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Conserved domains on  [gi|4826690|ref|NP_004932|]
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ATP-dependent RNA helicase DHX8 isoform 1 [Homo sapiens]

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];
556-1187 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: 574.72  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   556 MSILEQRESLPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFG 635
Cdd:COG1643    1 MSLITYPPDLPVSAVLPELLAALRAHQVVVLAAPPGAGKTTQLPLALLELGWGAGGRIGMLEPRRLAARAAAERMAEELG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   636 CCLGQEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQK-RQDMKLI 714
Cdd:COG1643   81 EPVGETVGYRVRFEDKVSAATRIEVVTEGILLRELQRDPELEGVDTVIFDEFHERSLNADLLLALLLDLQPAlRPDLKLL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   715 VTSATLDAVKFSQYFYEAPIFTIPGRTYPVEILYT--KEPETDYLDASLITVMQIhLTEPPGDILVFLTGQEEIDTACEI 792
Cdd:COG1643  161 VMSATLDAERFARLLGDAPVIESSGRTYPVEVRYRplPADERDLEDAVADAVREA-LAEEPGDILVFLPGEREIRRTAEA 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   793 LyerMKSLGPDVpelIILPVYSALPSEMQTRIFDPAPPGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKVYNSKTGID 872
Cdd:COG1643  240 L---RGRLPPDT---EILPLYGRLSAAEQDRAFAPAPHGRRRIVLATNIAETSLTVPGIRYVIDSGLARIPRYDPRSGVT 313

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   873 QLVVTPISQAQAKQRAGRAGRTGPGKCYRLYTE------RAYRDemlttnvPEIQRTNLASTVLSLKAMGINDLLSFDFM 946
Cdd:COG1643  314 RLPTERISQASANQRAGRAGRLAPGICYRLWSEedfarrPAFTD-------PEILRADLASLILELAAWGLGDPEDLPFL 386

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   947 DAPPMETLITAMEQLYTLGALDDEGLLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQNVFYRpkdkqa 1026
Cdd:COG1643  387 DPPPARAIADARALLQELGALDADGRLTPLGRALARLPLDPRLARMLLAAAELGCLREAAILAALLSERDPRRG------ 460

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690  1027 ladqkkakfhQTEGDHLTLLAVYNSWKNNKfsnpwcyENFIQARSLRRAQDIRKQMLGIMDRHKLDVVScgkSTVRVQKA 1106
Cdd:COG1643  461 ----------AAGSDLLARLNLWRRLREQQ-------REFLSYLRLREWRDLARQLRRLLGEGANEEPA---DYEAIGLL 520

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690  1107 ICSGFFRNAAKKDPQEGYRTLIDQQVVYIHPSSALFNRqpEWVVYHELVLTTKEY-MREVTTIDPRWLVEFAPAFFK-VS 1184
Cdd:COG1643  521 LALAYPDRIARRRGEGGRYLLARGRGAALFPGSPLAKK--EWLVAAELVGGAAEArIRLAAPIDPEWLEELAAHLIKrYS 598


                 ...
gi 4826690  1185 DPT 1187
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 ...
 265-343 1.70e-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: 1.70e-43
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 4826690   265 GDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTGTKTSLSMKDVDQETG 343
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 2.06e-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: 143.07  E-value: 2.06e-40
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 4826690    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];
556-1187 0e+00

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


Pssm-ID: 441249 [Multi-domain]  Cd Length: 836  Bit Score: 574.72  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   556 MSILEQRESLPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFG 635
Cdd:COG1643    1 MSLITYPPDLPVSAVLPELLAALRAHQVVVLAAPPGAGKTTQLPLALLELGWGAGGRIGMLEPRRLAARAAAERMAEELG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   636 CCLGQEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQK-RQDMKLI 714
Cdd:COG1643   81 EPVGETVGYRVRFEDKVSAATRIEVVTEGILLRELQRDPELEGVDTVIFDEFHERSLNADLLLALLLDLQPAlRPDLKLL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   715 VTSATLDAVKFSQYFYEAPIFTIPGRTYPVEILYT--KEPETDYLDASLITVMQIhLTEPPGDILVFLTGQEEIDTACEI 792
Cdd:COG1643  161 VMSATLDAERFARLLGDAPVIESSGRTYPVEVRYRplPADERDLEDAVADAVREA-LAEEPGDILVFLPGEREIRRTAEA 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   793 LyerMKSLGPDVpelIILPVYSALPSEMQTRIFDPAPPGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKVYNSKTGID 872
Cdd:COG1643  240 L---RGRLPPDT---EILPLYGRLSAAEQDRAFAPAPHGRRRIVLATNIAETSLTVPGIRYVIDSGLARIPRYDPRSGVT 313

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   873 QLVVTPISQAQAKQRAGRAGRTGPGKCYRLYTE------RAYRDemlttnvPEIQRTNLASTVLSLKAMGINDLLSFDFM 946
Cdd:COG1643  314 RLPTERISQASANQRAGRAGRLAPGICYRLWSEedfarrPAFTD-------PEILRADLASLILELAAWGLGDPEDLPFL 386

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   947 DAPPMETLITAMEQLYTLGALDDEGLLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQNVFYRpkdkqa 1026
Cdd:COG1643  387 DPPPARAIADARALLQELGALDADGRLTPLGRALARLPLDPRLARMLLAAAELGCLREAAILAALLSERDPRRG------ 460

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690  1027 ladqkkakfhQTEGDHLTLLAVYNSWKNNKfsnpwcyENFIQARSLRRAQDIRKQMLGIMDRHKLDVVScgkSTVRVQKA 1106
Cdd:COG1643  461 ----------AAGSDLLARLNLWRRLREQQ-------REFLSYLRLREWRDLARQLRRLLGEGANEEPA---DYEAIGLL 520

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690  1107 ICSGFFRNAAKKDPQEGYRTLIDQQVVYIHPSSALFNRqpEWVVYHELVLTTKEY-MREVTTIDPRWLVEFAPAFFK-VS 1184
Cdd:COG1643  521 LALAYPDRIARRRGEGGRYLLARGRGAALFPGSPLAKK--EWLVAAELVGGAAEArIRLAAPIDPEWLEELAAHLIKrYS 598


                 ...
gi 4826690  1185 DPT 1187
Cdd:COG1643  599 EPH 601
DEAH_box_HrpA TIGR01967
RNA helicase HrpA; This model represents HrpA, one of two related but uncharacterized DEAH-box ...
 563-1182 2.07e-157

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: 504.69  E-value: 2.07e-157
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690     563 ESLPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQEV 642
Cdd:TIGR01967   64 DNLPVSAKREDIAEAIAENQVVIIAGETGSGKTTQLPKICLELGRGSHGLIGHTQPRRLAARTVAQRIAEELGTPLGEKV 143

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690     643 GYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSATLDA 722
Cdd:TIGR01967  144 GYKVRFHDQVSSNTLVKLMTDGILLAETQQDRFLSRYDTIIIDEAHERSLNIDFLLGYLKQLLPRRPDLKIIITSATIDP 223

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690     723 VKFSQYFYEAPIFTIPGRTYPVEILY------TKEPETDYLDASLITVMQIhLTEPPGDILVFLTGQEEIDTACEILYER 796
Cdd:TIGR01967  224 ERFSRHFNNAPIIEVSGRTYPVEVRYrplveeQEDDDLDQLEAILDAVDEL-FAEGPGDILIFLPGEREIRDAAEILRKR 302

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690     797 mkslgpDVPELIILPVYSALPSEMQTRIFDPAppGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKVYNSKTGIDQLVV 876
Cdd:TIGR01967  303 ------NLRHTEILPLYARLSNKEQQRVFQPH--SGRRIVLATNVAETSLTVPGIHYVIDTGTARISRYSYRTKVQRLPI 374

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690     877 TPISQAQAKQRAGRAGRTGPGKCYRLYTERAYRDEMLTTNvPEIQRTNLASTVLSLKAMGINDLLSFDFMDAPPMETLIT 956
Cdd:TIGR01967  375 EPISQASANQRKGRCGRVAPGICIRLYSEEDFNSRPEFTD-PEILRTNLASVILQMLALRLGDIAAFPFIEAPDPRAIRD 453

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690     957 AMEQLYTLGALDDE---GLLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQNVFYRPKDKQALADQKKA 1033
Cdd:TIGR01967  454 GFRLLEELGALDDDeaePQLTPIGRQLAQLPVDPRLARMLLEAHRLGCLQEVLIIASALSIQDPRERPMEKQQAADQAHA 533

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690    1034 KFHQTEGDHLTLLAVYNSWKN-------NKFSNpWCYENFIQARSLRRAQDIRKQMLGIMDRHKLDVVSCGKSTVRVQKA 1106
Cdd:TIGR01967  534 RFKDPRSDFLSRVNLWRHIEEqrqalsaNQFRN-ACRKQYLNYLRVREWQDIYRQLTQVVKELGLKLNEEPADYDAIHKA 612

                          570       580       590       600       610       620       630
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 4826690    1107 ICSGFFRNAAKKDPQEGYrTLIDQQVVYIHPSSALFNRQPEWVVYHELVLTTKEYMREVTTIDPRWLVEFAPAFFK 1182
Cdd:TIGR01967  613 LLSGLLSQIGMKDEKHEY-DGARGRKFHIFPGSPLFKKPPKWVMAAELVETSKLYARLVAKIEPEWVEPVAGHLIK 687
PRK11131 PRK11131
ATP-dependent RNA helicase HrpA; Provisional
 563-1186 7.63e-148

ATP-dependent RNA helicase HrpA; Provisional


Pssm-ID: 182986 [Multi-domain]  Cd Length: 1294  Bit Score: 479.17  E-value: 7.63e-148
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690    563 ESLPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQEV 642
Cdd:PRK11131   71 ENLPVSQKKQDILEAIRDHQVVIVAGETGSGKTTQLPKICLELGRGVKGLIGHTQPRRLAARTVANRIAEELETELGGCV 150

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690    643 GYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSATLDA 722
Cdd:PRK11131  151 GYKVRFNDQVSDNTMVKLMTDGILLAEIQQDRLLMQYDTIIIDEAHERSLNIDFILGYLKELLPRRPDLKVIITSATIDP 230

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690    723 VKFSQYFYEAPIFTIPGRTYPVEILY------TKEPETDYLDASLITVMQIHlTEPPGDILVFLTGQEEI-DTAcEILYE 795
Cdd:PRK11131  231 ERFSRHFNNAPIIEVSGRTYPVEVRYrpiveeADDTERDQLQAIFDAVDELG-REGPGDILIFMSGEREIrDTA-DALNK 308

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690    796 RmkslgpDVPELIILPVYSALPSEMQTRIFDPAppGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKVYNSKTGIDQLV 875
Cdd:PRK11131  309 L------NLRHTEILPLYARLSNSEQNRVFQSH--SGRRIVLATNVAETSLTVPGIKYVIDPGTARISRYSYRTKVQRLP 380

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690    876 VTPISQAQAKQRAGRAGRTGPGKCYRLYTERAYRDEMLTTNvPEIQRTNLASTVLSLKAMGINDLLSFDFMDAPPMETLI 955
Cdd:PRK11131  381 IEPISQASANQRKGRCGRVSEGICIRLYSEDDFLSRPEFTD-PEILRTNLASVILQMTALGLGDIAAFPFVEAPDKRNIQ 459

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690    956 TAMEQLYTLGALDDEG-----LLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQNVFYRPKDKQALADQ 1030
Cdd:PRK11131  460 DGVRLLEELGAITTDEqasayKLTPLGRQLAQLPVDPRLARMVLEAQKHGCVREVMIITSALSIQDPRERPMDKQQASDE 539

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   1031 KKAKFHQTEGDHLTLLAVYNSWK-------NNKFSNpWCYENFIQARSLRRAQDIRKQMLGIMDRHKLDVVSCGKSTVRV 1103
Cdd:PRK11131  540 KHRRFADKESDFLAFVNLWNYLQeqqkalsSNQFRR-LCRTDYLNYLRVREWQDIYTQLRQVVKELGIPVNSEPAEYREI 618

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   1104 QKAICSGFFRNAAKKDPQEGYRTLIDQQVVYIHPSSALFNRQPEWVVYHELVLTTKEYMREVTTIDPRWLVEFAPAFFK- 1182
Cdd:PRK11131  619 HTALLTGLLSHIGMKDAEKQEYTGARNARFSIFPGSGLFKKPPKWVMVAELVETSRLWGRIAARIEPEWIEPLAQHLIKr 698


                  ....*
gi 4826690   1183 -VSDP 1186
Cdd:PRK11131  699 sYSEP 703
DEXHc_DHX8 cd17971
DEXH-box helicase domain of DEAH-box helicase 8; DEAH-box helicase 8 (DHX8 ,also known as ...
 560-738 3.73e-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: 3.73e-127
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   560 EQRESLPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLG 639
Cdd:cd17971    1 EQRESLPIYKLKEQLIQAVHDNQILVVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVAEEFGCCLG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   640 QEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSAT 719
Cdd:cd17971   81 QEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLSQYSVIMLDEAHERTIHTDVLFGLLKKTVQKRPDLKLIVTSAT 160

                        170
                 ....*....|....*....
gi 4826690   720 LDAVKFSQYFYEAPIFTIP 738
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 ...
 265-343 1.70e-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: 1.70e-43
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 4826690   265 GDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTGTKTSLSMKDVDQETG 343
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 2.06e-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: 143.07  E-value: 2.06e-40
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 4826690    25 LEYLSLVSKVCTELDNHLGINDKDLAEFVISLAEKNTTFDTFKASLVKNGAEFTDSLISNLLRLIQTM 92
Cdd:cd21691    1 LEYLSLVSKVCTELENHLGISDKDLAEFIIDLAEKSKTLDEFKKALKENGAEFPDSFVESLLRLIQRM 68
HA2 smart00847
Helicase associated domain (HA2) Add an annotation; This presumed domain is about 90 amino ...
 964-1046 7.94e-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: 7.94e-34
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690      964 LGALDDEGLLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQNvfYRPKDKQALADQKKAKFHQTEGDHL 1043
Cdd:smart00847    2 LGALDDDGRLTPLGRKMAELPLDPRLAKMLLAAAEFGCLDEILTIVAMLSVGD--PRPKEKREDADAARRRFADPESDHL 79


                    ...
gi 4826690     1044 TLL 1046
Cdd:smart00847   80 TLL 82
HA2 pfam04408
Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in ...
 957-1045 1.20e-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: 1.20e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690     957 AMEQLYTLGALDDEGLLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQNVFYRP------KDKQALADQ 1030
Cdd:pfam04408    1 ALELLYYLGALDEDGELTPLGRKMAELPLDPRLAKMLLAAAELGCLDEVLTIVAALSVRDPFVQPnfldprSAAKAARRR 80

                           90       100
                   ....*....|....*....|....
gi 4826690    1031 KKAKFHQ---------TEGDHLTL 1045
Cdd:pfam04408   81 RRAADEKarakfarldLEGDHLTL 104
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 261-339 2.34e-21

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 100.51  E-value: 2.34e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690    261 EPTIGDIYNGKVTSIMQFGCFVQLegLRKRwEGLVHISELRREgRVANVADVVSKGQRVKVKVLSFT-GTKTSLSMKDVD 339
Cdd:PRK11824  618 EPEVGEIYEGKVVRIVDFGAFVEI--LPGK-DGLVHISEIADE-RVEKVEDVLKEGDEVKVKVLEIDkRGRIRLSRKAVL 693
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 260-353 5.02e-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: 87.16  E-value: 5.02e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   260 EEPTIGDIYNGKVTSIMQFGCFVQLEGlrkRWEGLVHISELrREGRVANVADVVSKGQRVKVKVLSFTGT-KTSLSMKDV 338
Cdd:COG1098    1 MSIEVGDIVEGKVTGITPFGAFVELPE---GTTGLVHISEI-ADGYVKDINDYLKVGDEVKVKVLSIDEDgKISLSIKQA 76

                         90
                 ....*....|....*
gi 4826690   339 DQETGEDLNPNRRRN 353
Cdd:COG1098   77 EEKPKRPPRPRRNSR 91
S1_dom_CvfD NF040579
CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ...
 264-352 2.98e-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: 2.98e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690    264 IGDIYNGKVTSIMQFGCFVQLEglrKRWEGLVHISELrREGRVANVADVVSKGQRVKVKVLS---FTGtKTSLSMKDVDQ 340
Cdd:NF040579    3 IGDIVEGKVTGIQPYGAFVALD---EHTQGLIHISEI-KHGYVKDINDFLKVGQEVKVKVLDideYTG-KISLSLRALEE 77

                          90
                  ....*....|..
gi 4826690    341 ETGEDLNPNRRR 352
Cdd:NF040579   78 APEKHRKRRKHR 89
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
264-336 3.06e-14

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 68.78  E-value: 3.06e-14
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 4826690      264 IGDIYNGKVTSIMQFGCFVQLEGlrkRWEGLVHISELRREgRVANVADVVSKGQRVKVKVLSFTGTK--TSLSMK 336
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 ...
 262-324 1.23e-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: 1.23e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 4826690     262 PTIGDIYNGKVTSIMQFGCFVQLEGLRkrwEGLVHISELRREgRVANVADVVSKGQRVKVKVL 324
Cdd:pfam00575    1 PEKGDVVEGEVTRVTKGGAFVDLGNGV---EGFIPISELSDD-HVEDPDEVIKVGDEVKVKVL 59
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 260-336 6.57e-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: 59.75  E-value: 6.57e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690     260 EEPTIGDIYNGKVTSIMQFGCFVQL-EGLrkrwEGLVHISELRREGRVANVADVVSKGQRVKVKVLSF--TGTKTSLSMK 336
Cdd:TIGR00717  268 KKFPVGDKITGRVTNLTDYGVFVEIeEGI----EGLVHVSEMSWVKKNSHPSKVVKKGDEVEVMILDIdpERRRLSLGLK 343
 
Name Accession Description Interval E-value
HrpA COG1643
HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];
556-1187 0e+00

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


Pssm-ID: 441249 [Multi-domain]  Cd Length: 836  Bit Score: 574.72  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   556 MSILEQRESLPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFG 635
Cdd:COG1643    1 MSLITYPPDLPVSAVLPELLAALRAHQVVVLAAPPGAGKTTQLPLALLELGWGAGGRIGMLEPRRLAARAAAERMAEELG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   636 CCLGQEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQK-RQDMKLI 714
Cdd:COG1643   81 EPVGETVGYRVRFEDKVSAATRIEVVTEGILLRELQRDPELEGVDTVIFDEFHERSLNADLLLALLLDLQPAlRPDLKLL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   715 VTSATLDAVKFSQYFYEAPIFTIPGRTYPVEILYT--KEPETDYLDASLITVMQIhLTEPPGDILVFLTGQEEIDTACEI 792
Cdd:COG1643  161 VMSATLDAERFARLLGDAPVIESSGRTYPVEVRYRplPADERDLEDAVADAVREA-LAEEPGDILVFLPGEREIRRTAEA 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   793 LyerMKSLGPDVpelIILPVYSALPSEMQTRIFDPAPPGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKVYNSKTGID 872
Cdd:COG1643  240 L---RGRLPPDT---EILPLYGRLSAAEQDRAFAPAPHGRRRIVLATNIAETSLTVPGIRYVIDSGLARIPRYDPRSGVT 313

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   873 QLVVTPISQAQAKQRAGRAGRTGPGKCYRLYTE------RAYRDemlttnvPEIQRTNLASTVLSLKAMGINDLLSFDFM 946
Cdd:COG1643  314 RLPTERISQASANQRAGRAGRLAPGICYRLWSEedfarrPAFTD-------PEILRADLASLILELAAWGLGDPEDLPFL 386

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   947 DAPPMETLITAMEQLYTLGALDDEGLLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQNVFYRpkdkqa 1026
Cdd:COG1643  387 DPPPARAIADARALLQELGALDADGRLTPLGRALARLPLDPRLARMLLAAAELGCLREAAILAALLSERDPRRG------ 460

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690  1027 ladqkkakfhQTEGDHLTLLAVYNSWKNNKfsnpwcyENFIQARSLRRAQDIRKQMLGIMDRHKLDVVScgkSTVRVQKA 1106
Cdd:COG1643  461 ----------AAGSDLLARLNLWRRLREQQ-------REFLSYLRLREWRDLARQLRRLLGEGANEEPA---DYEAIGLL 520

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690  1107 ICSGFFRNAAKKDPQEGYRTLIDQQVVYIHPSSALFNRqpEWVVYHELVLTTKEY-MREVTTIDPRWLVEFAPAFFK-VS 1184
Cdd:COG1643  521 LALAYPDRIARRRGEGGRYLLARGRGAALFPGSPLAKK--EWLVAAELVGGAAEArIRLAAPIDPEWLEELAAHLIKrYS 598


                 ...
gi 4826690  1185 DPT 1187
Cdd:COG1643  599 EPH 601
DEAH_box_HrpA TIGR01967
RNA helicase HrpA; This model represents HrpA, one of two related but uncharacterized DEAH-box ...
 563-1182 2.07e-157

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: 504.69  E-value: 2.07e-157
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690     563 ESLPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQEV 642
Cdd:TIGR01967   64 DNLPVSAKREDIAEAIAENQVVIIAGETGSGKTTQLPKICLELGRGSHGLIGHTQPRRLAARTVAQRIAEELGTPLGEKV 143

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690     643 GYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSATLDA 722
Cdd:TIGR01967  144 GYKVRFHDQVSSNTLVKLMTDGILLAETQQDRFLSRYDTIIIDEAHERSLNIDFLLGYLKQLLPRRPDLKIIITSATIDP 223

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690     723 VKFSQYFYEAPIFTIPGRTYPVEILY------TKEPETDYLDASLITVMQIhLTEPPGDILVFLTGQEEIDTACEILYER 796
Cdd:TIGR01967  224 ERFSRHFNNAPIIEVSGRTYPVEVRYrplveeQEDDDLDQLEAILDAVDEL-FAEGPGDILIFLPGEREIRDAAEILRKR 302

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690     797 mkslgpDVPELIILPVYSALPSEMQTRIFDPAppGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKVYNSKTGIDQLVV 876
Cdd:TIGR01967  303 ------NLRHTEILPLYARLSNKEQQRVFQPH--SGRRIVLATNVAETSLTVPGIHYVIDTGTARISRYSYRTKVQRLPI 374

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690     877 TPISQAQAKQRAGRAGRTGPGKCYRLYTERAYRDEMLTTNvPEIQRTNLASTVLSLKAMGINDLLSFDFMDAPPMETLIT 956
Cdd:TIGR01967  375 EPISQASANQRKGRCGRVAPGICIRLYSEEDFNSRPEFTD-PEILRTNLASVILQMLALRLGDIAAFPFIEAPDPRAIRD 453

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690     957 AMEQLYTLGALDDE---GLLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQNVFYRPKDKQALADQKKA 1033
Cdd:TIGR01967  454 GFRLLEELGALDDDeaePQLTPIGRQLAQLPVDPRLARMLLEAHRLGCLQEVLIIASALSIQDPRERPMEKQQAADQAHA 533

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690    1034 KFHQTEGDHLTLLAVYNSWKN-------NKFSNpWCYENFIQARSLRRAQDIRKQMLGIMDRHKLDVVSCGKSTVRVQKA 1106
Cdd:TIGR01967  534 RFKDPRSDFLSRVNLWRHIEEqrqalsaNQFRN-ACRKQYLNYLRVREWQDIYRQLTQVVKELGLKLNEEPADYDAIHKA 612

                          570       580       590       600       610       620       630
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 4826690    1107 ICSGFFRNAAKKDPQEGYrTLIDQQVVYIHPSSALFNRQPEWVVYHELVLTTKEYMREVTTIDPRWLVEFAPAFFK 1182
Cdd:TIGR01967  613 LLSGLLSQIGMKDEKHEY-DGARGRKFHIFPGSPLFKKPPKWVMAAELVETSKLYARLVAKIEPEWVEPVAGHLIK 687
PRK11131 PRK11131
ATP-dependent RNA helicase HrpA; Provisional
 563-1186 7.63e-148

ATP-dependent RNA helicase HrpA; Provisional


Pssm-ID: 182986 [Multi-domain]  Cd Length: 1294  Bit Score: 479.17  E-value: 7.63e-148
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690    563 ESLPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQEV 642
Cdd:PRK11131   71 ENLPVSQKKQDILEAIRDHQVVIVAGETGSGKTTQLPKICLELGRGVKGLIGHTQPRRLAARTVANRIAEELETELGGCV 150

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690    643 GYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSATLDA 722
Cdd:PRK11131  151 GYKVRFNDQVSDNTMVKLMTDGILLAEIQQDRLLMQYDTIIIDEAHERSLNIDFILGYLKELLPRRPDLKVIITSATIDP 230

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690    723 VKFSQYFYEAPIFTIPGRTYPVEILY------TKEPETDYLDASLITVMQIHlTEPPGDILVFLTGQEEI-DTAcEILYE 795
Cdd:PRK11131  231 ERFSRHFNNAPIIEVSGRTYPVEVRYrpiveeADDTERDQLQAIFDAVDELG-REGPGDILIFMSGEREIrDTA-DALNK 308

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690    796 RmkslgpDVPELIILPVYSALPSEMQTRIFDPAppGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKVYNSKTGIDQLV 875
Cdd:PRK11131  309 L------NLRHTEILPLYARLSNSEQNRVFQSH--SGRRIVLATNVAETSLTVPGIKYVIDPGTARISRYSYRTKVQRLP 380

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690    876 VTPISQAQAKQRAGRAGRTGPGKCYRLYTERAYRDEMLTTNvPEIQRTNLASTVLSLKAMGINDLLSFDFMDAPPMETLI 955
Cdd:PRK11131  381 IEPISQASANQRKGRCGRVSEGICIRLYSEDDFLSRPEFTD-PEILRTNLASVILQMTALGLGDIAAFPFVEAPDKRNIQ 459

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690    956 TAMEQLYTLGALDDEG-----LLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQNVFYRPKDKQALADQ 1030
Cdd:PRK11131  460 DGVRLLEELGAITTDEqasayKLTPLGRQLAQLPVDPRLARMVLEAQKHGCVREVMIITSALSIQDPRERPMDKQQASDE 539

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   1031 KKAKFHQTEGDHLTLLAVYNSWK-------NNKFSNpWCYENFIQARSLRRAQDIRKQMLGIMDRHKLDVVSCGKSTVRV 1103
Cdd:PRK11131  540 KHRRFADKESDFLAFVNLWNYLQeqqkalsSNQFRR-LCRTDYLNYLRVREWQDIYTQLRQVVKELGIPVNSEPAEYREI 618

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   1104 QKAICSGFFRNAAKKDPQEGYRTLIDQQVVYIHPSSALFNRQPEWVVYHELVLTTKEYMREVTTIDPRWLVEFAPAFFK- 1182
Cdd:PRK11131  619 HTALLTGLLSHIGMKDAEKQEYTGARNARFSIFPGSGLFKKPPKWVMVAELVETSRLWGRIAARIEPEWIEPLAQHLIKr 698


                  ....*
gi 4826690   1183 -VSDP 1186
Cdd:PRK11131  699 sYSEP 703
DEXHc_DHX8 cd17971
DEXH-box helicase domain of DEAH-box helicase 8; DEAH-box helicase 8 (DHX8 ,also known as ...
 560-738 3.73e-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: 3.73e-127
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   560 EQRESLPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLG 639
Cdd:cd17971    1 EQRESLPIYKLKEQLIQAVHDNQILVVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVAEEFGCCLG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   640 QEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSAT 719
Cdd:cd17971   81 QEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLSQYSVIMLDEAHERTIHTDVLFGLLKKTVQKRPDLKLIVTSAT 160

                        170
                 ....*....|....*....
gi 4826690   720 LDAVKFSQYFYEAPIFTIP 738
Cdd:cd17971  161 LDAVKFSQYFYEAPIFTIP 179
DEAH_box_HrpB TIGR01970
ATP-dependent helicase HrpB; This model represents HrpB, one of two related but ...
 565-1012 1.28e-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: 1.28e-103
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690     565 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQIT-QYLAEAGYTsrGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQEVG 643
Cdd:TIGR01970    1 LPIHAVLPALRDALAAHPQVVLEAPPGAGKSTAVPlALLDAPGIG--GKIIMLEPRRLAARSAAQRLASQLGEAVGQTVG 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690     644 YTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKtVQK--RQDMKLIVTSATLD 721
Cdd:TIGR01970   79 YRVRGENKVSRRTRLEVVTEGILTRMIQDDPELDGVGALIFDEFHERSLDADLGLALALD-VQSslREDLKILAMSATLD 157

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690     722 AVKFSQYFYEAPIFTIPGRTYPVEILYTKEPETDYLDASLITVMQIHLTEPPGDILVFLTGQEEIDTACEILYERmksLG 801
Cdd:TIGR01970  158 GERLSSLLPDAPVVESEGRSFPVEIRYLPLRGDQRLEDAVSRAVEHALASETGSILVFLPGQAEIRRVQEQLAER---LD 234

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690     802 PDVpelIILPVYSALPSEMQTRIFDPAPPGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKVYNSKTGIDQLVVTPISQ 881
Cdd:TIGR01970  235 SDV---LICPLYGELSLAAQDRAIKPDPQGRRKVVLATNIAETSLTIEGIRVVIDSGLARVARFDPKTGITRLETVRISQ 311

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690     882 AQAKQRAGRAGRTGPGKCYRLYTErAYRDEMLTTNVPEIQRTNLASTVLSLKAMGINDLLSFDFMDAPPMETLITAMEQL 961
Cdd:TIGR01970  312 ASATQRAGRAGRLEPGVCYRLWSE-EQHQRLPAQDEPEILQADLSGLALELAQWGAKDPSDLRWLDAPPSVALAAARQLL 390

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|.
gi 4826690     962 YTLGALDDEGLLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSML 1012
Cdd:TIGR01970  391 QRLGALDAQGRLTAHGKAMAALGCHPRLAAMLLSAHSTGLAALACDLAALL 441
DEXHc_DHX38 cd17983
DEXH-box helicase domain of DEAH-box helicase 38; DEAH-box helicase 38 (DHX38, also known as ...
 565-737 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 4826690   565 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQEVGY 644
Cdd:cd17983    1 LPIFAVRQELLNVIRDNNVVIVVGETGSGKTTQLTQYLHEDGYTDYGMIGCTQPRRVAAMSVAKRVSEEMGVELGEEVGY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   645 TIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSATLDAVK 724
Cdd:cd17983   81 AIRFEDCTSENTVIKYMTDGILLRESLRDPDLDKYSAIIMDEAHERSLNTDVLFGLLREVVARRRDLKLIVTSATMDADK 160

                        170
                 ....*....|...
gi 4826690   725 FSQYFYEAPIFTI 737
Cdd:cd17983  161 FADFFGNVPIFTI 173
PRK11664 PRK11664
ATP-dependent RNA helicase HrpB; Provisional
 564-994 2.48e-94

ATP-dependent RNA helicase HrpB; Provisional


Pssm-ID: 236950 [Multi-domain]  Cd Length: 812  Bit Score: 321.10  E-value: 2.48e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690    564 SLPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQIT-QYLAEAGYTsrGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQEV 642
Cdd:PRK11664    3 SLPVAAVLPELLTALKTAPQVLLKAPTGAGKSTWLPlQLLQHGGIN--GKIIMLEPRRLAARNVAQRLAEQLGEKPGETV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690    643 GYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKtVQK--RQDMKLIVTSATL 720
Cdd:PRK11664   81 GYRMRAESKVGPNTRLEVVTEGILTRMIQRDPELSGVGLVILDEFHERSLQADLALALLLD-VQQglRDDLKLLIMSATL 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690    721 DAVKFSQYFYEAPIFTIPGRTYPVEILYTKEPETDYLDASLITVMQIHLTEPPGDILVFLTGQEEIDTACEILYERmksL 800
Cdd:PRK11664  160 DNDRLQQLLPDAPVIVSEGRSFPVERRYQPLPAHQRFDEAVARATAELLRQESGSLLLFLPGVGEIQRVQEQLASR---V 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690    801 GPDVpelIILPVYSALPSEMQTRIFDPAPPGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKVYNSKTGIDQLVVTPIS 880
Cdd:PRK11664  237 ASDV---LLCPLYGALSLAEQQKAILPAPAGRRKVVLATNIAETSLTIEGIRLVVDSGLERVARFDPKTGLTRLVTQRIS 313

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690    881 QAQAKQRAGRAGRTGPGKCYRLYTERAYrDEMLTTNVPEIQRTNLASTVLSLKAMGINDLLSFDFMDAPPMETLITAMEQ 960
Cdd:PRK11664  314 QASMTQRAGRAGRLEPGICLHLYSKEQA-ERAAAQSEPEILHSDLSGLLLELLQWGCHDPAQLSWLDQPPAAALAAAKRL 392

                         410       420       430
                  ....*....|....*....|....*....|....
gi 4826690    961 LYTLGALDDEGLLTRLGRRMAEFPLEPMLCKMLI 994
Cdd:PRK11664  393 LQQLGALDGQGRLTARGRKMAALGNDPRLAAMLV 426
DEXHc_DHX16 cd17974
DEXH-box helicase domain of DEAH-box helicase 16; DEAH-box helicase 16 (DHX16) is probably ...
 565-737 4.00e-89

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


Pssm-ID: 350732 [Multi-domain]  Cd Length: 174  Bit Score: 285.17  E-value: 4.00e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   565 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRG-KIGCTQPRRVAAMSVAKRVSEEFGCCLGQEVG 643
Cdd:cd17974    1 LPVYPYRDDLLAAVKEHQVLIIVGETGSGKTTQIPQYLHEAGYTKGGgKIGCTQPRRVAAMSVAARVAEEMGVKLGNEVG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   644 YTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSATLDAV 723
Cdd:cd17974   81 YSIRFEDCTSEKTVLKYMTDGMLLREFLTEPDLASYSVMIIDEAHERTLHTDILFGLVKDIARFRPDLKLLISSATMDAE 160

                        170
                 ....*....|....
gi 4826690   724 KFSQYFYEAPIFTI 737
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) ...
 581-737 1.20e-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: 1.20e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   581 NQILIVIGETGSGKTTQITQYLAEAGYTS--RGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQEVGYTIRFEDCTSPETVI 658
Cdd:cd17917    1 NQVVVIVGETGSGKTTQVPQFLLEDGLAKggKGRIVCTQPRRIAAISVAERVAEERGEKLGEEVGYQIRFESKTSSKTRI 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 4826690   659 KYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSATLDAVKFSQYFYEAPIFTI 737
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 ...
 742-903 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 4826690   742 YPVEILYTKEP-----------ETDYLDASLITVMQIHLTEPPGDILVFLTGQEEIDTACEILYERMKSlgPDVPELIIL 810
Cdd:cd18791    1 FPVEVYYLEDIlellgissekeDPDYVDAAVRLILQIHRTEEPGDILVFLPGQEEIERLCELLREELLS--PDLGKLLVL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   811 PVYSALPSEMQTRIFDPAPPGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKVYNSKTGIDQLVVTPISQAQAKQRAGR 890
Cdd:cd18791   79 PLHSSLPPEEQQRVFEPPPPGVRKVVLATNIAETSITIPGVVYVIDSGLVKEKVYDPRTGLSSLVTVWISKASAEQRAGR 158

                        170
                 ....*....|...
gi 4826690   891 AGRTGPGKCYRLY 903
Cdd:cd18791  159 AGRTRPGKCYRLY 171
DEXHc_DHX33 cd17978
DEXH-box helicase domain of DEAH-box helicase 33; DEAH-box helicase 33 (DHX33) stimulates RNA ...
 565-737 5.18e-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: 5.18e-86
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   565 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQEVGY 644
Cdd:cd17978    1 LPIYSARKRLLEELRKHDTVIIIGETGSGKTTQIPQYLYEAGFARGGMIGITQPRRVAAVSVAKRVAEEMGVELGQLVGY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   645 TIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKtVQKR------QDMKLIVTSA 718
Cdd:cd17978   81 SVRFDDVTSEETRIKYMTDGMLLREAIGDPLLSKYSVIILDEAHERTVHTDVLFGLVKS-AQRRrkeqklSPLKVIIMSA 159

                        170
                 ....*....|....*....
gi 4826690   719 TLDAVKFSQYFYEAPIFTI 737
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 ...
 558-737 3.37e-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: 269.29  E-value: 3.37e-83
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   558 ILEQRESLPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGK--IGCTQPRRVAAMSVAKRVSEEFG 635
Cdd:cd17973    6 ILEKRRELPVWEQKEDFLKLLKNNQILVLVGETGSGKTTQIPQFVLDDELPHQPKklVACTQPRRVAAMSVAQRVAEEMD 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   636 CCLGQEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIV 715
Cdd:cd17973   86 VKLGEEVGYSIRFEDCSSAKTILKYMTDGMLLREAMSDPLLSRYSVIILDEAHERTLATDILMGLLKEVVRRRPDLKLIV 165

                        170       180
                 ....*....|....*....|..
gi 4826690   716 TSATLDAVKFSQYFYEAPIFTI 737
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 ...
 565-729 9.15e-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: 9.15e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   565 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGK-IGCTQPRRVAAMSVAKRVSEEFGCCLGQEVG 643
Cdd:cd17980    1 LPVFKLRNHILYLVENYQTIVIVGETGCGKSTQIPQYLAEAGWTAGGRvVGCTQPRRVAAVTVAGRVAEEMGAVLGHEVG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   644 YTIRFEDCTSP-ETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSATLDA 722
Cdd:cd17980   81 YCIRFDDCTDPqATRIKFLTDGMLVREMMLDPLLTKYSVIMLDEAHERTLYTDILIGLLKKIQKKRGDLRLIVASATLDA 160


                 ....*..
gi 4826690   723 VKFSQYF 729
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 ...
 565-737 1.84e-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: 247.08  E-value: 1.84e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   565 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQEVGY 644
Cdd:cd17984    1 LPIQKQRKKLVQAVRDNSFLIVTGNTGSGKTTQLPKYLYEAGFSQHGMIGVTQPRRVAAISVAQRVAEEMKCTLGSKVGY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   645 TIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQ-----DMKLIVTSAT 719
Cdd:cd17984   81 QVRFDDCSSKETAIKYMTDGCLLRHILADPNLTKYSVIILDEAHERSLTTDILFGLLKKLFQEKSpnrkeHLKVVVMSAT 160

                        170
                 ....*....|....*...
gi 4826690   720 LDAVKFSQYFYEAPIFTI 737
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 ...
 565-734 2.83e-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: 203.84  E-value: 2.83e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   565 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQEVGY 644
Cdd:cd17989    1 LPVSQKRDEIAKAIAENQVVIIAGETGSGKTTQLPKICLELGRGIRGLIGHTQPRRLAARSVAERIAEELKTELGGAVGY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   645 TIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSATLDAVK 724
Cdd:cd17989   81 KVRFTDQTSDETCVKLMTDGILLAETQTDRYLRAYDTIIIDEAHERSLNIDFLLGYLKQLLPRRPDLKVIITSATIDAER 160

                        170
                 ....*....|
gi 4826690   725 FSQYFYEAPI 734
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 ...
 565-727 7.38e-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: 197.96  E-value: 7.38e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   565 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSR-----GKIGCTQPRRVAAMSVAKRVSEEFGCcLG 639
Cdd:cd17982    1 LPILAEEQEIMEAINENPVVIICGETGSGKTTQVPQFLYEAGFGSPesdnpGMIGITQPRRVAAVSMAKRVAEELNV-FG 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   640 QEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDM-------- 711
Cdd:cd17982   80 KEVSYQIRYDSTVSENTKIKFMTDGVLLKEIQTDFLLRKYSVIIIDEAHERSVNTDILIGMLSRIVPLRAKLylqdqtvk 159

                        170
                 ....*....|....*...
gi 4826690   712 --KLIVTSATLDAVKFSQ 727
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 ...
 565-734 1.90e-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: 1.90e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   565 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSrgkIGCTQPRRVAAMSVAKRVSEEFGCCLGQEVGY 644
Cdd:cd17979    1 LPIAQYREKIIELLKTHQVVIVAGDTGCGKSTQVPQYLLAAGFRH---IACTQPRRIACISLAKRVAFESLNQYGSKVAY 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   645 TIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSATLDAVK 724
Cdd:cd17979   78 QIRFERTRTLATKLLFLTEGLLLRQIQRDASLPQYNVLILDEVHERHLHGDFLLGVLRCLLRLRPDLKLILMSATINIEL 157

                        170
                 ....*....|
gi 4826690   725 FSQYFYEAPI 734
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 ...
 565-737 7.50e-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: 7.50e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   565 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEaGYTSRGK-----IGCTQPRRVAAMSVAKRVSEEFG--CC 637
Cdd:cd17981    1 LPSYGMKQEIINMIDNNQVTVISGETGCGKTTQVTQFILD-DAIERGKgsscrIVCTQPRRISAISVAERVAAERAesCG 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   638 LGQEVGYTIRFEDCTSPETV-IKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVT 716
Cdd:cd17981   80 LGNSTGYQIRLESRKPRKQGsILYCTTGIVLQWLQSDPHLSNVSHLVLDEIHERNLQSDVLMGIVKDLLPFRSDLKVILM 159

                        170       180
                 ....*....|....*....|.
gi 4826690   717 SATLDAVKFSQYFYEAPIFTI 737
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 ...
 565-737 7.04e-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: 7.04e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   565 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAE-----AGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLG 639
Cdd:cd17975    1 LPVFKHRESILETLKRHRVVVVAGETGSGKSTQVPQFLLEdlllnGGTAQKCNIVCTQPRRISAMSLATRVCEELGCESG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   640 -----QEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLI 714
Cdd:cd17975   81 pggknSLCGYQIRMESRTGEATRLLYCTTGVLLRKLQEDGLLSSISHIIVDEVHERSVQSDFLLIILKEILHKRSDLHLI 160

                        170       180
                 ....*....|....*....|...
gi 4826690   715 VTSATLDAVKFSQYFYEAPIFTI 737
Cdd:cd17975  161 LMSATVDCEKFSSYFTHCPILRI 183
DEXHc_YTHDC2 cd17987
DEXH-box helicase domain of YTH domain containing 2; YTH domain containing 2 (YTHDC2) ...
 565-737 3.59e-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: 3.59e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   565 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRG--KIGCTQPRRVAAMSVAKRVSEEFGCCLGQEV 642
Cdd:cd17987    1 LPVFEKQEQIVRIIKENKVVLIVGETGSGKTTQIPQFLLDDCYANGIpcRIFCTQPRRLAAIAVAERVAAERGEKIGQTV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   643 GYTIRFEDCTSPETVIKYMTDGMLLRECLI-DPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSATLD 721
Cdd:cd17987   81 GYQIRLESRVSPKTLLTFCTNGVLLRTLMAgDSALSTVTHVIVDEVHERDRFSDFLLTKLRDILQKHPNLKLILSSAALD 160

                        170
                 ....*....|....*.
gi 4826690   722 AVKFSQYFYEAPIFTI 737
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 ...
 265-343 1.70e-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: 1.70e-43
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 4826690   265 GDIYNGKVTSIMQFGCFVQLEGLRKRWEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTGTKTSLSMKDVDQETG 343
Cdd:cd05684    1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQNGKISLSMKDVDQDTG 79
DEXHc_DHX9 cd17972
DEXH-box helicase domain of DEAH-box helicase 9; DEAH-box helicase 9 (DHX9, also known as ...
 558-737 8.79e-43

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: 156.15  E-value: 8.79e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   558 ILEQRESLPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAE----AGYTSRGKIGCTQPRRVAAMSVAKRVSEE 633
Cdd:cd17972   52 ILQERELLPVKKFREEILEAISNNPVVIIRGATGCGKTTQVPQYILDdfiqNDRAAECNIVVTQPRRISAVSVAERVAFE 131

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   634 FGCCLGQEVGYTIRFEDCT-SPETVIKYMTDGMLLREclIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMK 712
Cdd:cd17972  132 RGEEVGKSCGYSVRFESVLpRPHASILFCTVGVLLRK--LEAGIRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPDLR 209

                        170       180
                 ....*....|....*....|....*
gi 4826690   713 LIVTSATLDAVKFSQYFYEAPIFTI 737
Cdd:cd17972  210 VILMSATIDTSMFCEYFFNCPVIEV 234
DEXHc_DHX32 cd17977
DEXH-box helicase domain of DEAH-box helicase 32; DEAH-box helicase 32 (DHX32) belongs to the ...
 565-734 1.98e-42

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


Pssm-ID: 350735 [Multi-domain]  Cd Length: 176  Bit Score: 153.06  E-value: 1.98e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   565 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAE---AGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQE 641
Cdd:cd17977    1 LPVWEAKYEFMESLAHNQIVIVSGDAKTGKSSQIPQWCAEyclSAHYQHGVVVCTQVHKQTAVWLALRVADEMDVNIGHE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   642 VGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSATLD 721
Cdd:cd17977   81 VGYVIPFENCCTNETILRYCTDDMLLREMMSDPLLESYGVIILDDAHERTVSTDVLLGLLKDVLLSRPELKLVIITCPHL 160

                        170
                 ....*....|...
gi 4826690   722 AVKFSQYFYEAPI 734
Cdd:cd17977  161 SSKLLSYYGNVPL 173
DEXHc_HrpB cd17990
DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA ...
 565-735 1.24e-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: 1.24e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   565 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQEVGY 644
Cdd:cd17990    1 LPIAAVLPALRAALDAGGQVVLEAPPGAGKTTRVPLALLAELWIAGGKIIVLEPRRVAARAAARRLATLLGEAPGETVGY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   645 TIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQ-KRQDMKLIVTSATLDAV 723
Cdd:cd17990   81 RVRGESRVGRRTRVEVVTEGVLLRRLQRDPELSGVGAVILDEFHERSLDADLALALLLEVQQlLRDDLRLLAMSATLDGD 160

                        170
                 ....*....|..
gi 4826690   724 KFSQYFYEAPIF 735
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 ...
 565-737 5.40e-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: 5.40e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   565 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEA----GYTSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQ 640
Cdd:cd17985    1 LPAWQERETILELLEKHQVLVISGMTGCGKTTQIPQFILDNslqgPPLPVANIICTQPRRISAISVAERVAQERAERVGQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   641 EVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSATL 720
Cdd:cd17985   81 SVGYQIRLESVKSSATRLLYCTTGVLLRRLEGDPTLQGVTHVIVDEVHERTEESDFLLLVLKDLMVQRPDLKVILMSATL 160

                        170
                 ....*....|....*..
gi 4826690   721 DAVKFSQYFYEAPIFTI 737
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 2.06e-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: 143.07  E-value: 2.06e-40
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 4826690    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 ...
 565-737 1.03e-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: 1.03e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   565 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAgYTSRGK---IGCTQPRRVAAMSVAKRVSEEFGCCLGQE 641
Cdd:cd17988    1 LPIYAKREEILSLIEANSVVIIKGATGCGKTTQLPQFILDH-YYKRGKycnIVVTQPRRIAAISIARRVSQEREWTLGSL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   642 VGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQ-KRQDMKLIVTSATL 720
Cdd:cd17988   80 VGYQVGLERPASEETRLIYCTTGVLLQKLINNKTLTEYTHIILDEVHERDQELDFLLLVVRRLLRtNSRHVKIILMSATI 159

                        170       180
                 ....*....|....*....|.
gi 4826690   721 DAVKFSQYF----YEAPIFTI 737
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 ...
 565-737 3.80e-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: 143.88  E-value: 3.80e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   565 LPIYKLKEQLVQAVHDNQ-ILIVIGETGSGKTTQITQYLAEAGYT---SRGKIGCTQPRRVAAMSVAKRVSEEFGCCLGQ 640
Cdd:cd17986    1 LPIWAAKFTFLEQLESPSgIVLVSGEPGSGKSTQVPQWCAEFALSrgfQKGQVTVTQPHPLAARSLALRVADEMDLNLGH 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   641 EVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKL-IVTSAT 719
Cdd:cd17986   81 EVGYSIPQEDCTGPNTILRFCWDRLLLQEMTSTPLLGAWGVVVLDEAQERSVASDSLLGLLKDVRLQRPELRVvVVTSPA 160

                        170
                 ....*....|....*...
gi 4826690   720 LDAvKFSQYFYEAPIFTI 737
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 ...
 565-734 5.62e-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: 5.62e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   565 LPIYKLKEQLVQAVHDNQILIVIGETGSGKTTQITQYLAEAGYTSRGKIGC----TQPRRVAAMSVAKRVSEEFGCCLGQ 640
Cdd:cd17976    1 LPVDSHKESILSAIEQNPVVVISGDTGCGKTTRIPQFILEDYVLRGRGARCnvviTQPRRISAVSVAQRVAHELGPNLRR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   641 EVGYTIRFEDCTSPET-VIKYMTDGMLLRECLIDPDLTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIVTSAT 719
Cdd:cd17976   81 NVGYQVRLESRPPPRGgALLFCTVGVLLKKLQSNPRLEGVSHVIVDEVHERDVNTDFLLILLKGVLQLNPELRVVLMSAT 160

                        170
                 ....*....|....*
gi 4826690   720 LDAVKFSQYFYEAPI 734
Cdd:cd17976  161 GDNQRLSRYFGGCPV 175
HA2 smart00847
Helicase associated domain (HA2) Add an annotation; This presumed domain is about 90 amino ...
 964-1046 7.94e-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: 7.94e-34
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690      964 LGALDDEGLLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQNvfYRPKDKQALADQKKAKFHQTEGDHL 1043
Cdd:smart00847    2 LGALDDDGRLTPLGRKMAELPLDPRLAKMLLAAAEFGCLDEILTIVAMLSVGD--PRPKEKREDADAARRRFADPESDHL 79


                    ...
gi 4826690     1044 TLL 1046
Cdd:smart00847   80 TLL 82
HA2 pfam04408
Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in ...
 957-1045 1.20e-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: 1.20e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690     957 AMEQLYTLGALDDEGLLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQNVFYRP------KDKQALADQ 1030
Cdd:pfam04408    1 ALELLYYLGALDEDGELTPLGRKMAELPLDPRLAKMLLAAAELGCLDEVLTIVAALSVRDPFVQPnfldprSAAKAARRR 80

                           90       100
                   ....*....|....*....|....
gi 4826690    1031 KKAKFHQ---------TEGDHLTL 1045
Cdd:pfam04408   81 RRAADEKarakfarldLEGDHLTL 104
OB_NTP_bind pfam07717
Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus ...
 1103-1179 1.70e-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: 1.70e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690    1103 VQKAICSGFFRNAAKKDPQE-GYRTLIDQQVVYIHPSSALFN---RQPEWVVYHELVLTTKEYMREVTTIDPRWLVEFAP 1178
Cdd:pfam07717    1 LRAALAAGLYPNVARRDPKGkGYTTLSDNQRVFIHPSSVLFNektFPPEWVVYQELVETTKVYIRTVTAISPEWLLLFAP 80


                   .
gi 4826690    1179 A 1179
Cdd:pfam07717   81 H 81
DEXDc smart00487
DEAD-like helicases superfamily;
561-746 4.93e-27

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 109.89  E-value: 4.93e-27
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690      561 QRESLPIyklkeqlvqAVHDNQILIVIGETGSGKTTQITQYLAEAGY-TSRGKIGCTQPRRVAAMSVAKRVSEEFGCCLG 639
Cdd:smart00487   13 QKEAIEA---------LLSGLRDVILAAPTGSGKTLAALLPALEALKrGKGGRVLVLVPTRELAEQWAEELKKLGPSLGL 83

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690      640 QEVGYT------IRFEDCTSPETVIKYMTDGMLLRECLIDP-DLTQYAIIMLDEAHERT--IHTDVLFGLLKKTVQKRQd 710
Cdd:smart00487   84 KVVGLYggdskrEQLRKLESGKTDILVTTPGRLLDLLENDKlSLSNVDLVILDEAHRLLdgGFGDQLEKLLKLLPKNVQ- 162

                           170       180       190
                    ....*....|....*....|....*....|....*...
gi 4826690      711 mkLIVTSATL--DAVKFSQYFYEAPIFTIPGRTYPVEI 746
Cdd:smart00487  163 --LLLLSATPpeEIENLLELFLNDPVFIDVGFTPLEPI 198
GH2_like cd21690
GIPC homology 2 (GH2) domain-like family; The GIPC (GAIP C-terminus-interacting protein) ...
 28-89 9.58e-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: 95.23  E-value: 9.58e-24
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 4826690    28 LSLVSKVCTELDNHLGINDKDLAEFVISLAEKNTTFDTFKASLVKNGAEFTDSLISNLLRLI 89
Cdd:cd21690    1 LSAIEKVDDLLKNYLGIDDPELAEFVISLAKKKKNPDEFAEALDENDAAFPDEFVFDLYRAI 62
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 261-339 2.34e-21

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 100.51  E-value: 2.34e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690    261 EPTIGDIYNGKVTSIMQFGCFVQLegLRKRwEGLVHISELRREgRVANVADVVSKGQRVKVKVLSFT-GTKTSLSMKDVD 339
Cdd:PRK11824  618 EPEVGEIYEGKVVRIVDFGAFVEI--LPGK-DGLVHISEIADE-RVEKVEDVLKEGDEVKVKVLEIDkRGRIRLSRKAVL 693
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 265-335 1.24e-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: 1.24e-20
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 4826690   265 GDIYNGKVTSIMQFGCFVQLEGLRkrwEGLVHISELRREgRVANVADVVSKGQRVKVKVLSF-TGTKTSLSM 335
Cdd:cd04472    1 GKIYEGKVVKIKDFGAFVEILPGK---DGLVHISELSDE-RVEKVEDVLKVGDEVKVKVIEVdDRGRISLSR 68
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 260-353 5.02e-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: 87.16  E-value: 5.02e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   260 EEPTIGDIYNGKVTSIMQFGCFVQLEGlrkRWEGLVHISELrREGRVANVADVVSKGQRVKVKVLSFTGT-KTSLSMKDV 338
Cdd:COG1098    1 MSIEVGDIVEGKVTGITPFGAFVELPE---GTTGLVHISEI-ADGYVKDINDYLKVGDEVKVKVLSIDEDgKISLSIKQA 76

                         90
                 ....*....|....*
gi 4826690   339 DQETGEDLNPNRRRN 353
Cdd:COG1098   77 EEKPKRPPRPRRNSR 91
S1_dom_CvfD NF040579
CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ...
 264-352 2.98e-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: 2.98e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690    264 IGDIYNGKVTSIMQFGCFVQLEglrKRWEGLVHISELrREGRVANVADVVSKGQRVKVKVLS---FTGtKTSLSMKDVDQ 340
Cdd:NF040579    3 IGDIVEGKVTGIQPYGAFVALD---EHTQGLIHISEI-KHGYVKDINDFLKVGQEVKVKVLDideYTG-KISLSLRALEE 77

                          90
                  ....*....|..
gi 4826690    341 ETGEDLNPNRRR 352
Cdd:NF040579   78 APEKHRKRRKHR 89
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 264-338 1.47e-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: 1.47e-18
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 4826690   264 IGDIYNGKVTSIMQFGCFVQLE-GLrkrwEGLVHISELRREGRVANVADVVSKGQRVKVKVLSF--TGTKTSLSMKDV 338
Cdd:COG0539  274 VGDVVKGKVTRLTDFGAFVELEpGV----EGLVHISEMSWTKRVAHPSDVVKVGDEVEVKVLDIdpEERRISLSIKQL 347
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 264-337 9.55e-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: 9.55e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 4826690   264 IGDIYNGKVTSIMQFGCFVQLEGLrkrwEGLVHISELRReGRVANVADVVSKGQRVKVKVLSF--TGTKTSLSMKD 337
Cdd:COG0539  189 EGDVVEGTVKNITDFGAFVDLGGV----DGLLHISEISW-GRVKHPSEVLKVGDEVEVKVLKIdrEKERISLSLKQ 259
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
259-344 2.78e-16

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 83.84  E-value: 2.78e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690    259 PEEPTIGDIYNGKVTSIMQFGCFVQLE-GLrkrwEGLVHISELrREGRVANVADVVSKGQRVKVKVLSFTGT--KTSLSM 335
Cdd:PRK00087  557 EEKYPVGSIVLGKVVRIAPFGAFVELEpGV----DGLVHISQI-SWKRIDKPEDVLSEGEEVKAKILEVDPEekRIRLSI 631


                  ....*....
gi 4826690    336 KDVDQETGE 344
Cdd:PRK00087  632 KEVEEEPGD 640
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 265-336 4.56e-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: 4.56e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 4826690   265 GDIYNGKVTSIMQFGCFVQL-EGLrkrwEGLVHISELRREgRVANVADVVSKGQRVKVKVLSFTGT-KTSLSMK 336
Cdd:cd05692    1 GSVVEGTVTRLKPFGAFVELgGGI----SGLVHISQIAHK-RVKDVKDVLKEGDKVKVKVLSIDARgRISLSIK 69
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 265-338 4.70e-15

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 78.76  E-value: 4.70e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 4826690    265 GDIYNGKVTSIMQFGCFVQLEGLrkrwEGLVHISELRREgRVANVADVVSKGQRVKVKVLSF---TGtKTSLSMKDV 338
Cdd:PRK06676  193 GDVVEGTVARLTDFGAFVDIGGV----DGLVHISELSHE-RVEKPSEVVSVGQEVEVKVLSIdweTE-RISLSLKDT 263
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 265-364 8.65e-15

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 77.99  E-value: 8.65e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690    265 GDIYNGKVTSIMQFGCFVQL-EGLrkrwEGLVHISELRREgRVANVADVVSKGQRVKVKVLSF--TGTKTSLSMKDVDQE 341
Cdd:PRK06676  278 GDVIEGTVKRLTDFGAFVEVlPGV----EGLVHISQISHK-HIATPSEVLEEGQEVKVKVLEVneEEKRISLSIKALEEA 352

                          90       100
                  ....*....|....*....|...
gi 4826690    342 TGEDLNPNRRRNLVGETNEETSM 364
Cdd:PRK06676  353 PAEEEDRREEYRQYELPEEETGF 375
HELICc smart00490
helicase superfamily c-terminal domain;
791-895 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 4826690      791 EILYERMKSLGpdvpeLIILPVYSALPSEMQTRIFDPAPPGSRKVVIATNIAETSLTIDGIYYVVDPGFvkqkvynsktg 870
Cdd:smart00490    1 EELAELLKELG-----IKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDL----------- 64

                            90       100
                    ....*....|....*....|....*
gi 4826690      871 idqlvvtPISQAQAKQRAGRAGRTG 895
Cdd:smart00490   65 -------PWSPASYIQRIGRAGRAG 82
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
264-336 3.06e-14

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 68.78  E-value: 3.06e-14
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 4826690      264 IGDIYNGKVTSIMQFGCFVQLEGlrkRWEGLVHISELRREgRVANVADVVSKGQRVKVKVLSFTGTK--TSLSMK 336
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGN---GVEGLIPISELSDK-RVKDPEEVLKVGDEVKVKVLSVDEEKgrIILSLK 72
PRK08059 PRK08059
general stress protein 13; Validated
 263-367 8.61e-14

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 69.31  E-value: 8.61e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690    263 TIGDIYNGKVTSIMQFGCFVQLEGlrkRWEGLVHISELrREGRVANVADVVSKGQRVKVKVLSF--TGTKTSLSMKdvdq 340
Cdd:PRK08059    6 EVGSVVTGKVTGIQPYGAFVALDE---ETQGLVHISEI-THGFVKDIHDFLSVGDEVKVKVLSVdeEKGKISLSIR---- 77

                          90       100
                  ....*....|....*....|....*..
gi 4826690    341 ETGEDLNPNRRRNLVGETNEETSMRNP 367
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 ...
 264-336 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 4826690   264 IGDIYNGKVTSIMQFGCFVQLEGLrkrwEGLVHISELRReGRVANVADVVSKGQRVKVKVLSFTGTKTSLSMK 336
Cdd:cd05688    1 EGDVVEGTVKSITDFGAFVDLGGV----DGLLHISDMSW-GRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 761-895 1.38e-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: 1.38e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690     761 LITVMQIHLTEPPGDILVFLTGQEEIDtaCEILYERMKslgpdvpeLIILPVYSALPSEMQTRIFDPAPPGSRKVVIATN 840
Cdd:pfam00271    3 LEALLELLKKERGGKVLIFSQTKKTLE--AELLLEKEG--------IKVARLHGDLSQEEREEILEDFRKGKIDVLVATD 72

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 4826690     841 IAETSLTIDGIYYVVDpgfvkqkvYNSKTGIDQLVvtpisqaqakQRAGRAGRTG 895
Cdd:pfam00271   73 VAERGLDLPDVDLVIN--------YDLPWNPASYI----------QRIGRAGRAG 109
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 264-336 5.84e-12

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 69.81  E-value: 5.84e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 4826690    264 IGDIYNGKVTSIMQFGCFVQLE-GLrkrwEGLVHISELRREGRVANVADVVSKGQRVKVKVLS--FTGTKTSLSMK 336
Cdd:PRK06299  286 VGSKVKGKVTNITDYGAFVELEeGI----EGLVHVSEMSWTKKNKHPSKVVSVGQEVEVMVLEidEEKRRISLGLK 357
PRK08582 PRK08582
RNA-binding protein S1;
270-361 6.01e-12

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 64.28  E-value: 6.01e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690    270 GKVTSIMQFGCFVQLEGLRKrweGLVHISELrREGRVANVADVVSKGQRVKVKVLSFTGT-KTSLSM-KDVDQETGEDLN 347
Cdd:PRK08582   11 GKVTGITNFGAFVELPEGKT---GLVHISEV-ADNYVKDINDHLKVGDEVEVKVLNVEDDgKIGLSIkKAKDRPKRQHDR 86

                          90
                  ....*....|....
gi 4826690    348 PNRRRNLVGETNEE 361
Cdd:PRK08582   87 PRHEDNRGGGNDVA 100
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 268-335 1.87e-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: 1.87e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 4826690   268 YNGKVTSIMQFGCFVQLEGlrkRWEGLVHISELRREgRVANVADVVSKGQRVKVKVLSFTGTKTSLSM 335
Cdd:cd00164    1 VTGKVVSITKFGVFVELED---GVEGLVHISELSDK-FVKDPSEVFKVGDEVEVKVLEVDPEKGRISL 64
rpsA PRK13806
30S ribosomal protein S1; Provisional
 265-348 2.04e-11

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 67.83  E-value: 2.04e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690    265 GDIYNGKVTSIMQFGCFVQLE-GLrkrwEGLVHISELRReGRVANVADVVSKGQRVKVKVLSF------TGTKTSLSMKD 337
Cdd:PRK13806  203 GDVVEGTVTRLAPFGAFVELApGV----EGMVHISELSW-SRVQKADEAVSVGDTVRVKVLGIerakkgKGLRISLSIKQ 277

                          90
                  ....*....|....*
gi 4826690    338 VD----QETGEDLNP 348
Cdd:PRK13806  278 AGgdpwDTVGDRLKA 292
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
265-338 2.08e-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: 2.08e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 4826690    265 GDIYNGKVTSIMQFGCFVQLEGLrkrwEGLVHISELRReGRVANVADVVSKGQRVKVKVLSF--TGTKTSLSMKDV 338
Cdd:PRK00087  478 GDVVEGEVKRLTDFGAFVDIGGV----DGLLHVSEISW-GRVEKPSDVLKVGDEIKVYILDIdkENKKLSLSLKKL 548
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 262-324 1.23e-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: 1.23e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 4826690     262 PTIGDIYNGKVTSIMQFGCFVQLEGLRkrwEGLVHISELRREgRVANVADVVSKGQRVKVKVL 324
Cdd:pfam00575    1 PEKGDVVEGEVTRVTKGGAFVDLGNGV---EGFIPISELSDD-HVEDPDEVIKVGDEVKVKVL 59
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
264-341 4.65e-10

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 58.56  E-value: 4.65e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690    264 IGDIYNGKVTSIMQFGCFVQLEGLRKrweGLVHISELrREGRVANVADVVSKGQRVKVKVL---SFTGtKTSLSMKDVDQ 340
Cdd:PRK07252    3 IGDKLKGTITGIKPYGAFVALENGTT---GLIHISEI-KTGFIDNIHQLLKVGEEVLVQVVdfdEYTG-KASLSLRTLEE 77


                  .
gi 4826690    341 E 341
Cdd:PRK07252   78 E 78
PRK05807 PRK05807
RNA-binding protein S1;
265-336 5.82e-10

RNA-binding protein S1;


Pssm-ID: 235614 [Multi-domain]  Cd Length: 136  Bit Score: 58.60  E-value: 5.82e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 4826690    265 GDIYNGKVTSIMQFGCFVQLEGLrkrwEGLVHISELrREGRVANVADVVSKGQRVKVKVLSF-TGTKTSLSMK 336
Cdd:PRK05807    6 GSILEGTVVNITNFGAFVEVEGK----TGLVHISEV-ADTYVKDIREHLKEQDKVKVKVISIdDNGKISLSIK 73
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 265-336 1.64e-09

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 62.10  E-value: 1.64e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 4826690    265 GDIYNGKVTSIMQFGCFVQLEGLrkrwEGLVHISELRReGRVANVADVVSKGQRVKVKVLSFTGTKT--SLSMK 336
Cdd:PRK06299  202 GQVVEGVVKNITDYGAFVDLGGV----DGLLHITDISW-KRVNHPSEVVNVGDEVKVKVLKFDKEKKrvSLGLK 270
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 262-341 1.73e-09

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 59.84  E-value: 1.73e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690    262 PTIGDIYNGKVTSIMQFGCFVQLE---GLrkrwEGLVHISELRReGRVANVADVVSKGQRVKVKVLSFTGTKTS--LSMK 336
Cdd:PRK03987    6 PEEGELVVGTVKEVKDFGAFVTLDeypGK----EGFIHISEVAS-GWVKNIRDHVKEGQKVVCKVIRVDPRKGHidLSLK 80


                  ....*.
gi 4826690    337 DV-DQE 341
Cdd:PRK03987   81 RVnEHQ 86
rpsA PRK13806
30S ribosomal protein S1; Provisional
 265-337 2.05e-09

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 61.66  E-value: 2.05e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 4826690    265 GDIYNGKVTSIMQFGCFVQLE-GLrkrwEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTGTK--TSLSMKD 337
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 ...
 265-325 2.60e-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: 2.60e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 4826690   265 GDIYNGKVTSIMQFGCFVQLeGLRKrwEGLVHISELRrEGRVANVADVVSKGQRVKVKVLS 325
Cdd:cd05685    1 GMVLEGVVTNVTDFGAFVDI-GVKQ--DGLIHISKMA-DRFVSHPSDVVSVGDIVEVKVIS 57
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
264-344 4.13e-09

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 60.81  E-value: 4.13e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   264 IGDIYNGKVTSIMQFGCFV-----QleglrkrwEGLVHISELRrEGRVANVADVVSKGQRVKVKVLSFTGTK--TSLSMK 336
Cdd:COG2183  641 PGMILEGTVTNVTDFGAFVdigvhQ--------DGLVHISQLS-DRFVKDPREVVKVGDIVKVKVLEVDLKRkrISLSMK 711


                 ....*...
gi 4826690   337 DVDQETGE 344
Cdd:COG2183  712 LDDEAGAA 719
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 264-348 4.91e-09

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 60.44  E-value: 4.91e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690    264 IGDIYNGKVTSIMQFGCFVQLE-GLrkrwEGLVHISELrREGRVANVADVVSKGQRVKVKV--LSFTGTKTSLSMKDVDQ 340
Cdd:PRK07899  293 IGQIVPGKVTKLVPFGAFVRVEeGI----EGLVHISEL-AERHVEVPEQVVQVGDEVFVKVidIDLERRRISLSLKQANE 367

                          90
                  ....*....|.
gi 4826690    341 ---ETGEDLNP 348
Cdd:PRK07899  368 gvtPESEDFDP 378
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 260-336 6.57e-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: 59.75  E-value: 6.57e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690     260 EEPTIGDIYNGKVTSIMQFGCFVQL-EGLrkrwEGLVHISELRREGRVANVADVVSKGQRVKVKVLSF--TGTKTSLSMK 336
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. ...
 262-324 8.85e-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: 8.85e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 4826690   262 PTIGDIYNGKVTSIMQFGCFVQLEGLRKRwEGLVHISELRReGRVANVADVVSKGQRVKVKVL 324
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, ...
 264-344 1.04e-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: 1.04e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   264 IGDIYNGKVTSIMQFGCFVQLEGLRKrwEGLVHISEL----------------RREGRVANVadvvskGQRVKVKVlsft 327
Cdd:cd04471    1 VGEEFDGVISGVTSFGLFVELDNLTV--EGLVHVSTLgddyyefdeenhalvgERTGKVFRL------GDKVKVRV---- 68

                         90
                 ....*....|....*..
gi 4826690   328 gtktslsmKDVDQETGE 344
Cdd:cd04471   69 --------VRVDLDRRK 77
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 264-336 2.38e-08

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 58.25  E-value: 2.38e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 4826690    264 IGDIYNGKVTSIMQFGCFVQLE-GLrkrwEGLVHISELRREGRVANVADVVSKGQRVKVKVLSF--TGTKTSLSMK 336
Cdd:PRK06299  373 VGDVVEGKVKNITDFGAFVGLEgGI----DGLVHLSDISWDKKGEEAVELYKKGDEVEAVVLKVdvEKERISLGIK 444
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 263-346 2.50e-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: 2.50e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690     263 TIGDIYNGKVTSIMQFGCFVQLEGLrkrwEGLVHISELRReGRVANVADVVSKGQRVKVKVLSFTGTKT--SLSMKDVDQ 340
Cdd:TIGR00717  186 KEGDVVKGVVKNITDFGAFVDLGGV----DGLLHITDMSW-KRVKHPSEYVKVGQEVKVKVIKFDKEKGriSLSLKQLGE 260


                   ....*.
gi 4826690     341 ETGEDL 346
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 ...
 263-336 2.51e-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: 2.51e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 4826690   263 TIGDIYNGKVTSIMQFGCFVQLEGlrKRWEGLVHISELRrEGRVANVADVVSKGQRVKVKVLSF--TGTKTSLSMK 336
Cdd:cd05708    1 KVGQKIDGTVRRVEDYGVFIDIDG--TNVSGLCHKSEIS-DNRVADASKLFRVGDKVRAKVLKIdaEKKRISLGLK 73
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
 262-393 2.71e-08

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 58.37  E-value: 2.71e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690    262 PTIGDIY-NGKVTSIMQFGCFVQLEGLRkrwEGLVHISELrREGRVANVADVVSKGQRVKVKVLSFT-GTKTSLSMKDVD 339
Cdd:PLN00207  751 PTVGDIYrNCEIKSIAPYGAFVEIAPGR---EGLCHISEL-SSNWLAKPEDAFKVGDRIDVKLIEVNdKGQLRLSRRALL 826

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 4826690    340 QETGEDLNPNRRRNlvGETNEETSMRN----PDRPTHLSLVSAPEVEDDSLERKRLTR 393
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 ...
 265-335 5.30e-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: 5.30e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 4826690   265 GDIYNGKVTSIMQFGCFVQLEGlrkRWEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTGTKTSLSM 335
Cdd:cd05690    1 GTVVSGKIKSITDFGIFVGLDG---GIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDVERERISL 68
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 265-341 3.46e-07

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 54.40  E-value: 3.46e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690    265 GDIYNGKVTSIMQFGCFVQLEGLRkrwEGLVHISELRREgRVANVADVVSKGQRVKVKVLSFtGTKT---SLSMKDVDQE 341
Cdd:PRK06299  461 GSIVTGTVTEVKDKGAFVELEDGV---EGLIRASELSRD-RVEDATEVLKVGDEVEAKVINI-DRKNrriSLSIKALDEA 535
PHA02653 PHA02653
RNA helicase NPH-II; Provisional
 676-904 4.49e-07

RNA helicase NPH-II; Provisional


Pssm-ID: 177443 [Multi-domain]  Cd Length: 675  Bit Score: 54.21  E-value: 4.49e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690    676 LTQYAIIMLDEAHERTIHTDVLFGLLKKTVQKRQDMKLIvtSATL-DAVKFSQYFYEAPIFT-IPGRT-YPVEILYTK-- 750
Cdd:PHA02653  289 LFDYGTVIIDEVHEHDQIGDIIIAVARKHIDKIRSLFLM--TATLeDDRDRIKEFFPNPAFVhIPGGTlFPISEVYVKnk 366

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690    751 ----------EPETDYLDASLITvmqihLTEPPG-DILVFLTGQEEIDTACEILYERMkslgpdvPELIILPVYSALPS- 818
Cdd:PHA02653  367 ynpknkrayiEEEKKNIVTALKK-----YTPPKGsSGIVFVASVSQCEEYKKYLEKRL-------PIYDFYIIHGKVPNi 434

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690    819 -EMQTRIFDPAPPgsrKVVIATNIAETSLTIDGIYYVVDPGfvkqKVYNSKT-GIDQLVvtpISQAQAKQRAGRAGRTGP 896
Cdd:PHA02653  435 dEILEKVYSSKNP---SIIISTPYLESSVTIRNATHVYDTG----RVYVPEPfGGKEMF---ISKSMRTQRKGRVGRVSP 504


                  ....*...
gi 4826690    897 GKCYRLYT 904
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 ...
 270-335 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 4826690   270 GKVTSIMQFGCFVQLE-GLrkrwEGLVHISELRREGRVANVADVVSKGQRVKVKVLSFTGTKTSLSM 335
Cdd:cd05689    9 GKVTNLTDYGCFVELEeGV----EGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERRRISL 71
VacB COG0557
Exoribonuclease R [Transcription];
264-325 2.84e-06

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 51.65  E-value: 2.84e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 4826690   264 IGDIYNGKVTSIMQFGCFVQLEGLRKrwEGLVHISEL----------------RREGRVANVadvvskGQRVKVKVLS 325
Cdd:COG0557  622 VGEEFEGVISGVTSFGLFVELDELGV--EGLVHVSSLgddyyeyderrqalvgERTGKRYRL------GDRVEVRVVR 691
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 265-345 3.54e-06

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 51.20  E-value: 3.54e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690    265 GDIYNGKVTSIMQFGCFVQLEGLrkrwEGLVHISELRREgRVANVADVVSKGQRVKVKVLS--FTGTKTSLSMKdvdqET 342
Cdd:PRK07899  209 GQVRKGVVSSIVNFGAFVDLGGV----DGLVHVSELSWK-HIDHPSEVVEVGQEVTVEVLDvdMDRERVSLSLK----AT 279


                  ...
gi 4826690    343 GED 345
Cdd:PRK07899  280 QED 282
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 584-719 1.06e-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: 1.06e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   584 LIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGccLGQEVGYTIRFedcTSPETV------ 657
Cdd:cd00046    4 VLITAPTGSGKTLAALLAALLLLLKKGKKVLVLVPTKALALQTAERLRELFG--PGIRVAVLVGG---SSAEEReknklg 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 4826690   658 ---IKYMTDGMLLRECLID--PDLTQYAIIMLDEAHERTIHTDVLFgLLKKTVQKRQ--DMKLIVTSAT 719
Cdd:cd00046   79 dadIIIATPDMLLNLLLREdrLFLKDLKLIIVDEAHALLIDSRGAL-ILDLAVRKAGlkNAQVILLSAT 146
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
 590-688 1.93e-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: 46.00  E-value: 1.93e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   590 TGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSeefgcclGQEVGY-TIRFEDCTSPETVIKYMTDGMLLR 668
Cdd:cd17931   10 PGAGKTTRVLPQIIREAIKKRLRTLVLAPTRVVAAEMYEALR-------GLPIRYrTGAVKEEHGGNEIVDYMCHGTFTC 82

                         90       100
                 ....*....|....*....|
gi 4826690   669 ECLIDPDLTQYAIIMLDEAH 688
Cdd:cd17931   83 RLLSPKRVPNYNLIIMDEAH 102
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 265-336 3.61e-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: 47.81  E-value: 3.61e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 4826690     265 GDIYNGKVTSIMQFGCFVQLEGlrkRWEGLVHISELRREgRVANVADVVSKGQRVKVKVLSF--TGTKTSLSMK 336
Cdd:TIGR00717  447 GSVVKGKVTEIKDFGAFVELPG---GVEGLIRNSELSEN-RDEDKTDEIKVGDEVEAKVVDIdkKNRKVSLSVK 516
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 264-346 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 4826690    264 IGDIYNGKVTSIMQFGCFVQL-EGLrkrwEGLVHISELRREGRVANVADVVSKGQRVKVKVLSF--TGTKTSLSMKDVDQ 340
Cdd:PRK12269  578 VNDVVKGRVTKIADFGAFIELaEGI----EGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGYdiQAGRVSLGLKQVTA 653


                  ....*.
gi 4826690    341 ETGEDL 346
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 ...
 260-330 1.83e-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: 1.83e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 4826690   260 EEPTIGDIYNGKVTSI---MQfGCFVQLeGLRKrwEGLVHISELRR--EGRVANVADVVSKGQRVKVKVL-SFTGTK 330
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 ...
 834-903 2.21e-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: 2.21e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 4826690   834 KVVIATNIAETSLTIDGIYYVVDPGFvkqkvynsktgidqlvvtPISQAQAKQRAGRAGRTG--PGKCYRLY 903
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 ...
 260-325 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 4826690   260 EEPTIGDIYNGKVTSIMQFGCFVQLEGlrkRWEGLVHISELRREgRVANVADVVSKGQRVKVKVLS 325
Cdd:cd04461   10 SDLKPGMVVHGYVRNITPYGVFVEFLG---GLTGLAPKSYISDE-FVTDPSFGFKKGQSVTAKVTS 71
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 260-341 1.69e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 42.17  E-value: 1.69e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690    260 EEPTIGDIYNGKVTSIMQFGCFVQLEGlrKRWEGLVHISELRREgRVANVADVVSKGQRVKVKVLSFTGTKTS--LSMKD 337
Cdd:PRK06676   13 KEVEVGDVVTGEVLKVEDKQVFVNIEG--YKVEGVIPISELSND-HIEDINDVVKVGDELEVYVLKVEDGEGNllLSKRR 89


                  ....
gi 4826690    338 VDQE 341
Cdd:PRK06676   90 LEAE 93
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 264-336 2.65e-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: 2.65e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 4826690     264 IGDIYNGKVTSIMQFGCFVQLEGlrkRWEGLVHISELRREGRVANVADVVSKGQRVKVKVLS--FTGTKTSLSMK 336
Cdd:TIGR00717  359 VGDRVTGKIKKITDFGAFVELEG---GIDGLIHLSDISWDKDGREADHLYKKGDEIEAVVLAvdKEKKRISLGVK 430
AAA_22 pfam13401
AAA domain;
582-688 2.69e-03

AAA domain;


Pssm-ID: 379165 [Multi-domain]  Cd Length: 129  Bit Score: 39.25  E-value: 2.69e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690     582 QILIVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVSEEFGcclgqevgytIRFEDCTSPETVIKYM 661
Cdd:pfam13401    6 GILVLTGESGTGKTTLLRRLLEQLPEVRDSVVFVDLPSGTSPKDLLRALLRALG----------LPLSGRLSKEELLAAL 75

                           90       100
                   ....*....|....*....|....*..
gi 4826690     662 TDgmLLRECLIDPdltqyaIIMLDEAH 688
Cdd:pfam13401   76 QQ--LLLALAVAV------VLIIDEAQ 94
Cas3_I cd09639
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short ...
 583-903 3.19e-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: 41.26  E-value: 3.19e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   583 ILIVIGETGSGKTTQITQYLAEAGYTS-RGKIGCTQPRRVAAMSVAKRVSEEFG-CCLGQEVGYTIRFEDCTSPETVIK- 659
Cdd:cd09639    1 LLVIEAPTGYGKTEAALLWALHSLKSQkADRVIIALPTRATINAMYRRAKEAFGeTGLYHSSILSSRIKEMGDSEEFEHl 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   660 ---YMTDGML-----LRECLIDP------------DLTQ----YAIIMLDEAHERTIHTDVLF-GLLKktVQKRQDMKLI 714
Cdd:cd09639   81 fplYIHSNDTlfldpITVCTIDQvlksvfgefghyEFTLasiaNSLLIFDEVHFYDEYTLALIlAVLE--VLKDNDVPIL 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   715 VTSATLDAVkFSQYF--YEAPIFTIPGRTYPVEILYT-KEPETDYLDASLITVMqIHLTEPPGDILVFLTgqeEIDTACE 791
Cdd:cd09639  159 LMSATLPKF-LKEYAekIGYVEENEPLDLKPNERAPFiKIESDKVGEISSLERL-LEFIKKGGSVAIIVN---TVDRAQE 233

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4826690   792 IlYERMKSLGPDVPELII----LPVYSALPSEMQTRIFDPAPPGsrkVVIATNIAETSLTIDGIYYVVDPgfvkqkvyns 867
Cdd:cd09639  234 F-YQQLKEKGPEEEIMLIhsrfTEKDRAKKEAELLLEFKKSEKF---VIVATQVIEASLDISVDVMITEL---------- 299

                        330       340       350
                 ....*....|....*....|....*....|....*.
gi 4826690   868 kTGIDQLVvtpisqaqakQRAGRAGRTGPGKCYRLY 903
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 ...
 259-325 5.35e-03

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


Pssm-ID: 239919 [Multi-domain]  Cd Length: 77  Bit Score: 36.82  E-value: 5.35e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 4826690   259 PEEPTIGDIYNGKVTSIMQFGCFVQLEglrKRWEGLVHISELRREGRVanvadvvskGQRVKVKVLS 325
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 ...
 265-326 6.39e-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: 6.39e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 4826690   265 GDIYNGKVTSIMQFGCFVQ-LEGLRkrweGLVHISELrREGRVANVADVVSKGQRVKVKVLSF 326
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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