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Conserved domains on  [gi|941644392|gb|JAM24740|]
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Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 [Daphnia magna]

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];
516-965 8.54e-174

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: 533.12  E-value: 8.54e-174
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  516 SLPIYKLRDELIKAVSDNQILIVIGETGSGKTTQITQYLSESGFTARGKIGCTQPRRVAAMSVAKRVSEEFGCRLGQEVG 595
Cdd:COG1643     9 DLPVSAVLPELLAALRAHQVVVLAAPPGAGKTTQLPLALLELGWGAGGRIGMLEPRRLAARAAAERMAEELGEPVGETVG 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  596 YTIRFEDCTSPETLIKYMTDGMLLRECLIDPDLQTYSCIMLDEAHERTIHTDVLFGLLKQAVQK-RAELKLIVTSATLDA 674
Cdd:COG1643    89 YRVRFEDKVSAATRIEVVTEGILLRELQRDPELEGVDTVIFDEFHERSLNADLLLALLLDLQPAlRPDLKLLVMSATLDA 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  675 VKFSQYFFEAPIFTIPGRTFPVEILYT--REPETDYLDASLITVMQIhLNEPPGDILLFLTGQEEIDTACEILyerMKSM 752
Cdd:COG1643   169 ERFARLLGDAPVIESSGRTYPVEVRYRplPADERDLEDAVADAVREA-LAEEPGDILVFLPGEREIRRTAEAL---RGRL 244

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  753 GPDVpelIILPVYSALPSEMQTRIFEPAPPGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKVYNSKTGMDSLVVTPIS 832
Cdd:COG1643   245 PPDT---EILPLYGRLSAAEQDRAFAPAPHGRRRIVLATNIAETSLTVPGIRYVIDSGLARIPRYDPRSGVTRLPTERIS 321

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  833 QAQAKQRAGRAGRTGPGKTYRLYTERAYRdEMLATPVPEIQRTNLASTVLQLKAMGINDLLNFDFMDAPPVESLIMALEQ 912
Cdd:COG1643   322 QASANQRAGRAGRLAPGICYRLWSEEDFA-RRPAFTDPEILRADLASLILELAAWGLGDPEDLPFLDPPPARAIADARAL 400

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|...
gi 941644392  913 LHSLSALDDEGLLTRLGRRMAEFPLEPSLSKMLIMSVHLMCSDEILTVVSMLS 965
Cdd:COG1643   401 LQELGALDADGRLTPLGRALARLPLDPRLARMLLAAAELGCLREAAILAALLS 453
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 212-290 3.23e-39

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: 140.07  E-value: 3.23e-39
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 941644392  212 GNVYAGKVMNLAAFGCFVQLEGIRKKCEGLVHISQLRREGRVNSVAEVVNRGDKVYVKVMSIAGQKISLSMKDVDQDSG 290
Cdd:cd05684     1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQNGKISLSMKDVDQDTG 79
OB_NTP_bind pfam07717
Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus ...
 1044-1120 3.62e-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: 111.58  E-value: 3.62e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  1044 VQKAICSGFFRNAAKKDPQE-GYRTLVDGQVVYIHPSSAIFN---RQPEWVVYHELVQTTKEYMREVTVIDAKWLVEFAP 1119
Cdd:pfam07717    1 LRAALAAGLYPNVARRDPKGkGYTTLSDNQRVFIHPSSVLFNektFPPEWVVYQELVETTKVYIRTVTAISPEWLLLFAP 80


                   .
gi 941644392  1120 A 1120
Cdd:pfam07717   81 H 81
GH2_like super family cl41749
GIPC homology 2 (GH2) domain-like family; The GIPC (GAIP C-terminus-interacting protein) ...
 1-23 2.67e-05

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.


The actual alignment was detected with superfamily member cd21691:

Pssm-ID: 425380  Cd Length: 68  Bit Score: 43.30  E-value: 2.67e-05
                          10        20
                  ....*....|....*....|...
gi 941644392    1 MIENGAEFSDSLIANLLRLIKHM 23
Cdd:cd21691    46 LKENGAEFPDSFVESLLRLIQRM 68
 
Name Accession Description Interval E-value
HrpA COG1643
HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];
516-965 8.54e-174

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


Pssm-ID: 441249 [Multi-domain]  Cd Length: 836  Bit Score: 533.12  E-value: 8.54e-174
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  516 SLPIYKLRDELIKAVSDNQILIVIGETGSGKTTQITQYLSESGFTARGKIGCTQPRRVAAMSVAKRVSEEFGCRLGQEVG 595
Cdd:COG1643     9 DLPVSAVLPELLAALRAHQVVVLAAPPGAGKTTQLPLALLELGWGAGGRIGMLEPRRLAARAAAERMAEELGEPVGETVG 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  596 YTIRFEDCTSPETLIKYMTDGMLLRECLIDPDLQTYSCIMLDEAHERTIHTDVLFGLLKQAVQK-RAELKLIVTSATLDA 674
Cdd:COG1643    89 YRVRFEDKVSAATRIEVVTEGILLRELQRDPELEGVDTVIFDEFHERSLNADLLLALLLDLQPAlRPDLKLLVMSATLDA 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  675 VKFSQYFFEAPIFTIPGRTFPVEILYT--REPETDYLDASLITVMQIhLNEPPGDILLFLTGQEEIDTACEILyerMKSM 752
Cdd:COG1643   169 ERFARLLGDAPVIESSGRTYPVEVRYRplPADERDLEDAVADAVREA-LAEEPGDILVFLPGEREIRRTAEAL---RGRL 244

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  753 GPDVpelIILPVYSALPSEMQTRIFEPAPPGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKVYNSKTGMDSLVVTPIS 832
Cdd:COG1643   245 PPDT---EILPLYGRLSAAEQDRAFAPAPHGRRRIVLATNIAETSLTVPGIRYVIDSGLARIPRYDPRSGVTRLPTERIS 321

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  833 QAQAKQRAGRAGRTGPGKTYRLYTERAYRdEMLATPVPEIQRTNLASTVLQLKAMGINDLLNFDFMDAPPVESLIMALEQ 912
Cdd:COG1643   322 QASANQRAGRAGRLAPGICYRLWSEEDFA-RRPAFTDPEILRADLASLILELAAWGLGDPEDLPFLDPPPARAIADARAL 400

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|...
gi 941644392  913 LHSLSALDDEGLLTRLGRRMAEFPLEPSLSKMLIMSVHLMCSDEILTVVSMLS 965
Cdd:COG1643   401 LQELGALDADGRLTPLGRALARLPLDPRLARMLLAAAELGCLREAAILAALLS 453
DEAH_box_HrpA TIGR01967
RNA helicase HrpA; This model represents HrpA, one of two related but uncharacterized DEAH-box ...
 488-1119 5.52e-127

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: 420.71  E-value: 5.52e-127
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392   488 EWKKHITggpkgASFGKKT----SLSIVEQRQSLPIYKLRDELIKAVSDNQILIVIGETGSGKTTQITQYLSESGFTARG 563
Cdd:TIGR01967   38 KFRERID-----AACDKVEarrqAVPEIRYPDNLPVSAKREDIAEAIAENQVVIIAGETGSGKTTQLPKICLELGRGSHG 112

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392   564 KIGCTQPRRVAAMSVAKRVSEEFGCRLGQEVGYTIRFEDCTSPETLIKYMTDGMLLRECLIDPDLQTYSCIMLDEAHERT 643
Cdd:TIGR01967  113 LIGHTQPRRLAARTVAQRIAEELGTPLGEKVGYKVRFHDQVSSNTLVKLMTDGILLAETQQDRFLSRYDTIIIDEAHERS 192

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392   644 IHTDVLFGLLKQAVQKRAELKLIVTSATLDAVKFSQYFFEAPIFTIPGRTFPVEILY------TREPETDYLDASLITVM 717
Cdd:TIGR01967  193 LNIDFLLGYLKQLLPRRPDLKIIITSATIDPERFSRHFNNAPIIEVSGRTYPVEVRYrplveeQEDDDLDQLEAILDAVD 272

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392   718 QIhLNEPPGDILLFLTGQEEIDTACEILYERmksmgpDVPELIILPVYSALPSEMQTRIFEPAppGSRKVVIATNIAETS 797
Cdd:TIGR01967  273 EL-FAEGPGDILIFLPGEREIRDAAEILRKR------NLRHTEILPLYARLSNKEQQRVFQPH--SGRRIVLATNVAETS 343

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392   798 LTIDGIYYVVDPGFVKQKVYNSKTGMDSLVVTPISQAQAKQRAGRAGRTGPGKTYRLYTERAYRDEMLATPvPEIQRTNL 877
Cdd:TIGR01967  344 LTVPGIHYVIDTGTARISRYSYRTKVQRLPIEPISQASANQRKGRCGRVAPGICIRLYSEEDFNSRPEFTD-PEILRTNL 422

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392   878 ASTVLQLKAMGINDLLNFDFMDAPPVESLIMALEQLHSLSALDDE---GLLTRLGRRMAEFPLEPSLSKMLIMSVHLMCS 954
Cdd:TIGR01967  423 ASVILQMLALRLGDIAAFPFIEAPDPRAIRDGFRLLEELGALDDDeaePQLTPIGRQLAQLPVDPRLARMLLEAHRLGCL 502

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392   955 DEILTVVSMLS**********************************************************----------- 1023
Cdd:TIGR01967  503 QEVLIIASALSIQDPRERPMEKQQAADQAHARFKDPRSDFLSRVNLWRHIEEQRQALSANQFRNACRKQylnylrvrewq 582

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  1024 ------*************AGKNTARVQKAICSGFFRNAAKKDPQEGYrTLVDGQVVYIHPSSAIFNRQPEWVVYHELVQ 1097
Cdd:TIGR01967  583 diyrqlTQVVKELGLKLNEEPADYDAIHKALLSGLLSQIGMKDEKHEY-DGARGRKFHIFPGSPLFKKPPKWVMAAELVE 661

                          650       660
                   ....*....|....*....|..
gi 941644392  1098 TTKEYMREVTVIDAKWLVEFAP 1119
Cdd:TIGR01967  662 TSKLYARLVAKIEPEWVEPVAG 683
PRK11131 PRK11131
ATP-dependent RNA helicase HrpA; Provisional
 511-965 1.06e-123

ATP-dependent RNA helicase HrpA; Provisional


Pssm-ID: 182986 [Multi-domain]  Cd Length: 1294  Bit Score: 412.15  E-value: 1.06e-123
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  511 VEQRQS----------LPIYKLRDELIKAVSDNQILIVIGETGSGKTTQITQYLSESGFTARGKIGCTQPRRVAAMSVAK 580
Cdd:PRK11131   57 VLLREAarpeitypenLPVSQKKQDILEAIRDHQVVIVAGETGSGKTTQLPKICLELGRGVKGLIGHTQPRRLAARTVAN 136

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  581 RVSEEFGCRLGQEVGYTIRFEDCTSPETLIKYMTDGMLLRECLIDPDLQTYSCIMLDEAHERTIHTDVLFGLLKQAVQKR 660
Cdd:PRK11131  137 RIAEELETELGGCVGYKVRFNDQVSDNTMVKLMTDGILLAEIQQDRLLMQYDTIIIDEAHERSLNIDFILGYLKELLPRR 216

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  661 AELKLIVTSATLDAVKFSQYFFEAPIFTIPGRTFPVEILY------TREPETDYLDASLITVMQIHlNEPPGDILLFLTG 734
Cdd:PRK11131  217 PDLKVIITSATIDPERFSRHFNNAPIIEVSGRTYPVEVRYrpiveeADDTERDQLQAIFDAVDELG-REGPGDILIFMSG 295

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  735 QEEI-DTAcEILYERmksmgpDVPELIILPVYSALPSEMQTRIFEPAppGSRKVVIATNIAETSLTIDGIYYVVDPGFVK 813
Cdd:PRK11131  296 EREIrDTA-DALNKL------NLRHTEILPLYARLSNSEQNRVFQSH--SGRRIVLATNVAETSLTVPGIKYVIDPGTAR 366

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  814 QKVYNSKTGMDSLVVTPISQAQAKQRAGRAGRTGPGKTYRLYTErayrDEMLATPV---PEIQRTNLASTVLQLKAMGIN 890
Cdd:PRK11131  367 ISRYSYRTKVQRLPIEPISQASANQRKGRCGRVSEGICIRLYSE----DDFLSRPEftdPEILRTNLASVILQMTALGLG 442

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  891 DLLNFDFMDAPP---VESLIMALEQLHSLSALDDEGL--LTRLGRRMAEFPLEPSLSKMLIMSVHLMCSDEILTVVSMLS 965
Cdd:PRK11131  443 DIAAFPFVEAPDkrnIQDGVRLLEELGAITTDEQASAykLTPLGRQLAQLPVDPRLARMVLEAQKHGCVREVMIITSALS 522
DEXHc_DHX8 cd17971
DEXH-box helicase domain of DEAH-box helicase 8; DEAH-box helicase 8 (DHX8 ,also known as ...
 512-690 1.14e-123

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: 377.21  E-value: 1.14e-123
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  512 EQRQSLPIYKLRDELIKAVSDNQILIVIGETGSGKTTQITQYLSESGFTARGKIGCTQPRRVAAMSVAKRVSEEFGCRLG 591
Cdd:cd17971     1 EQRESLPIYKLKEQLIQAVHDNQILVVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVAEEFGCCLG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  592 QEVGYTIRFEDCTSPETLIKYMTDGMLLRECLIDPDLQTYSCIMLDEAHERTIHTDVLFGLLKQAVQKRAELKLIVTSAT 671
Cdd:cd17971    81 QEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLSQYSVIMLDEAHERTIHTDVLFGLLKKTVQKRPDLKLIVTSAT 160

                         170
                  ....*....|....*....
gi 941644392  672 LDAVKFSQYFFEAPIFTIP 690
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 ...
 212-290 3.23e-39

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: 140.07  E-value: 3.23e-39
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 941644392  212 GNVYAGKVMNLAAFGCFVQLEGIRKKCEGLVHISQLRREGRVNSVAEVVNRGDKVYVKVMSIAGQKISLSMKDVDQDSG 290
Cdd:cd05684     1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQNGKISLSMKDVDQDTG 79
OB_NTP_bind pfam07717
Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus ...
 1044-1120 3.62e-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: 111.58  E-value: 3.62e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  1044 VQKAICSGFFRNAAKKDPQE-GYRTLVDGQVVYIHPSSAIFN---RQPEWVVYHELVQTTKEYMREVTVIDAKWLVEFAP 1119
Cdd:pfam07717    1 LRAALAAGLYPNVARRDPKGkGYTTLSDNQRVFIHPSSVLFNektFPPEWVVYQELVETTKVYIRTVTAISPEWLLLFAP 80


                   .
gi 941644392  1120 A 1120
Cdd:pfam07717   81 H 81
DEXDc smart00487
DEAD-like helicases superfamily;
513-698 9.97e-26

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 106.04  E-value: 9.97e-26
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392    513 QRQSLPiyklrdeliKAVSDNQILIVIGETGSGKTTQITQYLSESGF-TARGKIGCTQPRRVAAMSVAKRVSEEFGCRLG 591
Cdd:smart00487   13 QKEAIE---------ALLSGLRDVILAAPTGSGKTLAALLPALEALKrGKGGRVLVLVPTRELAEQWAEELKKLGPSLGL 83

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392    592 QEVGYT------IRFEDCTSPETLIKYMTDGMLLRECLIDP-DLQTYSCIMLDEAHERT--IHTDVLFGLLKQAVQKRae 662
Cdd:smart00487   84 KVVGLYggdskrEQLRKLESGKTDILVTTPGRLLDLLENDKlSLSNVDLVILDEAHRLLdgGFGDQLEKLLKLLPKNV-- 161

                           170       180       190
                    ....*....|....*....|....*....|....*...
gi 941644392    663 lKLIVTSATL--DAVKFSQYFFEAPIFTIPGRTFPVEI 698
Cdd:smart00487  162 -QLLLLSATPpeEIENLLELFLNDPVFIDVGFTPLEPI 198
HA2 pfam04408
Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in ...
 909-965 5.07e-23

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: 94.61  E-value: 5.07e-23
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 941644392   909 ALEQLHSLSALDDEGLLTRLGRRMAEFPLEPSLSKMLIMSVHLMCSDEILTVVSMLS 965
Cdd:pfam04408    1 ALELLYYLGALDEDGELTPLGRKMAELPLDPRLAKMLLAAAELGCLDEVLTIVAALS 57
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 201-285 2.75e-20

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: 93.96  E-value: 2.75e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  201 PQKDFPENAEVGNVYAGKVMNLAAFGCFVQLE-GIrkkcEGLVHISQLRREGRVNSVAEVVNRGDKVYVKVMSI--AGQK 277
Cdd:COG0539   264 PWENIAEKYPVGDVVKGKVTRLTDFGAFVELEpGV----EGLVHISEMSWTKRVAHPSDVVKVGDEVEVKVLDIdpEERR 339


                  ....*...
gi 941644392  278 ISLSMKDV 285
Cdd:COG0539   340 ISLSIKQL 347
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 209-286 8.38e-19

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 92.03  E-value: 8.38e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 941644392  209 AEVGNVYAGKVMNLAAFGCFVQLEGIRkkcEGLVHISQLRREgRVNSVAEVVNRGDKVYVKVMSIAGQ-KISLSMKDVD 286
Cdd:PRK11824  619 PEVGEIYEGKVVRIVDFGAFVEILPGK---DGLVHISEIADE-RVEKVEDVLKEGDEVKVKVLEIDKRgRIRLSRKAVL 693
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
210-283 6.51e-12

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 61.85  E-value: 6.51e-12
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 941644392    210 EVGNVYAGKVMNLAAFGCFVQLEGirkKCEGLVHISQLRREgRVNSVAEVVNRGDKVYVKVMSI--AGQKISLSMK 283
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGN---GVEGLIPISELSDK-RVKDPEEVLKVGDEVKVKVLSVdeEKGRIILSLK 72
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 201-283 9.66e-11

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: 65.91  E-value: 9.66e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392   201 PQKDFPENAEVGNVYAGKVMNLAAFGCFVQL-EGIrkkcEGLVHISQLRREGRVNSVAEVVNRGDKVYVKVMSIAGQ--K 277
Cdd:TIGR00717  262 PWEAIEKKFPVGDKITGRVTNLTDYGVFVEIeEGI----EGLVHVSEMSWVKKNSHPSKVVKKGDEVEVMILDIDPErrR 337


                   ....*.
gi 941644392   278 ISLSMK 283
Cdd:TIGR00717  338 LSLGLK 343
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 210-282 7.97e-07

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: 47.67  E-value: 7.97e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 941644392   210 EVGNVYAGKVMNLAAFGCFVQLEGirkKCEGLVHISQLRREGRVNSvAEVVNRGDKVYVKVMSI--AGQKISLSM 282
Cdd:pfam00575    2 EKGDVVEGEVTRVTKGGAFVDLGN---GVEGFIPISELSDDHVEDP-DEVIKVGDEVKVKVLKVdkDRRRIILSI 72
GH2-like_DHX8 cd21691
GIPC-homology 2 (GH2)-like domain found in DEAH box protein 8 (DHX8) and similar proteins; ...
 1-23 2.67e-05

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: 43.30  E-value: 2.67e-05
                          10        20
                  ....*....|....*....|...
gi 941644392    1 MIENGAEFSDSLIANLLRLIKHM 23
Cdd:cd21691    46 LKENGAEFPDSFVESLLRLIQRM 68
 
Name Accession Description Interval E-value
HrpA COG1643
HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];
516-965 8.54e-174

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


Pssm-ID: 441249 [Multi-domain]  Cd Length: 836  Bit Score: 533.12  E-value: 8.54e-174
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  516 SLPIYKLRDELIKAVSDNQILIVIGETGSGKTTQITQYLSESGFTARGKIGCTQPRRVAAMSVAKRVSEEFGCRLGQEVG 595
Cdd:COG1643     9 DLPVSAVLPELLAALRAHQVVVLAAPPGAGKTTQLPLALLELGWGAGGRIGMLEPRRLAARAAAERMAEELGEPVGETVG 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  596 YTIRFEDCTSPETLIKYMTDGMLLRECLIDPDLQTYSCIMLDEAHERTIHTDVLFGLLKQAVQK-RAELKLIVTSATLDA 674
Cdd:COG1643    89 YRVRFEDKVSAATRIEVVTEGILLRELQRDPELEGVDTVIFDEFHERSLNADLLLALLLDLQPAlRPDLKLLVMSATLDA 168

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  675 VKFSQYFFEAPIFTIPGRTFPVEILYT--REPETDYLDASLITVMQIhLNEPPGDILLFLTGQEEIDTACEILyerMKSM 752
Cdd:COG1643   169 ERFARLLGDAPVIESSGRTYPVEVRYRplPADERDLEDAVADAVREA-LAEEPGDILVFLPGEREIRRTAEAL---RGRL 244

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  753 GPDVpelIILPVYSALPSEMQTRIFEPAPPGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKVYNSKTGMDSLVVTPIS 832
Cdd:COG1643   245 PPDT---EILPLYGRLSAAEQDRAFAPAPHGRRRIVLATNIAETSLTVPGIRYVIDSGLARIPRYDPRSGVTRLPTERIS 321

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  833 QAQAKQRAGRAGRTGPGKTYRLYTERAYRdEMLATPVPEIQRTNLASTVLQLKAMGINDLLNFDFMDAPPVESLIMALEQ 912
Cdd:COG1643   322 QASANQRAGRAGRLAPGICYRLWSEEDFA-RRPAFTDPEILRADLASLILELAAWGLGDPEDLPFLDPPPARAIADARAL 400

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|...
gi 941644392  913 LHSLSALDDEGLLTRLGRRMAEFPLEPSLSKMLIMSVHLMCSDEILTVVSMLS 965
Cdd:COG1643   401 LQELGALDADGRLTPLGRALARLPLDPRLARMLLAAAELGCLREAAILAALLS 453
DEAH_box_HrpA TIGR01967
RNA helicase HrpA; This model represents HrpA, one of two related but uncharacterized DEAH-box ...
 488-1119 5.52e-127

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: 420.71  E-value: 5.52e-127
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392   488 EWKKHITggpkgASFGKKT----SLSIVEQRQSLPIYKLRDELIKAVSDNQILIVIGETGSGKTTQITQYLSESGFTARG 563
Cdd:TIGR01967   38 KFRERID-----AACDKVEarrqAVPEIRYPDNLPVSAKREDIAEAIAENQVVIIAGETGSGKTTQLPKICLELGRGSHG 112

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392   564 KIGCTQPRRVAAMSVAKRVSEEFGCRLGQEVGYTIRFEDCTSPETLIKYMTDGMLLRECLIDPDLQTYSCIMLDEAHERT 643
Cdd:TIGR01967  113 LIGHTQPRRLAARTVAQRIAEELGTPLGEKVGYKVRFHDQVSSNTLVKLMTDGILLAETQQDRFLSRYDTIIIDEAHERS 192

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392   644 IHTDVLFGLLKQAVQKRAELKLIVTSATLDAVKFSQYFFEAPIFTIPGRTFPVEILY------TREPETDYLDASLITVM 717
Cdd:TIGR01967  193 LNIDFLLGYLKQLLPRRPDLKIIITSATIDPERFSRHFNNAPIIEVSGRTYPVEVRYrplveeQEDDDLDQLEAILDAVD 272

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392   718 QIhLNEPPGDILLFLTGQEEIDTACEILYERmksmgpDVPELIILPVYSALPSEMQTRIFEPAppGSRKVVIATNIAETS 797
Cdd:TIGR01967  273 EL-FAEGPGDILIFLPGEREIRDAAEILRKR------NLRHTEILPLYARLSNKEQQRVFQPH--SGRRIVLATNVAETS 343

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392   798 LTIDGIYYVVDPGFVKQKVYNSKTGMDSLVVTPISQAQAKQRAGRAGRTGPGKTYRLYTERAYRDEMLATPvPEIQRTNL 877
Cdd:TIGR01967  344 LTVPGIHYVIDTGTARISRYSYRTKVQRLPIEPISQASANQRKGRCGRVAPGICIRLYSEEDFNSRPEFTD-PEILRTNL 422

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392   878 ASTVLQLKAMGINDLLNFDFMDAPPVESLIMALEQLHSLSALDDE---GLLTRLGRRMAEFPLEPSLSKMLIMSVHLMCS 954
Cdd:TIGR01967  423 ASVILQMLALRLGDIAAFPFIEAPDPRAIRDGFRLLEELGALDDDeaePQLTPIGRQLAQLPVDPRLARMLLEAHRLGCL 502

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392   955 DEILTVVSMLS**********************************************************----------- 1023
Cdd:TIGR01967  503 QEVLIIASALSIQDPRERPMEKQQAADQAHARFKDPRSDFLSRVNLWRHIEEQRQALSANQFRNACRKQylnylrvrewq 582

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  1024 ------*************AGKNTARVQKAICSGFFRNAAKKDPQEGYrTLVDGQVVYIHPSSAIFNRQPEWVVYHELVQ 1097
Cdd:TIGR01967  583 diyrqlTQVVKELGLKLNEEPADYDAIHKALLSGLLSQIGMKDEKHEY-DGARGRKFHIFPGSPLFKKPPKWVMAAELVE 661

                          650       660
                   ....*....|....*....|..
gi 941644392  1098 TTKEYMREVTVIDAKWLVEFAP 1119
Cdd:TIGR01967  662 TSKLYARLVAKIEPEWVEPVAG 683
PRK11131 PRK11131
ATP-dependent RNA helicase HrpA; Provisional
 511-965 1.06e-123

ATP-dependent RNA helicase HrpA; Provisional


Pssm-ID: 182986 [Multi-domain]  Cd Length: 1294  Bit Score: 412.15  E-value: 1.06e-123
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  511 VEQRQS----------LPIYKLRDELIKAVSDNQILIVIGETGSGKTTQITQYLSESGFTARGKIGCTQPRRVAAMSVAK 580
Cdd:PRK11131   57 VLLREAarpeitypenLPVSQKKQDILEAIRDHQVVIVAGETGSGKTTQLPKICLELGRGVKGLIGHTQPRRLAARTVAN 136

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  581 RVSEEFGCRLGQEVGYTIRFEDCTSPETLIKYMTDGMLLRECLIDPDLQTYSCIMLDEAHERTIHTDVLFGLLKQAVQKR 660
Cdd:PRK11131  137 RIAEELETELGGCVGYKVRFNDQVSDNTMVKLMTDGILLAEIQQDRLLMQYDTIIIDEAHERSLNIDFILGYLKELLPRR 216

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  661 AELKLIVTSATLDAVKFSQYFFEAPIFTIPGRTFPVEILY------TREPETDYLDASLITVMQIHlNEPPGDILLFLTG 734
Cdd:PRK11131  217 PDLKVIITSATIDPERFSRHFNNAPIIEVSGRTYPVEVRYrpiveeADDTERDQLQAIFDAVDELG-REGPGDILIFMSG 295

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  735 QEEI-DTAcEILYERmksmgpDVPELIILPVYSALPSEMQTRIFEPAppGSRKVVIATNIAETSLTIDGIYYVVDPGFVK 813
Cdd:PRK11131  296 EREIrDTA-DALNKL------NLRHTEILPLYARLSNSEQNRVFQSH--SGRRIVLATNVAETSLTVPGIKYVIDPGTAR 366

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  814 QKVYNSKTGMDSLVVTPISQAQAKQRAGRAGRTGPGKTYRLYTErayrDEMLATPV---PEIQRTNLASTVLQLKAMGIN 890
Cdd:PRK11131  367 ISRYSYRTKVQRLPIEPISQASANQRKGRCGRVSEGICIRLYSE----DDFLSRPEftdPEILRTNLASVILQMTALGLG 442

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  891 DLLNFDFMDAPP---VESLIMALEQLHSLSALDDEGL--LTRLGRRMAEFPLEPSLSKMLIMSVHLMCSDEILTVVSMLS 965
Cdd:PRK11131  443 DIAAFPFVEAPDkrnIQDGVRLLEELGAITTDEQASAykLTPLGRQLAQLPVDPRLARMVLEAQKHGCVREVMIITSALS 522
DEXHc_DHX8 cd17971
DEXH-box helicase domain of DEAH-box helicase 8; DEAH-box helicase 8 (DHX8 ,also known as ...
 512-690 1.14e-123

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: 377.21  E-value: 1.14e-123
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  512 EQRQSLPIYKLRDELIKAVSDNQILIVIGETGSGKTTQITQYLSESGFTARGKIGCTQPRRVAAMSVAKRVSEEFGCRLG 591
Cdd:cd17971     1 EQRESLPIYKLKEQLIQAVHDNQILVVIGETGSGKTTQITQYLAEAGYTSRGKIGCTQPRRVAAMSVAKRVAEEFGCCLG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  592 QEVGYTIRFEDCTSPETLIKYMTDGMLLRECLIDPDLQTYSCIMLDEAHERTIHTDVLFGLLKQAVQKRAELKLIVTSAT 671
Cdd:cd17971    81 QEVGYTIRFEDCTSPETVIKYMTDGMLLRECLIDPDLSQYSVIMLDEAHERTIHTDVLFGLLKKTVQKRPDLKLIVTSAT 160

                         170
                  ....*....|....*....
gi 941644392  672 LDAVKFSQYFFEAPIFTIP 690
Cdd:cd17971   161 LDAVKFSQYFYEAPIFTIP 179
DEAH_box_HrpB TIGR01970
ATP-dependent helicase HrpB; This model represents HrpB, one of two related but ...
 517-946 3.29e-100

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: 336.74  E-value: 3.29e-100
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392   517 LPIYKLRDELIKAVSDNQILIVIGETGSGKTTQIT-QYLSESGFTarGKIGCTQPRRVAAMSVAKRVSEEFGCRLGQEVG 595
Cdd:TIGR01970    1 LPIHAVLPALRDALAAHPQVVLEAPPGAGKSTAVPlALLDAPGIG--GKIIMLEPRRLAARSAAQRLASQLGEAVGQTVG 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392   596 YTIRFEDCTSPETLIKYMTDGMLLRECLIDPDLQTYSCIMLDEAHERTIHTDVLFGLLKQaVQK--RAELKLIVTSATLD 673
Cdd:TIGR01970   79 YRVRGENKVSRRTRLEVVTEGILTRMIQDDPELDGVGALIFDEFHERSLDADLGLALALD-VQSslREDLKILAMSATLD 157

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392   674 AVKFSQYFFEAPIFTIPGRTFPVEILYTREPETDYLDASLITVMQIHLNEPPGDILLFLTGQEEIDTACEILYERMKsmg 753
Cdd:TIGR01970  158 GERLSSLLPDAPVVESEGRSFPVEIRYLPLRGDQRLEDAVSRAVEHALASETGSILVFLPGQAEIRRVQEQLAERLD--- 234

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392   754 pdvPELIILPVYSALPSEMQTRIFEPAPPGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKVYNSKTGMDSLVVTPISQ 833
Cdd:TIGR01970  235 ---SDVLICPLYGELSLAAQDRAIKPDPQGRRKVVLATNIAETSLTIEGIRVVIDSGLARVARFDPKTGITRLETVRISQ 311

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392   834 AQAKQRAGRAGRTGPGKTYRLYTErAYRDEMLATPVPEIQRTNLASTVLQLKAMGINDLLNFDFMDAPPVESLIMALEQL 913
Cdd:TIGR01970  312 ASATQRAGRAGRLEPGVCYRLWSE-EQHQRLPAQDEPEILQADLSGLALELAQWGAKDPSDLRWLDAPPSVALAAARQLL 390

                          410       420       430
                   ....*....|....*....|....*....|...
gi 941644392   914 HSLSALDDEGLLTRLGRRMAEFPLEPSLSKMLI 946
Cdd:TIGR01970  391 QRLGALDAQGRLTAHGKAMAALGCHPRLAAMLL 423
PRK11664 PRK11664
ATP-dependent RNA helicase HrpB; Provisional
 516-946 1.59e-94

ATP-dependent RNA helicase HrpB; Provisional


Pssm-ID: 236950 [Multi-domain]  Cd Length: 812  Bit Score: 320.72  E-value: 1.59e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  516 SLPIYKLRDELIKAVSDNQILIVIGETGSGKTTQIT-QYLSESGFTarGKIGCTQPRRVAAMSVAKRVSEEFGCRLGQEV 594
Cdd:PRK11664    3 SLPVAAVLPELLTALKTAPQVLLKAPTGAGKSTWLPlQLLQHGGIN--GKIIMLEPRRLAARNVAQRLAEQLGEKPGETV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  595 GYTIRFEDCTSPETLIKYMTDGMLLRECLIDPDLQTYSCIMLDEAHERTIHTDVLFGLLKQaVQK--RAELKLIVTSATL 672
Cdd:PRK11664   81 GYRMRAESKVGPNTRLEVVTEGILTRMIQRDPELSGVGLVILDEFHERSLQADLALALLLD-VQQglRDDLKLLIMSATL 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  673 DAVKFSQYFFEAPIFTIPGRTFPVEILYTREPETDYLDASLITVMQIHLNEPPGDILLFLTGQEEIDTACEILYERMKSm 752
Cdd:PRK11664  160 DNDRLQQLLPDAPVIVSEGRSFPVERRYQPLPAHQRFDEAVARATAELLRQESGSLLLFLPGVGEIQRVQEQLASRVAS- 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  753 gpDVpelIILPVYSALPSEMQTRIFEPAPPGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKVYNSKTGMDSLVVTPIS 832
Cdd:PRK11664  239 --DV---LLCPLYGALSLAEQQKAILPAPAGRRKVVLATNIAETSLTIEGIRLVVDSGLERVARFDPKTGLTRLVTQRIS 313

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  833 QAQAKQRAGRAGRTGPGKTYRLYTERAYrDEMLATPVPEIQRTNLASTVLQLKAMGINDLLNFDFMDAPPVESLIMALEQ 912
Cdd:PRK11664  314 QASMTQRAGRAGRLEPGICLHLYSKEQA-ERAAAQSEPEILHSDLSGLLLELLQWGCHDPAQLSWLDQPPAAALAAAKRL 392

                         410       420       430
                  ....*....|....*....|....*....|....
gi 941644392  913 LHSLSALDDEGLLTRLGRRMAEFPLEPSLSKMLI 946
Cdd:PRK11664  393 LQQLGALDGQGRLTARGRKMAALGNDPRLAAMLV 426
DEXHc_DHX38 cd17983
DEXH-box helicase domain of DEAH-box helicase 38; DEAH-box helicase 38 (DHX38, also known as ...
 517-689 5.42e-93

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: 294.76  E-value: 5.42e-93
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  517 LPIYKLRDELIKAVSDNQILIVIGETGSGKTTQITQYLSESGFTARGKIGCTQPRRVAAMSVAKRVSEEFGCRLGQEVGY 596
Cdd:cd17983     1 LPIFAVRQELLNVIRDNNVVIVVGETGSGKTTQLTQYLHEDGYTDYGMIGCTQPRRVAAMSVAKRVSEEMGVELGEEVGY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  597 TIRFEDCTSPETLIKYMTDGMLLRECLIDPDLQTYSCIMLDEAHERTIHTDVLFGLLKQAVQKRAELKLIVTSATLDAVK 676
Cdd:cd17983    81 AIRFEDCTSENTVIKYMTDGILLRESLRDPDLDKYSAIIMDEAHERSLNTDVLFGLLREVVARRRDLKLIVTSATMDADK 160

                         170
                  ....*....|...
gi 941644392  677 FSQYFFEAPIFTI 689
Cdd:cd17983   161 FADFFGNVPIFTI 173
DEXHc_DHX16 cd17974
DEXH-box helicase domain of DEAH-box helicase 16; DEAH-box helicase 16 (DHX16) is probably ...
 517-689 6.54e-90

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: 286.71  E-value: 6.54e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  517 LPIYKLRDELIKAVSDNQILIVIGETGSGKTTQITQYLSESGFTARG-KIGCTQPRRVAAMSVAKRVSEEFGCRLGQEVG 595
Cdd:cd17974     1 LPVYPYRDDLLAAVKEHQVLIIVGETGSGKTTQIPQYLHEAGYTKGGgKIGCTQPRRVAAMSVAARVAEEMGVKLGNEVG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  596 YTIRFEDCTSPETLIKYMTDGMLLRECLIDPDLQTYSCIMLDEAHERTIHTDVLFGLLKQAVQKRAELKLIVTSATLDAV 675
Cdd:cd17974    81 YSIRFEDCTSEKTVLKYMTDGMLLREFLTEPDLASYSVMIIDEAHERTLHTDILFGLVKDIARFRPDLKLLISSATMDAE 160

                         170
                  ....*....|....
gi 941644392  676 KFSQYFFEAPIFTI 689
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) ...
 533-689 6.27e-89

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: 283.20  E-value: 6.27e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  533 NQILIVIGETGSGKTTQITQYLSESGFT--ARGKIGCTQPRRVAAMSVAKRVSEEFGCRLGQEVGYTIRFEDCTSPETLI 610
Cdd:cd17917     1 NQVVVIVGETGSGKTTQVPQFLLEDGLAkgGKGRIVCTQPRRIAAISVAERVAEERGEKLGEEVGYQIRFESKTSSKTRI 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 941644392  611 KYMTDGMLLRECLIDPDLQTYSCIMLDEAHERTIHTDVLFGLLKQAVQKRAELKLIVTSATLDAVKFSQYFFEAPIFTI 689
Cdd:cd17917    81 KFCTDGILLRELLSDPLLSGYSHVILDEAHERSLDTDFLLGLLKDLLRKRPDLKVILMSATLDAEKFSSYFGGAPVIHI 159
DEXHc_DHX33 cd17978
DEXH-box helicase domain of DEAH-box helicase 33; DEAH-box helicase 33 (DHX33) stimulates RNA ...
 517-689 1.81e-88

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: 282.71  E-value: 1.81e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  517 LPIYKLRDELIKAVSDNQILIVIGETGSGKTTQITQYLSESGFTARGKIGCTQPRRVAAMSVAKRVSEEFGCRLGQEVGY 596
Cdd:cd17978     1 LPIYSARKRLLEELRKHDTVIIIGETGSGKTTQIPQYLYEAGFARGGMIGITQPRRVAAVSVAKRVAEEMGVELGQLVGY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  597 TIRFEDCTSPETLIKYMTDGMLLRECLIDPDLQTYSCIMLDEAHERTIHTDVLFGLLKQAVQKR-----AELKLIVTSAT 671
Cdd:cd17978    81 SVRFDDVTSEETRIKYMTDGMLLREAIGDPLLSKYSVIILDEAHERTVHTDVLFGLVKSAQRRRkeqklSPLKVIIMSAT 160

                         170
                  ....*....|....*...
gi 941644392  672 LDAVKFSQYFFEAPIFTI 689
Cdd:cd17978   161 LDADLFSEYFNGAPVLYI 178
DEXHc_DHX15 cd17973
DEXH-box helicase domain of DEAH-box helicase 15; DEAH-box helicase 15 (DHX15) is a pre-mRNA ...
 508-689 4.58e-85

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: 273.91  E-value: 4.58e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  508 LSIVEQRQSLPIYKLRDELIKAVSDNQILIVIGETGSGKTTQITQYLSESGFTARGK--IGCTQPRRVAAMSVAKRVSEE 585
Cdd:cd17973     4 FEILEKRRELPVWEQKEDFLKLLKNNQILVLVGETGSGKTTQIPQFVLDDELPHQPKklVACTQPRRVAAMSVAQRVAEE 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  586 FGCRLGQEVGYTIRFEDCTSPETLIKYMTDGMLLRECLIDPDLQTYSCIMLDEAHERTIHTDVLFGLLKQAVQKRAELKL 665
Cdd:cd17973    84 MDVKLGEEVGYSIRFEDCSSAKTILKYMTDGMLLREAMSDPLLSRYSVIILDEAHERTLATDILMGLLKEVVRRRPDLKL 163

                         170       180
                  ....*....|....*....|....
gi 941644392  666 IVTSATLDAVKFSQYFFEAPIFTI 689
Cdd:cd17973   164 IVMSATLDAGKFQKYFDNAPLLKV 187
SF2_C_RHA cd18791
C-terminal helicase domain of the RNA helicase A (RHA) family helicases; The RNA helicase A ...
 694-855 5.49e-84

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: 270.17  E-value: 5.49e-84
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  694 FPVEILYTREP-----------ETDYLDASLITVMQIHLNEPPGDILLFLTGQEEIDTACEILYERMKSmgPDVPELIIL 762
Cdd:cd18791     1 FPVEVYYLEDIlellgissekeDPDYVDAAVRLILQIHRTEEPGDILVFLPGQEEIERLCELLREELLS--PDLGKLLVL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  763 PVYSALPSEMQTRIFEPAPPGSRKVVIATNIAETSLTIDGIYYVVDPGFVKQKVYNSKTGMDSLVVTPISQAQAKQRAGR 842
Cdd:cd18791    79 PLHSSLPPEEQQRVFEPPPPGVRKVVLATNIAETSITIPGVVYVIDSGLVKEKVYDPRTGLSSLVTVWISKASAEQRAGR 158

                         170
                  ....*....|...
gi 941644392  843 AGRTGPGKTYRLY 855
Cdd:cd18791   159 AGRTRPGKCYRLY 171
DEXHc_DHX35 cd17980
DEXH-box helicase domain of DEAH-box helicase 35; DHX35 plays a role in colorectal cancers and ...
 517-681 1.05e-75

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: 247.77  E-value: 1.05e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  517 LPIYKLRDELIKAVSDNQILIVIGETGSGKTTQITQYLSESGFTARGK-IGCTQPRRVAAMSVAKRVSEEFGCRLGQEVG 595
Cdd:cd17980     1 LPVFKLRNHILYLVENYQTIVIVGETGCGKSTQIPQYLAEAGWTAGGRvVGCTQPRRVAAVTVAGRVAEEMGAVLGHEVG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  596 YTIRFEDCTSP-ETLIKYMTDGMLLRECLIDPDLQTYSCIMLDEAHERTIHTDVLFGLLKQAVQKRAELKLIVTSATLDA 674
Cdd:cd17980    81 YCIRFDDCTDPqATRIKFLTDGMLVREMMLDPLLTKYSVIMLDEAHERTLYTDILIGLLKKIQKKRGDLRLIVASATLDA 160


                  ....*..
gi 941644392  675 VKFSQYF 681
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 ...
 517-689 1.80e-74

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


Pssm-ID: 350742 [Multi-domain]  Cd Length: 178  Bit Score: 243.99  E-value: 1.80e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  517 LPIYKLRDELIKAVSDNQILIVIGETGSGKTTQITQYLSESGFTARGKIGCTQPRRVAAMSVAKRVSEEFGCRLGQEVGY 596
Cdd:cd17984     1 LPIQKQRKKLVQAVRDNSFLIVTGNTGSGKTTQLPKYLYEAGFSQHGMIGVTQPRRVAAISVAQRVAEEMKCTLGSKVGY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  597 TIRFEDCTSPETLIKYMTDGMLLRECLIDPDLQTYSCIMLDEAHERTIHTDVLFGLLKQAVQKRA-----ELKLIVTSAT 671
Cdd:cd17984    81 QVRFDDCSSKETAIKYMTDGCLLRHILADPNLTKYSVIILDEAHERSLTTDILFGLLKKLFQEKSpnrkeHLKVVVMSAT 160

                         170
                  ....*....|....*...
gi 941644392  672 LDAVKFSQYFFEAPIFTI 689
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 ...
 517-686 8.19e-64

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: 213.86  E-value: 8.19e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  517 LPIYKLRDELIKAVSDNQILIVIGETGSGKTTQITQYLSESGFTARGKIGCTQPRRVAAMSVAKRVSEEFGCRLGQEVGY 596
Cdd:cd17989     1 LPVSQKRDEIAKAIAENQVVIIAGETGSGKTTQLPKICLELGRGIRGLIGHTQPRRLAARSVAERIAEELKTELGGAVGY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  597 TIRFEDCTSPETLIKYMTDGMLLRECLIDPDLQTYSCIMLDEAHERTIHTDVLFGLLKQAVQKRAELKLIVTSATLDAVK 676
Cdd:cd17989    81 KVRFTDQTSDETCVKLMTDGILLAETQTDRYLRAYDTIIIDEAHERSLNIDFLLGYLKQLLPRRPDLKVIITSATIDAER 160

                         170
                  ....*....|
gi 941644392  677 FSQYFFEAPI 686
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 ...
 517-679 4.29e-55

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: 189.87  E-value: 4.29e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  517 LPIYKLRDELIKAVSDNQILIVIGETGSGKTTQITQYLSESGFTAR-----GKIGCTQPRRVAAMSVAKRVSEEFGcRLG 591
Cdd:cd17982     1 LPILAEEQEIMEAINENPVVIICGETGSGKTTQVPQFLYEAGFGSPesdnpGMIGITQPRRVAAVSMAKRVAEELN-VFG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  592 QEVGYTIRFEDCTSPETLIKYMTDGMLLRECLIDPDLQTYSCIMLDEAHERTIHTDVLFGLLKQAVQKRAE--------- 662
Cdd:cd17982    80 KEVSYQIRYDSTVSENTKIKFMTDGVLLKEIQTDFLLRKYSVIIIDEAHERSVNTDILIGMLSRIVPLRAKlylqdqtvk 159

                         170
                  ....*....|....*...
gi 941644392  663 -LKLIVTSATLDAVKFSQ 679
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 ...
 517-686 1.18e-53

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: 184.95  E-value: 1.18e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  517 LPIYKLRDELIKAVSDNQILIVIGETGSGKTTQITQYLSESGFTargKIGCTQPRRVAAMSVAKRVSEEFGCRLGQEVGY 596
Cdd:cd17979     1 LPIAQYREKIIELLKTHQVVIVAGDTGCGKSTQVPQYLLAAGFR---HIACTQPRRIACISLAKRVAFESLNQYGSKVAY 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  597 TIRFEDCTSPETLIKYMTDGMLLRECLIDPDLQTYSCIMLDEAHERTIHTDVLFGLLKQAVQKRAELKLIVTSATLDAVK 676
Cdd:cd17979    78 QIRFERTRTLATKLLFLTEGLLLRQIQRDASLPQYNVLILDEVHERHLHGDFLLGVLRCLLRLRPDLKLILMSATINIEL 157

                         170
                  ....*....|
gi 941644392  677 FSQYFFEAPI 686
Cdd:cd17979   158 FSGYFEGAPV 167
DEXHc_YTHDC2 cd17987
DEXH-box helicase domain of YTH domain containing 2; YTH domain containing 2 (YTHDC2) ...
 517-689 2.40e-48

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: 170.01  E-value: 2.40e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  517 LPIYKLRDELIKAVSDNQILIVIGETGSGKTTQITQYL----SESGFTARgkIGCTQPRRVAAMSVAKRVSEEFGCRLGQ 592
Cdd:cd17987     1 LPVFEKQEQIVRIIKENKVVLIVGETGSGKTTQIPQFLlddcYANGIPCR--IFCTQPRRLAAIAVAERVAAERGEKIGQ 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  593 EVGYTIRFEDCTSPETLIKYMTDGMLLRECLI-DPDLQTYSCIMLDEAHERTIHTDVLFGLLKQAVQKRAELKLIVTSAT 671
Cdd:cd17987    79 TVGYQIRLESRVSPKTLLTFCTNGVLLRTLMAgDSALSTVTHVIVDEVHERDRFSDFLLTKLRDILQKHPNLKLILSSAA 158

                         170
                  ....*....|....*...
gi 941644392  672 LDAVKFSQYFFEAPIFTI 689
Cdd:cd17987   159 LDVNLFIRYFGSCPVIYI 176
DEXHc_DHX29 cd17975
DEXH-box helicase domain of DEAH-box helicase 29; DEAH-box helicase 29 (DHX29) is a part of ...
 517-689 1.63e-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: 167.78  E-value: 1.63e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  517 LPIYKLRDELIKAVSDNQILIVIGETGSGKTTQITQYLSES-----GFTARGKIGCTQPRRVAAMSVAKRVSEEFGCRLG 591
Cdd:cd17975     1 LPVFKHRESILETLKRHRVVVVAGETGSGKSTQVPQFLLEDlllngGTAQKCNIVCTQPRRISAMSLATRVCEELGCESG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  592 -----QEVGYTIRFEDCTSPETLIKYMTDGMLLRECLIDPDLQTYSCIMLDEAHERTIHTDVLFGLLKQAVQKRAELKLI 666
Cdd:cd17975    81 pggknSLCGYQIRMESRTGEATRLLYCTTGVLLRKLQEDGLLSSISHIIVDEVHERSVQSDFLLIILKEILHKRSDLHLI 160

                         170       180
                  ....*....|....*....|...
gi 941644392  667 VTSATLDAVKFSQYFFEAPIFTI 689
Cdd:cd17975   161 LMSATVDCEKFSSYFTHCPILRI 183
DEXHc_DHX36 cd17981
DEXH-box helicase domain of DEAH-box helicase 36; DEAH-box helicase 36 (DHX36, also known as ...
 517-689 2.06e-47

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


Pssm-ID: 350739 [Multi-domain]  Cd Length: 180  Bit Score: 167.33  E-value: 2.06e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  517 LPIYKLRDELIKAVSDNQILIVIGETGSGKTTQITQYLSESgFTARGK-----IGCTQPRRVAAMSVAKRVSEEFG--CR 589
Cdd:cd17981     1 LPSYGMKQEIINMIDNNQVTVISGETGCGKTTQVTQFILDD-AIERGKgsscrIVCTQPRRISAISVAERVAAERAesCG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  590 LGQEVGYTIRFEDCTSPE-TLIKYMTDGMLLRECLIDPDLQTYSCIMLDEAHERTIHTDVLFGLLKQAVQKRAELKLIVT 668
Cdd:cd17981    80 LGNSTGYQIRLESRKPRKqGSILYCTTGIVLQWLQSDPHLSNVSHLVLDEIHERNLQSDVLMGIVKDLLPFRSDLKVILM 159

                         170       180
                  ....*....|....*....|.
gi 941644392  669 SATLDAVKFSQYFFEAPIFTI 689
Cdd:cd17981   160 SATLNAEKFSDYFNNCPMIHI 180
DEXHc_DHX57 cd17985
DEXH-box helicase domain of DEAH-box helicase 57; DEAH-box helicase 57 (DHX57) belongs to the ...
 517-689 9.09e-44

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: 156.92  E-value: 9.09e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  517 LPIYKLRDELIKAVSDNQILIVIGETGSGKTTQITQY-LSESGFTARGK---IGCTQPRRVAAMSVAKRVSEEFGCRLGQ 592
Cdd:cd17985     1 LPAWQERETILELLEKHQVLVISGMTGCGKTTQIPQFiLDNSLQGPPLPvanIICTQPRRISAISVAERVAQERAERVGQ 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  593 EVGYTIRFEDCTSPETLIKYMTDGMLLRECLIDPDLQTYSCIMLDEAHERTIHTDVLFGLLKQAVQKRAELKLIVTSATL 672
Cdd:cd17985    81 SVGYQIRLESVKSSATRLLYCTTGVLLRRLEGDPTLQGVTHVIVDEVHERTEESDFLLLVLKDLMVQRPDLKVILMSATL 160

                         170
                  ....*....|....*..
gi 941644392  673 DAVKFSQYFFEAPIFTI 689
Cdd:cd17985   161 NAELFSDYFNSCPVIHI 177
DEXHc_DHX9 cd17972
DEXH-box helicase domain of DEAH-box helicase 9; DEAH-box helicase 9 (DHX9, also known as ...
 510-689 1.85e-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: 158.07  E-value: 1.85e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  510 IVEQRQSLPIYKLRDELIKAVSDNQILIVIGETGSGKTTQITQYLSE----SGFTARGKIGCTQPRRVAAMSVAKRVSEE 585
Cdd:cd17972    52 ILQERELLPVKKFREEILEAISNNPVVIIRGATGCGKTTQVPQYILDdfiqNDRAAECNIVVTQPRRISAVSVAERVAFE 131

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  586 FGCRLGQEVGYTIRFEDCT-SPETLIKYMTDGMLLREclIDPDLQTYSCIMLDEAHERTIHTDVLFGLLKQAVQKRAELK 664
Cdd:cd17972   132 RGEEVGKSCGYSVRFESVLpRPHASILFCTVGVLLRK--LEAGIRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPDLR 209

                         170       180
                  ....*....|....*....|....*
gi 941644392  665 LIVTSATLDAVKFSQYFFEAPIFTI 689
Cdd:cd17972   210 VILMSATIDTSMFCEYFFNCPVIEV 234
DEXHc_HrpB cd17990
DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA ...
 517-687 9.16e-43

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: 154.03  E-value: 9.16e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  517 LPIYKLRDELIKAVSDNQILIVIGETGSGKTTQIT-QYLSESGFTArGKIGCTQPRRVAAMSVAKRVSEEFGCRLGQEVG 595
Cdd:cd17990     1 LPIAAVLPALRAALDAGGQVVLEAPPGAGKTTRVPlALLAELWIAG-GKIIVLEPRRVAARAAARRLATLLGEAPGETVG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  596 YTIRFEDCTSPETLIKYMTDGMLLRECLIDPDLQTYSCIMLDEAHERTIHTDVLFGLLKQAVQ-KRAELKLIVTSATLDA 674
Cdd:cd17990    80 YRVRGESRVGRRTRVEVVTEGVLLRRLQRDPELSGVGAVILDEFHERSLDADLALALLLEVQQlLRDDLRLLAMSATLDG 159

                         170
                  ....*....|...
gi 941644392  675 VKFSQYFFEAPIF 687
Cdd:cd17990   160 DGLAALLPEAPVV 172
DEXHc_DHX32 cd17977
DEXH-box helicase domain of DEAH-box helicase 32; DEAH-box helicase 32 (DHX32) belongs to the ...
 517-686 3.69e-42

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


Pssm-ID: 350735 [Multi-domain]  Cd Length: 176  Bit Score: 152.29  E-value: 3.69e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  517 LPIYKLRDELIKAVSDNQILIVIGETGSGKTTQITQYLSE---SGFTARGKIGCTQPRRVAAMSVAKRVSEEFGCRLGQE 593
Cdd:cd17977     1 LPVWEAKYEFMESLAHNQIVIVSGDAKTGKSSQIPQWCAEyclSAHYQHGVVVCTQVHKQTAVWLALRVADEMDVNIGHE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  594 VGYTIRFEDCTSPETLIKYMTDGMLLRECLIDPDLQTYSCIMLDEAHERTIHTDVLFGLLKQAVQKRAELKLIVTSATLD 673
Cdd:cd17977    81 VGYVIPFENCCTNETILRYCTDDMLLREMMSDPLLESYGVIILDDAHERTVSTDVLLGLLKDVLLSRPELKLVIITCPHL 160

                         170
                  ....*....|...
gi 941644392  674 AVKFSQYFFEAPI 686
Cdd:cd17977   161 SSKLLSYYGNVPL 173
DEXHc_TDRD9 cd17988
DEXH-box helicase domain of tudor domain containing 9; Tudor domain containing 9 (TDRD9, also ...
 517-689 8.86e-40

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: 145.72  E-value: 8.86e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  517 LPIYKLRDELIKAVSDNQILIVIGETGSGKTTQITQYLSESgFTARGK---IGCTQPRRVAAMSVAKRVSEEFGCRLGQE 593
Cdd:cd17988     1 LPIYAKREEILSLIEANSVVIIKGATGCGKTTQLPQFILDH-YYKRGKycnIVVTQPRRIAAISIARRVSQEREWTLGSL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  594 VGYTIRFEDCTSPETLIKYMTDGMLLRECLIDPDLQTYSCIMLDEAHERTIHTDVLFGLLKQAVQKRA-ELKLIVTSATL 672
Cdd:cd17988    80 VGYQVGLERPASEETRLIYCTTGVLLQKLINNKTLTEYTHIILDEVHERDQELDFLLLVVRRLLRTNSrHVKIILMSATI 159

                         170       180
                  ....*....|....*....|.
gi 941644392  673 DAVKFSQYF----FEAPIFTI 689
Cdd:cd17988   160 SCKEFADYFttpnNPAYVFEV 180
DEXHc_DHX30 cd17976
DEXH-box helicase domain of DEAH-box helicase 30; DEAH-box helicase 30 (DHX30) plays an ...
 517-686 1.35e-39

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: 144.94  E-value: 1.35e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  517 LPIYKLRDELIKAVSDNQILIVIGETGSGKTTQITQYLSESGFT----ARGKIGCTQPRRVAAMSVAKRVSEEFGCRLGQ 592
Cdd:cd17976     1 LPVDSHKESILSAIEQNPVVVISGDTGCGKTTRIPQFILEDYVLrgrgARCNVVITQPRRISAVSVAQRVAHELGPNLRR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  593 EVGYTIRFEDCTSPET-LIKYMTDGMLLRECLIDPDLQTYSCIMLDEAHERTIHTDVLFGLLKQAVQKRAELKLIVTSAT 671
Cdd:cd17976    81 NVGYQVRLESRPPPRGgALLFCTVGVLLKKLQSNPRLEGVSHVIVDEVHERDVNTDFLLILLKGVLQLNPELRVVLMSAT 160

                         170
                  ....*....|....*
gi 941644392  672 LDAVKFSQYFFEAPI 686
Cdd:cd17976   161 GDNQRLSRYFGGCPV 175
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 212-290 3.23e-39

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: 140.07  E-value: 3.23e-39
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 941644392  212 GNVYAGKVMNLAAFGCFVQLEGIRKKCEGLVHISQLRREGRVNSVAEVVNRGDKVYVKVMSIAGQKISLSMKDVDQDSG 290
Cdd:cd05684     1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQNGKISLSMKDVDQDTG 79
DEXQc_DQX1 cd17986
DEXQ-box helicase domain of DEAQ-box RNA dependent ATPase 1; DEAQ-box RNA dependent ATPase 1 ...
 517-689 5.01e-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: 143.11  E-value: 5.01e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  517 LPIYKLRDELIKAV-SDNQILIVIGETGSGKTTQITQYLSESGFT---ARGKIGCTQPRRVAAMSVAKRVSEEFGCRLGQ 592
Cdd:cd17986     1 LPIWAAKFTFLEQLeSPSGIVLVSGEPGSGKSTQVPQWCAEFALSrgfQKGQVTVTQPHPLAARSLALRVADEMDLNLGH 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  593 EVGYTIRFEDCTSPETLIKYMTDGMLLRECLIDPDLQTYSCIMLDEAHERTIHTDVLFGLLKQAVQKRAELKL-IVTSAT 671
Cdd:cd17986    81 EVGYSIPQEDCTGPNTILRFCWDRLLLQEMTSTPLLGAWGVVVLDEAQERSVASDSLLGLLKDVRLQRPELRVvVVTSPA 160

                         170
                  ....*....|....*...
gi 941644392  672 LDAvKFSQYFFEAPIFTI 689
Cdd:cd17986   161 LEP-KLRAFWGNPPVVHV 177
OB_NTP_bind pfam07717
Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus ...
 1044-1120 3.62e-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: 111.58  E-value: 3.62e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  1044 VQKAICSGFFRNAAKKDPQE-GYRTLVDGQVVYIHPSSAIFN---RQPEWVVYHELVQTTKEYMREVTVIDAKWLVEFAP 1119
Cdd:pfam07717    1 LRAALAAGLYPNVARRDPKGkGYTTLSDNQRVFIHPSSVLFNektFPPEWVVYQELVETTKVYIRTVTAISPEWLLLFAP 80


                   .
gi 941644392  1120 A 1120
Cdd:pfam07717   81 H 81
DEXDc smart00487
DEAD-like helicases superfamily;
513-698 9.97e-26

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 106.04  E-value: 9.97e-26
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392    513 QRQSLPiyklrdeliKAVSDNQILIVIGETGSGKTTQITQYLSESGF-TARGKIGCTQPRRVAAMSVAKRVSEEFGCRLG 591
Cdd:smart00487   13 QKEAIE---------ALLSGLRDVILAAPTGSGKTLAALLPALEALKrGKGGRVLVLVPTRELAEQWAEELKKLGPSLGL 83

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392    592 QEVGYT------IRFEDCTSPETLIKYMTDGMLLRECLIDP-DLQTYSCIMLDEAHERT--IHTDVLFGLLKQAVQKRae 662
Cdd:smart00487   84 KVVGLYggdskrEQLRKLESGKTDILVTTPGRLLDLLENDKlSLSNVDLVILDEAHRLLdgGFGDQLEKLLKLLPKNV-- 161

                           170       180       190
                    ....*....|....*....|....*....|....*...
gi 941644392    663 lKLIVTSATL--DAVKFSQYFFEAPIFTIPGRTFPVEI 698
Cdd:smart00487  162 -QLLLLSATPpeEIENLLELFLNDPVFIDVGFTPLEPI 198
HA2 pfam04408
Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in ...
 909-965 5.07e-23

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: 94.61  E-value: 5.07e-23
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 941644392   909 ALEQLHSLSALDDEGLLTRLGRRMAEFPLEPSLSKMLIMSVHLMCSDEILTVVSMLS 965
Cdd:pfam04408    1 ALELLYYLGALDEDGELTPLGRKMAELPLDPRLAKMLLAAAELGCLDEVLTIVAALS 57
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 201-285 2.75e-20

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: 93.96  E-value: 2.75e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  201 PQKDFPENAEVGNVYAGKVMNLAAFGCFVQLE-GIrkkcEGLVHISQLRREGRVNSVAEVVNRGDKVYVKVMSI--AGQK 277
Cdd:COG0539   264 PWENIAEKYPVGDVVKGKVTRLTDFGAFVELEpGV----EGLVHISEMSWTKRVAHPSDVVKVGDEVEVKVLDIdpEERR 339


                  ....*...
gi 941644392  278 ISLSMKDV 285
Cdd:COG0539   340 ISLSIKQL 347
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 209-286 8.38e-19

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 92.03  E-value: 8.38e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 941644392  209 AEVGNVYAGKVMNLAAFGCFVQLEGIRkkcEGLVHISQLRREgRVNSVAEVVNRGDKVYVKVMSIAGQ-KISLSMKDVD 286
Cdd:PRK11824  619 PEVGEIYEGKVVRIVDFGAFVEILPGK---DGLVHISEIADE-RVEKVEDVLKEGDEVKVKVLEIDKRgRIRLSRKAVL 693
Pnp COG1185
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ...
 209-284 1.45e-18

Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440798 [Multi-domain]  Cd Length: 686  Bit Score: 91.22  E-value: 1.45e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 941644392  209 AEVGNVYAGKVMNLAAFGCFVQLEGIRkkcEGLVHISQLRREgRVNSVAEVVNRGDKVYVKVMSIAGQ-KISLSMKD 284
Cdd:COG1185   614 PEVGEIYEGKVVRIMDFGAFVEILPGK---DGLVHISELADE-RVEKVEDVLKEGDEVKVKVLEIDDQgRIKLSRKA 686
HA2 smart00847
Helicase associated domain (HA2) Add an annotation; This presumed domain is about 90 amino ...
 915-965 2.12e-18

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: 80.78  E-value: 2.12e-18
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|.
gi 941644392    915 SLSALDDEGLLTRLGRRMAEFPLEPSLSKMLIMSVHLMCSDEILTVVSMLS 965
Cdd:smart00847    1 ELGALDDDGRLTPLGRKMAELPLDPRLAKMLLAAAEFGCLDEILTIVAMLS 51
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 210-304 3.40e-18

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


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 81.76  E-value: 3.40e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  210 EVGNVYAGKVMNLAAFGCFVQLEGirkKCEGLVHISQLrREGRVNSVAEVVNRGDKVYVKVMSIAG-QKISLSMKDVDQD 288
Cdd:COG1098     4 EVGDIVEGKVTGITPFGAFVELPE---GTTGLVHISEI-ADGYVKDINDYLKVGDEVKVKVLSIDEdGKISLSIKQAEEK 79

                          90
                  ....*....|....*.
gi 941644392  289 SGEDLNPAPSTSSRPG 304
Cdd:COG1098    80 PKRPPRPRRNSRPKAG 95
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 194-288 1.85e-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: 85.10  E-value: 1.85e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  194 DDRREKKpqKDFPENAEVGNVYAGKVMNLAAFGCFVQLEGIrkkcEGLVHISQLRReGRVNSVAEVVNRGDKVYVKVMSI 273
Cdd:COG0539   174 EEREEKR--EELLEKLEEGDVVEGTVKNITDFGAFVDLGGV----DGLLHISEISW-GRVKHPSEVLKVGDEVEVKVLKI 246

                          90
                  ....*....|....*..
gi 941644392  274 --AGQKISLSMKDVDQD 288
Cdd:COG0539   247 drEKERISLSLKQLQPD 263
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 212-282 3.11e-17

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: 76.81  E-value: 3.11e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 941644392  212 GNVYAGKVMNLAAFGCFVQLEGIRkkcEGLVHISQLRREgRVNSVAEVVNRGDKVYVKVMSIAGQ-KISLSM 282
Cdd:cd04472     1 GKIYEGKVVKIKDFGAFVEILPGK---DGLVHISELSDE-RVEKVEDVLKVGDEVKVKVIEVDDRgRISLSR 68
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
198-291 5.70e-17

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 86.15  E-value: 5.70e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  198 EKKPQKDFPENAEVGNVYAGKVMNLAAFGCFVQLE-GIrkkcEGLVHISQLrREGRVNSVAEVVNRGDKVYVKVMSI--A 274
Cdd:PRK00087  549 LPDPWENVEEKYPVGSIVLGKVVRIAPFGAFVELEpGV----DGLVHISQI-SWKRIDKPEDVLSEGEEVKAKILEVdpE 623

                          90
                  ....*....|....*..
gi 941644392  275 GQKISLSMKDVDQDSGE 291
Cdd:PRK00087  624 EKRIRLSIKEVEEEPGD 640
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 212-283 1.01e-14

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: 70.01  E-value: 1.01e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 941644392  212 GNVYAGKVMNLAAFGCFVQL-EGIrkkcEGLVHISQLRREgRVNSVAEVVNRGDKVYVKVMSIAGQ-KISLSMK 283
Cdd:cd05692     1 GSVVEGTVTRLKPFGAFVELgGGI----SGLVHISQIAHK-RVKDVKDVLKEGDKVKVKVLSIDARgRISLSIK 69
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 207-301 1.12e-14

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 77.22  E-value: 1.12e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  207 ENAEVGNVYAGKVMNLAAFGCFVQL-EGIrkkcEGLVHISQLRREgRVNSVAEVVNRGDKVYVKVMSI--AGQKISLSMK 283
Cdd:PRK06676  273 EKLPEGDVIEGTVKRLTDFGAFVEVlPGV----EGLVHISQISHK-HIATPSEVLEEGQEVKVKVLEVneEEKRISLSIK 347

                          90
                  ....*....|....*...
gi 941644392  284 DVDQDSGEDLNPAPSTSS 301
Cdd:PRK06676  348 ALEEAPAEEEDRREEYRQ 365
HELICc smart00490
helicase superfamily c-terminal domain;
743-847 1.76e-14

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 69.55  E-value: 1.76e-14
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392    743 EILYERMKSMGpdvpeLIILPVYSALPSEMQTRIFEPAPPGSRKVVIATNIAETSLTIDGIYYVVDPGFvkqkvynsktg 822
Cdd:smart00490    1 EELAELLKELG-----IKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDL----------- 64

                            90       100
                    ....*....|....*....|....*
gi 941644392    823 mdslvvtPISQAQAKQRAGRAGRTG 847
Cdd:smart00490   65 -------PWSPASYIQRIGRAGRAG 82
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 196-285 5.08e-14

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 75.30  E-value: 5.08e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  196 RREKKpqKDFPENAEVGNVYAGKVMNLAAFGCFVQLEGIrkkcEGLVHISQLRREgRVNSVAEVVNRGDKVYVKVMSI-- 273
Cdd:PRK06676  179 RAAKK--EELLSSLKEGDVVEGTVARLTDFGAFVDIGGV----DGLVHISELSHE-RVEKPSEVVSVGQEVEVKVLSIdw 251

                          90
                  ....*....|..
gi 941644392  274 AGQKISLSMKDV 285
Cdd:PRK06676  252 ETERISLSLKDT 263
S1_pNO40 cd05686
S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function ...
 210-283 3.81e-13

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


Pssm-ID: 240191 [Multi-domain]  Cd Length: 73  Bit Score: 65.58  E-value: 3.81e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 941644392  210 EVGNVYAGKVMNLAAFGCFVQLEGIRKkcEGLVHISQLRrEGRVNSVAEVVNRGDKVYVKVMSIA-GQKISLSMK 283
Cdd:cd05686     2 ALYQIFKGEVASVTEYGAFVKIPGCRK--QGLVHKSHMS-SCRVDDPSEVVDVGEKVWVKVIGREmKDKMKLSLS 73
PRK08059 PRK08059
general stress protein 13; Validated
 207-283 4.09e-13

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 66.99  E-value: 4.09e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 941644392  207 ENAEVGNVYAGKVMNLAAFGCFVQLEGirkKCEGLVHISQLrREGRVNSVAEVVNRGDKVYVKVMSIAGQ--KISLSMK 283
Cdd:PRK08059    3 SQYEVGSVVTGKVTGIQPYGAFVALDE---ETQGLVHISEI-THGFVKDIHDFLSVGDEVKVKVLSVDEEkgKISLSIR 77
rpsA PRK13806
30S ribosomal protein S1; Provisional
 201-288 1.08e-12

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 72.06  E-value: 1.08e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  201 PQKDFPENAEVGNVYAGKVMNLAAFGCFVQLE-GIrkkcEGLVHISQLRREGRVNSVAEVVNRGDKVYVKVMSI--AGQK 277
Cdd:PRK13806  282 PWDTVGDRLKAGDKVTGKVVRLAPFGAFVEILpGI----EGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDIdpAKRR 357

                          90
                  ....*....|.
gi 941644392  278 ISLSMKDVDQD 288
Cdd:PRK13806  358 ISLSLRDAEGD 368
PRK08582 PRK08582
RNA-binding protein S1;
210-340 1.18e-12

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 66.21  E-value: 1.18e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  210 EVGNVYAGKVMNLAAFGCFVQLEGirkKCEGLVHISQLrREGRVNSVAEVVNRGDKVYVKVMSIAGQ-KISLSM-KDVDQ 287
Cdd:PRK08582    4 EVGSKLQGKVTGITNFGAFVELPE---GKTGLVHISEV-ADNYVKDINDHLKVGDEVEVKVLNVEDDgKIGLSIkKAKDR 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 941644392  288 DSGEDLNPapstssrpgltSHESETALRNPDRPLSLLDLKTNV----EEDELTNRKR 340
Cdd:PRK08582   80 PKRQHDRP-----------RHEDNRGGGNDVAPKEDFEQKMSRflkdSEDRLTSIKR 125
rpsA PRK13806
30S ribosomal protein S1; Provisional
 195-288 1.39e-12

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 71.68  E-value: 1.39e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  195 DRREKKPQKDFPENAEVGNVYAGKVMNLAAFGCFVQLE-GIrkkcEGLVHISQLRReGRVNSVAEVVNRGDKVYVKVMSI 273
Cdd:PRK13806  186 EREQKEALEAFMETVKEGDVVEGTVTRLAPFGAFVELApGV----EGMVHISELSW-SRVQKADEAVSVGDTVRVKVLGI 260

                          90       100
                  ....*....|....*....|.
gi 941644392  274 A------GQKISLSMKDVDQD 288
Cdd:PRK13806  261 ErakkgkGLRISLSIKQAGGD 281
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
189-287 2.66e-12

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 71.21  E-value: 2.66e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  189 DKRGKDDRRE-KKPQkdFPENAE------VGNVYAGKVMNLAAFGCFVQLeGIrkKCEGLVHISQLRrEGRVNSVAEVVN 261
Cdd:COG2183   614 EKPGRDPRPEfKTPT--FREGVLkiedlkPGMILEGTVTNVTDFGAFVDI-GV--HQDGLVHISQLS-DRFVKDPREVVK 687

                          90       100
                  ....*....|....*....|....*...
gi 941644392  262 RGDKVYVKVMSI--AGQKISLSMKDVDQ 287
Cdd:COG2183   688 VGDIVKVKVLEVdlKRKRISLSMKLDDE 715
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
210-283 6.51e-12

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 61.85  E-value: 6.51e-12
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 941644392    210 EVGNVYAGKVMNLAAFGCFVQLEGirkKCEGLVHISQLRREgRVNSVAEVVNRGDKVYVKVMSI--AGQKISLSMK 283
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGN---GVEGLIPISELSDK-RVKDPEEVLKVGDEVKVKVLSVdeEKGRIILSLK 72
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 713-847 7.85e-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: 63.00  E-value: 7.85e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392   713 LITVMQIHLNEPPGDILLFLTGQEEIDtaCEILYERMKsmgpdvpeLIILPVYSALPSEMQTRIFEPAPPGSRKVVIATN 792
Cdd:pfam00271    3 LEALLELLKKERGGKVLIFSQTKKTLE--AELLLEKEG--------IKVARLHGDLSQEEREEILEDFRKGKIDVLVATD 72

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 941644392   793 IAETSLTIDGIYYVVDpgfvkqkvYNSKTGMDSLVvtpisqaqakQRAGRAGRTG 847
Cdd:pfam00271   73 VAERGLDLPDVDLVIN--------YDLPWNPASYI----------QRIGRAGRAG 109
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 211-281 8.55e-12

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: 61.49  E-value: 8.55e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 941644392  211 VGNVYAGKVMNLAAFGCFVQLEGIrkkcEGLVHISQLRReGRVNSVAEVVNRGDKVYVKVMSI--AGQKISLS 281
Cdd:cd05688     1 EGDVVEGTVKSITDFGAFVDLGGV----DGLLHISDMSW-GRVKHPSEVVNVGDEVEVKVLKIdkERKRISLG 68
PRK05807 PRK05807
RNA-binding protein S1;
210-283 1.71e-11

RNA-binding protein S1;


Pssm-ID: 235614 [Multi-domain]  Cd Length: 136  Bit Score: 62.84  E-value: 1.71e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 941644392  210 EVGNVYAGKVMNLAAFGCFVQLEGIrkkcEGLVHISQLrREGRVNSVAEVVNRGDKVYVKVMSI-AGQKISLSMK 283
Cdd:PRK05807    4 KAGSILEGTVVNITNFGAFVEVEGK----TGLVHISEV-ADTYVKDIREHLKEQDKVKVKVISIdDNGKISLSIK 73
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 210-283 1.93e-11

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 68.27  E-value: 1.93e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 941644392  210 EVGNVYAGKVMNLAAFGCFVQLE-GIrkkcEGLVHISQLRREGRVNSVAEVVNRGDKVYVKVMSI--AGQKISLSMK 283
Cdd:PRK06299  285 PVGSKVKGKVTNITDYGAFVELEeGI----EGLVHVSEMSWTKKNKHPSKVVSVGQEVEVMVLEIdeEKRRISLGLK 357
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 201-296 4.65e-11

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 66.61  E-value: 4.65e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  201 PQKDFPENAEVGNVYAGKVMNLAAFGCFVQLE-GIrkkcEGLVHISQLrREGRVNSVAEVVNRGDKVYVKVMSI--AGQK 277
Cdd:PRK07899  283 PWQQFARTHAIGQIVPGKVTKLVPFGAFVRVEeGI----EGLVHISEL-AERHVEVPEQVVQVGDEVFVKVIDIdlERRR 357

                          90       100
                  ....*....|....*....|...
gi 941644392  278 ISLSMK----DVDQDSgEDLNPA 296
Cdd:PRK07899  358 ISLSLKqaneGVTPES-EDFDPA 379
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 201-283 9.66e-11

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: 65.91  E-value: 9.66e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392   201 PQKDFPENAEVGNVYAGKVMNLAAFGCFVQL-EGIrkkcEGLVHISQLRREGRVNSVAEVVNRGDKVYVKVMSIAGQ--K 277
Cdd:TIGR00717  262 PWEAIEKKFPVGDKITGRVTNLTDYGVFVEIeEGI----EGLVHVSEMSWVKKNSHPSKVVKKGDEVEVMILDIDPErrR 337


                   ....*.
gi 941644392   278 ISLSMK 283
Cdd:TIGR00717  338 LSLGLK 343
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 194-288 1.18e-10

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 65.57  E-value: 1.18e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  194 DDRREKKpqKDFPENAEVGNVYAGKVMNLAAFGCFVQLEGIrkkcEGLVHISQLRReGRVNSVAEVVNRGDKVYVKVMSI 273
Cdd:PRK06299  186 EERAEER--EELLENLEEGQVVEGVVKNITDYGAFVDLGGV----DGLLHITDISW-KRVNHPSEVVNVGDEVKVKVLKF 258

                          90
                  ....*....|....*..
gi 941644392  274 --AGQKISLSMKDVDQD 288
Cdd:PRK06299  259 dkEKKRVSLGLKQLGED 275
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
197-285 1.26e-10

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 65.74  E-value: 1.26e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  197 REKKPQKDFpENAEVGNVYAGKVMNLAAFGCFVQLEGIrkkcEGLVHISQLRReGRVNSVAEVVNRGDKVYVKVMSI--A 274
Cdd:PRK00087  464 KEKKKEETW-NSLEEGDVVEGEVKRLTDFGAFVDIGGV----DGLLHVSEISW-GRVEKPSDVLKVGDEIKVYILDIdkE 537

                          90
                  ....*....|.
gi 941644392  275 GQKISLSMKDV 285
Cdd:PRK00087  538 NKKLSLSLKKL 548
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 200-288 1.45e-10

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 65.19  E-value: 1.45e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  200 KPQKDFPENAEVGNVYAGKVMNLAAFGCFVQLE-GIrkkcEGLVHISQLRREGRVNSVAEVVNRGDKVYVKVMSI--AGQ 276
Cdd:PRK06299  362 NPWEEFAEKYPVGDVVEGKVKNITDFGAFVGLEgGI----DGLVHLSDISWDKKGEEAVELYKKGDEVEAVVLKVdvEKE 437

                          90
                  ....*....|..
gi 941644392  277 KISLSMKDVDQD 288
Cdd:PRK06299  438 RISLGIKQLEED 449
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 179-293 2.21e-10

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: 64.76  E-value: 2.21e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392   179 DRHRGNDRFEDKRGKDDRREKKPQkDFPENAEVGNVYAGKVMNLAAFGCFVQLEGIrkkcEGLVHISQLRReGRVNSVAE 258
Cdd:TIGR00717  156 DQKRNNIVVSRRAYLEEERSQARE-ELLENLKEGDVVKGVVKNITDFGAFVDLGGV----DGLLHITDMSW-KRVKHPSE 229

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 941644392   259 VVNRGDKVYVKVMSIAGQK--ISLSMKDVDQDSGEDL 293
Cdd:TIGR00717  230 YVKVGQEVKVKVIKFDKEKgrISLSLKQLGEDPWEAI 266
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 212-281 2.22e-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: 2.22e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 941644392  212 GNVYAGKVMNLAAFGCFVQLeGIRKKceGLVHISQLRrEGRVNSVAEVVNRGDKVYVKVMSI--AGQKISLS 281
Cdd:cd05685     1 GMVLEGVVTNVTDFGAFVDI-GVKQD--GLIHISKMA-DRFVSHPSDVVSVGDIVEVKVISIdeERGRISLS 68
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 212-280 4.58e-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: 4.58e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 941644392  212 GNVYAGKVMNLAAFGCFVQLE-GIrkkcEGLVHISQLRREGRVNSVAEVVNRGDKVYVKVMSI--AGQKISL 280
Cdd:cd05690     1 GTVVSGKIKSITDFGIFVGLDgGI----DGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIdvERERISL 68
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 215-282 1.00e-07

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: 50.07  E-value: 1.00e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 941644392  215 YAGKVMNLAAFGCFVQLEGirkKCEGLVHISQLRREgRVNSVAEVVNRGDKVYVKVMSIAGQKISLSM 282
Cdd:cd00164     1 VTGKVVSITKFGVFVELED---GVEGLVHISELSDK-FVKDPSEVFKVGDEVEVKVLEVDPEKGRISL 64
S1_RNase_R cd04471
S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, ...
 211-273 2.30e-07

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: 49.32  E-value: 2.30e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 941644392  211 VGNVYAGKVMNLAAFGCFVQLEGIrkKCEGLVHISQL----------------RREGRVNSVaevvnrGDKVYVKVMSI 273
Cdd:cd04471     1 VGEEFDGVISGVTSFGLFVELDNL--TVEGLVHVSTLgddyyefdeenhalvgERTGKVFRL------GDKVKVRVVRV 71
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 201-288 2.46e-07

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 54.79  E-value: 2.46e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  201 PQKDFPENAEVGNVYAGKVMNLAAFGCFVQLEGirkKCEGLVHISQLRREgRVNSVAEVVNRGDKVYVKVMSI--AGQKI 278
Cdd:PRK06299  450 PFEEFAKKHKKGSIVTGTVTEVKDKGAFVELED---GVEGLIRASELSRD-RVEDATEVLKVGDEVEAKVINIdrKNRRI 525

                          90
                  ....*....|
gi 941644392  279 SLSMKDVDQD 288
Cdd:PRK06299  526 SLSIKALDEA 535
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 203-288 3.33e-07

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 52.90  E-value: 3.33e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  203 KDFPEnaeVGNVYAGKVMNLAAFGCFVQLEGIRKKcEGLVHISQLRReGRVNSVAEVVNRGDKVYVKVMSI---AGQkIS 279
Cdd:PRK03987    3 KEWPE---EGELVVGTVKEVKDFGAFVTLDEYPGK-EGFIHISEVAS-GWVKNIRDHVKEGQKVVCKVIRVdprKGH-ID 76


                  ....*....
gi 941644392  280 LSMKDVDQD 288
Cdd:PRK03987   77 LSLKRVNEH 85
S1_RPS1_repeat_ec4 cd05689
S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 217-282 3.62e-07

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


Pssm-ID: 240194 [Multi-domain]  Cd Length: 72  Bit Score: 48.73  E-value: 3.62e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 941644392  217 GKVMNLAAFGCFVQLEgirKKCEGLVHISQLRREGRVNSVAEVVNRGDKVYVKVMSIAGQKISLSM 282
Cdd:cd05689     9 GKVTNLTDYGCFVELE---EGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEERRRISL 71
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 210-282 7.97e-07

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: 47.67  E-value: 7.97e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 941644392   210 EVGNVYAGKVMNLAAFGCFVQLEGirkKCEGLVHISQLRREGRVNSvAEVVNRGDKVYVKVMSI--AGQKISLSM 282
Cdd:pfam00575    2 EKGDVVEGEVTRVTKGGAFVDLGN---GVEGFIPISELSDDHVEDP-DEVIKVGDEVKVKVLKVdkDRRRIILSI 72
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 210-284 2.12e-06

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: 46.42  E-value: 2.12e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  210 EVGNVYAGKVMNLAAFGCFVQLE---GIrkkcEGLVHISQLRReGRVNSVAEVVNRGDKVYVKVMSIAGQK--ISLSMKD 284
Cdd:cd04452     2 EEGELVVVTVKSIADMGAYVSLLeygNI----EGMILLSELSR-RRIRSIRKLVKVGRKEVVKVIRVDKEKgyIDLSKKR 76
PHA02653 PHA02653
RNA helicase NPH-II; Provisional
 628-856 2.70e-06

RNA helicase NPH-II; Provisional


Pssm-ID: 177443 [Multi-domain]  Cd Length: 675  Bit Score: 51.52  E-value: 2.70e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  628 LQTYSCIMLDEAHERTIHTDVLFGLLKQAVQKRAELKLIvtSATL-DAVKFSQYFFEAPIFT-IPGRT-FPVEILYTREP 704
Cdd:PHA02653  289 LFDYGTVIIDEVHEHDQIGDIIIAVARKHIDKIRSLFLM--TATLeDDRDRIKEFFPNPAFVhIPGGTlFPISEVYVKNK 366

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  705 ET-----DYLDASLITVMQIHLNEPPGD---ILLFLTGQEEIDTACEILYERMksmgpdvPELIILPVYSALPS--EMQT 774
Cdd:PHA02653  367 YNpknkrAYIEEEKKNIVTALKKYTPPKgssGIVFVASVSQCEEYKKYLEKRL-------PIYDFYIIHGKVPNidEILE 439

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  775 RIFEPAPPgsrKVVIATNIAETSLTIDGIYYVVDPGfvkqKVYNSK--TGMDSLvvtpISQAQAKQRAGRAGRTGPGkTY 852
Cdd:PHA02653  440 KVYSSKNP---SIIISTPYLESSVTIRNATHVYDTG----RVYVPEpfGGKEMF----ISKSMRTQRKGRVGRVSPG-TY 507


                  ....*
gi 941644392  853 -RLYT 856
Cdd:PHA02653  508 vYFYD 512
S1_RecJ_like cd04473
S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of ...
 206-273 1.39e-05

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: 44.13  E-value: 1.39e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 941644392  206 PENAEVGNVYAGKVMNLAAFGCFVQL-EGIRkkceGLVHISQLRREGRVnsvaevvnrGDKVYVKVMSI 273
Cdd:cd04473    11 MEDLEVGKLYKGKVNGVAKYGVFVDLnDHVR----GLIHRSNLLRDYEV---------GDEVIVQVTDI 66
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 536-671 1.41e-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: 46.24  E-value: 1.41e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  536 LIVIGETGSGKTTQITQYLSESGFTARGKIGCTQPRRVAAMSVAKRVSEEFgcRLGQEVGYTIRFedcTSPETL------ 609
Cdd:cd00046     4 VLITAPTGSGKTLAALLAALLLLLKKGKKVLVLVPTKALALQTAERLRELF--GPGIRVAVLVGG---SSAEEReknklg 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 941644392  610 ---IKYMTDGMLLRECLID--PDLQTYSCIMLDEAHERTIHTDVLFgLLKQAVQKRA--ELKLIVTSAT 671
Cdd:cd00046    79 dadIIIATPDMLLNLLLREdrLFLKDLKLIIVDEAHALLIDSRGAL-ILDLAVRKAGlkNAQVILLSAT 146
VacB COG0557
Exoribonuclease R [Transcription];
211-273 1.47e-05

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 49.33  E-value: 1.47e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 941644392  211 VGNVYAGKVMNLAAFGCFVQLEGIrkKCEGLVHISQL----------------RREGRVNSVaevvnrGDKVYVKVMSI 273
Cdd:COG0557   622 VGEEFEGVISGVTSFGLFVELDEL--GVEGLVHVSSLgddyyeyderrqalvgERTGKRYRL------GDRVEVRVVRV 692
GH2-like_DHX8 cd21691
GIPC-homology 2 (GH2)-like domain found in DEAH box protein 8 (DHX8) and similar proteins; ...
 1-23 2.67e-05

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: 43.30  E-value: 2.67e-05
                          10        20
                  ....*....|....*....|...
gi 941644392    1 MIENGAEFSDSLIANLLRLIKHM 23
Cdd:cd21691    46 LKENGAEFPDSFVESLLRLIQRM 68
cas3_core TIGR01587
CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an ...
 535-871 5.50e-05

CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not included within this model.


Pssm-ID: 273707 [Multi-domain]  Cd Length: 359  Bit Score: 46.68  E-value: 5.50e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392   535 ILIVIGETGSGKTT--------QITQYLSESGFTArgkigctQPRRVAAMSVAKRVSEEFGCRLGQEVG--YTIRFEDCT 604
Cdd:TIGR01587    1 LLVIEAPTGYGKTEaallwalhSIKSQKADRVIIA-------LPTRATINAMYRRAKELFGSELVGLHHssSFSRIKEMG 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392   605 SPETLIK----YMTDGML-----LRECLIDPDLQT----------------YSCIMLDEAHERTIHTDVLF-GLLKqaVQ 658
Cdd:TIGR01587   74 DSEEFEHlfplYIHSNDKlfldpITVCTIDQVLKSvfgefghyeftlasiaNSLLIFDEVHFYDEYTLALIlAVLE--VL 151

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392   659 KRAELKLIVTSATLDA--VKFSQ----YFFEAPIFTIPGRTFpveilyTREPETDYLDASL--ITVMQ--IHLNEPPGDI 728
Cdd:TIGR01587  152 KDNDVPILLMSATLPKflKEYAEkigyVEFNEPLDLKEERRF------ENHRFILIESDKVgeISSLErlLEFIKKGGSI 225

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392   729 LLFLTgqeEIDTACEIlYERMKSMGPDvpELIILpvYSALPSEMQTR------IFEPAPPGSRKVVIATNIAETSLTIDG 802
Cdd:TIGR01587  226 AIIVN---TVDRAQEF-YQQLKEKAPE--EEIIL--YHSRFTEKDRAkkeaelLREMKKSNEKFVIVATQVIEASLDISA 297

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 941644392   803 IYYVVDPgfvkqkvynskTGMDSLVvtpisqaqakQRAGRAGRTGPGktyrlytERAYRDEMLATPVPE 871
Cdd:TIGR01587  298 DVMITEL-----------APIDSLI----------QRLGRLHRYGRK-------IGENFEVYIITIAPE 338
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 201-283 8.20e-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: 46.65  E-value: 8.20e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392   201 PQKDFPENAEVGNVYAGKVMNLAAFGCFVQLE-GIrkkcEGLVHISQLRREGRVNSVAEVVNRGDKVYVKVMSI--AGQK 277
Cdd:TIGR00717  349 PWEQFEEKHPVGDRVTGKIKKITDFGAFVELEgGI----DGLIHLSDISWDKDGREADHLYKKGDEIEAVVLAVdkEKKR 424


                   ....*.
gi 941644392   278 ISLSMK 283
Cdd:TIGR00717  425 ISLGVK 430
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
211-288 1.15e-04

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 42.77  E-value: 1.15e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  211 VGNVYAGKVMNLAAFGCFVQLEGIRKkceGLVHISQLrREGRVNSVAEVVNRGDKVYVKVMSIA--GQKISLSMKDVDQD 288
Cdd:PRK07252    3 IGDKLKGTITGIKPYGAFVALENGTT---GLIHISEI-KTGFIDNIHQLLKVGEEVLVQVVDFDeyTGKASLSLRTLEEE 78
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 198-302 1.26e-04

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 46.24  E-value: 1.26e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  198 EKKPQKDFPENAEVGNVYAGKVMNLAAFGCFVQL-EGIrkkcEGLVHISQLRREGRVNSVAEVVNRGDKVYVKVM--SIA 274
Cdd:PRK12269  565 QPDPWLEFENKFGVNDVVKGRVTKIADFGAFIELaEGI----EGLAHISEFSWVKKTSKPSDMVKIGDEVECMILgyDIQ 640

                          90       100
                  ....*....|....*....|....*...
gi 941644392  275 GQKISLSMKDVDQDSGEDLNPAPSTSSR 302
Cdd:PRK12269  641 AGRVSLGLKQVTANPWEEIEARYPVGAR 668
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 212-288 1.40e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 45.81  E-value: 1.40e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 941644392  212 GNVYAGKVMNLAAFGCFVQLEGIrkkcEGLVHISQLRREgRVNSVAEVVNRGDKVYVKVMSI--AGQKISLSMKDVDQD 288
Cdd:PRK07899  209 GQVRKGVVSSIVNFGAFVDLGGV----DGLVHVSELSWK-HIDHPSEVVEVGQEVTVEVLDVdmDRERVSLSLKATQED 282
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 201-283 1.56e-04

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: 45.88  E-value: 1.56e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392   201 PQKDFPENAEVGNVYAGKVMNLAAFGCFVQLEGirkKCEGLVHISQLRREgRVNSVAEVVNRGDKVYVKVMSI--AGQKI 278
Cdd:TIGR00717  436 PWEKFAAKYKVGSVVKGKVTEIKDFGAFVELPG---GVEGLIRNSELSEN-RDEDKTDEIKVGDEVEAKVVDIdkKNRKV 511


                   ....*
gi 941644392   279 SLSMK 283
Cdd:TIGR00717  512 SLSVK 516
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
 211-343 2.05e-04

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 45.66  E-value: 2.05e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  211 VGNVYAG-KVMNLAAFGCFVQLEGIRkkcEGLVHISQLrREGRVNSVAEVVNRGDKVYVKVMSIAGQ-KISLSMKDVDQD 288
Cdd:PLN00207  753 VGDIYRNcEIKSIAPYGAFVEIAPGR---EGLCHISEL-SSNWLAKPEDAFKVGDRIDVKLIEVNDKgQLRLSRRALLPE 828

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 941644392  289 SGEDlnpAPSTSSRPGLTSHESET--ALRNPDRPLSLLDLKTNVEEDELTNRKRVQR 343
Cdd:PLN00207  829 ANSE---KSSQKQQGGSTKDKAPQkkYVNTSSRPRRAAQAEKNSAENAAVPKKKDYK 882
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 786-848 5.78e-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: 39.61  E-value: 5.78e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 941644392  786 KVVIATNIAETSLTIDGIYYVVDPGFvkqkvynsktgmdslvvtPISQAQAKQRAGRAGRTGP 848
Cdd:cd18785    24 EILVATNVLGEGIDVPSLDTVIFFDP------------------PSSAASYIQRVGRAGRGGK 68
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
 542-640 9.49e-04

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: 41.00  E-value: 9.49e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  542 TGSGKTTQITQYLSESGFTARGKIGCTQPRRVAAMSVAKRVSeefgcrlGQEVGY-TIRFEDCTSPETLIKYMTDGMLLR 620
Cdd:cd17931    10 PGAGKTTRVLPQIIREAIKKRLRTLVLAPTRVVAAEMYEALR-------GLPIRYrTGAVKEEHGGNEIVDYMCHGTFTC 82

                          90       100
                  ....*....|....*....|
gi 941644392  621 ECLIDPDLQTYSCIMLDEAH 640
Cdd:cd17931    83 RLLSPKRVPNYNLIIMDEAH 102
rpsA PRK13806
30S ribosomal protein S1; Provisional
 198-292 1.35e-03

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 42.79  E-value: 1.35e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  198 EKKPQKDFPENAEVGNVYAGKVMNLAAFGCFVQLE-GIrkkcEGLVHISQLRREGRVNSVAEvVNRGDKVYVKVMSI--A 274
Cdd:PRK13806  366 EGDPWADVAERFAPGTTVTGTVEKRAQFGLFVNLApGV----TGLLPASVISRAGKPATYEK-LKPGDSVTLVVEEIdtA 440

                          90
                  ....*....|....*...
gi 941644392  275 GQKISLSMKDVDQDSGED 292
Cdd:PRK13806  441 KRKISLAPAGAAGSGADD 458
Cas3_I cd09639
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short ...
 535-855 1.52e-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: 42.03  E-value: 1.52e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  535 ILIVIGETGSGKTT--------QITQYLSESGFTArgkigctQPRRVAAMSVAKRVSEEFG-CRLGQEVGYTIRFEDCTS 605
Cdd:cd09639     1 LLVIEAPTGYGKTEaallwalhSLKSQKADRVIIA-------LPTRATINAMYRRAKEAFGeTGLYHSSILSSRIKEMGD 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  606 PETLIK----YMTDGML-----LRECLIDPDLQT----------------YSCIMLDEAHERTIHTDVLF-GLLKqaVQK 659
Cdd:cd09639    74 SEEFEHlfplYIHSNDTlfldpITVCTIDQVLKSvfgefghyeftlasiaNSLLIFDEVHFYDEYTLALIlAVLE--VLK 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  660 RAELKLIVTSATLDavKFSQYFFEA---PIFTIPGRTFPVEILYTREPETDYL-DASLITVMqIHLNEPPGDILLFLTgq 735
Cdd:cd09639   152 DNDVPILLMSATLP--KFLKEYAEKigyVEENEPLDLKPNERAPFIKIESDKVgEISSLERL-LEFIKKGGSVAIIVN-- 226

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392  736 eEIDTACEIlYERMKSMGPDVPELII----LPVYSALPSEMQTRIFEPAPPGsrkVVIATNIAETSLTIDGIYYVVDPgf 811
Cdd:cd09639   227 -TVDRAQEF-YQQLKEKGPEEEIMLIhsrfTEKDRAKKEAELLLEFKKSEKF---VIVATQVIEASLDISVDVMITEL-- 299

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....
gi 941644392  812 vkqkvynskTGMDSLVvtpisqaqakQRAGRAGRTGPGKTYRLY 855
Cdd:cd09639   300 ---------APIDSLI----------QRLGRLHRYGEKNGEEVY 324
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 212-286 2.53e-03

S1_RPS1_repeat_ec6: 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 6 (ec6) 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: 240196 [Multi-domain]  Cd Length: 73  Bit Score: 37.64  E-value: 2.53e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 941644392  212 GNVYAGKVMNLAAFGCFVQL-EGIrkkcEGLVHISQLRREgRVNSVAEVVNRGDKVYVKVMSI--AGQKISLSMKDVD 286
Cdd:cd05691     1 GSIVTGKVTEVDAKGATVKLgDGV----EGFLRAAELSRD-RVEDATERFKVGDEVEAKITNVdrKNRKISLSIKAKE 73
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 513-673 2.77e-03

DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.


Pssm-ID: 425570 [Multi-domain]  Cd Length: 165  Bit Score: 39.92  E-value: 2.77e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392   513 QRQSLP-IYKLRDelikavsdnqiLIVIGETGSGKTT--QITqYLSESGFTARGKIG-CTQPRRVAA---MSVAKRVSEE 585
Cdd:pfam00270    4 QAEAIPaILEGRD-----------VLVQAPTGSGKTLafLLP-ALEALDKLDNGPQAlVLAPTRELAeqiYEELKKLGKG 71

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392   586 FGCRLGQEVG---YTIRFEDCTSPEtlIKYMTDGMLLRECLIDPDLQTYSCIMLDEAHErtiHTDVLFG--LLKQAVQKR 660
Cdd:pfam00270   72 LGLKVASLLGgdsRKEQLEKLKGPD--ILVGTPGRLLDLLQERKLLKNLKLLVLDEAHR---LLDMGFGpdLEEILRRLP 146

                          170
                   ....*....|...
gi 941644392   661 AELKLIVTSATLD 673
Cdd:pfam00270  147 KKRQILLLSATLP 159
AAA_22 pfam13401
AAA domain;
534-667 3.12e-03

AAA domain;


Pssm-ID: 379165 [Multi-domain]  Cd Length: 129  Bit Score: 38.86  E-value: 3.12e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 941644392   534 QILIVIGETGSGKTTQITQYLSESGFTARGKIGCTQPRRVAAMSVAKRVSEEFGCRLgqevgytirfEDCTSPETLIKYM 613
Cdd:pfam13401    6 GILVLTGESGTGKTTLLRRLLEQLPEVRDSVVFVDLPSGTSPKDLLRALLRALGLPL----------SGRLSKEELLAAL 75

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 941644392   614 TDGMLlreclidpDLQTYSCIMLDEAHErtIHTDVLFGLLKQAVQKRAELKLIV 667
Cdd:pfam13401   76 QQLLL--------ALAVAVVLIIDEAQH--LSLEALEELRDLLNLSSKLLQLIL 119
 
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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