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Conserved domains on  [gi|157824876|gb|ABV82517|]
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maleless [Drosophila melanogaster]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DEXHc_DHX9 cd17972
DEXH-box helicase domain of DEAH-box helicase 9; DEAH-box helicase 9 (DHX9, also known as ...
 326-559 9.22e-157

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: 469.31  E-value: 9.22e-157
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  326 IPWAPPQANWNTWHACNIDEGELATTSIDDLSMDYERSLRDRRQNDNEYRQFLEFREKLPIAAMRSEILTAINDNPVVII 405
Cdd:cd17972     1 VPWSPPQSNWNPWTSSNIDEGPLAFATPEQISMDLKNELMYQREQDHNLQQILQERELLPVKKFREEILEAISNNPVVII 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  406 RGNTGCGKTTQIAQYILDDYICSGQGGYANIYVTQPRRISAISVAERVARERCEQLGDTVGYSVRFESVFPRPYGAILFC 485
Cdd:cd17972    81 RGATGCGKTTQVPQYILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEVGKSCGYSVRFESVLPRPHASILFC 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 157824876  486 TVGVLLRKLEAGLRGVSHIIVDEIHERDVNSDFLLVILRDMVDTYPDLHVILMSATIDTTKFSKYFGICPVLEV 559
Cdd:cd17972   161 TVGVLLRKLEAGIRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPDLRVILMSATIDTSMFCEYFFNCPVIEV 234
HrpA super family cl34328
HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];
378-889 3.49e-116

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: 383.28  E-value: 3.49e-116
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  378 LEFREKLPIAAMRSEILTAINDNPVVIIRGNTGCGKTTQIAQYILDdyicSGQGGYANIYVTQPRRISAISVAERVARER 457
Cdd:COG1643     4 ITYPPDLPVSAVLPELLAALRAHQVVVLAAPPGAGKTTQLPLALLE----LGWGAGGRIGMLEPRRLAARAAAERMAEEL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  458 CEQLGDTVGYSVRFES-VFPRPYgaILFCTVGVLLRKLEA--GLRGVSHIIVDEIHERDVNSDFLLVILRDMVDTY-PDL 533
Cdd:COG1643    80 GEPVGETVGYRVRFEDkVSAATR--IEVVTEGILLRELQRdpELEGVDTVIFDEFHERSLNADLLLALLLDLQPALrPDL 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  534 HVILMSATIDTTKFSKYFGICPVLEVPGRAFPVqqfflediiqmtdfvpsaeSRRKRKEVEDEEQLLSedkdeaeinynk 613
Cdd:COG1643   158 KLLVMSATLDAERFARLLGDAPVIESSGRTYPV-------------------EVRYRPLPADERDLED------------ 206

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  614 vcedkysqktrnAMAMLsesdvsfeLLEALLMHikskniPGAILVFLPGWNLIFALMKFLQNTnIFGDTsqyQILPCHSQ 693
Cdd:COG1643   207 ------------AVADA--------VREALAEE------PGDILVFLPGEREIRRTAEALRGR-LPPDT---EILPLYGR 256

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  694 IPRDEQRKVFEPVPEGVTKIILSTNIAETSITIDDIVFVIDICKARMKLFtSHNN-LTSYATVWASKTNLEQRKGRAGRV 772
Cdd:COG1643   257 LSAAEQDRAFAPAPHGRRRIVLATNIAETSLTVPGIRYVIDSGLARIPRY-DPRSgVTRLPTERISQASANQRAGRAGRL 335

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  773 RPGFCFTLCSRARFQALEDNLTPEMFRTPLHEMALTIKLLRLGSIHHFlsKALEPPPVDAVIEAEVLLREMRCLDANDEL 852
Cdd:COG1643   336 APGICYRLWSEEDFARRPAFTDPEILRADLASLILELAAWGLGDPEDL--PFLDPPPARAIADARALLQELGALDADGRL 413

                         490       500       510
                  ....*....|....*....|....*....|....*..
gi 157824876  853 TPLGRLLARLPIEPRLGKMMVLGAVFGCADLMAIMAS 889
Cdd:COG1643   414 TPLGRALARLPLDPRLARMLLAAAELGCLREAAILAA 450
DSRM_DHX9_rpt2 cd19855
second double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; ...
 167-241 3.54e-37

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


:

Pssm-ID: 380684  Cd Length: 75  Bit Score: 134.27  E-value: 3.54e-37
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 157824876  167 IENAKERLNIYKQTNNIRDDYKYTPVGPEHARSFLAELSIYVPALNRTVTARESGSNKKSASKSCALSLVRQLFH 241
Cdd:cd19855     1 LDNAKSRLNEFLQKNKIPAEYKYTSVGPDHNRSFIAELSIFVKQLGKTIYARETGSNKKLASQSCALSLVRQLYH 75
DSRM_DHX9_rpt1 cd19854
first double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; ...
 2-70 3.47e-31

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


:

Pssm-ID: 380683  Cd Length: 69  Bit Score: 116.99  E-value: 3.47e-31
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 157824876    2 DIKSFLYQFCAKSQIEPKFDIRQTGPKNRQRFLCEVRVEPNTYIGVGNSTNKKDAEKNACRDFVNYLVR 70
Cdd:cd19854     1 EIKAFLYAWCGKKKLTPEYDIKEAGNKHRQRFKCEVRVEGFDYVGTGNATNKKDAQTNAARDFLNYLVR 69
OB_NTP_bind pfam07717
Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus ...
 1002-1079 6.91e-20

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: 85.00  E-value: 6.91e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  1002 ALLCLGLYPNICVHKEKRKVLTT--ESKAALLHKTSVNCSnlAVTFPYPFFVFGEKIRTRAVSCKQLSMVSPLQVILFGS 1079
Cdd:pfam07717    3 AALAAGLYPNVARRDPKGKGYTTlsDNQRVFIHPSSVLFN--EKTFPPEWVVYQELVETTKVYIRTVTAISPEWLLLFAP 80
 
Name Accession Description Interval E-value
DEXHc_DHX9 cd17972
DEXH-box helicase domain of DEAH-box helicase 9; DEAH-box helicase 9 (DHX9, also known as ...
 326-559 9.22e-157

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: 469.31  E-value: 9.22e-157
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  326 IPWAPPQANWNTWHACNIDEGELATTSIDDLSMDYERSLRDRRQNDNEYRQFLEFREKLPIAAMRSEILTAINDNPVVII 405
Cdd:cd17972     1 VPWSPPQSNWNPWTSSNIDEGPLAFATPEQISMDLKNELMYQREQDHNLQQILQERELLPVKKFREEILEAISNNPVVII 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  406 RGNTGCGKTTQIAQYILDDYICSGQGGYANIYVTQPRRISAISVAERVARERCEQLGDTVGYSVRFESVFPRPYGAILFC 485
Cdd:cd17972    81 RGATGCGKTTQVPQYILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEVGKSCGYSVRFESVLPRPHASILFC 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 157824876  486 TVGVLLRKLEAGLRGVSHIIVDEIHERDVNSDFLLVILRDMVDTYPDLHVILMSATIDTTKFSKYFGICPVLEV 559
Cdd:cd17972   161 TVGVLLRKLEAGIRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPDLRVILMSATIDTSMFCEYFFNCPVIEV 234
HrpA COG1643
HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];
378-889 3.49e-116

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


Pssm-ID: 441249 [Multi-domain]  Cd Length: 836  Bit Score: 383.28  E-value: 3.49e-116
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  378 LEFREKLPIAAMRSEILTAINDNPVVIIRGNTGCGKTTQIAQYILDdyicSGQGGYANIYVTQPRRISAISVAERVARER 457
Cdd:COG1643     4 ITYPPDLPVSAVLPELLAALRAHQVVVLAAPPGAGKTTQLPLALLE----LGWGAGGRIGMLEPRRLAARAAAERMAEEL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  458 CEQLGDTVGYSVRFES-VFPRPYgaILFCTVGVLLRKLEA--GLRGVSHIIVDEIHERDVNSDFLLVILRDMVDTY-PDL 533
Cdd:COG1643    80 GEPVGETVGYRVRFEDkVSAATR--IEVVTEGILLRELQRdpELEGVDTVIFDEFHERSLNADLLLALLLDLQPALrPDL 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  534 HVILMSATIDTTKFSKYFGICPVLEVPGRAFPVqqfflediiqmtdfvpsaeSRRKRKEVEDEEQLLSedkdeaeinynk 613
Cdd:COG1643   158 KLLVMSATLDAERFARLLGDAPVIESSGRTYPV-------------------EVRYRPLPADERDLED------------ 206

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  614 vcedkysqktrnAMAMLsesdvsfeLLEALLMHikskniPGAILVFLPGWNLIFALMKFLQNTnIFGDTsqyQILPCHSQ 693
Cdd:COG1643   207 ------------AVADA--------VREALAEE------PGDILVFLPGEREIRRTAEALRGR-LPPDT---EILPLYGR 256

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  694 IPRDEQRKVFEPVPEGVTKIILSTNIAETSITIDDIVFVIDICKARMKLFtSHNN-LTSYATVWASKTNLEQRKGRAGRV 772
Cdd:COG1643   257 LSAAEQDRAFAPAPHGRRRIVLATNIAETSLTVPGIRYVIDSGLARIPRY-DPRSgVTRLPTERISQASANQRAGRAGRL 335

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  773 RPGFCFTLCSRARFQALEDNLTPEMFRTPLHEMALTIKLLRLGSIHHFlsKALEPPPVDAVIEAEVLLREMRCLDANDEL 852
Cdd:COG1643   336 APGICYRLWSEEDFARRPAFTDPEILRADLASLILELAAWGLGDPEDL--PFLDPPPARAIADARALLQELGALDADGRL 413

                         490       500       510
                  ....*....|....*....|....*....|....*..
gi 157824876  853 TPLGRLLARLPIEPRLGKMMVLGAVFGCADLMAIMAS 889
Cdd:COG1643   414 TPLGRALARLPLDPRLARMLLAAAELGCLREAAILAA 450
DEAH_box_HrpA TIGR01967
RNA helicase HrpA; This model represents HrpA, one of two related but uncharacterized DEAH-box ...
 378-917 7.90e-85

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: 303.23  E-value: 7.90e-85
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876   378 LEFREKLPIAAMRSEILTAINDNPVVIIRGNTGCGKTTQIAQyilddyICS--GQGGYANIYVTQPRRISAISVAERVAR 455
Cdd:TIGR01967   60 IRYPDNLPVSAKREDIAEAIAENQVVIIAGETGSGKTTQLPK------ICLelGRGSHGLIGHTQPRRLAARTVAQRIAE 133

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876   456 ERCEQLGDTVGYSVRFESVFpRPYGAILFCTVGVLLRKLEAG--LRGVSHIIVDEIHERDVNSDFLLVILRDMVDTYPDL 533
Cdd:TIGR01967  134 ELGTPLGEKVGYKVRFHDQV-SSNTLVKLMTDGILLAETQQDrfLSRYDTIIIDEAHERSLNIDFLLGYLKQLLPRRPDL 212

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876   534 HVILMSATIDTTKFSKYFGICPVLEVPGRAFPVqqfflediiqmtdfvpsaesrrkrkevedeeqllsedkdeaEINYNK 613
Cdd:TIGR01967  213 KIIITSATIDPERFSRHFNNAPIIEVSGRTYPV-----------------------------------------EVRYRP 251

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876   614 VCEDkysqktrnamamlsESDVSFELLEALLMHIK--SKNIPGAILVFLPGWNLIFALMKFLQNTNIFGdtsqYQILPCH 691
Cdd:TIGR01967  252 LVEE--------------QEDDDLDQLEAILDAVDelFAEGPGDILIFLPGEREIRDAAEILRKRNLRH----TEILPLY 313

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876   692 SQIPRDEQRKVFEpvPEGVTKIILSTNIAETSITIDDIVFVIDICKARMKLFTSHNNLTSYATVWASKTNLEQRKGRAGR 771
Cdd:TIGR01967  314 ARLSNKEQQRVFQ--PHSGRRIVLATNVAETSLTVPGIHYVIDTGTARISRYSYRTKVQRLPIEPISQASANQRKGRCGR 391

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876   772 VRPGFCFTLCSRARFQALEDNLTPEMFRTPLHEMALTIKLLRLGSIHHFlsKALEPPPVDAVIEAEVLLREMRCLD---A 848
Cdd:TIGR01967  392 VAPGICIRLYSEEDFNSRPEFTDPEILRTNLASVILQMLALRLGDIAAF--PFIEAPDPRAIRDGFRLLEELGALDddeA 469

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876   849 NDELTPLGRLLARLPIEPRLGKMMVLGAVFGCADLMAIMASYSST--------------------FSEVFSLDIGQRRLA 908
Cdd:TIGR01967  470 EPQLTPIGRQLAQLPVDPRLARMLLEAHRLGCLQEVLIIASALSIqdprerpmekqqaadqaharFKDPRSDFLSRVNLW 549

                          570
                   ....*....|...
gi 157824876   909 NH----QKALSGT 917
Cdd:TIGR01967  550 RHieeqRQALSAN 562
PRK11131 PRK11131
ATP-dependent RNA helicase HrpA; Provisional
 353-891 8.82e-77

ATP-dependent RNA helicase HrpA; Provisional


Pssm-ID: 182986 [Multi-domain]  Cd Length: 1294  Bit Score: 278.87  E-value: 8.82e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  353 IDDLSMDYERSlRDRRQNDNEYRQFLEFREKLPIAAMRSEILTAINDNPVVIIRGNTGCGKTTQIAQyilddyICS--GQ 430
Cdd:PRK11131   43 FQEIAKEIAQA-AQRVLLREAARPEITYPENLPVSQKKQDILEAIRDHQVVIVAGETGSGKTTQLPK------ICLelGR 115

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  431 GGYANIYVTQPRRISAISVAERVARERCEQLGDTVGYSVRF-ESVFPRPYgaILFCTVGVLLRKLEAG--LRGVSHIIVD 507
Cdd:PRK11131  116 GVKGLIGHTQPRRLAARTVANRIAEELETELGGCVGYKVRFnDQVSDNTM--VKLMTDGILLAEIQQDrlLMQYDTIIID 193

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  508 EIHERDVNSDFLLVILRDMVDTYPDLHVILMSATIDTTKFSKYFGICPVLEVPGRAFPVQQfflediiqmtdfvpsaesr 587
Cdd:PRK11131  194 EAHERSLNIDFILGYLKELLPRRPDLKVIITSATIDPERFSRHFNNAPIIEVSGRTYPVEV------------------- 254

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  588 RKRKEVEDEEqllSEDKDEAEINYNKVCEdkysqktrnamaMLSESdvsfelleallmhikskniPGAILVFLPGWNLIF 667
Cdd:PRK11131  255 RYRPIVEEAD---DTERDQLQAIFDAVDE------------LGREG-------------------PGDILIFMSGEREIR 300

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  668 ----ALMKflQNtniFGDTsqyQILPCHSQIPRDEQRKVFEpvPEGVTKIILSTNIAETSITIDDIVFVIDICKARMKLF 743
Cdd:PRK11131  301 dtadALNK--LN---LRHT---EILPLYARLSNSEQNRVFQ--SHSGRRIVLATNVAETSLTVPGIKYVIDPGTARISRY 370

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  744 tshnnltSYATVWA-------SKTNLEQRKGRAGRVRPGFCFTLCSRARFQALEDNLTPEMFRTPLHEMALTIKLLRLGS 816
Cdd:PRK11131  371 -------SYRTKVQrlpiepiSQASANQRKGRCGRVSEGICIRLYSEDDFLSRPEFTDPEILRTNLASVILQMTALGLGD 443

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  817 IHHFlskalepPPVDAV----IEAEV-LLREMRCLDAND-----ELTPLGRLLARLPIEPRLGKMMVLGAVFGCA-DLMA 885
Cdd:PRK11131  444 IAAF-------PFVEAPdkrnIQDGVrLLEELGAITTDEqasayKLTPLGRQLAQLPVDPRLARMVLEAQKHGCVrEVMI 516


                  ....*.
gi 157824876  886 IMASYS 891
Cdd:PRK11131  517 ITSALS 522
SF2_C_RHA cd18791
C-terminal helicase domain of the RNA helicase A (RHA) family helicases; The RNA helicase A ...
 564-781 1.45e-68

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: 227.80  E-value: 1.45e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  564 FPVQQFFLEDIIQMTDfvpsaesrrkrkevedeeqllsedkdeaeinynkvcedkysqktrnaMAMLSESDVSFELLEAL 643
Cdd:cd18791     1 FPVEVYYLEDILELLG-----------------------------------------------ISSEKEDPDYVDAAVRL 33

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  644 LMHIKSKNIPGAILVFLPGWNLIFALMKFLQNTNIFGDTSQYQILPCHSQIPRDEQRKVFEPVPEGVTKIILSTNIAETS 723
Cdd:cd18791    34 ILQIHRTEEPGDILVFLPGQEEIERLCELLREELLSPDLGKLLVLPLHSSLPPEEQQRVFEPPPPGVRKVVLATNIAETS 113

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 157824876  724 ITIDDIVFVIDICKARMKLFTSHNNLTSYATVWASKTNLEQRKGRAGRVRPGFCFTLC 781
Cdd:cd18791   114 ITIPGVVYVIDSGLVKEKVYDPRTGLSSLVTVWISKASAEQRAGRAGRTRPGKCYRLY 171
DSRM_DHX9_rpt2 cd19855
second double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; ...
 167-241 3.54e-37

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


Pssm-ID: 380684  Cd Length: 75  Bit Score: 134.27  E-value: 3.54e-37
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 157824876  167 IENAKERLNIYKQTNNIRDDYKYTPVGPEHARSFLAELSIYVPALNRTVTARESGSNKKSASKSCALSLVRQLFH 241
Cdd:cd19855     1 LDNAKSRLNEFLQKNKIPAEYKYTSVGPDHNRSFIAELSIFVKQLGKTIYARETGSNKKLASQSCALSLVRQLYH 75
DSRM_DHX9_rpt1 cd19854
first double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; ...
 2-70 3.47e-31

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


Pssm-ID: 380683  Cd Length: 69  Bit Score: 116.99  E-value: 3.47e-31
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 157824876    2 DIKSFLYQFCAKSQIEPKFDIRQTGPKNRQRFLCEVRVEPNTYIGVGNSTNKKDAEKNACRDFVNYLVR 70
Cdd:cd19854     1 EIKAFLYAWCGKKKLTPEYDIKEAGNKHRQRFKCEVRVEGFDYVGTGNATNKKDAQTNAARDFLNYLVR 69
DEXDc smart00487
DEAD-like helicases superfamily;
393-569 6.42e-22

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 95.25  E-value: 6.42e-22
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876    393 ILTAINDNPVVIIRGNTGCGKTTQIAQYILDDYIcsgQGGYANIYVTQPRRISAISVAERVARERCEQLGDTVGY----- 467
Cdd:smart00487   17 IEALLSGLRDVILAAPTGSGKTLAALLPALEALK---RGKGGRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLyggds 93

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876    468 SVRFESVFPRPYGAILFCTVGVLLRKLEAG---LRGVSHIIVDEIHERDvNSDFLLVILRDMVDTYPDLHVILMSATI-- 542
Cdd:smart00487   94 KREQLRKLESGKTDILVTTPGRLLDLLENDklsLSNVDLVILDEAHRLL-DGGFGDQLEKLLKLLPKNVQLLLLSATPpe 172

                           170       180
                    ....*....|....*....|....*....
gi 157824876    543 DTTKFSKYFGICPVLEVPGRA--FPVQQF 569
Cdd:smart00487  173 EIENLLELFLNDPVFIDVGFTplEPIEQF 201
OB_NTP_bind pfam07717
Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus ...
 1002-1079 6.91e-20

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: 85.00  E-value: 6.91e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  1002 ALLCLGLYPNICVHKEKRKVLTT--ESKAALLHKTSVNCSnlAVTFPYPFFVFGEKIRTRAVSCKQLSMVSPLQVILFGS 1079
Cdd:pfam07717    3 AALAAGLYPNVARRDPKGKGYTTlsDNQRVFIHPSSVLFN--EKTFPPEWVVYQELVETTKVYIRTVTAISPEWLLLFAP 80
HA2 smart00847
Helicase associated domain (HA2) Add an annotation; This presumed domain is about 90 amino ...
 842-926 1.38e-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: 81.55  E-value: 1.38e-18
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876    842 EMRCLDANDELTPLGRLLARLPIEPRLGKMMVLGAVFGCADLMAIMASYSSTFSeVFSLDIGQrRLANHQKALSGtKCSD 921
Cdd:smart00847    1 ELGALDDDGRLTPLGRKMAELPLDPRLAKMLLAAAEFGCLDEILTIVAMLSVGD-PRPKEKRE-DADAARRRFAD-PESD 77


                    ....*
gi 157824876    922 HVAMI 926
Cdd:smart00847   78 HLTLL 82
HA2 pfam04408
Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in ...
 836-925 2.16e-16

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: 76.12  E-value: 2.16e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876   836 AEVLLREMRCLDANDELTPLGRLLARLPIEPRLGKMMVLGAVFGCADLMAIMA---SYSSTFSEVFSLDIGQRRLAN--- 909
Cdd:pfam04408    1 ALELLYYLGALDEDGELTPLGRKMAELPLDPRLAKMLLAAAELGCLDEVLTIVaalSVRDPFVQPNFLDPRSAAKAArrr 80

                           90       100
                   ....*....|....*....|....
gi 157824876   910 --------HQKALSGTKCSDHVAM 925
Cdd:pfam04408   81 rraadekaRAKFARLDLEGDHLTL 104
DSRM smart00358
Double-stranded RNA binding motif;
4-68 2.91e-16

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 74.22  E-value: 2.91e-16
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 157824876      4 KSFLYQFCAKSQIEPKFD-IRQTGPKNRQRFLCEVRVEpNTYIGVGNSTNKKDAEKNACRDFVNYL 68
Cdd:smart00358    2 KSLLQELAQKRKLPPEYElVKEEGPDHAPRFTVTVKVG-GKRTGEGEGSSKKEAKQRAAEAALRSL 66
PHA02653 PHA02653
RNA helicase NPH-II; Provisional
 382-775 9.31e-12

RNA helicase NPH-II; Provisional


Pssm-ID: 177443 [Multi-domain]  Cd Length: 675  Bit Score: 69.62  E-value: 9.31e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  382 EKLPIAAMR----SEILTAINDNPVVIIRGNTGCGKTTQIAQYIL-DDYICSGQGGYANIYVTQPRRISAISVAeRVA-- 454
Cdd:PHA02653  157 SKIPLASLQpdvqLKIFEAWISRKPVVLTGGTGVGKTSQVPKLLLwFNYLFGGFDNLDKIDPNFIERPIVLSLP-RVAlv 235

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  455 RERCEQLGDTVGY--------SVRFESV-------FPRPYGaILFCTVGVLLRKLeaglRGVSHIIVDEIHERDVNSDFL 519
Cdd:PHA02653  236 RLHSITLLKSLGFdeidgspiSLKYGSIpdelintNPKPYG-LVFSTHKLTLNKL----FDYGTVIIDEVHEHDQIGDII 310

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  520 LVILRDMVDTYPDLhvILMSATI--DTTKFSKYFGICPVLEVPGRA-FPVQQFFLEDIIQMTDfvpsaesrrKRKEVEDE 596
Cdd:PHA02653  311 IAVARKHIDKIRSL--FLMTATLedDRDRIKEFFPNPAFVHIPGGTlFPISEVYVKNKYNPKN---------KRAYIEEE 379

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  597 EQLLSEdkdeaeinynkvcedkysqktrnamamlsesdvsfelleALLMHIKSKNIPGaiLVFLPGWNLIFALMKFLQNT 676
Cdd:PHA02653  380 KKNIVT---------------------------------------ALKKYTPPKGSSG--IVFVASVSQCEEYKKYLEKR 418

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  677 NifgdtSQYQILPCHSQIPRDEQ--RKVFEPvpEGVTkIILSTNIAETSITIDDIVFVIDICKARMKLFTSHNnltsyaT 754
Cdd:PHA02653  419 L-----PIYDFYIIHGKVPNIDEilEKVYSS--KNPS-IIISTPYLESSVTIRNATHVYDTGRVYVPEPFGGK------E 484

                         410       420
                  ....*....|....*....|.
gi 157824876  755 VWASKTNLEQRKGRAGRVRPG 775
Cdd:PHA02653  485 MFISKSMRTQRKGRVGRVSPG 505
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 4-68 7.63e-10

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


Pssm-ID: 425434 [Multi-domain]  Cd Length: 66  Bit Score: 56.08  E-value: 7.63e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 157824876     4 KSFLYQFCAKSQIEPKFD-IRQTGPKNRQRFLCEVRVEpNTYIGVGNSTNKKDAEKNACRDFVNYL 68
Cdd:pfam00035    2 KSLLQEYAQKNGKPPPYEyVSEEGPPHSPKFTVTVKVD-GKLYGSGTGSSKKEAEQLAAEKALEKL 66
DSRM smart00358
Double-stranded RNA binding motif;
170-240 5.73e-07

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 48.03  E-value: 5.73e-07
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 157824876    170 AKERLNIYKQTNNIRDDYKYTPV-GPEHARSFLAELSIyvpalNRTVTARESGSNKKSASKSCALSLVRQLF 240
Cdd:smart00358    1 PKSLLQELAQKRKLPPEYELVKEeGPDHAPRFTVTVKV-----GGKRTGEGEGSSKKEAKQRAAEAALRSLK 67
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 403-545 1.89e-06

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: 49.16  E-value: 1.89e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876   403 VIIRGNTGCGKTTqIAQYILDDYICSGQGGYANIYVTqPRRISAISVAERvARERCEQLGDTVGYSV---RFESVFPRPY 479
Cdd:pfam00270   17 VLVQAPTGSGKTL-AFLLPALEALDKLDNGPQALVLA-PTRELAEQIYEE-LKKLGKGLGLKVASLLggdSRKEQLEKLK 93

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 157824876   480 GA-ILFCTVGVLLR--KLEAGLRGVSHIIVDEIHERDVNS--DFLLVILRDMvdtYPDLHVILMSATIDTT 545
Cdd:pfam00270   94 GPdILVGTPGRLLDllQERKLLKNLKLLVLDEAHRLLDMGfgPDLEEILRRL---PKKRQILLLSATLPRN 161
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 170-239 1.31e-04

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


Pssm-ID: 425434 [Multi-domain]  Cd Length: 66  Bit Score: 41.06  E-value: 1.31e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 157824876   170 AKERLNIYKQTNNIRDDYKYTPV-GPEHARSFLAELSIyvpalNRTVTARESGSNKKSASKSCALSLVRQL 239
Cdd:pfam00035    1 PKSLLQEYAQKNGKPPPYEYVSEeGPPHSPKFTVTVKV-----DGKLYGSGTGSSKKEAEQLAAEKALEKL 66
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
22-68 9.58e-03

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 39.31  E-value: 9.58e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 157824876   22 IRQTGPKNRQRFLCEVRVEpNTYIGVGNSTNKKDAEKNACRDFVNYL 68
Cdd:COG0571   180 VEEEGPDHAKTFTVEVLVG-GKVLGEGTGRSKKEAEQAAAKAALEKL 225
 
Name Accession Description Interval E-value
DEXHc_DHX9 cd17972
DEXH-box helicase domain of DEAH-box helicase 9; DEAH-box helicase 9 (DHX9, also known as ...
 326-559 9.22e-157

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: 469.31  E-value: 9.22e-157
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  326 IPWAPPQANWNTWHACNIDEGELATTSIDDLSMDYERSLRDRRQNDNEYRQFLEFREKLPIAAMRSEILTAINDNPVVII 405
Cdd:cd17972     1 VPWSPPQSNWNPWTSSNIDEGPLAFATPEQISMDLKNELMYQREQDHNLQQILQERELLPVKKFREEILEAISNNPVVII 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  406 RGNTGCGKTTQIAQYILDDYICSGQGGYANIYVTQPRRISAISVAERVARERCEQLGDTVGYSVRFESVFPRPYGAILFC 485
Cdd:cd17972    81 RGATGCGKTTQVPQYILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEVGKSCGYSVRFESVLPRPHASILFC 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 157824876  486 TVGVLLRKLEAGLRGVSHIIVDEIHERDVNSDFLLVILRDMVDTYPDLHVILMSATIDTTKFSKYFGICPVLEV 559
Cdd:cd17972   161 TVGVLLRKLEAGIRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPDLRVILMSATIDTSMFCEYFFNCPVIEV 234
HrpA COG1643
HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];
378-889 3.49e-116

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


Pssm-ID: 441249 [Multi-domain]  Cd Length: 836  Bit Score: 383.28  E-value: 3.49e-116
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  378 LEFREKLPIAAMRSEILTAINDNPVVIIRGNTGCGKTTQIAQYILDdyicSGQGGYANIYVTQPRRISAISVAERVARER 457
Cdd:COG1643     4 ITYPPDLPVSAVLPELLAALRAHQVVVLAAPPGAGKTTQLPLALLE----LGWGAGGRIGMLEPRRLAARAAAERMAEEL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  458 CEQLGDTVGYSVRFES-VFPRPYgaILFCTVGVLLRKLEA--GLRGVSHIIVDEIHERDVNSDFLLVILRDMVDTY-PDL 533
Cdd:COG1643    80 GEPVGETVGYRVRFEDkVSAATR--IEVVTEGILLRELQRdpELEGVDTVIFDEFHERSLNADLLLALLLDLQPALrPDL 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  534 HVILMSATIDTTKFSKYFGICPVLEVPGRAFPVqqfflediiqmtdfvpsaeSRRKRKEVEDEEQLLSedkdeaeinynk 613
Cdd:COG1643   158 KLLVMSATLDAERFARLLGDAPVIESSGRTYPV-------------------EVRYRPLPADERDLED------------ 206

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  614 vcedkysqktrnAMAMLsesdvsfeLLEALLMHikskniPGAILVFLPGWNLIFALMKFLQNTnIFGDTsqyQILPCHSQ 693
Cdd:COG1643   207 ------------AVADA--------VREALAEE------PGDILVFLPGEREIRRTAEALRGR-LPPDT---EILPLYGR 256

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  694 IPRDEQRKVFEPVPEGVTKIILSTNIAETSITIDDIVFVIDICKARMKLFtSHNN-LTSYATVWASKTNLEQRKGRAGRV 772
Cdd:COG1643   257 LSAAEQDRAFAPAPHGRRRIVLATNIAETSLTVPGIRYVIDSGLARIPRY-DPRSgVTRLPTERISQASANQRAGRAGRL 335

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  773 RPGFCFTLCSRARFQALEDNLTPEMFRTPLHEMALTIKLLRLGSIHHFlsKALEPPPVDAVIEAEVLLREMRCLDANDEL 852
Cdd:COG1643   336 APGICYRLWSEEDFARRPAFTDPEILRADLASLILELAAWGLGDPEDL--PFLDPPPARAIADARALLQELGALDADGRL 413

                         490       500       510
                  ....*....|....*....|....*....|....*..
gi 157824876  853 TPLGRLLARLPIEPRLGKMMVLGAVFGCADLMAIMAS 889
Cdd:COG1643   414 TPLGRALARLPLDPRLARMLLAAAELGCLREAAILAA 450
DEAH_box_HrpA TIGR01967
RNA helicase HrpA; This model represents HrpA, one of two related but uncharacterized DEAH-box ...
 378-917 7.90e-85

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: 303.23  E-value: 7.90e-85
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876   378 LEFREKLPIAAMRSEILTAINDNPVVIIRGNTGCGKTTQIAQyilddyICS--GQGGYANIYVTQPRRISAISVAERVAR 455
Cdd:TIGR01967   60 IRYPDNLPVSAKREDIAEAIAENQVVIIAGETGSGKTTQLPK------ICLelGRGSHGLIGHTQPRRLAARTVAQRIAE 133

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876   456 ERCEQLGDTVGYSVRFESVFpRPYGAILFCTVGVLLRKLEAG--LRGVSHIIVDEIHERDVNSDFLLVILRDMVDTYPDL 533
Cdd:TIGR01967  134 ELGTPLGEKVGYKVRFHDQV-SSNTLVKLMTDGILLAETQQDrfLSRYDTIIIDEAHERSLNIDFLLGYLKQLLPRRPDL 212

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876   534 HVILMSATIDTTKFSKYFGICPVLEVPGRAFPVqqfflediiqmtdfvpsaesrrkrkevedeeqllsedkdeaEINYNK 613
Cdd:TIGR01967  213 KIIITSATIDPERFSRHFNNAPIIEVSGRTYPV-----------------------------------------EVRYRP 251

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876   614 VCEDkysqktrnamamlsESDVSFELLEALLMHIK--SKNIPGAILVFLPGWNLIFALMKFLQNTNIFGdtsqYQILPCH 691
Cdd:TIGR01967  252 LVEE--------------QEDDDLDQLEAILDAVDelFAEGPGDILIFLPGEREIRDAAEILRKRNLRH----TEILPLY 313

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876   692 SQIPRDEQRKVFEpvPEGVTKIILSTNIAETSITIDDIVFVIDICKARMKLFTSHNNLTSYATVWASKTNLEQRKGRAGR 771
Cdd:TIGR01967  314 ARLSNKEQQRVFQ--PHSGRRIVLATNVAETSLTVPGIHYVIDTGTARISRYSYRTKVQRLPIEPISQASANQRKGRCGR 391

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876   772 VRPGFCFTLCSRARFQALEDNLTPEMFRTPLHEMALTIKLLRLGSIHHFlsKALEPPPVDAVIEAEVLLREMRCLD---A 848
Cdd:TIGR01967  392 VAPGICIRLYSEEDFNSRPEFTDPEILRTNLASVILQMLALRLGDIAAF--PFIEAPDPRAIRDGFRLLEELGALDddeA 469

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876   849 NDELTPLGRLLARLPIEPRLGKMMVLGAVFGCADLMAIMASYSST--------------------FSEVFSLDIGQRRLA 908
Cdd:TIGR01967  470 EPQLTPIGRQLAQLPVDPRLARMLLEAHRLGCLQEVLIIASALSIqdprerpmekqqaadqaharFKDPRSDFLSRVNLW 549

                          570
                   ....*....|...
gi 157824876   909 NH----QKALSGT 917
Cdd:TIGR01967  550 RHieeqRQALSAN 562
DEXHc_RHA-like cd17917
DEXH-box helicase domain of DEAD-like helicase RHA family proteins; The RNA helicase A (RHA) ...
 400-559 3.44e-79

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: 257.39  E-value: 3.44e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  400 NPVVIIRGNTGCGKTTQIAQYILDDYICSGQGGyaNIYVTQPRRISAISVAERVARERCEQLGDTVGYSVRFESVFPRPy 479
Cdd:cd17917     1 NQVVVIVGETGSGKTTQVPQFLLEDGLAKGGKG--RIVCTQPRRIAAISVAERVAEERGEKLGEEVGYQIRFESKTSSK- 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  480 GAILFCTVGVLLRKLEAG--LRGVSHIIVDEIHERDVNSDFLLVILRDMVDTYPDLHVILMSATIDTTKFSKYFGICPVL 557
Cdd:cd17917    78 TRIKFCTDGILLRELLSDplLSGYSHVILDEAHERSLDTDFLLGLLKDLLRKRPDLKVILMSATLDAEKFSSYFGGAPVI 157


                  ..
gi 157824876  558 EV 559
Cdd:cd17917   158 HI 159
PRK11131 PRK11131
ATP-dependent RNA helicase HrpA; Provisional
 353-891 8.82e-77

ATP-dependent RNA helicase HrpA; Provisional


Pssm-ID: 182986 [Multi-domain]  Cd Length: 1294  Bit Score: 278.87  E-value: 8.82e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  353 IDDLSMDYERSlRDRRQNDNEYRQFLEFREKLPIAAMRSEILTAINDNPVVIIRGNTGCGKTTQIAQyilddyICS--GQ 430
Cdd:PRK11131   43 FQEIAKEIAQA-AQRVLLREAARPEITYPENLPVSQKKQDILEAIRDHQVVIVAGETGSGKTTQLPK------ICLelGR 115

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  431 GGYANIYVTQPRRISAISVAERVARERCEQLGDTVGYSVRF-ESVFPRPYgaILFCTVGVLLRKLEAG--LRGVSHIIVD 507
Cdd:PRK11131  116 GVKGLIGHTQPRRLAARTVANRIAEELETELGGCVGYKVRFnDQVSDNTM--VKLMTDGILLAEIQQDrlLMQYDTIIID 193

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  508 EIHERDVNSDFLLVILRDMVDTYPDLHVILMSATIDTTKFSKYFGICPVLEVPGRAFPVQQfflediiqmtdfvpsaesr 587
Cdd:PRK11131  194 EAHERSLNIDFILGYLKELLPRRPDLKVIITSATIDPERFSRHFNNAPIIEVSGRTYPVEV------------------- 254

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  588 RKRKEVEDEEqllSEDKDEAEINYNKVCEdkysqktrnamaMLSESdvsfelleallmhikskniPGAILVFLPGWNLIF 667
Cdd:PRK11131  255 RYRPIVEEAD---DTERDQLQAIFDAVDE------------LGREG-------------------PGDILIFMSGEREIR 300

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  668 ----ALMKflQNtniFGDTsqyQILPCHSQIPRDEQRKVFEpvPEGVTKIILSTNIAETSITIDDIVFVIDICKARMKLF 743
Cdd:PRK11131  301 dtadALNK--LN---LRHT---EILPLYARLSNSEQNRVFQ--SHSGRRIVLATNVAETSLTVPGIKYVIDPGTARISRY 370

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  744 tshnnltSYATVWA-------SKTNLEQRKGRAGRVRPGFCFTLCSRARFQALEDNLTPEMFRTPLHEMALTIKLLRLGS 816
Cdd:PRK11131  371 -------SYRTKVQrlpiepiSQASANQRKGRCGRVSEGICIRLYSEDDFLSRPEFTDPEILRTNLASVILQMTALGLGD 443

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  817 IHHFlskalepPPVDAV----IEAEV-LLREMRCLDAND-----ELTPLGRLLARLPIEPRLGKMMVLGAVFGCA-DLMA 885
Cdd:PRK11131  444 IAAF-------PFVEAPdkrnIQDGVrLLEELGAITTDEqasayKLTPLGRQLAQLPVDPRLARMVLEAQKHGCVrEVMI 516


                  ....*.
gi 157824876  886 IMASYS 891
Cdd:PRK11131  517 ITSALS 522
DEXHc_DHX30 cd17976
DEXH-box helicase domain of DEAH-box helicase 30; DEAH-box helicase 30 (DHX30) plays an ...
 384-559 1.23e-74

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: 245.09  E-value: 1.23e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  384 LPIAAMRSEILTAINDNPVVIIRGNTGCGKTTQIAQYILDDYICSGQGGYANIYVTQPRRISAISVAERVARERCEQLGD 463
Cdd:cd17976     1 LPVDSHKESILSAIEQNPVVVISGDTGCGKTTRIPQFILEDYVLRGRGARCNVVITQPRRISAVSVAQRVAHELGPNLRR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  464 TVGYSVRFESVFPRPYGAILFCTVGVLLRKLE--AGLRGVSHIIVDEIHERDVNSDFLLVILRDMVDTYPDLHVILMSAT 541
Cdd:cd17976    81 NVGYQVRLESRPPPRGGALLFCTVGVLLKKLQsnPRLEGVSHVIVDEVHERDVNTDFLLILLKGVLQLNPELRVVLMSAT 160

                         170
                  ....*....|....*...
gi 157824876  542 IDTTKFSKYFGICPVLEV 559
Cdd:cd17976   161 GDNQRLSRYFGGCPVVRV 178
DEAH_box_HrpB TIGR01970
ATP-dependent helicase HrpB; This model represents HrpB, one of two related but ...
 384-888 4.83e-73

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: 261.24  E-value: 4.83e-73
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876   384 LPIAAMRSEILTAINDNPVVIIRGNTGCGKTTQIAQYILDDYICSGQggyanIYVTQPRRISAISVAERVARERCEQLGD 463
Cdd:TIGR01970    1 LPIHAVLPALRDALAAHPQVVLEAPPGAGKSTAVPLALLDAPGIGGK-----IIMLEPRRLAARSAAQRLASQLGEAVGQ 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876   464 TVGYSVRFES-VFPRPygAILFCTVGVLLRKLEA--GLRGVSHIIVDEIHERDVNSDFLLVILRDMVDTY-PDLHVILMS 539
Cdd:TIGR01970   76 TVGYRVRGENkVSRRT--RLEVVTEGILTRMIQDdpELDGVGALIFDEFHERSLDADLGLALALDVQSSLrEDLKILAMS 153

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876   540 ATIDTTKFSKYFGICPVLEVPGRAFPVQqfflediiqmtdfvpsaesRRKRKEVEDEEqllsedkdeaeinynkvCEDKY 619
Cdd:TIGR01970  154 ATLDGERLSSLLPDAPVVESEGRSFPVE-------------------IRYLPLRGDQR-----------------LEDAV 197

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876   620 SQKTRNAMAmlsesdvsfelleallmhikskNIPGAILVFLPGWNLIFALMKFLQNTNifgdTSQYQILPCHSQIPRDEQ 699
Cdd:TIGR01970  198 SRAVEHALA----------------------SETGSILVFLPGQAEIRRVQEQLAERL----DSDVLICPLYGELSLAAQ 251

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876   700 RKVFEPVPEGVTKIILSTNIAETSITIDDIVFVIDICKARMKLFTSHNNLTSYATVWASKTNLEQRKGRAGRVRPGFCFT 779
Cdd:TIGR01970  252 DRAIKPDPQGRRKVVLATNIAETSLTIEGIRVVIDSGLARVARFDPKTGITRLETVRISQASATQRAGRAGRLEPGVCYR 331

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876   780 LCSRARFQALEDNLTPEMFRTPLHEMALtiKLLRLGSIHHFLSKALEPPPVDAVIEAEVLLREMRCLDANDELTPLGRLL 859
Cdd:TIGR01970  332 LWSEEQHQRLPAQDEPEILQADLSGLAL--ELAQWGAKDPSDLRWLDAPPSVALAAARQLLQRLGALDAQGRLTAHGKAM 409

                          490       500
                   ....*....|....*....|....*....
gi 157824876   860 ARLPIEPRLGKMMVLGAVFGCADLMAIMA 888
Cdd:TIGR01970  410 AALGCHPRLAAMLLSAHSTGLAALACDLA 438
SF2_C_RHA cd18791
C-terminal helicase domain of the RNA helicase A (RHA) family helicases; The RNA helicase A ...
 564-781 1.45e-68

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: 227.80  E-value: 1.45e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  564 FPVQQFFLEDIIQMTDfvpsaesrrkrkevedeeqllsedkdeaeinynkvcedkysqktrnaMAMLSESDVSFELLEAL 643
Cdd:cd18791     1 FPVEVYYLEDILELLG-----------------------------------------------ISSEKEDPDYVDAAVRL 33

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  644 LMHIKSKNIPGAILVFLPGWNLIFALMKFLQNTNIFGDTSQYQILPCHSQIPRDEQRKVFEPVPEGVTKIILSTNIAETS 723
Cdd:cd18791    34 ILQIHRTEEPGDILVFLPGQEEIERLCELLREELLSPDLGKLLVLPLHSSLPPEEQQRVFEPPPPGVRKVVLATNIAETS 113

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 157824876  724 ITIDDIVFVIDICKARMKLFTSHNNLTSYATVWASKTNLEQRKGRAGRVRPGFCFTLC 781
Cdd:cd18791   114 ITIPGVVYVIDSGLVKEKVYDPRTGLSSLVTVWISKASAEQRAGRAGRTRPGKCYRLY 171
DEXHc_DHX36 cd17981
DEXH-box helicase domain of DEAH-box helicase 36; DEAH-box helicase 36 (DHX36, also known as ...
 384-559 7.18e-67

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: 223.18  E-value: 7.18e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  384 LPIAAMRSEILTAINDNPVVIIRGNTGCGKTTQIAQYILDDYICSGQGGYANIYVTQPRRISAISVAERVARERCEQ--L 461
Cdd:cd17981     1 LPSYGMKQEIINMIDNNQVTVISGETGCGKTTQVTQFILDDAIERGKGSSCRIVCTQPRRISAISVAERVAAERAEScgL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  462 GDTVGYSVRFESVFPRPYGAILFCTVGVLLRKLEAG--LRGVSHIIVDEIHERDVNSDFLLVILRDMVDTYPDLHVILMS 539
Cdd:cd17981    81 GNSTGYQIRLESRKPRKQGSILYCTTGIVLQWLQSDphLSNVSHLVLDEIHERNLQSDVLMGIVKDLLPFRSDLKVILMS 160

                         170       180
                  ....*....|....*....|
gi 157824876  540 ATIDTTKFSKYFGICPVLEV 559
Cdd:cd17981   161 ATLNAEKFSDYFNNCPMIHI 180
DEXHc_DHX57 cd17985
DEXH-box helicase domain of DEAH-box helicase 57; DEAH-box helicase 57 (DHX57) belongs to the ...
 384-559 1.11e-62

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: 211.24  E-value: 1.11e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  384 LPIAAMRSEILTAINDNPVVIIRGNTGCGKTTQIAQYILDDYICSGQGGYANIYVTQPRRISAISVAERVARERCEQLGD 463
Cdd:cd17985     1 LPAWQERETILELLEKHQVLVISGMTGCGKTTQIPQFILDNSLQGPPLPVANIICTQPRRISAISVAERVAQERAERVGQ 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  464 TVGYSVRFESVFPRPyGAILFCTVGVLLRKLEAG--LRGVSHIIVDEIHERDVNSDFLLVILRDMVDTYPDLHVILMSAT 541
Cdd:cd17985    81 SVGYQIRLESVKSSA-TRLLYCTTGVLLRRLEGDptLQGVTHVIVDEVHERTEESDFLLLVLKDLMVQRPDLKVILMSAT 159

                         170
                  ....*....|....*...
gi 157824876  542 IDTTKFSKYFGICPVLEV 559
Cdd:cd17985   160 LNAELFSDYFNSCPVIHI 177
PRK11664 PRK11664
ATP-dependent RNA helicase HrpB; Provisional
 384-873 8.91e-61

ATP-dependent RNA helicase HrpB; Provisional


Pssm-ID: 236950 [Multi-domain]  Cd Length: 812  Bit Score: 224.42  E-value: 8.91e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  384 LPIAAMRSEILTAINDNPVVIIRGNTGCGKTTQIAQYILDDYICSGQggyanIYVTQPRRISAISVAERVARERCEQLGD 463
Cdd:PRK11664    4 LPVAAVLPELLTALKTAPQVLLKAPTGAGKSTWLPLQLLQHGGINGK-----IIMLEPRRLAARNVAQRLAEQLGEKPGE 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  464 TVGYSVRFES-VFPRPYGAILfcTVGVLLRKLE--AGLRGVSHIIVDEIHERDVNSD----FLLVI---LRDmvdtypDL 533
Cdd:PRK11664   79 TVGYRMRAESkVGPNTRLEVV--TEGILTRMIQrdPELSGVGLVILDEFHERSLQADlalaLLLDVqqgLRD------DL 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  534 HVILMSATIDTTKFSKYFGICPVLEVPGRAFPVqqfflediiqmtdfvpsaesrrkrkevedeeqllsedkdeaEINYNK 613
Cdd:PRK11664  151 KLLIMSATLDNDRLQQLLPDAPVIVSEGRSFPV-----------------------------------------ERRYQP 189

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  614 VcedKYSQKTRNAMAMLSEsdvsfELLEallmhikskNIPGAILVFLPGWNLIFALMKFLQNtNIFGDTsqyQILPCHSQ 693
Cdd:PRK11664  190 L---PAHQRFDEAVARATA-----ELLR---------QESGSLLLFLPGVGEIQRVQEQLAS-RVASDV---LLCPLYGA 248

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  694 IPRDEQRKVFEPVPEGVTKIILSTNIAETSITIDDIVFVIDICKARMKLFTSHNNLTSYATVWASKTNLEQRKGRAGRVR 773
Cdd:PRK11664  249 LSLAEQQKAILPAPAGRRKVVLATNIAETSLTIEGIRLVVDSGLERVARFDPKTGLTRLVTQRISQASMTQRAGRAGRLE 328

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  774 PGFCFTLCSRARFQALEDNLTPEMFRTPLHemALTIKLLRLG--SIHHFlsKALEPPPVDAVIEAEVLLREMRCLDANDE 851
Cdd:PRK11664  329 PGICLHLYSKEQAERAAAQSEPEILHSDLS--GLLLELLQWGchDPAQL--SWLDQPPAAALAAAKRLLQQLGALDGQGR 404

                         490       500
                  ....*....|....*....|..
gi 157824876  852 LTPLGRLLARLPIEPRLGKMMV 873
Cdd:PRK11664  405 LTARGRKMAALGNDPRLAAMLV 426
DEXHc_YTHDC2 cd17987
DEXH-box helicase domain of YTH domain containing 2; YTH domain containing 2 (YTHDC2) ...
 384-559 1.91e-59

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: 201.98  E-value: 1.91e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  384 LPIAAMRSEILTAINDNPVVIIRGNTGCGKTTQIAQYILDDyiCSGQGGYANIYVTQPRRISAISVAERVARERCEQLGD 463
Cdd:cd17987     1 LPVFEKQEQIVRIIKENKVVLIVGETGSGKTTQIPQFLLDD--CYANGIPCRIFCTQPRRLAAIAVAERVAAERGEKIGQ 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  464 TVGYSVRFES-VFPRPygAILFCTVGVLLRKLEAG---LRGVSHIIVDEIHERDVNSDFLLVILRDMVDTYPDLHVILMS 539
Cdd:cd17987    79 TVGYQIRLESrVSPKT--LLTFCTNGVLLRTLMAGdsaLSTVTHVIVDEVHERDRFSDFLLTKLRDILQKHPNLKLILSS 156

                         170       180
                  ....*....|....*....|
gi 157824876  540 ATIDTTKFSKYFGICPVLEV 559
Cdd:cd17987   157 AALDVNLFIRYFGSCPVIYI 176
DEXHc_TDRD9 cd17988
DEXH-box helicase domain of tudor domain containing 9; Tudor domain containing 9 (TDRD9, also ...
 384-559 1.51e-53

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: 185.01  E-value: 1.51e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  384 LPIAAMRSEILTAINDNPVVIIRGNTGCGKTTQIAQYILDDYICSGQggYANIYVTQPRRISAISVAERVARERCEQLGD 463
Cdd:cd17988     1 LPIYAKREEILSLIEANSVVIIKGATGCGKTTQLPQFILDHYYKRGK--YCNIVVTQPRRIAAISIARRVSQEREWTLGS 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  464 TVGYSVRFESVFPRpYGAILFCTVGVLLRKL--EAGLRGVSHIIVDEIHERDVNSDFLLVILRDMVDTYPD-LHVILMSA 540
Cdd:cd17988    79 LVGYQVGLERPASE-ETRLIYCTTGVLLQKLinNKTLTEYTHIILDEVHERDQELDFLLLVVRRLLRTNSRhVKIILMSA 157

                         170       180
                  ....*....|....*....|...
gi 157824876  541 TIDTTKFSKYFG----ICPVLEV 559
Cdd:cd17988   158 TISCKEFADYFTtpnnPAYVFEV 180
DEXHc_DHX34 cd17979
DEXH-box helicase domain of DEAH-box helicase 34; DEAH-box helicase 34 (DHX34) plays a role in ...
 384-559 1.17e-52

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: 182.26  E-value: 1.17e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  384 LPIAAMRSEILTAINDNPVVIIRGNTGCGKTTQIAQYILDdyicsgqGGYANIYVTQPRRISAISVAERVARERCEQLGD 463
Cdd:cd17979     1 LPIAQYREKIIELLKTHQVVIVAGDTGCGKSTQVPQYLLA-------AGFRHIACTQPRRIACISLAKRVAFESLNQYGS 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  464 TVGYSVRFESVfPRPYGAILFCTVGVLLRKLE--AGLRGVSHIIVDEIHERDVNSDFLLVILRDMVDTYPDLHVILMSAT 541
Cdd:cd17979    74 KVAYQIRFERT-RTLATKLLFLTEGLLLRQIQrdASLPQYNVLILDEVHERHLHGDFLLGVLRCLLRLRPDLKLILMSAT 152

                         170
                  ....*....|....*...
gi 157824876  542 IDTTKFSKYFGICPVLEV 559
Cdd:cd17979   153 INIELFSGYFEGAPVVQV 170
DEXHc_DHX29 cd17975
DEXH-box helicase domain of DEAH-box helicase 29; DEAH-box helicase 29 (DHX29) is a part of ...
 384-559 3.61e-52

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: 181.27  E-value: 3.61e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  384 LPIAAMRSEILTAINDNPVVIIRGNTGCGKTTQIAQYILDDYICSG-QGGYANIYVTQPRRISAISVAERVarerCEQLG 462
Cdd:cd17975     1 LPVFKHRESILETLKRHRVVVVAGETGSGKSTQVPQFLLEDLLLNGgTAQKCNIVCTQPRRISAMSLATRV----CEELG 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  463 ---------DTVGYSVRFESvfpRPYGA--ILFCTVGVLLRKLEAG--LRGVSHIIVDEIHERDVNSDFLLVILRDMVDT 529
Cdd:cd17975    77 cesgpggknSLCGYQIRMES---RTGEAtrLLYCTTGVLLRKLQEDglLSSISHIIVDEVHERSVQSDFLLIILKEILHK 153

                         170       180       190
                  ....*....|....*....|....*....|
gi 157824876  530 YPDLHVILMSATIDTTKFSKYFGICPVLEV 559
Cdd:cd17975   154 RSDLHLILMSATVDCEKFSSYFTHCPILRI 183
DEXHc_DHX33 cd17978
DEXH-box helicase domain of DEAH-box helicase 33; DEAH-box helicase 33 (DHX33) stimulates RNA ...
 384-557 1.99e-50

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: 176.01  E-value: 1.99e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  384 LPIAAMRSEILTAINDNPVVIIRGNTGCGKTTQIAQYILDDYICSGQggyaNIYVTQPRRISAISVAERVARERCEQLGD 463
Cdd:cd17978     1 LPIYSARKRLLEELRKHDTVIIIGETGSGKTTQIPQYLYEAGFARGG----MIGITQPRRVAAVSVAKRVAEEMGVELGQ 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  464 TVGYSVRFESVfPRPYGAILFCTVGVLLRK--LEAGLRGVSHIIVDEIHERDVNSDFLLVILRDMVDT-----YPDLHVI 536
Cdd:cd17978    77 LVGYSVRFDDV-TSEETRIKYMTDGMLLREaiGDPLLSKYSVIILDEAHERTVHTDVLFGLVKSAQRRrkeqkLSPLKVI 155

                         170       180
                  ....*....|....*....|.
gi 157824876  537 LMSATIDTTKFSKYFGICPVL 557
Cdd:cd17978   156 IMSATLDADLFSEYFNGAPVL 176
DEXHc_DHX8 cd17971
DEXH-box helicase domain of DEAH-box helicase 8; DEAH-box helicase 8 (DHX8 ,also known as ...
 379-560 3.89e-48

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: 169.59  E-value: 3.89e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  379 EFREKLPIAAMRSEILTAINDNPVVIIRGNTGCGKTTQIAQYILDdyicSGQGGYANIYVTQPRRISAISVAERVARERC 458
Cdd:cd17971     1 EQRESLPIYKLKEQLIQAVHDNQILVVIGETGSGKTTQITQYLAE----AGYTSRGKIGCTQPRRVAAMSVAKRVAEEFG 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  459 EQLGDTVGYSVRFESVfPRPYGAILFCTVGVLLRK--LEAGLRGVSHIIVDEIHERDVNSDFLLVILRDMVDTYPDLHVI 536
Cdd:cd17971    77 CCLGQEVGYTIRFEDC-TSPETVIKYMTDGMLLREclIDPDLSQYSVIMLDEAHERTIHTDVLFGLLKKTVQKRPDLKLI 155

                         170       180
                  ....*....|....*....|....
gi 157824876  537 LMSATIDTTKFSKYFGICPVLEVP 560
Cdd:cd17971   156 VTSATLDAVKFSQYFYEAPIFTIP 179
DEXHc_DHX38 cd17983
DEXH-box helicase domain of DEAH-box helicase 38; DEAH-box helicase 38 (DHX38, also known as ...
 384-559 6.49e-47

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: 165.71  E-value: 6.49e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  384 LPIAAMRSEILTAINDNPVVIIRGNTGCGKTTQIAQYILDDyicsGQGGYANIYVTQPRRISAISVAERVARERCEQLGD 463
Cdd:cd17983     1 LPIFAVRQELLNVIRDNNVVIVVGETGSGKTTQLTQYLHED----GYTDYGMIGCTQPRRVAAMSVAKRVSEEMGVELGE 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  464 TVGYSVRFESVfPRPYGAILFCTVGVLLRK--LEAGLRGVSHIIVDEIHERDVNSDFLLVILRDMVDTYPDLHVILMSAT 541
Cdd:cd17983    77 EVGYAIRFEDC-TSENTVIKYMTDGILLREslRDPDLDKYSAIIMDEAHERSLNTDVLFGLLREVVARRRDLKLIVTSAT 155

                         170
                  ....*....|....*...
gi 157824876  542 IDTTKFSKYFGICPVLEV 559
Cdd:cd17983   156 MDADKFADFFGNVPIFTI 173
DEXHc_HrpA cd17989
DEXH-box helicase domain of ATP-dependent RNA helicase HrpA; HrpA is part of the HrpB-HrpA ...
 384-559 3.76e-45

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: 160.70  E-value: 3.76e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  384 LPIAAMRSEILTAINDNPVVIIRGNTGCGKTTQIAQYILDdyicSGQGGYANIYVTQPRRISAISVAERVARERCEQLGD 463
Cdd:cd17989     1 LPVSQKRDEIAKAIAENQVVIIAGETGSGKTTQLPKICLE----LGRGIRGLIGHTQPRRLAARSVAERIAEELKTELGG 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  464 TVGYSVRFE-SVFPRPYgaILFCTVGVLLRKLEAG--LRGVSHIIVDEIHERDVNSDFLLVILRDMVDTYPDLHVILMSA 540
Cdd:cd17989    77 AVGYKVRFTdQTSDETC--VKLMTDGILLAETQTDryLRAYDTIIIDEAHERSLNIDFLLGYLKQLLPRRPDLKVIITSA 154

                         170
                  ....*....|....*....
gi 157824876  541 TIDTTKFSKYFGICPVLEV 559
Cdd:cd17989   155 TIDAERFSRHFNNAPIIEV 173
DEXHc_DHX15 cd17973
DEXH-box helicase domain of DEAH-box helicase 15; DEAH-box helicase 15 (DHX15) is a pre-mRNA ...
 372-559 7.39e-44

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: 157.58  E-value: 7.39e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  372 NEYRQFLEFREKLPIAAMRSEILTAINDNPVVIIRGNTGCGKTTQIAQYILDDYICSGQGgyANIYVTQPRRISAISVAE 451
Cdd:cd17973     1 QRYFEILEKRRELPVWEQKEDFLKLLKNNQILVLVGETGSGKTTQIPQFVLDDELPHQPK--KLVACTQPRRVAAMSVAQ 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  452 RVARERCEQLGDTVGYSVRFESVfPRPYGAILFCTVGVLLRKLEAG--LRGVSHIIVDEIHERDVNSDFLLVILRDMVDT 529
Cdd:cd17973    79 RVAEEMDVKLGEEVGYSIRFEDC-SSAKTILKYMTDGMLLREAMSDplLSRYSVIILDEAHERTLATDILMGLLKEVVRR 157

                         170       180       190
                  ....*....|....*....|....*....|
gi 157824876  530 YPDLHVILMSATIDTTKFSKYFGICPVLEV 559
Cdd:cd17973   158 RPDLKLIVMSATLDAGKFQKYFDNAPLLKV 187
DEXHc_DHX16 cd17974
DEXH-box helicase domain of DEAH-box helicase 16; DEAH-box helicase 16 (DHX16) is probably ...
 384-559 4.51e-43

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: 154.97  E-value: 4.51e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  384 LPIAAMRSEILTAINDNPVVIIRGNTGCGKTTQIAQYILDDYICSGQGgyaNIYVTQPRRISAISVAERVARERCEQLGD 463
Cdd:cd17974     1 LPVYPYRDDLLAAVKEHQVLIIVGETGSGKTTQIPQYLHEAGYTKGGG---KIGCTQPRRVAAMSVAARVAEEMGVKLGN 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  464 TVGYSVRFESVfPRPYGAILFCTVGVLLRKL--EAGLRGVSHIIVDEIHERDVNSDFLLVILRDMVDTYPDLHVILMSAT 541
Cdd:cd17974    78 EVGYSIRFEDC-TSEKTVLKYMTDGMLLREFltEPDLASYSVMIIDEAHERTLHTDILFGLVKDIARFRPDLKLLISSAT 156

                         170
                  ....*....|....*...
gi 157824876  542 IDTTKFSKYFGICPVLEV 559
Cdd:cd17974   157 MDAEKFSAFFDDAPIFRI 174
DEXHc_DHX35 cd17980
DEXH-box helicase domain of DEAH-box helicase 35; DHX35 plays a role in colorectal cancers and ...
 384-551 1.29e-41

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: 151.08  E-value: 1.29e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  384 LPIAAMRSEILTAINDNPVVIIRGNTGCGKTTQIAQYILDdyicSG-QGGYANIYVTQPRRISAISVAERVARERCEQLG 462
Cdd:cd17980     1 LPVFKLRNHILYLVENYQTIVIVGETGCGKSTQIPQYLAE----AGwTAGGRVVGCTQPRRVAAVTVAGRVAEEMGAVLG 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  463 DTVGYSVRFESVFPRPYGAILFCTVGVLLRKLEAG--LRGVSHIIVDEIHERDVNSDFLLVILRDMVDTYPDLHVILMSA 540
Cdd:cd17980    77 HEVGYCIRFDDCTDPQATRIKFLTDGMLVREMMLDplLTKYSVIMLDEAHERTLYTDILIGLLKKIQKKRGDLRLIVASA 156

                         170
                  ....*....|.
gi 157824876  541 TIDTTKFSKYF 551
Cdd:cd17980   157 TLDAEKFRDFF 167
DEXHc_HrpB cd17990
DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA ...
 384-559 1.89e-40

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


Pssm-ID: 438711 [Multi-domain]  Cd Length: 174  Bit Score: 147.48  E-value: 1.89e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  384 LPIAAMRSEILTAINDNPVVIIRGNTGCGKTTQIAQYILDdyICSGQGGyaNIYVTQPRRISAISVAERVARERCEQLGD 463
Cdd:cd17990     1 LPIAAVLPALRAALDAGGQVVLEAPPGAGKTTRVPLALLA--ELWIAGG--KIIVLEPRRVAARAAARRLATLLGEAPGE 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  464 TVGYSVRFESVFPRPyGAILFCTVGVLLRKLEA--GLRGVSHIIVDEIHERDVNSDFLLVILRDMVDTY-PDLHVILMSA 540
Cdd:cd17990    77 TVGYRVRGESRVGRR-TRVEVVTEGVLLRRLQRdpELSGVGAVILDEFHERSLDADLALALLLEVQQLLrDDLRLLAMSA 155

                         170
                  ....*....|....*....
gi 157824876  541 TIDTTKFSKYFGICPVLEV 559
Cdd:cd17990   156 TLDGDGLAALLPEAPVVES 174
DEXHc_DHX37 cd17982
DEXH-box helicase domain of DEAH-box helicase 37; DHX37 plays a role in the development of the ...
 384-559 3.28e-40

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: 147.50  E-value: 3.28e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  384 LPIAAMRSEILTAINDNPVVIIRGNTGCGKTTQIAQYILDDYICSGQGGYAN-IYVTQPRRISAISVAERVARErCEQLG 462
Cdd:cd17982     1 LPILAEEQEIMEAINENPVVIICGETGSGKTTQVPQFLYEAGFGSPESDNPGmIGITQPRRVAAVSMAKRVAEE-LNVFG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  463 DTVGYSVRFES-VFPRPygAILFCTVGVLLRKLEAG--LRGVSHIIVDEIHERDVNSDFLL------VILRDMVDTYPD- 532
Cdd:cd17982    80 KEVSYQIRYDStVSENT--KIKFMTDGVLLKEIQTDflLRKYSVIIIDEAHERSVNTDILIgmlsriVPLRAKLYLQDQt 157

                         170       180       190
                  ....*....|....*....|....*....|....
gi 157824876  533 ---LHVILMSATIDTTKFSK----YFGICPVLEV 559
Cdd:cd17982   158 vkpLKLVIMSATLRVEDFTEnkllFPRPPPVIKV 191
DEXHc_DHX40 cd17984
DEXH-box helicase domain of DEAH-box helicase 40; DEAH-box helicase 40 (DHX40) belongs to the ...
 384-559 5.69e-38

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: 140.37  E-value: 5.69e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  384 LPIAAMRSEILTAINDNPVVIIRGNTGCGKTTQIAQYILDdyicSGQGGYANIYVTQPRRISAISVAERVARERCEQLGD 463
Cdd:cd17984     1 LPIQKQRKKLVQAVRDNSFLIVTGNTGSGKTTQLPKYLYE----AGFSQHGMIGVTQPRRVAAISVAQRVAEEMKCTLGS 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  464 TVGYSVRFESVFPRPyGAILFCTVGVLLRKLEA--GLRGVSHIIVDEIHERDVNSDFLLVILRDMV------DTYPdLHV 535
Cdd:cd17984    77 KVGYQVRFDDCSSKE-TAIKYMTDGCLLRHILAdpNLTKYSVIILDEAHERSLTTDILFGLLKKLFqekspnRKEH-LKV 154

                         170       180
                  ....*....|....*....|....
gi 157824876  536 ILMSATIDTTKFSKYFGICPVLEV 559
Cdd:cd17984   155 VVMSATLELAKLSAFFGNCPVFDI 178
DSRM_DHX9_rpt2 cd19855
second double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; ...
 167-241 3.54e-37

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


Pssm-ID: 380684  Cd Length: 75  Bit Score: 134.27  E-value: 3.54e-37
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 157824876  167 IENAKERLNIYKQTNNIRDDYKYTPVGPEHARSFLAELSIYVPALNRTVTARESGSNKKSASKSCALSLVRQLFH 241
Cdd:cd19855     1 LDNAKSRLNEFLQKNKIPAEYKYTSVGPDHNRSFIAELSIFVKQLGKTIYARETGSNKKLASQSCALSLVRQLYH 75
DSRM_DHX9_rpt1 cd19854
first double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; ...
 2-70 3.47e-31

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


Pssm-ID: 380683  Cd Length: 69  Bit Score: 116.99  E-value: 3.47e-31
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 157824876    2 DIKSFLYQFCAKSQIEPKFDIRQTGPKNRQRFLCEVRVEPNTYIGVGNSTNKKDAEKNACRDFVNYLVR 70
Cdd:cd19854     1 EIKAFLYAWCGKKKLTPEYDIKEAGNKHRQRFKCEVRVEGFDYVGTGNATNKKDAQTNAARDFLNYLVR 69
DEXHc_DHX32 cd17977
DEXH-box helicase domain of DEAH-box helicase 32; DEAH-box helicase 32 (DHX32) belongs to the ...
 384-559 6.21e-24

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: 99.90  E-value: 6.21e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  384 LPIAAMRSEILTAINDNPVVIIRGNTGCGKTTQIAQYILDdYICSGQGGYANIYVTQPRRISAISVAERVARERCEQLGD 463
Cdd:cd17977     1 LPVWEAKYEFMESLAHNQIVIVSGDAKTGKSSQIPQWCAE-YCLSAHYQHGVVVCTQVHKQTAVWLALRVADEMDVNIGH 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  464 TVGYSVRFESVFPRPygAIL-FCTVGVLLRKLEAG--LRGVSHIIVDEIHERDVNSDFLLVILRDMVDTYPDLHVILMSA 540
Cdd:cd17977    80 EVGYVIPFENCCTNE--TILrYCTDDMLLREMMSDplLESYGVIILDDAHERTVSTDVLLGLLKDVLLSRPELKLVIITC 157

                         170
                  ....*....|....*....
gi 157824876  541 TIDTTKFSKYFGICPVLEV 559
Cdd:cd17977   158 PHLSSKLLSYYGNVPLIEV 176
DEXDc smart00487
DEAD-like helicases superfamily;
393-569 6.42e-22

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 95.25  E-value: 6.42e-22
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876    393 ILTAINDNPVVIIRGNTGCGKTTQIAQYILDDYIcsgQGGYANIYVTQPRRISAISVAERVARERCEQLGDTVGY----- 467
Cdd:smart00487   17 IEALLSGLRDVILAAPTGSGKTLAALLPALEALK---RGKGGRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLyggds 93

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876    468 SVRFESVFPRPYGAILFCTVGVLLRKLEAG---LRGVSHIIVDEIHERDvNSDFLLVILRDMVDTYPDLHVILMSATI-- 542
Cdd:smart00487   94 KREQLRKLESGKTDILVTTPGRLLDLLENDklsLSNVDLVILDEAHRLL-DGGFGDQLEKLLKLLPKNVQLLLLSATPpe 172

                           170       180
                    ....*....|....*....|....*....
gi 157824876    543 DTTKFSKYFGICPVLEVPGRA--FPVQQF 569
Cdd:smart00487  173 EIENLLELFLNDPVFIDVGFTplEPIEQF 201
DEXQc_DQX1 cd17986
DEXQ-box helicase domain of DEAQ-box RNA dependent ATPase 1; DEAQ-box RNA dependent ATPase 1 ...
 384-559 3.73e-20

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: 89.19  E-value: 3.73e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  384 LPIAAMRSEILTAI-NDNPVVIIRGNTGCGKTTQIAQYILDdYICSGQGGYANIYVTQPRRISAISVAERVARERCEQLG 462
Cdd:cd17986     1 LPIWAAKFTFLEQLeSPSGIVLVSGEPGSGKSTQVPQWCAE-FALSRGFQKGQVTVTQPHPLAARSLALRVADEMDLNLG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  463 DTVGYSVRFESVfPRPYGAILFCTVGVLLRKLEA--GLRGVSHIIVDEIHERDVNSDFLLVILRDMVDTYPDLHVILMSA 540
Cdd:cd17986    80 HEVGYSIPQEDC-TGPNTILRFCWDRLLLQEMTStpLLGAWGVVVLDEAQERSVASDSLLGLLKDVRLQRPELRVVVVTS 158

                         170
                  ....*....|....*....
gi 157824876  541 TIDTTKFSKYFGICPVLEV 559
Cdd:cd17986   159 PALEPKLRAFWGNPPVVHV 177
OB_NTP_bind pfam07717
Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus ...
 1002-1079 6.91e-20

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: 85.00  E-value: 6.91e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  1002 ALLCLGLYPNICVHKEKRKVLTT--ESKAALLHKTSVNCSnlAVTFPYPFFVFGEKIRTRAVSCKQLSMVSPLQVILFGS 1079
Cdd:pfam07717    3 AALAAGLYPNVARRDPKGKGYTTlsDNQRVFIHPSSVLFN--EKTFPPEWVVYQELVETTKVYIRTVTAISPEWLLLFAP 80
HA2 smart00847
Helicase associated domain (HA2) Add an annotation; This presumed domain is about 90 amino ...
 842-926 1.38e-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: 81.55  E-value: 1.38e-18
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876    842 EMRCLDANDELTPLGRLLARLPIEPRLGKMMVLGAVFGCADLMAIMASYSSTFSeVFSLDIGQrRLANHQKALSGtKCSD 921
Cdd:smart00847    1 ELGALDDDGRLTPLGRKMAELPLDPRLAKMLLAAAEFGCLDEILTIVAMLSVGD-PRPKEKRE-DADAARRRFAD-PESD 77


                    ....*
gi 157824876    922 HVAMI 926
Cdd:smart00847   78 HLTLL 82
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 403-541 1.94e-17

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: 80.53  E-value: 1.94e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  403 VIIRGNTGCGKTTqIAQYILDDYICSgQGGyaNIYVTQPRRISAISVAERVARERceQLGDTVGYSVRFESVFPRPYGA- 481
Cdd:cd00046     4 VLITAPTGSGKTL-AALLAALLLLLK-KGK--KVLVLVPTKALALQTAERLRELF--GPGIRVAVLVGGSSAEEREKNKl 77

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 157824876  482 ----ILFCTVGVLLRKLEA----GLRGVSHIIVDEIHERDVNSDFLLVI-LRDMVDTYPDLHVILMSAT 541
Cdd:cd00046    78 gdadIIIATPDMLLNLLLRedrlFLKDLKLIIVDEAHALLIDSRGALILdLAVRKAGLKNAQVILLSAT 146
HA2 pfam04408
Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in ...
 836-925 2.16e-16

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: 76.12  E-value: 2.16e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876   836 AEVLLREMRCLDANDELTPLGRLLARLPIEPRLGKMMVLGAVFGCADLMAIMA---SYSSTFSEVFSLDIGQRRLAN--- 909
Cdd:pfam04408    1 ALELLYYLGALDEDGELTPLGRKMAELPLDPRLAKMLLAAAELGCLDEVLTIVaalSVRDPFVQPNFLDPRSAAKAArrr 80

                           90       100
                   ....*....|....*....|....
gi 157824876   910 --------HQKALSGTKCSDHVAM 925
Cdd:pfam04408   81 rraadekaRAKFARLDLEGDHLTL 104
DSRM smart00358
Double-stranded RNA binding motif;
4-68 2.91e-16

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 74.22  E-value: 2.91e-16
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 157824876      4 KSFLYQFCAKSQIEPKFD-IRQTGPKNRQRFLCEVRVEpNTYIGVGNSTNKKDAEKNACRDFVNYL 68
Cdd:smart00358    2 KSLLQELAQKRKLPPEYElVKEEGPDHAPRFTVTVKVG-GKRTGEGEGSSKKEAKQRAAEAALRSL 66
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 642-772 1.25e-13

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: 68.39  E-value: 1.25e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876   642 ALLMHIKSKNIPGAILVFLPGWNLIfalmkflqNTNIFGDTSQYQILPCHSQIPRDEQRKVFEPVPEGVTKIILSTNIAE 721
Cdd:pfam00271    4 EALLELLKKERGGKVLIFSQTKKTL--------EAELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAE 75

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|.
gi 157824876   722 TSITIDDIVFVIDickarmklFTSHNNLTSYatvwasktnlEQRKGRAGRV 772
Cdd:pfam00271   76 RGLDLPDVDLVIN--------YDLPWNPASY----------IQRIGRAGRA 108
HELICc smart00490
helicase superfamily c-terminal domain;
685-771 8.05e-13

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 64.93  E-value: 8.05e-13
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876    685 YQILPCHSQIPRDEQRKVFEPVPEGVTKIILSTNIAETSITIDDIVFVIDICkarmklftshnnltsyatVWASKTNLEQ 764
Cdd:smart00490   12 IKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYD------------------LPWSPASYIQ 73


                    ....*..
gi 157824876    765 RKGRAGR 771
Cdd:smart00490   74 RIGRAGR 80
PHA02653 PHA02653
RNA helicase NPH-II; Provisional
 382-775 9.31e-12

RNA helicase NPH-II; Provisional


Pssm-ID: 177443 [Multi-domain]  Cd Length: 675  Bit Score: 69.62  E-value: 9.31e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  382 EKLPIAAMR----SEILTAINDNPVVIIRGNTGCGKTTQIAQYIL-DDYICSGQGGYANIYVTQPRRISAISVAeRVA-- 454
Cdd:PHA02653  157 SKIPLASLQpdvqLKIFEAWISRKPVVLTGGTGVGKTSQVPKLLLwFNYLFGGFDNLDKIDPNFIERPIVLSLP-RVAlv 235

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  455 RERCEQLGDTVGY--------SVRFESV-------FPRPYGaILFCTVGVLLRKLeaglRGVSHIIVDEIHERDVNSDFL 519
Cdd:PHA02653  236 RLHSITLLKSLGFdeidgspiSLKYGSIpdelintNPKPYG-LVFSTHKLTLNKL----FDYGTVIIDEVHEHDQIGDII 310

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  520 LVILRDMVDTYPDLhvILMSATI--DTTKFSKYFGICPVLEVPGRA-FPVQQFFLEDIIQMTDfvpsaesrrKRKEVEDE 596
Cdd:PHA02653  311 IAVARKHIDKIRSL--FLMTATLedDRDRIKEFFPNPAFVHIPGGTlFPISEVYVKNKYNPKN---------KRAYIEEE 379

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  597 EQLLSEdkdeaeinynkvcedkysqktrnamamlsesdvsfelleALLMHIKSKNIPGaiLVFLPGWNLIFALMKFLQNT 676
Cdd:PHA02653  380 KKNIVT---------------------------------------ALKKYTPPKGSSG--IVFVASVSQCEEYKKYLEKR 418

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  677 NifgdtSQYQILPCHSQIPRDEQ--RKVFEPvpEGVTkIILSTNIAETSITIDDIVFVIDICKARMKLFTSHNnltsyaT 754
Cdd:PHA02653  419 L-----PIYDFYIIHGKVPNIDEilEKVYSS--KNPS-IIISTPYLESSVTIRNATHVYDTGRVYVPEPFGGK------E 484

                         410       420
                  ....*....|....*....|.
gi 157824876  755 VWASKTNLEQRKGRAGRVRPG 775
Cdd:PHA02653  485 MFISKSMRTQRKGRVGRVSPG 505
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 4-68 7.63e-10

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


Pssm-ID: 425434 [Multi-domain]  Cd Length: 66  Bit Score: 56.08  E-value: 7.63e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 157824876     4 KSFLYQFCAKSQIEPKFD-IRQTGPKNRQRFLCEVRVEpNTYIGVGNSTNKKDAEKNACRDFVNYL 68
Cdd:pfam00035    2 KSLLQEYAQKNGKPPPYEyVSEEGPPHSPKFTVTVKVD-GKLYGSGTGSSKKEAEQLAAEKALEKL 66
DSRM_SF cd00048
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
 8-62 6.67e-08

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


Pssm-ID: 380679 [Multi-domain]  Cd Length: 57  Bit Score: 50.36  E-value: 6.67e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 157824876    8 YQFCAKSQI-EPKFDIRQTGPKNRQRFLCEVRVEPNTYIGVGNStnKKDAEKNACR 62
Cdd:cd00048     1 NELCQKNKWpPPEYETVEEGGPHNPRFTCTVTVNGQTFEGEGKS--KKEAKQAAAE 54
DSRM_EIF2AK2-like cd19875
double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...
 5-68 1.18e-07

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


Pssm-ID: 380704  Cd Length: 67  Bit Score: 49.96  E-value: 1.18e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 157824876    5 SFLYQFCAKSQIEPKFDIRQTGPKNRQRFLCEVRVEPNTYiGVGNSTNKKDAEKNACRDFVNYL 68
Cdd:cd19875     5 SALNEYCQKRGLSLEFVDVSVGPDHCPGFTASATIDGIVF-ASATGTSKKEAKRAAAKLALKKL 67
DSRM_RNAse_III_family cd10845
double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...
 1-68 2.84e-07

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


Pssm-ID: 380682 [Multi-domain]  Cd Length: 69  Bit Score: 49.03  E-value: 2.84e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876    1 MDIKSFLYQFC-AKSQIEPKFD-IRQTGPKNRQRFLCEVRVEpNTYIGVGNSTNKKDAEKNACRDFVNYL 68
Cdd:cd10845     1 KDYKTALQEYLqKRGLPLPEYElVEEEGPDHNKTFTVEVKVN-GKVIGEGTGRSKKEAEQAAAKAALEKL 69
DSRM smart00358
Double-stranded RNA binding motif;
170-240 5.73e-07

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 48.03  E-value: 5.73e-07
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 157824876    170 AKERLNIYKQTNNIRDDYKYTPV-GPEHARSFLAELSIyvpalNRTVTARESGSNKKSASKSCALSLVRQLF 240
Cdd:smart00358    1 PKSLLQELAQKRKLPPEYELVKEeGPDHAPRFTVTVKV-----GGKRTGEGEGSSKKEAKQRAAEAALRSLK 67
DSRM_SON-like cd19870
double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known ...
 5-62 1.59e-06

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


Pssm-ID: 380699  Cd Length: 75  Bit Score: 46.89  E-value: 1.59e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876    5 SFLYQFCAKSQ-IEPKFDIRQ-TGPKNRQRFLCEVRVEPNTYIGVGNSTNKKDAEKNACR 62
Cdd:cd19870     6 SALMELCNKRKwGPPEFRLVEeSGPPHRKHFLFKVVVNGVEYQPSVASGNKKDAKAQAAT 65
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 403-545 1.89e-06

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: 49.16  E-value: 1.89e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876   403 VIIRGNTGCGKTTqIAQYILDDYICSGQGGYANIYVTqPRRISAISVAERvARERCEQLGDTVGYSV---RFESVFPRPY 479
Cdd:pfam00270   17 VLVQAPTGSGKTL-AFLLPALEALDKLDNGPQALVLA-PTRELAEQIYEE-LKKLGKGLGLKVASLLggdSRKEQLEKLK 93

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 157824876   480 GA-ILFCTVGVLLR--KLEAGLRGVSHIIVDEIHERDVNS--DFLLVILRDMvdtYPDLHVILMSATIDTT 545
Cdd:pfam00270   94 GPdILVGTPGRLLDllQERKLLKNLKLLVLDEAHRLLDMGfgPDLEEILRRL---PKKRQILLLSATLPRN 161
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 170-239 1.31e-04

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


Pssm-ID: 425434 [Multi-domain]  Cd Length: 66  Bit Score: 41.06  E-value: 1.31e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 157824876   170 AKERLNIYKQTNNIRDDYKYTPV-GPEHARSFLAELSIyvpalNRTVTARESGSNKKSASKSCALSLVRQL 239
Cdd:pfam00035    1 PKSLLQEYAQKNGKPPPYEYVSEeGPPHSPKFTVTVKV-----DGKLYGSGTGSSKKEAEQLAAEKALEKL 66
DSRM_EIF2AK2-like cd19875
double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...
 169-239 1.64e-04

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


Pssm-ID: 380704  Cd Length: 67  Bit Score: 41.10  E-value: 1.64e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 157824876  169 NAKERLNIYKQTNNIRDDYKYTPVGPEHARSFLAELSIyvpalNRTVTARESGSNKKSASKSCALSLVRQL 239
Cdd:cd19875     2 NPVSALNEYCQKRGLSLEFVDVSVGPDHCPGFTASATI-----DGIVFASATGTSKKEAKRAAAKLALKKL 67
DEXHc_LHR-like cd17922
DEXH-box helicase domain of LHR; Large helicase-related protein (LHR) is a DNA ...
 403-542 1.66e-04

DEXH-box helicase domain of LHR; Large helicase-related protein (LHR) is a DNA damage-inducible helicase that uses ATP hydrolysis to drive unidirectional 3'-to-5' translocation along single-stranded DNA (ssDNA) and to unwind RNA:DNA duplexes. This group also includes related bacterial and archaeal helicases from 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: 350680 [Multi-domain]  Cd Length: 166  Bit Score: 43.73  E-value: 1.66e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  403 VIIRGNTGCGKTTQIAQYILDDYICSGQGGYANIYVT--------QPRRISA--------ISVAER----VARERCEQLG 462
Cdd:cd17922     4 VLIAAPTGSGKTEAAFLPALSSLADEPEKGVQVLYISplkalindQERRLEEpldeidleIPVAVRhgdtSQSEKAKQLK 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  463 DTVGysvrfesvfprpygaILFCT---VGVLL--RKLEAGLRGVSHIIVDEIHE-----RDVNSDFLLVILRDMVDtyPD 532
Cdd:cd17922    84 NPPG---------------ILITTpesLELLLvnKKLRELFAGLRYVVVDEIHAllgskRGVQLELLLERLRKLTG--RP 146

                         170
                  ....*....|
gi 157824876  533 LHVILMSATI 542
Cdd:cd17922   147 LRRIGLSATL 156
DEXHc_Ski2 cd17921
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ...
 409-543 5.80e-03

DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases play an important role in RNA degradation, processing, and splicing pathways. They belong to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350679 [Multi-domain]  Cd Length: 181  Bit Score: 39.17  E-value: 5.80e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157824876  409 TGCGKTTqIAQYILDDYICSGQGgyaNIYVTQPRRisAIsVAERVA--RERCEQLGDTVGYSVRFESVFPRPYGA--ILF 484
Cdd:cd17921    26 TSSGKTL-IAELAILRALATSGG---KAVYIAPTR--AL-VNQKEAdlRERFGPLGKNVGLLTGDPSVNKLLLAEadILV 98

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 157824876  485 CT---VGVLLRKL-EAGLRGVSHIIVDEIH--ERDVNSDFLLVILRDMVDTYPDLHVILMSATID 543
Cdd:cd17921    99 ATpekLDLLLRNGgERLIQDVRLVVVDEAHliGDGERGVVLELLLSRLLRINKNARFVGLSATLP 163
DSRM_DHX9_rpt1 cd19854
first double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; ...
 169-239 7.72e-03

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


Pssm-ID: 380683  Cd Length: 69  Bit Score: 36.48  E-value: 7.72e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 157824876  169 NAKERLNIYKQTNNIRDDYKYTPVGPEHARSFLAELSIYvpalNRTVTARESGSNKKSASKSCALSLVRQL 239
Cdd:cd19854     1 EIKAFLYAWCGKKKLTPEYDIKEAGNKHRQRFKCEVRVE----GFDYVGTGNATNKKDAQTNAARDFLNYL 67
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
22-68 9.58e-03

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 39.31  E-value: 9.58e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 157824876   22 IRQTGPKNRQRFLCEVRVEpNTYIGVGNSTNKKDAEKNACRDFVNYL 68
Cdd:COG0571   180 VEEEGPDHAKTFTVEVLVG-GKVLGEGTGRSKKEAEQAAAKAALEKL 225
 
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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