoint in the cell cycle (CAS depletion blocks the cell in the G2 phase), and has been shown to be associated with the microtubule network and the mitotic spindle, as is the protein MEK, which is thought to regulate the intracellular localization (predominantly nuclear vs. predominantly cytosolic) of CAS. In the nucleus, CAS acts as a nuclear transport factor in the importin pathway. The importin pathway mediates the nuclear transport of several proteins that are necessary for mitosis and further progression. CAS is therefore thought to affect the cell cycle through its effect on the nuclear transport of these proteins. Since apoptosis also requires the nuclear import of several proteins (such as P53 and transcription factors), it has been suggested that CAS also enables apoptosis by facilitating the nuclear import of at least a subset of these essential proteins.


Pssm-ID: 367469  Cd Length: 435  Bit Score: 656.30  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  486 ERLFTMRGTNNATLITAAEMAPYVEVLLTNLFKALTLPGSSENEYIMKAIMRSFSLLQESIIPYIPSVITQLTQKLLAVS 565
Cdd:pfam03378    1 ERLLTLRDEQGQPIFTSADIAPFAKDLLTHLFAAIEKPGSQENEYLMKCIMRVLIVIQEAVLPVADVVLQHLTNILQEVS 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  566 KNPSKPHFNHYMFESICLSIRITCKANPEAVGSFEEALFMVFTEILQNDVQEFIPYVFQVMSLLLEMHKNE-IPTSYMAL 644
Cdd:pfam03378   81 KNPSNPRFNHYLFEAIGALIRFACKADPAAVSKFEEALFPPFQAILQEDVTEFMPYVFQLLAQLLEANPSGtLPDYYMAL 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  645 FPHLLQPVLWERTGNIPPLVRLLQAYLERGASTIasAAADKIPGLLGVFQKLIASKANDHQGFYLLNSIIEHMPPESVDQ 724
Cdd:pfam03378  161 FPPLLSPALWERRGNVPALVRLLSAFIPKASQEI--VANNKLEPVLGIFQKLIASKANDHQGFYLLESVIENFPPEVLEP 238

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  725 YRKQIFILLFQRLQNSKTTKFIKSFLVFINLYCVRYGALALQEIFDSIQPKMFGMVLEKIIIPEIQKVSGQVEKKICAVG 804
Cdd:pfam03378  239 YFKTIFSLLFQRLQNSKTEKFVKRFVIFYHLYSAKHGADFLIQLIDAIQPGVFGMIYLNVILPETQKLAGPLDRKLAAVS 318

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  805 ITKILTECPPMMDTeYTKLWIPLLQALIGLFELPEDDTIPDEEHFIDIEDTP--GYQTAFSQLAFAGKKEHDPVGQmVNN 882
Cdd:pfam03378  319 YTKLLCESPAFADR-YPKGWGFLLQSLLKLLELPPDPAAADEDDIIDEADVDdmGYGVGFTQLNTAGKKERDPFPD-IPD 396

                          410       420
                   ....*....|....*....|....*
gi 1707477765  883 PRIHLAQSLHKLSTACPGRVSNLVS 907
Cdd:pfam03378  397 VKQWVGQSLKEASQAHPGRISQIIS 421
Cse1 pfam08506
Cse1; This domain is present in Cse1 nuclear export receptor proteins. Cse1 mediates the ...
 115-485 4.61e-177

Cse1; This domain is present in Cse1 nuclear export receptor proteins. Cse1 mediates the nuclear export of importin alpha. This domain contains HEAT repeats.


Pssm-ID: 430038 [Multi-domain]  Cd Length: 370  Bit Score: 534.58  E-value: 4.61e-177
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  115 LFKRYRHEFKSNELWTEIKLVLDAFALPLTNLFKATIELCSTHANDASALKVLFSSLILIAKLFYSLNFQDLPEFFEDNM 194
Cdd:pfam08506    1 IFKRWRPLFRSDELFLEIKLVLDKFAEPFLTLLQKVDELIEANKNNKASLKILFEVLLLLCKLFYDLNCQDIPEFFEDNM 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  195 ETWMTNFHSLLTLDNKLLQTDDEEEAGLLELLKSQICDNAALYAQKYDEEFQPYLPRFVTAIWNLLVTTGQEVKYDLLVS 274
Cdd:pfam08506   81 KEWMGIFHKYLSYDNPLLETDDDEEATVLEKLKASICELVQLYTLRYEEEFGPMVNDFIQAVWNLLVSTSPQPKYDILVS 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  275 NAIQFLASVCERPHYKHLFEDQNTLTSICEKVIVPNMEFRAADEEAFEDNSEEYIRRDLEGSDIDTRRRAACDLVRGLCK 354
Cdd:pfam08506  161 KALSFLTSVARRPKYAELFNNESVLKQIIEKVVLPNVTLRESDEELFEDDPIEYIRRDLEGSDSDTRRRAATDFLKELKE 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  355 FFEGPVTGIFSGYVNSMLQEYAKNPSVNWKHKDAAIYLVTSLASKAQTQKHGITQANELVNLTEFFVNHIQPDLKSAtVN 434
Cdd:pfam08506  241 KFEALVTNVVLEYIQRLLEKYSANPSLNWKAKDTAIYLFTSIAAKGAVTKSGVTSTNPLVDVVDFFQQQIAPDLMAN-VN 319

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1707477765  435 EFPVLKADGIKYIMIFRNQVPKEQLLVSIPLLINHLQAESIVVHTYAAHAL 485
Cdd:pfam08506  320 QHPILKADAIKYIYTFRNQLTKEQLIEIFPLLINFLQSSSYVVYTYAAITI 370
CSE1 COG5657
CAS/CSE protein involved in chromosome segregation [Cell division and chromosome partitioning]; ...
 36-894 2.80e-120

CAS/CSE protein involved in chromosome segregation [Cell division and chromosome partitioning];


Pssm-ID: 227944 [Multi-domain]  Cd Length: 947  Bit Score: 402.27  E-value: 2.80e-120
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765   36 VEDEPNKICESDRIAIKANIVPLMLSSPEQIQKQLSDAISIIGREDFPQKWPDLLTEMVNRFQSGDFHVINGVLRTAHSL 115
Cdd:COG5657     71 REENGNSILPDENVLIRDELFSLIISSSNQLQIQNALAVSRIARLDFPDEWPTLVPDLLSLLSEKDMVTNENSLRVLHHI 150

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  116 FKRYRHEFKSNELWTEIKLVLDAFALPLTNLFKATIELCSthaNDASALKVLFSSLILIAKLFYSLNFQDLPEFFEDNME 195
Cdd:COG5657    151 FKRLRRLFRSDALFLEIAPVLLSILCPFLFSSAYFWSMSE---NLDESLLSLFQVCLKLIRRYYDLGFQDIPEFFEDNLD 227

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  196 TWMTNFHSLLTLDNKLLQtDDEEEAGLLELLKSQICDNAALYAQKYDEEFQPYLPRFVTAIWNLLVTTGQEVKYDLLVSN 275
Cdd:COG5657    228 KFMEHFCKLLSYSNPVLQ-KDCLEDCVYFKLKGSICEIFNLYTTKYPEVITYLIYDFVEIVWNLLTTITRPYIRDYLVSK 306

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  276 AIQFLASVCERPHYKH----LFEDQNTLTSICEKVIVPNMEFRAADEEAFEDNSEEYIRrdlEGSDIDTRRRAACDLVRG 351
Cdd:COG5657    307 SLTVLINVIKYPIRKTaevlSNVSENLINNLVDLLILPNLILREEDLEEWEDDPLEYIR---EQSKTDYEVNVRPCIENE 383

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  352 LCKFFEGpVTGIFSGYVNSMLQEYAKNPsvnwKHKDAAIYLVTSLASKAQtqkhGITQANELVNLTEFFVNHIQPDLKSA 431
Cdd:COG5657    384 LKDLFDV-FGRIAVGHELTVIESEATTP----NILDEARQLFAAYASFGL----GVEAVNRMVDFVKFLGSIIYPDLLSP 454

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  432 TVNEFPVLKADGIKYIMIFRNQVPKEQLLVSiplliNHLQAESIVVHTYAAHALERLFTMRGTNNATLITAAEMAPYVEV 511
Cdd:COG5657    455 NEIIHLRILRSRIAYILTFRNQLDSSELSES-----KFLASQFFVNYTTACIDAVVLLTTREAYSTIFDDWNFSVCSKIG 529

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  512 LLTNLFKALTLPGSS-----ENEYIMKAIMRSFSLLQESIIPYIPSVITQLTQKLLAVSKNPSKPHFNHYMFESICLSIR 586
Cdd:COG5657    530 LLENLILLVLSLMASpssleEREFLLQLISRIIIIDPELIAPLGSEILQLLDNLVEINAKNPSNPQFAHYTFEDIGALVF 609

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  587 ITCKANPEAVGSFEEALFMVFTEILQNDVQEFIPYVFQVMSLLLEMHKNE-IPTSYMALFPHLLQPVLWERTGNIPPLVR 665
Cdd:COG5657    610 LKSGMCEITIPTLVLALVPEFPVLLSEDATELWSYVLQLLSILPEHFSGDvLPSVVKILRQPSLATELLPTKLEILKSYR 689

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  666 LLQAYLERGASTIASAAADKIpglLGVFQKLIASKANDHQGFyLLNSIIEHMPPE-SVDQYRKQIFILLFQRLQNSKTTK 744
Cdd:COG5657    690 LLDNPILTTGYIFKSSGFQPV---LGILQYLLGSEPHDALCF-LNLTVVETLYLEnIYEPYVNLIFVLLLSRLKNSKTER 765

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  745 FIKSFLVFINLYCVRYGALALQEIF----DSIQPKMFGMVLEKIIIPEIQkVSGQVEKKICAVGITKIL-TECPPMM-DT 818
Cdd:COG5657    766 FVIKIIHVFSLVSFKDSLTVGCDNLiskiNQTKNILIVQLYGNWILGFDE-IHDSKDRKIHLIGLSNLLrTLHPEVLsYV 844

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  819 EYTKLWIPLLQALIGLFELP----EDDTIPDEEHFIDIEDtpgyQTAFSQLAFAGKKeHDPVGQmVNNPRIHLAQSLHKL 894
Cdd:COG5657    845 SVTNLIISLLSEIFETASGDaiiyELNDDYADDWFDGEIS----AEEFSRLAQLEFK-VDPVHD-IDNTKYFISFFMEAM 918
Staufen_C pfam16482
Staufen C-terminal domain; This is the C-terminal domain of Staufen proteins. It consists of ...
 1466-1575 6.43e-58

Staufen C-terminal domain; This is the C-terminal domain of Staufen proteins. It consists of an N-terminal Staufen-swapping motif (SSM) comprising two alpha helices, connected by a linker region to a dsRNA-binding-like domain ('RBD'). The 'RBD' has the fold of a functional dsRNA-binding domain, but lacks the residues required to bind RNA. This domain is responsible for dimerization, the SSM from one molecule interacts with the 'RBD' of another.


Pssm-ID: 465131  Cd Length: 110  Bit Score: 195.12  E-value: 6.43e-58
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765 1466 KATVTAMIARELLYGGTSPTAETILKSSNSSGHVPHGPlTRPSEQLDYLSNVQGIQVEYKDFPKNNKNEFVSLINCSSQP 1545
Cdd:pfam16482    2 KATVTAAIARELLYGGTSPTAEAILKNNGKTGAVPCGL-VQPSQQLEYLARVQGFQVEYSDFPRQNKNEFLSLLTLSSQP 80

                           90       100       110
                   ....*....|....*....|....*....|
gi 1707477765 1546 PLISHGIGKDVESCHDMAALNILKLLSELD 1575
Cdd:pfam16482   81 VQMTHGIGSSLEASHDQAALSALKQLSEQG 110
DSRM_STAU1_rpt4 cd19885
fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen ...
 1295-1373 4.72e-53

fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 1 (Staufen 1) and similar proteins; Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 1 contains five double-stranded RNA binding motifs (DSRMs). This model describes the fourth motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380714  Cd Length: 86  Bit Score: 180.28  E-value: 4.72e-53
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1707477765 1295 QTSPEYGQGMNPISRLAQIQQAKKEKEPEYMLITERGLPRRREFVMQVKVGVHTAEGMGTNKKVAKRNAAENMLEILGF 1373
Cdd:cd19885      1 QTSPEYGQGMNPISRLAQIQQAKKEKEPEYTLITERGLPRRREFVMQVKVGNQTAEGMGPNKKVAKRNAAEKMLELLGF 79
DSRM_STAU1_rpt2 cd19881
second double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen ...
 1101-1165 2.79e-44

second double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 1 (Staufen 1) and similar proteins; Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 1 contains five double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380710  Cd Length: 79  Bit Score: 155.04  E-value: 2.79e-44
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1707477765 1101 MKLGKKPMYKPIDPYTGMRSTYNYTMRG-GTYPPRYFYPF-PVGPLLYQVELSIGGQQFHGKGRTRQ 1165
Cdd:cd19881      1 MKLGKKPIYKPIDPYTGMRSAYNYNMRGnGAYPPRYFYPFpPVGPVLYQVELSIGGQQFHGKGRTRQ 67
DSRM_STAU1_rpt1 cd19879
first double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...
 1002-1067 1.13e-43

first double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 1 (Staufen 1) and similar proteins; Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 1 contains five double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380708  Cd Length: 66  Bit Score: 152.92  E-value: 1.13e-43
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1707477765 1002 KEKTPMCLVNELARFNKIQPEYKLLSEQGPAHSKVFTVQLTLGDQHWEAEGTSIKKAQHAAAAKAL 1067
Cdd:cd19879      1 KEKTPMCLVNELARFNKIQPEYKLLSEQGPAHSKVFTVQLTLGDQHWEAEGTSIKKAQHAAAAKAL 66
DSRM_STAU1_rpt3 cd19883
third double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...
 1202-1268 7.28e-41

third double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 1 (Staufen 1) and similar proteins; Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 1 contains five double-stranded RNA binding motifs (DSRMs). This model describes the third motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380712  Cd Length: 67  Bit Score: 144.77  E-value: 7.28e-41
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1707477765 1202 KSEISQVFEIALKRNLPVNFEVTKESGPPHMKSFVTKVSVGEFMGEGEGKSKKISKKNAAIAVLEEL 1268
Cdd:cd19883      1 KSEISQVFEIALKRNMPVNFEVTKETGPPHMKSFVTKVSVGEFAGEGEGKSKKISKKNAAIAVLEEL 67
DSRM_STAU1_rpt5 cd19887
fifth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...
 1506-1575 3.67e-39

fifth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 1 (Staufen 1) and similar proteins; Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 1 contains five double-stranded RNA binding motifs (DSRMs). This model describes the fifth motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380716  Cd Length: 70  Bit Score: 140.19  E-value: 3.67e-39
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765 1506 RPSEQLDYLSNVQGIQVEYKDFPKNNKNEFVSLINCSSQPPLISHGIGKDVESCHDMAALNILKLLSELD 1575
Cdd:cd19887      1 RPSEQLDYLSRVQGLQVEYKDFPKNNKNEFVSLINCSSQPPLISHGIGKDVESCHDMAALNILKLLSELD 70
DSRM smart00358
Double-stranded RNA binding motif;
1205-1269 7.28e-18

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 79.23  E-value: 7.28e-18
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1707477765  1205 ISQVFEIALKRNLPVNFEVTKESGPPHMKSFVTKVSVGEFM-GEGEGKSKKISKKNAAIAVLEELK 1269
Cdd:smart00358    2 KSLLQELAQKRKLPPEYELVKEEGPDHAPRFTVTVKVGGKRtGEGEGSSKKEAKQRAAEAALRSLK 67
DSRM smart00358
Double-stranded RNA binding motif;
1306-1372 2.99e-17

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 77.30  E-value: 2.99e-17
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1707477765  1306 PISRLAQIQQAKKeKEPEYMLITERGLPRRREFVMQVKV-GVHTAEGMGTNKKVAKRNAAENMLEILG 1372
Cdd:smart00358    1 PKSLLQELAQKRK-LPPEYELVKEEGPDHAPRFTVTVKVgGKRTGEGEGSSKKEAKQRAAEAALRSLK 67
SXM1 COG5656
Importin, protein involved in nuclear import [Posttranslational modification, protein turnover, ...
 54-661 2.52e-16

Importin, protein involved in nuclear import [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 227943 [Multi-domain]  Cd Length: 970  Bit Score: 85.29  E-value: 2.52e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765   54 NIVPLMLSSPEQIQKQLSDAISIIGREDFPQKWPDLLTEMVNRFQSGDFHVINGVLRTAHSLFKRYRhefksnelwteIK 133
Cdd:COG5656     92 NILDVFLYSPEVTRTALNAILVNIFSEDKPSDLWGLFPKAANLLRSSEANHVYTGLLCLEELFKAYR-----------WK 160

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  134 LVLD-AFALPL-TNLFKATIELCS---THANDASAlkvlfSSLILIAKLFYSLNFQDLPEFFEDNmETWMTNFHSLLTLD 208
Cdd:COG5656    161 YNDEqVDILMLiTALFPILEKVGGnleSQGNYGSV-----ETLMLILKSFKSVCYYSLPDFLSAI-ETFSSWFQLSLRIL 234

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  209 NK-LLQTDDEEEAGLLELLKSQICDNAALY--------------AQKYDEEFQPYLPRF---------VTAIWnllvTTG 264
Cdd:COG5656    235 QKpLPNEVLSLDPEVRSLSKWVKCKKWAAYnlyrsfqryikksyKKSYLSFYITFMTRVpmilatffkQIEEW----GQG 310

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  265 Q-----EVKYDLL-----VSNAIQFLASVceRPHYKHLFEDqntltsicekVIVPNMEFRAADEEAFEDNSEEYIRRDLE 334
Cdd:COG5656    311 QlwlsdIELYFIDffvelCVDADQTWRLM--EPHLQYIISG----------VIFPLLCLSEEEEELFENDPDEYIRRYYD 378

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  335 GSDIDTRRRAACDLVRGLCKFFEGPVT--GIFSgYVNSMLQEYAKNPS--VNWKHKDAAIYLVTSLASKaqtqkhgITQA 410
Cdd:COG5656    379 FFDNGLSPDLAALFFLIISKSKRKEETfqGILS-FLLSILGQSAATPSniDNARQAEGALRLLASIKSF-------ITKM 450

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  411 NELVNLTEFF-VNHIQPDLKSatvnEFPVLKADGIKYIMIFRNQVP-KEQLLVSIPLLINHLQAESIVVHTYAAHALERL 488
Cdd:COG5656    451 SPAANVMEYFiVNHVIPAFRS----NYGFLKSRACEFISTIEEDFKdNGILLEAYENTHNCLKNNHLPVMIEAALALQFF 526

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  489 FTMRGTNNAtliTAAEMAPYVEVL--LTNLFKALTLPGsseneyIMKAIMRSFSllqESIIPYIPSVITQLTQKLLAVS- 565
Cdd:COG5656    527 IFNEQSHEK---FSAHVPETMEKLlsLSNTFEIDPLSM------VMESFVEYFS---EELSPFAPELAGSLVRQFLKIAq 594

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  566 ---KNPSKPHFNH-----------YMFESICLSIRITckanPEAVGSFEEALFMVFTEILQNDVQEFIPYVFQVMSLLLE 631
Cdd:COG5656    595 sllENSSDTSSVVddkqmaasgilRTIESMILSLENR----PLVLKYLEVSLYPVISFILKNEISDFYQEALDILDGYTF 670

                          650       660       670
                   ....*....|....*....|....*....|
gi 1707477765  632 MHKNEIPTSymalfphllqPVLWERTGNIP 661
Cdd:COG5656    671 MSKEIEPIM----------WGIFELLLNLL 690
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 1205-1268 9.30e-14

Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training Putative motif shared by proteins that bind to dsRNA. At least some DSRM proteins seem to bind to specific RNA targets. Exemplified by Staufen, which is involved in localization of at least five different mRNAs in the early Drosophila embryo. Also by interferon-induced protein kinase in humans, which is part of the cellular response to dsRNA.


Pssm-ID: 425434 [Multi-domain]  Cd Length: 66  Bit Score: 67.26  E-value: 9.30e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1707477765 1205 ISQVFEIALKRNLPVNFEVTKESGPPHMKSFVTKVSV-GEFMGEGEGKSKKISKKNAAIAVLEEL 1268
Cdd:pfam00035    2 KSLLQEYAQKNGKPPPYEYVSEEGPPHSPKFTVTVKVdGKLYGSGTGSSKKEAEQLAAEKALEKL 66
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1293-1372 8.95e-12

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 66.66  E-value: 8.95e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765 1293 KLQTSPEYGQGMNPISRLAQIQQAKKEKEPEYMLITERGLPRRREFVMQVKV-GVHTAEGMGTNKKVAKRNAAENMLEIL 1371
Cdd:COG0571    146 RLEEIAPGGAGKDYKTALQEWLQARGLPLPEYEVVEEEGPDHAKTFTVEVLVgGKVLGEGTGRSKKEAEQAAAKAALEKL 225


                   .
gi 1707477765 1372 G 1372
Cdd:COG0571    226 G 226
DSRM smart00358
Double-stranded RNA binding motif;
1006-1055 1.40e-11

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 61.12  E-value: 1.40e-11
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|.
gi 1707477765  1006 PMCLVNELARFNKIQPEYKLLSEQGPAHSKVFTVQLTLGDQHW-EAEGTSI 1055
Cdd:smart00358    1 PKSLLQELAQKRKLPPEYELVKEEGPDHAPRFTVTVKVGGKRTgEGEGSSK 51
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 1210-1268 6.66e-11

ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. This enzyme cleaves double-stranded rRNA. It is involved in processing ribosomal RNA precursors. It is found even in minimal genones such as Mycoplasma genitalium and Buchnera aphidicola, and in some cases has been shown to be an essential gene. These bacterial proteins contain a double-stranded RNA binding motif (pfam00035) and a ribonuclease III domain (pfam00636). Eukaryotic homologs tend to be much longer proteins with additional domains, localized to the nucleus, and not included in this family. [Transcription, RNA processing]


Pssm-ID: 274024 [Multi-domain]  Cd Length: 220  Bit Score: 63.76  E-value: 6.66e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1707477765 1210 EIALKRNLP-VNFEVTKESGPPHMKSFVTKVSV-GEFMGEGEGKSKKISKKNAAIAVLEEL 1268
Cdd:TIGR02191  160 EWAQARGKPlPEYRLIKEEGPDHDKEFTVEVSVnGEPYGEGKGKSKKEAEQNAAKAALEKL 220
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 1306-1371 7.05e-11

Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training Putative motif shared by proteins that bind to dsRNA. At least some DSRM proteins seem to bind to specific RNA targets. Exemplified by Staufen, which is involved in localization of at least five different mRNAs in the early Drosophila embryo. Also by interferon-induced protein kinase in humans, which is part of the cellular response to dsRNA.


Pssm-ID: 425434 [Multi-domain]  Cd Length: 66  Bit Score: 59.17  E-value: 7.05e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1707477765 1306 PISRLAQIQQaKKEKEPEYMLITERGLPRRREFVMQVKV-GVHTAEGMGTNKKVAKRNAAENMLEIL 1371
Cdd:pfam00035    1 PKSLLQEYAQ-KNGKPPPYEYVSEEGPPHSPKFTVTVKVdGKLYGSGTGSSKKEAEQLAAEKALEKL 66
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1187-1270 8.61e-11

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 63.58  E-value: 8.61e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765 1187 KPEVNGKEPDDENLN-KSEIsQvfEIALKRNLPV-NFEVTKESGPPHMKSFVTKVSV-GEFMGEGEGKSKKISKKNAAIA 1263
Cdd:COG0571    144 EPRLEEIAPGGAGKDyKTAL-Q--EWLQARGLPLpEYEVVEEEGPDHAKTFTVEVLVgGKVLGEGTGRSKKEAEQAAAKA 220


                   ....*..
gi 1707477765 1264 VLEELKK 1270
Cdd:COG0571    221 ALEKLGK 227
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1013-1054 7.08e-07

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 52.02  E-value: 7.08e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1707477765 1013 LARFNKIQPEYKLLSEQGPAHSKVFTVQLTLGDQHW-EAEGTS 1054
Cdd:COG0571    167 LQARGLPLPEYEVVEEEGPDHAKTFTVEVLVGGKVLgEGTGRS 209
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 1006-1055 7.54e-07

Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training Putative motif shared by proteins that bind to dsRNA. At least some DSRM proteins seem to bind to specific RNA targets. Exemplified by Staufen, which is involved in localization of at least five different mRNAs in the early Drosophila embryo. Also by interferon-induced protein kinase in humans, which is part of the cellular response to dsRNA.


Pssm-ID: 425434 [Multi-domain]  Cd Length: 66  Bit Score: 48.00  E-value: 7.54e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1707477765 1006 PMCLVNELARFNKIQPEYKLLSEQGPAHSKVFTVQLTLGDQHW-EAEGTSI 1055
Cdd:pfam00035    1 PKSLLQEYAQKNGKPPPYEYVSEEGPPHSPKFTVTVKVDGKLYgSGTGSSK 51
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 1013-1054 4.54e-05

ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. This enzyme cleaves double-stranded rRNA. It is involved in processing ribosomal RNA precursors. It is found even in minimal genones such as Mycoplasma genitalium and Buchnera aphidicola, and in some cases has been shown to be an essential gene. These bacterial proteins contain a double-stranded RNA binding motif (pfam00035) and a ribonuclease III domain (pfam00636). Eukaryotic homologs tend to be much longer proteins with additional domains, localized to the nucleus, and not included in this family. [Transcription, RNA processing]


Pssm-ID: 274024 [Multi-domain]  Cd Length: 220  Bit Score: 46.43  E-value: 4.54e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1707477765 1013 LARFNKIQPEYKLLSEQGPAHSKVFTVQLTLGDQHW-EAEGTS 1054
Cdd:TIGR02191  162 AQARGKPLPEYRLIKEEGPDHDKEFTVEVSVNGEPYgEGKGKS 204
 
Name Accession Description Interval E-value
CAS_CSE1 pfam03378
CAS/CSE protein, C-terminus; Mammalian cellular apoptosis susceptibility (CAS) proteins are ...
 486-907 0e+00

CAS/CSE protein, C-terminus; Mammalian cellular apoptosis susceptibility (CAS) proteins are homologous to the yeast chromosome-segregation protein, CSE1. This family aligns the C-terminal halves (approximately). CAS is involved in both cellular apoptosis and proliferation. Apoptosis is inhibited in CAS-depleted cells, while the expression of CAS correlates to the degree of cellular proliferation. Like CSE1, it is essential for the mitotic checkpoint in the cell cycle (CAS depletion blocks the cell in the G2 phase), and has been shown to be associated with the microtubule network and the mitotic spindle, as is the protein MEK, which is thought to regulate the intracellular localization (predominantly nuclear vs. predominantly cytosolic) of CAS. In the nucleus, CAS acts as a nuclear transport factor in the importin pathway. The importin pathway mediates the nuclear transport of several proteins that are necessary for mitosis and further progression. CAS is therefore thought to affect the cell cycle through its effect on the nuclear transport of these proteins. Since apoptosis also requires the nuclear import of several proteins (such as P53 and transcription factors), it has been suggested that CAS also enables apoptosis by facilitating the nuclear import of at least a subset of these essential proteins.


Pssm-ID: 367469  Cd Length: 435  Bit Score: 656.30  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  486 ERLFTMRGTNNATLITAAEMAPYVEVLLTNLFKALTLPGSSENEYIMKAIMRSFSLLQESIIPYIPSVITQLTQKLLAVS 565
Cdd:pfam03378    1 ERLLTLRDEQGQPIFTSADIAPFAKDLLTHLFAAIEKPGSQENEYLMKCIMRVLIVIQEAVLPVADVVLQHLTNILQEVS 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  566 KNPSKPHFNHYMFESICLSIRITCKANPEAVGSFEEALFMVFTEILQNDVQEFIPYVFQVMSLLLEMHKNE-IPTSYMAL 644
Cdd:pfam03378   81 KNPSNPRFNHYLFEAIGALIRFACKADPAAVSKFEEALFPPFQAILQEDVTEFMPYVFQLLAQLLEANPSGtLPDYYMAL 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  645 FPHLLQPVLWERTGNIPPLVRLLQAYLERGASTIasAAADKIPGLLGVFQKLIASKANDHQGFYLLNSIIEHMPPESVDQ 724
Cdd:pfam03378  161 FPPLLSPALWERRGNVPALVRLLSAFIPKASQEI--VANNKLEPVLGIFQKLIASKANDHQGFYLLESVIENFPPEVLEP 238

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  725 YRKQIFILLFQRLQNSKTTKFIKSFLVFINLYCVRYGALALQEIFDSIQPKMFGMVLEKIIIPEIQKVSGQVEKKICAVG 804
Cdd:pfam03378  239 YFKTIFSLLFQRLQNSKTEKFVKRFVIFYHLYSAKHGADFLIQLIDAIQPGVFGMIYLNVILPETQKLAGPLDRKLAAVS 318

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  805 ITKILTECPPMMDTeYTKLWIPLLQALIGLFELPEDDTIPDEEHFIDIEDTP--GYQTAFSQLAFAGKKEHDPVGQmVNN 882
Cdd:pfam03378  319 YTKLLCESPAFADR-YPKGWGFLLQSLLKLLELPPDPAAADEDDIIDEADVDdmGYGVGFTQLNTAGKKERDPFPD-IPD 396

                          410       420
                   ....*....|....*....|....*
gi 1707477765  883 PRIHLAQSLHKLSTACPGRVSNLVS 907
Cdd:pfam03378  397 VKQWVGQSLKEASQAHPGRISQIIS 421
Cse1 pfam08506
Cse1; This domain is present in Cse1 nuclear export receptor proteins. Cse1 mediates the ...
 115-485 4.61e-177

Cse1; This domain is present in Cse1 nuclear export receptor proteins. Cse1 mediates the nuclear export of importin alpha. This domain contains HEAT repeats.


Pssm-ID: 430038 [Multi-domain]  Cd Length: 370  Bit Score: 534.58  E-value: 4.61e-177
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  115 LFKRYRHEFKSNELWTEIKLVLDAFALPLTNLFKATIELCSTHANDASALKVLFSSLILIAKLFYSLNFQDLPEFFEDNM 194
Cdd:pfam08506    1 IFKRWRPLFRSDELFLEIKLVLDKFAEPFLTLLQKVDELIEANKNNKASLKILFEVLLLLCKLFYDLNCQDIPEFFEDNM 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  195 ETWMTNFHSLLTLDNKLLQTDDEEEAGLLELLKSQICDNAALYAQKYDEEFQPYLPRFVTAIWNLLVTTGQEVKYDLLVS 274
Cdd:pfam08506   81 KEWMGIFHKYLSYDNPLLETDDDEEATVLEKLKASICELVQLYTLRYEEEFGPMVNDFIQAVWNLLVSTSPQPKYDILVS 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  275 NAIQFLASVCERPHYKHLFEDQNTLTSICEKVIVPNMEFRAADEEAFEDNSEEYIRRDLEGSDIDTRRRAACDLVRGLCK 354
Cdd:pfam08506  161 KALSFLTSVARRPKYAELFNNESVLKQIIEKVVLPNVTLRESDEELFEDDPIEYIRRDLEGSDSDTRRRAATDFLKELKE 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  355 FFEGPVTGIFSGYVNSMLQEYAKNPSVNWKHKDAAIYLVTSLASKAQTQKHGITQANELVNLTEFFVNHIQPDLKSAtVN 434
Cdd:pfam08506  241 KFEALVTNVVLEYIQRLLEKYSANPSLNWKAKDTAIYLFTSIAAKGAVTKSGVTSTNPLVDVVDFFQQQIAPDLMAN-VN 319

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1707477765  435 EFPVLKADGIKYIMIFRNQVPKEQLLVSIPLLINHLQAESIVVHTYAAHAL 485
Cdd:pfam08506  320 QHPILKADAIKYIYTFRNQLTKEQLIEIFPLLINFLQSSSYVVYTYAAITI 370
CSE1 COG5657
CAS/CSE protein involved in chromosome segregation [Cell division and chromosome partitioning]; ...
 36-894 2.80e-120

CAS/CSE protein involved in chromosome segregation [Cell division and chromosome partitioning];


Pssm-ID: 227944 [Multi-domain]  Cd Length: 947  Bit Score: 402.27  E-value: 2.80e-120
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765   36 VEDEPNKICESDRIAIKANIVPLMLSSPEQIQKQLSDAISIIGREDFPQKWPDLLTEMVNRFQSGDFHVINGVLRTAHSL 115
Cdd:COG5657     71 REENGNSILPDENVLIRDELFSLIISSSNQLQIQNALAVSRIARLDFPDEWPTLVPDLLSLLSEKDMVTNENSLRVLHHI 150

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  116 FKRYRHEFKSNELWTEIKLVLDAFALPLTNLFKATIELCSthaNDASALKVLFSSLILIAKLFYSLNFQDLPEFFEDNME 195
Cdd:COG5657    151 FKRLRRLFRSDALFLEIAPVLLSILCPFLFSSAYFWSMSE---NLDESLLSLFQVCLKLIRRYYDLGFQDIPEFFEDNLD 227

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  196 TWMTNFHSLLTLDNKLLQtDDEEEAGLLELLKSQICDNAALYAQKYDEEFQPYLPRFVTAIWNLLVTTGQEVKYDLLVSN 275
Cdd:COG5657    228 KFMEHFCKLLSYSNPVLQ-KDCLEDCVYFKLKGSICEIFNLYTTKYPEVITYLIYDFVEIVWNLLTTITRPYIRDYLVSK 306

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  276 AIQFLASVCERPHYKH----LFEDQNTLTSICEKVIVPNMEFRAADEEAFEDNSEEYIRrdlEGSDIDTRRRAACDLVRG 351
Cdd:COG5657    307 SLTVLINVIKYPIRKTaevlSNVSENLINNLVDLLILPNLILREEDLEEWEDDPLEYIR---EQSKTDYEVNVRPCIENE 383

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  352 LCKFFEGpVTGIFSGYVNSMLQEYAKNPsvnwKHKDAAIYLVTSLASKAQtqkhGITQANELVNLTEFFVNHIQPDLKSA 431
Cdd:COG5657    384 LKDLFDV-FGRIAVGHELTVIESEATTP----NILDEARQLFAAYASFGL----GVEAVNRMVDFVKFLGSIIYPDLLSP 454

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  432 TVNEFPVLKADGIKYIMIFRNQVPKEQLLVSiplliNHLQAESIVVHTYAAHALERLFTMRGTNNATLITAAEMAPYVEV 511
Cdd:COG5657    455 NEIIHLRILRSRIAYILTFRNQLDSSELSES-----KFLASQFFVNYTTACIDAVVLLTTREAYSTIFDDWNFSVCSKIG 529

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  512 LLTNLFKALTLPGSS-----ENEYIMKAIMRSFSLLQESIIPYIPSVITQLTQKLLAVSKNPSKPHFNHYMFESICLSIR 586
Cdd:COG5657    530 LLENLILLVLSLMASpssleEREFLLQLISRIIIIDPELIAPLGSEILQLLDNLVEINAKNPSNPQFAHYTFEDIGALVF 609

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  587 ITCKANPEAVGSFEEALFMVFTEILQNDVQEFIPYVFQVMSLLLEMHKNE-IPTSYMALFPHLLQPVLWERTGNIPPLVR 665
Cdd:COG5657    610 LKSGMCEITIPTLVLALVPEFPVLLSEDATELWSYVLQLLSILPEHFSGDvLPSVVKILRQPSLATELLPTKLEILKSYR 689

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  666 LLQAYLERGASTIASAAADKIpglLGVFQKLIASKANDHQGFyLLNSIIEHMPPE-SVDQYRKQIFILLFQRLQNSKTTK 744
Cdd:COG5657    690 LLDNPILTTGYIFKSSGFQPV---LGILQYLLGSEPHDALCF-LNLTVVETLYLEnIYEPYVNLIFVLLLSRLKNSKTER 765

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  745 FIKSFLVFINLYCVRYGALALQEIF----DSIQPKMFGMVLEKIIIPEIQkVSGQVEKKICAVGITKIL-TECPPMM-DT 818
Cdd:COG5657    766 FVIKIIHVFSLVSFKDSLTVGCDNLiskiNQTKNILIVQLYGNWILGFDE-IHDSKDRKIHLIGLSNLLrTLHPEVLsYV 844

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  819 EYTKLWIPLLQALIGLFELP----EDDTIPDEEHFIDIEDtpgyQTAFSQLAFAGKKeHDPVGQmVNNPRIHLAQSLHKL 894
Cdd:COG5657    845 SVTNLIISLLSEIFETASGDaiiyELNDDYADDWFDGEIS----AEEFSRLAQLEFK-VDPVHD-IDNTKYFISFFMEAM 918
Staufen_C pfam16482
Staufen C-terminal domain; This is the C-terminal domain of Staufen proteins. It consists of ...
 1466-1575 6.43e-58

Staufen C-terminal domain; This is the C-terminal domain of Staufen proteins. It consists of an N-terminal Staufen-swapping motif (SSM) comprising two alpha helices, connected by a linker region to a dsRNA-binding-like domain ('RBD'). The 'RBD' has the fold of a functional dsRNA-binding domain, but lacks the residues required to bind RNA. This domain is responsible for dimerization, the SSM from one molecule interacts with the 'RBD' of another.


Pssm-ID: 465131  Cd Length: 110  Bit Score: 195.12  E-value: 6.43e-58
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765 1466 KATVTAMIARELLYGGTSPTAETILKSSNSSGHVPHGPlTRPSEQLDYLSNVQGIQVEYKDFPKNNKNEFVSLINCSSQP 1545
Cdd:pfam16482    2 KATVTAAIARELLYGGTSPTAEAILKNNGKTGAVPCGL-VQPSQQLEYLARVQGFQVEYSDFPRQNKNEFLSLLTLSSQP 80

                           90       100       110
                   ....*....|....*....|....*....|
gi 1707477765 1546 PLISHGIGKDVESCHDMAALNILKLLSELD 1575
Cdd:pfam16482   81 VQMTHGIGSSLEASHDQAALSALKQLSEQG 110
DSRM_STAU1_rpt4 cd19885
fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen ...
 1295-1373 4.72e-53

fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 1 (Staufen 1) and similar proteins; Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 1 contains five double-stranded RNA binding motifs (DSRMs). This model describes the fourth motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380714  Cd Length: 86  Bit Score: 180.28  E-value: 4.72e-53
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1707477765 1295 QTSPEYGQGMNPISRLAQIQQAKKEKEPEYMLITERGLPRRREFVMQVKVGVHTAEGMGTNKKVAKRNAAENMLEILGF 1373
Cdd:cd19885      1 QTSPEYGQGMNPISRLAQIQQAKKEKEPEYTLITERGLPRRREFVMQVKVGNQTAEGMGPNKKVAKRNAAEKMLELLGF 79
DSRM_STAU1_rpt2 cd19881
second double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen ...
 1101-1165 2.79e-44

second double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 1 (Staufen 1) and similar proteins; Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 1 contains five double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380710  Cd Length: 79  Bit Score: 155.04  E-value: 2.79e-44
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1707477765 1101 MKLGKKPMYKPIDPYTGMRSTYNYTMRG-GTYPPRYFYPF-PVGPLLYQVELSIGGQQFHGKGRTRQ 1165
Cdd:cd19881      1 MKLGKKPIYKPIDPYTGMRSAYNYNMRGnGAYPPRYFYPFpPVGPVLYQVELSIGGQQFHGKGRTRQ 67
DSRM_STAU1_rpt1 cd19879
first double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...
 1002-1067 1.13e-43

first double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 1 (Staufen 1) and similar proteins; Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 1 contains five double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380708  Cd Length: 66  Bit Score: 152.92  E-value: 1.13e-43
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1707477765 1002 KEKTPMCLVNELARFNKIQPEYKLLSEQGPAHSKVFTVQLTLGDQHWEAEGTSIKKAQHAAAAKAL 1067
Cdd:cd19879      1 KEKTPMCLVNELARFNKIQPEYKLLSEQGPAHSKVFTVQLTLGDQHWEAEGTSIKKAQHAAAAKAL 66
DSRM_STAU1_rpt3 cd19883
third double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...
 1202-1268 7.28e-41

third double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 1 (Staufen 1) and similar proteins; Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 1 contains five double-stranded RNA binding motifs (DSRMs). This model describes the third motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380712  Cd Length: 67  Bit Score: 144.77  E-value: 7.28e-41
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1707477765 1202 KSEISQVFEIALKRNLPVNFEVTKESGPPHMKSFVTKVSVGEFMGEGEGKSKKISKKNAAIAVLEEL 1268
Cdd:cd19883      1 KSEISQVFEIALKRNMPVNFEVTKETGPPHMKSFVTKVSVGEFAGEGEGKSKKISKKNAAIAVLEEL 67
DSRM_STAU1_rpt5 cd19887
fifth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...
 1506-1575 3.67e-39

fifth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 1 (Staufen 1) and similar proteins; Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 1 contains five double-stranded RNA binding motifs (DSRMs). This model describes the fifth motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380716  Cd Length: 70  Bit Score: 140.19  E-value: 3.67e-39
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765 1506 RPSEQLDYLSNVQGIQVEYKDFPKNNKNEFVSLINCSSQPPLISHGIGKDVESCHDMAALNILKLLSELD 1575
Cdd:cd19887      1 RPSEQLDYLSRVQGLQVEYKDFPKNNKNEFVSLINCSSQPPLISHGIGKDVESCHDMAALNILKLLSELD 70
DSRM_STAU2_rpt4 cd19886
fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen ...
 1302-1373 1.04e-38

fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 2 (Staufen 2) and similar proteins; Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite. Staufen 2 contains five double-stranded RNA binding motifs (DSRMs). This model describes the fourth motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380715  Cd Length: 86  Bit Score: 139.32  E-value: 1.04e-38
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1707477765 1302 QGMNPISRLAQIQQAKKEKEPEYMLITERGLPRRREFVMQVKVGVHTAEGMGTNKKVAKRNAAENMLEILGF 1373
Cdd:cd19886      1 QGMNPISRLAQIQQAKKEKEPEYVLLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKRNAAEAMLLQLGY 72
DSRM_STAU_rpt4 cd19860
fourth double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 1305-1372 9.30e-38

fourth double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein Staufen and similar proteins; Staufen is a double-stranded RNA binding protein required both for the localization of maternal determinants to the posterior pole of the egg, oskar (osk) RNA, and for correct localization to the anterior pole, anchoring bicoid (bcd) RNA. The family also includes two Staufen homologs from vertebrates, Staufen 1 and Staufen 2. They are present in distinct ribonucleoprotein complexes and associate with different mRNAs. Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite. Staufen proteins contain five double-stranded RNA binding motifs (DSRMs). This model describes the fourth motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380689  Cd Length: 68  Bit Score: 135.92  E-value: 9.30e-38
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1707477765 1305 NPISRLAQIQQAKKEKEPEYMLITERGLPRRREFVMQVKVGVHTAEGMGTNKKVAKRNAAENMLEILG 1372
Cdd:cd19860      1 NPISRLIQIQQARKEKEPVYSLVAERGTPRRREFVMQVTVGDKTATGTGPNKKLAKRNAAEAMLELLG 68
DSRM_STAU_rpt3 cd19859
third double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 1204-1268 8.39e-33

third double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein Staufen and similar proteins; Staufen is a double-stranded RNA binding protein required both for the localization of maternal determinants to the posterior pole of the egg, oskar (osk) RNA, and for correct localization to the anterior pole, anchoring bicoid (bcd) RNA. The family also includes two Staufen homologs from vertebrates, Staufen 1 and Staufen 2. They are present in distinct ribonucleoprotein complexes and associate with different mRNAs. Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite. Staufen proteins contain five double-stranded RNA binding motifs (DSRMs). This model describes the third motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380688  Cd Length: 65  Bit Score: 121.74  E-value: 8.39e-33
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1707477765 1204 EISQVFEIALKRNLPVNFEVTKESGPPHMKSFVTKVSVGEFMGEGEGKSKKISKKNAAIAVLEEL 1268
Cdd:cd19859      1 EISLVHEIALKRNLTVNFEVLRESGPPHMKNFITRCTVGSFVTEGEGNSKKVSKKRAAEKMLEEL 65
DSRM_STAU2_rpt3 cd19884
third double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...
 1202-1268 1.35e-32

third double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 2 (Staufen 2) and similar proteins; Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite. Staufen 2 contains five double-stranded RNA binding motifs (DSRMs). This model describes the third motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380713  Cd Length: 67  Bit Score: 121.27  E-value: 1.35e-32
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1707477765 1202 KSEISQVFEIALKRNLPVNFEVTKESGPPHMKSFVTKVSVGEFMGEGEGKSKKISKKNAAIAVLEEL 1268
Cdd:cd19884      1 KSEISLVFEIALKRNMPVSFEVIKESGPPHMKSFVTRVTVGEFTAEGEGNSKKLSKKRAATSVLQEL 67
DSRM_STAU2_rpt1 cd19880
first double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...
 1000-1055 5.44e-32

first double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 2 (Staufen 2) and similar proteins; Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite. Staufen 2 contains five double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380709  Cd Length: 68  Bit Score: 119.44  E-value: 5.44e-32
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1707477765 1000 NPKEKTPMCLVNELARFNKIQPEYKLLSEQGPAHSKVFTVQLTLGDQHWEAEGTSI 1055
Cdd:cd19880      1 NPKEKTPMCLVNELARFNRIQPQYKLLNERGPAHAKIFTVQLTLGEQTWEAEGSSI 56
DSRM_STAU_rpt5 cd19861
fifth double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 1507-1574 3.09e-27

fifth double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein Staufen and similar proteins; Staufen is a double-stranded RNA binding protein required both for the localization of maternal determinants to the posterior pole of the egg, oskar (osk) RNA, and for correct localization to the anterior pole, anchoring bicoid (bcd) RNA. The family also includes two Staufen homologs from vertebrates, Staufen 1 and Staufen 2. They are present in distinct ribonucleoprotein complexes and associate with different mRNAs. Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite. Staufen proteins contain five double-stranded RNA binding motifs (DSRMs). This model describes the fifth motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380690  Cd Length: 68  Bit Score: 105.77  E-value: 3.09e-27
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1707477765 1507 PSEQLDYLSNVQGIQVEYKDFPKNNKNEFVSLINCSSQPPLISHGIGKDVESCHDMAALNILKLLSEL 1574
Cdd:cd19861      1 PKEQLEYLAKVLGFSVEFTDFPKGNKSEYLSLVSLGTEPPQVCHGSGSSVEESRDAAALNALKLLKEL 68
DSRM_STAU_rpt1 cd19857
first double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 1005-1055 6.45e-25

first double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein Staufen and similar proteins; Staufen is a double-stranded RNA binding protein required both for the localization of maternal determinants to the posterior pole of the egg, oskar (osk) RNA, and for correct localization to the anterior pole, anchoring bicoid (bcd) RNA. The family also includes two Staufen homologs from vertebrates, Staufen 1 and Staufen 2. They are present in distinct ribonucleoprotein complexes and associate with different mRNAs. Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite. Staufen proteins contain five double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380686  Cd Length: 64  Bit Score: 99.26  E-value: 6.45e-25
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1707477765 1005 TPMCLVNELARFNKIQPEYKLLSEQGPAHSKVFTVQLTLGDQ-HWEAEGTSI 1055
Cdd:cd19857      1 TPMCLLNELARFNKIRPQYTLVDEEGPAHKKTFTVKLTLGDEeEYEASGSSI 52
DSRM smart00358
Double-stranded RNA binding motif;
1205-1269 7.28e-18

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 79.23  E-value: 7.28e-18
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1707477765  1205 ISQVFEIALKRNLPVNFEVTKESGPPHMKSFVTKVSVGEFM-GEGEGKSKKISKKNAAIAVLEELK 1269
Cdd:smart00358    2 KSLLQELAQKRKLPPEYELVKEEGPDHAPRFTVTVKVGGKRtGEGEGSSKKEAKQRAAEAALRSLK 67
DSRM smart00358
Double-stranded RNA binding motif;
1306-1372 2.99e-17

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 77.30  E-value: 2.99e-17
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1707477765  1306 PISRLAQIQQAKKeKEPEYMLITERGLPRRREFVMQVKV-GVHTAEGMGTNKKVAKRNAAENMLEILG 1372
Cdd:smart00358    1 PKSLLQELAQKRK-LPPEYELVKEEGPDHAPRFTVTVKVgGKRTGEGEGSSKKEAKQRAAEAALRSLK 67
SXM1 COG5656
Importin, protein involved in nuclear import [Posttranslational modification, protein turnover, ...
 54-661 2.52e-16

Importin, protein involved in nuclear import [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 227943 [Multi-domain]  Cd Length: 970  Bit Score: 85.29  E-value: 2.52e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765   54 NIVPLMLSSPEQIQKQLSDAISIIGREDFPQKWPDLLTEMVNRFQSGDFHVINGVLRTAHSLFKRYRhefksnelwteIK 133
Cdd:COG5656     92 NILDVFLYSPEVTRTALNAILVNIFSEDKPSDLWGLFPKAANLLRSSEANHVYTGLLCLEELFKAYR-----------WK 160

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  134 LVLD-AFALPL-TNLFKATIELCS---THANDASAlkvlfSSLILIAKLFYSLNFQDLPEFFEDNmETWMTNFHSLLTLD 208
Cdd:COG5656    161 YNDEqVDILMLiTALFPILEKVGGnleSQGNYGSV-----ETLMLILKSFKSVCYYSLPDFLSAI-ETFSSWFQLSLRIL 234

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  209 NK-LLQTDDEEEAGLLELLKSQICDNAALY--------------AQKYDEEFQPYLPRF---------VTAIWnllvTTG 264
Cdd:COG5656    235 QKpLPNEVLSLDPEVRSLSKWVKCKKWAAYnlyrsfqryikksyKKSYLSFYITFMTRVpmilatffkQIEEW----GQG 310

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  265 Q-----EVKYDLL-----VSNAIQFLASVceRPHYKHLFEDqntltsicekVIVPNMEFRAADEEAFEDNSEEYIRRDLE 334
Cdd:COG5656    311 QlwlsdIELYFIDffvelCVDADQTWRLM--EPHLQYIISG----------VIFPLLCLSEEEEELFENDPDEYIRRYYD 378

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  335 GSDIDTRRRAACDLVRGLCKFFEGPVT--GIFSgYVNSMLQEYAKNPS--VNWKHKDAAIYLVTSLASKaqtqkhgITQA 410
Cdd:COG5656    379 FFDNGLSPDLAALFFLIISKSKRKEETfqGILS-FLLSILGQSAATPSniDNARQAEGALRLLASIKSF-------ITKM 450

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  411 NELVNLTEFF-VNHIQPDLKSatvnEFPVLKADGIKYIMIFRNQVP-KEQLLVSIPLLINHLQAESIVVHTYAAHALERL 488
Cdd:COG5656    451 SPAANVMEYFiVNHVIPAFRS----NYGFLKSRACEFISTIEEDFKdNGILLEAYENTHNCLKNNHLPVMIEAALALQFF 526

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  489 FTMRGTNNAtliTAAEMAPYVEVL--LTNLFKALTLPGsseneyIMKAIMRSFSllqESIIPYIPSVITQLTQKLLAVS- 565
Cdd:COG5656    527 IFNEQSHEK---FSAHVPETMEKLlsLSNTFEIDPLSM------VMESFVEYFS---EELSPFAPELAGSLVRQFLKIAq 594

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765  566 ---KNPSKPHFNH-----------YMFESICLSIRITckanPEAVGSFEEALFMVFTEILQNDVQEFIPYVFQVMSLLLE 631
Cdd:COG5656    595 sllENSSDTSSVVddkqmaasgilRTIESMILSLENR----PLVLKYLEVSLYPVISFILKNEISDFYQEALDILDGYTF 670

                          650       660       670
                   ....*....|....*....|....*....|
gi 1707477765  632 MHKNEIPTSymalfphllqPVLWERTGNIP 661
Cdd:COG5656    671 MSKEIEPIM----------WGIFELLLNLL 690
DSRM_RNAse_III_family cd10845
double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...
 1304-1371 4.85e-14

double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase III (EC 3.1.26.3; also known as ribonuclease 3) digests double-stranded RNA formed within single-strand substrates, but not RNA-DNA hybrids. It is involved in the processing of rRNA precursors, viral transcripts, some mRNAs, and at least 1 tRNA (metY, a minor form of tRNA-init-Met). It cleaves the 30S primary rRNA transcript to yield the immediate precursors to the 16S and 23S rRNAs. The cleavage can occur in assembled 30S, 50S, and even 70S subunits and is influenced by the presence of ribosomal proteins. The RNase III family also includes the mitochondrion-specific ribosomal protein mL44 subfamily, which is composed of mitochondrial 54S ribosomal protein L3 (MRPL3) and mitochondrial 39S ribosomal protein L44 (MRPL44). Members of this family contain an RNase III domain and a C-terminal double-stranded RNA binding motif (DSRM). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380682 [Multi-domain]  Cd Length: 69  Bit Score: 68.29  E-value: 4.85e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1707477765 1304 MNPISRLAQIQQAKKEKEPEYMLITERGLPRRREFVMQVKV-GVHTAEGMGTNKKVAKRNAAENMLEIL 1371
Cdd:cd10845      1 KDYKTALQEYLQKRGLPLPEYELVEEEGPDHNKTFTVEVKVnGKVIGEGTGRSKKEAEQAAAKAALEKL 69
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 1205-1268 9.30e-14

Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training Putative motif shared by proteins that bind to dsRNA. At least some DSRM proteins seem to bind to specific RNA targets. Exemplified by Staufen, which is involved in localization of at least five different mRNAs in the early Drosophila embryo. Also by interferon-induced protein kinase in humans, which is part of the cellular response to dsRNA.


Pssm-ID: 425434 [Multi-domain]  Cd Length: 66  Bit Score: 67.26  E-value: 9.30e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1707477765 1205 ISQVFEIALKRNLPVNFEVTKESGPPHMKSFVTKVSV-GEFMGEGEGKSKKISKKNAAIAVLEEL 1268
Cdd:pfam00035    2 KSLLQEYAQKNGKPPPYEYVSEEGPPHSPKFTVTVKVdGKLYGSGTGSSKKEAEQLAAEKALEKL 66
DSRM_PRKRA-like_rpt1 cd19862
first double-stranded RNA binding motif of protein activator of the interferon-induced protein ...
 1202-1269 1.69e-13

first double-stranded RNA binding motif of protein activator of the interferon-induced protein kinase (PRKRA) and similar proteins; This family includes protein activator of the interferon-induced protein kinase (PRKRA) and the RISC-loading complex subunit TARBP2. PRKRA (also known as interferon-inducible double-stranded RNA-dependent protein kinase activator A, PKR-associated protein X (RAX), PKR-associating protein X, protein kinase, interferon-inducible double-stranded RNA-dependent activator, PACT, or HSD14) is a cellular activator for double-stranded RNA-dependent protein kinase during stress signaling. TARBP2 (also called TAR RNA-binding protein 2, or trans-activation-responsive RNA-binding protein (TRBP)), participates in the formation of the RNA-induced silencing complex (RISC). It is part of the RISC-loading complex (RLC), together with dicer1 and eif2c2/ago2, and is required to process precursor miRNAs. This family also includes Drosophila melanogaster Loquacious and similar proteins. Loquacious (Loqs) is a double-stranded RNA-binding domain (dsRBD) protein, a homolog of human TAR RNA binding protein (TRBP) that is a protein first identified as binding the HIV trans-activator RNA (TAR). Loqs interacts with Dicer1 (dmDcr1) to facilitate miRNA processing. PRKRA family proteins contain three double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380691 [Multi-domain]  Cd Length: 70  Bit Score: 66.90  E-value: 1.69e-13
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1707477765 1202 KSEISQVFEIALKRNLPVNFEVTKESGPPHMKSFVTKVSVGEFMGEGEGKSKKISKKNAAIAVLEELK 1269
Cdd:cd19862      1 KTPISVLQELCAKRGITPKYELISSEGAVHEPTFTFRVTVGDITATGSGTSKKKAKHAAAENALEQLK 68
DSRM_STAU2_rpt2 cd19882
second double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen ...
 1094-1166 1.85e-13

second double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 2 (Staufen 2) and similar proteins; Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite. Staufen 2 contains five double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380711  Cd Length: 82  Bit Score: 67.05  E-value: 1.85e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1707477765 1094 VELNALCMKLGKKPMYKPIDPYTGMRSTYNYTMRGgTYPPRYFYPFPvgPLLYqVELSIGGQQFHGKGRTRQA 1166
Cdd:cd19882      1 VELNGLAMKRGEPAIYRPIDPKPPPNYRPNYNFRG-MYNQRYHYPMP--KTFY-VSLTVGNREFIGEGRTRQA 69
DSRM_RNAse_III_family cd10845
double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...
 1206-1268 5.00e-12

double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase III (EC 3.1.26.3; also known as ribonuclease 3) digests double-stranded RNA formed within single-strand substrates, but not RNA-DNA hybrids. It is involved in the processing of rRNA precursors, viral transcripts, some mRNAs, and at least 1 tRNA (metY, a minor form of tRNA-init-Met). It cleaves the 30S primary rRNA transcript to yield the immediate precursors to the 16S and 23S rRNAs. The cleavage can occur in assembled 30S, 50S, and even 70S subunits and is influenced by the presence of ribosomal proteins. The RNase III family also includes the mitochondrion-specific ribosomal protein mL44 subfamily, which is composed of mitochondrial 54S ribosomal protein L3 (MRPL3) and mitochondrial 39S ribosomal protein L44 (MRPL44). Members of this family contain an RNase III domain and a C-terminal double-stranded RNA binding motif (DSRM). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380682 [Multi-domain]  Cd Length: 69  Bit Score: 62.51  E-value: 5.00e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1707477765 1206 SQVFEIALKRNLP-VNFEVTKESGPPHMKSFVTKVSV-GEFMGEGEGKSKKISKKNAAIAVLEEL 1268
Cdd:cd10845      5 TALQEYLQKRGLPlPEYELVEEEGPDHNKTFTVEVKVnGKVIGEGTGRSKKEAEQAAAKAALEKL 69
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1293-1372 8.95e-12

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 66.66  E-value: 8.95e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765 1293 KLQTSPEYGQGMNPISRLAQIQQAKKEKEPEYMLITERGLPRRREFVMQVKV-GVHTAEGMGTNKKVAKRNAAENMLEIL 1371
Cdd:COG0571    146 RLEEIAPGGAGKDYKTALQEWLQARGLPLPEYEVVEEEGPDHAKTFTVEVLVgGKVLGEGTGRSKKEAEQAAAKAALEKL 225


                   .
gi 1707477765 1372 G 1372
Cdd:COG0571    226 G 226
DSRM_PRKRA-like_rpt2 cd19863
second double-stranded RNA binding motif of PRKRA, TARBP2 and similar proteins; The family ...
 1305-1368 9.83e-12

second double-stranded RNA binding motif of PRKRA, TARBP2 and similar proteins; The family includes protein activator of the interferon-induced protein kinase (PRKRA) and the RISC-loading complex subunit TARBP2. PRKRA (also known as interferon-inducible double-stranded RNA-dependent protein kinase activator A, PKR-associated protein X (RAX), PKR-associating protein X, protein kinase, interferon-inducible double-stranded RNA-dependent activator, PACT, or HSD14) is a cellular activator for double-stranded RNA-dependent protein kinase during stress signaling. TARBP2 (also called TAR RNA-binding protein 2, or trans-activation-responsive RNA-binding protein (TRBP)) participates in the formation of the RNA-induced silencing complex (RISC). It is part of the RISC-loading complex (RLC), together with dicer1 and eif2c2/ago2, and is required to process precursor miRNAs. The family also includes Drosophila melanogaster Loquacious and similar proteins. Loquacious (Loqs) is a double-stranded RNA-binding domain (dsRBD) protein, a homolog of human TAR RNA binding protein (TRBP) that is a protein first identified as binding the HIV trans-activator RNA (TAR). Loqs interacts with Dicer1 (dmDcr1) to facilitate miRNA processing. PRKRA family proteins contain three double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380692  Cd Length: 67  Bit Score: 61.62  E-value: 9.83e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1707477765 1305 NPISRLAQIQQAKKEKEPEYMLITERGLPRRREFVMQVKVGVHTAEGMGTNKKVAKRNAAENML 1368
Cdd:cd19863      1 NPVGILQELCVQRRWRLPEYEVEQESGPPHEKEFTIACRVENFSETGSGKSKKLAKRAAAEKML 64
DSRM_STAU2_rpt5 cd19888
fifth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...
 1506-1573 1.19e-11

fifth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 2 (Staufen 2) and similar proteins; Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite. Staufen 2 contains five double-stranded RNA binding motifs (DSRMs). This model describes the fifth motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380717  Cd Length: 68  Bit Score: 61.51  E-value: 1.19e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1707477765 1506 RPSEQLDYLSNVQGIQVEYKDfpKNNKNEFVSLINCSSQpPLISHGIGKDVESCHDMAALNILKLLSE 1573
Cdd:cd19888      2 QPSKQLEYLARIQGFQVQYSD--RQNGKECMTCLTLSPV-QMTFHGIGSSIEASHDQAALSALKQLSE 66
DSRM smart00358
Double-stranded RNA binding motif;
1006-1055 1.40e-11

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 61.12  E-value: 1.40e-11
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|.
gi 1707477765  1006 PMCLVNELARFNKIQPEYKLLSEQGPAHSKVFTVQLTLGDQHW-EAEGTSI 1055
Cdd:smart00358    1 PKSLLQELAQKRKLPPEYELVKEEGPDHAPRFTVTVKVGGKRTgEGEGSSK 51
DSRM_PRKRA_rpt2 cd19891
second double-stranded RNA binding motif of protein activator of the interferon-induced ...
 1305-1368 4.74e-11

second double-stranded RNA binding motif of protein activator of the interferon-induced protein kinase (PRKRA) and similar proteins; PRKRA (also known as interferon-inducible double-stranded RNA-dependent protein kinase activator A, PKR-associated protein X (RAX), PKR-associating protein X, protein kinase, interferon-inducible double-stranded RNA-dependent activator, PACT, or HSD14) is a cellular activator for double-stranded RNA-dependent protein kinase during stress signaling. PRKRA contains three double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380720  Cd Length: 67  Bit Score: 59.95  E-value: 4.74e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1707477765 1305 NPISRLAQIQQAKKEKEPEYMLITERGLPRRREFVMQVKVGVHTAEGMGTNKKVAKRNAAENML 1368
Cdd:cd19891      1 NPIGSLQELAVQKGWRLPEYTLAQESGPPHKREFTITCRVETFVETGTGTSKKVAKRNAAEKLL 64
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 1210-1268 6.66e-11

ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. This enzyme cleaves double-stranded rRNA. It is involved in processing ribosomal RNA precursors. It is found even in minimal genones such as Mycoplasma genitalium and Buchnera aphidicola, and in some cases has been shown to be an essential gene. These bacterial proteins contain a double-stranded RNA binding motif (pfam00035) and a ribonuclease III domain (pfam00636). Eukaryotic homologs tend to be much longer proteins with additional domains, localized to the nucleus, and not included in this family. [Transcription, RNA processing]


Pssm-ID: 274024 [Multi-domain]  Cd Length: 220  Bit Score: 63.76  E-value: 6.66e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1707477765 1210 EIALKRNLP-VNFEVTKESGPPHMKSFVTKVSV-GEFMGEGEGKSKKISKKNAAIAVLEEL 1268
Cdd:TIGR02191  160 EWAQARGKPlPEYRLIKEEGPDHDKEFTVEVSVnGEPYGEGKGKSKKEAEQNAAKAALEKL 220
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 1306-1371 7.05e-11

Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training Putative motif shared by proteins that bind to dsRNA. At least some DSRM proteins seem to bind to specific RNA targets. Exemplified by Staufen, which is involved in localization of at least five different mRNAs in the early Drosophila embryo. Also by interferon-induced protein kinase in humans, which is part of the cellular response to dsRNA.


Pssm-ID: 425434 [Multi-domain]  Cd Length: 66  Bit Score: 59.17  E-value: 7.05e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1707477765 1306 PISRLAQIQQaKKEKEPEYMLITERGLPRRREFVMQVKV-GVHTAEGMGTNKKVAKRNAAENMLEIL 1371
Cdd:pfam00035    1 PKSLLQEYAQ-KNGKPPPYEYVSEEGPPHSPKFTVTVKVdGKLYGSGTGSSKKEAEQLAAEKALEKL 66
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1187-1270 8.61e-11

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 63.58  E-value: 8.61e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765 1187 KPEVNGKEPDDENLN-KSEIsQvfEIALKRNLPV-NFEVTKESGPPHMKSFVTKVSV-GEFMGEGEGKSKKISKKNAAIA 1263
Cdd:COG0571    144 EPRLEEIAPGGAGKDyKTAL-Q--EWLQARGLPLpEYEVVEEEGPDHAKTFTVEVLVgGKVLGEGTGRSKKEAEQAAAKA 220


                   ....*..
gi 1707477765 1264 VLEELKK 1270
Cdd:COG0571    221 ALEKLGK 227
DSRM_SF cd00048
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
 1312-1368 1.32e-10

double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 amino acid domain that adopts an alpha-beta-beta-beta-alpha fold. It is not sequence specific, but highly specific for double-stranded RNAs (dsRNAs) of various origin and structure. The DSRM domains are found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila Staufen protein, E. coli RNase III, RNase H1, and dsRNA dependent adenosine deaminases. They are involved in numerous cellular mechanisms ranging from localization and transport of messenger RNAs, through maturation and degradation of RNAs, to viral response and signal transduction. Some members harbor tandem DSRMs that act in small RNA biogenesis.


Pssm-ID: 380679 [Multi-domain]  Cd Length: 57  Bit Score: 58.07  E-value: 1.32e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1707477765 1312 QIQQAKKEKEPEYMLITERGlPRRREFVMQVKVGVHTAEGMGTNKKVAKRNAAENML 1368
Cdd:cd00048      2 ELCQKNKWPPPEYETVEEGG-PHNPRFTCTVTVNGQTFEGEGKSKKEAKQAAAEKAL 57
DSRM_STAU_rpt2 cd19858
second double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 1118-1166 1.43e-10

second double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein Staufen and similar proteins; Staufen is a double-stranded RNA binding protein required both for the localization of maternal determinants to the posterior pole of the egg, oskar (osk) RNA, and for correct localization to the anterior pole, anchoring bicoid (bcd) RNA. The family also includes two Staufen homologs from vertebrates, Staufen 1 and Staufen 2. They are present in distinct ribonucleoprotein complexes and associate with different mRNAs. Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite. Staufen proteins contain five double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380687  Cd Length: 67  Bit Score: 58.57  E-value: 1.43e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1707477765 1118 MRSTYNYTM-----RGGTYPPRYFYPFPVG--PLLYQVELSIGGQQFHGKGRTRQA 1166
Cdd:cd19858      1 RQEHPNYNNygmpqRRGDYRFRYPYPNNPSgpPPPFYVTLTVGEREFIGEGRTRQA 56
DSRM_SF cd00048
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
 1209-1265 2.48e-10

double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 amino acid domain that adopts an alpha-beta-beta-beta-alpha fold. It is not sequence specific, but highly specific for double-stranded RNAs (dsRNAs) of various origin and structure. The DSRM domains are found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila Staufen protein, E. coli RNase III, RNase H1, and dsRNA dependent adenosine deaminases. They are involved in numerous cellular mechanisms ranging from localization and transport of messenger RNAs, through maturation and degradation of RNAs, to viral response and signal transduction. Some members harbor tandem DSRMs that act in small RNA biogenesis.


Pssm-ID: 380679 [Multi-domain]  Cd Length: 57  Bit Score: 57.29  E-value: 2.48e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1707477765 1209 FEIALKRNLP-VNFEvTKESGPPHMKSFVTKVSVGEFMGEGEGKSKKISKKNAAIAVL 1265
Cdd:cd00048      1 NELCQKNKWPpPEYE-TVEEGGPHNPRFTCTVTVNGQTFEGEGKSKKEAKQAAAEKAL 57
DSRM_PRKRA-like_rpt1 cd19862
first double-stranded RNA binding motif of protein activator of the interferon-induced protein ...
 1305-1371 4.56e-10

first double-stranded RNA binding motif of protein activator of the interferon-induced protein kinase (PRKRA) and similar proteins; This family includes protein activator of the interferon-induced protein kinase (PRKRA) and the RISC-loading complex subunit TARBP2. PRKRA (also known as interferon-inducible double-stranded RNA-dependent protein kinase activator A, PKR-associated protein X (RAX), PKR-associating protein X, protein kinase, interferon-inducible double-stranded RNA-dependent activator, PACT, or HSD14) is a cellular activator for double-stranded RNA-dependent protein kinase during stress signaling. TARBP2 (also called TAR RNA-binding protein 2, or trans-activation-responsive RNA-binding protein (TRBP)), participates in the formation of the RNA-induced silencing complex (RISC). It is part of the RISC-loading complex (RLC), together with dicer1 and eif2c2/ago2, and is required to process precursor miRNAs. This family also includes Drosophila melanogaster Loquacious and similar proteins. Loquacious (Loqs) is a double-stranded RNA-binding domain (dsRBD) protein, a homolog of human TAR RNA binding protein (TRBP) that is a protein first identified as binding the HIV trans-activator RNA (TAR). Loqs interacts with Dicer1 (dmDcr1) to facilitate miRNA processing. PRKRA family proteins contain three double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380691 [Multi-domain]  Cd Length: 70  Bit Score: 57.27  E-value: 4.56e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1707477765 1305 NPISRLAQIQqAKKEKEPEYMLITERGLPRRREFVMQVKVGVHTAEGMGTNKKVAKRNAAENMLEIL 1371
Cdd:cd19862      2 TPISVLQELC-AKRGITPKYELISSEGAVHEPTFTFRVTVGDITATGSGTSKKKAKHAAAENALEQL 67
DSRM_PRKRA-like_rpt2 cd19863
second double-stranded RNA binding motif of PRKRA, TARBP2 and similar proteins; The family ...
 1210-1268 3.71e-09

second double-stranded RNA binding motif of PRKRA, TARBP2 and similar proteins; The family includes protein activator of the interferon-induced protein kinase (PRKRA) and the RISC-loading complex subunit TARBP2. PRKRA (also known as interferon-inducible double-stranded RNA-dependent protein kinase activator A, PKR-associated protein X (RAX), PKR-associating protein X, protein kinase, interferon-inducible double-stranded RNA-dependent activator, PACT, or HSD14) is a cellular activator for double-stranded RNA-dependent protein kinase during stress signaling. TARBP2 (also called TAR RNA-binding protein 2, or trans-activation-responsive RNA-binding protein (TRBP)) participates in the formation of the RNA-induced silencing complex (RISC). It is part of the RISC-loading complex (RLC), together with dicer1 and eif2c2/ago2, and is required to process precursor miRNAs. The family also includes Drosophila melanogaster Loquacious and similar proteins. Loquacious (Loqs) is a double-stranded RNA-binding domain (dsRBD) protein, a homolog of human TAR RNA binding protein (TRBP) that is a protein first identified as binding the HIV trans-activator RNA (TAR). Loqs interacts with Dicer1 (dmDcr1) to facilitate miRNA processing. PRKRA family proteins contain three double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380692  Cd Length: 67  Bit Score: 54.31  E-value: 3.71e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1707477765 1210 EIALKRN--LPVnFEVTKESGPPHMKSFVTKVSVGEFMGEGEGKSKKISKKNAAIAVLEEL 1268
Cdd:cd19863      8 ELCVQRRwrLPE-YEVEQESGPPHEKEFTIACRVENFSETGSGKSKKLAKRAAAEKMLTRL 67
DSRM_SON-like cd19870
double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known ...
 1201-1272 5.03e-09

double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known as Bax antagonist selected in saccharomyces 1 (BASS1), negative regulatory element-binding protein (NRE-binding protein), or protein DBP-5, or SON3) is an RNA-binding protein which acts as an mRNA splicing cofactor by promoting efficient splicing of transcripts that possess weak splice sites. It specifically promotes splicing of many cell-cycle and DNA-repair transcripts that possess weak splice sites, such as TUBG1, KATNB1, TUBGCP2, AURKB, PCNT, AKT1, RAD23A, and FANCG. Members of this group contain a double-stranded RNA binding motif (DSRM) at the C-terminus. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380699  Cd Length: 75  Bit Score: 54.21  E-value: 5.03e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1707477765 1201 NKSEISQVFEIALKRNL-PVNFEVTKESGPPHMKSFVTKVSVG--EFMGEGEGKSKKISKKNAAIAVLEELKKLP 1272
Cdd:cd19870      1 GKHPVSALMELCNKRKWgPPEFRLVEESGPPHRKHFLFKVVVNgvEYQPSVASGNKKDAKAQAATVALQALGLVP 75
DSRM_STAU_rpt4 cd19860
fourth double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 1205-1268 9.31e-09

fourth double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein Staufen and similar proteins; Staufen is a double-stranded RNA binding protein required both for the localization of maternal determinants to the posterior pole of the egg, oskar (osk) RNA, and for correct localization to the anterior pole, anchoring bicoid (bcd) RNA. The family also includes two Staufen homologs from vertebrates, Staufen 1 and Staufen 2. They are present in distinct ribonucleoprotein complexes and associate with different mRNAs. Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite. Staufen proteins contain five double-stranded RNA binding motifs (DSRMs). This model describes the fourth motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380689  Cd Length: 68  Bit Score: 53.49  E-value: 9.31e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1707477765 1205 ISQVFEI--ALKRNLPVnFEVTKESGPPHMKSFVTKVSVGEFMGEGEGKSKKISKKNAAIAVLEEL 1268
Cdd:cd19860      3 ISRLIQIqqARKEKEPV-YSLVAERGTPRRREFVMQVTVGDKTATGTGPNKKLAKRNAAEAMLELL 67
DSRM_EIF2AK2-like cd19875
double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...
 1202-1268 1.66e-08

double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2) and similar proteins; The family includes EIF2AK2 and adenosine deaminase domain-containing proteins, ADAD1 and ADAD2. EIF2AK2 (EC 2.7.11.1/EC 2.7.10.2; also known as interferon-induced, double-stranded RNA-activated protein kinase, eIF-2A protein kinase 2, interferon-inducible RNA-dependent protein kinase, P1/eIF-2A protein kinase, protein kinase RNA-activated (PKR), protein kinase R, tyrosine-protein kinase EIF2AK2, or p68 kinase) acts as an IFN-induced dsRNA-dependent serine/threonine-protein kinase which plays a key role in the innate immune response to viral infection and is also involved in the regulation of signal transduction, apoptosis, cell proliferation and differentiation. ADAD1 (also called testis nuclear RNA-binding protein (TENR)) and ADAD2 (also called testis nuclear RNA-binding protein-like (TENRL)) are phylogenetically related to a family of adenosine deaminases involved in RNA editing. ADAD1 plays an essential function in spermatid morphogenesis. It may be involved in testis-specific nuclear post-transcriptional processes such as heterogeneous nuclear RNA (hnRNA) packaging, alternative splicing, or nuclear/cytoplasmic transport of mRNAs. ADAD2 is a double-stranded RNA binding protein with unclear biological function. Members of this group contains varying numbers of double-stranded RNA binding motifs (DSRMs). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380704  Cd Length: 67  Bit Score: 52.65  E-value: 1.66e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1707477765 1202 KSEISQVFEIALKRNLPVNFEVTkESGPPHMKSFVTKVSV-GEFMGEGEGKSKKISKKNAAIAVLEEL 1268
Cdd:cd19875      1 KNPVSALNEYCQKRGLSLEFVDV-SVGPDHCPGFTASATIdGIVFASATGTSKKEAKRAAAKLALKKL 67
DSRM_EIF2AK2 cd20314
double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...
 1205-1268 4.75e-08

double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2) and similar proteins; EIF2AK2 (EC 2.7.11.1/EC 2.7.10.2; also known as interferon-induced, double-stranded RNA-activated protein kinase, eIF-2A protein kinase 2, interferon-inducible RNA-dependent protein kinase, P1/eIF-2A protein kinase, protein kinase RNA-activated (PKR), protein kinase R, tyrosine-protein kinase EIF2AK2, or p68 kinase) acts as an IFN-induced dsRNA-dependent serine/threonine-protein kinase which plays a key role in the innate immune response to viral infection and is also involved in the regulation of signal transduction, apoptosis, cell proliferation and differentiation. EIF2AK2 proteins contain two to three double-stranded RNA binding motifs (DSRMs). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380746  Cd Length: 68  Bit Score: 51.24  E-value: 4.75e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1707477765 1205 ISQVFEIALKRNLPVNFEVTKESGPPHMKSFVTKVSVGEFM-GEGEGKSKKISKKNAAIAVLEEL 1268
Cdd:cd20314      4 VSLLNEYCQKERLTVKYEEEKRSGPTHKPRFFCKYIIDGKEyPEGEGKSKKEAKQAAARLAYEEL 68
DSRM_TARBP2_rpt2 cd10844
second double-stranded RNA binding motif of the RISC-loading complex subunit TARBP2 and ...
 1305-1368 6.67e-08

second double-stranded RNA binding motif of the RISC-loading complex subunit TARBP2 and similar proteins; TARBP2 (also known as TAR RNA-binding protein 2, or trans-activation-responsive RNA-binding protein (TRBP)) participates in the formation of the RNA-induced silencing complex (RISC). It is part of the RISC-loading complex (RLC), together with dicer1 and eif2c2/ago2, and is required to process precursor miRNAs. TARBP2 contains three double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380681  Cd Length: 67  Bit Score: 50.88  E-value: 6.67e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1707477765 1305 NPISRLAQIQQAKKEKEPEYMLITERGLPRRREFVMQVKVGVHTAEGMGTNKKVAKRNAAENML 1368
Cdd:cd10844      1 NPVGALQELVVQKGWRLPEYTVTQESGPAHRKEFTMTCRVERFIEIGSGTSKKLAKRNAAAKML 64
DSRM_PRKRA-like_rpt3 cd19864
third double-stranded RNA binding motif of PRKRA, TARBP2 and similar proteins; The family ...
 1507-1571 7.75e-08

third double-stranded RNA binding motif of PRKRA, TARBP2 and similar proteins; The family includes protein activator of the interferon-induced protein kinase (PRKRA) and the RISC-loading complex subunit TARBP2. PRKRA (also known as interferon-inducible double-stranded RNA-dependent protein kinase activator A, PKR-associated protein X (RAX), PKR-associating protein X, protein kinase, interferon-inducible double-stranded RNA-dependent activator, PACT, or HSD14) is a cellular activator for double-stranded RNA-dependent protein kinase during stress signaling. TARBP2 (also called TAR RNA-binding protein 2, or trans-activation-responsive RNA-binding protein (TRBP)) participates in the formation of the RNA-induced silencing complex (RISC). It is part of the RISC-loading complex (RLC), together with dicer1 and eif2c2/ago2, and is required to process precursor miRNAs. The family also includes Drosophila melanogaster Loquacious and similar proteins. Loquacious (Loqs) is a double-stranded RNA-binding domain (dsRBD) protein, a homolog of human TAR RNA binding protein (TRBP) that is a protein first identified as binding the HIV trans-activator RNA (TAR). Loqs interacts with Dicer1 (dmDcr1) to facilitate miRNA processing. PRKRA family proteins contain three double-stranded RNA binding motifs (DSRMs). This model describes the third motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380693  Cd Length: 72  Bit Score: 50.69  E-value: 7.75e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1707477765 1507 PSEQLDYLSNVQGIQVEYKDFPKNNKN-EFVSLINCSSQPPLISHGIGKDVESCHDMAALNILKLL 1571
Cdd:cd19864      3 YCELLQELAEEQKFKVTYVDIEELSSSgKYQCLVQLSTLPPTVCHGSGASLEEAKEEAARNALEYL 68
DSRM_STRBP_RED-like_rpt2 cd19866
second double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This ...
 1305-1371 1.51e-07

second double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This family includes spermatid perinuclear RNA-binding protein (STRBP) and interleukin enhancer-binding factor 3 (ILF3), as well as two RNA-editing deaminases, RED1 and RED2. STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. ILF3 (also known as double-stranded RNA-binding protein 76 (DRBP76), M-phase phosphoprotein 4 (MPP4), nuclear factor associated with dsRNA (NFAR), nuclear factor of activated T-cells 90 kDa (NF-AT-90), or translational control protein 80 (TCP80)) is an RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. RED1 (EC 3.5.4.37; also called double-stranded RNA-specific editase 1, RNA-editing enzyme 1, dsRNA adenosine deaminase, ADARB1, ADAR2, or DRADA2) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. RED2 (also called double-stranded RNA-specific editase B2, RNA-dependent adenosine deaminase 3, RNA-editing enzyme 2, dsRNA adenosine deaminase B2, ADAR3, or ADARB2) prevents the binding of other ADAR enzymes to targets in vitro, and decreases the efficiency of these enzymes. It is capable of binding to dsRNA but also to ssRNA. RED2 lacks editing activity for currently known substrate RNAs. Members of this group contain two double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380695  Cd Length: 63  Bit Score: 49.86  E-value: 1.51e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1707477765 1305 NPISRLAQIQQAKKekepeYMLITERGLPRRREFVMQVKVGVHTAEGMGTNKKVAKRNAAENMLEIL 1371
Cdd:cd19866      2 NPVMLLNELRPGLK-----YKCLSESGESHAKSFVMSVTVDGQTFEGTGRSKKLAKAAAAQAALAKL 63
DSRM_RNAse_III_family cd10845
double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...
 1000-1055 3.24e-07

double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase III (EC 3.1.26.3; also known as ribonuclease 3) digests double-stranded RNA formed within single-strand substrates, but not RNA-DNA hybrids. It is involved in the processing of rRNA precursors, viral transcripts, some mRNAs, and at least 1 tRNA (metY, a minor form of tRNA-init-Met). It cleaves the 30S primary rRNA transcript to yield the immediate precursors to the 16S and 23S rRNAs. The cleavage can occur in assembled 30S, 50S, and even 70S subunits and is influenced by the presence of ribosomal proteins. The RNase III family also includes the mitochondrion-specific ribosomal protein mL44 subfamily, which is composed of mitochondrial 54S ribosomal protein L3 (MRPL3) and mitochondrial 39S ribosomal protein L44 (MRPL44). Members of this family contain an RNase III domain and a C-terminal double-stranded RNA binding motif (DSRM). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380682 [Multi-domain]  Cd Length: 69  Bit Score: 49.03  E-value: 3.24e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1707477765 1000 NPKEKtpmcLVNELARFNKIQPEYKLLSEQGPAHSKVFTVQLTLGDQHW-EAEGTSI 1055
Cdd:cd10845      2 DYKTA----LQEYLQKRGLPLPEYELVEEEGPDHNKTFTVEVKVNGKVIgEGTGRSK 54
DSRM_STRBP_rpt1 cd19909
first double-stranded RNA binding motif of spermatid perinuclear RNA-binding protein (STRBP) ...
 1006-1054 3.83e-07

first double-stranded RNA binding motif of spermatid perinuclear RNA-binding protein (STRBP) and similar proteins; STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. STRBP contains an N-terminal DZF domain and two double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380738  Cd Length: 84  Bit Score: 49.26  E-value: 3.83e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1707477765 1006 PMclvNELARFNKIQP--EYKLLSEQGPAHSKVFTVQLTLGDQHWEAEGTS 1054
Cdd:cd19909      5 PM---NALMRLNQIRPglQYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPS 52
DSRM_PRKRA_rpt2 cd19891
second double-stranded RNA binding motif of protein activator of the interferon-induced ...
 1205-1268 4.37e-07

second double-stranded RNA binding motif of protein activator of the interferon-induced protein kinase (PRKRA) and similar proteins; PRKRA (also known as interferon-inducible double-stranded RNA-dependent protein kinase activator A, PKR-associated protein X (RAX), PKR-associating protein X, protein kinase, interferon-inducible double-stranded RNA-dependent activator, PACT, or HSD14) is a cellular activator for double-stranded RNA-dependent protein kinase during stress signaling. PRKRA contains three double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380720  Cd Length: 67  Bit Score: 48.78  E-value: 4.37e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1707477765 1205 ISQVFEIALKRN--LPvNFEVTKESGPPHMKSFVTKVSVGEFMGEGEGKSKKISKKNAAIAVLEEL 1268
Cdd:cd19891      3 IGSLQELAVQKGwrLP-EYTLAQESGPPHKREFTITCRVETFVETGTGTSKKVAKRNAAEKLLAKF 67
DSRM_STRBP_RED-like_rpt2 cd19866
second double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This ...
 1219-1268 4.95e-07

second double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This family includes spermatid perinuclear RNA-binding protein (STRBP) and interleukin enhancer-binding factor 3 (ILF3), as well as two RNA-editing deaminases, RED1 and RED2. STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. ILF3 (also known as double-stranded RNA-binding protein 76 (DRBP76), M-phase phosphoprotein 4 (MPP4), nuclear factor associated with dsRNA (NFAR), nuclear factor of activated T-cells 90 kDa (NF-AT-90), or translational control protein 80 (TCP80)) is an RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. RED1 (EC 3.5.4.37; also called double-stranded RNA-specific editase 1, RNA-editing enzyme 1, dsRNA adenosine deaminase, ADARB1, ADAR2, or DRADA2) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. RED2 (also called double-stranded RNA-specific editase B2, RNA-dependent adenosine deaminase 3, RNA-editing enzyme 2, dsRNA adenosine deaminase B2, ADAR3, or ADARB2) prevents the binding of other ADAR enzymes to targets in vitro, and decreases the efficiency of these enzymes. It is capable of binding to dsRNA but also to ssRNA. RED2 lacks editing activity for currently known substrate RNAs. Members of this group contain two double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380695  Cd Length: 63  Bit Score: 48.32  E-value: 4.95e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1707477765 1219 VNFEVTKESGPPHMKSFVTKVSV-GEFMgEGEGKSKKISKKNAAIAVLEEL 1268
Cdd:cd19866     14 LKYKCLSESGESHAKSFVMSVTVdGQTF-EGTGRSKKLAKAAAAQAALAKL 63
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
1013-1054 7.08e-07

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 52.02  E-value: 7.08e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1707477765 1013 LARFNKIQPEYKLLSEQGPAHSKVFTVQLTLGDQHW-EAEGTS 1054
Cdd:COG0571    167 LQARGLPLPEYEVVEEEGPDHAKTFTVEVLVGGKVLgEGTGRS 209
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 1006-1055 7.54e-07

Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training Putative motif shared by proteins that bind to dsRNA. At least some DSRM proteins seem to bind to specific RNA targets. Exemplified by Staufen, which is involved in localization of at least five different mRNAs in the early Drosophila embryo. Also by interferon-induced protein kinase in humans, which is part of the cellular response to dsRNA.


Pssm-ID: 425434 [Multi-domain]  Cd Length: 66  Bit Score: 48.00  E-value: 7.54e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1707477765 1006 PMCLVNELARFNKIQPEYKLLSEQGPAHSKVFTVQLTLGDQHW-EAEGTSI 1055
Cdd:pfam00035    1 PKSLLQEYAQKNGKPPPYEYVSEEGPPHSPKFTVTVKVDGKLYgSGTGSSK 51
DSRM_EIF2AK2_rpt1 cd19903
first double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha ...
 1305-1371 9.10e-07

first double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2) and similar proteins; EIF2AK2 (EC 2.7.11.1/EC 2.7.10.2; also known as interferon-induced, double-stranded RNA-activated protein kinase, eIF-2A protein kinase 2, interferon-inducible RNA-dependent protein kinase, P1/eIF-2A protein kinase, protein kinase RNA-activated (PKR), protein kinase R, tyrosine-protein kinase EIF2AK2, or p68 kinase) acts as an IFN-induced dsRNA-dependent serine/threonine-protein kinase which plays a key role in the innate immune response to viral infection and is also involved in the regulation of signal transduction, apoptosis, cell proliferation and differentiation. EIF2AK2 proteins contain two to three double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380732  Cd Length: 68  Bit Score: 47.77  E-value: 9.10e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1707477765 1305 NPISRLAQIQQAKKEKEpEYMLITERGLPRRREFVMQVKV-GVHTAEGMGTNKKVAKRNAAENMLEIL 1371
Cdd:cd19903      2 NYMGKLNEYCQKQKVVL-DYVEVPTSGPSHDPRFTFQVVIdGKEYPEGEGKSKKEAKQAAAKLALEIL 68
DSRM_EIF2AK2_rpt1 cd19903
first double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha ...
 1214-1268 1.21e-06

first double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2) and similar proteins; EIF2AK2 (EC 2.7.11.1/EC 2.7.10.2; also known as interferon-induced, double-stranded RNA-activated protein kinase, eIF-2A protein kinase 2, interferon-inducible RNA-dependent protein kinase, P1/eIF-2A protein kinase, protein kinase RNA-activated (PKR), protein kinase R, tyrosine-protein kinase EIF2AK2, or p68 kinase) acts as an IFN-induced dsRNA-dependent serine/threonine-protein kinase which plays a key role in the innate immune response to viral infection and is also involved in the regulation of signal transduction, apoptosis, cell proliferation and differentiation. EIF2AK2 proteins contain two to three double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380732  Cd Length: 68  Bit Score: 47.38  E-value: 1.21e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1707477765 1214 KRNLPVNFEVTKESGPPHMKSFVTKVSV-GEFMGEGEGKSKKISKKNAAIAVLEEL 1268
Cdd:cd19903     13 KQKVVLDYVEVPTSGPSHDPRFTFQVVIdGKEYPEGEGKSKKEAKQAAAKLALEIL 68
DSRM_SON-like cd19870
double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known ...
 1303-1373 1.60e-06

double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known as Bax antagonist selected in saccharomyces 1 (BASS1), negative regulatory element-binding protein (NRE-binding protein), or protein DBP-5, or SON3) is an RNA-binding protein which acts as an mRNA splicing cofactor by promoting efficient splicing of transcripts that possess weak splice sites. It specifically promotes splicing of many cell-cycle and DNA-repair transcripts that possess weak splice sites, such as TUBG1, KATNB1, TUBGCP2, AURKB, PCNT, AKT1, RAD23A, and FANCG. Members of this group contain a double-stranded RNA binding motif (DSRM) at the C-terminus. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380699  Cd Length: 75  Bit Score: 47.28  E-value: 1.60e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1707477765 1303 GMNPISRLAQIQQAKKEKEPEYMLITERGLPRRREFVMQVKVG--VHTAEGMGTNKKVAKRNAAENMLEILGF 1373
Cdd:cd19870      1 GKHPVSALMELCNKRKWGPPEFRLVEESGPPHRKHFLFKVVVNgvEYQPSVASGNKKDAKAQAATVALQALGL 73
DSRM_STAU1_rpt4 cd19885
fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen ...
 1205-1275 1.99e-06

fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 1 (Staufen 1) and similar proteins; Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 1 contains five double-stranded RNA binding motifs (DSRMs). This model describes the fourth motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380714  Cd Length: 86  Bit Score: 47.39  E-value: 1.99e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1707477765 1205 ISQVFEI--ALKRNLPvNFEVTKESGPPHMKSFVTKVSVGEFMGEGEGKSKKISKKNAAIAVLEEL--KKLPPLP 1275
Cdd:cd19885     13 ISRLAQIqqAKKEKEP-EYTLITERGLPRRREFVMQVKVGNQTAEGMGPNKKVAKRNAAEKMLELLgfKVPQPQP 86
DSRM_STRBP-like_rpt2 cd19897
second double-stranded RNA binding motif of STRBP, ILF3 and similar proteins; This family ...
 1305-1371 2.22e-06

second double-stranded RNA binding motif of STRBP, ILF3 and similar proteins; This family includes spermatid perinuclear RNA-binding protein (STRBP) and interleukin enhancer-binding factor 3 (ILF3). STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. ILF3 (also known as double-stranded RNA-binding protein 76 (DRBP76), M-phase phosphoprotein 4 (MPP4), nuclear factor associated with dsRNA (NFAR), nuclear factor of activated T-cells 90 kDa (NF-AT-90), or translational control protein 80 (TCP80)) is an RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. Members of this STRBP/ILF3 group contain an N-terminal DZF domain and two double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380726  Cd Length: 64  Bit Score: 46.59  E-value: 2.22e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1707477765 1305 NPISRLAQiqqakKEKEPEYMLITERGLPRRREFVMQVKVGVHTAEGMGTNKKVAKRNAAENMLEIL 1371
Cdd:cd19897      2 NPVMELNE-----KRRGLKYELISETGGSHDKRFVMEVEVDGQKFQGAGSNKKVAKANAALAALEKL 63
DSRM_TARBP2_rpt2 cd10844
second double-stranded RNA binding motif of the RISC-loading complex subunit TARBP2 and ...
 1217-1265 2.38e-06

second double-stranded RNA binding motif of the RISC-loading complex subunit TARBP2 and similar proteins; TARBP2 (also known as TAR RNA-binding protein 2, or trans-activation-responsive RNA-binding protein (TRBP)) participates in the formation of the RNA-induced silencing complex (RISC). It is part of the RISC-loading complex (RLC), together with dicer1 and eif2c2/ago2, and is required to process precursor miRNAs. TARBP2 contains three double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380681  Cd Length: 67  Bit Score: 46.64  E-value: 2.38e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1707477765 1217 LPvNFEVTKESGPPHMKSFVTKVSVGEFMGEGEGKSKKISKKNAAIAVL 1265
Cdd:cd10844     17 LP-EYTVTQESGPAHRKEFTMTCRVERFIEIGSGTSKKLAKRNAAAKML 64
DSRM_PRKRA_rpt1 cd19889
first double-stranded RNA binding motif of protein activator of the interferon-induced protein ...
 1202-1269 2.54e-06

first double-stranded RNA binding motif of protein activator of the interferon-induced protein kinase (PRKRA) and similar proteins; PRKRA (also known as interferon-inducible double-stranded RNA-dependent protein kinase activator A, PKR-associated protein X (RAX), PKR-associating protein X, protein kinase, interferon-inducible double-stranded RNA-dependent activator, PACT, or HSD14) is a cellular activator for double-stranded RNA-dependent protein kinase during stress signaling. PRKRA contains three double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380718 [Multi-domain]  Cd Length: 71  Bit Score: 46.44  E-value: 2.54e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1707477765 1202 KSEISQVFEIALK-RNLPVnFEVTKESGPPHMKSFVTKVSVGEFMGEGEGKSKKISKKNAAIAVLEELK 1269
Cdd:cd19889      2 KTPIQLLHEYGTKtGNIPV-YELEKSEGQAHLPSFTFRVTVGDITCTGEGTSKKLAKHRAAEAALNILK 69
DSRM_EIF2AK2-like cd19875
double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...
 1305-1371 2.75e-06

double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2) and similar proteins; The family includes EIF2AK2 and adenosine deaminase domain-containing proteins, ADAD1 and ADAD2. EIF2AK2 (EC 2.7.11.1/EC 2.7.10.2; also known as interferon-induced, double-stranded RNA-activated protein kinase, eIF-2A protein kinase 2, interferon-inducible RNA-dependent protein kinase, P1/eIF-2A protein kinase, protein kinase RNA-activated (PKR), protein kinase R, tyrosine-protein kinase EIF2AK2, or p68 kinase) acts as an IFN-induced dsRNA-dependent serine/threonine-protein kinase which plays a key role in the innate immune response to viral infection and is also involved in the regulation of signal transduction, apoptosis, cell proliferation and differentiation. ADAD1 (also called testis nuclear RNA-binding protein (TENR)) and ADAD2 (also called testis nuclear RNA-binding protein-like (TENRL)) are phylogenetically related to a family of adenosine deaminases involved in RNA editing. ADAD1 plays an essential function in spermatid morphogenesis. It may be involved in testis-specific nuclear post-transcriptional processes such as heterogeneous nuclear RNA (hnRNA) packaging, alternative splicing, or nuclear/cytoplasmic transport of mRNAs. ADAD2 is a double-stranded RNA binding protein with unclear biological function. Members of this group contains varying numbers of double-stranded RNA binding motifs (DSRMs). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380704  Cd Length: 67  Bit Score: 46.11  E-value: 2.75e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1707477765 1305 NPISRLAQIQQaKKEKEPEYMlITERGLPRRREFVMQVKV-GVHTAEGMGTNKKVAKRNAAENMLEIL 1371
Cdd:cd19875      2 NPVSALNEYCQ-KRGLSLEFV-DVSVGPDHCPGFTASATIdGIVFASATGTSKKEAKRAAAKLALKKL 67
DSRM_DCL_plant cd19869
double-stranded RNA binding motif of plant Dicer-like proteins; The family includes plant ...
 1210-1270 3.69e-06

double-stranded RNA binding motif of plant Dicer-like proteins; The family includes plant Dicer-like (DCL) proteins and other ribonuclease (RNase) III-like (RTL) proteins. DCLs are endoribonucleases involved in RNA-mediated post-transcriptional gene silencing (PTGS). They function in the microRNA (miRNA) biogenesis pathway by cleaving primary miRNAs (pri-miRNAs) and precursor miRNAs (pre-miRNAs). Family members contain a double-stranded RNA binding motif (DSRM) at the C-terminus. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380698  Cd Length: 70  Bit Score: 46.21  E-value: 3.69e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765 1210 EIALKRNLPV-NFEVTKESGPPHMKSFVTKVSVG--------EFMGEGEgKSKKISKKNAAIAVLEELKK 1270
Cdd:cd19869      2 EICLKRRWPMpVYRCVEEEGPAHAKRFTYMVRVKipergwtiECEGEPM-RSKKRAKDSAALLLLEYLKK 70
DSRM_STRBP_RED-like_rpt1 cd19865
first double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This ...
 1304-1369 3.75e-06

first double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This family includes spermatid perinuclear RNA-binding protein (STRBP) and interleukin enhancer-binding factor 3 (ILF3), as well as two RNA-editing deaminases, RED1 and RED2. STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. ILF3 (also known as double-stranded RNA-binding protein 76 (DRBP76), M-phase phosphoprotein 4 (MPP4), nuclear factor associated with dsRNA (NFAR), nuclear factor of activated T-cells 90 kDa (NF-AT-90), or translational control protein 80 (TCP80)) is an RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. RED1 (EC 3.5.4.37; also called double-stranded RNA-specific editase 1, RNA-editing enzyme 1, dsRNA adenosine deaminase, ADARB1, ADAR2, or DRADA2) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. RED2 (also called double-stranded RNA-specific editase B2, RNA-dependent adenosine deaminase 3, RNA-editing enzyme 2, dsRNA adenosine deaminase B2, ADAR3, or ADARB2) prevents the binding of other ADAR enzymes to targets in vitro, and decreases the efficiency of these enzymes. It is capable of binding to dsRNA, but also to ssRNA. RED2 lacks editing activity for currently known substrate RNAs. Members of this group contain two double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380694  Cd Length: 63  Bit Score: 45.80  E-value: 3.75e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1707477765 1304 MNPISRLAQIQQAKKekepeYMLITERGLPRRREFVMQVKVGVHTAEGMGTNKKVAKRNAAENMLE 1369
Cdd:cd19865      1 KNALMQLNELRPGLQ-----YKLTSQTGPVHAPVFTMSVEVNGQTFEGTGRSKKKAKLEAAEKALR 61
DSRM_PRKRA-like_rpt1 cd19862
first double-stranded RNA binding motif of protein activator of the interferon-induced protein ...
 1004-1054 5.50e-06

first double-stranded RNA binding motif of protein activator of the interferon-induced protein kinase (PRKRA) and similar proteins; This family includes protein activator of the interferon-induced protein kinase (PRKRA) and the RISC-loading complex subunit TARBP2. PRKRA (also known as interferon-inducible double-stranded RNA-dependent protein kinase activator A, PKR-associated protein X (RAX), PKR-associating protein X, protein kinase, interferon-inducible double-stranded RNA-dependent activator, PACT, or HSD14) is a cellular activator for double-stranded RNA-dependent protein kinase during stress signaling. TARBP2 (also called TAR RNA-binding protein 2, or trans-activation-responsive RNA-binding protein (TRBP)), participates in the formation of the RNA-induced silencing complex (RISC). It is part of the RISC-loading complex (RLC), together with dicer1 and eif2c2/ago2, and is required to process precursor miRNAs. This family also includes Drosophila melanogaster Loquacious and similar proteins. Loquacious (Loqs) is a double-stranded RNA-binding domain (dsRBD) protein, a homolog of human TAR RNA binding protein (TRBP) that is a protein first identified as binding the HIV trans-activator RNA (TAR). Loqs interacts with Dicer1 (dmDcr1) to facilitate miRNA processing. PRKRA family proteins contain three double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380691 [Multi-domain]  Cd Length: 70  Bit Score: 45.71  E-value: 5.50e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1707477765 1004 KTPMCLVNELARFNKIQPEYKLLSEQGPAHSKVFTVQLTLGDQHWEAEGTS 1054
Cdd:cd19862      1 KTPISVLQELCAKRGITPKYELISSEGAVHEPTFTFRVTVGDITATGSGTS 51
DSRM_ILF3_rpt2 cd19912
second double-stranded RNA binding motif of interleukin enhancer-binding factor 3 (ILF3) and ...
 1302-1371 6.64e-06

second double-stranded RNA binding motif of interleukin enhancer-binding factor 3 (ILF3) and similar proteins; ILF3 (also known as double-stranded RNA-binding protein 76 (DRBP76), M-phase phosphoprotein 4 (MPP4), nuclear factor associated with dsRNA (NFAR), nuclear factor of activated T-cells 90 kDa (NF-AT-90), or translational control protein 80 (TCP80)) is an RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. ILF3 contains an N-terminal DZF domain and two double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380741  Cd Length: 72  Bit Score: 45.41  E-value: 6.64e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765 1302 QGMNPISRLAQiqqakKEKEPEYMLITERGLPRRREFVMQVKVGVHTAEGMGTNKKVAKRNAAENMLEIL 1371
Cdd:cd19912      5 HGKNPVMELNE-----KRRGLKYELISETGGSHDKRFVMEVEVDGQKFQGAGSNKKVAKAYAALAALEKL 69
DSRM_STRBP-like_rpt1 cd19894
first double-stranded RNA binding motif of STRBP, ILF3 and similar proteins; This family ...
 1011-1054 7.54e-06

first double-stranded RNA binding motif of STRBP, ILF3 and similar proteins; This family includes spermatid perinuclear RNA-binding protein (STRBP) and interleukin enhancer-binding factor 3 (ILF3). STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. ILF3 (also known as double-stranded RNA-binding protein 76 (DRBP76), M-phase phosphoprotein 4 (MPP4), nuclear factor associated with dsRNA (NFAR), nuclear factor of activated T-cells 90 kDa (NF-AT-90), or translational control protein 80 (TCP80)) is an RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. Members of this STRBP/ILF3 group contain an N-terminal DZF domain and two double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380723  Cd Length: 63  Bit Score: 45.07  E-value: 7.54e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1707477765 1011 NELARFNKIQP--EYKLLSEQGPAHSKVFTVQLTLGDQHWEAEGTS 1054
Cdd:cd19894      2 NALMRLNQLRPglQYKLASQTGPVHAPQFTMSVEVDGVTYEASGPS 47
DSRM_DHX9_rpt1 cd19854
first double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; ...
 1317-1371 9.85e-06

first double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; DHX9 (EC 3.6.4.13; also known as ATP-dependent RNA helicase A, DExH-box helicase 9 (DDX9), Leukophysin (LKP), nuclear DNA helicase II (NDH II), NDH2, or RNA helicase A) is a multifunctional ATP-dependent nucleic acid helicase that unwinds DNA and RNA in a 3' to 5' direction and plays important roles in many processes, such as DNA replication, transcriptional activation, post-transcriptional RNA regulation, mRNA translation, and RNA-mediated gene silencing. It contains two double-stranded RNA binding motifs (DSRMs) at the N-terminal region. This model corresponds to the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380683  Cd Length: 69  Bit Score: 44.96  E-value: 9.85e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1707477765 1317 KKEKEPEYmLITERGLPRRREFVMQVKVGVHT--AEGMGTNKKVAKRNAAENMLEIL 1371
Cdd:cd19854     12 KKKLTPEY-DIKEAGNKHRQRFKCEVRVEGFDyvGTGNATNKKDAQTNAARDFLNYL 67
DSRM_ILF3_rpt1 cd19910
first double-stranded RNA binding motif of interleukin enhancer-binding factor 3 (ILF3) and ...
 1006-1054 1.21e-05

first double-stranded RNA binding motif of interleukin enhancer-binding factor 3 (ILF3) and similar proteins; ILF3 (also known as double-stranded RNA-binding protein 76 (DRBP76), M-phase phosphoprotein 4 (MPP4), nuclear factor associated with dsRNA (NFAR), nuclear factor of activated T-cells 90 kDa (NF-AT-90), or translational control protein 80 (TCP80)) is an RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. ILF3 contains an N-terminal DZF domain and two double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380739  Cd Length: 73  Bit Score: 44.75  E-value: 1.21e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1707477765 1006 PMCLVNELARFNKIQP--EYKLLSEQGPAHSKVFTVQLTLGDQHWEAEGTS 1054
Cdd:cd19910      2 PPQAMNALMRLNQLKPglQYKLISQTGPVHAPVFTMSVEVDGKTFEASGPS 52
DSRM_STAU_rpt3 cd19859
third double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 1006-1054 1.42e-05

third double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein Staufen and similar proteins; Staufen is a double-stranded RNA binding protein required both for the localization of maternal determinants to the posterior pole of the egg, oskar (osk) RNA, and for correct localization to the anterior pole, anchoring bicoid (bcd) RNA. The family also includes two Staufen homologs from vertebrates, Staufen 1 and Staufen 2. They are present in distinct ribonucleoprotein complexes and associate with different mRNAs. Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite. Staufen proteins contain five double-stranded RNA binding motifs (DSRMs). This model describes the third motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380688  Cd Length: 65  Bit Score: 44.31  E-value: 1.42e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1707477765 1006 PMCLVNELARFNKIQPEYKLLSEQGPAHSKVFTVQLTLGDQHWEAEGTS 1054
Cdd:cd19859      1 EISLVHEIALKRNLTVNFEVLRESGPPHMKNFITRCTVGSFVTEGEGNS 49
DSRM_STRBP-like_rpt2 cd19897
second double-stranded RNA binding motif of STRBP, ILF3 and similar proteins; This family ...
 1208-1268 1.49e-05

second double-stranded RNA binding motif of STRBP, ILF3 and similar proteins; This family includes spermatid perinuclear RNA-binding protein (STRBP) and interleukin enhancer-binding factor 3 (ILF3). STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. ILF3 (also known as double-stranded RNA-binding protein 76 (DRBP76), M-phase phosphoprotein 4 (MPP4), nuclear factor associated with dsRNA (NFAR), nuclear factor of activated T-cells 90 kDa (NF-AT-90), or translational control protein 80 (TCP80)) is an RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. Members of this STRBP/ILF3 group contain an N-terminal DZF domain and two double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380726  Cd Length: 64  Bit Score: 44.27  E-value: 1.49e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1707477765 1208 VFEIALKRNlPVNFEVTKESGPPHMKSFVTKVSVGEFMGEGEGKSKKISKKNAAIAVLEEL 1268
Cdd:cd19897      4 VMELNEKRR-GLKYELISETGGSHDKRFVMEVEVDGQKFQGAGSNKKVAKANAALAALEKL 63
DSRM_STAU2_rpt4 cd19886
fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen ...
 1205-1268 1.84e-05

fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 2 (Staufen 2) and similar proteins; Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite. Staufen 2 contains five double-stranded RNA binding motifs (DSRMs). This model describes the fourth motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380715  Cd Length: 86  Bit Score: 44.56  E-value: 1.84e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1707477765 1205 ISQVFEI--ALKRNLPvNFEVTKESGPPHMKSFVTKVSVGEFMGEGEGKSKKISKKNAAIAVLEEL 1268
Cdd:cd19886      6 ISRLAQIqqAKKEKEP-EYVLLSERGMPRRREFVMQVKVGNEVATGTGPNKKIAKRNAAEAMLLQL 70
DSRM_DRADA cd19902
double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA) ...
 1305-1371 2.04e-05

double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA) and similar proteins; DRADA (EC 3.5.4.37; also known as 136 kDa double-stranded RNA-binding protein (p136), interferon-inducible protein 4 (IFI-4), K88DSRBP, ADAR1, G1P1, or ADAR) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. DRADA family members contain at least one double-stranded RNA binding motifs (DSRM); vertebrate proteins contain three. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380731  Cd Length: 71  Bit Score: 43.82  E-value: 2.04e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1707477765 1305 NPISRLAQIQQAKKEkEPEYMLITERGLPRRREFVMQVKVGVHT-AEGMGTNKKVAKRNAAENMLEIL 1371
Cdd:cd19902      2 NPVSALMEYAQSRGV-TAEIEVLSQSGPPHNPRFKAAVFVGGRRfPSVEASSKKDAKQEAADLALRAL 68
DSRM_AtDRB-like_rpt2 cd19908
second double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding ...
 1210-1269 2.51e-05

second double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding proteins (AtDRBs)and similar proteins; This family includes a group of Arabidopsis thaliana double-stranded RNA-binding proteins (AtDRB1-5). They bind double-stranded RNA (dsRNA) and may be involved in RNA-mediated silencing. Members of this family contain two to three double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380737 [Multi-domain]  Cd Length: 69  Bit Score: 43.62  E-value: 2.51e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1707477765 1210 EIALKRNLPVNFEVTKESGPPHMKSFVTKVSVG--EFMGEgEGKSKKISKKNAAIAVLEELK 1269
Cdd:cd19908      9 EYAQKAGLPLPLYTTVRSGPGHVPTFTCTVEIAgiTFTGE-AAKTKKQAEKSAARTAWSSIK 69
DSRM_STAU_rpt1 cd19857
first double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 1205-1265 3.74e-05

first double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein Staufen and similar proteins; Staufen is a double-stranded RNA binding protein required both for the localization of maternal determinants to the posterior pole of the egg, oskar (osk) RNA, and for correct localization to the anterior pole, anchoring bicoid (bcd) RNA. The family also includes two Staufen homologs from vertebrates, Staufen 1 and Staufen 2. They are present in distinct ribonucleoprotein complexes and associate with different mRNAs. Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite. Staufen proteins contain five double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380686  Cd Length: 64  Bit Score: 43.02  E-value: 3.74e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1707477765 1205 ISQVFEIALKRNLPVNFEVTKESGPPHMKSFVTKVSVG-EFMGEGEGKSKKISKKNAAIAVL 1265
Cdd:cd19857      3 MCLLNELARFNKIRPQYTLVDEEGPAHKKTFTVKLTLGdEEEYEASGSSIKKAQHAAAEKAL 64
RNaseIII TIGR02191
ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. ...
 1013-1054 4.54e-05

ribonuclease III, bacterial; This family consists of bacterial examples of ribonuclease III. This enzyme cleaves double-stranded rRNA. It is involved in processing ribosomal RNA precursors. It is found even in minimal genones such as Mycoplasma genitalium and Buchnera aphidicola, and in some cases has been shown to be an essential gene. These bacterial proteins contain a double-stranded RNA binding motif (pfam00035) and a ribonuclease III domain (pfam00636). Eukaryotic homologs tend to be much longer proteins with additional domains, localized to the nucleus, and not included in this family. [Transcription, RNA processing]


Pssm-ID: 274024 [Multi-domain]  Cd Length: 220  Bit Score: 46.43  E-value: 4.54e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1707477765 1013 LARFNKIQPEYKLLSEQGPAHSKVFTVQLTLGDQHW-EAEGTS 1054
Cdd:TIGR02191  162 AQARGKPLPEYRLIKEEGPDHDKEFTVEVSVNGEPYgEGKGKS 204
DSRM_STRBP_rpt2 cd19911
second double-stranded RNA binding motif of spermatid perinuclear RNA-binding protein (STRBP) ...
 1305-1371 5.57e-05

second double-stranded RNA binding motif of spermatid perinuclear RNA-binding protein (STRBP) and similar proteins; STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. STRBP contains an N-terminal DZF domain and two double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380740  Cd Length: 64  Bit Score: 42.43  E-value: 5.57e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1707477765 1305 NPISRLAQiqqakKEKEPEYMLITERGLPRRREFVMQVKVGVHTAEGMGTNKKVAKRNAAENMLEIL 1371
Cdd:cd19911      2 NPVMELNE-----KRRGLKYELISETGGSHDKRFVMEVEVDGQKFRGAGPNKKVAKASAALAALEKL 63
DSRM_DHX9_rpt1 cd19854
first double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; ...
 1214-1270 9.78e-05

first double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; DHX9 (EC 3.6.4.13; also known as ATP-dependent RNA helicase A, DExH-box helicase 9 (DDX9), Leukophysin (LKP), nuclear DNA helicase II (NDH II), NDH2, or RNA helicase A) is a multifunctional ATP-dependent nucleic acid helicase that unwinds DNA and RNA in a 3' to 5' direction and plays important roles in many processes, such as DNA replication, transcriptional activation, post-transcriptional RNA regulation, mRNA translation, and RNA-mediated gene silencing. It contains two double-stranded RNA binding motifs (DSRMs) at the N-terminal region. This model corresponds to the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380683  Cd Length: 69  Bit Score: 41.87  E-value: 9.78e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1707477765 1214 KRNLPVNFEVtKESGPPHMKSFVTKVSVG--EFMGEGEGKSKKISKKNAAIAVLEELKK 1270
Cdd:cd19854     12 KKKLTPEYDI-KEAGNKHRQRFKCEVRVEgfDYVGTGNATNKKDAQTNAARDFLNYLVR 69
DSRM_STRBP_rpt2 cd19911
second double-stranded RNA binding motif of spermatid perinuclear RNA-binding protein (STRBP) ...
 1208-1268 1.44e-04

second double-stranded RNA binding motif of spermatid perinuclear RNA-binding protein (STRBP) and similar proteins; STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. STRBP contains an N-terminal DZF domain and two double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380740  Cd Length: 64  Bit Score: 41.27  E-value: 1.44e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1707477765 1208 VFEIALKRNlPVNFEVTKESGPPHMKSFVTKVSVGEFMGEGEGKSKKISKKNAAIAVLEEL 1268
Cdd:cd19911      4 VMELNEKRR-GLKYELISETGGSHDKRFVMEVEVDGQKFRGAGPNKKVAKASAALAALEKL 63
DSRM_RED1_rpt2 cd19898
second double-stranded RNA binding motif of RNA-editing deaminase 1 (RED1) and similar ...
 1221-1273 1.45e-04

second double-stranded RNA binding motif of RNA-editing deaminase 1 (RED1) and similar proteins; RED1 (EC 3.5.4.37; also known as double-stranded RNA-specific editase 1, RNA-editing enzyme 1, dsRNA adenosine deaminase, ADARB1, ADAR2, or DRADA2) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. It contains two double-stranded RNA binding motifs (DSRMs) and a C-terminal RNA-specific adenosine-deaminase (editase) domain. This model describes the second DSRM. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380727  Cd Length: 70  Bit Score: 41.71  E-value: 1.45e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1707477765 1221 FEVTKESGPPHMKSFVTKVSVGEFMGEGEGKSKKISKKNAAIAVLEELKKLPP 1273
Cdd:cd19898     18 YEFVSESGESHAKNFVMSVTVDGQTFEGSGRNKKLAKARAAQAALAKLFNLQL 70
DSRM_RED1_rpt2 cd19898
second double-stranded RNA binding motif of RNA-editing deaminase 1 (RED1) and similar ...
 1302-1371 1.49e-04

second double-stranded RNA binding motif of RNA-editing deaminase 1 (RED1) and similar proteins; RED1 (EC 3.5.4.37; also known as double-stranded RNA-specific editase 1, RNA-editing enzyme 1, dsRNA adenosine deaminase, ADARB1, ADAR2, or DRADA2) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. It contains two double-stranded RNA binding motifs (DSRMs) and a C-terminal RNA-specific adenosine-deaminase (editase) domain. This model describes the second DSRM. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380727  Cd Length: 70  Bit Score: 41.33  E-value: 1.49e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1707477765 1302 QGMNPISRLAQIQQAKKekepeYMLITERGLPRRREFVMQVKVGVHTAEGMGTNKKVAKRNAAENMLEIL 1371
Cdd:cd19898      1 SGKNPVMILNELRPGLK-----YEFVSESGESHAKNFVMSVTVDGQTFEGSGRNKKLAKARAAQAALAKL 65
DSRM_RED2_rpt2 cd19899
second double-stranded RNA binding motif of RNA-editing deaminase 2 (RED2) and similar ...
 1231-1268 2.09e-04

second double-stranded RNA binding motif of RNA-editing deaminase 2 (RED2) and similar proteins; RED2 (also known as double-stranded RNA-specific editase B2, RNA-dependent adenosine deaminase 3, RNA-editing enzyme 2, dsRNA adenosine deaminase B2, ADAR3, or ADARB2) prevents the binding of other ADAR enzymes to targets in vitro, and decreases the efficiency of these enzymes. It is capable of binding to dsRNA but also to ssRNA. RED2 contains two double-stranded RNA binding motifs (DSRMs) and a C-terminal RNA-specific adenosine-deaminase (editase) domain. This model describes the second DSRM. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. RED2 lacks editing activity for currently known substrate RNAs, and may have an inactive editase domain.


Pssm-ID: 380728  Cd Length: 74  Bit Score: 41.40  E-value: 2.09e-04
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 1707477765 1231 HMKSFVTKVSVGEFMGEGEGKSKKISKKNAAIAVLEEL 1268
Cdd:cd19899     33 HIKSFVMAVRVDGRTFEGSGRSKKLAKAQAAQAALQAL 70
DSRM_STRBP_RED-like_rpt1 cd19865
first double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This ...
 1011-1054 2.21e-04

first double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This family includes spermatid perinuclear RNA-binding protein (STRBP) and interleukin enhancer-binding factor 3 (ILF3), as well as two RNA-editing deaminases, RED1 and RED2. STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. ILF3 (also known as double-stranded RNA-binding protein 76 (DRBP76), M-phase phosphoprotein 4 (MPP4), nuclear factor associated with dsRNA (NFAR), nuclear factor of activated T-cells 90 kDa (NF-AT-90), or translational control protein 80 (TCP80)) is an RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. RED1 (EC 3.5.4.37; also called double-stranded RNA-specific editase 1, RNA-editing enzyme 1, dsRNA adenosine deaminase, ADARB1, ADAR2, or DRADA2) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. RED2 (also called double-stranded RNA-specific editase B2, RNA-dependent adenosine deaminase 3, RNA-editing enzyme 2, dsRNA adenosine deaminase B2, ADAR3, or ADARB2) prevents the binding of other ADAR enzymes to targets in vitro, and decreases the efficiency of these enzymes. It is capable of binding to dsRNA, but also to ssRNA. RED2 lacks editing activity for currently known substrate RNAs. Members of this group contain two double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380694  Cd Length: 63  Bit Score: 40.79  E-value: 2.21e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1707477765 1011 NELARFNKIQP--EYKLLSEQGPAHSKVFTVQLTLGDQHWEAEGTS 1054
Cdd:cd19865      2 NALMQLNELRPglQYKLTSQTGPVHAPVFTMSVEVNGQTFEGTGRS 47
DSRM_ILF3_rpt2 cd19912
second double-stranded RNA binding motif of interleukin enhancer-binding factor 3 (ILF3) and ...
 1200-1268 2.29e-04

second double-stranded RNA binding motif of interleukin enhancer-binding factor 3 (ILF3) and similar proteins; ILF3 (also known as double-stranded RNA-binding protein 76 (DRBP76), M-phase phosphoprotein 4 (MPP4), nuclear factor associated with dsRNA (NFAR), nuclear factor of activated T-cells 90 kDa (NF-AT-90), or translational control protein 80 (TCP80)) is an RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. ILF3 contains an N-terminal DZF domain and two double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380741  Cd Length: 72  Bit Score: 41.17  E-value: 2.29e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1707477765 1200 LNKSEISQVFEIALKRNlPVNFEVTKESGPPHMKSFVTKVSVGEFMGEGEGKSKKISKKNAAIAVLEEL 1268
Cdd:cd19912      2 LTKHGKNPVMELNEKRR-GLKYELISETGGSHDKRFVMEVEVDGQKFQGAGSNKKVAKAYAALAALEKL 69
DSRM_DRADA_rpt2 cd19914
second double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase ...
 1305-1371 3.07e-04

second double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA) and similar proteins; DRADA (EC 3.5.4.37; also known as 136 kDa double-stranded RNA-binding protein (p136), interferon-inducible protein 4 (IFI-4), K88DSRBP, ADAR1, G1P1, or ADAR) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. Vertebrate DRADA contains three double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380743  Cd Length: 71  Bit Score: 40.60  E-value: 3.07e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1707477765 1305 NPISRLAQIQQaKKEKEPEYMLITERGLPRRREFVMQVKVGVHT-AEGMGTNKKVAKRNAAENMLEIL 1371
Cdd:cd19914      2 NPISVLMEHSQ-KSGNMCEFQLLSQEGPPHDPKFTYCVKVGEQTfPSVVANSKKVAKQMAAEEAVKEL 68
DSRM_RED2_rpt2 cd19899
second double-stranded RNA binding motif of RNA-editing deaminase 2 (RED2) and similar ...
 1324-1371 3.32e-04

second double-stranded RNA binding motif of RNA-editing deaminase 2 (RED2) and similar proteins; RED2 (also known as double-stranded RNA-specific editase B2, RNA-dependent adenosine deaminase 3, RNA-editing enzyme 2, dsRNA adenosine deaminase B2, ADAR3, or ADARB2) prevents the binding of other ADAR enzymes to targets in vitro, and decreases the efficiency of these enzymes. It is capable of binding to dsRNA but also to ssRNA. RED2 contains two double-stranded RNA binding motifs (DSRMs) and a C-terminal RNA-specific adenosine-deaminase (editase) domain. This model describes the second DSRM. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. RED2 lacks editing activity for currently known substrate RNAs, and may have an inactive editase domain.


Pssm-ID: 380728  Cd Length: 74  Bit Score: 40.63  E-value: 3.32e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1707477765 1324 YMLITERGLPRR-REFVMQVKVGVHTAEGMGTNKKVAKRNAAENMLEIL 1371
Cdd:cd19899     22 YVCLSETAEKQHiKSFVMAVRVDGRTFEGSGRSKKLAKAQAAQAALQAL 70
DSRM_DRADA cd19902
double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA) ...
 1202-1268 3.87e-04

double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA) and similar proteins; DRADA (EC 3.5.4.37; also known as 136 kDa double-stranded RNA-binding protein (p136), interferon-inducible protein 4 (IFI-4), K88DSRBP, ADAR1, G1P1, or ADAR) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. DRADA family members contain at least one double-stranded RNA binding motifs (DSRM); vertebrate proteins contain three. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380731  Cd Length: 71  Bit Score: 40.35  E-value: 3.87e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1707477765 1202 KSEISQVFEIALKRNLPVNFEVTKESGPPHMKSFVTKVSVGE-FMGEGEGKSKKISKKNAAIAVLEEL 1268
Cdd:cd19902      1 KNPVSALMEYAQSRGVTAEIEVLSQSGPPHNPRFKAAVFVGGrRFPSVEASSKKDAKQEAADLALRAL 68
DSRM_DRADA_rpt2 cd19914
second double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase ...
 1202-1268 3.92e-04

second double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA) and similar proteins; DRADA (EC 3.5.4.37; also known as 136 kDa double-stranded RNA-binding protein (p136), interferon-inducible protein 4 (IFI-4), K88DSRBP, ADAR1, G1P1, or ADAR) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. Vertebrate DRADA contains three double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380743  Cd Length: 71  Bit Score: 40.22  E-value: 3.92e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1707477765 1202 KSEISQVFEIALKRNLPVNFEVTKESGPPHMKSFVTKVSVGEFM-GEGEGKSKKISKKNAAIAVLEEL 1268
Cdd:cd19914      1 KNPISVLMEHSQKSGNMCEFQLLSQEGPPHDPKFTYCVKVGEQTfPSVVANSKKVAKQMAAEEAVKEL 68
DSRM_RED1_rpt1 cd19895
first double-stranded RNA binding motif of RNA-editing deaminase 1 (RED1) and similar proteins; ...
 1006-1054 4.64e-04

first double-stranded RNA binding motif of RNA-editing deaminase 1 (RED1) and similar proteins; RED1 (EC 3.5.4.37; also known as double-stranded RNA-specific editase 1, RNA-editing enzyme 1, dsRNA adenosine deaminase, ADARB1, ADAR2, or DRADA2) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. It contains two double-stranded RNA binding motifs (DSRMs) and a C-terminal RNA-specific adenosine-deaminase (editase) domain. This model describes the first DSRM. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380724  Cd Length: 72  Bit Score: 40.06  E-value: 4.64e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1707477765 1006 PMCLVNELARFNKIQP--EYKLLSEQGPAHSKVFTVQLTLGDQHWEAEGTS 1054
Cdd:cd19895      2 PVLPKNALMQLNEIKPglQYKLLSQTGPVHAPVFVMSVEVNGQVFEGSGPT 52
seadorna_dsRNA TIGR04238
seadornavirus double-stranded RNA-binding protein; This protein family occurs in the ...
 1205-1282 4.72e-04

seadornavirus double-stranded RNA-binding protein; This protein family occurs in the seadornavirus virus group, with an N-terminal domain for binding double-stranded RNA, is designated VP12 in Banna virus, VP8 in Kadipiro virus, and VP11 in Liao ning virus.


Pssm-ID: 275074 [Multi-domain]  Cd Length: 201  Bit Score: 43.01  E-value: 4.72e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1707477765 1205 ISQVFEIALKRNLPV-NFEVTKESGPPHMKSFVTKVSVGEFMGEGEGKSKKISKKNAAIAVLEELKKLPPLPTVEKMKP 1282
Cdd:TIGR04238    3 VGMLQELAVKRGLELpVYEKVGKEGPDHAPTFTIKLTANDIEVIEAASSKKQAEKLAAATIYEDMKENGLLEVHDTRKS 81
DSRM_DGCR8_rpt1 cd19867
first double-stranded RNA binding motif of DiGeorge syndrome critical region 8 (DGCR8) and ...
 1300-1372 5.35e-04

first double-stranded RNA binding motif of DiGeorge syndrome critical region 8 (DGCR8) and similar proteins; DGCR8 is a component of the microprocessor complex that acts as an RNA- and heme-binding protein that is involved in the initial step of microRNA (miRNA) biogenesis. Within the microprocessor complex, DGCR8 functions as a molecular anchor necessary for the recognition of pri-miRNA at dsRNA-ssRNA junction and directs DROSHA to cleave 11bp away from the junction to release hairpin-shaped pre-miRNAs that are subsequently cut by the cytoplasmic DICER to generate mature miRNAs. DGCR8 contains two double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380696  Cd Length: 74  Bit Score: 40.01  E-value: 5.35e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1707477765 1300 YGQGMNPISRLAQIQQAKKEKEPEY--MLITERGLPrrreFVMQVKV-GVHTAEGMGTNKKVAKRNAAENMLEILG 1372
Cdd:cd19867      2 NPDGKSPVCILHEYCQRVLKVQPEYnfTETENAATP----FSAEVFInGVEYGSGEASSKKLAKQKAARATLEILI 73
DSRM_STRBP_rpt1 cd19909
first double-stranded RNA binding motif of spermatid perinuclear RNA-binding protein (STRBP) ...
 1302-1373 6.06e-04

first double-stranded RNA binding motif of spermatid perinuclear RNA-binding protein (STRBP) and similar proteins; STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. STRBP contains an N-terminal DZF domain and two double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380738  Cd Length: 84  Bit Score: 40.40  E-value: 6.06e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1707477765 1302 QGMNPISRLAQIQQAKkekepEYMLITERGLPRRREFVMQVKVGVHTAEGMGTNKKVAKRNAAENMLEILGF 1373
Cdd:cd19909      4 QPMNALMRLNQIRPGL-----QYKLLSQSGPVHAPVFTMSVDVDGTTYEASGPSKKTAKLHVAVKVLQAMGY 70
DSRM_DCL_plant cd19869
double-stranded RNA binding motif of plant Dicer-like proteins; The family includes plant ...
 1021-1051 7.69e-04

double-stranded RNA binding motif of plant Dicer-like proteins; The family includes plant Dicer-like (DCL) proteins and other ribonuclease (RNase) III-like (RTL) proteins. DCLs are endoribonucleases involved in RNA-mediated post-transcriptional gene silencing (PTGS). They function in the microRNA (miRNA) biogenesis pathway by cleaving primary miRNAs (pri-miRNAs) and precursor miRNAs (pre-miRNAs). Family members contain a double-stranded RNA binding motif (DSRM) at the C-terminus. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380698  Cd Length: 70  Bit Score: 39.66  E-value: 7.69e-04
                           10        20        30
                   ....*....|....*....|....*....|...
gi 1707477765 1021 PEYKLLSEQGPAHSKVFT--VQLTLGDQHWEAE 1051
Cdd:cd19869     12 PVYRCVEEEGPAHAKRFTymVRVKIPERGWTIE 44
DSRM_EIF2AK2_rpt2 cd19904
second double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha ...
 1205-1261 8.74e-04

second double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2) and similar proteins; EIF2AK2 (EC 2.7.11.1/EC 2.7.10.2; also known as interferon-induced, double-stranded RNA-activated protein kinase, eIF-2A protein kinase 2, interferon-inducible RNA-dependent protein kinase, P1/eIF-2A protein kinase, protein kinase RNA-activated (PKR), protein kinase R, tyrosine-protein kinase EIF2AK2, or p68 kinase) acts as an IFN-induced dsRNA-dependent serine/threonine-protein kinase which plays a key role in the innate immune response to viral infection and is also involved in the regulation of signal transduction, apoptosis, cell proliferation and differentiation. EIF2AK2 proteins contain two to three double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380733  Cd Length: 69  Bit Score: 39.42  E-value: 8.74e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1707477765 1205 ISQVFEIALKRNLPVNFEVTKESGPPHMKSFVTKVSVGE-FMGEGEGKSKKISKKNAA 1261
Cdd:cd19904      4 ISLLNQYAQKKRLTVNYEQCASTGVPGPPRFSCKCKIGQkEYGIGTGSTKQEAKQAAA 61
DSRM_STRBP_RED-like_rpt1 cd19865
first double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This ...
 1221-1266 9.65e-04

first double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This family includes spermatid perinuclear RNA-binding protein (STRBP) and interleukin enhancer-binding factor 3 (ILF3), as well as two RNA-editing deaminases, RED1 and RED2. STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. ILF3 (also known as double-stranded RNA-binding protein 76 (DRBP76), M-phase phosphoprotein 4 (MPP4), nuclear factor associated with dsRNA (NFAR), nuclear factor of activated T-cells 90 kDa (NF-AT-90), or translational control protein 80 (TCP80)) is an RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. RED1 (EC 3.5.4.37; also called double-stranded RNA-specific editase 1, RNA-editing enzyme 1, dsRNA adenosine deaminase, ADARB1, ADAR2, or DRADA2) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. RED2 (also called double-stranded RNA-specific editase B2, RNA-dependent adenosine deaminase 3, RNA-editing enzyme 2, dsRNA adenosine deaminase B2, ADAR3, or ADARB2) prevents the binding of other ADAR enzymes to targets in vitro, and decreases the efficiency of these enzymes. It is capable of binding to dsRNA, but also to ssRNA. RED2 lacks editing activity for currently known substrate RNAs. Members of this group contain two double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380694  Cd Length: 63  Bit Score: 38.87  E-value: 9.65e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1707477765 1221 FEVTKESGPPHMKSFVTKVSVGEFMGEGEGKSKKISKKNAAIAVLE 1266
Cdd:cd19865     16 YKLTSQTGPVHAPVFTMSVEVNGQTFEGTGRSKKKAKLEAAEKALR 61
DSRM_DHX9_rpt2 cd19855
second double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; ...
 1206-1268 1.29e-03

second double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; DHX9 (EC 3.6.4.13; also known as ATP-dependent RNA helicase A, DExH-box helicase 9 (DDX9), Leukophysin (LKP), nuclear DNA helicase II (NDH II), NDH2, or RNA helicase A) is a multifunctional ATP-dependent nucleic acid helicase that unwinds DNA and RNA in a 3' to 5' direction and plays important roles in many processes, such as DNA replication, transcriptional activation, post-transcriptional RNA regulation, mRNA translation and RNA-mediated gene silencing. It contains two double-stranded RNA binding motifs (DSRMs) at the N-terminal region. This model corresponds to the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380684  Cd Length: 75  Bit Score: 39.12  E-value: 1.29e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1707477765 1206 SQVFEIALKRNLPVNFEvTKESGPPHMKSFVTKVSV------GEFMGEGEGKSKKISKKNAAIAVLEEL 1268
Cdd:cd19855      6 SRLNEFLQKNKIPAEYK-YTSVGPDHNRSFIAELSIfvkqlgKTIYARETGSNKKLASQSCALSLVRQL 73
DSRM_STRBP_RED-like_rpt2 cd19866
second double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This ...
 1004-1054 1.58e-03

second double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins; This family includes spermatid perinuclear RNA-binding protein (STRBP) and interleukin enhancer-binding factor 3 (ILF3), as well as two RNA-editing deaminases, RED1 and RED2. STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. ILF3 (also known as double-stranded RNA-binding protein 76 (DRBP76), M-phase phosphoprotein 4 (MPP4), nuclear factor associated with dsRNA (NFAR), nuclear factor of activated T-cells 90 kDa (NF-AT-90), or translational control protein 80 (TCP80)) is an RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. RED1 (EC 3.5.4.37; also called double-stranded RNA-specific editase 1, RNA-editing enzyme 1, dsRNA adenosine deaminase, ADARB1, ADAR2, or DRADA2) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. RED2 (also called double-stranded RNA-specific editase B2, RNA-dependent adenosine deaminase 3, RNA-editing enzyme 2, dsRNA adenosine deaminase B2, ADAR3, or ADARB2) prevents the binding of other ADAR enzymes to targets in vitro, and decreases the efficiency of these enzymes. It is capable of binding to dsRNA but also to ssRNA. RED2 lacks editing activity for currently known substrate RNAs. Members of this group contain two double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380695  Cd Length: 63  Bit Score: 38.30  E-value: 1.58e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1707477765 1004 KTPMCLVNELARfnkiQPEYKLLSEQGPAHSKVFTVQLTLGDQHWEAEGTS 1054
Cdd:cd19866      1 KNPVMLLNELRP----GLKYKCLSESGESHAKSFVMSVTVDGQTFEGTGRS 47
DSRM_STAU_rpt1 cd19857
first double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 1305-1368 1.80e-03

first double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein Staufen and similar proteins; Staufen is a double-stranded RNA binding protein required both for the localization of maternal determinants to the posterior pole of the egg, oskar (osk) RNA, and for correct localization to the anterior pole, anchoring bicoid (bcd) RNA. The family also includes two Staufen homologs from vertebrates, Staufen 1 and Staufen 2. They are present in distinct ribonucleoprotein complexes and associate with different mRNAs. Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite. Staufen proteins contain five double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380686  Cd Length: 64  Bit Score: 38.40  E-value: 1.80e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1707477765 1305 NPISRLAQIqqAKKEK-EPEYMLITERGLPRRREFVMQVKVGVHTA-EGMGTNKKVAKRNAAENML 1368
Cdd:cd19857      1 TPMCLLNEL--ARFNKiRPQYTLVDEEGPAHKKTFTVKLTLGDEEEyEASGSSIKKAQHAAAEKAL 64
DSRM_TARBP2_rpt1 cd19890
first double-stranded RNA binding motif of the RISC-loading complex subunit TARBP2 and similar ...
 1303-1371 2.35e-03

first double-stranded RNA binding motif of the RISC-loading complex subunit TARBP2 and similar proteins; TARBP2 (also known as TAR RNA-binding protein 2, or trans-activation-responsive RNA-binding protein (TRBP)), participates in the formation of the RNA-induced silencing complex (RISC). It is part of the RISC-loading complex (RLC), together with dicer1 and eif2c2/ago2, and is required to process precursor miRNAs. TARBP2 contains three double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380719  Cd Length: 72  Bit Score: 38.19  E-value: 2.35e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1707477765 1303 GMNPISrLAQIQQAKKEKEPEYMLITERGLPRRREFVMQVKVGVHTAEGMGTNKKVAKRNAAENMLEIL 1371
Cdd:cd19890      2 GKTPIS-LLQEYGTRIGKTPVYDLLKAEGQAHQPNFTFRVTVGDISCTGQGPSKKAAKHKAAEVALKLL 69
DSRM_TARBP2_rpt1 cd19890
first double-stranded RNA binding motif of the RISC-loading complex subunit TARBP2 and similar ...
 1202-1269 2.50e-03

first double-stranded RNA binding motif of the RISC-loading complex subunit TARBP2 and similar proteins; TARBP2 (also known as TAR RNA-binding protein 2, or trans-activation-responsive RNA-binding protein (TRBP)), participates in the formation of the RNA-induced silencing complex (RISC). It is part of the RISC-loading complex (RLC), together with dicer1 and eif2c2/ago2, and is required to process precursor miRNAs. TARBP2 contains three double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380719  Cd Length: 72  Bit Score: 38.19  E-value: 2.50e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1707477765 1202 KSEISQVFEIALKRNLPVNFEVTKESGPPHMKSFVTKVSVGEFMGEGEGKSKKISKKNAAIAVLEELK 1269
Cdd:cd19890      3 KTPISLLQEYGTRIGKTPVYDLLKAEGQAHQPNFTFRVTVGDISCTGQGPSKKAAKHKAAEVALKLLK 70
DSRM_PRKRA_rpt1 cd19889
first double-stranded RNA binding motif of protein activator of the interferon-induced protein ...
 1303-1371 5.32e-03

first double-stranded RNA binding motif of protein activator of the interferon-induced protein kinase (PRKRA) and similar proteins; PRKRA (also known as interferon-inducible double-stranded RNA-dependent protein kinase activator A, PKR-associated protein X (RAX), PKR-associating protein X, protein kinase, interferon-inducible double-stranded RNA-dependent activator, PACT, or HSD14) is a cellular activator for double-stranded RNA-dependent protein kinase during stress signaling. PRKRA contains three double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380718 [Multi-domain]  Cd Length: 71  Bit Score: 37.20  E-value: 5.32e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1707477765 1303 GMNPISRLAQIQqAKKEKEPEYMLITERGLPRRREFVMQVKVGVHTAEGMGTNKKVAKRNAAENMLEIL 1371
Cdd:cd19889      1 GKTPIQLLHEYG-TKTGNIPVYELEKSEGQAHLPSFTFRVTVGDITCTGEGTSKKLAKHRAAEAALNIL 68
DSRM_STAU1_rpt4 cd19885
fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen ...
 1010-1075 5.59e-03

fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 1 (Staufen 1) and similar proteins; Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 1 contains five double-stranded RNA binding motifs (DSRMs). This model describes the fourth motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380714  Cd Length: 86  Bit Score: 37.76  E-value: 5.59e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1707477765 1010 VNELARFNKIQ-------PEYKLLSEQGPAHSKVFTVQLTLGDQHWEAEGTSIKKAQHAAAAKALE--GTKFPKP 1075
Cdd:cd19885     10 MNPISRLAQIQqakkekePEYTLITERGLPRRREFVMQVKVGNQTAEGMGPNKKVAKRNAAEKMLEllGFKVPQP 84
DSRM_DRADA_rpt1 cd19913
first double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase ...
 1305-1371 6.40e-03

first double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA); DRADA (EC 3.5.4.37; also known as 136 kDa double-stranded RNA-binding protein (p136), interferon-inducible protein 4 (IFI-4), K88DSRBP, ADAR1, G1P1, or ADAR) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. Vertebrate DRADA contains three double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380742  Cd Length: 71  Bit Score: 36.77  E-value: 6.40e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1707477765 1305 NPISRLAQIQQAKKEkEPEYMLITERGLPRRREFVMQVKV-GVHTAEGMGTNKKVAKRNAAENMLEIL 1371
Cdd:cd19913      2 NPVSGLMEYAQFLGQ-TCEFLLLEQSGPSHDPRFKFQAVIdGRRFPPAEASSKKVAKKDAAAIALKIL 68
DSRM_PRKRA_rpt1 cd19889
first double-stranded RNA binding motif of protein activator of the interferon-induced protein ...
 1004-1056 6.93e-03

first double-stranded RNA binding motif of protein activator of the interferon-induced protein kinase (PRKRA) and similar proteins; PRKRA (also known as interferon-inducible double-stranded RNA-dependent protein kinase activator A, PKR-associated protein X (RAX), PKR-associating protein X, protein kinase, interferon-inducible double-stranded RNA-dependent activator, PACT, or HSD14) is a cellular activator for double-stranded RNA-dependent protein kinase during stress signaling. PRKRA contains three double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380718 [Multi-domain]  Cd Length: 71  Bit Score: 36.81  E-value: 6.93e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1707477765 1004 KTPMCLVNELARFNKIQPEYKLLSEQGPAHSKVFTVQLTLGDQHWEAEGTSIK 1056
Cdd:cd19889      2 KTPIQLLHEYGTKTGNIPVYELEKSEGQAHLPSFTFRVTVGDITCTGEGTSKK 54
 
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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