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Conserved domains on  [gi|3650397|emb|CAA77038|]
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maleless protein [Sciara ocellaris]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DEAD-like_helicase_N super family cl28899
N-terminal helicase domain of the DEAD-box helicase superfamily; The DEAD-like helicase ...
 325-558 6.02e-136

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


The actual alignment was detected with superfamily member cd17972:

Pssm-ID: 475120 [Multi-domain]  Cd Length: 234  Bit Score: 413.85  E-value: 6.02e-136
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   325 ISWSPPQPNWNPWTACNIDEGYLATATLEQLSEELLQISRDKLQNDNELIERMKFRETLPVAAMKNEIMTLINDNSVVIV 404
Cdd:cd17972    1 VPWSPPQSNWNPWTSSNIDEGPLAFATPEQISMDLKNELMYQREQDHNLQQILQERELLPVKKFREEILEAISNNPVVII 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   405 KGATGCGKTTQIAQYILEDYVNSGQGAWCNIAITQPRRISAISVSERIAVERNENIGESVGYSVRFESCLPRPFGAIMFC 484
Cdd:cd17972   81 RGATGCGKTTQVPQYILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEVGKSCGYSVRFESVLPRPHASILFC 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 3650397   485 TIGVLLRKLEAGLRGVSHVIVDEIHERDVNSDFILVVLRDMVHTYPDLRVILMSATIDTTLFSDYFGKCPVIEI 558
Cdd:cd17972  161 TVGVLLRKLEAGIRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPDLRVILMSATIDTSMFCEYFFNCPVIEV 234
HrpA super family cl34328
HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];
377-870 6.50e-107

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: 357.08  E-value: 6.50e-107
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   377 MKFRETLPVAAMKNEIMTLINDNSVVIVKGATGCGKTTQIAQYILEdyvnsgQGaWCN---IAITQPRRISAISVSERIA 453
Cdd:COG1643    4 ITYPPDLPVSAVLPELLAALRAHQVVVLAAPPGAGKTTQLPLALLE------LG-WGAggrIGMLEPRRLAARAAAERMA 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   454 VERNENIGESVGYSVRFESCLprpfGA---IMFCTIGVLLRKLEA--GLRGVSHVIVDEIHERDVNSDFILVVLRDMVHT 528
Cdd:COG1643   77 EELGEPVGETVGYRVRFEDKV----SAatrIEVVTEGILLRELQRdpELEGVDTVIFDEFHERSLNADLLLALLLDLQPA 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   529 Y-PDLRVILMSATIDTTLFSDYFGKCPVIEIPGRAHPVtqlfledciemtkfvpspESRKRKRDDESEmvgietdgDQnl 607
Cdd:COG1643  153 LrPDLKLLVMSATLDAERFARLLGDAPVIESSGRTYPV------------------EVRYRPLPADER--------DL-- 204

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   608 nktvlagnysnetVTAMAsmsesevsfELIEALLifikqKNVPGAVLVFLPGWNLIFALMKHLQsGRFGgSDFRILPCHS 687
Cdd:COG1643  205 -------------EDAVA---------DAVREAL-----AEEPGDILVFLPGEREIRRTAEALR-GRLP-PDTEILPLYG 255

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   688 QIPREDQRKVFEPVPPGVTKIILSTNIAETSITIDDIVYVIDICKARMKLFtSHNN-MTSYATVWASKTNLEQRKGRAGR 766
Cdd:COG1643  256 RLSAAEQDRAFAPAPHGRRRIVLATNIAETSLTVPGIRYVIDSGLARIPRY-DPRSgVTRLPTERISQASANQRAGRAGR 334

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   767 VRPGFCFTLCSRARYAKLDEHLTPEMFRTPLHELALSIKLLRLGAIGQFlsKAIEPPPLDAVIEAEVVLRDLKCLNQNDD 846
Cdd:COG1643  335 LAPGICYRLWSEEDFARRPAFTDPEILRADLASLILELAAWGLGDPEDL--PFLDPPPARAIADARALLQELGALDADGR 412

                        490       500
                 ....*....|....*....|....
gi 3650397   847 LSPLGKILARLPIEPRLGKMMVLG 870
Cdd:COG1643  413 LTPLGRALARLPLDPRLARMLLAA 436
DSRM_DHX9_rpt2 cd19855
second double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; ...
 164-238 7.36e-42

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: 147.36  E-value: 7.36e-42
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 3650397   164 IENAKAKLHQFMQMNKIQADYRYTPVGPDHARSFMAEMKIFVKQLNRTITGRESGSNKQTASKSCALSLVRQLYH 238
Cdd:cd19855    1 LDNAKSRLNEFLQKNKIPAEYKYTSVGPDHNRSFIAELSIFVKQLGKTIYARETGSNKKLASQSCALSLVRQLYH 75
DSRM_DHX9_rpt1 cd19854
first double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; ...
 3-71 1.89e-32

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: 120.45  E-value: 1.89e-32
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 3650397     3 DIKSFFHSWCNKTKVEPQFESRPTGPKHRQRFLCELRVAGFNYVGAGNSTVKKDAEKNAARDFVNFLVR 71
Cdd:cd19854    1 EIKAFLYAWCGKKKLTPEYDIKEAGNKHRQRFKCEVRVEGFDYVGTGNATNKKDAQTNAARDFLNYLVR 69
OB_NTP_bind pfam07717
Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus ...
 995-1072 5.56e-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: 85.38  E-value: 5.56e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397     995 ALLCMGLYPNVCYHKEKRKVLTT--ESKAALIHKTSVNCTNLaiTFPYPFFVFGEKIRTRAVSCKQMSMVAPIHLILFGS 1072
Cdd:pfam07717    3 AALAAGLYPNVARRDPKGKGYTTlsDNQRVFIHPSSVLFNEK--TFPPEWVVYQELVETTKVYIRTVTAISPEWLLLFAP 80
HA2 smart00847
Helicase associated domain (HA2) Add an annotation; This presumed domain is about 90 amino ...
 838-921 1.47e-12

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: 64.21  E-value: 1.47e-12
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397      838 LKCLNQNDDLSPLGKILARLPIEPRLGKMMVLGCIFLCGDALGAMAAYSGTFSeVFTLDLGQRRLSNHQKALGGtkHSDH 917
Cdd:smart00847    2 LGALDDDGRLTPLGRKMAELPLDPRLAKMLLAAAEFGCLDEILTIVAMLSVGD-PRPKEKREDADAARRRFADP--ESDH 78


                    ....
gi 3650397      918 VAML 921
Cdd:smart00847   79 LTLL 82
 
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 ...
 325-558 6.02e-136

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: 413.85  E-value: 6.02e-136
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   325 ISWSPPQPNWNPWTACNIDEGYLATATLEQLSEELLQISRDKLQNDNELIERMKFRETLPVAAMKNEIMTLINDNSVVIV 404
Cdd:cd17972    1 VPWSPPQSNWNPWTSSNIDEGPLAFATPEQISMDLKNELMYQREQDHNLQQILQERELLPVKKFREEILEAISNNPVVII 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   405 KGATGCGKTTQIAQYILEDYVNSGQGAWCNIAITQPRRISAISVSERIAVERNENIGESVGYSVRFESCLPRPFGAIMFC 484
Cdd:cd17972   81 RGATGCGKTTQVPQYILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEVGKSCGYSVRFESVLPRPHASILFC 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 3650397   485 TIGVLLRKLEAGLRGVSHVIVDEIHERDVNSDFILVVLRDMVHTYPDLRVILMSATIDTTLFSDYFGKCPVIEI 558
Cdd:cd17972  161 TVGVLLRKLEAGIRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPDLRVILMSATIDTSMFCEYFFNCPVIEV 234
HrpA COG1643
HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];
377-870 6.50e-107

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


Pssm-ID: 441249 [Multi-domain]  Cd Length: 836  Bit Score: 357.08  E-value: 6.50e-107
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   377 MKFRETLPVAAMKNEIMTLINDNSVVIVKGATGCGKTTQIAQYILEdyvnsgQGaWCN---IAITQPRRISAISVSERIA 453
Cdd:COG1643    4 ITYPPDLPVSAVLPELLAALRAHQVVVLAAPPGAGKTTQLPLALLE------LG-WGAggrIGMLEPRRLAARAAAERMA 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   454 VERNENIGESVGYSVRFESCLprpfGA---IMFCTIGVLLRKLEA--GLRGVSHVIVDEIHERDVNSDFILVVLRDMVHT 528
Cdd:COG1643   77 EELGEPVGETVGYRVRFEDKV----SAatrIEVVTEGILLRELQRdpELEGVDTVIFDEFHERSLNADLLLALLLDLQPA 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   529 Y-PDLRVILMSATIDTTLFSDYFGKCPVIEIPGRAHPVtqlfledciemtkfvpspESRKRKRDDESEmvgietdgDQnl 607
Cdd:COG1643  153 LrPDLKLLVMSATLDAERFARLLGDAPVIESSGRTYPV------------------EVRYRPLPADER--------DL-- 204

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   608 nktvlagnysnetVTAMAsmsesevsfELIEALLifikqKNVPGAVLVFLPGWNLIFALMKHLQsGRFGgSDFRILPCHS 687
Cdd:COG1643  205 -------------EDAVA---------DAVREAL-----AEEPGDILVFLPGEREIRRTAEALR-GRLP-PDTEILPLYG 255

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   688 QIPREDQRKVFEPVPPGVTKIILSTNIAETSITIDDIVYVIDICKARMKLFtSHNN-MTSYATVWASKTNLEQRKGRAGR 766
Cdd:COG1643  256 RLSAAEQDRAFAPAPHGRRRIVLATNIAETSLTVPGIRYVIDSGLARIPRY-DPRSgVTRLPTERISQASANQRAGRAGR 334

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   767 VRPGFCFTLCSRARYAKLDEHLTPEMFRTPLHELALSIKLLRLGAIGQFlsKAIEPPPLDAVIEAEVVLRDLKCLNQNDD 846
Cdd:COG1643  335 LAPGICYRLWSEEDFARRPAFTDPEILRADLASLILELAAWGLGDPEDL--PFLDPPPARAIADARALLQELGALDADGR 412

                        490       500
                 ....*....|....*....|....
gi 3650397   847 LSPLGKILARLPIEPRLGKMMVLG 870
Cdd:COG1643  413 LTPLGRALARLPLDPRLARMLLAA 436
DEAH_box_HrpA TIGR01967
RNA helicase HrpA; This model represents HrpA, one of two related but uncharacterized DEAH-box ...
 348-872 2.64e-81

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: 292.44  E-value: 2.64e-81
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397     348 ATATLEQLSEELlQISRDKLQNDNELIERMKFRETLPVAAMKNEIMTLINDNSVVIVKGATGCGKTTQIAQYILEdyvnS 427
Cdd:TIGR01967   32 AIAALAKFRERI-DAACDKVEARRQAVPEIRYPDNLPVSAKREDIAEAIAENQVVIIAGETGSGKTTQLPKICLE----L 106

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397     428 GQGAWCNIAITQPRRISAISVSERIAVERNENIGESVGYSVRFESCLpRPFGAIMFCTIGVLLRKLEAG--LRGVSHVIV 505
Cdd:TIGR01967  107 GRGSHGLIGHTQPRRLAARTVAQRIAEELGTPLGEKVGYKVRFHDQV-SSNTLVKLMTDGILLAETQQDrfLSRYDTIII 185

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397     506 DEIHERDVNSDFILVVLRDMVHTYPDLRVILMSATIDTTLFSDYFGKCPVIEIPGRAHPVtqlfledciemtkfvpspES 585
Cdd:TIGR01967  186 DEAHERSLNIDFLLGYLKQLLPRRPDLKIIITSATIDPERFSRHFNNAPIIEVSGRTYPV------------------EV 247

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397     586 RKRKRDDESEmvgiETDGDQnlnktvlagnysnetvtamasmsesevsfelIEALLIFIKQ--KNVPGAVLVFLPGWNLI 663
Cdd:TIGR01967  248 RYRPLVEEQE----DDDLDQ-------------------------------LEAILDAVDElfAEGPGDILIFLPGEREI 292

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397     664 FALMKHLQSGRFGGSDfrILPCHSQIPREDQRKVFEpvPPGVTKIILSTNIAETSITIDDIVYVIDICKARMKLFTSHNN 743
Cdd:TIGR01967  293 RDAAEILRKRNLRHTE--ILPLYARLSNKEQQRVFQ--PHSGRRIVLATNVAETSLTVPGIHYVIDTGTARISRYSYRTK 368

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397     744 MTSYATVWASKTNLEQRKGRAGRVRPGFCFTLCSRARYAKLDEHLTPEMFRTPLHELALSIKLLRLGAIGQFlsKAIEPP 823
Cdd:TIGR01967  369 VQRLPIEPISQASANQRKGRCGRVAPGICIRLYSEEDFNSRPEFTDPEILRTNLASVILQMLALRLGDIAAF--PFIEAP 446

                          490       500       510       520       530
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 3650397     824 PLDAVIEAEVVLRDLKCLNQNDD---LSPLGKILARLPIEPRLGKMMV----LGCI 872
Cdd:TIGR01967  447 DPRAIRDGFRLLEELGALDDDEAepqLTPIGRQLAQLPVDPRLARMLLeahrLGCL 502
PRK11131 PRK11131
ATP-dependent RNA helicase HrpA; Provisional
 350-872 1.42e-71

ATP-dependent RNA helicase HrpA; Provisional


Pssm-ID: 182986 [Multi-domain]  Cd Length: 1294  Bit Score: 262.69  E-value: 1.42e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397    350 ATLEQLSEELlQISRDKLQNDNELIERMKFRETLPVAAMKNEIMTLINDNSVVIVKGATGCGKTTQIAQYILEdyvnSGQ 429
Cdd:PRK11131   41 AIFQEIAKEI-AQAAQRVLLREAARPEITYPENLPVSQKKQDILEAIRDHQVVIVAGETGSGKTTQLPKICLE----LGR 115

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397    430 GAWCNIAITQPRRISAISVSERIAVERNENIGESVGYSVRF-----ESCLprpfgaIMFCTIGVLLRKLEAG--LRGVSH 502
Cdd:PRK11131  116 GVKGLIGHTQPRRLAARTVANRIAEELETELGGCVGYKVRFndqvsDNTM------VKLMTDGILLAEIQQDrlLMQYDT 189

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397    503 VIVDEIHERDVNSDFILVVLRDMVHTYPDLRVILMSATIDTTLFSDYFGKCPVIEIPGRAHPVtqlfledciemtkfvps 582
Cdd:PRK11131  190 IIIDEAHERSLNIDFILGYLKELLPRRPDLKVIITSATIDPERFSRHFNNAPIIEVSGRTYPV----------------- 252

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397    583 pESRKRKRDDESEmvgiETDGDQnlnktvlagnysnetvtamasmseSEVSFELIEALlifikQKNVPGAVLVFLPGWNL 662
Cdd:PRK11131  253 -EVRYRPIVEEAD----DTERDQ------------------------LQAIFDAVDEL-----GREGPGDILIFMSGERE 298

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397    663 IF----ALMKHlqsgrfggsDFR---ILPCHSQIPREDQRKVFEpvPPGVTKIILSTNIAETSITIDDIVYVIDICKARM 735
Cdd:PRK11131  299 IRdtadALNKL---------NLRhteILPLYARLSNSEQNRVFQ--SHSGRRIVLATNVAETSLTVPGIKYVIDPGTARI 367

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397    736 KLFtshnnmtSYATVWA-------SKTNLEQRKGRAGRVRPGFCFTLCSRARYAKLDEHLTPEMFRTPLHELALSIKLLR 808
Cdd:PRK11131  368 SRY-------SYRTKVQrlpiepiSQASANQRKGRCGRVSEGICIRLYSEDDFLSRPEFTDPEILRTNLASVILQMTALG 440

                         490       500       510       520       530       540       550
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 3650397    809 LGAIGQFlsKAIEPPPLDAVIEAEVVLRDLKCLNQNDD-----LSPLGKILARLPIEPRLGKMMV----LGCI 872
Cdd:PRK11131  441 LGDIAAF--PFVEAPDKRNIQDGVRLLEELGAITTDEQasaykLTPLGRQLAQLPVDPRLARMVLeaqkHGCV 511
SF2_C_RHA cd18791
C-terminal helicase domain of the RNA helicase A (RHA) family helicases; The RNA helicase A ...
 622-776 1.18e-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: 1.18e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   622 TAMASMSESEVSFELIEALLIFIKQKNVPGAVLVFLPGWNLIFALMKHLQS--GRFGGSDFRILPCHSQIPREDQRKVFE 699
Cdd:cd18791   15 LGISSEKEDPDYVDAAVRLILQIHRTEEPGDILVFLPGQEEIERLCELLREelLSPDLGKLLVLPLHSSLPPEEQQRVFE 94

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 3650397   700 PVPPGVTKIILSTNIAETSITIDDIVYVIDICKARMKLFTSHNNMTSYATVWASKTNLEQRKGRAGRVRPGFCFTLC 776
Cdd:cd18791   95 PPPPGVRKVVLATNIAETSITIPGVVYVIDSGLVKEKVYDPRTGLSSLVTVWISKASAEQRAGRAGRTRPGKCYRLY 171
DSRM_DHX9_rpt2 cd19855
second double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; ...
 164-238 7.36e-42

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: 147.36  E-value: 7.36e-42
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 3650397   164 IENAKAKLHQFMQMNKIQADYRYTPVGPDHARSFMAEMKIFVKQLNRTITGRESGSNKQTASKSCALSLVRQLYH 238
Cdd:cd19855    1 LDNAKSRLNEFLQKNKIPAEYKYTSVGPDHNRSFIAELSIFVKQLGKTIYARETGSNKKLASQSCALSLVRQLYH 75
DSRM_DHX9_rpt1 cd19854
first double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; ...
 3-71 1.89e-32

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: 120.45  E-value: 1.89e-32
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 3650397     3 DIKSFFHSWCNKTKVEPQFESRPTGPKHRQRFLCELRVAGFNYVGAGNSTVKKDAEKNAARDFVNFLVR 71
Cdd:cd19854    1 EIKAFLYAWCGKKKLTPEYDIKEAGNKHRQRFKCEVRVEGFDYVGTGNATNKKDAQTNAARDFLNYLVR 69
DEXDc smart00487
DEAD-like helicases superfamily;
374-567 1.92e-21

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 93.71  E-value: 1.92e-21
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397      374 IERMKFRETLPVAamKNEIMTLINDNSVVIVKGATGCGKTTQIAQYILEDYvnsGQGAWCNIAITQPRRISAISVSERIA 453
Cdd:smart00487    1 IEKFGFEPLRPYQ--KEAIEALLSGLRDVILAAPTGSGKTLAALLPALEAL---KRGKGGRVLVLVPTRELAEQWAEELK 75

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397      454 VE----RNENIGESVGYSVRFE-SCLPRPFGAIMFCTIGVLLRKLEAG---LRGVSHVIVDEIHERDvNSDFILVVLRDM 525
Cdd:smart00487   76 KLgpslGLKVVGLYGGDSKREQlRKLESGKTDILVTTPGRLLDLLENDklsLSNVDLVILDEAHRLL-DGGFGDQLEKLL 154

                           170       180       190       200
                    ....*....|....*....|....*....|....*....|....*.
gi 3650397      526 VHTYPDLRVILMSATIDTTL--FSDYFGKCPVIEIPGRA--HPVTQ 567
Cdd:smart00487  155 KLLPKNVQLLLLSATPPEEIenLLELFLNDPVFIDVGFTplEPIEQ 200
OB_NTP_bind pfam07717
Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus ...
 995-1072 5.56e-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: 85.38  E-value: 5.56e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397     995 ALLCMGLYPNVCYHKEKRKVLTT--ESKAALIHKTSVNCTNLaiTFPYPFFVFGEKIRTRAVSCKQMSMVAPIHLILFGS 1072
Cdd:pfam07717    3 AALAAGLYPNVARRDPKGKGYTTlsDNQRVFIHPSSVLFNEK--TFPPEWVVYQELVETTKVYIRTVTAISPEWLLLFAP 80
DSRM smart00358
Double-stranded RNA binding motif;
5-69 9.83e-16

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 72.68  E-value: 9.83e-16
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 3650397        5 KSFFHSWCNKTKVEPQFES-RPTGPKHRQRFLCELRVAGFnYVGAGNSTVKKDAEKNAARDFVNFL 69
Cdd:smart00358    2 KSLLQELAQKRKLPPEYELvKEEGPDHAPRFTVTVKVGGK-RTGEGEGSSKKEAKQRAAEAALRSL 66
HELICc smart00490
helicase superfamily c-terminal domain;
679-766 2.37e-13

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 66.47  E-value: 2.37e-13
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397      679 DFRILPCHSQIPREDQRKVFEPVPPGVTKIILSTNIAETSITIDDIVYVIDICkarmklftshnnmtsyatVWASKTNLE 758
Cdd:smart00490   11 GIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYD------------------LPWSPASYI 72


                    ....*...
gi 3650397      759 QRKGRAGR 766
Cdd:smart00490   73 QRIGRAGR 80
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 635-767 4.12e-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: 66.85  E-value: 4.12e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397     635 ELIEALLIFIKQKNvPGAVLVFLPGWNLIFALMKHLQSGrfggsdFRILPCHSQIPREDQRKVFEPVPPGVTKIILSTNI 714
Cdd:pfam00271    1 EKLEALLELLKKER-GGKVLIFSQTKKTLEAELLLEKEG------IKVARLHGDLSQEEREEILEDFRKGKIDVLVATDV 73

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 3650397     715 AETSITIDDIVYVIDickarmklFTSHNNMTSYatvwasktnlEQRKGRAGRV 767
Cdd:pfam00271   74 AERGLDLPDVDLVIN--------YDLPWNPASY----------IQRIGRAGRA 108
DSRM smart00358
Double-stranded RNA binding motif;
167-237 9.46e-13

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 64.21  E-value: 9.46e-13
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 3650397      167 AKAKLHQFMQMNKIQADYRYTPV-GPDHARSFMAEMKIfvkqlNRTITGRESGSNKQTASKSCALSLVRQLY 237
Cdd:smart00358    1 PKSLLQELAQKRKLPPEYELVKEeGPDHAPRFTVTVKV-----GGKRTGEGEGSSKKEAKQRAAEAALRSLK 67
HA2 smart00847
Helicase associated domain (HA2) Add an annotation; This presumed domain is about 90 amino ...
 838-921 1.47e-12

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: 64.21  E-value: 1.47e-12
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397      838 LKCLNQNDDLSPLGKILARLPIEPRLGKMMVLGCIFLCGDALGAMAAYSGTFSeVFTLDLGQRRLSNHQKALGGtkHSDH 917
Cdd:smart00847    2 LGALDDDGRLTPLGRKMAELPLDPRLAKMLLAAAEFGCLDEILTIVAMLSVGD-PRPKEKREDADAARRRFADP--ESDH 78


                    ....
gi 3650397      918 VAML 921
Cdd:smart00847   79 LTLL 82
HA2 pfam04408
Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in ...
 831-920 1.63e-11

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: 61.87  E-value: 1.63e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397     831 AEVVLRDLKCLNQNDDLSPLGKILARLPIEPRLGKMMVLGCIFLCGD---ALGAMAAYSGTFSEVFTLDLGQRRLSN--- 904
Cdd:pfam04408    1 ALELLYYLGALDEDGELTPLGRKMAELPLDPRLAKMLLAAAELGCLDevlTIVAALSVRDPFVQPNFLDPRSAAKAArrr 80

                           90       100
                   ....*....|....*....|....
gi 3650397     905 --------HQKALGGTKHSDHVAM 920
Cdd:pfam04408   81 rraadekaRAKFARLDLEGDHLTL 104
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 5-69 4.42e-11

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: 59.55  E-value: 4.42e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 3650397       5 KSFFHSWCNKTKVEPQFE-SRPTGPKHRQRFLCELRVAGFNYvGAGNSTVKKDAEKNAARDFVNFL 69
Cdd:pfam00035    2 KSLLQEYAQKNGKPPPYEyVSEEGPPHSPKFTVTVKVDGKLY-GSGTGSSKKEAEQLAAEKALEKL 66
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 167-236 4.85e-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: 56.47  E-value: 4.85e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 3650397     167 AKAKLHQFMQMNKIQADYRYTPV-GPDHARSFMAEMKIfvkqlNRTITGRESGSNKQTASKSCALSLVRQL 236
Cdd:pfam00035    1 PKSLLQEYAQKNGKPPPYEYVSEeGPPHSPKFTVTVKV-----DGKLYGSGTGSSKKEAEQLAAEKALEKL 66
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 402-545 6.28e-05

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: 44.93  E-value: 6.28e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397     402 VIVKGATGCGKTTqIAQYILEDYVNSGQGAwCNIAITQPRRISAISVSERIaVERNENIGESVGYSV---RFESCLPRPF 478
Cdd:pfam00270   17 VLVQAPTGSGKTL-AFLLPALEALDKLDNG-PQALVLAPTRELAEQIYEEL-KKLGKGLGLKVASLLggdSRKEQLEKLK 93

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397     479 GA-IMFCTIGVLLR--KLEAGLRGVSHVIVDEIHERDVNsDFILVVLRDMVHTYPDLRVILMSATIDTTL 545
Cdd:pfam00270   94 GPdILVGTPGRLLDllQERKLLKNLKLLVLDEAHRLLDM-GFGPDLEEILRRLPKKRQILLLSATLPRNL 162
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
26-64 8.63e-04

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 42.39  E-value: 8.63e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 3650397    26 TGPKHRQRFLCELRVAGFNY-VGAGNStvKKDAEKNAARD 64
Cdd:COG0571  183 EGPDHAKTFTVEVLVGGKVLgEGTGRS--KKEAEQAAAKA 220
 
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 ...
 325-558 6.02e-136

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: 413.85  E-value: 6.02e-136
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   325 ISWSPPQPNWNPWTACNIDEGYLATATLEQLSEELLQISRDKLQNDNELIERMKFRETLPVAAMKNEIMTLINDNSVVIV 404
Cdd:cd17972    1 VPWSPPQSNWNPWTSSNIDEGPLAFATPEQISMDLKNELMYQREQDHNLQQILQERELLPVKKFREEILEAISNNPVVII 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   405 KGATGCGKTTQIAQYILEDYVNSGQGAWCNIAITQPRRISAISVSERIAVERNENIGESVGYSVRFESCLPRPFGAIMFC 484
Cdd:cd17972   81 RGATGCGKTTQVPQYILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEVGKSCGYSVRFESVLPRPHASILFC 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 3650397   485 TIGVLLRKLEAGLRGVSHVIVDEIHERDVNSDFILVVLRDMVHTYPDLRVILMSATIDTTLFSDYFGKCPVIEI 558
Cdd:cd17972  161 TVGVLLRKLEAGIRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPDLRVILMSATIDTSMFCEYFFNCPVIEV 234
HrpA COG1643
HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];
377-870 6.50e-107

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


Pssm-ID: 441249 [Multi-domain]  Cd Length: 836  Bit Score: 357.08  E-value: 6.50e-107
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   377 MKFRETLPVAAMKNEIMTLINDNSVVIVKGATGCGKTTQIAQYILEdyvnsgQGaWCN---IAITQPRRISAISVSERIA 453
Cdd:COG1643    4 ITYPPDLPVSAVLPELLAALRAHQVVVLAAPPGAGKTTQLPLALLE------LG-WGAggrIGMLEPRRLAARAAAERMA 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   454 VERNENIGESVGYSVRFESCLprpfGA---IMFCTIGVLLRKLEA--GLRGVSHVIVDEIHERDVNSDFILVVLRDMVHT 528
Cdd:COG1643   77 EELGEPVGETVGYRVRFEDKV----SAatrIEVVTEGILLRELQRdpELEGVDTVIFDEFHERSLNADLLLALLLDLQPA 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   529 Y-PDLRVILMSATIDTTLFSDYFGKCPVIEIPGRAHPVtqlfledciemtkfvpspESRKRKRDDESEmvgietdgDQnl 607
Cdd:COG1643  153 LrPDLKLLVMSATLDAERFARLLGDAPVIESSGRTYPV------------------EVRYRPLPADER--------DL-- 204

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   608 nktvlagnysnetVTAMAsmsesevsfELIEALLifikqKNVPGAVLVFLPGWNLIFALMKHLQsGRFGgSDFRILPCHS 687
Cdd:COG1643  205 -------------EDAVA---------DAVREAL-----AEEPGDILVFLPGEREIRRTAEALR-GRLP-PDTEILPLYG 255

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   688 QIPREDQRKVFEPVPPGVTKIILSTNIAETSITIDDIVYVIDICKARMKLFtSHNN-MTSYATVWASKTNLEQRKGRAGR 766
Cdd:COG1643  256 RLSAAEQDRAFAPAPHGRRRIVLATNIAETSLTVPGIRYVIDSGLARIPRY-DPRSgVTRLPTERISQASANQRAGRAGR 334

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   767 VRPGFCFTLCSRARYAKLDEHLTPEMFRTPLHELALSIKLLRLGAIGQFlsKAIEPPPLDAVIEAEVVLRDLKCLNQNDD 846
Cdd:COG1643  335 LAPGICYRLWSEEDFARRPAFTDPEILRADLASLILELAAWGLGDPEDL--PFLDPPPARAIADARALLQELGALDADGR 412

                        490       500
                 ....*....|....*....|....
gi 3650397   847 LSPLGKILARLPIEPRLGKMMVLG 870
Cdd:COG1643  413 LTPLGRALARLPLDPRLARMLLAA 436
DEAH_box_HrpA TIGR01967
RNA helicase HrpA; This model represents HrpA, one of two related but uncharacterized DEAH-box ...
 348-872 2.64e-81

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: 292.44  E-value: 2.64e-81
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397     348 ATATLEQLSEELlQISRDKLQNDNELIERMKFRETLPVAAMKNEIMTLINDNSVVIVKGATGCGKTTQIAQYILEdyvnS 427
Cdd:TIGR01967   32 AIAALAKFRERI-DAACDKVEARRQAVPEIRYPDNLPVSAKREDIAEAIAENQVVIIAGETGSGKTTQLPKICLE----L 106

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397     428 GQGAWCNIAITQPRRISAISVSERIAVERNENIGESVGYSVRFESCLpRPFGAIMFCTIGVLLRKLEAG--LRGVSHVIV 505
Cdd:TIGR01967  107 GRGSHGLIGHTQPRRLAARTVAQRIAEELGTPLGEKVGYKVRFHDQV-SSNTLVKLMTDGILLAETQQDrfLSRYDTIII 185

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397     506 DEIHERDVNSDFILVVLRDMVHTYPDLRVILMSATIDTTLFSDYFGKCPVIEIPGRAHPVtqlfledciemtkfvpspES 585
Cdd:TIGR01967  186 DEAHERSLNIDFLLGYLKQLLPRRPDLKIIITSATIDPERFSRHFNNAPIIEVSGRTYPV------------------EV 247

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397     586 RKRKRDDESEmvgiETDGDQnlnktvlagnysnetvtamasmsesevsfelIEALLIFIKQ--KNVPGAVLVFLPGWNLI 663
Cdd:TIGR01967  248 RYRPLVEEQE----DDDLDQ-------------------------------LEAILDAVDElfAEGPGDILIFLPGEREI 292

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397     664 FALMKHLQSGRFGGSDfrILPCHSQIPREDQRKVFEpvPPGVTKIILSTNIAETSITIDDIVYVIDICKARMKLFTSHNN 743
Cdd:TIGR01967  293 RDAAEILRKRNLRHTE--ILPLYARLSNKEQQRVFQ--PHSGRRIVLATNVAETSLTVPGIHYVIDTGTARISRYSYRTK 368

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397     744 MTSYATVWASKTNLEQRKGRAGRVRPGFCFTLCSRARYAKLDEHLTPEMFRTPLHELALSIKLLRLGAIGQFlsKAIEPP 823
Cdd:TIGR01967  369 VQRLPIEPISQASANQRKGRCGRVAPGICIRLYSEEDFNSRPEFTDPEILRTNLASVILQMLALRLGDIAAF--PFIEAP 446

                          490       500       510       520       530
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 3650397     824 PLDAVIEAEVVLRDLKCLNQNDD---LSPLGKILARLPIEPRLGKMMV----LGCI 872
Cdd:TIGR01967  447 DPRAIRDGFRLLEELGALDDDEAepqLTPIGRQLAQLPVDPRLARMLLeahrLGCL 502
DEXHc_RHA-like cd17917
DEXH-box helicase domain of DEAD-like helicase RHA family proteins; The RNA helicase A (RHA) ...
 399-558 1.48e-80

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: 260.85  E-value: 1.48e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   399 NSVVIVKGATGCGKTTQIAQYILEDYVNSGQGawCNIAITQPRRISAISVSERIAVERNENIGESVGYSVRFESCLPRPf 478
Cdd:cd17917    1 NQVVVIVGETGSGKTTQVPQFLLEDGLAKGGK--GRIVCTQPRRIAAISVAERVAEERGEKLGEEVGYQIRFESKTSSK- 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   479 GAIMFCTIGVLLRKLEAG--LRGVSHVIVDEIHERDVNSDFILVVLRDMVHTYPDLRVILMSATIDTTLFSDYFGKCPVI 556
Cdd:cd17917   78 TRIKFCTDGILLRELLSDplLSGYSHVILDEAHERSLDTDFLLGLLKDLLRKRPDLKVILMSATLDAEKFSSYFGGAPVI 157


                 ..
gi 3650397   557 EI 558
Cdd:cd17917  158 HI 159
DEXHc_DHX30 cd17976
DEXH-box helicase domain of DEAH-box helicase 30; DEAH-box helicase 30 (DHX30) plays an ...
 383-558 9.05e-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: 242.78  E-value: 9.05e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   383 LPVAAMKNEIMTLINDNSVVIVKGATGCGKTTQIAQYILEDYVNSGQGAWCNIAITQPRRISAISVSERIAVERNENIGE 462
Cdd:cd17976    1 LPVDSHKESILSAIEQNPVVVISGDTGCGKTTRIPQFILEDYVLRGRGARCNVVITQPRRISAVSVAQRVAHELGPNLRR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   463 SVGYSVRFESCLPRPFGAIMFCTIGVLLRKLE--AGLRGVSHVIVDEIHERDVNSDFILVVLRDMVHTYPDLRVILMSAT 540
Cdd:cd17976   81 NVGYQVRLESRPPPRGGALLFCTVGVLLKKLQsnPRLEGVSHVIVDEVHERDVNTDFLLILLKGVLQLNPELRVVLMSAT 160

                        170
                 ....*....|....*...
gi 3650397   541 IDTTLFSDYFGKCPVIEI 558
Cdd:cd17976  161 GDNQRLSRYFGGCPVVRV 178
PRK11131 PRK11131
ATP-dependent RNA helicase HrpA; Provisional
 350-872 1.42e-71

ATP-dependent RNA helicase HrpA; Provisional


Pssm-ID: 182986 [Multi-domain]  Cd Length: 1294  Bit Score: 262.69  E-value: 1.42e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397    350 ATLEQLSEELlQISRDKLQNDNELIERMKFRETLPVAAMKNEIMTLINDNSVVIVKGATGCGKTTQIAQYILEdyvnSGQ 429
Cdd:PRK11131   41 AIFQEIAKEI-AQAAQRVLLREAARPEITYPENLPVSQKKQDILEAIRDHQVVIVAGETGSGKTTQLPKICLE----LGR 115

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397    430 GAWCNIAITQPRRISAISVSERIAVERNENIGESVGYSVRF-----ESCLprpfgaIMFCTIGVLLRKLEAG--LRGVSH 502
Cdd:PRK11131  116 GVKGLIGHTQPRRLAARTVANRIAEELETELGGCVGYKVRFndqvsDNTM------VKLMTDGILLAEIQQDrlLMQYDT 189

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397    503 VIVDEIHERDVNSDFILVVLRDMVHTYPDLRVILMSATIDTTLFSDYFGKCPVIEIPGRAHPVtqlfledciemtkfvps 582
Cdd:PRK11131  190 IIIDEAHERSLNIDFILGYLKELLPRRPDLKVIITSATIDPERFSRHFNNAPIIEVSGRTYPV----------------- 252

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397    583 pESRKRKRDDESEmvgiETDGDQnlnktvlagnysnetvtamasmseSEVSFELIEALlifikQKNVPGAVLVFLPGWNL 662
Cdd:PRK11131  253 -EVRYRPIVEEAD----DTERDQ------------------------LQAIFDAVDEL-----GREGPGDILIFMSGERE 298

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397    663 IF----ALMKHlqsgrfggsDFR---ILPCHSQIPREDQRKVFEpvPPGVTKIILSTNIAETSITIDDIVYVIDICKARM 735
Cdd:PRK11131  299 IRdtadALNKL---------NLRhteILPLYARLSNSEQNRVFQ--SHSGRRIVLATNVAETSLTVPGIKYVIDPGTARI 367

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397    736 KLFtshnnmtSYATVWA-------SKTNLEQRKGRAGRVRPGFCFTLCSRARYAKLDEHLTPEMFRTPLHELALSIKLLR 808
Cdd:PRK11131  368 SRY-------SYRTKVQrlpiepiSQASANQRKGRCGRVSEGICIRLYSEDDFLSRPEFTDPEILRTNLASVILQMTALG 440

                         490       500       510       520       530       540       550
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 3650397    809 LGAIGQFlsKAIEPPPLDAVIEAEVVLRDLKCLNQNDD-----LSPLGKILARLPIEPRLGKMMV----LGCI 872
Cdd:PRK11131  441 LGDIAAF--PFVEAPDKRNIQDGVRLLEELGAITTDEQasaykLTPLGRQLAQLPVDPRLARMVLeaqkHGCV 511
DEAH_box_HrpB TIGR01970
ATP-dependent helicase HrpB; This model represents HrpB, one of two related but ...
 383-935 2.90e-69

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: 249.68  E-value: 2.90e-69
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397     383 LPVAAMKNEIMTLINDNSVVIVKGATGCGKTTQIAQYILEDYVNSGQgawcnIAITQPRRISAISVSERIAVERNENIGE 462
Cdd:TIGR01970    1 LPIHAVLPALRDALAAHPQVVLEAPPGAGKSTAVPLALLDAPGIGGK-----IIMLEPRRLAARSAAQRLASQLGEAVGQ 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397     463 SVGYSVRFESCLPRPfGAIMFCTIGVLLRKLEA--GLRGVSHVIVDEIHERDVNSDFILVVLRDMVHTY-PDLRVILMSA 539
Cdd:TIGR01970   76 TVGYRVRGENKVSRR-TRLEVVTEGILTRMIQDdpELDGVGALIFDEFHERSLDADLGLALALDVQSSLrEDLKILAMSA 154

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397     540 TIDTTLFSDYFGKCPVIEIPGRAHPVtqlfledciemtkfvpspESRKRKRDdesemvgietdGDQNLnktvlagnysne 619
Cdd:TIGR01970  155 TLDGERLSSLLPDAPVVESEGRSFPV------------------EIRYLPLR-----------GDQRL------------ 193

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397     620 tvtamasmsESEVSFELIEALlifikqKNVPGAVLVFLPGWNLIFALMKHLQSGRfgGSDFRILPCHSQIPREDQRKVFE 699
Cdd:TIGR01970  194 ---------EDAVSRAVEHAL------ASETGSILVFLPGQAEIRRVQEQLAERL--DSDVLICPLYGELSLAAQDRAIK 256

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397     700 PVPPGVTKIILSTNIAETSITIDDIVYVIDICKARMKLFTSHNNMTSYATVWASKTNLEQRKGRAGRVRPGFCFTLCSRA 779
Cdd:TIGR01970  257 PDPQGRRKVVLATNIAETSLTIEGIRVVIDSGLARVARFDPKTGITRLETVRISQASATQRAGRAGRLEPGVCYRLWSEE 336

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397     780 RYAKLDEHLTPEMFRTPLHELALsiKLLRLGAIGQFLSKAIEPPPLDAVIEAEVVLRDLKCLNQNDDLSPLGKILARLPI 859
Cdd:TIGR01970  337 QHQRLPAQDEPEILQADLSGLAL--ELAQWGAKDPSDLRWLDAPPSVALAAARQLLQRLGALDAQGRLTAHGKAMAALGC 414

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397     860 EPRLGKMMVLGciflCGDALGAMAA-YSGTFSEVFTL-----DLGQRRLSNHQKALGGTKHSDHVAmlvasHMWNRARDK 933
Cdd:TIGR01970  415 HPRLAAMLLSA----HSTGLAALACdLAALLEERGLPrqggaDLMNRLHRLQQGRQGRGQRAQQLA-----KKLRRRLRF 485


                   ..
gi 3650397     934 GE 935
Cdd:TIGR01970  486 SQ 487
SF2_C_RHA cd18791
C-terminal helicase domain of the RNA helicase A (RHA) family helicases; The RNA helicase A ...
 622-776 1.18e-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: 1.18e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   622 TAMASMSESEVSFELIEALLIFIKQKNVPGAVLVFLPGWNLIFALMKHLQS--GRFGGSDFRILPCHSQIPREDQRKVFE 699
Cdd:cd18791   15 LGISSEKEDPDYVDAAVRLILQIHRTEEPGDILVFLPGQEEIERLCELLREelLSPDLGKLLVLPLHSSLPPEEQQRVFE 94

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 3650397   700 PVPPGVTKIILSTNIAETSITIDDIVYVIDICKARMKLFTSHNNMTSYATVWASKTNLEQRKGRAGRVRPGFCFTLC 776
Cdd:cd18791   95 PPPPGVRKVVLATNIAETSITIPGVVYVIDSGLVKEKVYDPRTGLSSLVTVWISKASAEQRAGRAGRTRPGKCYRLY 171
DEXHc_DHX36 cd17981
DEXH-box helicase domain of DEAH-box helicase 36; DEAH-box helicase 36 (DHX36, also known as ...
 383-558 5.63e-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: 223.57  E-value: 5.63e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   383 LPVAAMKNEIMTLINDNSVVIVKGATGCGKTTQIAQYILEDYVNSGQGAWCNIAITQPRRISAISVSERIAVERNEN--I 460
Cdd:cd17981    1 LPSYGMKQEIINMIDNNQVTVISGETGCGKTTQVTQFILDDAIERGKGSSCRIVCTQPRRISAISVAERVAAERAEScgL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   461 GESVGYSVRFESCLPRPFGAIMFCTIGVLLRKLEAG--LRGVSHVIVDEIHERDVNSDFILVVLRDMVHTYPDLRVILMS 538
Cdd:cd17981   81 GNSTGYQIRLESRKPRKQGSILYCTTGIVLQWLQSDphLSNVSHLVLDEIHERNLQSDVLMGIVKDLLPFRSDLKVILMS 160

                        170       180
                 ....*....|....*....|
gi 3650397   539 ATIDTTLFSDYFGKCPVIEI 558
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 ...
 383-558 4.54e-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: 209.31  E-value: 4.54e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   383 LPVAAMKNEIMTLINDNSVVIVKGATGCGKTTQIAQYILEDYVNSGQGAWCNIAITQPRRISAISVSERIAVERNENIGE 462
Cdd:cd17985    1 LPAWQERETILELLEKHQVLVISGMTGCGKTTQIPQFILDNSLQGPPLPVANIICTQPRRISAISVAERVAQERAERVGQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   463 SVGYSVRFEScLPRPFGAIMFCTIGVLLRKLEAG--LRGVSHVIVDEIHERDVNSDFILVVLRDMVHTYPDLRVILMSAT 540
Cdd:cd17985   81 SVGYQIRLES-VKSSATRLLYCTTGVLLRRLEGDptLQGVTHVIVDEVHERTEESDFLLLVLKDLMVQRPDLKVILMSAT 159

                        170
                 ....*....|....*...
gi 3650397   541 IDTTLFSDYFGKCPVIEI 558
Cdd:cd17985  160 LNAELFSDYFNSCPVIHI 177
PRK11664 PRK11664
ATP-dependent RNA helicase HrpB; Provisional
 383-868 1.70e-61

ATP-dependent RNA helicase HrpB; Provisional


Pssm-ID: 236950 [Multi-domain]  Cd Length: 812  Bit Score: 226.34  E-value: 1.70e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397    383 LPVAAMKNEIMTLINDNSVVIVKGATGCGKTTQIAQYILEDYVNSGQgawcnIAITQPRRISAISVSERIAVERNENIGE 462
Cdd:PRK11664    4 LPVAAVLPELLTALKTAPQVLLKAPTGAGKSTWLPLQLLQHGGINGK-----IIMLEPRRLAARNVAQRLAEQLGEKPGE 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397    463 SVGYSVRFESCLPrPFGAIMFCTIGVLLRKLE--AGLRGVSHVIVDEIHERDVNSD----FILVV---LRDmvhtypDLR 533
Cdd:PRK11664   79 TVGYRMRAESKVG-PNTRLEVVTEGILTRMIQrdPELSGVGLVILDEFHERSLQADlalaLLLDVqqgLRD------DLK 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397    534 VILMSATIDTTLFSDYFGKCPVIEIPGRAHPVTqlfledciemTKFVPspesrkrkrddesemvgietdgdqnlnktvLA 613
Cdd:PRK11664  152 LLIMSATLDNDRLQQLLPDAPVIVSEGRSFPVE----------RRYQP------------------------------LP 191

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397    614 GNYSNETVTAMAsmsesevsfelIEALLifikqKNVPGAVLVFLPGWNLIFALMKHLqSGRFGgSDFRILPCHSQIPRED 693
Cdd:PRK11664  192 AHQRFDEAVARA-----------TAELL-----RQESGSLLLFLPGVGEIQRVQEQL-ASRVA-SDVLLCPLYGALSLAE 253

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397    694 QRKVFEPVPPGVTKIILSTNIAETSITIDDIVYVIDICKARMKLFTSHNNMTSYATVWASKTNLEQRKGRAGRVRPGFCF 773
Cdd:PRK11664  254 QQKAILPAPAGRRKVVLATNIAETSLTIEGIRLVVDSGLERVARFDPKTGLTRLVTQRISQASMTQRAGRAGRLEPGICL 333

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397    774 TLCSRARYAKLDEHLTPEMFRTPLHELALSikLLRLGA--IGQFlsKAIEPPPLDAVIEAEVVLRDLKCLNQNDDLSPLG 851
Cdd:PRK11664  334 HLYSKEQAERAAAQSEPEILHSDLSGLLLE--LLQWGChdPAQL--SWLDQPPAAALAAAKRLLQQLGALDGQGRLTARG 409

                         490
                  ....*....|....*..
gi 3650397    852 KILARLPIEPRLGKMMV 868
Cdd:PRK11664  410 RKMAALGNDPRLAAMLV 426
DEXHc_YTHDC2 cd17987
DEXH-box helicase domain of YTH domain containing 2; YTH domain containing 2 (YTHDC2) ...
 383-558 7.38e-61

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: 205.83  E-value: 7.38e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   383 LPVAAMKNEIMTLINDNSVVIVKGATGCGKTTQIAQYILEDyvNSGQGAWCNIAITQPRRISAISVSERIAVERNENIGE 462
Cdd:cd17987    1 LPVFEKQEQIVRIIKENKVVLIVGETGSGKTTQIPQFLLDD--CYANGIPCRIFCTQPRRLAAIAVAERVAAERGEKIGQ 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   463 SVGYSVRFESCLpRPFGAIMFCTIGVLLRKLEAG---LRGVSHVIVDEIHERDVNSDFILVVLRDMVHTYPDLRVILMSA 539
Cdd:cd17987   79 TVGYQIRLESRV-SPKTLLTFCTNGVLLRTLMAGdsaLSTVTHVIVDEVHERDRFSDFLLTKLRDILQKHPNLKLILSSA 157

                        170
                 ....*....|....*....
gi 3650397   540 TIDTTLFSDYFGKCPVIEI 558
Cdd:cd17987  158 ALDVNLFIRYFGSCPVIYI 176
DEXHc_DHX29 cd17975
DEXH-box helicase domain of DEAH-box helicase 29; DEAH-box helicase 29 (DHX29) is a part of ...
 383-558 5.03e-51

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: 178.18  E-value: 5.03e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   383 LPVAAMKNEIMTLINDNSVVIVKGATGCGKTTQIAQYILEDYV-NSGQGAWCNIAITQPRRISAISVSERIAVERNENIG 461
Cdd:cd17975    1 LPVFKHRESILETLKRHRVVVVAGETGSGKSTQVPQFLLEDLLlNGGTAQKCNIVCTQPRRISAMSLATRVCEELGCESG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   462 ES-----VGYSVRFESclpRPFGA--IMFCTIGVLLRKLEAG--LRGVSHVIVDEIHERDVNSDFILVVLRDMVHTYPDL 532
Cdd:cd17975   81 PGgknslCGYQIRMES---RTGEAtrLLYCTTGVLLRKLQEDglLSSISHIIVDEVHERSVQSDFLLIILKEILHKRSDL 157

                        170       180
                 ....*....|....*....|....*.
gi 3650397   533 RVILMSATIDTTLFSDYFGKCPVIEI 558
Cdd:cd17975  158 HLILMSATVDCEKFSSYFTHCPILRI 183
DEXHc_DHX34 cd17979
DEXH-box helicase domain of DEAH-box helicase 34; DEAH-box helicase 34 (DHX34) plays a role in ...
 383-558 1.72e-49

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: 173.01  E-value: 1.72e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   383 LPVAAMKNEIMTLINDNSVVIVKGATGCGKTTQIAQYILEDYVNsgqgawcNIAITQPRRISAISVSERIAVERNENIGE 462
Cdd:cd17979    1 LPIAQYREKIIELLKTHQVVIVAGDTGCGKSTQVPQYLLAAGFR-------HIACTQPRRIACISLAKRVAFESLNQYGS 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   463 SVGYSVRFESClPRPFGAIMFCTIGVLLRKLE--AGLRGVSHVIVDEIHERDVNSDFILVVLRDMVHTYPDLRVILMSAT 540
Cdd:cd17979   74 KVAYQIRFERT-RTLATKLLFLTEGLLLRQIQrdASLPQYNVLILDEVHERHLHGDFLLGVLRCLLRLRPDLKLILMSAT 152

                        170
                 ....*....|....*...
gi 3650397   541 IDTTLFSDYFGKCPVIEI 558
Cdd:cd17979  153 INIELFSGYFEGAPVVQV 170
DEXHc_TDRD9 cd17988
DEXH-box helicase domain of tudor domain containing 9; Tudor domain containing 9 (TDRD9, also ...
 383-551 3.00e-49

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: 172.69  E-value: 3.00e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   383 LPVAAMKNEIMTLINDNSVVIVKGATGCGKTTQIAQYILEDYVNSgqGAWCNIAITQPRRISAISVSERIAVERNENIGE 462
Cdd:cd17988    1 LPIYAKREEILSLIEANSVVIIKGATGCGKTTQLPQFILDHYYKR--GKYCNIVVTQPRRIAAISIARRVSQEREWTLGS 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   463 SVGYSVRFEsclpRPFGA---IMFCTIGVLLRKL--EAGLRGVSHVIVDEIHERDVNSDFILVVLRDMVHTYPD-LRVIL 536
Cdd:cd17988   79 LVGYQVGLE----RPASEetrLIYCTTGVLLQKLinNKTLTEYTHIILDEVHERDQELDFLLLVVRRLLRTNSRhVKIIL 154

                        170
                 ....*....|....*
gi 3650397   537 MSATIDTTLFSDYFG 551
Cdd:cd17988  155 MSATISCKEFADYFT 169
DEXHc_DHX33 cd17978
DEXH-box helicase domain of DEAH-box helicase 33; DEAH-box helicase 33 (DHX33) stimulates RNA ...
 383-558 5.37e-48

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: 169.07  E-value: 5.37e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   383 LPVAAMKNEIMTLINDNSVVIVKGATGCGKTTQIAQYILEDYVNSGQgawcNIAITQPRRISAISVSERIAVERNENIGE 462
Cdd:cd17978    1 LPIYSARKRLLEELRKHDTVIIIGETGSGKTTQIPQYLYEAGFARGG----MIGITQPRRVAAVSVAKRVAEEMGVELGQ 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   463 SVGYSVRFESCLPRPfGAIMFCTIGVLLRK--LEAGLRGVSHVIVDEIHERDVNSDFILVVLRDMVHT-----YPDLRVI 535
Cdd:cd17978   77 LVGYSVRFDDVTSEE-TRIKYMTDGMLLREaiGDPLLSKYSVIILDEAHERTVHTDVLFGLVKSAQRRrkeqkLSPLKVI 155

                        170       180
                 ....*....|....*....|...
gi 3650397   536 LMSATIDTTLFSDYFGKCPVIEI 558
Cdd:cd17978  156 IMSATLDADLFSEYFNGAPVLYI 178
DEXHc_DHX38 cd17983
DEXH-box helicase domain of DEAH-box helicase 38; DEAH-box helicase 38 (DHX38, also known as ...
 383-558 9.67e-48

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: 168.02  E-value: 9.67e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   383 LPVAAMKNEIMTLINDNSVVIVKGATGCGKTTQIAQYILED-YVNSGQgawcnIAITQPRRISAISVSERIAVERNENIG 461
Cdd:cd17983    1 LPIFAVRQELLNVIRDNNVVIVVGETGSGKTTQLTQYLHEDgYTDYGM-----IGCTQPRRVAAMSVAKRVSEEMGVELG 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   462 ESVGYSVRFESClPRPFGAIMFCTIGVLLRK--LEAGLRGVSHVIVDEIHERDVNSDFILVVLRDMVHTYPDLRVILMSA 539
Cdd:cd17983   76 EEVGYAIRFEDC-TSENTVIKYMTDGILLREslRDPDLDKYSAIIMDEAHERSLNTDVLFGLLREVVARRRDLKLIVTSA 154

                        170
                 ....*....|....*....
gi 3650397   540 TIDTTLFSDYFGKCPVIEI 558
Cdd:cd17983  155 TMDADKFADFFGNVPIFTI 173
DEXHc_DHX8 cd17971
DEXH-box helicase domain of DEAH-box helicase 8; DEAH-box helicase 8 (DHX8 ,also known as ...
 380-559 2.16e-47

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: 167.27  E-value: 2.16e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   380 RETLPVAAMKNEIMTLINDNSVVIVKGATGCGKTTQIAQYILEdyvnSGQGAWCNIAITQPRRISAISVSERIAVERNEN 459
Cdd:cd17971    3 RESLPIYKLKEQLIQAVHDNQILVVIGETGSGKTTQITQYLAE----AGYTSRGKIGCTQPRRVAAMSVAKRVAEEFGCC 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   460 IGESVGYSVRFESClPRPFGAIMFCTIGVLLRK--LEAGLRGVSHVIVDEIHERDVNSDFILVVLRDMVHTYPDLRVILM 537
Cdd:cd17971   79 LGQEVGYTIRFEDC-TSPETVIKYMTDGMLLREclIDPDLSQYSVIMLDEAHERTIHTDVLFGLLKKTVQKRPDLKLIVT 157

                        170       180
                 ....*....|....*....|..
gi 3650397   538 SATIDTTLFSDYFGKCPVIEIP 559
Cdd:cd17971  158 SATLDAVKFSQYFYEAPIFTIP 179
DEXHc_HrpA cd17989
DEXH-box helicase domain of ATP-dependent RNA helicase HrpA; HrpA is part of the HrpB-HrpA ...
 383-558 1.64e-44

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: 158.77  E-value: 1.64e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   383 LPVAAMKNEIMTLINDNSVVIVKGATGCGKTTQIAQYILEdyvnSGQGAWCNIAITQPRRISAISVSERIAVERNENIGE 462
Cdd:cd17989    1 LPVSQKRDEIAKAIAENQVVIIAGETGSGKTTQLPKICLE----LGRGIRGLIGHTQPRRLAARSVAERIAEELKTELGG 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   463 SVGYSVRFESCL-PRPFGAIMfcTIGVLLRKLEAG--LRGVSHVIVDEIHERDVNSDFILVVLRDMVHTYPDLRVILMSA 539
Cdd:cd17989   77 AVGYKVRFTDQTsDETCVKLM--TDGILLAETQTDryLRAYDTIIIDEAHERSLNIDFLLGYLKQLLPRRPDLKVIITSA 154

                        170
                 ....*....|....*....
gi 3650397   540 TIDTTLFSDYFGKCPVIEI 558
Cdd:cd17989  155 TIDAERFSRHFNNAPIIEV 173
DEXHc_DHX35 cd17980
DEXH-box helicase domain of DEAH-box helicase 35; DHX35 plays a role in colorectal cancers and ...
 383-550 1.96e-42

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: 153.39  E-value: 1.96e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   383 LPVAAMKNEIMTLINDNSVVIVKGATGCGKTTQIAQYILEDYVNSGQGAwcnIAITQPRRISAISVSERIAVERNENIGE 462
Cdd:cd17980    1 LPVFKLRNHILYLVENYQTIVIVGETGCGKSTQIPQYLAEAGWTAGGRV---VGCTQPRRVAAVTVAGRVAEEMGAVLGH 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   463 SVGYSVRFESCLPRPFGAIMFCTIGVLLRKLEAG--LRGVSHVIVDEIHERDVNSDFILVVLRDMVHTYPDLRVILMSAT 540
Cdd:cd17980   78 EVGYCIRFDDCTDPQATRIKFLTDGMLVREMMLDplLTKYSVIMLDEAHERTLYTDILIGLLKKIQKKRGDLRLIVASAT 157

                        170
                 ....*....|
gi 3650397   541 IDTTLFSDYF 550
Cdd:cd17980  158 LDAEKFRDFF 167
DEXHc_DHX15 cd17973
DEXH-box helicase domain of DEAH-box helicase 15; DEAH-box helicase 15 (DHX15) is a pre-mRNA ...
 377-558 2.62e-42

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: 153.34  E-value: 2.62e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   377 MKFRETLPVAAMKNEIMTLINDNSVVIVKGATGCGKTTQIAQYILEDYVnSGQGAWcNIAITQPRRISAISVSERIAVER 456
Cdd:cd17973    7 LEKRRELPVWEQKEDFLKLLKNNQILVLVGETGSGKTTQIPQFVLDDEL-PHQPKK-LVACTQPRRVAAMSVAQRVAEEM 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   457 NENIGESVGYSVRFESCL-PRPFgaIMFCTIGVLLRKLEAG--LRGVSHVIVDEIHERDVNSDFILVVLRDMVHTYPDLR 533
Cdd:cd17973   85 DVKLGEEVGYSIRFEDCSsAKTI--LKYMTDGMLLREAMSDplLSRYSVIILDEAHERTLATDILMGLLKEVVRRRPDLK 162

                        170       180
                 ....*....|....*....|....*
gi 3650397   534 VILMSATIDTTLFSDYFGKCPVIEI 558
Cdd:cd17973  163 LIVMSATLDAGKFQKYFDNAPLLKV 187
DSRM_DHX9_rpt2 cd19855
second double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; ...
 164-238 7.36e-42

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: 147.36  E-value: 7.36e-42
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 3650397   164 IENAKAKLHQFMQMNKIQADYRYTPVGPDHARSFMAEMKIFVKQLNRTITGRESGSNKQTASKSCALSLVRQLYH 238
Cdd:cd19855    1 LDNAKSRLNEFLQKNKIPAEYKYTSVGPDHNRSFIAELSIFVKQLGKTIYARETGSNKKLASQSCALSLVRQLYH 75
DEXHc_DHX16 cd17974
DEXH-box helicase domain of DEAH-box helicase 16; DEAH-box helicase 16 (DHX16) is probably ...
 383-558 2.32e-41

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: 149.96  E-value: 2.32e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   383 LPVAAMKNEIMTLINDNSVVIVKGATGCGKTTQIAQYILEDYVNSGQGawcNIAITQPRRISAISVSERIAVERNENIGE 462
Cdd:cd17974    1 LPVYPYRDDLLAAVKEHQVLIIVGETGSGKTTQIPQYLHEAGYTKGGG---KIGCTQPRRVAAMSVAARVAEEMGVKLGN 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   463 SVGYSVRFESClPRPFGAIMFCTIGVLLRKL--EAGLRGVSHVIVDEIHERDVNSDFILVVLRDMVHTYPDLRVILMSAT 540
Cdd:cd17974   78 EVGYSIRFEDC-TSEKTVLKYMTDGMLLREFltEPDLASYSVMIIDEAHERTLHTDILFGLVKDIARFRPDLKLLISSAT 156

                        170
                 ....*....|....*...
gi 3650397   541 IDTTLFSDYFGKCPVIEI 558
Cdd:cd17974  157 MDAEKFSAFFDDAPIFRI 174
DEXHc_DHX37 cd17982
DEXH-box helicase domain of DEAH-box helicase 37; DHX37 plays a role in the development of the ...
 383-558 3.36e-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: 147.12  E-value: 3.36e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   383 LPVAAMKNEIMTLINDNSVVIVKGATGCGKTTQIAQYILE------DYVNSGQgawcnIAITQPRRISAISVSERIAVER 456
Cdd:cd17982    1 LPILAEEQEIMEAINENPVVIICGETGSGKTTQVPQFLYEagfgspESDNPGM-----IGITQPRRVAAVSMAKRVAEEL 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   457 NEnIGESVGYSVRFESCLPRPFgAIMFCTIGVLLRKLEAG--LRGVSHVIVDEIHERDVNSDFIL------VVLRDMVHT 528
Cdd:cd17982   76 NV-FGKEVSYQIRYDSTVSENT-KIKFMTDGVLLKEIQTDflLRKYSVIIIDEAHERSVNTDILIgmlsriVPLRAKLYL 153

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 3650397   529 YPD----LRVILMSATI-------DTTLFSdyfGKCPVIEI 558
Cdd:cd17982  154 QDQtvkpLKLVIMSATLrvedfteNKLLFP---RPPPVIKV 191
DEXHc_HrpB cd17990
DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA ...
 383-557 5.12e-36

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: 134.77  E-value: 5.12e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   383 LPVAAMKNEIMTLINDNSVVIVKGATGCGKTTQIAQYILEDYVNSGQgawcNIAITQPRRISAISVSERIAVERNENIGE 462
Cdd:cd17990    1 LPIAAVLPALRAALDAGGQVVLEAPPGAGKTTRVPLALLAELWIAGG----KIIVLEPRRVAARAAARRLATLLGEAPGE 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   463 SVGYSVRFESCLPRPfGAIMFCTIGVLLRKLEA--GLRGVSHVIVDEIHERDVNSDFILVVLRDMVHTY-PDLRVILMSA 539
Cdd:cd17990   77 TVGYRVRGESRVGRR-TRVEVVTEGVLLRRLQRdpELSGVGAVILDEFHERSLDADLALALLLEVQQLLrDDLRLLAMSA 155

                        170
                 ....*....|....*...
gi 3650397   540 TIDTTLFSDYFGKCPVIE 557
Cdd:cd17990  156 TLDGDGLAALLPEAPVVE 173
DEXHc_DHX40 cd17984
DEXH-box helicase domain of DEAH-box helicase 40; DEAH-box helicase 40 (DHX40) belongs to the ...
 383-558 1.15e-35

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: 133.83  E-value: 1.15e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   383 LPVAAMKNEIMTLINDNSVVIVKGATGCGKTTQIAQYILEdyvnSGQGAWCNIAITQPRRISAISVSERIAVERNENIGE 462
Cdd:cd17984    1 LPIQKQRKKLVQAVRDNSFLIVTGNTGSGKTTQLPKYLYE----AGFSQHGMIGVTQPRRVAAISVAQRVAEEMKCTLGS 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   463 SVGYSVRFESCLPRPfGAIMFCTIGVLLRKLEA--GLRGVSHVIVDEIHERDVNSDFILVVLRDMV------HTYPdLRV 534
Cdd:cd17984   77 KVGYQVRFDDCSSKE-TAIKYMTDGCLLRHILAdpNLTKYSVIILDEAHERSLTTDILFGLLKKLFqekspnRKEH-LKV 154

                        170       180
                 ....*....|....*....|....
gi 3650397   535 ILMSATIDTTLFSDYFGKCPVIEI 558
Cdd:cd17984  155 VVMSATLELAKLSAFFGNCPVFDI 178
DSRM_DHX9_rpt1 cd19854
first double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; ...
 3-71 1.89e-32

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: 120.45  E-value: 1.89e-32
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 3650397     3 DIKSFFHSWCNKTKVEPQFESRPTGPKHRQRFLCELRVAGFNYVGAGNSTVKKDAEKNAARDFVNFLVR 71
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 ...
 383-558 5.35e-26

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: 106.06  E-value: 5.35e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   383 LPVAAMKNEIMTLINDNSVVIVKGATGCGKTTQIAQYILEdYVNSGQGAWCNIAITQPRRISAISVSERIAVERNENIGE 462
Cdd:cd17977    1 LPVWEAKYEFMESLAHNQIVIVSGDAKTGKSSQIPQWCAE-YCLSAHYQHGVVVCTQVHKQTAVWLALRVADEMDVNIGH 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   463 SVGYSVRFESCLPRPfGAIMFCTIGVLLRKLEAG--LRGVSHVIVDEIHERDVNSDFILVVLRDMVHTYPDLRVILMSAT 540
Cdd:cd17977   80 EVGYVIPFENCCTNE-TILRYCTDDMLLREMMSDplLESYGVIILDDAHERTVSTDVLLGLLKDVLLSRPELKLVIITCP 158

                        170
                 ....*....|....*...
gi 3650397   541 IDTTLFSDYFGKCPVIEI 558
Cdd:cd17977  159 HLSSKLLSYYGNVPLIEV 176
DEXQc_DQX1 cd17986
DEXQ-box helicase domain of DEAQ-box RNA dependent ATPase 1; DEAQ-box RNA dependent ATPase 1 ...
 383-558 2.73e-25

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: 103.82  E-value: 2.73e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   383 LPVAAMKNEIMTLINDNS-VVIVKGATGCGKTTQIAQYILEdYVNSGQGAWCNIAITQPRRISAISVSERIAVERNENIG 461
Cdd:cd17986    1 LPIWAAKFTFLEQLESPSgIVLVSGEPGSGKSTQVPQWCAE-FALSRGFQKGQVTVTQPHPLAARSLALRVADEMDLNLG 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   462 ESVGYSVRFESCLPrPFGAIMFCTIGVLLRKLEA--GLRGVSHVIVDEIHERDVNSDFILVVLRDMVHTYPDLRVILMSA 539
Cdd:cd17986   80 HEVGYSIPQEDCTG-PNTILRFCWDRLLLQEMTStpLLGAWGVVVLDEAQERSVASDSLLGLLKDVRLQRPELRVVVVTS 158

                        170
                 ....*....|....*....
gi 3650397   540 TIDTTLFSDYFGKCPVIEI 558
Cdd:cd17986  159 PALEPKLRAFWGNPPVVHV 177
DEXDc smart00487
DEAD-like helicases superfamily;
374-567 1.92e-21

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 93.71  E-value: 1.92e-21
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397      374 IERMKFRETLPVAamKNEIMTLINDNSVVIVKGATGCGKTTQIAQYILEDYvnsGQGAWCNIAITQPRRISAISVSERIA 453
Cdd:smart00487    1 IEKFGFEPLRPYQ--KEAIEALLSGLRDVILAAPTGSGKTLAALLPALEAL---KRGKGGRVLVLVPTRELAEQWAEELK 75

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397      454 VE----RNENIGESVGYSVRFE-SCLPRPFGAIMFCTIGVLLRKLEAG---LRGVSHVIVDEIHERDvNSDFILVVLRDM 525
Cdd:smart00487   76 KLgpslGLKVVGLYGGDSKREQlRKLESGKTDILVTTPGRLLDLLENDklsLSNVDLVILDEAHRLL-DGGFGDQLEKLL 154

                           170       180       190       200
                    ....*....|....*....|....*....|....*....|....*.
gi 3650397      526 VHTYPDLRVILMSATIDTTL--FSDYFGKCPVIEIPGRA--HPVTQ 567
Cdd:smart00487  155 KLLPKNVQLLLLSATPPEEIenLLELFLNDPVFIDVGFTplEPIEQ 200
OB_NTP_bind pfam07717
Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus ...
 995-1072 5.56e-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: 85.38  E-value: 5.56e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397     995 ALLCMGLYPNVCYHKEKRKVLTT--ESKAALIHKTSVNCTNLaiTFPYPFFVFGEKIRTRAVSCKQMSMVAPIHLILFGS 1072
Cdd:pfam07717    3 AALAAGLYPNVARRDPKGKGYTTlsDNQRVFIHPSSVLFNEK--TFPPEWVVYQELVETTKVYIRTVTAISPEWLLLFAP 80
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 399-540 3.96e-19

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: 85.15  E-value: 3.96e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   399 NSVVIVKGATGCGKTTqIAQYILEDYVNSgQGawCNIAITQPRRISAISVSERIAVERNENIgeSVGYSVRFESCLPRPF 478
Cdd:cd00046    1 GENVLITAPTGSGKTL-AALLAALLLLLK-KG--KKVLVLVPTKALALQTAERLRELFGPGI--RVAVLVGGSSAEEREK 74

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 3650397   479 GA-----IMFCTIGVLLRKLEA----GLRGVSHVIVDEIHERDVNSDFILVV-LRDMVHTYPDLRVILMSAT 540
Cdd:cd00046   75 NKlgdadIIIATPDMLLNLLLRedrlFLKDLKLIIVDEAHALLIDSRGALILdLAVRKAGLKNAQVILLSAT 146
PHA02653 PHA02653
RNA helicase NPH-II; Provisional
 375-770 6.21e-16

RNA helicase NPH-II; Provisional


Pssm-ID: 177443 [Multi-domain]  Cd Length: 675  Bit Score: 83.10  E-value: 6.21e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397    375 ERMKFRETLPvaAMKNEIMTLINDNSVVIVKGATGCGKTTQIAQYILE-DYVNSGQGAWCNIAITQPRRISAISVSeRIA 453
Cdd:PHA02653  157 SKIPLASLQP--DVQLKIFEAWISRKPVVLTGGTGVGKTSQVPKLLLWfNYLFGGFDNLDKIDPNFIERPIVLSLP-RVA 233

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397    454 VER--NENIGESVGYSVRFESCL---------------PRPFGaIMFCTIGVLLRKleagLRGVSHVIVDEIHERDVNSD 516
Cdd:PHA02653  234 LVRlhSITLLKSLGFDEIDGSPIslkygsipdelintnPKPYG-LVFSTHKLTLNK----LFDYGTVIIDEVHEHDQIGD 308

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397    517 FILVVLR---DMVHTypdlrVILMSATI--DTTLFSDYFGKCPVIEIPGRA-HPVTQLFLedciemtKFVPSPESRKRKR 590
Cdd:PHA02653  309 IIIAVARkhiDKIRS-----LFLMTATLedDRDRIKEFFPNPAFVHIPGGTlFPISEVYV-------KNKYNPKNKRAYI 376

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397    591 DDEsemvgietdgDQNLNKTVLagnysneTVTAMASMSesevsfelieallifikqknvpgaVLVFLPGWNLIFALMKHL 670
Cdd:PHA02653  377 EEE----------KKNIVTALK-------KYTPPKGSS------------------------GIVFVASVSQCEEYKKYL 415

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397    671 QSgRFGGSDFRILpcHSQIPREDQ--RKVFEPVPPgvtKIILSTNIAETSITIDDIVYVIDICKARMKLFTSHNNMtsya 748
Cdd:PHA02653  416 EK-RLPIYDFYII--HGKVPNIDEilEKVYSSKNP---SIIISTPYLESSVTIRNATHVYDTGRVYVPEPFGGKEM---- 485

                         410       420
                  ....*....|....*....|..
gi 3650397    749 tvWASKTNLEQRKGRAGRVRPG 770
Cdd:PHA02653  486 --FISKSMRTQRKGRVGRVSPG 505
DSRM smart00358
Double-stranded RNA binding motif;
5-69 9.83e-16

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 72.68  E-value: 9.83e-16
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 3650397        5 KSFFHSWCNKTKVEPQFES-RPTGPKHRQRFLCELRVAGFnYVGAGNSTVKKDAEKNAARDFVNFL 69
Cdd:smart00358    2 KSLLQELAQKRKLPPEYELvKEEGPDHAPRFTVTVKVGGK-RTGEGEGSSKKEAKQRAAEAALRSL 66
HELICc smart00490
helicase superfamily c-terminal domain;
679-766 2.37e-13

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 66.47  E-value: 2.37e-13
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397      679 DFRILPCHSQIPREDQRKVFEPVPPGVTKIILSTNIAETSITIDDIVYVIDICkarmklftshnnmtsyatVWASKTNLE 758
Cdd:smart00490   11 GIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYD------------------LPWSPASYI 72


                    ....*...
gi 3650397      759 QRKGRAGR 766
Cdd:smart00490   73 QRIGRAGR 80
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 635-767 4.12e-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: 66.85  E-value: 4.12e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397     635 ELIEALLIFIKQKNvPGAVLVFLPGWNLIFALMKHLQSGrfggsdFRILPCHSQIPREDQRKVFEPVPPGVTKIILSTNI 714
Cdd:pfam00271    1 EKLEALLELLKKER-GGKVLIFSQTKKTLEAELLLEKEG------IKVARLHGDLSQEEREEILEDFRKGKIDVLVATDV 73

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 3650397     715 AETSITIDDIVYVIDickarmklFTSHNNMTSYatvwasktnlEQRKGRAGRV 767
Cdd:pfam00271   74 AERGLDLPDVDLVIN--------YDLPWNPASY----------IQRIGRAGRA 108
DSRM smart00358
Double-stranded RNA binding motif;
167-237 9.46e-13

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 64.21  E-value: 9.46e-13
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 3650397      167 AKAKLHQFMQMNKIQADYRYTPV-GPDHARSFMAEMKIfvkqlNRTITGRESGSNKQTASKSCALSLVRQLY 237
Cdd:smart00358    1 PKSLLQELAQKRKLPPEYELVKEeGPDHAPRFTVTVKV-----GGKRTGEGEGSSKKEAKQRAAEAALRSLK 67
HA2 smart00847
Helicase associated domain (HA2) Add an annotation; This presumed domain is about 90 amino ...
 838-921 1.47e-12

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: 64.21  E-value: 1.47e-12
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397      838 LKCLNQNDDLSPLGKILARLPIEPRLGKMMVLGCIFLCGDALGAMAAYSGTFSeVFTLDLGQRRLSNHQKALGGtkHSDH 917
Cdd:smart00847    2 LGALDDDGRLTPLGRKMAELPLDPRLAKMLLAAAEFGCLDEILTIVAMLSVGD-PRPKEKREDADAARRRFADP--ESDH 78


                    ....
gi 3650397      918 VAML 921
Cdd:smart00847   79 LTLL 82
HA2 pfam04408
Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in ...
 831-920 1.63e-11

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: 61.87  E-value: 1.63e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397     831 AEVVLRDLKCLNQNDDLSPLGKILARLPIEPRLGKMMVLGCIFLCGD---ALGAMAAYSGTFSEVFTLDLGQRRLSN--- 904
Cdd:pfam04408    1 ALELLYYLGALDEDGELTPLGRKMAELPLDPRLAKMLLAAAELGCLDevlTIVAALSVRDPFVQPNFLDPRSAAKAArrr 80

                           90       100
                   ....*....|....*....|....
gi 3650397     905 --------HQKALGGTKHSDHVAM 920
Cdd:pfam04408   81 rraadekaRAKFARLDLEGDHLTL 104
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 5-69 4.42e-11

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: 59.55  E-value: 4.42e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 3650397       5 KSFFHSWCNKTKVEPQFE-SRPTGPKHRQRFLCELRVAGFNYvGAGNSTVKKDAEKNAARDFVNFL 69
Cdd:pfam00035    2 KSLLQEYAQKNGKPPPYEyVSEEGPPHSPKFTVTVKVDGKLY-GSGTGSSKKEAEQLAAEKALEKL 66
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 167-236 4.85e-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: 56.47  E-value: 4.85e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 3650397     167 AKAKLHQFMQMNKIQADYRYTPV-GPDHARSFMAEMKIfvkqlNRTITGRESGSNKQTASKSCALSLVRQL 236
Cdd:pfam00035    1 PKSLLQEYAQKNGKPPPYEYVSEeGPPHSPKFTVTVKV-----DGKLYGSGTGSSKKEAEQLAAEKALEKL 66
DSRM_SF cd00048
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
 9-63 4.20e-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: 50.75  E-value: 4.20e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 3650397     9 HSWCNKTK-VEPQFESRPTGPKHRQRFLCELRVAGFNYVGAGNStvKKDAEKNAAR 63
Cdd:cd00048    1 NELCQKNKwPPPEYETVEEGGPHNPRFTCTVTVNGQTFEGEGKS--KKEAKQAAAE 54
DSRM_SON-like cd19870
double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known ...
 6-63 4.35e-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: 45.73  E-value: 4.35e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397     6 SFFHSWCNKTKV-EPQFES-RPTGPKHRQRFLCELRVAGFNYVGAGNSTVKKDAEKNAAR 63
Cdd:cd19870    6 SALMELCNKRKWgPPEFRLvEESGPPHRKHFLFKVVVNGVEYQPSVASGNKKDAKAQAAT 65
DSRM_EIF2AK2-like cd19875
double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...
 6-69 4.43e-05

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: 42.64  E-value: 4.43e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 3650397     6 SFFHSWCNKTKVEPQFESRPTGPKHRQRFLCELRVaGFNYVGAGNSTVKKDAEKNAARDFVNFL 69
Cdd:cd19875    5 SALNEYCQKRGLSLEFVDVSVGPDHCPGFTASATI-DGIVFASATGTSKKEAKRAAAKLALKKL 67
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 402-545 6.28e-05

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: 44.93  E-value: 6.28e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397     402 VIVKGATGCGKTTqIAQYILEDYVNSGQGAwCNIAITQPRRISAISVSERIaVERNENIGESVGYSV---RFESCLPRPF 478
Cdd:pfam00270   17 VLVQAPTGSGKTL-AFLLPALEALDKLDNG-PQALVLAPTRELAEQIYEEL-KKLGKGLGLKVASLLggdSRKEQLEKLK 93

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397     479 GA-IMFCTIGVLLR--KLEAGLRGVSHVIVDEIHERDVNsDFILVVLRDMVHTYPDLRVILMSATIDTTL 545
Cdd:pfam00270   94 GPdILVGTPGRLLDllQERKLLKNLKLLVLDEAHRLLDM-GFGPDLEEILRRLPKKRQILLLSATLPRNL 162
DSRM_RNAse_III_family cd10845
double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...
 11-69 9.96e-05

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: 41.71  E-value: 9.96e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 3650397    11 WCNKTK-VEPQFES-RPTGPKHRQRFLCELRVAGFNY-VGAGNStvKKDAEKNAARDFVNFL 69
Cdd:cd10845   10 YLQKRGlPLPEYELvEEEGPDHNKTFTVEVKVNGKVIgEGTGRS--KKEAEQAAAKAALEKL 69
DSRM_EIF2AK2-like cd19875
double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...
 171-236 1.03e-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: 41.48  E-value: 1.03e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 3650397   171 LHQFMQMNKIQADYRYTPVGPDHARSFMAEMKIfvkqlNRTITGRESGSNKQTASKSCALSLVRQL 236
Cdd:cd19875    7 LNEYCQKRGLSLEFVDVSVGPDHCPGFTASATI-----DGIVFASATGTSKKEAKRAAAKLALKKL 67
DSRM_AtDRB-like_rpt2 cd19908
second double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding ...
 19-63 1.04e-04

second double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding proteins (AtDRBs)and similar proteins; This family includes a group of Arabidopsis thaliana double-stranded RNA-binding proteins (AtDRB1-5). They bind double-stranded RNA (dsRNA) and may be involved in RNA-mediated silencing. Members of this family contain two to three double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380737 [Multi-domain]  Cd Length: 69  Bit Score: 41.70  E-value: 1.04e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 3650397    19 PQFESRPTGPKHRQRFLCELRVAGFNYVGAGNSTvKKDAEKNAAR 63
Cdd:cd19908   19 PLYTTVRSGPGHVPTFTCTVEIAGITFTGEAAKT-KKQAEKSAAR 62
DSRM_AtDRB-like cd19878
double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding proteins ...
 5-62 4.13e-04

double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding proteins (AtDRBs)and similar proteins; This family includes a group of Arabidopsis thaliana double-stranded RNA-binding proteins (AtDRB1-5). They bind double-stranded RNA (dsRNA) and may be involved in RNA-mediated silencing. Members of this family contain two to three double-stranded RNA binding motifs (DSRMs). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380707 [Multi-domain]  Cd Length: 67  Bit Score: 39.81  E-value: 4.13e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 3650397     5 KSFFHSWCNKTKVE-PQFESRPTGPKHRQRFLCELRVAGFNYVGAGNSTvKKDAEKNAA 62
Cdd:cd19878    2 KNLLQEYAQKKKIPlPKYESAKSGPSHQPTFVSTVIVLGVRFSSEGAKN-KKQAEQSAA 59
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
26-64 8.63e-04

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 42.39  E-value: 8.63e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 3650397    26 TGPKHRQRFLCELRVAGFNY-VGAGNStvKKDAEKNAARD 64
Cdd:COG0571  183 EGPDHAKTFTVEVLVGGKVLgEGTGRS--KKEAEQAAAKA 220
DEXHc_Ski2 cd17921
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ...
 398-559 3.15e-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: 39.94  E-value: 3.15e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   398 DNSVVIVKGaTGCGKTTqIAQYILEDYVNSGQGawcNIAITQPRRisAIsVSERIA--VERNENIGESVGYSVRFESCLP 475
Cdd:cd17921   17 GDSVLVSAP-TSSGKTL-IAELAILRALATSGG---KAVYIAPTR--AL-VNQKEAdlRERFGPLGKNVGLLTGDPSVNK 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3650397   476 RPFGA--IMFCT---IGVLLRKL-EAGLRGVSHVIVDEIH-----ERDVnsdfIL-VVLRDMVHTYPDLRVILMSATID- 542
Cdd:cd17921   89 LLLAEadILVATpekLDLLLRNGgERLIQDVRLVVVDEAHligdgERGV----VLeLLLSRLLRINKNARFVGLSATLPn 164

                        170
                 ....*....|....*..
gi 3650397   543 TTLFSDYFGKCPVIEIP 559
Cdd:cd17921  165 AEDLAEWLGVEDLIRFD 181
DEXHc_LHR-like cd17922
DEXH-box helicase domain of LHR; Large helicase-related protein (LHR) is a DNA ...
 491-541 8.55e-03

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: 38.33  E-value: 8.55e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 3650397   491 RKLEAGLRGVSHVIVDEIHE-----RDVNSDFILVVLRDMVHtyPDLRVILMSATI 541
Cdd:cd17922  103 KKLRELFAGLRYVVVDEIHAllgskRGVQLELLLERLRKLTG--RPLRRIGLSATL 156
 
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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