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Conserved domains on  [gi|1044440465|ref|XP_017371606|]
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ATP-dependent RNA helicase DHX8 isoform X1 [Cebus imitator]

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];
552-1183 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: 576.26  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  552 MSIIEQRESLPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFG 631
Cdd:COG1643      1 MSLITYPPDLPVSAVLPELLAALRAHQVVVLAAPPGAGKTTQLPLALLELGWGAGGRIGMLEPRRLAARAAAERMAEELG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  632 CCLGQEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQK-RQDMKLI 710
Cdd:COG1643     81 EPVGETVGYRVRFEDKVSAATRIEVVTEGILLRELQRDPELEGVDTVIFDEFHERSLNADLLLALLLDLQPAlRPDLKLL 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  711 VTSATLDAVKFSQYFYEAPIFTIPGRTYPVEILYT--KEPETDYLDASLITVMQIhLTEPPGDILVFLTGQEEIDTACEI 788
Cdd:COG1643    161 VMSATLDAERFARLLGDAPVIESSGRTYPVEVRYRplPADERDLEDAVADAVREA-LAEEPGDILVFLPGEREIRRTAEA 239

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  789 LyerMKSLGPDVpelIILPVYSALPSEMQTRIFDPAPPGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKVYNSKTGID 868
Cdd:COG1643    240 L---RGRLPPDT---EILPLYGRLSAAEQDRAFAPAPHGRRRIVLATNIAETSLTVPGIRYVIDSGLARIPRYDPRSGVT 313

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  869 QLVVTPISQAQAKQRAGRAGRTGPGKCYRLYTE------RAYRDemlttnvPEIQRTNLASTVLSLKAMGINDLLSFDFM 942
Cdd:COG1643    314 RLPTERISQASANQRAGRAGRLAPGICYRLWSEedfarrPAFTD-------PEILRADLASLILELAAWGLGDPEDLPFL 386

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  943 DAPPMETLITAMEQLYTLGALDDEGLLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQNVFYRpkdkqa 1022
Cdd:COG1643    387 DPPPARAIADARALLQELGALDADGRLTPLGRALARLPLDPRLARMLLAAAELGCLREAAILAALLSERDPRRG------ 460

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465 1023 ladqkkakfhQTEGDHLTLLAVYNSWKNNKfsnpwcyENFIQARSLRRAQDIRKQMLGIMDRHKLDVVScgkSTVRVQKA 1102
Cdd:COG1643    461 ----------AAGSDLLARLNLWRRLREQQ-------REFLSYLRLREWRDLARQLRRLLGEGANEEPA---DYEAIGLL 520

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465 1103 ICSGFFRNAAKKDPQEGYRTLIDQQVVYIHPSSALFNRqpEWVVYHELVLTTKEY-MREVTTIDPRWLVEFAPAFFK-VS 1180
Cdd:COG1643    521 LALAYPDRIARRRGEGGRYLLARGRGAALFPGSPLAKK--EWLVAAELVGGAAEArIRLAAPIDPEWLEELAAHLIKrYS 598


                   ...
gi 1044440465 1181 DPT 1183
Cdd:COG1643    599 EPH 601
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 261-339 1.69e-43

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: 152.39  E-value: 1.69e-43
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1044440465  261 GDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTGTKTSLSMKDVDQETG 339
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; ...
 25-92 1.63e-40

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: 143.45  E-value: 1.63e-40
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1044440465   25 LEYLSLVSKVCTELDNHLGINDKDLAEFVISLAEKNTTFDTFKASLVKNGAEFTDSLISNLLRLIQTM 92
Cdd:cd21691      1 LEYLSLVSKVCTELENHLGISDKDLAEFIIDLAEKSKTLDEFKKALKENGAEFPDSFVESLLRLIQRM 68
 
Name Accession Description Interval E-value
HrpA COG1643
HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];
552-1183 0e+00

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


Pssm-ID: 441249 [Multi-domain]  Cd Length: 836  Bit Score: 576.26  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  552 MSIIEQRESLPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFG 631
Cdd:COG1643      1 MSLITYPPDLPVSAVLPELLAALRAHQVVVLAAPPGAGKTTQLPLALLELGWGAGGRIGMLEPRRLAARAAAERMAEELG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  632 CCLGQEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQK-RQDMKLI 710
Cdd:COG1643     81 EPVGETVGYRVRFEDKVSAATRIEVVTEGILLRELQRDPELEGVDTVIFDEFHERSLNADLLLALLLDLQPAlRPDLKLL 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  711 VTSATLDAVKFSQYFYEAPIFTIPGRTYPVEILYT--KEPETDYLDASLITVMQIhLTEPPGDILVFLTGQEEIDTACEI 788
Cdd:COG1643    161 VMSATLDAERFARLLGDAPVIESSGRTYPVEVRYRplPADERDLEDAVADAVREA-LAEEPGDILVFLPGEREIRRTAEA 239

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  789 LyerMKSLGPDVpelIILPVYSALPSEMQTRIFDPAPPGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKVYNSKTGID 868
Cdd:COG1643    240 L---RGRLPPDT---EILPLYGRLSAAEQDRAFAPAPHGRRRIVLATNIAETSLTVPGIRYVIDSGLARIPRYDPRSGVT 313

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  869 QLVVTPISQAQAKQRAGRAGRTGPGKCYRLYTE------RAYRDemlttnvPEIQRTNLASTVLSLKAMGINDLLSFDFM 942
Cdd:COG1643    314 RLPTERISQASANQRAGRAGRLAPGICYRLWSEedfarrPAFTD-------PEILRADLASLILELAAWGLGDPEDLPFL 386

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  943 DAPPMETLITAMEQLYTLGALDDEGLLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQNVFYRpkdkqa 1022
Cdd:COG1643    387 DPPPARAIADARALLQELGALDADGRLTPLGRALARLPLDPRLARMLLAAAELGCLREAAILAALLSERDPRRG------ 460

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465 1023 ladqkkakfhQTEGDHLTLLAVYNSWKNNKfsnpwcyENFIQARSLRRAQDIRKQMLGIMDRHKLDVVScgkSTVRVQKA 1102
Cdd:COG1643    461 ----------AAGSDLLARLNLWRRLREQQ-------REFLSYLRLREWRDLARQLRRLLGEGANEEPA---DYEAIGLL 520

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465 1103 ICSGFFRNAAKKDPQEGYRTLIDQQVVYIHPSSALFNRqpEWVVYHELVLTTKEY-MREVTTIDPRWLVEFAPAFFK-VS 1180
Cdd:COG1643    521 LALAYPDRIARRRGEGGRYLLARGRGAALFPGSPLAKK--EWLVAAELVGGAAEArIRLAAPIDPEWLEELAAHLIKrYS 598


                   ...
gi 1044440465 1181 DPT 1183
Cdd:COG1643    599 EPH 601
DEAH_box_HrpA TIGR01967
RNA helicase HrpA; This model represents HrpA, one of two related but uncharacterized DEAH-box ...
 548-1178 4.71e-158

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: 506.23  E-value: 4.71e-158
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  548 KKTQMSIIEQRESLPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVS 627
Cdd:TIGR01967   53 RRQAVPEIRYPDNLPVSAKREDIAEAIAENQVVIIAGETGSGKTTQLPKICLELGRGSHGLIGHTQPRRLAARTVAQRIA 132

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  628 EEFGCCLGQEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDM 707
Cdd:TIGR01967  133 EELGTPLGEKVGYKVRFHDQVSSNTLVKLMTDGILLAETQQDRFLSRYDTIIIDEAHERSLNIDFLLGYLKQLLPRRPDL 212

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  708 KLIVTSATLDAVKFSQYFYEAPIFTIPGRTYPVEILY------TKEPETDYLDASLITVMQIhLTEPPGDILVFLTGQEE 781
Cdd:TIGR01967  213 KIIITSATIDPERFSRHFNNAPIIEVSGRTYPVEVRYrplveeQEDDDLDQLEAILDAVDEL-FAEGPGDILIFLPGERE 291

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  782 IDTACEILYERmkslgpDVPELIILPVYSALPSEMQTRIFDPAppGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKVY 861
Cdd:TIGR01967  292 IRDAAEILRKR------NLRHTEILPLYARLSNKEQQRVFQPH--SGRRIVLATNVAETSLTVPGIHYVIDTGTARISRY 363

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  862 NSKTGIDQLVVTPISQAQAKQRAGRAGRTGPGKCYRLYTERAYRDEMLTTNvPEIQRTNLASTVLSLKAMGINDLLSFDF 941
Cdd:TIGR01967  364 SYRTKVQRLPIEPISQASANQRKGRCGRVAPGICIRLYSEEDFNSRPEFTD-PEILRTNLASVILQMLALRLGDIAAFPF 442

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  942 MDAPPMETLITAMEQLYTLGALDDE---GLLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQNVFYRPK 1018
Cdd:TIGR01967  443 IEAPDPRAIRDGFRLLEELGALDDDeaePQLTPIGRQLAQLPVDPRLARMLLEAHRLGCLQEVLIIASALSIQDPRERPM 522

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465 1019 DKQALADQKKAKFHQTEGDHLTLLAVYNSWKN-------NKFSNpWCYENFIQARSLRRAQDIRKQMLGIMDRHKLDVVS 1091
Cdd:TIGR01967  523 EKQQAADQAHARFKDPRSDFLSRVNLWRHIEEqrqalsaNQFRN-ACRKQYLNYLRVREWQDIYRQLTQVVKELGLKLNE 601

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465 1092 CGKSTVRVQKAICSGFFRNAAKKDPQEGYrTLIDQQVVYIHPSSALFNRQPEWVVYHELVLTTKEYMREVTTIDPRWLVE 1171
Cdd:TIGR01967  602 EPADYDAIHKALLSGLLSQIGMKDEKHEY-DGARGRKFHIFPGSPLFKKPPKWVMAAELVETSKLYARLVAKIEPEWVEP 680


                   ....*..
gi 1044440465 1172 FAPAFFK 1178
Cdd:TIGR01967  681 VAGHLIK 687
PRK11131 PRK11131
ATP-dependent RNA helicase HrpA; Provisional
 548-1182 5.56e-149

ATP-dependent RNA helicase HrpA; Provisional


Pssm-ID: 182986 [Multi-domain]  Cd Length: 1294  Bit Score: 482.25  E-value: 5.56e-149
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  548 KKTQMSIIEQRESLPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVS 627
Cdd:PRK11131    60 REAARPEITYPENLPVSQKKQDILEAIRDHQVVIVAGETGSGKTTQLPKICLELGRGVKGLIGHTQPRRLAARTVANRIA 139

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  628 EEFGCCLGQEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDM 707
Cdd:PRK11131   140 EELETELGGCVGYKVRFNDQVSDNTMVKLMTDGILLAEIQQDRLLMQYDTIIIDEAHERSLNIDFILGYLKELLPRRPDL 219

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  708 KLIVTSATLDAVKFSQYFYEAPIFTIPGRTYPVEILY------TKEPETDYLDASLITVMQIHlTEPPGDILVFLTGQEE 781
Cdd:PRK11131   220 KVIITSATIDPERFSRHFNNAPIIEVSGRTYPVEVRYrpiveeADDTERDQLQAIFDAVDELG-REGPGDILIFMSGERE 298

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  782 I-DTAcEILYERmkslgpDVPELIILPVYSALPSEMQTRIFDPAppGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKV 860
Cdd:PRK11131   299 IrDTA-DALNKL------NLRHTEILPLYARLSNSEQNRVFQSH--SGRRIVLATNVAETSLTVPGIKYVIDPGTARISR 369

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  861 YNSKTGIDQLVVTPISQAQAKQRAGRAGRTGPGKCYRLYTERAYRDEMLTTNvPEIQRTNLASTVLSLKAMGINDLLSFD 940
Cdd:PRK11131   370 YSYRTKVQRLPIEPISQASANQRKGRCGRVSEGICIRLYSEDDFLSRPEFTD-PEILRTNLASVILQMTALGLGDIAAFP 448

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  941 FMDAPPMETLITAMEQLYTLGALDDEG-----LLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQNVFY 1015
Cdd:PRK11131   449 FVEAPDKRNIQDGVRLLEELGAITTDEqasayKLTPLGRQLAQLPVDPRLARMVLEAQKHGCVREVMIITSALSIQDPRE 528

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465 1016 RPKDKQALADQKKAKFHQTEGDHLTLLAVYNSWK-------NNKFSNpWCYENFIQARSLRRAQDIRKQMLGIMDRHKLD 1088
Cdd:PRK11131   529 RPMDKQQASDEKHRRFADKESDFLAFVNLWNYLQeqqkalsSNQFRR-LCRTDYLNYLRVREWQDIYTQLRQVVKELGIP 607

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465 1089 VVSCGKSTVRVQKAICSGFFRNAAKKDPQEGYRTLIDQQVVYIHPSSALFNRQPEWVVYHELVLTTKEYMREVTTIDPRW 1168
Cdd:PRK11131   608 VNSEPAEYREIHTALLTGLLSHIGMKDAEKQEYTGARNARFSIFPGSGLFKKPPKWVMVAELVETSRLWGRIAARIEPEW 687

                          650
                   ....*....|....*.
gi 1044440465 1169 LVEFAPAFFK--VSDP 1182
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 ...
 556-734 3.34e-127

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: 387.61  E-value: 3.34e-127
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  556 EQRESLPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLG 635
Cdd:cd17971      1 EQRESLPIYKLKEQLIQAVHDNQILVVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVAEEFGCCLG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  636 QEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSAT 715
Cdd:cd17971     81 QEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLSQYSVIMLDEAHERTIHTDVLFGLLKKTVQKRPDLKLIVTSAT 160

                          170
                   ....*....|....*....
gi 1044440465  716 LDAVKFSQYFYEAPIFTIP 734
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 ...
 261-339 1.69e-43

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: 152.39  E-value: 1.69e-43
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1044440465  261 GDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTGTKTSLSMKDVDQETG 339
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; ...
 25-92 1.63e-40

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: 143.45  E-value: 1.63e-40
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1044440465   25 LEYLSLVSKVCTELDNHLGINDKDLAEFVISLAEKNTTFDTFKASLVKNGAEFTDSLISNLLRLIQTM 92
Cdd:cd21691      1 LEYLSLVSKVCTELENHLGISDKDLAEFIIDLAEKSKTLDEFKKALKENGAEFPDSFVESLLRLIQRM 68
HA2 smart00847
Helicase associated domain (HA2) Add an annotation; This presumed domain is about 90 amino ...
 960-1042 8.72e-34

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: 124.69  E-value: 8.72e-34
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465   960 LGALDDEGLLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQNvfYRPKDKQALADQKKAKFHQTEGDHL 1039
Cdd:smart00847    2 LGALDDDGRLTPLGRKMAELPLDPRLAKMLLAAAEFGCLDEILTIVAMLSVGD--PRPKEKREDADAARRRFADPESDHL 79


                    ...
gi 1044440465  1040 TLL 1042
Cdd:smart00847   80 TLL 82
HA2 pfam04408
Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in ...
 953-1041 1.22e-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: 119.26  E-value: 1.22e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  953 AMEQLYTLGALDDEGLLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQNVFYRP------KDKQALADQ 1026
Cdd:pfam04408    1 ALELLYYLGALDEDGELTPLGRKMAELPLDPRLAKMLLAAAELGCLDEVLTIVAALSVRDPFVQPnfldprSAAKAARRR 80

                           90       100
                   ....*....|....*....|....
gi 1044440465 1027 KKAKFHQ---------TEGDHLTL 1041
Cdd:pfam04408   81 RRAADEKarakfarldLEGDHLTL 104
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 257-335 2.65e-21

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 100.12  E-value: 2.65e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  257 EPTIGDIYNGKVTSIMQFGCFVQLegLRKRwEGLVHISELRREgRVANVADVVSKGQRVKVKVLSFT-GTKTSLSMKDVD 335
Cdd:PRK11824   618 EPEVGEIYEGKVVRIVDFGAFVEI--LPGK-DGLVHISEIADE-RVEKVEDVLKEGDEVKVKVLEIDkRGRIRLSRKAVL 693
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 256-349 3.82e-20

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


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 87.54  E-value: 3.82e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  256 EEPTIGDIYNGKVTSIMQFGCFVQLEGlrkRWEGLVHISELrREGRVANVADVVSKGQRVKVKVLSFTGT-KTSLSMKDV 334
Cdd:COG1098      1 MSIEVGDIVEGKVTGITPFGAFVELPE---GTTGLVHISEI-ADGYVKDINDYLKVGDEVKVKVLSIDEDgKISLSIKQA 76

                           90
                   ....*....|....*
gi 1044440465  335 DQETGEDLNPNRRRN 349
Cdd:COG1098     77 EEKPKRPPRPRRNSR 91
S1_dom_CvfD NF040579
CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ...
 260-348 2.61e-19

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: 84.40  E-value: 2.61e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  260 IGDIYNGKVTSIMQFGCFVQLEglrKRWEGLVHISELrREGRVANVADVVSKGQRVKVKVLS---FTGtKTSLSMKDVDQ 336
Cdd:NF040579     3 IGDIVEGKVTGIQPYGAFVALD---EHTQGLIHISEI-KHGYVKDINDFLKVGQEVKVKVLDideYTG-KISLSLRALEE 77

                           90
                   ....*....|..
gi 1044440465  337 ETGEDLNPNRRR 348
Cdd:NF040579    78 APEKHRKRRKHR 89
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
260-332 2.66e-14

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 68.78  E-value: 2.66e-14
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1044440465   260 IGDIYNGKVTSIMQFGCFVQLEGlrkRWEGLVHISELRREgRVANVADVVSKGQRVKVKVLSFTGTK--TSLSMK 332
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 ...
 258-320 1.19e-10

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: 58.45  E-value: 1.19e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1044440465  258 PTIGDIYNGKVTSIMQFGCFVQLEGLRkrwEGLVHISELRREgRVANVADVVSKGQRVKVKVL 320
Cdd:pfam00575    1 PEKGDVVEGEVTRVTKGGAFVDLGNGV---EGFIPISELSDD-HVEDPDEVIKVGDEVKVKVL 59
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 256-332 5.60e-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: 60.13  E-value: 5.60e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  256 EEPTIGDIYNGKVTSIMQFGCFVQL-EGLrkrwEGLVHISELRREGRVANVADVVSKGQRVKVKVLSF--TGTKTSLSMK 332
Cdd:TIGR00717  268 KKFPVGDKITGRVTNLTDYGVFVEIeEGI----EGLVHVSEMSWVKKNSHPSKVVKKGDEVEVMILDIdpERRRLSLGLK 343
 
Name Accession Description Interval E-value
HrpA COG1643
HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];
552-1183 0e+00

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


Pssm-ID: 441249 [Multi-domain]  Cd Length: 836  Bit Score: 576.26  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  552 MSIIEQRESLPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFG 631
Cdd:COG1643      1 MSLITYPPDLPVSAVLPELLAALRAHQVVVLAAPPGAGKTTQLPLALLELGWGAGGRIGMLEPRRLAARAAAERMAEELG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  632 CCLGQEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQK-RQDMKLI 710
Cdd:COG1643     81 EPVGETVGYRVRFEDKVSAATRIEVVTEGILLRELQRDPELEGVDTVIFDEFHERSLNADLLLALLLDLQPAlRPDLKLL 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  711 VTSATLDAVKFSQYFYEAPIFTIPGRTYPVEILYT--KEPETDYLDASLITVMQIhLTEPPGDILVFLTGQEEIDTACEI 788
Cdd:COG1643    161 VMSATLDAERFARLLGDAPVIESSGRTYPVEVRYRplPADERDLEDAVADAVREA-LAEEPGDILVFLPGEREIRRTAEA 239

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  789 LyerMKSLGPDVpelIILPVYSALPSEMQTRIFDPAPPGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKVYNSKTGID 868
Cdd:COG1643    240 L---RGRLPPDT---EILPLYGRLSAAEQDRAFAPAPHGRRRIVLATNIAETSLTVPGIRYVIDSGLARIPRYDPRSGVT 313

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  869 QLVVTPISQAQAKQRAGRAGRTGPGKCYRLYTE------RAYRDemlttnvPEIQRTNLASTVLSLKAMGINDLLSFDFM 942
Cdd:COG1643    314 RLPTERISQASANQRAGRAGRLAPGICYRLWSEedfarrPAFTD-------PEILRADLASLILELAAWGLGDPEDLPFL 386

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  943 DAPPMETLITAMEQLYTLGALDDEGLLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQNVFYRpkdkqa 1022
Cdd:COG1643    387 DPPPARAIADARALLQELGALDADGRLTPLGRALARLPLDPRLARMLLAAAELGCLREAAILAALLSERDPRRG------ 460

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465 1023 ladqkkakfhQTEGDHLTLLAVYNSWKNNKfsnpwcyENFIQARSLRRAQDIRKQMLGIMDRHKLDVVScgkSTVRVQKA 1102
Cdd:COG1643    461 ----------AAGSDLLARLNLWRRLREQQ-------REFLSYLRLREWRDLARQLRRLLGEGANEEPA---DYEAIGLL 520

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465 1103 ICSGFFRNAAKKDPQEGYRTLIDQQVVYIHPSSALFNRqpEWVVYHELVLTTKEY-MREVTTIDPRWLVEFAPAFFK-VS 1180
Cdd:COG1643    521 LALAYPDRIARRRGEGGRYLLARGRGAALFPGSPLAKK--EWLVAAELVGGAAEArIRLAAPIDPEWLEELAAHLIKrYS 598


                   ...
gi 1044440465 1181 DPT 1183
Cdd:COG1643    599 EPH 601
DEAH_box_HrpA TIGR01967
RNA helicase HrpA; This model represents HrpA, one of two related but uncharacterized DEAH-box ...
 548-1178 4.71e-158

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: 506.23  E-value: 4.71e-158
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  548 KKTQMSIIEQRESLPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVS 627
Cdd:TIGR01967   53 RRQAVPEIRYPDNLPVSAKREDIAEAIAENQVVIIAGETGSGKTTQLPKICLELGRGSHGLIGHTQPRRLAARTVAQRIA 132

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  628 EEFGCCLGQEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDM 707
Cdd:TIGR01967  133 EELGTPLGEKVGYKVRFHDQVSSNTLVKLMTDGILLAETQQDRFLSRYDTIIIDEAHERSLNIDFLLGYLKQLLPRRPDL 212

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  708 KLIVTSATLDAVKFSQYFYEAPIFTIPGRTYPVEILY------TKEPETDYLDASLITVMQIhLTEPPGDILVFLTGQEE 781
Cdd:TIGR01967  213 KIIITSATIDPERFSRHFNNAPIIEVSGRTYPVEVRYrplveeQEDDDLDQLEAILDAVDEL-FAEGPGDILIFLPGERE 291

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  782 IDTACEILYERmkslgpDVPELIILPVYSALPSEMQTRIFDPAppGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKVY 861
Cdd:TIGR01967  292 IRDAAEILRKR------NLRHTEILPLYARLSNKEQQRVFQPH--SGRRIVLATNVAETSLTVPGIHYVIDTGTARISRY 363

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  862 NSKTGIDQLVVTPISQAQAKQRAGRAGRTGPGKCYRLYTERAYRDEMLTTNvPEIQRTNLASTVLSLKAMGINDLLSFDF 941
Cdd:TIGR01967  364 SYRTKVQRLPIEPISQASANQRKGRCGRVAPGICIRLYSEEDFNSRPEFTD-PEILRTNLASVILQMLALRLGDIAAFPF 442

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  942 MDAPPMETLITAMEQLYTLGALDDE---GLLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQNVFYRPK 1018
Cdd:TIGR01967  443 IEAPDPRAIRDGFRLLEELGALDDDeaePQLTPIGRQLAQLPVDPRLARMLLEAHRLGCLQEVLIIASALSIQDPRERPM 522

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465 1019 DKQALADQKKAKFHQTEGDHLTLLAVYNSWKN-------NKFSNpWCYENFIQARSLRRAQDIRKQMLGIMDRHKLDVVS 1091
Cdd:TIGR01967  523 EKQQAADQAHARFKDPRSDFLSRVNLWRHIEEqrqalsaNQFRN-ACRKQYLNYLRVREWQDIYRQLTQVVKELGLKLNE 601

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465 1092 CGKSTVRVQKAICSGFFRNAAKKDPQEGYrTLIDQQVVYIHPSSALFNRQPEWVVYHELVLTTKEYMREVTTIDPRWLVE 1171
Cdd:TIGR01967  602 EPADYDAIHKALLSGLLSQIGMKDEKHEY-DGARGRKFHIFPGSPLFKKPPKWVMAAELVETSKLYARLVAKIEPEWVEP 680


                   ....*..
gi 1044440465 1172 FAPAFFK 1178
Cdd:TIGR01967  681 VAGHLIK 687
PRK11131 PRK11131
ATP-dependent RNA helicase HrpA; Provisional
 548-1182 5.56e-149

ATP-dependent RNA helicase HrpA; Provisional


Pssm-ID: 182986 [Multi-domain]  Cd Length: 1294  Bit Score: 482.25  E-value: 5.56e-149
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  548 KKTQMSIIEQRESLPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVS 627
Cdd:PRK11131    60 REAARPEITYPENLPVSQKKQDILEAIRDHQVVIVAGETGSGKTTQLPKICLELGRGVKGLIGHTQPRRLAARTVANRIA 139

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  628 EEFGCCLGQEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDM 707
Cdd:PRK11131   140 EELETELGGCVGYKVRFNDQVSDNTMVKLMTDGILLAEIQQDRLLMQYDTIIIDEAHERSLNIDFILGYLKELLPRRPDL 219

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  708 KLIVTSATLDAVKFSQYFYEAPIFTIPGRTYPVEILY------TKEPETDYLDASLITVMQIHlTEPPGDILVFLTGQEE 781
Cdd:PRK11131   220 KVIITSATIDPERFSRHFNNAPIIEVSGRTYPVEVRYrpiveeADDTERDQLQAIFDAVDELG-REGPGDILIFMSGERE 298

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  782 I-DTAcEILYERmkslgpDVPELIILPVYSALPSEMQTRIFDPAppGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKV 860
Cdd:PRK11131   299 IrDTA-DALNKL------NLRHTEILPLYARLSNSEQNRVFQSH--SGRRIVLATNVAETSLTVPGIKYVIDPGTARISR 369

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  861 YNSKTGIDQLVVTPISQAQAKQRAGRAGRTGPGKCYRLYTERAYRDEMLTTNvPEIQRTNLASTVLSLKAMGINDLLSFD 940
Cdd:PRK11131   370 YSYRTKVQRLPIEPISQASANQRKGRCGRVSEGICIRLYSEDDFLSRPEFTD-PEILRTNLASVILQMTALGLGDIAAFP 448

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  941 FMDAPPMETLITAMEQLYTLGALDDEG-----LLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQNVFY 1015
Cdd:PRK11131   449 FVEAPDKRNIQDGVRLLEELGAITTDEqasayKLTPLGRQLAQLPVDPRLARMVLEAQKHGCVREVMIITSALSIQDPRE 528

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465 1016 RPKDKQALADQKKAKFHQTEGDHLTLLAVYNSWK-------NNKFSNpWCYENFIQARSLRRAQDIRKQMLGIMDRHKLD 1088
Cdd:PRK11131   529 RPMDKQQASDEKHRRFADKESDFLAFVNLWNYLQeqqkalsSNQFRR-LCRTDYLNYLRVREWQDIYTQLRQVVKELGIP 607

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465 1089 VVSCGKSTVRVQKAICSGFFRNAAKKDPQEGYRTLIDQQVVYIHPSSALFNRQPEWVVYHELVLTTKEYMREVTTIDPRW 1168
Cdd:PRK11131   608 VNSEPAEYREIHTALLTGLLSHIGMKDAEKQEYTGARNARFSIFPGSGLFKKPPKWVMVAELVETSRLWGRIAARIEPEW 687

                          650
                   ....*....|....*.
gi 1044440465 1169 LVEFAPAFFK--VSDP 1182
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 ...
 556-734 3.34e-127

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: 387.61  E-value: 3.34e-127
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  556 EQRESLPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLG 635
Cdd:cd17971      1 EQRESLPIYKLKEQLIQAVHDNQILVVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVAEEFGCCLG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  636 QEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSAT 715
Cdd:cd17971     81 QEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLSQYSVIMLDEAHERTIHTDVLFGLLKKTVQKRPDLKLIVTSAT 160

                          170
                   ....*....|....*....
gi 1044440465  716 LDAVKFSQYFYEAPIFTIP 734
Cdd:cd17971    161 LDAVKFSQYFYEAPIFTIP 179
DEAH_box_HrpB TIGR01970
ATP-dependent helicase HrpB; This model represents HrpB, one of two related but ...
 561-1008 1.02e-103

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: 347.14  E-value: 1.02e-103
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  561 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQIT-QYLAEAGYTsrGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQEVG 639
Cdd:TIGR01970    1 LPIHAVLPALRDALAAHPQVVLEAPPGAGKSTAVPlALLDAPGIG--GKIIMLEPRRLAARSAAQRLASQLGEAVGQTVG 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  640 YTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKtVQK--RQDMKLIVTSATLD 717
Cdd:TIGR01970   79 YRVRGENKVSRRTRLEVVTEGILTRMIQDDPELDGVGALIFDEFHERSLDADLGLALALD-VQSslREDLKILAMSATLD 157

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  718 AVKFSQYFYEAPIFTIPGRTYPVEILYTKEPETDYLDASLITVMQIHLTEPPGDILVFLTGQEEIDTACEILYERmksLG 797
Cdd:TIGR01970  158 GERLSSLLPDAPVVESEGRSFPVEIRYLPLRGDQRLEDAVSRAVEHALASETGSILVFLPGQAEIRRVQEQLAER---LD 234

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  798 PDVpelIILPVYSALPSEMQTRIFDPAPPGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKVYNSKTGIDQLVVTPISQ 877
Cdd:TIGR01970  235 SDV---LICPLYGELSLAAQDRAIKPDPQGRRKVVLATNIAETSLTIEGIRVVIDSGLARVARFDPKTGITRLETVRISQ 311

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  878 AQAKQRAGRAGRTGPGKCYRLYTErAYRDEMLTTNVPEIQRTNLASTVLSLKAMGINDLLSFDFMDAPPMETLITAMEQL 957
Cdd:TIGR01970  312 ASATQRAGRAGRLEPGVCYRLWSE-EQHQRLPAQDEPEILQADLSGLALELAQWGAKDPSDLRWLDAPPSVALAAARQLL 390

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1044440465  958 YTLGALDDEGLLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSML 1008
Cdd:TIGR01970  391 QRLGALDAQGRLTAHGKAMAALGCHPRLAAMLLSAHSTGLAALACDLAALL 441
PRK11664 PRK11664
ATP-dependent RNA helicase HrpB; Provisional
 560-990 1.89e-94

ATP-dependent RNA helicase HrpB; Provisional


Pssm-ID: 236950 [Multi-domain]  Cd Length: 812  Bit Score: 321.49  E-value: 1.89e-94
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  560 SLPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQIT-QYLAEAGYTsrGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQEV 638
Cdd:PRK11664     3 SLPVAAVLPELLTALKTAPQVLLKAPTGAGKSTWLPlQLLQHGGIN--GKIIMLEPRRLAARNVAQRLAEQLGEKPGETV 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  639 GYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKtVQK--RQDMKLIVTSATL 716
Cdd:PRK11664    81 GYRMRAESKVGPNTRLEVVTEGILTRMIQRDPELSGVGLVILDEFHERSLQADLALALLLD-VQQglRDDLKLLIMSATL 159

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  717 DAVKFSQYFYEAPIFTIPGRTYPVEILYTKEPETDYLDASLITVMQIHLTEPPGDILVFLTGQEEIDTACEILYERmksL 796
Cdd:PRK11664   160 DNDRLQQLLPDAPVIVSEGRSFPVERRYQPLPAHQRFDEAVARATAELLRQESGSLLLFLPGVGEIQRVQEQLASR---V 236

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  797 GPDVpelIILPVYSALPSEMQTRIFDPAPPGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKVYNSKTGIDQLVVTPIS 876
Cdd:PRK11664   237 ASDV---LLCPLYGALSLAEQQKAILPAPAGRRKVVLATNIAETSLTIEGIRLVVDSGLERVARFDPKTGLTRLVTQRIS 313

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  877 QAQAKQRAGRAGRTGPGKCYRLYTERAYrDEMLTTNVPEIQRTNLASTVLSLKAMGINDLLSFDFMDAPPMETLITAMEQ 956
Cdd:PRK11664   314 QASMTQRAGRAGRLEPGICLHLYSKEQA-ERAAAQSEPEILHSDLSGLLLELLQWGCHDPAQLSWLDQPPAAALAAAKRL 392

                          410       420       430
                   ....*....|....*....|....*....|....
gi 1044440465  957 LYTLGALDDEGLLTRLGRRMAEFPLEPMLCKMLI 990
Cdd:PRK11664   393 LQQLGALDGQGRLTARGRKMAALGNDPRLAAMLV 426
DEXHc_DHX38 cd17983
DEXH-box helicase domain of DEAH-box helicase 38; DEAH-box helicase 38 (DHX38, also known as ...
 561-733 2.41e-94

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: 299.38  E-value: 2.41e-94
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  561 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQEVGY 640
Cdd:cd17983      1 LPIFAVRQELLNVIRDNNVVIVVGETGSGKTTQLTQYLHEDGYTDYGMIGCTQPRRVAAMSVAKRVSEEMGVELGEEVGY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  641 TIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSATLDAVK 720
Cdd:cd17983     81 AIRFEDCTSENTVIKYMTDGILLRESLRDPDLDKYSAIIMDEAHERSLNTDVLFGLLREVVARRRDLKLIVTSATMDADK 160

                          170
                   ....*....|...
gi 1044440465  721 FSQYFYEAPIFTI 733
Cdd:cd17983    161 FADFFGNVPIFTI 173
DEXHc_DHX16 cd17974
DEXH-box helicase domain of DEAH-box helicase 16; DEAH-box helicase 16 (DHX16) is probably ...
 561-733 4.08e-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: 284.78  E-value: 4.08e-89
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  561 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRG-KIGCTQPRRVAAMSVAKRVSEEFGCCLGQEVG 639
Cdd:cd17974      1 LPVYPYRDDLLAAVKEHQVLIIVGETGSGKTTQIPQYLHEAGYTKGGgKIGCTQPRRVAAMSVAARVAEEMGVKLGNEVG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  640 YTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSATLDAV 719
Cdd:cd17974     81 YSIRFEDCTSEKTVLKYMTDGMLLREFLTEPDLASYSVMIIDEAHERTLHTDILFGLVKDIARFRPDLKLLISSATMDAE 160

                          170
                   ....*....|....
gi 1044440465  720 KFSQYFYEAPIFTI 733
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) ...
 577-733 1.35e-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: 280.11  E-value: 1.35e-87
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  577 NQILIVIGETGSGKTTQITQYLAEAGYTS--RGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQEVGYTIRFEDCTSPETVI 654
Cdd:cd17917      1 NQVVVIVGETGSGKTTQVPQFLLEDGLAKggKGRIVCTQPRRIAAISVAERVAEERGEKLGEEVGYQIRFESKTSSKTRI 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1044440465  655 KYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSATLDAVKFSQYFYEAPIFTI 733
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 ...
 738-899 2.35e-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: 277.11  E-value: 2.35e-86
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  738 YPVEILYTKEP-----------ETDYLDASLITVMQIHLTEPPGDILVFLTGQEEIDTACEILYERMKSlgPDVPELIIL 806
Cdd:cd18791      1 FPVEVYYLEDIlellgissekeDPDYVDAAVRLILQIHRTEEPGDILVFLPGQEEIERLCELLREELLS--PDLGKLLVL 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  807 PVYSALPSEMQTRIFDPAPPGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKVYNSKTGIDQLVVTPISQAQAKQRAGR 886
Cdd:cd18791     79 PLHSSLPPEEQQRVFEPPPPGVRKVVLATNIAETSITIPGVVYVIDSGLVKEKVYDPRTGLSSLVTVWISKASAEQRAGR 158

                          170
                   ....*....|...
gi 1044440465  887 AGRTGPGKCYRLY 899
Cdd:cd18791    159 AGRTRPGKCYRLY 171
DEXHc_DHX33 cd17978
DEXH-box helicase domain of DEAH-box helicase 33; DEAH-box helicase 33 (DHX33) stimulates RNA ...
 561-733 4.88e-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: 276.54  E-value: 4.88e-86
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  561 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQEVGY 640
Cdd:cd17978      1 LPIYSARKRLLEELRKHDTVIIIGETGSGKTTQIPQYLYEAGFARGGMIGITQPRRVAAVSVAKRVAEEMGVELGQLVGY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  641 TIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKtVQKR------QDMKLIVTSA 714
Cdd:cd17978     81 SVRFDDVTSEETRIKYMTDGMLLREAIGDPLLSKYSVIILDEAHERTVHTDVLFGLVKS-AQRRrkeqklSPLKVIIMSA 159

                          170
                   ....*....|....*....
gi 1044440465  715 TLDAVKFSQYFYEAPIFTI 733
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 ...
 554-733 9.39e-83

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: 267.74  E-value: 9.39e-83
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  554 IIEQRESLPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGK--IGCTQPRRVAAMSVAKRVSEEFG 631
Cdd:cd17973      6 ILEKRRELPVWEQKEDFLKLLKNNQILVLVGETGSGKTTQIPQFVLDDELPHQPKklVACTQPRRVAAMSVAQRVAEEMD 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  632 CCLGQEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIV 711
Cdd:cd17973     86 VKLGEEVGYSIRFEDCSSAKTILKYMTDGMLLREAMSDPLLSRYSVIILDEAHERTLATDILMGLLKEVVRRRPDLKLIV 165

                          170       180
                   ....*....|....*....|..
gi 1044440465  712 TSATLDAVKFSQYFYEAPIFTI 733
Cdd:cd17973    166 MSATLDAGKFQKYFDNAPLLKV 187
DEXHc_DHX35 cd17980
DEXH-box helicase domain of DEAH-box helicase 35; DHX35 plays a role in colorectal cancers and ...
 561-725 8.73e-76

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: 248.54  E-value: 8.73e-76
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  561 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGK-IGCTQPRRVAAMSVAKRVSEEFGCCLGQEVG 639
Cdd:cd17980      1 LPVFKLRNHILYLVENYQTIVIVGETGCGKSTQIPQYLAEAGWTAGGRvVGCTQPRRVAAVTVAGRVAEEMGAVLGHEVG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  640 YTIRFEDCTSP-ETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSATLDA 718
Cdd:cd17980     81 YCIRFDDCTDPqATRIKFLTDGMLVREMMLDPLLTKYSVIMLDEAHERTLYTDILIGLLKKIQKKRGDLRLIVASATLDA 160


                   ....*..
gi 1044440465  719 VKFSQYF 725
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 ...
 561-733 1.44e-75

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: 247.46  E-value: 1.44e-75
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  561 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQEVGY 640
Cdd:cd17984      1 LPIQKQRKKLVQAVRDNSFLIVTGNTGSGKTTQLPKYLYEAGFSQHGMIGVTQPRRVAAISVAQRVAEEMKCTLGSKVGY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  641 TIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQ-----DMKLIVTSAT 715
Cdd:cd17984     81 QVRFDDCSSKETAIKYMTDGCLLRHILADPNLTKYSVIILDEAHERSLTTDILFGLLKKLFQEKSpnrkeHLKVVVMSAT 160

                          170
                   ....*....|....*...
gi 1044440465  716 LDAVKFSQYFYEAPIFTI 733
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 ...
 561-730 2.76e-60

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: 204.23  E-value: 2.76e-60
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  561 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQEVGY 640
Cdd:cd17989      1 LPVSQKRDEIAKAIAENQVVIIAGETGSGKTTQLPKICLELGRGIRGLIGHTQPRRLAARSVAERIAEELKTELGGAVGY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  641 TIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSATLDAVK 720
Cdd:cd17989     81 KVRFTDQTSDETCVKLMTDGILLAETQTDRYLRAYDTIIIDEAHERSLNIDFLLGYLKQLLPRRPDLKVIITSATIDAER 160

                          170
                   ....*....|
gi 1044440465  721 FSQYFYEAPI 730
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 ...
 561-723 9.26e-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: 197.58  E-value: 9.26e-58
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  561 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSR-----GKIGCTQPRRVAAMSVAKRVSEEFGCcLG 635
Cdd:cd17982      1 LPILAEEQEIMEAINENPVVIICGETGSGKTTQVPQFLYEAGFGSPesdnpGMIGITQPRRVAAVSMAKRVAEELNV-FG 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  636 QEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDM-------- 707
Cdd:cd17982     80 KEVSYQIRYDSTVSENTKIKFMTDGVLLKEIQTDFLLRKYSVIIIDEAHERSVNTDILIGMLSRIVPLRAKLylqdqtvk 159

                          170
                   ....*....|....*...
gi 1044440465  708 --KLIVTSATLDAVKFSQ 723
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 ...
 561-730 1.73e-54

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: 187.26  E-value: 1.73e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  561 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSrgkIGCTQPRRVAAMSVAKRVSEEFGCCLGQEVGY 640
Cdd:cd17979      1 LPIAQYREKIIELLKTHQVVIVAGDTGCGKSTQVPQYLLAAGFRH---IACTQPRRIACISLAKRVAFESLNQYGSKVAY 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  641 TIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSATLDAVK 720
Cdd:cd17979     78 QIRFERTRTLATKLLFLTEGLLLRQIQRDASLPQYNVLILDEVHERHLHGDFLLGVLRCLLRLRPDLKLILMSATINIEL 157

                          170
                   ....*....|
gi 1044440465  721 FSQYFYEAPI 730
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 ...
 561-733 7.77e-48

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: 168.87  E-value: 7.77e-48
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  561 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEaGYTSRGK-----IGCTQPRRVAAMSVAKRVSEEFG--CC 633
Cdd:cd17981      1 LPSYGMKQEIINMIDNNQVTVISGETGCGKTTQVTQFILD-DAIERGKgsscrIVCTQPRRISAISVAERVAAERAesCG 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  634 LGQEVGYTIRFEDCTSPETV-IKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVT 712
Cdd:cd17981     80 LGNSTGYQIRLESRKPRKQGsILYCTTGIVLQWLQSDPHLSNVSHLVLDEIHERNLQSDVLMGIVKDLLPFRSDLKVILM 159

                          170       180
                   ....*....|....*....|.
gi 1044440465  713 SATLDAVKFSQYFYEAPIFTI 733
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 ...
 561-733 7.02e-47

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: 166.24  E-value: 7.02e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  561 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAE-----AGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLG 635
Cdd:cd17975      1 LPVFKHRESILETLKRHRVVVVAGETGSGKSTQVPQFLLEdlllnGGTAQKCNIVCTQPRRISAMSLATRVCEELGCESG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  636 -----QEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLI 710
Cdd:cd17975     81 pggknSLCGYQIRMESRTGEATRLLYCTTGVLLRKLQEDGLLSSISHIIVDEVHERSVQSDFLLIILKEILHKRSDLHLI 160

                          170       180
                   ....*....|....*....|...
gi 1044440465  711 VTSATLDAVKFSQYFYEAPIFTI 733
Cdd:cd17975    161 LMSATVDCEKFSSYFTHCPILRI 183
DEXHc_YTHDC2 cd17987
DEXH-box helicase domain of YTH domain containing 2; YTH domain containing 2 (YTHDC2) ...
 561-733 3.58e-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: 163.85  E-value: 3.58e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  561 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRG--KIGCTQPRRVAAMSVAKRVSEEFGCCLGQEV 638
Cdd:cd17987      1 LPVFEKQEQIVRIIKENKVVLIVGETGSGKTTQIPQFLLDDCYANGIpcRIFCTQPRRLAAIAVAERVAAERGEKIGQTV 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  639 GYTIRFEDCTSPETVIKYMTDGMLLRECLI-DPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSATLD 717
Cdd:cd17987     81 GYQIRLESRVSPKTLLTFCTNGVLLRTLMAgDSALSTVTHVIVDEVHERDRFSDFLLTKLRDILQKHPNLKLILSSAALD 160

                          170
                   ....*....|....*.
gi 1044440465  718 AVKFSQYFYEAPIFTI 733
Cdd:cd17987    161 VNLFIRYFGSCPVIYI 176
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 261-339 1.69e-43

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: 152.39  E-value: 1.69e-43
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1044440465  261 GDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTGTKTSLSMKDVDQETG 339
Cdd:cd05684      1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQNGKISLSMKDVDQDTG 79
DEXHc_DHX32 cd17977
DEXH-box helicase domain of DEAH-box helicase 32; DEAH-box helicase 32 (DHX32) belongs to the ...
 561-730 2.51e-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: 152.67  E-value: 2.51e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  561 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAE---AGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQE 637
Cdd:cd17977      1 LPVWEAKYEFMESLAHNQIVIVSGDAKTGKSSQIPQWCAEyclSAHYQHGVVVCTQVHKQTAVWLALRVADEMDVNIGHE 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  638 VGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSATLD 717
Cdd:cd17977     81 VGYVIPFENCCTNETILRYCTDDMLLREMMSDPLLESYGVIILDDAHERTVSTDVLLGLLKDVLLSRPELKLVIITCPHL 160

                          170
                   ....*....|...
gi 1044440465  718 AVKFSQYFYEAPI 730
Cdd:cd17977    161 SSKLLSYYGNVPL 173
DEXHc_DHX9 cd17972
DEXH-box helicase domain of DEAH-box helicase 9; DEAH-box helicase 9 (DHX9, also known as ...
 554-733 2.68e-42

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: 154.99  E-value: 2.68e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  554 IIEQRESLPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAE----AGYTSRGKIGCTQPRRVAAMSVAKRVSEE 629
Cdd:cd17972     52 ILQERELLPVKKFREEILEAISNNPVVIIRGATGCGKTTQVPQYILDdfiqNDRAAECNIVVTQPRRISAVSVAERVAFE 131

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  630 FGCCLGQEVGYTIRFEDCT-SPETVIKYMTDGMLLREclIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMK 708
Cdd:cd17972    132 RGEEVGKSCGYSVRFESVLpRPHASILFCTVGVLLRK--LEAGIRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPDLR 209

                          170       180
                   ....*....|....*....|....*
gi 1044440465  709 LIVTSATLDAVKFSQYFYEAPIFTI 733
Cdd:cd17972    210 VILMSATIDTSMFCEYFFNCPVIEV 234
DEXHc_HrpB cd17990
DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA ...
 561-731 1.43e-41

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: 150.56  E-value: 1.43e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  561 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQEVGY 640
Cdd:cd17990      1 LPIAAVLPALRAALDAGGQVVLEAPPGAGKTTRVPLALLAELWIAGGKIIVLEPRRVAARAAARRLATLLGEAPGETVGY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  641 TIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQ-KRQDMKLIVTSATLDAV 719
Cdd:cd17990     81 RVRGESRVGRRTRVEVVTEGVLLRRLQRDPELSGVGAVILDEFHERSLDADLALALLLEVQQlLRDDLRLLAMSATLDGD 160

                          170
                   ....*....|..
gi 1044440465  720 KFSQYFYEAPIF 731
Cdd:cd17990    161 GLAALLPEAPVV 172
DEXHc_DHX57 cd17985
DEXH-box helicase domain of DEAH-box helicase 57; DEAH-box helicase 57 (DHX57) belongs to the ...
 561-733 5.39e-41

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: 148.84  E-value: 5.39e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  561 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEA----GYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQ 636
Cdd:cd17985      1 LPAWQERETILELLEKHQVLVISGMTGCGKTTQIPQFILDNslqgPPLPVANIICTQPRRISAISVAERVAQERAERVGQ 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  637 EVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSATL 716
Cdd:cd17985     81 SVGYQIRLESVKSSATRLLYCTTGVLLRRLEGDPTLQGVTHVIVDEVHERTEESDFLLLVLKDLMVQRPDLKVILMSATL 160

                          170
                   ....*....|....*..
gi 1044440465  717 DAVKFSQYFYEAPIFTI 733
Cdd:cd17985    161 NAELFSDYFNSCPVIHI 177
GH2-like_DHX8 cd21691
GIPC-homology 2 (GH2)-like domain found in DEAH box protein 8 (DHX8) and similar proteins; ...
 25-92 1.63e-40

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: 143.45  E-value: 1.63e-40
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1044440465   25 LEYLSLVSKVCTELDNHLGINDKDLAEFVISLAEKNTTFDTFKASLVKNGAEFTDSLISNLLRLIQTM 92
Cdd:cd21691      1 LEYLSLVSKVCTELENHLGISDKDLAEFIIDLAEKSKTLDEFKKALKENGAEFPDSFVESLLRLIQRM 68
DEXHc_TDRD9 cd17988
DEXH-box helicase domain of tudor domain containing 9; Tudor domain containing 9 (TDRD9, also ...
 561-733 1.07e-39

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: 145.34  E-value: 1.07e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  561 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAgYTSRGK---IGCTQPRRVAAMSVAKRVSEEFGCCLGQE 637
Cdd:cd17988      1 LPIYAKREEILSLIEANSVVIIKGATGCGKTTQLPQFILDH-YYKRGKycnIVVTQPRRIAAISIARRVSQEREWTLGSL 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  638 VGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQ-KRQDMKLIVTSATL 716
Cdd:cd17988     80 VGYQVGLERPASEETRLIYCTTGVLLQKLINNKTLTEYTHIILDEVHERDQELDFLLLVVRRLLRtNSRHVKIILMSATI 159

                          170       180
                   ....*....|....*....|.
gi 1044440465  717 DAVKFSQYF----YEAPIFTI 733
Cdd:cd17988    160 SCKEFADYFttpnNPAYVFEV 180
DEXQc_DQX1 cd17986
DEXQ-box helicase domain of DEAQ-box RNA dependent ATPase 1; DEAQ-box RNA dependent ATPase 1 ...
 561-733 4.18e-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: 143.50  E-value: 4.18e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  561 LPIYKLKEQLVQAVHDNQ-ILIVIGETGSGKTTQITQYLAEAGYT---SRGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQ 636
Cdd:cd17986      1 LPIWAAKFTFLEQLESPSgIVLVSGEPGSGKSTQVPQWCAEFALSrgfQKGQVTVTQPHPLAARSLALRVADEMDLNLGH 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  637 EVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKL-IVTSAT 715
Cdd:cd17986     81 EVGYSIPQEDCTGPNTILRFCWDRLLLQEMTSTPLLGAWGVVVLDEAQERSVASDSLLGLLKDVRLQRPELRVvVVTSPA 160

                          170
                   ....*....|....*...
gi 1044440465  716 LDAvKFSQYFYEAPIFTI 733
Cdd:cd17986    161 LEP-KLRAFWGNPPVVHV 177
DEXHc_DHX30 cd17976
DEXH-box helicase domain of DEAH-box helicase 30; DEAH-box helicase 30 (DHX30) plays an ...
 561-730 5.60e-37

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: 137.62  E-value: 5.60e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  561 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGC----TQPRRVAAMSVAKRVSEEFGCCLGQ 636
Cdd:cd17976      1 LPVDSHKESILSAIEQNPVVVISGDTGCGKTTRIPQFILEDYVLRGRGARCnvviTQPRRISAVSVAQRVAHELGPNLRR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  637 EVGYTIRFEDCTSPET-VIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSAT 715
Cdd:cd17976     81 NVGYQVRLESRPPPRGgALLFCTVGVLLKKLQSNPRLEGVSHVIVDEVHERDVNTDFLLILLKGVLQLNPELRVVLMSAT 160

                          170
                   ....*....|....*
gi 1044440465  716 LDAVKFSQYFYEAPI 730
Cdd:cd17976    161 GDNQRLSRYFGGCPV 175
HA2 smart00847
Helicase associated domain (HA2) Add an annotation; This presumed domain is about 90 amino ...
 960-1042 8.72e-34

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: 124.69  E-value: 8.72e-34
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465   960 LGALDDEGLLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQNvfYRPKDKQALADQKKAKFHQTEGDHL 1039
Cdd:smart00847    2 LGALDDDGRLTPLGRKMAELPLDPRLAKMLLAAAEFGCLDEILTIVAMLSVGD--PRPKEKREDADAARRRFADPESDHL 79


                    ...
gi 1044440465  1040 TLL 1042
Cdd:smart00847   80 TLL 82
HA2 pfam04408
Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in ...
 953-1041 1.22e-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: 119.26  E-value: 1.22e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  953 AMEQLYTLGALDDEGLLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQNVFYRP------KDKQALADQ 1026
Cdd:pfam04408    1 ALELLYYLGALDEDGELTPLGRKMAELPLDPRLAKMLLAAAELGCLDEVLTIVAALSVRDPFVQPnfldprSAAKAARRR 80

                           90       100
                   ....*....|....*....|....
gi 1044440465 1027 KKAKFHQ---------TEGDHLTL 1041
Cdd:pfam04408   81 RRAADEKarakfarldLEGDHLTL 104
OB_NTP_bind pfam07717
Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus ...
 1099-1175 1.69e-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: 1.69e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465 1099 VQKAICSGFFRNAAKKDPQE-GYRTLIDQQVVYIHPSSALFN---RQPEWVVYHELVLTTKEYMREVTTIDPRWLVEFAP 1174
Cdd:pfam07717    1 LRAALAAGLYPNVARRDPKGkGYTTLSDNQRVFIHPSSVLFNektFPPEWVVYQELVETTKVYIRTVTAISPEWLLLFAP 80


                   .
gi 1044440465 1175 A 1175
Cdd:pfam07717   81 H 81
DEXDc smart00487
DEAD-like helicases superfamily;
557-742 4.78e-27

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 109.89  E-value: 4.78e-27
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465   557 QRESLPIyklkeqlvqAVHDNQILIVIGETGSGKTTQITQYLAEAGY-TSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLG 635
Cdd:smart00487   13 QKEAIEA---------LLSGLRDVILAAPTGSGKTLAALLPALEALKrGKGGRVLVLVPTRELAEQWAEELKKLGPSLGL 83

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465   636 QEVGYT------IRFEDCTSPETVIKYMTDGMLLRECLIDP-DLTQYAIIMLDEAHERT--IHTDVLFGLLKKTVQKRQd 706
Cdd:smart00487   84 KVVGLYggdskrEQLRKLESGKTDILVTTPGRLLDLLENDKlSLSNVDLVILDEAHRLLdgGFGDQLEKLLKLLPKNVQ- 162

                           170       180       190
                    ....*....|....*....|....*....|....*...
gi 1044440465   707 mkLIVTSATL--DAVKFSQYFYEAPIFTIPGRTYPVEI 742
Cdd:smart00487  163 --LLLLSATPpeEIENLLELFLNDPVFIDVGFTPLEPI 198
GH2_like cd21690
GIPC homology 2 (GH2) domain-like family; The GIPC (GAIP C-terminus-interacting protein) ...
 28-89 7.71e-24

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: 95.62  E-value: 7.71e-24
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1044440465   28 LSLVSKVCTELDNHLGINDKDLAEFVISLAEKNTTFDTFKASLVKNGAEFTDSLISNLLRLI 89
Cdd:cd21690      1 LSAIEKVDDLLKNYLGIDDPELAEFVISLAKKKKNPDEFAEALDENDAAFPDEFVFDLYRAI 62
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 257-335 2.65e-21

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 100.12  E-value: 2.65e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  257 EPTIGDIYNGKVTSIMQFGCFVQLegLRKRwEGLVHISELRREgRVANVADVVSKGQRVKVKVLSFT-GTKTSLSMKDVD 335
Cdd:PRK11824   618 EPEVGEIYEGKVVRIVDFGAFVEI--LPGK-DGLVHISEIADE-RVEKVEDVLKEGDEVKVKVLEIDkRGRIRLSRKAVL 693
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 261-331 1.22e-20

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: 86.83  E-value: 1.22e-20
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1044440465  261 GDIYNGKVTSIMQFGCFVQLEGLRkrwEGLVHISELRREgRVANVADVVSKGQRVKVKVLSF-TGTKTSLSM 331
Cdd:cd04472      1 GKIYEGKVVKIKDFGAFVEILPGK---DGLVHISELSDE-RVEKVEDVLKVGDEVKVKVIEVdDRGRISLSR 68
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 256-349 3.82e-20

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


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 87.54  E-value: 3.82e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  256 EEPTIGDIYNGKVTSIMQFGCFVQLEGlrkRWEGLVHISELrREGRVANVADVVSKGQRVKVKVLSFTGT-KTSLSMKDV 334
Cdd:COG1098      1 MSIEVGDIVEGKVTGITPFGAFVELPE---GTTGLVHISEI-ADGYVKDINDYLKVGDEVKVKVLSIDEDgKISLSIKQA 76

                           90
                   ....*....|....*
gi 1044440465  335 DQETGEDLNPNRRRN 349
Cdd:COG1098     77 EEKPKRPPRPRRNSR 91
S1_dom_CvfD NF040579
CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ...
 260-348 2.61e-19

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: 84.40  E-value: 2.61e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  260 IGDIYNGKVTSIMQFGCFVQLEglrKRWEGLVHISELrREGRVANVADVVSKGQRVKVKVLS---FTGtKTSLSMKDVDQ 336
Cdd:NF040579     3 IGDIVEGKVTGIQPYGAFVALD---EHTQGLIHISEI-KHGYVKDINDFLKVGQEVKVKVLDideYTG-KISLSLRALEE 77

                           90
                   ....*....|..
gi 1044440465  337 ETGEDLNPNRRR 348
Cdd:NF040579    78 APEKHRKRRKHR 89
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 260-334 1.39e-18

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: 88.56  E-value: 1.39e-18
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1044440465  260 IGDIYNGKVTSIMQFGCFVQLE-GLrkrwEGLVHISELRREGRVANVADVVSKGQRVKVKVLSF--TGTKTSLSMKDV 334
Cdd:COG0539    274 VGDVVKGKVTRLTDFGAFVELEpGV----EGLVHISEMSWTKRVAHPSDVVKVGDEVEVKVLDIdpEERRISLSIKQL 347
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 260-333 9.08e-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: 83.17  E-value: 9.08e-17
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1044440465  260 IGDIYNGKVTSIMQFGCFVQLEGLrkrwEGLVHISELRReGRVANVADVVSKGQRVKVKVLSF--TGTKTSLSMKD 333
Cdd:COG0539    189 EGDVVEGTVKNITDFGAFVDLGGV----DGLLHISEISW-GRVKHPSEVLKVGDEVEVKVLKIdrEKERISLSLKQ 259
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
255-340 2.47e-16

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 84.23  E-value: 2.47e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  255 PEEPTIGDIYNGKVTSIMQFGCFVQLE-GLrkrwEGLVHISELrREGRVANVADVVSKGQRVKVKVLSFTGT--KTSLSM 331
Cdd:PRK00087   557 EEKYPVGSIVLGKVVRIAPFGAFVELEpGV----DGLVHISQI-SWKRIDKPEDVLSEGEEVKAKILEVDPEekRIRLSI 631


                   ....*....
gi 1044440465  332 KDVDQETGE 340
Cdd:PRK00087   632 KEVEEEPGD 640
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 261-334 4.12e-15

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 78.76  E-value: 4.12e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1044440465  261 GDIYNGKVTSIMQFGCFVQLEGLrkrwEGLVHISELRREgRVANVADVVSKGQRVKVKVLSF---TGtKTSLSMKDV 334
Cdd:PRK06676   193 GDVVEGTVARLTDFGAFVDIGGV----DGLVHISELSHE-RVEKPSEVVSVGQEVEVKVLSIdweTE-RISLSLKDT 263
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 261-332 4.54e-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: 70.78  E-value: 4.54e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1044440465  261 GDIYNGKVTSIMQFGCFVQL-EGLrkrwEGLVHISELRREgRVANVADVVSKGQRVKVKVLSFTGT-KTSLSMK 332
Cdd:cd05692      1 GSVVEGTVTRLKPFGAFVELgGGI----SGLVHISQIAHK-RVKDVKDVLKEGDKVKVKVLSIDARgRISLSIK 69
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 261-360 7.74e-15

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 77.99  E-value: 7.74e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  261 GDIYNGKVTSIMQFGCFVQL-EGLrkrwEGLVHISELRREgRVANVADVVSKGQRVKVKVLSF--TGTKTSLSMKDVDQE 337
Cdd:PRK06676   278 GDVIEGTVKRLTDFGAFVEVlPGV----EGLVHISQISHK-HIATPSEVLEEGQEVKVKVLEVneEEKRISLSIKALEEA 352

                           90       100
                   ....*....|....*....|...
gi 1044440465  338 TGEDLNPNRRRNLVGETNEETSM 360
Cdd:PRK06676   353 PAEEEDRREEYRQYELPEEETGF 375
HELICc smart00490
helicase superfamily c-terminal domain;
787-891 1.03e-14

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 70.32  E-value: 1.03e-14
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465   787 EILYERMKSLGpdvpeLIILPVYSALPSEMQTRIFDPAPPGSRKVVIATNIAETSLTIDGIYYVVDPGFvkqkvynsktg 866
Cdd:smart00490    1 EELAELLKELG-----IKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDL----------- 64

                            90       100
                    ....*....|....*....|....*
gi 1044440465   867 idqlvvtPISQAQAKQRAGRAGRTG 891
Cdd:smart00490   65 -------PWSPASYIQRIGRAGRAG 82
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
260-332 2.66e-14

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 68.78  E-value: 2.66e-14
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1044440465   260 IGDIYNGKVTSIMQFGCFVQLEGlrkRWEGLVHISELRREgRVANVADVVSKGQRVKVKVLSFTGTK--TSLSMK 332
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGN---GVEGLIPISELSDK-RVKDPEEVLKVGDEVKVKVLSVDEEKgrIILSLK 72
PRK08059 PRK08059
general stress protein 13; Validated
 259-363 7.34e-14

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 69.31  E-value: 7.34e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  259 TIGDIYNGKVTSIMQFGCFVQLEGlrkRWEGLVHISELrREGRVANVADVVSKGQRVKVKVLSF--TGTKTSLSMKdvdq 336
Cdd:PRK08059     6 EVGSVVTGKVTGIQPYGAFVALDE---ETQGLVHISEI-THGFVKDIHDFLSVGDEVKVKVLSVdeEKGKISLSIR---- 77

                           90       100
                   ....*....|....*....|....*..
gi 1044440465  337 ETGEDLNPNRRRNLVGETNEETSMRNP 363
Cdd:PRK08059    78 ATEEAPEAKRKKGKILIPNPSEQGFNT 104
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 260-332 1.67e-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: 66.50  E-value: 1.67e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1044440465  260 IGDIYNGKVTSIMQFGCFVQLEGLrkrwEGLVHISELRReGRVANVADVVSKGQRVKVKVLSFTGTKTSLSMK 332
Cdd:cd05688      1 EGDVVEGTVKSITDFGAFVDLGGV----DGLLHISDMSW-GRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 757-891 1.26e-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: 1.26e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  757 LITVMQIHLTEPPGDILVFLTGQEEIDtaCEILYERMKslgpdvpeLIILPVYSALPSEMQTRIFDPAPPGSRKVVIATN 836
Cdd:pfam00271    3 LEALLELLKKERGGKVLIFSQTKKTLE--AELLLEKEG--------IKVARLHGDLSQEEREEILEDFRKGKIDVLVATD 72

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1044440465  837 IAETSLTIDGIYYVVDpgfvkqkvYNSKTGIDQLVvtpisqaqakQRAGRAGRTG 891
Cdd:pfam00271   73 VAERGLDLPDVDLVIN--------YDLPWNPASYI----------QRIGRAGRAG 109
PRK08582 PRK08582
RNA-binding protein S1;
266-357 4.61e-12

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 64.67  E-value: 4.61e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  266 GKVTSIMQFGCFVQLEGLRKrweGLVHISELrREGRVANVADVVSKGQRVKVKVLSFTGT-KTSLSM-KDVDQETGEDLN 343
Cdd:PRK08582    11 GKVTGITNFGAFVELPEGKT---GLVHISEV-ADNYVKDINDHLKVGDEVEVKVLNVEDDgKIGLSIkKAKDRPKRQHDR 86

                           90
                   ....*....|....
gi 1044440465  344 PNRRRNLVGETNEE 357
Cdd:PRK08582    87 PRHEDNRGGGNDVA 100
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 260-332 5.38e-12

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 69.81  E-value: 5.38e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1044440465  260 IGDIYNGKVTSIMQFGCFVQLE-GLrkrwEGLVHISELRREGRVANVADVVSKGQRVKVKVLS--FTGTKTSLSMK 332
Cdd:PRK06299   286 VGSKVKGKVTNITDYGAFVELEeGI----EGLVHVSEMSWTKKNKHPSKVVSVGQEVEVMVLEidEEKRRISLGLK 357
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 264-331 1.79e-11

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: 60.47  E-value: 1.79e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1044440465  264 YNGKVTSIMQFGCFVQLEGlrkRWEGLVHISELRREgRVANVADVVSKGQRVKVKVLSFTGTKTSLSM 331
Cdd:cd00164      1 VTGKVVSITKFGVFVELED---GVEGLVHISELSDK-FVKDPSEVFKVGDEVEVKVLEVDPEKGRISL 64
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
261-334 1.84e-11

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 68.43  E-value: 1.84e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1044440465  261 GDIYNGKVTSIMQFGCFVQLEGLrkrwEGLVHISELRReGRVANVADVVSKGQRVKVKVLSF--TGTKTSLSMKDV 334
Cdd:PRK00087   478 GDVVEGEVKRLTDFGAFVDIGGV----DGLLHVSEISW-GRVEKPSDVLKVGDEIKVYILDIdkENKKLSLSLKKL 548
rpsA PRK13806
30S ribosomal protein S1; Provisional
 261-344 2.09e-11

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 67.83  E-value: 2.09e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  261 GDIYNGKVTSIMQFGCFVQLE-GLrkrwEGLVHISELRReGRVANVADVVSKGQRVKVKVLSF------TGTKTSLSMKD 333
Cdd:PRK13806   203 GDVVEGTVTRLAPFGAFVELApGV----EGMVHISELSW-SRVQKADEAVSVGDTVRVKVLGIerakkgKGLRISLSIKQ 277

                           90
                   ....*....|....*
gi 1044440465  334 VD----QETGEDLNP 344
Cdd:PRK13806   278 AGgdpwDTVGDRLKA 292
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 258-320 1.19e-10

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: 58.45  E-value: 1.19e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1044440465  258 PTIGDIYNGKVTSIMQFGCFVQLEGLRkrwEGLVHISELRREgRVANVADVVSKGQRVKVKVL 320
Cdd:pfam00575    1 PEKGDVVEGEVTRVTKGGAFVDLGNGV---EGFIPISELSDD-HVEDPDEVIKVGDEVKVKVL 59
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
260-337 3.78e-10

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 58.56  E-value: 3.78e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  260 IGDIYNGKVTSIMQFGCFVQLEGLRKrweGLVHISELrREGRVANVADVVSKGQRVKVKVL---SFTGtKTSLSMKDVDQ 336
Cdd:PRK07252     3 IGDKLKGTITGIKPYGAFVALENGTT---GLIHISEI-KTGFIDNIHQLLKVGEEVLVQVVdfdEYTG-KASLSLRTLEE 77


                   .
gi 1044440465  337 E 337
Cdd:PRK07252    78 E 78
PRK05807 PRK05807
RNA-binding protein S1;
261-332 4.51e-10

RNA-binding protein S1;


Pssm-ID: 235614 [Multi-domain]  Cd Length: 136  Bit Score: 58.99  E-value: 4.51e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1044440465  261 GDIYNGKVTSIMQFGCFVQLEGLrkrwEGLVHISELrREGRVANVADVVSKGQRVKVKVLSF-TGTKTSLSMK 332
Cdd:PRK05807     6 GSILEGTVVNITNFGAFVEVEGK----TGLVHISEV-ADTYVKDIREHLKEQDKVKVKVISIdDNGKISLSIK 73
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 261-332 1.45e-09

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 62.10  E-value: 1.45e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1044440465  261 GDIYNGKVTSIMQFGCFVQLEGLrkrwEGLVHISELRReGRVANVADVVSKGQRVKVKVLSFTGTKT--SLSMK 332
Cdd:PRK06299   202 GQVVEGVVKNITDYGAFVDLGGV----DGLLHITDISW-KRVNHPSEVVNVGDEVKVKVLKFDKEKKrvSLGLK 270
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 258-337 1.59e-09

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 60.22  E-value: 1.59e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  258 PTIGDIYNGKVTSIMQFGCFVQLE---GLrkrwEGLVHISELRReGRVANVADVVSKGQRVKVKVLSFTGTKTS--LSMK 332
Cdd:PRK03987     6 PEEGELVVGTVKEVKDFGAFVTLDeypGK----EGFIHISEVAS-GWVKNIRDHVKEGQKVVCKVIRVDPRKGHidLSLK 80


                   ....*.
gi 1044440465  333 DV-DQE 337
Cdd:PRK03987    81 RVnEHQ 86
rpsA PRK13806
30S ribosomal protein S1; Provisional
 261-333 2.12e-09

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 61.28  E-value: 2.12e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1044440465  261 GDIYNGKVTSIMQFGCFVQLE-GLrkrwEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTGTK--TSLSMKD 333
Cdd:PRK13806   293 GDKVTGKVVRLAPFGAFVEILpGI----EGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKrrISLSLRD 364
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 261-321 2.80e-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: 54.55  E-value: 2.80e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1044440465  261 GDIYNGKVTSIMQFGCFVQLeGLRKrwEGLVHISELRrEGRVANVADVVSKGQRVKVKVLS 321
Cdd:cd05685      1 GMVLEGVVTNVTDFGAFVDI-GVKQ--DGLIHISKMA-DRFVSHPSDVVSVGDIVEVKVIS 57
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
260-340 4.01e-09

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 60.81  E-value: 4.01e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  260 IGDIYNGKVTSIMQFGCFV-----QleglrkrwEGLVHISELRrEGRVANVADVVSKGQRVKVKVLSFTGTK--TSLSMK 332
Cdd:COG2183    641 PGMILEGTVTNVTDFGAFVdigvhQ--------DGLVHISQLS-DRFVKDPREVVKVGDIVKVKVLEVDLKRkrISLSMK 711


                   ....*...
gi 1044440465  333 DVDQETGE 340
Cdd:COG2183    712 LDDEAGAA 719
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 260-344 4.89e-09

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 60.44  E-value: 4.89e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  260 IGDIYNGKVTSIMQFGCFVQLE-GLrkrwEGLVHISELrREGRVANVADVVSKGQRVKVKV--LSFTGTKTSLSMKDVDQ 336
Cdd:PRK07899   293 IGQIVPGKVTKLVPFGAFVRVEeGI----EGLVHISEL-AERHVEVPEQVVQVGDEVFVKVidIDLERRRISLSLKQANE 367

                           90
                   ....*....|.
gi 1044440465  337 ---ETGEDLNP 344
Cdd:PRK07899   368 gvtPESEDFDP 378
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 256-332 5.60e-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: 60.13  E-value: 5.60e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  256 EEPTIGDIYNGKVTSIMQFGCFVQL-EGLrkrwEGLVHISELRREGRVANVADVVSKGQRVKVKVLSF--TGTKTSLSMK 332
Cdd:TIGR00717  268 KKFPVGDKITGRVTNLTDYGVFVEIeEGI----EGLVHVSEMSWVKKNSHPSKVVKKGDEVEVMILDIdpERRRLSLGLK 343
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 258-320 8.16e-09

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: 53.36  E-value: 8.16e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1044440465  258 PTIGDIYNGKVTSIMQFGCFVQLEGLRKRwEGLVHISELRReGRVANVADVVSKGQRVKVKVL 320
Cdd:cd04452      1 PEEGELVVVTVKSIADMGAYVSLLEYGNI-EGMILLSELSR-RRIRSIRKLVKVGRKEVVKVI 61
S1_RNase_R cd04471
S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, ...
 260-340 1.03e-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: 53.17  E-value: 1.03e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  260 IGDIYNGKVTSIMQFGCFVQLEGLRKrwEGLVHISEL----------------RREGRVANVadvvskGQRVKVKVlsft 323
Cdd:cd04471      1 VGEEFDGVISGVTSFGLFVELDNLTV--EGLVHVSTLgddyyefdeenhalvgERTGKVFRL------GDKVKVRV---- 68

                           90
                   ....*....|....*..
gi 1044440465  324 gtktslsmKDVDQETGE 340
Cdd:cd04471     69 --------VRVDLDRRK 77
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 260-332 2.18e-08

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 58.25  E-value: 2.18e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1044440465  260 IGDIYNGKVTSIMQFGCFVQLE-GLrkrwEGLVHISELRREGRVANVADVVSKGQRVKVKVLSF--TGTKTSLSMK 332
Cdd:PRK06299   373 VGDVVEGKVKNITDFGAFVGLEgGI----DGLVHLSDISWDKKGEEAVELYKKGDEVEAVVLKVdvEKERISLGIK 444
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 259-342 2.20e-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: 58.21  E-value: 2.20e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  259 TIGDIYNGKVTSIMQFGCFVQLEGLrkrwEGLVHISELRReGRVANVADVVSKGQRVKVKVLSFTGTKT--SLSMKDVDQ 336
Cdd:TIGR00717  186 KEGDVVKGVVKNITDFGAFVDLGGV----DGLLHITDMSW-KRVKHPSEYVKVGQEVKVKVIKFDKEKGriSLSLKQLGE 260


                   ....*.
gi 1044440465  337 ETGEDL 342
Cdd:TIGR00717  261 DPWEAI 266
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 259-332 2.38e-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: 2.38e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1044440465  259 TIGDIYNGKVTSIMQFGCFVQLEGlrKRWEGLVHISELRrEGRVANVADVVSKGQRVKVKVLSF--TGTKTSLSMK 332
Cdd:cd05708      1 KVGQKIDGTVRRVEDYGVFIDIDG--TNVSGLCHKSEIS-DNRVADASKLFRVGDKVRAKVLKIdaEKKRISLGLK 73
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
 258-389 2.70e-08

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 58.37  E-value: 2.70e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  258 PTIGDIY-NGKVTSIMQFGCFVQLEGLRkrwEGLVHISELrREGRVANVADVVSKGQRVKVKVLSFT-GTKTSLSMKDVD 335
Cdd:PLN00207   751 PTVGDIYrNCEIKSIAPYGAFVEIAPGR---EGLCHISEL-SSNWLAKPEDAFKVGDRIDVKLIEVNdKGQLRLSRRALL 826

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1044440465  336 QETGEDLNPNRRRNlvGETNEETSMRN----PDRPTHLSLVSAPEVEDDSLERKRLTR 389
Cdd:PLN00207   827 PEANSEKSSQKQQG--GSTKDKAPQKKyvntSSRPRRAAQAEKNSAENAAVPKKKDYK 882
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 261-331 5.28e-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: 50.96  E-value: 5.28e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1044440465  261 GDIYNGKVTSIMQFGCFVQLEGlrkRWEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTGTKTSLSM 331
Cdd:cd05690      1 GTVVSGKIKSITDFGIFVGLDG---GIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERERISL 68
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 261-337 3.11e-07

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 54.79  E-value: 3.11e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  261 GDIYNGKVTSIMQFGCFVQLEGLRkrwEGLVHISELRREgRVANVADVVSKGQRVKVKVLSFtGTKT---SLSMKDVDQE 337
Cdd:PRK06299   461 GSIVTGTVTEVKDKGAFVELEDGV---EGLIRASELSRD-RVEDATEVLKVGDEVEAKVINI-DRKNrriSLSIKALDEA 535
PHA02653 PHA02653
RNA helicase NPH-II; Provisional
 672-900 4.59e-07

RNA helicase NPH-II; Provisional


Pssm-ID: 177443 [Multi-domain]  Cd Length: 675  Bit Score: 54.21  E-value: 4.59e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  672 LTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIvtSATL-DAVKFSQYFYEAPIFT-IPGRT-YPVEILYTK-- 746
Cdd:PHA02653   289 LFDYGTVIIDEVHEHDQIGDIIIAVARKHIDKIRSLFLM--TATLeDDRDRIKEFFPNPAFVhIPGGTlFPISEVYVKnk 366

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  747 ----------EPETDYLDASLITvmqihLTEPPG-DILVFLTGQEEIDTACEILYERMkslgpdvPELIILPVYSALPS- 814
Cdd:PHA02653   367 ynpknkrayiEEEKKNIVTALKK-----YTPPKGsSGIVFVASVSQCEEYKKYLEKRL-------PIYDFYIIHGKVPNi 434

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  815 -EMQTRIFDPAPPgsrKVVIATNIAETSLTIDGIYYVVDPGfvkqKVYNSKT-GIDQLVvtpISQAQAKQRAGRAGRTGP 892
Cdd:PHA02653   435 dEILEKVYSSKNP---SIIISTPYLESSVTIRNATHVYDTG----RVYVPEPfGGKEMF---ISKSMRTQRKGRVGRVSP 504


                   ....*...
gi 1044440465  893 GKCYRLYT 900
Cdd:PHA02653   505 GTYVYFYD 512
S1_RPS1_repeat_ec4 cd05689
S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 266-331 1.07e-06

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: 47.19  E-value: 1.07e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1044440465  266 GKVTSIMQFGCFVQLE-GLrkrwEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTGTKTSLSM 331
Cdd:cd05689      9 GKVTNLTDYGCFVELEeGV----EGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERRRISL 71
VacB COG0557
Exoribonuclease R [Transcription];
260-321 2.60e-06

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 51.65  E-value: 2.60e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1044440465  260 IGDIYNGKVTSIMQFGCFVQLEGLRKrwEGLVHISEL----------------RREGRVANVadvvskGQRVKVKVLS 321
Cdd:COG0557    622 VGEEFEGVISGVTSFGLFVELDELGV--EGLVHVSSLgddyyeyderrqalvgERTGKRYRL------GDRVEVRVVR 691
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 261-341 3.53e-06

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 51.20  E-value: 3.53e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  261 GDIYNGKVTSIMQFGCFVQLEGLrkrwEGLVHISELRREgRVANVADVVSKGQRVKVKVLS--FTGTKTSLSMKdvdqET 338
Cdd:PRK07899   209 GQVRKGVVSSIVNFGAFVDLGGV----DGLVHVSELSWK-HIDHPSEVVEVGQEVTVEVLDvdMDRERVSLSLK----AT 279


                   ...
gi 1044440465  339 GED 341
Cdd:PRK07899   280 QED 282
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 580-715 1.08e-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: 46.63  E-value: 1.08e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  580 LIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGccLGQEVGYTIRFedcTSPETV------ 653
Cdd:cd00046      4 VLITAPTGSGKTLAALLAALLLLLKKGKKVLVLVPTKALALQTAERLRELFG--PGIRVAVLVGG---SSAEEReknklg 78

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1044440465  654 ---IKYMTDGMLLRECLID--PDLTQYAIIMLDEAHERTIHTDVLFgLLKKTVQKRQ--DMKLIVTSAT 715
Cdd:cd00046     79 dadIIIATPDMLLNLLLREdrLFLKDLKLIIVDEAHALLIDSRGAL-ILDLAVRKAGlkNAQVILLSAT 146
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
 586-684 2.23e-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: 45.62  E-value: 2.23e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  586 TGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSeefgcclGQEVGY-TIRFEDCTSPETVIKYMTDGMLLR 664
Cdd:cd17931     10 PGAGKTTRVLPQIIREAIKKRLRTLVLAPTRVVAAEMYEALR-------GLPIRYrTGAVKEEHGGNEIVDYMCHGTFTC 82

                           90       100
                   ....*....|....*....|
gi 1044440465  665 ECLIDPDLTQYAIIMLDEAH 684
Cdd:cd17931     83 RLLSPKRVPNYNLIIMDEAH 102
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 261-332 3.19e-05

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: 48.19  E-value: 3.19e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1044440465  261 GDIYNGKVTSIMQFGCFVQLEGlrkRWEGLVHISELRREgRVANVADVVSKGQRVKVKVLSF--TGTKTSLSMK 332
Cdd:TIGR00717  447 GSVVKGKVTEIKDFGAFVELPG---GVEGLIRNSELSEN-RDEDKTDEIKVGDEVEAKVVDIdkKNRKVSLSVK 516
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 260-342 1.23e-04

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 46.24  E-value: 1.23e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  260 IGDIYNGKVTSIMQFGCFVQL-EGLrkrwEGLVHISELRREGRVANVADVVSKGQRVKVKVLSF--TGTKTSLSMKDVDQ 336
Cdd:PRK12269   578 VNDVVKGRVTKIADFGAFIELaEGI----EGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGYdiQAGRVSLGLKQVTA 653


                   ....*.
gi 1044440465  337 ETGEDL 342
Cdd:PRK12269   654 NPWEEI 659
S1_RNase_E cd04453
S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential ...
 256-326 1.70e-04

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: 41.43  E-value: 1.70e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1044440465  256 EEPTIGDIYNGKVTSI---MQfGCFVQLeGLRKrwEGLVHISELRR--EGRVANVADVVSKGQRVKVKVL-SFTGTK 326
Cdd:cd04453      3 REPIVGNIYLGRVKKIvpgLQ-AAFVDI-GLGK--NGFLHLSDILPayFKKHKKIAKLLKEGQEILVQVVkEPIGTK 75
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 830-899 2.20e-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: 2.20e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1044440465  830 KVVIATNIAETSLTIDGIYYVVDPGFvkqkvynsktgidqlvvtPISQAQAKQRAGRAGRTG--PGKCYRLY 899
Cdd:cd18785     24 EILVATNVLGEGIDVPSLDTVIFFDP------------------PSSAASYIQRVGRAGRGGkdEGEVILFV 77
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 256-321 1.44e-03

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: 38.72  E-value: 1.44e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1044440465  256 EEPTIGDIYNGKVTSIMQFGCFVQLEGlrkRWEGLVHISELRREgRVANVADVVSKGQRVKVKVLS 321
Cdd:cd04461     10 SDLKPGMVVHGYVRNITPYGVFVEFLG---GLTGLAPKSYISDE-FVTDPSFGFKKGQSVTAKVTS 71
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 256-337 1.61e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 42.17  E-value: 1.61e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  256 EEPTIGDIYNGKVTSIMQFGCFVQLEGlrKRWEGLVHISELRREgRVANVADVVSKGQRVKVKVLSFTGTKTS--LSMKD 333
Cdd:PRK06676    13 KEVEVGDVVTGEVLKVEDKQVFVNIEG--YKVEGVIPISELSND-HIEDINDVVKVGDELEVYVLKVEDGEGNllLSKRR 89


                   ....
gi 1044440465  334 VDQE 337
Cdd:PRK06676    90 LEAE 93
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 260-332 2.61e-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: 42.03  E-value: 2.61e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1044440465  260 IGDIYNGKVTSIMQFGCFVQLEGlrkRWEGLVHISELR--REGRVANVadVVSKGQRVKVKVLS--FTGTKTSLSMK 332
Cdd:TIGR00717  359 VGDRVTGKIKKITDFGAFVELEG---GIDGLIHLSDISwdKDGREADH--LYKKGDEIEAVVLAvdKEKKRISLGVK 430
AAA_22 pfam13401
AAA domain;
578-684 2.68e-03

AAA domain;


Pssm-ID: 379165 [Multi-domain]  Cd Length: 129  Bit Score: 39.25  E-value: 2.68e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  578 QILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGcclgqevgytIRFEDCTSPETVIKYM 657
Cdd:pfam13401    6 GILVLTGESGTGKTTLLRRLLEQLPEVRDSVVFVDLPSGTSPKDLLRALLRALG----------LPLSGRLSKEELLAAL 75

                           90       100
                   ....*....|....*....|....*..
gi 1044440465  658 TDgmLLRECLIDPdltqyaIIMLDEAH 684
Cdd:pfam13401   76 QQ--LLLALAVAV------VLIIDEAQ 94
Cas3_I cd09639
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short ...
 579-899 2.70e-03

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: 41.65  E-value: 2.70e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  579 ILIVIGETGSGKTTQITQYLAEAGYTS-RGKIGCTQPRRVAAMSVAKRVSEEFG-CCLGQEVGYTIRFEDCTSPETVIK- 655
Cdd:cd09639      1 LLVIEAPTGYGKTEAALLWALHSLKSQkADRVIIALPTRATINAMYRRAKEAFGeTGLYHSSILSSRIKEMGDSEEFEHl 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  656 ---YMTDGML-----LRECLIDP------------DLTQ----YAIIMLDEAHERTIHTDVLF-GLLKktVQKRQDMKLI 710
Cdd:cd09639     81 fplYIHSNDTlfldpITVCTIDQvlksvfgefghyEFTLasiaNSLLIFDEVHFYDEYTLALIlAVLE--VLKDNDVPIL 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  711 VTSATLDAVkFSQYF--YEAPIFTIPGRTYPVEILYT-KEPETDYLDASLITVMqIHLTEPPGDILVFLTgqeEIDTACE 787
Cdd:cd09639    159 LMSATLPKF-LKEYAekIGYVEENEPLDLKPNERAPFiKIESDKVGEISSLERL-LEFIKKGGSVAIIVN---TVDRAQE 233

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1044440465  788 IlYERMKSLGPDVPELII----LPVYSALPSEMQTRIFDPAPPGsrkVVIATNIAETSLTIDGIYYVVDPgfvkqkvyns 863
Cdd:cd09639    234 F-YQQLKEKGPEEEIMLIhsrfTEKDRAKKEAELLLEFKKSEKF---VIVATQVIEASLDISVDVMITEL---------- 299

                          330       340       350
                   ....*....|....*....|....*....|....*.
gi 1044440465  864 kTGIDQLVvtpisqaqakQRAGRAGRTGPGKCYRLY 899
Cdd:cd09639    300 -APIDSLI----------QRLGRLHRYGEKNGEEVY 324
S1_RecJ_like cd04473
S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of ...
 255-321 5.03e-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: 37.20  E-value: 5.03e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1044440465  255 PEEPTIGDIYNGKVTSIMQFGCFVQLEglrKRWEGLVHISELRREGRVanvadvvskGQRVKVKVLS 321
Cdd:cd04473     11 MEDLEVGKLYKGKVNGVAKYGVFVDLN---DHVRGLIHRSNLLRDYEV---------GDEVIVQVTD 65
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 261-322 6.37e-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: 6.37e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1044440465  261 GDIYNGKVTSIMQFGCFVQ-LEGLRkrweGLVHISELrREGRVANVADVVSKGQRVKVKVLSF 322
Cdd:cd05698      1 GLKTHGTIVKVKPNGCIVSfYNNVK----GFLPKSEL-SEAFIKDPEEHFRVGQVVKVKVLSC 58
 
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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