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Conserved domains on  [gi|1952420370|ref|XP_038610052|]
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ATP-dependent RNA helicase DHX8 [Tachyglossus aculeatus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HrpA super family cl34328
HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];
535-1160 0e+00

HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];


The actual alignment was detected with superfamily member COG1643:

Pssm-ID: 441249 [Multi-domain]  Cd Length: 836  Bit Score: 563.55  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  535 SIIEQRESLPIFRLKEQLIQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGC 614
Cdd:COG1643      2 SLITYPPDLPVSAVLPELLAALRAHQVVVLAAPPGAGKTTQLPLALLELGWGAGGRIGMLEPRRLAARAAAERMAEELGE 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  615 CLGQEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLGQYAIIMLDEAHERTIHTDVLFGLLKKTVQK-RQDMKLIV 693
Cdd:COG1643     82 PVGETVGYRVRFEDKVSAATRIEVVTEGILLRELQRDPELEGVDTVIFDEFHERSLNADLLLALLLDLQPAlRPDLKLLV 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  694 TSATLDAVKFSQYFYEAPIFTIPGRTYPVEILYT--KEPETDYLDASLITVMQIhLTEPPGDILVFLTGQEEIDTACEIL 771
Cdd:COG1643    162 MSATLDAERFARLLGDAPVIESSGRTYPVEVRYRplPADERDLEDAVADAVREA-LAEEPGDILVFLPGEREIRRTAEAL 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  772 yerMKSLGPDVpelIILPVYSALPSEMQTRIFDPAPPGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKVYNSKTGIDQ 851
Cdd:COG1643    241 ---RGRLPPDT---EILPLYGRLSAAEQDRAFAPAPHGRRRIVLATNIAETSLTVPGIRYVIDSGLARIPRYDPRSGVTR 314

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  852 LVVTPISQAQAKQRAGRAGRTGPGKCYRLYTE------RAYRDemlttnvPEIQRTNLASTVLSLKAMGINDLLSFDFMD 925
Cdd:COG1643    315 LPTERISQASANQRAGRAGRLAPGICYRLWSEedfarrPAFTD-------PEILRADLASLILELAAWGLGDPEDLPFLD 387

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  926 APPMETLITAMEQLYTLGALDDEGLLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQNVFYRpkdkqal 1005
Cdd:COG1643    388 PPPARAIADARALLQELGALDADGRLTPLGRALARLPLDPRLARMLLAAAELGCLREAAILAALLSERDPRRG------- 460

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370 1006 adqkkakfhQTEGDHLTLLAVYNSWKNNKfanpwcyENFIQARSLRRAQDIRKQMLGIMDRHKLDVVScgkATVRVQKAI 1085
Cdd:COG1643    461 ---------AAGSDLLARLNLWRRLREQQ-------REFLSYLRLREWRDLARQLRRLLGEGANEEPA---DYEAIGLLL 521

                          570       580       590       600       610       620       630
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1952420370 1086 CSGFFRNAAKKDPQEGYRTLIDQQVVYIHPSSALFNRqpEWVVYHELVLTTKEY-MREVTTIDPRWLVEFAPAFFK 1160
Cdd:COG1643    522 ALAYPDRIARRRGEGGRYLLARGRGAALFPGSPLAKK--EWLVAAELVGGAAEArIRLAAPIDPEWLEELAAHLIK 595
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 243-321 2.25e-42

S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.


:

Pssm-ID: 240189 [Multi-domain]  Cd Length: 79  Bit Score: 148.93  E-value: 2.25e-42
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1952420370  243 GDIYQGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTGTKTSLSMKDVEQETG 321
Cdd:cd05684      1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQNGKISLSMKDVDQDTG 79
GH2-like_DHX8 cd21691
GIPC-homology 2 (GH2)-like domain found in DEAH box protein 8 (DHX8) and similar proteins; ...
 13-80 8.21e-41

GIPC-homology 2 (GH2)-like domain found in DEAH box protein 8 (DHX8) and similar proteins; DHX8 (a human homolog of yeast Prp22), also called RNA helicase HRH1, is an ATP-dependent RNA helicase involved in pre-mRNA splicing as a component of the spliceosome. It facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. This model corresponds to the GH2-like domain that shows high sequence similarity with the GH2 domain found in GIPC (GAIP C-terminus-interacting protein) family of proteins, which mediate endocytosis by tethering cargo proteins to the motor myosin VI.


:

Pssm-ID: 409668  Cd Length: 68  Bit Score: 144.23  E-value: 8.21e-41
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1952420370   13 LEYLSLVSKVCTELDNHLGINDKDLAEFVISLAEKNTTFDTFKASLAKNGAEFTDSLISNLLRLIQTM 80
Cdd:cd21691      1 LEYLSLVSKVCTELENHLGISDKDLAEFIIDLAEKSKTLDEFKKALKENGAEFPDSFVESLLRLIQRM 68
 
Name Accession Description Interval E-value
HrpA COG1643
HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];
535-1160 0e+00

HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441249 [Multi-domain]  Cd Length: 836  Bit Score: 563.55  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  535 SIIEQRESLPIFRLKEQLIQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGC 614
Cdd:COG1643      2 SLITYPPDLPVSAVLPELLAALRAHQVVVLAAPPGAGKTTQLPLALLELGWGAGGRIGMLEPRRLAARAAAERMAEELGE 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  615 CLGQEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLGQYAIIMLDEAHERTIHTDVLFGLLKKTVQK-RQDMKLIV 693
Cdd:COG1643     82 PVGETVGYRVRFEDKVSAATRIEVVTEGILLRELQRDPELEGVDTVIFDEFHERSLNADLLLALLLDLQPAlRPDLKLLV 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  694 TSATLDAVKFSQYFYEAPIFTIPGRTYPVEILYT--KEPETDYLDASLITVMQIhLTEPPGDILVFLTGQEEIDTACEIL 771
Cdd:COG1643    162 MSATLDAERFARLLGDAPVIESSGRTYPVEVRYRplPADERDLEDAVADAVREA-LAEEPGDILVFLPGEREIRRTAEAL 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  772 yerMKSLGPDVpelIILPVYSALPSEMQTRIFDPAPPGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKVYNSKTGIDQ 851
Cdd:COG1643    241 ---RGRLPPDT---EILPLYGRLSAAEQDRAFAPAPHGRRRIVLATNIAETSLTVPGIRYVIDSGLARIPRYDPRSGVTR 314

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  852 LVVTPISQAQAKQRAGRAGRTGPGKCYRLYTE------RAYRDemlttnvPEIQRTNLASTVLSLKAMGINDLLSFDFMD 925
Cdd:COG1643    315 LPTERISQASANQRAGRAGRLAPGICYRLWSEedfarrPAFTD-------PEILRADLASLILELAAWGLGDPEDLPFLD 387

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  926 APPMETLITAMEQLYTLGALDDEGLLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQNVFYRpkdkqal 1005
Cdd:COG1643    388 PPPARAIADARALLQELGALDADGRLTPLGRALARLPLDPRLARMLLAAAELGCLREAAILAALLSERDPRRG------- 460

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370 1006 adqkkakfhQTEGDHLTLLAVYNSWKNNKfanpwcyENFIQARSLRRAQDIRKQMLGIMDRHKLDVVScgkATVRVQKAI 1085
Cdd:COG1643    461 ---------AAGSDLLARLNLWRRLREQQ-------REFLSYLRLREWRDLARQLRRLLGEGANEEPA---DYEAIGLLL 521

                          570       580       590       600       610       620       630
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1952420370 1086 CSGFFRNAAKKDPQEGYRTLIDQQVVYIHPSSALFNRqpEWVVYHELVLTTKEY-MREVTTIDPRWLVEFAPAFFK 1160
Cdd:COG1643    522 ALAYPDRIARRRGEGGRYLLARGRGAALFPGSPLAKK--EWLVAAELVGGAAEArIRLAAPIDPEWLEELAAHLIK 595
DEAH_box_HrpA TIGR01967
RNA helicase HrpA; This model represents HrpA, one of two related but uncharacterized DEAH-box ...
 530-1160 1.11e-156

RNA helicase HrpA; This model represents HrpA, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria and a few high-GC Gram-positive bacteria. HrpA is about 1300 amino acids long, while its paralog HrpB, also uncharacterized, is about 800 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing. The HrpA/B homolog from Borrelia is 500 amino acids shorter but appears to be derived from HrpA rather than HrpB. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 273900 [Multi-domain]  Cd Length: 1283  Bit Score: 501.99  E-value: 1.11e-156
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  530 KKTQLSIIEQRESLPIFRLKEQLIQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVS 609
Cdd:TIGR01967   53 RRQAVPEIRYPDNLPVSAKREDIAEAIAENQVVIIAGETGSGKTTQLPKICLELGRGSHGLIGHTQPRRLAARTVAQRIA 132

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  610 EEFGCCLGQEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLGQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDM 689
Cdd:TIGR01967  133 EELGTPLGEKVGYKVRFHDQVSSNTLVKLMTDGILLAETQQDRFLSRYDTIIIDEAHERSLNIDFLLGYLKQLLPRRPDL 212

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  690 KLIVTSATLDAVKFSQYFYEAPIFTIPGRTYPVEILY------TKEPETDYLDASLITVMQIhLTEPPGDILVFLTGQEE 763
Cdd:TIGR01967  213 KIIITSATIDPERFSRHFNNAPIIEVSGRTYPVEVRYrplveeQEDDDLDQLEAILDAVDEL-FAEGPGDILIFLPGERE 291

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  764 IDTACEILYERmkslgpDVPELIILPVYSALPSEMQTRIFDPAppGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKVY 843
Cdd:TIGR01967  292 IRDAAEILRKR------NLRHTEILPLYARLSNKEQQRVFQPH--SGRRIVLATNVAETSLTVPGIHYVIDTGTARISRY 363

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  844 NSKTGIDQLVVTPISQAQAKQRAGRAGRTGPGKCYRLYTERAYRDEMLTTNvPEIQRTNLASTVLSLKAMGINDLLSFDF 923
Cdd:TIGR01967  364 SYRTKVQRLPIEPISQASANQRKGRCGRVAPGICIRLYSEEDFNSRPEFTD-PEILRTNLASVILQMLALRLGDIAAFPF 442

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  924 MDAPPMETLITAMEQLYTLGALDDE---GLLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQNVFYRPK 1000
Cdd:TIGR01967  443 IEAPDPRAIRDGFRLLEELGALDDDeaePQLTPIGRQLAQLPVDPRLARMLLEAHRLGCLQEVLIIASALSIQDPRERPM 522

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370 1001 DKQALADQKKAKFHQTEGDHLTLLAVYNSWKN-------NKFANpWCYENFIQARSLRRAQDIRKQMLGIMDRHKLDVVS 1073
Cdd:TIGR01967  523 EKQQAADQAHARFKDPRSDFLSRVNLWRHIEEqrqalsaNQFRN-ACRKQYLNYLRVREWQDIYRQLTQVVKELGLKLNE 601

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370 1074 CGKATVRVQKAICSGFFRNAAKKDPQEGYrTLIDQQVVYIHPSSALFNRQPEWVVYHELVLTTKEYMREVTTIDPRWLVE 1153
Cdd:TIGR01967  602 EPADYDAIHKALLSGLLSQIGMKDEKHEY-DGARGRKFHIFPGSPLFKKPPKWVMAAELVETSKLYARLVAKIEPEWVEP 680


                   ....*..
gi 1952420370 1154 FAPAFFK 1160
Cdd:TIGR01967  681 VAGHLIK 687
PRK11131 PRK11131
ATP-dependent RNA helicase HrpA; Provisional
 530-1164 1.25e-147

ATP-dependent RNA helicase HrpA; Provisional


Pssm-ID: 182986 [Multi-domain]  Cd Length: 1294  Bit Score: 478.02  E-value: 1.25e-147
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  530 KKTQLSIIEQRESLPIFRLKEQLIQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVS 609
Cdd:PRK11131    60 REAARPEITYPENLPVSQKKQDILEAIRDHQVVIVAGETGSGKTTQLPKICLELGRGVKGLIGHTQPRRLAARTVANRIA 139

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  610 EEFGCCLGQEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLGQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDM 689
Cdd:PRK11131   140 EELETELGGCVGYKVRFNDQVSDNTMVKLMTDGILLAEIQQDRLLMQYDTIIIDEAHERSLNIDFILGYLKELLPRRPDL 219

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  690 KLIVTSATLDAVKFSQYFYEAPIFTIPGRTYPVEILY------TKEPETDYLDASLITVMQIHlTEPPGDILVFLTGQEE 763
Cdd:PRK11131   220 KVIITSATIDPERFSRHFNNAPIIEVSGRTYPVEVRYrpiveeADDTERDQLQAIFDAVDELG-REGPGDILIFMSGERE 298

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  764 I-DTAcEILYERmkslgpDVPELIILPVYSALPSEMQTRIFDPAppGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKV 842
Cdd:PRK11131   299 IrDTA-DALNKL------NLRHTEILPLYARLSNSEQNRVFQSH--SGRRIVLATNVAETSLTVPGIKYVIDPGTARISR 369

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  843 YNSKTGIDQLVVTPISQAQAKQRAGRAGRTGPGKCYRLYTERAYRDEMLTTNvPEIQRTNLASTVLSLKAMGINDLLSFD 922
Cdd:PRK11131   370 YSYRTKVQRLPIEPISQASANQRKGRCGRVSEGICIRLYSEDDFLSRPEFTD-PEILRTNLASVILQMTALGLGDIAAFP 448

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  923 FMDAPPMETLITAMEQLYTLGALDDEG-----LLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQNVFY 997
Cdd:PRK11131   449 FVEAPDKRNIQDGVRLLEELGAITTDEqasayKLTPLGRQLAQLPVDPRLARMVLEAQKHGCVREVMIITSALSIQDPRE 528

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  998 RPKDKQALADQKKAKFHQTEGDHLTLLAVYNSWK-------NNKFANpWCYENFIQARSLRRAQDIRKQMLGIMDRHKLD 1070
Cdd:PRK11131   529 RPMDKQQASDEKHRRFADKESDFLAFVNLWNYLQeqqkalsSNQFRR-LCRTDYLNYLRVREWQDIYTQLRQVVKELGIP 607

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370 1071 VVSCGKATVRVQKAICSGFFRNAAKKDPQEGYRTLIDQQVVYIHPSSALFNRQPEWVVYHELVLTTKEYMREVTTIDPRW 1150
Cdd:PRK11131   608 VNSEPAEYREIHTALLTGLLSHIGMKDAEKQEYTGARNARFSIFPGSGLFKKPPKWVMVAELVETSRLWGRIAARIEPEW 687

                          650
                   ....*....|....*.
gi 1952420370 1151 LVEFAPAFFK--VSDP 1164
Cdd:PRK11131   688 IEPLAQHLIKrsYSEP 703
DEXHc_DHX8 cd17971
DEXH-box helicase domain of DEAH-box helicase 8; DEAH-box helicase 8 (DHX8 ,also known as ...
 538-716 2.04e-126

DEXH-box helicase domain of DEAH-box helicase 8; DEAH-box helicase 8 (DHX8 ,also known as pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22) acts late in the splicing of pre-mRNA and mediates the release of the spliced mRNA from spliceosomes. DHX8 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350729 [Multi-domain]  Cd Length: 179  Bit Score: 385.30  E-value: 2.04e-126
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  538 EQRESLPIFRLKEQLIQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLG 617
Cdd:cd17971      1 EQRESLPIYKLKEQLIQAVHDNQILVVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVAEEFGCCLG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  618 QEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLGQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSAT 697
Cdd:cd17971     81 QEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLSQYSVIMLDEAHERTIHTDVLFGLLKKTVQKRPDLKLIVTSAT 160

                          170
                   ....*....|....*....
gi 1952420370  698 LDAVKFSQYFYEAPIFTIP 716
Cdd:cd17971    161 LDAVKFSQYFYEAPIFTIP 179
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 243-321 2.25e-42

S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.


Pssm-ID: 240189 [Multi-domain]  Cd Length: 79  Bit Score: 148.93  E-value: 2.25e-42
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1952420370  243 GDIYQGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTGTKTSLSMKDVEQETG 321
Cdd:cd05684      1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQNGKISLSMKDVDQDTG 79
GH2-like_DHX8 cd21691
GIPC-homology 2 (GH2)-like domain found in DEAH box protein 8 (DHX8) and similar proteins; ...
 13-80 8.21e-41

GIPC-homology 2 (GH2)-like domain found in DEAH box protein 8 (DHX8) and similar proteins; DHX8 (a human homolog of yeast Prp22), also called RNA helicase HRH1, is an ATP-dependent RNA helicase involved in pre-mRNA splicing as a component of the spliceosome. It facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. This model corresponds to the GH2-like domain that shows high sequence similarity with the GH2 domain found in GIPC (GAIP C-terminus-interacting protein) family of proteins, which mediate endocytosis by tethering cargo proteins to the motor myosin VI.


Pssm-ID: 409668  Cd Length: 68  Bit Score: 144.23  E-value: 8.21e-41
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1952420370   13 LEYLSLVSKVCTELDNHLGINDKDLAEFVISLAEKNTTFDTFKASLAKNGAEFTDSLISNLLRLIQTM 80
Cdd:cd21691      1 LEYLSLVSKVCTELENHLGISDKDLAEFIIDLAEKSKTLDEFKKALKENGAEFPDSFVESLLRLIQRM 68
HA2 smart00847
Helicase associated domain (HA2) Add an annotation; This presumed domain is about 90 amino ...
 942-1024 3.10e-33

Helicase associated domain (HA2) Add an annotation; This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding.


Pssm-ID: 214852 [Multi-domain]  Cd Length: 82  Bit Score: 123.15  E-value: 3.10e-33
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370   942 LGALDDEGLLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQNvfYRPKDKQALADQKKAKFHQTEGDHL 1021
Cdd:smart00847    2 LGALDDDGRLTPLGRKMAELPLDPRLAKMLLAAAEFGCLDEILTIVAMLSVGD--PRPKEKREDADAARRRFADPESDHL 79


                    ...
gi 1952420370  1022 TLL 1024
Cdd:smart00847   80 TLL 82
HA2 pfam04408
Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in ...
 935-1023 2.44e-31

Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding.


Pssm-ID: 461295 [Multi-domain]  Cd Length: 104  Bit Score: 118.49  E-value: 2.44e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  935 AMEQLYTLGALDDEGLLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQNVFYRP------KDKQALADQ 1008
Cdd:pfam04408    1 ALELLYYLGALDEDGELTPLGRKMAELPLDPRLAKMLLAAAELGCLDEVLTIVAALSVRDPFVQPnfldprSAAKAARRR 80

                           90       100
                   ....*....|....*....|....
gi 1952420370 1009 KKAKFHQ---------TEGDHLTL 1023
Cdd:pfam04408   81 RRAADEKarakfarldLEGDHLTL 104
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 239-317 2.39e-21

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 100.51  E-value: 2.39e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  239 EPSIGDIYQGKVTSIMQFGCFVQLegLRKRwEGLVHISELRREgRVANVADVVSKGQRVKVKVLSFT-GTKTSLSMKDVE 317
Cdd:PRK11824   618 EPEVGEIYEGKVVRIVDFGAFVEI--LPGK-DGLVHISEIADE-RVEKVEDVLKEGDEVKVKVLEIDkRGRIRLSRKAVL 693
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 238-340 3.49e-21

Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function prediction only];


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 90.62  E-value: 3.49e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  238 EEPSIGDIYQGKVTSIMQFGCFVQLEGlrkRWEGLVHISELrREGRVANVADVVSKGQRVKVKVLSFTGT-KTSLSMKDV 316
Cdd:COG1098      1 MSIEVGDIVEGKVTGITPFGAFVELPE---GTTGLVHISEI-ADGYVKDINDYLKVGDEVKVKVLSIDEDgKISLSIKQA 76

                           90       100
                   ....*....|....*....|....
gi 1952420370  317 EQETGEDLNPNRRRTTagEAGEET 340
Cdd:COG1098     77 EEKPKRPPRPRRNSRP--KAGFES 98
S1_dom_CvfD NF040579
CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ...
 242-332 2.57e-20

CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a family of full-length homologs of RNA-binding proteins from the Firmicutes with a single copy of the S1 domain. Several members of the family have been characterized as general stress proteins, and the most recently characterized, CvfD, was shown to act as a post-transcriptional regulator.


Pssm-ID: 468553 [Multi-domain]  Cd Length: 113  Bit Score: 87.48  E-value: 2.57e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  242 IGDIYQGKVTSIMQFGCFVQLEglrKRWEGLVHISELrREGRVANVADVVSKGQRVKVKVLS---FTGtKTSLSMKDVEQ 318
Cdd:NF040579     3 IGDIVEGKVTGIQPYGAFVALD---EHTQGLIHISEI-KHGYVKDINDFLKVGQEVKVKVLDideYTG-KISLSLRALEE 77

                           90
                   ....*....|....
gi 1952420370  319 ETGEDLNPNRRRTT 332
Cdd:NF040579    78 APEKHRKRRKHRWT 91
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
242-314 6.25e-15

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 70.71  E-value: 6.25e-15
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1952420370   242 IGDIYQGKVTSIMQFGCFVQLEGlrkRWEGLVHISELRREgRVANVADVVSKGQRVKVKVLSFTGTK--TSLSMK 314
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGN---GVEGLIPISELSDK-RVKDPEEVLKVGDEVKVKVLSVDEEKgrIILSLK 72
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 240-302 2.63e-11

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 60.38  E-value: 2.63e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1952420370  240 PSIGDIYQGKVTSIMQFGCFVQLEGLRkrwEGLVHISELRREgRVANVADVVSKGQRVKVKVL 302
Cdd:pfam00575    1 PEKGDVVEGEVTRVTKGGAFVDLGNGV---EGFIPISELSDD-HVEDPDEVIKVGDEVKVKVL 59
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 238-314 2.28e-09

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 61.29  E-value: 2.28e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  238 EEPSIGDIYQGKVTSIMQFGCFVQL-EGLrkrwEGLVHISELRREGRVANVADVVSKGQRVKVKVLSF--TGTKTSLSMK 314
Cdd:TIGR00717  268 KKFPVGDKITGRVTNLTDYGVFVEIeEGI----EGLVHVSEMSWVKKNSHPSKVVKKGDEVEVMILDIdpERRRLSLGLK 343
 
Name Accession Description Interval E-value
HrpA COG1643
HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];
535-1160 0e+00

HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441249 [Multi-domain]  Cd Length: 836  Bit Score: 563.55  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  535 SIIEQRESLPIFRLKEQLIQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGC 614
Cdd:COG1643      2 SLITYPPDLPVSAVLPELLAALRAHQVVVLAAPPGAGKTTQLPLALLELGWGAGGRIGMLEPRRLAARAAAERMAEELGE 81

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  615 CLGQEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLGQYAIIMLDEAHERTIHTDVLFGLLKKTVQK-RQDMKLIV 693
Cdd:COG1643     82 PVGETVGYRVRFEDKVSAATRIEVVTEGILLRELQRDPELEGVDTVIFDEFHERSLNADLLLALLLDLQPAlRPDLKLLV 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  694 TSATLDAVKFSQYFYEAPIFTIPGRTYPVEILYT--KEPETDYLDASLITVMQIhLTEPPGDILVFLTGQEEIDTACEIL 771
Cdd:COG1643    162 MSATLDAERFARLLGDAPVIESSGRTYPVEVRYRplPADERDLEDAVADAVREA-LAEEPGDILVFLPGEREIRRTAEAL 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  772 yerMKSLGPDVpelIILPVYSALPSEMQTRIFDPAPPGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKVYNSKTGIDQ 851
Cdd:COG1643    241 ---RGRLPPDT---EILPLYGRLSAAEQDRAFAPAPHGRRRIVLATNIAETSLTVPGIRYVIDSGLARIPRYDPRSGVTR 314

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  852 LVVTPISQAQAKQRAGRAGRTGPGKCYRLYTE------RAYRDemlttnvPEIQRTNLASTVLSLKAMGINDLLSFDFMD 925
Cdd:COG1643    315 LPTERISQASANQRAGRAGRLAPGICYRLWSEedfarrPAFTD-------PEILRADLASLILELAAWGLGDPEDLPFLD 387

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  926 APPMETLITAMEQLYTLGALDDEGLLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQNVFYRpkdkqal 1005
Cdd:COG1643    388 PPPARAIADARALLQELGALDADGRLTPLGRALARLPLDPRLARMLLAAAELGCLREAAILAALLSERDPRRG------- 460

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370 1006 adqkkakfhQTEGDHLTLLAVYNSWKNNKfanpwcyENFIQARSLRRAQDIRKQMLGIMDRHKLDVVScgkATVRVQKAI 1085
Cdd:COG1643    461 ---------AAGSDLLARLNLWRRLREQQ-------REFLSYLRLREWRDLARQLRRLLGEGANEEPA---DYEAIGLLL 521

                          570       580       590       600       610       620       630
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1952420370 1086 CSGFFRNAAKKDPQEGYRTLIDQQVVYIHPSSALFNRqpEWVVYHELVLTTKEY-MREVTTIDPRWLVEFAPAFFK 1160
Cdd:COG1643    522 ALAYPDRIARRRGEGGRYLLARGRGAALFPGSPLAKK--EWLVAAELVGGAAEArIRLAAPIDPEWLEELAAHLIK 595
DEAH_box_HrpA TIGR01967
RNA helicase HrpA; This model represents HrpA, one of two related but uncharacterized DEAH-box ...
 530-1160 1.11e-156

RNA helicase HrpA; This model represents HrpA, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria and a few high-GC Gram-positive bacteria. HrpA is about 1300 amino acids long, while its paralog HrpB, also uncharacterized, is about 800 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing. The HrpA/B homolog from Borrelia is 500 amino acids shorter but appears to be derived from HrpA rather than HrpB. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 273900 [Multi-domain]  Cd Length: 1283  Bit Score: 501.99  E-value: 1.11e-156
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  530 KKTQLSIIEQRESLPIFRLKEQLIQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVS 609
Cdd:TIGR01967   53 RRQAVPEIRYPDNLPVSAKREDIAEAIAENQVVIIAGETGSGKTTQLPKICLELGRGSHGLIGHTQPRRLAARTVAQRIA 132

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  610 EEFGCCLGQEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLGQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDM 689
Cdd:TIGR01967  133 EELGTPLGEKVGYKVRFHDQVSSNTLVKLMTDGILLAETQQDRFLSRYDTIIIDEAHERSLNIDFLLGYLKQLLPRRPDL 212

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  690 KLIVTSATLDAVKFSQYFYEAPIFTIPGRTYPVEILY------TKEPETDYLDASLITVMQIhLTEPPGDILVFLTGQEE 763
Cdd:TIGR01967  213 KIIITSATIDPERFSRHFNNAPIIEVSGRTYPVEVRYrplveeQEDDDLDQLEAILDAVDEL-FAEGPGDILIFLPGERE 291

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  764 IDTACEILYERmkslgpDVPELIILPVYSALPSEMQTRIFDPAppGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKVY 843
Cdd:TIGR01967  292 IRDAAEILRKR------NLRHTEILPLYARLSNKEQQRVFQPH--SGRRIVLATNVAETSLTVPGIHYVIDTGTARISRY 363

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  844 NSKTGIDQLVVTPISQAQAKQRAGRAGRTGPGKCYRLYTERAYRDEMLTTNvPEIQRTNLASTVLSLKAMGINDLLSFDF 923
Cdd:TIGR01967  364 SYRTKVQRLPIEPISQASANQRKGRCGRVAPGICIRLYSEEDFNSRPEFTD-PEILRTNLASVILQMLALRLGDIAAFPF 442

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  924 MDAPPMETLITAMEQLYTLGALDDE---GLLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQNVFYRPK 1000
Cdd:TIGR01967  443 IEAPDPRAIRDGFRLLEELGALDDDeaePQLTPIGRQLAQLPVDPRLARMLLEAHRLGCLQEVLIIASALSIQDPRERPM 522

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370 1001 DKQALADQKKAKFHQTEGDHLTLLAVYNSWKN-------NKFANpWCYENFIQARSLRRAQDIRKQMLGIMDRHKLDVVS 1073
Cdd:TIGR01967  523 EKQQAADQAHARFKDPRSDFLSRVNLWRHIEEqrqalsaNQFRN-ACRKQYLNYLRVREWQDIYRQLTQVVKELGLKLNE 601

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370 1074 CGKATVRVQKAICSGFFRNAAKKDPQEGYrTLIDQQVVYIHPSSALFNRQPEWVVYHELVLTTKEYMREVTTIDPRWLVE 1153
Cdd:TIGR01967  602 EPADYDAIHKALLSGLLSQIGMKDEKHEY-DGARGRKFHIFPGSPLFKKPPKWVMAAELVETSKLYARLVAKIEPEWVEP 680


                   ....*..
gi 1952420370 1154 FAPAFFK 1160
Cdd:TIGR01967  681 VAGHLIK 687
PRK11131 PRK11131
ATP-dependent RNA helicase HrpA; Provisional
 530-1164 1.25e-147

ATP-dependent RNA helicase HrpA; Provisional


Pssm-ID: 182986 [Multi-domain]  Cd Length: 1294  Bit Score: 478.02  E-value: 1.25e-147
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  530 KKTQLSIIEQRESLPIFRLKEQLIQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVS 609
Cdd:PRK11131    60 REAARPEITYPENLPVSQKKQDILEAIRDHQVVIVAGETGSGKTTQLPKICLELGRGVKGLIGHTQPRRLAARTVANRIA 139

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  610 EEFGCCLGQEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLGQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDM 689
Cdd:PRK11131   140 EELETELGGCVGYKVRFNDQVSDNTMVKLMTDGILLAEIQQDRLLMQYDTIIIDEAHERSLNIDFILGYLKELLPRRPDL 219

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  690 KLIVTSATLDAVKFSQYFYEAPIFTIPGRTYPVEILY------TKEPETDYLDASLITVMQIHlTEPPGDILVFLTGQEE 763
Cdd:PRK11131   220 KVIITSATIDPERFSRHFNNAPIIEVSGRTYPVEVRYrpiveeADDTERDQLQAIFDAVDELG-REGPGDILIFMSGERE 298

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  764 I-DTAcEILYERmkslgpDVPELIILPVYSALPSEMQTRIFDPAppGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKV 842
Cdd:PRK11131   299 IrDTA-DALNKL------NLRHTEILPLYARLSNSEQNRVFQSH--SGRRIVLATNVAETSLTVPGIKYVIDPGTARISR 369

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  843 YNSKTGIDQLVVTPISQAQAKQRAGRAGRTGPGKCYRLYTERAYRDEMLTTNvPEIQRTNLASTVLSLKAMGINDLLSFD 922
Cdd:PRK11131   370 YSYRTKVQRLPIEPISQASANQRKGRCGRVSEGICIRLYSEDDFLSRPEFTD-PEILRTNLASVILQMTALGLGDIAAFP 448

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  923 FMDAPPMETLITAMEQLYTLGALDDEG-----LLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQNVFY 997
Cdd:PRK11131   449 FVEAPDKRNIQDGVRLLEELGAITTDEqasayKLTPLGRQLAQLPVDPRLARMVLEAQKHGCVREVMIITSALSIQDPRE 528

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  998 RPKDKQALADQKKAKFHQTEGDHLTLLAVYNSWK-------NNKFANpWCYENFIQARSLRRAQDIRKQMLGIMDRHKLD 1070
Cdd:PRK11131   529 RPMDKQQASDEKHRRFADKESDFLAFVNLWNYLQeqqkalsSNQFRR-LCRTDYLNYLRVREWQDIYTQLRQVVKELGIP 607

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370 1071 VVSCGKATVRVQKAICSGFFRNAAKKDPQEGYRTLIDQQVVYIHPSSALFNRQPEWVVYHELVLTTKEYMREVTTIDPRW 1150
Cdd:PRK11131   608 VNSEPAEYREIHTALLTGLLSHIGMKDAEKQEYTGARNARFSIFPGSGLFKKPPKWVMVAELVETSRLWGRIAARIEPEW 687

                          650
                   ....*....|....*.
gi 1952420370 1151 LVEFAPAFFK--VSDP 1164
Cdd:PRK11131   688 IEPLAQHLIKrsYSEP 703
DEXHc_DHX8 cd17971
DEXH-box helicase domain of DEAH-box helicase 8; DEAH-box helicase 8 (DHX8 ,also known as ...
 538-716 2.04e-126

DEXH-box helicase domain of DEAH-box helicase 8; DEAH-box helicase 8 (DHX8 ,also known as pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22) acts late in the splicing of pre-mRNA and mediates the release of the spliced mRNA from spliceosomes. DHX8 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350729 [Multi-domain]  Cd Length: 179  Bit Score: 385.30  E-value: 2.04e-126
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  538 EQRESLPIFRLKEQLIQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLG 617
Cdd:cd17971      1 EQRESLPIYKLKEQLIQAVHDNQILVVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVAEEFGCCLG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  618 QEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLGQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSAT 697
Cdd:cd17971     81 QEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLSQYSVIMLDEAHERTIHTDVLFGLLKKTVQKRPDLKLIVTSAT 160

                          170
                   ....*....|....*....
gi 1952420370  698 LDAVKFSQYFYEAPIFTIP 716
Cdd:cd17971    161 LDAVKFSQYFYEAPIFTIP 179
DEAH_box_HrpB TIGR01970
ATP-dependent helicase HrpB; This model represents HrpB, one of two related but ...
 543-990 1.21e-101

ATP-dependent helicase HrpB; This model represents HrpB, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria, but also in a few species of other lineages. The member from Rhizobium meliloti has been designated HelO. HrpB is typically about 800 residues in length, while its paralog HrpA (TIGR01967), also uncharacterized, is about 1300 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 273901 [Multi-domain]  Cd Length: 819  Bit Score: 341.36  E-value: 1.21e-101
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  543 LPIFRLKEQLIQAVHDNQILIVIGETGSGKTTQIT-QYLAEAGYTsrGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQEVG 621
Cdd:TIGR01970    1 LPIHAVLPALRDALAAHPQVVLEAPPGAGKSTAVPlALLDAPGIG--GKIIMLEPRRLAARSAAQRLASQLGEAVGQTVG 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  622 YTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLGQYAIIMLDEAHERTIHTDVLFGLLKKtVQK--RQDMKLIVTSATLD 699
Cdd:TIGR01970   79 YRVRGENKVSRRTRLEVVTEGILTRMIQDDPELDGVGALIFDEFHERSLDADLGLALALD-VQSslREDLKILAMSATLD 157

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  700 AVKFSQYFYEAPIFTIPGRTYPVEILYTKEPETDYLDASLITVMQIHLTEPPGDILVFLTGQEEIDTACEILYERmksLG 779
Cdd:TIGR01970  158 GERLSSLLPDAPVVESEGRSFPVEIRYLPLRGDQRLEDAVSRAVEHALASETGSILVFLPGQAEIRRVQEQLAER---LD 234

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  780 PDVpelIILPVYSALPSEMQTRIFDPAPPGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKVYNSKTGIDQLVVTPISQ 859
Cdd:TIGR01970  235 SDV---LICPLYGELSLAAQDRAIKPDPQGRRKVVLATNIAETSLTIEGIRVVIDSGLARVARFDPKTGITRLETVRISQ 311

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  860 AQAKQRAGRAGRTGPGKCYRLYTErAYRDEMLTTNVPEIQRTNLASTVLSLKAMGINDLLSFDFMDAPPMETLITAMEQL 939
Cdd:TIGR01970  312 ASATQRAGRAGRLEPGVCYRLWSE-EQHQRLPAQDEPEILQADLSGLALELAQWGAKDPSDLRWLDAPPSVALAAARQLL 390

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1952420370  940 YTLGALDDEGLLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSML 990
Cdd:TIGR01970  391 QRLGALDAQGRLTAHGKAMAALGCHPRLAAMLLSAHSTGLAALACDLAALL 441
DEXHc_DHX38 cd17983
DEXH-box helicase domain of DEAH-box helicase 38; DEAH-box helicase 38 (DHX38, also known as ...
 543-715 3.20e-95

DEXH-box helicase domain of DEAH-box helicase 38; DEAH-box helicase 38 (DHX38, also known as PRP16) is involved in pre-mRNA splicing. DHX38 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350741 [Multi-domain]  Cd Length: 173  Bit Score: 301.30  E-value: 3.20e-95
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  543 LPIFRLKEQLIQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQEVGY 622
Cdd:cd17983      1 LPIFAVRQELLNVIRDNNVVIVVGETGSGKTTQLTQYLHEDGYTDYGMIGCTQPRRVAAMSVAKRVSEEMGVELGEEVGY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  623 TIRFEDCTSPETVIKYMTDGMLLRECLIDPDLGQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSATLDAVK 702
Cdd:cd17983     81 AIRFEDCTSENTVIKYMTDGILLRESLRDPDLDKYSAIIMDEAHERSLNTDVLFGLLREVVARRRDLKLIVTSATMDADK 160

                          170
                   ....*....|...
gi 1952420370  703 FSQYFYEAPIFTI 715
Cdd:cd17983    161 FADFFGNVPIFTI 173
PRK11664 PRK11664
ATP-dependent RNA helicase HrpB; Provisional
 542-972 1.29e-93

ATP-dependent RNA helicase HrpB; Provisional


Pssm-ID: 236950 [Multi-domain]  Cd Length: 812  Bit Score: 318.79  E-value: 1.29e-93
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  542 SLPIFRLKEQLIQAVHDNQILIVIGETGSGKTTQIT-QYLAEAGYTsrGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQEV 620
Cdd:PRK11664     3 SLPVAAVLPELLTALKTAPQVLLKAPTGAGKSTWLPlQLLQHGGIN--GKIIMLEPRRLAARNVAQRLAEQLGEKPGETV 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  621 GYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLGQYAIIMLDEAHERTIHTDVLFGLLKKtVQK--RQDMKLIVTSATL 698
Cdd:PRK11664    81 GYRMRAESKVGPNTRLEVVTEGILTRMIQRDPELSGVGLVILDEFHERSLQADLALALLLD-VQQglRDDLKLLIMSATL 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  699 DAVKFSQYFYEAPIFTIPGRTYPVEILYTKEPETDYLDASLITVMQIHLTEPPGDILVFLTGQEEIDTACEILYERmksL 778
Cdd:PRK11664   160 DNDRLQQLLPDAPVIVSEGRSFPVERRYQPLPAHQRFDEAVARATAELLRQESGSLLLFLPGVGEIQRVQEQLASR---V 236

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  779 GPDVpelIILPVYSALPSEMQTRIFDPAPPGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKVYNSKTGIDQLVVTPIS 858
Cdd:PRK11664   237 ASDV---LLCPLYGALSLAEQQKAILPAPAGRRKVVLATNIAETSLTIEGIRLVVDSGLERVARFDPKTGLTRLVTQRIS 313

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  859 QAQAKQRAGRAGRTGPGKCYRLYTERAYrDEMLTTNVPEIQRTNLASTVLSLKAMGINDLLSFDFMDAPPMETLITAMEQ 938
Cdd:PRK11664   314 QASMTQRAGRAGRLEPGICLHLYSKEQA-ERAAAQSEPEILHSDLSGLLLELLQWGCHDPAQLSWLDQPPAAALAAAKRL 392

                          410       420       430
                   ....*....|....*....|....*....|....
gi 1952420370  939 LYTLGALDDEGLLTRLGRRMAEFPLEPMLCKMLI 972
Cdd:PRK11664   393 LQQLGALDGQGRLTARGRKMAALGNDPRLAAMLV 426
DEXHc_DHX16 cd17974
DEXH-box helicase domain of DEAH-box helicase 16; DEAH-box helicase 16 (DHX16) is probably ...
 543-715 3.44e-89

DEXH-box helicase domain of DEAH-box helicase 16; DEAH-box helicase 16 (DHX16) is probably involved in pre-mRNA splicing. DHX16 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350732 [Multi-domain]  Cd Length: 174  Bit Score: 285.17  E-value: 3.44e-89
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  543 LPIFRLKEQLIQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRG-KIGCTQPRRVAAMSVAKRVSEEFGCCLGQEVG 621
Cdd:cd17974      1 LPVYPYRDDLLAAVKEHQVLIIVGETGSGKTTQIPQYLHEAGYTKGGgKIGCTQPRRVAAMSVAARVAEEMGVKLGNEVG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  622 YTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLGQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSATLDAV 701
Cdd:cd17974     81 YSIRFEDCTSEKTVLKYMTDGMLLREFLTEPDLASYSVMIIDEAHERTLHTDILFGLVKDIARFRPDLKLLISSATMDAE 160

                          170
                   ....*....|....
gi 1952420370  702 KFSQYFYEAPIFTI 715
Cdd:cd17974    161 KFSAFFDDAPIFRI 174
DEXHc_RHA-like cd17917
DEXH-box helicase domain of DEAD-like helicase RHA family proteins; The RNA helicase A (RHA) ...
 559-715 2.79e-87

DEXH-box helicase domain of DEAD-like helicase RHA family proteins; The RNA helicase A (RHA) family includes RHA, also called DEAH-box helicase 9 (DHX9), DHX8, DHX15-16, DHX32-38, and many others. The RHA family belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438707 [Multi-domain]  Cd Length: 159  Bit Score: 278.96  E-value: 2.79e-87
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  559 NQILIVIGETGSGKTTQITQYLAEAGYTS--RGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQEVGYTIRFEDCTSPETVI 636
Cdd:cd17917      1 NQVVVIVGETGSGKTTQVPQFLLEDGLAKggKGRIVCTQPRRIAAISVAERVAEERGEKLGEEVGYQIRFESKTSSKTRI 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1952420370  637 KYMTDGMLLRECLIDPDLGQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSATLDAVKFSQYFYEAPIFTI 715
Cdd:cd17917     81 KFCTDGILLRELLSDPLLSGYSHVILDEAHERSLDTDFLLGLLKDLLRKRPDLKVILMSATLDAEKFSSYFGGAPVIHI 159
SF2_C_RHA cd18791
C-terminal helicase domain of the RNA helicase A (RHA) family helicases; The RNA helicase A ...
 720-881 1.84e-86

C-terminal helicase domain of the RNA helicase A (RHA) family helicases; The RNA helicase A (RHA) family includes RHA, also called DEAH-box helicase 9 (DHX9), DHX8, DHX15-16, DHX32-38, and many others. The RHA family members are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350178 [Multi-domain]  Cd Length: 171  Bit Score: 277.49  E-value: 1.84e-86
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  720 YPVEILYTKEP-----------ETDYLDASLITVMQIHLTEPPGDILVFLTGQEEIDTACEILYERMKSlgPDVPELIIL 788
Cdd:cd18791      1 FPVEVYYLEDIlellgissekeDPDYVDAAVRLILQIHRTEEPGDILVFLPGQEEIERLCELLREELLS--PDLGKLLVL 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  789 PVYSALPSEMQTRIFDPAPPGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKVYNSKTGIDQLVVTPISQAQAKQRAGR 868
Cdd:cd18791     79 PLHSSLPPEEQQRVFEPPPPGVRKVVLATNIAETSITIPGVVYVIDSGLVKEKVYDPRTGLSSLVTVWISKASAEQRAGR 158

                          170
                   ....*....|...
gi 1952420370  869 AGRTGPGKCYRLY 881
Cdd:cd18791    159 AGRTRPGKCYRLY 171
DEXHc_DHX33 cd17978
DEXH-box helicase domain of DEAH-box helicase 33; DEAH-box helicase 33 (DHX33) stimulates RNA ...
 543-715 7.34e-86

DEXH-box helicase domain of DEAH-box helicase 33; DEAH-box helicase 33 (DHX33) stimulates RNA polymerase I transcription of the 47S precursor rRNA. DHX33 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438710 [Multi-domain]  Cd Length: 178  Bit Score: 276.16  E-value: 7.34e-86
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  543 LPIFRLKEQLIQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQEVGY 622
Cdd:cd17978      1 LPIYSARKRLLEELRKHDTVIIIGETGSGKTTQIPQYLYEAGFARGGMIGITQPRRVAAVSVAKRVAEEMGVELGQLVGY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  623 TIRFEDCTSPETVIKYMTDGMLLRECLIDPDLGQYAIIMLDEAHERTIHTDVLFGLLKKtVQKR------QDMKLIVTSA 696
Cdd:cd17978     81 SVRFDDVTSEETRIKYMTDGMLLREAIGDPLLSKYSVIILDEAHERTVHTDVLFGLVKS-AQRRrkeqklSPLKVIIMSA 159

                          170
                   ....*....|....*....
gi 1952420370  697 TLDAVKFSQYFYEAPIFTI 715
Cdd:cd17978    160 TLDADLFSEYFNGAPVLYI 178
DEXHc_DHX15 cd17973
DEXH-box helicase domain of DEAH-box helicase 15; DEAH-box helicase 15 (DHX15) is a pre-mRNA ...
 534-715 3.71e-82

DEXH-box helicase domain of DEAH-box helicase 15; DEAH-box helicase 15 (DHX15) is a pre-mRNA processing factor involved in disassembly of spliceosomes after the release of mature mRNA. DHX15 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438709 [Multi-domain]  Cd Length: 187  Bit Score: 266.20  E-value: 3.71e-82
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  534 LSIIEQRESLPIFRLKEQLIQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGK--IGCTQPRRVAAMSVAKRVSEE 611
Cdd:cd17973      4 FEILEKRRELPVWEQKEDFLKLLKNNQILVLVGETGSGKTTQIPQFVLDDELPHQPKklVACTQPRRVAAMSVAQRVAEE 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  612 FGCCLGQEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLGQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKL 691
Cdd:cd17973     84 MDVKLGEEVGYSIRFEDCSSAKTILKYMTDGMLLREAMSDPLLSRYSVIILDEAHERTLATDILMGLLKEVVRRRPDLKL 163

                          170       180
                   ....*....|....*....|....
gi 1952420370  692 IVTSATLDAVKFSQYFYEAPIFTI 715
Cdd:cd17973    164 IVMSATLDAGKFQKYFDNAPLLKV 187
DEXHc_DHX35 cd17980
DEXH-box helicase domain of DEAH-box helicase 35; DHX35 plays a role in colorectal cancers and ...
 543-707 1.36e-74

DEXH-box helicase domain of DEAH-box helicase 35; DHX35 plays a role in colorectal cancers and seems to be associated with risk to thyroid cancers. It also has been shown to positively regulate poxviruses, such as Myxoma virus. DEAH-box helicase 35 (DHX35) belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350738 [Multi-domain]  Cd Length: 185  Bit Score: 245.07  E-value: 1.36e-74
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  543 LPIFRLKEQLIQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGK-IGCTQPRRVAAMSVAKRVSEEFGCCLGQEVG 621
Cdd:cd17980      1 LPVFKLRNHILYLVENYQTIVIVGETGCGKSTQIPQYLAEAGWTAGGRvVGCTQPRRVAAVTVAGRVAEEMGAVLGHEVG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  622 YTIRFEDCTSP-ETVIKYMTDGMLLRECLIDPDLGQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSATLDA 700
Cdd:cd17980     81 YCIRFDDCTDPqATRIKFLTDGMLVREMMLDPLLTKYSVIMLDEAHERTLYTDILIGLLKKIQKKRGDLRLIVASATLDA 160


                   ....*..
gi 1952420370  701 VKFSQYF 707
Cdd:cd17980    161 EKFRDFF 167
DEXHc_DHX40 cd17984
DEXH-box helicase domain of DEAH-box helicase 40; DEAH-box helicase 40 (DHX40) belongs to the ...
 543-715 3.41e-74

DEXH-box helicase domain of DEAH-box helicase 40; DEAH-box helicase 40 (DHX40) belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350742 [Multi-domain]  Cd Length: 178  Bit Score: 243.61  E-value: 3.41e-74
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  543 LPIFRLKEQLIQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQEVGY 622
Cdd:cd17984      1 LPIQKQRKKLVQAVRDNSFLIVTGNTGSGKTTQLPKYLYEAGFSQHGMIGVTQPRRVAAISVAQRVAEEMKCTLGSKVGY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  623 TIRFEDCTSPETVIKYMTDGMLLRECLIDPDLGQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQ-----DMKLIVTSAT 697
Cdd:cd17984     81 QVRFDDCSSKETAIKYMTDGCLLRHILADPNLTKYSVIILDEAHERSLTTDILFGLLKKLFQEKSpnrkeHLKVVVMSAT 160

                          170
                   ....*....|....*...
gi 1952420370  698 LDAVKFSQYFYEAPIFTI 715
Cdd:cd17984    161 LELAKLSAFFGNCPVFDI 178
DEXHc_HrpA cd17989
DEXH-box helicase domain of ATP-dependent RNA helicase HrpA; HrpA is part of the HrpB-HrpA ...
 543-712 1.82e-59

DEXH-box helicase domain of ATP-dependent RNA helicase HrpA; HrpA is part of the HrpB-HrpA two-partner secretion (TPS) system, a secretion pathway important to the secretion of large virulence-associated proteins. HrpA belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350747 [Multi-domain]  Cd Length: 173  Bit Score: 201.53  E-value: 1.82e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  543 LPIFRLKEQLIQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQEVGY 622
Cdd:cd17989      1 LPVSQKRDEIAKAIAENQVVIIAGETGSGKTTQLPKICLELGRGIRGLIGHTQPRRLAARSVAERIAEELKTELGGAVGY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  623 TIRFEDCTSPETVIKYMTDGMLLRECLIDPDLGQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSATLDAVK 702
Cdd:cd17989     81 KVRFTDQTSDETCVKLMTDGILLAETQTDRYLRAYDTIIIDEAHERSLNIDFLLGYLKQLLPRRPDLKVIITSATIDAER 160

                          170
                   ....*....|
gi 1952420370  703 FSQYFYEAPI 712
Cdd:cd17989    161 FSRHFNNAPI 170
DEXHc_DHX37 cd17982
DEXH-box helicase domain of DEAH-box helicase 37; DHX37 plays a role in the development of the ...
 543-705 4.69e-58

DEXH-box helicase domain of DEAH-box helicase 37; DHX37 plays a role in the development of the human nervous system and has been linked to schizophrenia. It also negatively regulates poxviruses such as Myxoma virus. DEAH-box helicase 37 (DHX37) belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350740 [Multi-domain]  Cd Length: 191  Bit Score: 198.35  E-value: 4.69e-58
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  543 LPIFRLKEQLIQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSR-----GKIGCTQPRRVAAMSVAKRVSEEFGCcLG 617
Cdd:cd17982      1 LPILAEEQEIMEAINENPVVIICGETGSGKTTQVPQFLYEAGFGSPesdnpGMIGITQPRRVAAVSMAKRVAEELNV-FG 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  618 QEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLGQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDM-------- 689
Cdd:cd17982     80 KEVSYQIRYDSTVSENTKIKFMTDGVLLKEIQTDFLLRKYSVIIIDEAHERSVNTDILIGMLSRIVPLRAKLylqdqtvk 159

                          170
                   ....*....|....*...
gi 1952420370  690 --KLIVTSATLDAVKFSQ 705
Cdd:cd17982    160 plKLVIMSATLRVEDFTE 177
DEXHc_DHX34 cd17979
DEXH-box helicase domain of DEAH-box helicase 34; DEAH-box helicase 34 (DHX34) plays a role in ...
 543-712 1.03e-55

DEXH-box helicase domain of DEAH-box helicase 34; DEAH-box helicase 34 (DHX34) plays a role in the nonsense-mediated decay (NMD), a surveillance mechanism that degrades aberrant mRNAs. DHX34 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350737 [Multi-domain]  Cd Length: 170  Bit Score: 190.73  E-value: 1.03e-55
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  543 LPIFRLKEQLIQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSrgkIGCTQPRRVAAMSVAKRVSEEFGCCLGQEVGY 622
Cdd:cd17979      1 LPIAQYREKIIELLKTHQVVIVAGDTGCGKSTQVPQYLLAAGFRH---IACTQPRRIACISLAKRVAFESLNQYGSKVAY 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  623 TIRFEDCTSPETVIKYMTDGMLLRECLIDPDLGQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSATLDAVK 702
Cdd:cd17979     78 QIRFERTRTLATKLLFLTEGLLLRQIQRDASLPQYNVLILDEVHERHLHGDFLLGVLRCLLRLRPDLKLILMSATINIEL 157

                          170
                   ....*....|
gi 1952420370  703 FSQYFYEAPI 712
Cdd:cd17979    158 FSGYFEGAPV 167
DEXHc_DHX36 cd17981
DEXH-box helicase domain of DEAH-box helicase 36; DEAH-box helicase 36 (DHX36, also known as ...
 543-715 3.42e-47

DEXH-box helicase domain of DEAH-box helicase 36; DEAH-box helicase 36 (DHX36, also known as G4-resolvase 1 or G4R1, MLE-like protein 1 and RNA helicase associated with AU-rich element or RHAU) unwinds a G4-quadruplex in human telomerase RNA. DHX36 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350739 [Multi-domain]  Cd Length: 180  Bit Score: 166.94  E-value: 3.42e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  543 LPIFRLKEQLIQAVHDNQILIVIGETGSGKTTQITQYLAEaGYTSRGK-----IGCTQPRRVAAMSVAKRVSEEFG--CC 615
Cdd:cd17981      1 LPSYGMKQEIINMIDNNQVTVISGETGCGKTTQVTQFILD-DAIERGKgsscrIVCTQPRRISAISVAERVAAERAesCG 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  616 LGQEVGYTIRFEDCTSPETV-IKYMTDGMLLRECLIDPDLGQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVT 694
Cdd:cd17981     80 LGNSTGYQIRLESRKPRKQGsILYCTTGIVLQWLQSDPHLSNVSHLVLDEIHERNLQSDVLMGIVKDLLPFRSDLKVILM 159

                          170       180
                   ....*....|....*....|.
gi 1952420370  695 SATLDAVKFSQYFYEAPIFTI 715
Cdd:cd17981    160 SATLNAEKFSDYFNNCPMIHI 180
DEXHc_DHX29 cd17975
DEXH-box helicase domain of DEAH-box helicase 29; DEAH-box helicase 29 (DHX29) is a part of ...
 543-715 1.04e-46

DEXH-box helicase domain of DEAH-box helicase 29; DEAH-box helicase 29 (DHX29) is a part of the 43S pre-initiation complex involved in translation initiation of mRNAs with structured 5'-UTRs. DHX29 is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350733 [Multi-domain]  Cd Length: 183  Bit Score: 165.47  E-value: 1.04e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  543 LPIFRLKEQLIQAVHDNQILIVIGETGSGKTTQITQYLAE-----AGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLG 617
Cdd:cd17975      1 LPVFKHRESILETLKRHRVVVVAGETGSGKSTQVPQFLLEdlllnGGTAQKCNIVCTQPRRISAMSLATRVCEELGCESG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  618 -----QEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLGQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLI 692
Cdd:cd17975     81 pggknSLCGYQIRMESRTGEATRLLYCTTGVLLRKLQEDGLLSSISHIIVDEVHERSVQSDFLLIILKEILHKRSDLHLI 160

                          170       180
                   ....*....|....*....|...
gi 1952420370  693 VTSATLDAVKFSQYFYEAPIFTI 715
Cdd:cd17975    161 LMSATVDCEKFSSYFTHCPILRI 183
DEXHc_YTHDC2 cd17987
DEXH-box helicase domain of YTH domain containing 2; YTH domain containing 2 (YTHDC2) ...
 543-715 6.86e-46

DEXH-box helicase domain of YTH domain containing 2; YTH domain containing 2 (YTHDC2) regulates mRNA translation and stability via binding to N6-methyladenosine, a modified RNA nucleotide enriched in the stop codons and 3' UTRs of eukaryotic messenger RNAs. YTHDC2 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350745 [Multi-domain]  Cd Length: 176  Bit Score: 163.08  E-value: 6.86e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  543 LPIFRLKEQLIQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRG--KIGCTQPRRVAAMSVAKRVSEEFGCCLGQEV 620
Cdd:cd17987      1 LPVFEKQEQIVRIIKENKVVLIVGETGSGKTTQIPQFLLDDCYANGIpcRIFCTQPRRLAAIAVAERVAAERGEKIGQTV 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  621 GYTIRFEDCTSPETVIKYMTDGMLLRECLI-DPDLGQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSATLD 699
Cdd:cd17987     81 GYQIRLESRVSPKTLLTFCTNGVLLRTLMAgDSALSTVTHVIVDEVHERDRFSDFLLTKLRDILQKHPNLKLILSSAALD 160

                          170
                   ....*....|....*.
gi 1952420370  700 AVKFSQYFYEAPIFTI 715
Cdd:cd17987    161 VNLFIRYFGSCPVIYI 176
DEXHc_DHX32 cd17977
DEXH-box helicase domain of DEAH-box helicase 32; DEAH-box helicase 32 (DHX32) belongs to the ...
 543-712 2.13e-42

DEXH-box helicase domain of DEAH-box helicase 32; DEAH-box helicase 32 (DHX32) belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350735 [Multi-domain]  Cd Length: 176  Bit Score: 153.06  E-value: 2.13e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  543 LPIFRLKEQLIQAVHDNQILIVIGETGSGKTTQITQYLAE---AGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQE 619
Cdd:cd17977      1 LPVWEAKYEFMESLAHNQIVIVSGDAKTGKSSQIPQWCAEyclSAHYQHGVVVCTQVHKQTAVWLALRVADEMDVNIGHE 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  620 VGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLGQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSATLD 699
Cdd:cd17977     81 VGYVIPFENCCTNETILRYCTDDMLLREMMSDPLLESYGVIILDDAHERTVSTDVLLGLLKDVLLSRPELKLVIITCPHL 160

                          170
                   ....*....|...
gi 1952420370  700 AVKFSQYFYEAPI 712
Cdd:cd17977    161 SSKLLSYYGNVPL 173
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 243-321 2.25e-42

S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.


Pssm-ID: 240189 [Multi-domain]  Cd Length: 79  Bit Score: 148.93  E-value: 2.25e-42
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1952420370  243 GDIYQGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTGTKTSLSMKDVEQETG 321
Cdd:cd05684      1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQNGKISLSMKDVDQDTG 79
DEXHc_DHX57 cd17985
DEXH-box helicase domain of DEAH-box helicase 57; DEAH-box helicase 57 (DHX57) belongs to the ...
 543-715 9.66e-42

DEXH-box helicase domain of DEAH-box helicase 57; DEAH-box helicase 57 (DHX57) belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350743 [Multi-domain]  Cd Length: 177  Bit Score: 151.15  E-value: 9.66e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  543 LPIFRLKEQLIQAVHDNQILIVIGETGSGKTTQITQYLAEA----GYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQ 618
Cdd:cd17985      1 LPAWQERETILELLEKHQVLVISGMTGCGKTTQIPQFILDNslqgPPLPVANIICTQPRRISAISVAERVAQERAERVGQ 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  619 EVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLGQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSATL 698
Cdd:cd17985     81 SVGYQIRLESVKSSATRLLYCTTGVLLRRLEGDPTLQGVTHVIVDEVHERTEESDFLLLVLKDLMVQRPDLKVILMSATL 160

                          170
                   ....*....|....*..
gi 1952420370  699 DAVKFSQYFYEAPIFTI 715
Cdd:cd17985    161 NAELFSDYFNSCPVIHI 177
DEXHc_DHX9 cd17972
DEXH-box helicase domain of DEAH-box helicase 9; DEAH-box helicase 9 (DHX9, also known as ...
 536-715 1.35e-41

DEXH-box helicase domain of DEAH-box helicase 9; DEAH-box helicase 9 (DHX9, also known as ATP-dependent RNA helicase A or RHA and leukophysin or LKP) plays an important role in many cellular processes, including regulation of DNA replication, transcription, translation, microRNA biogenesis, RNA processing and transport, and maintenance of genomic stability. DHX9 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350730 [Multi-domain]  Cd Length: 234  Bit Score: 152.68  E-value: 1.35e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  536 IIEQRESLPIFRLKEQLIQAVHDNQILIVIGETGSGKTTQITQYLAE----AGYTSRGKIGCTQPRRVAAMSVAKRVSEE 611
Cdd:cd17972     52 ILQERELLPVKKFREEILEAISNNPVVIIRGATGCGKTTQVPQYILDdfiqNDRAAECNIVVTQPRRISAVSVAERVAFE 131

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  612 FGCCLGQEVGYTIRFEDCT-SPETVIKYMTDGMLLREclIDPDLGQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMK 690
Cdd:cd17972    132 RGEEVGKSCGYSVRFESVLpRPHASILFCTVGVLLRK--LEAGIRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPDLR 209

                          170       180
                   ....*....|....*....|....*
gi 1952420370  691 LIVTSATLDAVKFSQYFYEAPIFTI 715
Cdd:cd17972    210 VILMSATIDTSMFCEYFFNCPVIEV 234
GH2-like_DHX8 cd21691
GIPC-homology 2 (GH2)-like domain found in DEAH box protein 8 (DHX8) and similar proteins; ...
 13-80 8.21e-41

GIPC-homology 2 (GH2)-like domain found in DEAH box protein 8 (DHX8) and similar proteins; DHX8 (a human homolog of yeast Prp22), also called RNA helicase HRH1, is an ATP-dependent RNA helicase involved in pre-mRNA splicing as a component of the spliceosome. It facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. This model corresponds to the GH2-like domain that shows high sequence similarity with the GH2 domain found in GIPC (GAIP C-terminus-interacting protein) family of proteins, which mediate endocytosis by tethering cargo proteins to the motor myosin VI.


Pssm-ID: 409668  Cd Length: 68  Bit Score: 144.23  E-value: 8.21e-41
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1952420370   13 LEYLSLVSKVCTELDNHLGINDKDLAEFVISLAEKNTTFDTFKASLAKNGAEFTDSLISNLLRLIQTM 80
Cdd:cd21691      1 LEYLSLVSKVCTELENHLGISDKDLAEFIIDLAEKSKTLDEFKKALKENGAEFPDSFVESLLRLIQRM 68
DEXHc_HrpB cd17990
DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA ...
 543-713 1.15e-40

DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA two-partner secretion (TPS) system, a secretion pathway important to the secretion of large virulence-associated proteins. HrpB belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438711 [Multi-domain]  Cd Length: 174  Bit Score: 147.86  E-value: 1.15e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  543 LPIFRLKEQLIQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQEVGY 622
Cdd:cd17990      1 LPIAAVLPALRAALDAGGQVVLEAPPGAGKTTRVPLALLAELWIAGGKIIVLEPRRVAARAAARRLATLLGEAPGETVGY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  623 TIRFEDCTSPETVIKYMTDGMLLRECLIDPDLGQYAIIMLDEAHERTIHTDVLFGLLKKTVQ-KRQDMKLIVTSATLDAV 701
Cdd:cd17990     81 RVRGESRVGRRTRVEVVTEGVLLRRLQRDPELSGVGAVILDEFHERSLDADLALALLLEVQQlLRDDLRLLAMSATLDGD 160

                          170
                   ....*....|..
gi 1952420370  702 KFSQYFYEAPIF 713
Cdd:cd17990    161 GLAALLPEAPVV 172
DEXQc_DQX1 cd17986
DEXQ-box helicase domain of DEAQ-box RNA dependent ATPase 1; DEAQ-box RNA dependent ATPase 1 ...
 543-715 1.49e-39

DEXQ-box helicase domain of DEAQ-box RNA dependent ATPase 1; DEAQ-box RNA dependent ATPase 1 (DQX1) belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350744 [Multi-domain]  Cd Length: 177  Bit Score: 144.66  E-value: 1.49e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  543 LPIFRLKEQLIQAVHDNQ-ILIVIGETGSGKTTQITQYLAEAGYT---SRGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQ 618
Cdd:cd17986      1 LPIWAAKFTFLEQLESPSgIVLVSGEPGSGKSTQVPQWCAEFALSrgfQKGQVTVTQPHPLAARSLALRVADEMDLNLGH 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  619 EVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLGQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKL-IVTSAT 697
Cdd:cd17986     81 EVGYSIPQEDCTGPNTILRFCWDRLLLQEMTSTPLLGAWGVVVLDEAQERSVASDSLLGLLKDVRLQRPELRVvVVTSPA 160

                          170
                   ....*....|....*...
gi 1952420370  698 LDAvKFSQYFYEAPIFTI 715
Cdd:cd17986    161 LEP-KLRAFWGNPPVVHV 177
DEXHc_TDRD9 cd17988
DEXH-box helicase domain of tudor domain containing 9; Tudor domain containing 9 (TDRD9, also ...
 543-715 3.15e-38

DEXH-box helicase domain of tudor domain containing 9; Tudor domain containing 9 (TDRD9, also known as HIG-1or NET54 or C14orf75) is a part of the nuclear PIWI-interacting RNA (piRNA) pathway essential for transposon silencing and male fertility TDRD9 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350746 [Multi-domain]  Cd Length: 180  Bit Score: 141.10  E-value: 3.15e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  543 LPIFRLKEQLIQAVHDNQILIVIGETGSGKTTQITQYLAEAgYTSRGK---IGCTQPRRVAAMSVAKRVSEEFGCCLGQE 619
Cdd:cd17988      1 LPIYAKREEILSLIEANSVVIIKGATGCGKTTQLPQFILDH-YYKRGKycnIVVTQPRRIAAISIARRVSQEREWTLGSL 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  620 VGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLGQYAIIMLDEAHERTIHTDVLFGLLKKTVQ-KRQDMKLIVTSATL 698
Cdd:cd17988     80 VGYQVGLERPASEETRLIYCTTGVLLQKLINNKTLTEYTHIILDEVHERDQELDFLLLVVRRLLRtNSRHVKIILMSATI 159

                          170       180
                   ....*....|....*....|.
gi 1952420370  699 DAVKFSQYF----YEAPIFTI 715
Cdd:cd17988    160 SCKEFADYFttpnNPAYVFEV 180
DEXHc_DHX30 cd17976
DEXH-box helicase domain of DEAH-box helicase 30; DEAH-box helicase 30 (DHX30) plays an ...
 543-712 2.07e-36

DEXH-box helicase domain of DEAH-box helicase 30; DEAH-box helicase 30 (DHX30) plays an important role in the assembly of the mitochondrial large ribosomal subunit. DHX30 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350734 [Multi-domain]  Cd Length: 178  Bit Score: 135.69  E-value: 2.07e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  543 LPIFRLKEQLIQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGC----TQPRRVAAMSVAKRVSEEFGCCLGQ 618
Cdd:cd17976      1 LPVDSHKESILSAIEQNPVVVISGDTGCGKTTRIPQFILEDYVLRGRGARCnvviTQPRRISAVSVAQRVAHELGPNLRR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  619 EVGYTIRFEDCTSPET-VIKYMTDGMLLRECLIDPDLGQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSAT 697
Cdd:cd17976     81 NVGYQVRLESRPPPRGgALLFCTVGVLLKKLQSNPRLEGVSHVIVDEVHERDVNTDFLLILLKGVLQLNPELRVVLMSAT 160

                          170
                   ....*....|....*
gi 1952420370  698 LDAVKFSQYFYEAPI 712
Cdd:cd17976    161 GDNQRLSRYFGGCPV 175
HA2 smart00847
Helicase associated domain (HA2) Add an annotation; This presumed domain is about 90 amino ...
 942-1024 3.10e-33

Helicase associated domain (HA2) Add an annotation; This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding.


Pssm-ID: 214852 [Multi-domain]  Cd Length: 82  Bit Score: 123.15  E-value: 3.10e-33
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370   942 LGALDDEGLLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQNvfYRPKDKQALADQKKAKFHQTEGDHL 1021
Cdd:smart00847    2 LGALDDDGRLTPLGRKMAELPLDPRLAKMLLAAAEFGCLDEILTIVAMLSVGD--PRPKEKREDADAARRRFADPESDHL 79


                    ...
gi 1952420370  1022 TLL 1024
Cdd:smart00847   80 TLL 82
HA2 pfam04408
Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in ...
 935-1023 2.44e-31

Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding.


Pssm-ID: 461295 [Multi-domain]  Cd Length: 104  Bit Score: 118.49  E-value: 2.44e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  935 AMEQLYTLGALDDEGLLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQNVFYRP------KDKQALADQ 1008
Cdd:pfam04408    1 ALELLYYLGALDEDGELTPLGRKMAELPLDPRLAKMLLAAAELGCLDEVLTIVAALSVRDPFVQPnfldprSAAKAARRR 80

                           90       100
                   ....*....|....*....|....
gi 1952420370 1009 KKAKFHQ---------TEGDHLTL 1023
Cdd:pfam04408   81 RRAADEKarakfarldLEGDHLTL 104
OB_NTP_bind pfam07717
Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus ...
 1081-1157 1.67e-29

Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus of the DEAD-box helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. There do seem to be a couple of instances where it occurs by itself -. The structure PDB:3i4u adopts an OB-fold. helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. This C-terminal domain of the yeast helicase contains an oligonucleotide/oligosaccharide-binding (OB)-fold which seems to be placed at the entrance of the putative nucleic acid cavity. It also constitutes the binding site for the G-patch-containing domain of Pfa1p. When found on DEAH/RHA helicases, this domain is central to the regulation of the helicase activity through its binding of both RNA and G-patch domain proteins.


Pssm-ID: 400182 [Multi-domain]  Cd Length: 82  Bit Score: 112.35  E-value: 1.67e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370 1081 VQKAICSGFFRNAAKKDPQE-GYRTLIDQQVVYIHPSSALFN---RQPEWVVYHELVLTTKEYMREVTTIDPRWLVEFAP 1156
Cdd:pfam07717    1 LRAALAAGLYPNVARRDPKGkGYTTLSDNQRVFIHPSSVLFNektFPPEWVVYQELVETTKVYIRTVTAISPEWLLLFAP 80


                   .
gi 1952420370 1157 A 1157
Cdd:pfam07717   81 H 81
DEXDc smart00487
DEAD-like helicases superfamily;
539-724 3.99e-27

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 109.89  E-value: 3.99e-27
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370   539 QRESLPIfrlkeqliqAVHDNQILIVIGETGSGKTTQITQYLAEAGY-TSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLG 617
Cdd:smart00487   13 QKEAIEA---------LLSGLRDVILAAPTGSGKTLAALLPALEALKrGKGGRVLVLVPTRELAEQWAEELKKLGPSLGL 83

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370   618 QEVGYT------IRFEDCTSPETVIKYMTDGMLLRECLIDP-DLGQYAIIMLDEAHERT--IHTDVLFGLLKKTVQKRQd 688
Cdd:smart00487   84 KVVGLYggdskrEQLRKLESGKTDILVTTPGRLLDLLENDKlSLSNVDLVILDEAHRLLdgGFGDQLEKLLKLLPKNVQ- 162

                           170       180       190
                    ....*....|....*....|....*....|....*...
gi 1952420370   689 mkLIVTSATL--DAVKFSQYFYEAPIFTIPGRTYPVEI 724
Cdd:smart00487  163 --LLLLSATPpeEIENLLELFLNDPVFIDVGFTPLEPI 198
GH2_like cd21690
GIPC homology 2 (GH2) domain-like family; The GIPC (GAIP C-terminus-interacting protein) ...
 16-77 1.15e-23

GIPC homology 2 (GH2) domain-like family; The GIPC (GAIP C-terminus-interacting protein) family of proteins mediate endocytosis by tethering cargo proteins to the motor myosin VI. This model represents the C-terminal GIPC homology 2 or GH2 domain (plus the linker to the PDZ domain located N-terminally of GH2), which mediates the interaction with myosin VI and is involved in homodimerization in the autoinhibited state. The family also includes DEAH box protein 8 (DHX8) and similar proteins. DHX8 (a human homolog of yeast Prp22), also called RNA helicase HRH1, is an ATP-dependent RNA helicase involved in pre-mRNA splicing as a component of the spliceosome. It facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 contains a GH2-like domain at the N-terminus, which shows high sequence similarity with the GH2 domain found in GIPC proteins.


Pssm-ID: 409667  Cd Length: 62  Bit Score: 95.23  E-value: 1.15e-23
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1952420370   16 LSLVSKVCTELDNHLGINDKDLAEFVISLAEKNTTFDTFKASLAKNGAEFTDSLISNLLRLI 77
Cdd:cd21690      1 LSAIEKVDDLLKNYLGIDDPELAEFVISLAKKKKNPDEFAEALDENDAAFPDEFVFDLYRAI 62
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 239-317 2.39e-21

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 100.51  E-value: 2.39e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  239 EPSIGDIYQGKVTSIMQFGCFVQLegLRKRwEGLVHISELRREgRVANVADVVSKGQRVKVKVLSFT-GTKTSLSMKDVE 317
Cdd:PRK11824   618 EPEVGEIYEGKVVRIVDFGAFVEI--LPGK-DGLVHISEIADE-RVEKVEDVLKEGDEVKVKVLEIDkRGRIRLSRKAVL 693
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 238-340 3.49e-21

Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function prediction only];


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 90.62  E-value: 3.49e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  238 EEPSIGDIYQGKVTSIMQFGCFVQLEGlrkRWEGLVHISELrREGRVANVADVVSKGQRVKVKVLSFTGT-KTSLSMKDV 316
Cdd:COG1098      1 MSIEVGDIVEGKVTGITPFGAFVELPE---GTTGLVHISEI-ADGYVKDINDYLKVGDEVKVKVLSIDEDgKISLSIKQA 76

                           90       100
                   ....*....|....*....|....
gi 1952420370  317 EQETGEDLNPNRRRTTagEAGEET 340
Cdd:COG1098     77 EEKPKRPPRPRRNSRP--KAGFES 98
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 243-313 8.43e-21

S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.


Pssm-ID: 239918 [Multi-domain]  Cd Length: 68  Bit Score: 87.21  E-value: 8.43e-21
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1952420370  243 GDIYQGKVTSIMQFGCFVQLEGLRkrwEGLVHISELRREgRVANVADVVSKGQRVKVKVLSF-TGTKTSLSM 313
Cdd:cd04472      1 GKIYEGKVVKIKDFGAFVEILPGK---DGLVHISELSDE-RVEKVEDVLKVGDEVKVKVIEVdDRGRISLSR 68
S1_dom_CvfD NF040579
CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ...
 242-332 2.57e-20

CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a family of full-length homologs of RNA-binding proteins from the Firmicutes with a single copy of the S1 domain. Several members of the family have been characterized as general stress proteins, and the most recently characterized, CvfD, was shown to act as a post-transcriptional regulator.


Pssm-ID: 468553 [Multi-domain]  Cd Length: 113  Bit Score: 87.48  E-value: 2.57e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  242 IGDIYQGKVTSIMQFGCFVQLEglrKRWEGLVHISELrREGRVANVADVVSKGQRVKVKVLS---FTGtKTSLSMKDVEQ 318
Cdd:NF040579     3 IGDIVEGKVTGIQPYGAFVALD---EHTQGLIHISEI-KHGYVKDINDFLKVGQEVKVKVLDideYTG-KISLSLRALEE 77

                           90
                   ....*....|....
gi 1952420370  319 ETGEDLNPNRRRTT 332
Cdd:NF040579    78 APEKHRKRRKHRWT 91
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 242-316 3.44e-19

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 90.49  E-value: 3.44e-19
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1952420370  242 IGDIYQGKVTSIMQFGCFVQLE-GLrkrwEGLVHISELRREGRVANVADVVSKGQRVKVKVLSF--TGTKTSLSMKDV 316
Cdd:COG0539    274 VGDVVKGKVTRLTDFGAFVELEpGV----EGLVHISEMSWTKRVAHPSDVVKVGDEVEVKVLDIdpEERRISLSIKQL 347
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 242-317 4.36e-17

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 84.33  E-value: 4.36e-17
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1952420370  242 IGDIYQGKVTSIMQFGCFVQLEGLrkrwEGLVHISELRReGRVANVADVVSKGQRVKVKVLSF--TGTKTSLSMKDVE 317
Cdd:COG0539    189 EGDVVEGTVKNITDFGAFVDLGGV----DGLLHISEISW-GRVKHPSEVLKVGDEVEVKVLKIdrEKERISLSLKQLQ 261
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
237-322 7.70e-17

bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 85.77  E-value: 7.70e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  237 PEEPSIGDIYQGKVTSIMQFGCFVQLE-GLrkrwEGLVHISELrREGRVANVADVVSKGQRVKVKVLSFTGT--KTSLSM 313
Cdd:PRK00087   557 EEKYPVGSIVLGKVVRIAPFGAFVELEpGV----DGLVHISQI-SWKRIDKPEDVLSEGEEVKAKILEVDPEekRIRLSI 631


                   ....*....
gi 1952420370  314 KDVEQETGE 322
Cdd:PRK00087   632 KEVEEEPGD 640
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 243-314 1.25e-15

S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240197 [Multi-domain]  Cd Length: 69  Bit Score: 72.32  E-value: 1.25e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1952420370  243 GDIYQGKVTSIMQFGCFVQL-EGLrkrwEGLVHISELRREgRVANVADVVSKGQRVKVKVLSFTGT-KTSLSMK 314
Cdd:cd05692      1 GSVVEGTVTRLKPFGAFVELgGGI----SGLVHISQIAHK-RVKDVKDVLKEGDKVKVKVLSIDARgRISLSIK 69
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 238-342 1.63e-15

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 79.92  E-value: 1.63e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  238 EEPSIGDIYQGKVTSIMQFGCFVQL-EGLrkrwEGLVHISELRREgRVANVADVVSKGQRVKVKVLSF--TGTKTSLSMK 314
Cdd:PRK06676   273 EKLPEGDVIEGTVKRLTDFGAFVEVlPGV----EGLVHISQISHK-HIATPSEVLEEGQEVKVKVLEVneEEKRISLSIK 347

                           90       100
                   ....*....|....*....|....*...
gi 1952420370  315 DVEQETGEDLNPNRRRTTAGEAGEETAM 342
Cdd:PRK06676   348 ALEEAPAEEEDRREEYRQYELPEEETGF 375
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 243-316 2.77e-15

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 79.15  E-value: 2.77e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1952420370  243 GDIYQGKVTSIMQFGCFVQLEGLrkrwEGLVHISELRREgRVANVADVVSKGQRVKVKVLSF---TGtKTSLSMKDV 316
Cdd:PRK06676   193 GDVVEGTVARLTDFGAFVDIGGV----DGLVHISELSHE-RVEKPSEVVSVGQEVEVKVLSIdweTE-RISLSLKDT 263
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
242-314 6.25e-15

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 70.71  E-value: 6.25e-15
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1952420370   242 IGDIYQGKVTSIMQFGCFVQLEGlrkRWEGLVHISELRREgRVANVADVVSKGQRVKVKVLSFTGTK--TSLSMK 314
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGN---GVEGLIPISELSDK-RVKDPEEVLKVGDEVKVKVLSVDEEKgrIILSLK 72
HELICc smart00490
helicase superfamily c-terminal domain;
769-873 1.11e-14

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 70.32  E-value: 1.11e-14
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370   769 EILYERMKSLGpdvpeLIILPVYSALPSEMQTRIFDPAPPGSRKVVIATNIAETSLTIDGIYYVVDPGFvkqkvynsktg 848
Cdd:smart00490    1 EELAELLKELG-----IKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDL----------- 64

                            90       100
                    ....*....|....*....|....*
gi 1952420370   849 idqlvvtPISQAQAKQRAGRAGRTG 873
Cdd:smart00490   65 -------PWSPASYIQRIGRAGRAG 82
PRK08059 PRK08059
general stress protein 13; Validated
 242-317 3.23e-14

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 70.46  E-value: 3.23e-14
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1952420370  242 IGDIYQGKVTSIMQFGCFVQLEGlrkRWEGLVHISELrREGRVANVADVVSKGQRVKVKVLSF---TGtKTSLSMKDVE 317
Cdd:PRK08059     7 VGSVVTGKVTGIQPYGAFVALDE---ETQGLVHISEI-THGFVKDIHDFLSVGDEVKVKVLSVdeeKG-KISLSIRATE 80
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 242-314 1.32e-13

S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240193 [Multi-domain]  Cd Length: 68  Bit Score: 66.88  E-value: 1.32e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1952420370  242 IGDIYQGKVTSIMQFGCFVQLEGLrkrwEGLVHISELRReGRVANVADVVSKGQRVKVKVLSFTGTKTSLSMK 314
Cdd:cd05688      1 EGDVVEGTVKSITDFGAFVDLGGV----DGLLHISDMSW-GRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 739-873 1.10e-12

Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.


Pssm-ID: 459740 [Multi-domain]  Cd Length: 109  Bit Score: 65.31  E-value: 1.10e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  739 LITVMQIHLTEPPGDILVFLTGQEEIDtaCEILYERMKslgpdvpeLIILPVYSALPSEMQTRIFDPAPPGSRKVVIATN 818
Cdd:pfam00271    3 LEALLELLKKERGGKVLIFSQTKKTLE--AELLLEKEG--------IKVARLHGDLSQEEREEILEDFRKGKIDVLVATD 72

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1952420370  819 IAETSLTIDGIYYVVDpgfvkqkvYNSKTGIDQLVvtpisqaqakQRAGRAGRTG 873
Cdd:pfam00271   73 VAERGLDLPDVDLVIN--------YDLPWNPASYI----------QRIGRAGRAG 109
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 242-314 2.25e-12

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 71.35  E-value: 2.25e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1952420370  242 IGDIYQGKVTSIMQFGCFVQLE-GLrkrwEGLVHISELRREGRVANVADVVSKGQRVKVKVLS--FTGTKTSLSMK 314
Cdd:PRK06299   286 VGSKVKGKVTNITDYGAFVELEeGI----EGLVHVSEMSWTKKNKHPSKVVSVGQEVEVMVLEidEEKRRISLGLK 357
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 246-313 2.98e-12

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 62.78  E-value: 2.98e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1952420370  246 YQGKVTSIMQFGCFVQLEGlrkRWEGLVHISELRREgRVANVADVVSKGQRVKVKVLSFTGTKTSLSM 313
Cdd:cd00164      1 VTGKVVSITKFGVFVELED---GVEGLVHISELSDK-FVKDPSEVFKVGDEVEVKVLEVDPEKGRISL 64
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
243-317 3.69e-12

bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 70.75  E-value: 3.69e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1952420370  243 GDIYQGKVTSIMQFGCFVQLEGLrkrwEGLVHISELRReGRVANVADVVSKGQRVKVKVLSF--TGTKTSLSMKDVE 317
Cdd:PRK00087   478 GDVVEGEVKRLTDFGAFVDIGGV----DGLLHVSEISW-GRVEKPSDVLKVGDEIKVYILDIdkENKKLSLSLKKLL 549
rpsA PRK13806
30S ribosomal protein S1; Provisional
 238-326 3.83e-12

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 70.14  E-value: 3.83e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  238 EEPSIGDIYQGKVTSIMQFGCFVQLE-GLrkrwEGLVHISELRReGRVANVADVVSKGQRVKVKVLSF------TGTKTS 310
Cdd:PRK13806   198 ETVKEGDVVEGTVTRLAPFGAFVELApGV----EGMVHISELSW-SRVQKADEAVSVGDTVRVKVLGIerakkgKGLRIS 272

                           90       100
                   ....*....|....*....|
gi 1952420370  311 LSMKDVE----QETGEDLNP 326
Cdd:PRK13806   273 LSIKQAGgdpwDTVGDRLKA 292
PRK08582 PRK08582
RNA-binding protein S1;
242-334 7.08e-12

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 64.28  E-value: 7.08e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  242 IGDIYQGKVTSIMQFGCFVQLEGLRKrweGLVHISELrREGRVANVADVVSKGQRVKVKVLSFTGT-KTSLSM-KDVEQE 319
Cdd:PRK08582     5 VGSKLQGKVTGITNFGAFVELPEGKT---GLVHISEV-ADNYVKDINDHLKVGDEVEVKVLNVEDDgKIGLSIkKAKDRP 80

                           90
                   ....*....|....*
gi 1952420370  320 TGEDLNPNRRRTTAG 334
Cdd:PRK08582    81 KRQHDRPRHEDNRGG 95
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 240-302 2.63e-11

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 60.38  E-value: 2.63e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1952420370  240 PSIGDIYQGKVTSIMQFGCFVQLEGLRkrwEGLVHISELRREgRVANVADVVSKGQRVKVKVL 302
Cdd:pfam00575    1 PEKGDVVEGEVTRVTKGGAFVDLGNGV---EGFIPISELSDD-HVEDPDEVIKVGDEVKVKVL 59
S1_pNO40 cd05686
S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function ...
 240-314 2.85e-11

S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.


Pssm-ID: 240191 [Multi-domain]  Cd Length: 73  Bit Score: 60.19  E-value: 2.85e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1952420370  240 PSIGDIYQGKVTSIMQFGCFVQLEGLRKrwEGLVHISELrREGRVANVADVVSKGQRVKVKVLSF-TGTKTSLSMK 314
Cdd:cd05686      1 PALYQIFKGEVASVTEYGAFVKIPGCRK--QGLVHKSHM-SSCRVDDPSEVVDVGEKVWVKVIGReMKDKMKLSLS 73
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
242-319 4.12e-11

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 61.26  E-value: 4.12e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  242 IGDIYQGKVTSIMQFGCFVQLEGLRKrweGLVHISELrREGRVANVADVVSKGQRVKVKVL---SFTGtKTSLSMKDVEQ 318
Cdd:PRK07252     3 IGDKLKGTITGIKPYGAFVALENGTT---GLIHISEI-KTGFIDNIHQLLKVGEEVLVQVVdfdEYTG-KASLSLRTLEE 77


                   .
gi 1952420370  319 E 319
Cdd:PRK07252    78 E 78
PRK05807 PRK05807
RNA-binding protein S1;
243-334 1.11e-10

RNA-binding protein S1;


Pssm-ID: 235614 [Multi-domain]  Cd Length: 136  Bit Score: 60.53  E-value: 1.11e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  243 GDIYQGKVTSIMQFGCFVQLEGLrkrwEGLVHISELrREGRVANVADVVSKGQRVKVKVLSF-TGTKTSLSMKDVEQETG 321
Cdd:PRK05807     6 GSILEGTVVNITNFGAFVEVEGK----TGLVHISEV-ADTYVKDIREHLKEQDKVKVKVISIdDNGKISLSIKQAMKQKK 80

                           90
                   ....*....|....*....
gi 1952420370  322 E------DLNPNRRRTTAG 334
Cdd:PRK05807    81 SvkpaeiDWQKEKNKNNNG 99
rpsA PRK13806
30S ribosomal protein S1; Provisional
 243-317 2.25e-10

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 64.36  E-value: 2.25e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1952420370  243 GDIYQGKVTSIMQFGCFVQLE-GLrkrwEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTGTK--TSLSMKDVE 317
Cdd:PRK13806   293 GDKVTGKVVRLAPFGAFVEILpGI----EGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKrrISLSLRDAE 366
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 240-302 3.39e-10

S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to complete the initiation complex, which is competent to begin translation. The IF2a subunit is a major site of control of the translation initiation process, via phosphorylation of a specific serine residue. This alpha subunit is well conserved in eukaryotes and archaea but is not present in bacteria. IF2 is a cold-shock-inducible protein.


Pssm-ID: 239899 [Multi-domain]  Cd Length: 76  Bit Score: 57.21  E-value: 3.39e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1952420370  240 PSIGDIYQGKVTSIMQFGCFVQLEGLRKRwEGLVHISELRReGRVANVADVVSKGQRVKVKVL 302
Cdd:cd04452      1 PEEGELVVVTVKSIADMGAYVSLLEYGNI-EGMILLSELSR-RRIRSIRKLVKVGRKEVVKVI 61
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 240-319 5.16e-10

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 61.38  E-value: 5.16e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  240 PSIGDIYQGKVTSIMQFGCFVQLE---GLrkrwEGLVHISELRReGRVANVADVVSKGQRVKVKVLSFTGTKTS--LSMK 314
Cdd:PRK03987     6 PEEGELVVGTVKEVKDFGAFVTLDeypGK----EGFIHISEVAS-GWVKNIRDHVKEGQKVVCKVIRVDPRKGHidLSLK 80


                   ....*.
gi 1952420370  315 DV-EQE 319
Cdd:PRK03987    81 RVnEHQ 86
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 243-303 1.11e-09

S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.


Pssm-ID: 240190 [Multi-domain]  Cd Length: 68  Bit Score: 55.70  E-value: 1.11e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1952420370  243 GDIYQGKVTSIMQFGCFVQLeGLRKrwEGLVHISELRrEGRVANVADVVSKGQRVKVKVLS 303
Cdd:cd05685      1 GMVLEGVVTNVTDFGAFVDI-GVKQ--DGLIHISKMA-DRFVSHPSDVVSVGDIVEVKVIS 57
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 243-318 1.20e-09

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 62.49  E-value: 1.20e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1952420370  243 GDIYQGKVTSIMQFGCFVQLEGLrkrwEGLVHISELRReGRVANVADVVSKGQRVKVKVLSFTGTKT--SLSMKDVEQ 318
Cdd:PRK06299   202 GQVVEGVVKNITDYGAFVDLGGV----DGLLHITDISW-KRVNHPSEVVNVGDEVKVKVLKFDKEKKrvSLGLKQLGE 274
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
242-322 2.00e-09

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 61.96  E-value: 2.00e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  242 IGDIYQGKVTSIMQFGCFV-----QleglrkrwEGLVHISELRrEGRVANVADVVSKGQRVKVKVLSFTGTK--TSLSMK 314
Cdd:COG2183    641 PGMILEGTVTNVTDFGAFVdigvhQ--------DGLVHISQLS-DRFVKDPREVVKVGDIVKVKVLEVDLKRkrISLSMK 711


                   ....*...
gi 1952420370  315 DVEQETGE 322
Cdd:COG2183    712 LDDEAGAA 719
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 242-318 2.09e-09

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 61.72  E-value: 2.09e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  242 IGDIYQGKVTSIMQFGCFVQLE-GLrkrwEGLVHISELRREGRVANVADVVSKGQRVKVKVLSF--TGTKTSLSMKDVEQ 318
Cdd:PRK06299   373 VGDVVEGKVKNITDFGAFVGLEgGI----DGLVHLSDISWDKKGEEAVELYKKGDEVEAVVLKVdvEKERISLGIKQLEE 448
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 238-314 2.28e-09

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 61.29  E-value: 2.28e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  238 EEPSIGDIYQGKVTSIMQFGCFVQL-EGLrkrwEGLVHISELRREGRVANVADVVSKGQRVKVKVLSF--TGTKTSLSMK 314
Cdd:TIGR00717  268 KKFPVGDKITGRVTNLTDYGVFVEIeEGI----EGLVHVSEMSWVKKNSHPSKVVKKGDEVEVMILDIdpERRRLSLGLK 343
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 241-326 4.85e-09

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 60.06  E-value: 4.85e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  241 SIGDIYQGKVTSIMQFGCFVQLE-GLrkrwEGLVHISELrREGRVANVADVVSKGQRVKVKV--LSFTGTKTSLSMKDVE 317
Cdd:PRK07899   292 AIGQIVPGKVTKLVPFGAFVRVEeGI----EGLVHISEL-AERHVEVPEQVVQVGDEVFVKVidIDLERRRISLSLKQAN 366

                           90
                   ....*....|..
gi 1952420370  318 Q---ETGEDLNP 326
Cdd:PRK07899   367 EgvtPESEDFDP 378
S1_RNase_R cd04471
S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, ...
 242-303 1.49e-08

S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.


Pssm-ID: 239917 [Multi-domain]  Cd Length: 83  Bit Score: 52.79  E-value: 1.49e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1952420370  242 IGDIYQGKVTSIMQFGCFVQLEGLRKrwEGLVHISEL----------------RREGRVANVadvvskGQRVKVKVLS 303
Cdd:cd04471      1 VGEEFDGVISGVTSFGLFVELDNLTV--EGLVHVSTLgddyyefdeenhalvgERTGKVFRL------GDKVKVRVVR 70
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 242-324 1.51e-08

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 58.59  E-value: 1.51e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  242 IGDIYQGKVTSIMQFGCFVQLEGLrkrwEGLVHISELRReGRVANVADVVSKGQRVKVKVLSFTGTKT--SLSMKDVEQE 319
Cdd:TIGR00717  187 EGDVVKGVVKNITDFGAFVDLGGV----DGLLHITDMSW-KRVKHPSEYVKVGQEVKVKVIKFDKEKGriSLSLKQLGED 261


                   ....*
gi 1952420370  320 TGEDL 324
Cdd:TIGR00717  262 PWEAI 266
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 243-314 2.46e-08

S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240213 [Multi-domain]  Cd Length: 77  Bit Score: 51.95  E-value: 2.46e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1952420370  243 GDIYQGKVTSIMQFGCFVQLEGlrKRWEGLVHISELRrEGRVANVADVVSKGQRVKVKVLSF--TGTKTSLSMK 314
Cdd:cd05708      3 GQKIDGTVRRVEDYGVFIDIDG--TNVSGLCHKSEIS-DNRVADASKLFRVGDKVRAKVLKIdaEKKRISLGLK 73
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 243-313 4.15e-08

S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240195 [Multi-domain]  Cd Length: 69  Bit Score: 51.34  E-value: 4.15e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1952420370  243 GDIYQGKVTSIMQFGCFVQLEGlrkRWEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTGTKTSLSM 313
Cdd:cd05690      1 GTVVSGKIKSITDFGIFVGLDG---GIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERERISL 68
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
 240-371 1.00e-07

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 56.44  E-value: 1.00e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  240 PSIGDIYQG-KVTSIMQFGCFVQLEGLRkrwEGLVHISELrREGRVANVADVVSKGQRVKVKVLSFT-GTKTSLSMKDVE 317
Cdd:PLN00207   751 PTVGDIYRNcEIKSIAPYGAFVEIAPGR---EGLCHISEL-SSNWLAKPEDAFKVGDRIDVKLIEVNdKGQLRLSRRALL 826

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1952420370  318 qetgedLNPNRRRTTAGEAGEETAMRNPD--------RPSHLALVSAPELEDDTLQRKRLTR 371
Cdd:PLN00207   827 ------PEANSEKSSQKQQGGSTKDKAPQkkyvntssRPRRAAQAEKNSAENAAVPKKKDYK 882
PHA02653 PHA02653
RNA helicase NPH-II; Provisional
 654-882 1.42e-07

RNA helicase NPH-II; Provisional


Pssm-ID: 177443 [Multi-domain]  Cd Length: 675  Bit Score: 55.75  E-value: 1.42e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  654 LGQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIvtSATL-DAVKFSQYFYEAPIFT-IPGRT-YPVEILYTK-- 728
Cdd:PHA02653   289 LFDYGTVIIDEVHEHDQIGDIIIAVARKHIDKIRSLFLM--TATLeDDRDRIKEFFPNPAFVhIPGGTlFPISEVYVKnk 366

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  729 ----------EPETDYLDASLITvmqihLTEPPG-DILVFLTGQEEIDTACEILYERMkslgpdvPELIILPVYSALPS- 796
Cdd:PHA02653   367 ynpknkrayiEEEKKNIVTALKK-----YTPPKGsSGIVFVASVSQCEEYKKYLEKRL-------PIYDFYIIHGKVPNi 434

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  797 -EMQTRIFDPAPPgsrKVVIATNIAETSLTIDGIYYVVDPGfvkqKVYNSKT-GIDQLVvtpISQAQAKQRAGRAGRTGP 874
Cdd:PHA02653   435 dEILEKVYSSKNP---SIIISTPYLESSVTIRNATHVYDTG----RVYVPEPfGGKEMF---ISKSMRTQRKGRVGRVSP 504


                   ....*...
gi 1952420370  875 GKCYRLYT 882
Cdd:PHA02653   505 GTYVYFYD 512
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 243-319 1.62e-07

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 55.56  E-value: 1.62e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  243 GDIYQGKVTSIMQFGCFVQLEGLRkrwEGLVHISELRREgRVANVADVVSKGQRVKVKVLSFtGTKT---SLSMKDVEQE 319
Cdd:PRK06299   461 GSIVTGTVTEVKDKGAFVELEDGV---EGLIRASELSRD-RVEDATEVLKVGDEVEAKVINI-DRKNrriSLSIKALDEA 535
S1_RPS1_repeat_ec4 cd05689
S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 248-313 7.48e-07

S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240194 [Multi-domain]  Cd Length: 72  Bit Score: 47.57  E-value: 7.48e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1952420370  248 GKVTSIMQFGCFVQLE-GLrkrwEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTGTKTSLSM 313
Cdd:cd05689      9 GKVTNLTDYGCFVELEeGV----EGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERRRISL 71
VacB COG0557
Exoribonuclease R [Transcription];
242-303 3.05e-06

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 51.65  E-value: 3.05e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1952420370  242 IGDIYQGKVTSIMQFGCFVQLEGLRKrwEGLVHISEL----------------RREGRVANVadvvskGQRVKVKVLS 303
Cdd:COG0557    622 VGEEFEGVISGVTSFGLFVELDELGV--EGLVHVSSLgddyyeyderrqalvgERTGKRYRL------GDRVEVRVVR 691
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 243-323 3.65e-06

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 50.81  E-value: 3.65e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  243 GDIYQGKVTSIMQFGCFVQLEGLrkrwEGLVHISELRREgRVANVADVVSKGQRVKVKVLS--FTGTKTSLSMKdveqET 320
Cdd:PRK07899   209 GQVRKGVVSSIVNFGAFVDLGGV----DGLVHVSELSWK-HIDHPSEVVEVGQEVTVEVLDvdMDRERVSLSLK----AT 279


                   ...
gi 1952420370  321 GED 323
Cdd:PRK07899   280 QED 282
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 243-314 7.05e-06

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 50.12  E-value: 7.05e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1952420370  243 GDIYQGKVTSIMQFGCFVQLEGlrkRWEGLVHISELRREgRVANVADVVSKGQRVKVKVLSF--TGTKTSLSMK 314
Cdd:TIGR00717  447 GSVVKGKVTEIKDFGAFVELPG---GVEGLIRNSELSEN-RDEDKTDEIKVGDEVEAKVVDIdkKNRKVSLSVK 516
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 562-697 1.91e-05

N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily 2 helicases comprise a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This N-terminal domain contains the ATP-binding region.


Pssm-ID: 350668 [Multi-domain]  Cd Length: 146  Bit Score: 45.86  E-value: 1.91e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  562 LIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGccLGQEVGYTIRFedcTSPETV------ 635
Cdd:cd00046      4 VLITAPTGSGKTLAALLAALLLLLKKGKKVLVLVPTKALALQTAERLRELFG--PGIRVAVLVGG---SSAEEReknklg 78

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1952420370  636 ---IKYMTDGMLLRECLIDPDLGQYAIIML--DEAHERTIHTDVLFgLLKKTVQKRQ--DMKLIVTSAT 697
Cdd:cd00046     79 dadIIIATPDMLLNLLLREDRLFLKDLKLIivDEAHALLIDSRGAL-ILDLAVRKAGlkNAQVILLSAT 146
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
 568-666 3.35e-05

DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional protein found in pestiviruses that contains an N-terminal protease and a C-terminal helicase. The N-terminal domain is a chymotrypsin-like serine protease, which is responsible for most of the maturation cleavages of the polyprotein precursor in the cytosolic side of the endoplasmic reticulum membrane. The C-terminal domain, about two-thirds of NS3, is a helicase belonging to superfamily 2 (SF2) thought to be important for unwinding highly structured regions of the RNA genome during replication. NS3 plays an essential role in viral polyprotein processing and genome replication. NS3 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350689 [Multi-domain]  Cd Length: 151  Bit Score: 45.23  E-value: 3.35e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  568 TGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSeefgcclGQEVGY-TIRFEDCTSPETVIKYMTDGMLLR 646
Cdd:cd17931     10 PGAGKTTRVLPQIIREAIKKRLRTLVLAPTRVVAAEMYEALR-------GLPIRYrTGAVKEEHGGNEIVDYMCHGTFTC 82

                           90       100
                   ....*....|....*....|
gi 1952420370  647 ECLIDPDLGQYAIIMLDEAH 666
Cdd:cd17931     83 RLLSPKRVPNYNLIIMDEAH 102
S1_RNase_E cd04453
S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential ...
 238-308 7.10e-05

S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain that is highly homologous to that of RNase E. RNase G not only shares sequence similarity with RNase E, but also functionally overlaps with RNase E. In Escherichia coli, RNase G is involved in the maturation of the 5' end of the 16S rRNA. RNase G plays a secondary role in mRNA decay.


Pssm-ID: 239900 [Multi-domain]  Cd Length: 88  Bit Score: 42.58  E-value: 7.10e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1952420370  238 EEPSIGDIYQGKVTSI---MQfGCFVQLeGLRKrwEGLVHISELRR--EGRVANVADVVSKGQRVKVKVL-SFTGTK 308
Cdd:cd04453      3 REPIVGNIYLGRVKKIvpgLQ-AAFVDI-GLGK--NGFLHLSDILPayFKKHKKIAKLLKEGQEILVQVVkEPIGTK 75
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 242-324 7.50e-05

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 47.01  E-value: 7.50e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  242 IGDIYQGKVTSIMQFGCFVQL-EGLrkrwEGLVHISELRREGRVANVADVVSKGQRVKVKVLSF--TGTKTSLSMKDVEQ 318
Cdd:PRK12269   578 VNDVVKGRVTKIADFGAFIELaEGI----EGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGYdiQAGRVSLGLKQVTA 653


                   ....*.
gi 1952420370  319 ETGEDL 324
Cdd:PRK12269   654 NPWEEI 659
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 812-881 2.17e-04

C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases include DEAD-box helicases, UvrB, RecG, Ski2, Sucrose Non-Fermenting (SNF) family helicases, and dicer proteins, among others. Similar to SF1 helicases, they do not form toroidal structures like SF3-6 helicases. SF2 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350172 [Multi-domain]  Cd Length: 77  Bit Score: 40.77  E-value: 2.17e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1952420370  812 KVVIATNIAETSLTIDGIYYVVDPGFvkqkvynsktgidqlvvtPISQAQAKQRAGRAGRTG--PGKCYRLY 881
Cdd:cd18785     24 EILVATNVLGEGIDVPSLDTVIFFDP------------------PSSAASYIQRVGRAGRGGkdEGEVILFV 77
Cas3_I cd09639
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short ...
 561-881 6.31e-04

CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; DEAD/DEAH box helicase DNA helicase cas3'; Often but not always is fused to HD nuclease domain; signature gene for Type I


Pssm-ID: 187770 [Multi-domain]  Cd Length: 353  Bit Score: 43.57  E-value: 6.31e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  561 ILIVIGETGSGKTTQITQYLAEAGYTS-RGKIGCTQPRRVAAMSVAKRVSEEFG-CCLGQEVGYTIRFEDCTSPETVIK- 637
Cdd:cd09639      1 LLVIEAPTGYGKTEAALLWALHSLKSQkADRVIIALPTRATINAMYRRAKEAFGeTGLYHSSILSSRIKEMGDSEEFEHl 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  638 ---YMTDGML-----LRECLID-------PDLGQY---------AIIMLDEAHERTIHTDVLF-GLLKktVQKRQDMKLI 692
Cdd:cd09639     81 fplYIHSNDTlfldpITVCTIDqvlksvfGEFGHYeftlasianSLLIFDEVHFYDEYTLALIlAVLE--VLKDNDVPIL 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  693 VTSATLDAVkFSQYF--YEAPIFTIPGRTYPVEILYT-KEPETDYLDASLITVMqIHLTEPPGDILVFLTgqeEIDTACE 769
Cdd:cd09639    159 LMSATLPKF-LKEYAekIGYVEENEPLDLKPNERAPFiKIESDKVGEISSLERL-LEFIKKGGSVAIIVN---TVDRAQE 233

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  770 IlYERMKSLGPDVPELII----LPVYSALPSEMQTRIFDPAPPGsrkVVIATNIAETSLTIDGIYYVVDPgfvkqkvyns 845
Cdd:cd09639    234 F-YQQLKEKGPEEEIMLIhsrfTEKDRAKKEAELLLEFKKSEKF---VIVATQVIEASLDISVDVMITEL---------- 299

                          330       340       350
                   ....*....|....*....|....*....|....*.
gi 1952420370  846 kTGIDQLVvtpisqaqakQRAGRAGRTGPGKCYRLY 881
Cdd:cd09639    300 -APIDSLI----------QRLGRLHRYGEKNGEEVY 324
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 238-303 6.80e-04

S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 239908 [Multi-domain]  Cd Length: 83  Bit Score: 39.49  E-value: 6.80e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1952420370  238 EEPSIGDIYQGKVTSIMQFGCFVQLEGlrkRWEGLVHISELRREgRVANVADVVSKGQRVKVKVLS 303
Cdd:cd04461     10 SDLKPGMVVHGYVRNITPYGVFVEFLG---GLTGLAPKSYISDE-FVTDPSFGFKKGQSVTAKVTS 71
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 242-314 1.29e-03

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 42.80  E-value: 1.29e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1952420370  242 IGDIYQGKVTSIMQFGCFVQLEGlrkRWEGLVHISELR--REGRVANVadVVSKGQRVKVKVLS--FTGTKTSLSMK 314
Cdd:TIGR00717  359 VGDRVTGKIKKITDFGAFVELEG---GIDGLIHLSDISwdKDGREADH--LYKKGDEIEAVVLAvdKEKKRISLGVK 430
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 238-319 1.30e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 42.55  E-value: 1.30e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  238 EEPSIGDIYQGKVTSIMQFGCFVQLEGlrKRWEGLVHISELRREgRVANVADVVSKGQRVKVKVLSFTGTKTS--LSMKD 315
Cdd:PRK06676    13 KEVEVGDVVTGEVLKVEDKQVFVNIEG--YKVEGVIPISELSND-HIEDINDVVKVGDELEVYVLKVEDGEGNllLSKRR 89


                   ....
gi 1952420370  316 VEQE 319
Cdd:PRK06676    90 LEAE 93
AAA_22 pfam13401
AAA domain;
560-666 1.74e-03

AAA domain;


Pssm-ID: 379165 [Multi-domain]  Cd Length: 129  Bit Score: 39.63  E-value: 1.74e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  560 QILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEfgccLGQEVGYTIRFEDCTSpetvikym 639
Cdd:pfam13401    6 GILVLTGESGTGKTTLLRRLLEQLPEVRDSVVFVDLPSGTSPKDLLRALLRA----LGLPLSGRLSKEELLA-------- 73

                           90       100
                   ....*....|....*....|....*..
gi 1952420370  640 tdgMLLRECLidpDLGQYAIIMLDEAH 666
Cdd:pfam13401   74 ---ALQQLLL---ALAVAVVLIIDEAQ 94
CafA COG1530
Ribonuclease G or E [Translation, ribosomal structure and biogenesis];
231-301 3.68e-03

Ribonuclease G or E [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441139 [Multi-domain]  Cd Length: 490  Bit Score: 41.29  E-value: 3.68e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1952420370  231 HVDRPPpEEPSIGDIYQGKVTSI---MQfGCFVQLeGLRKrwEGLVHISELRRE---------GRVANVADVVSKGQRVK 298
Cdd:COG1530     26 DIERPG-REQLVGNIYKGKVTRVlpgLQ-AAFVDI-GLER--HGFLHVKDISPEyfslgkedsGKRPNIQDVLKEGQEVL 100


                   ...
gi 1952420370  299 VKV 301
Cdd:COG1530    101 VQV 103
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 243-304 6.09e-03

S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240203 [Multi-domain]  Cd Length: 70  Bit Score: 36.43  E-value: 6.09e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1952420370  243 GDIYQGKVTSIMQFGCFVQ-LEGLRkrweGLVHISELrREGRVANVADVVSKGQRVKVKVLSF 304
Cdd:cd05698      1 GLKTHGTIVKVKPNGCIVSfYNNVK----GFLPKSEL-SEAFIKDPEEHFRVGQVVKVKVLSC 58
S1_RecJ_like cd04473
S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of ...
 242-303 8.67e-03

S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.


Pssm-ID: 239919 [Multi-domain]  Cd Length: 77  Bit Score: 36.43  E-value: 8.67e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1952420370  242 IGDIYQGKVTSIMQFGCFVQLEglrKRWEGLVHISELRREGRVanvadvvskGQRVKVKVLS 303
Cdd:cd04473     16 VGKLYKGKVNGVAKYGVFVDLN---DHVRGLIHRSNLLRDYEV---------GDEVIVQVTD 65
 
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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