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Conserved domains on  [gi|1764642986|gb|KAB5579853|]
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hypothetical protein PHYPO_G00199720 [Pangasianodon hypophthalmus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DEXHc_DHX9 cd17972
DEXH-box helicase domain of DEAH-box helicase 9; DEAH-box helicase 9 (DHX9, also known as ...
 335-568 1.34e-157

DEXH-box helicase domain of DEAH-box helicase 9; DEAH-box helicase 9 (DHX9, also known as ATP-dependent RNA helicase A or RHA and leukophysin or LKP) plays an important role in many cellular processes, including regulation of DNA replication, transcription, translation, microRNA biogenesis, RNA processing and transport, and maintenance of genomic stability. DHX9 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


:

Pssm-ID: 350730 [Multi-domain]  Cd Length: 234  Bit Score: 469.31  E-value: 1.34e-157
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  335 VQWSPPQVNWNPWTSSNIDEGPLAFCTPEQISSDLQSELHYQIDHDTNLQERLREREQLPVKKFEEEIMHTINSNPVVII 414
Cdd:cd17972      1 VPWSPPQSNWNPWTSSNIDEGPLAFATPEQISMDLKNELMYQREQDHNLQQILQERELLPVKKFREEILEAISNNPVVII 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  415 RGATGCGKTTQVPQYILDQYIRGGRASECNIVVTQPRRISAVSVAERVAYERGEDLGKSCGYSVRFESVLPRPHASVLFC 494
Cdd:cd17972     81 RGATGCGKTTQVPQYILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEVGKSCGYSVRFESVLPRPHASILFC 160

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1764642986  495 TVGVLLRKLEAGIRGISHVIVDEIHERDINTDFLMVVLRDVIHAFPDVRVVLMSATIDTTMFREYFFSCPIIEV 568
Cdd:cd17972    161 TVGVLLRKLEAGIRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPDLRVILMSATIDTSMFCEYFFNCPVIEV 234
HrpA super family cl34328
HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];
391-890 5.57e-118

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: 386.36  E-value: 5.57e-118
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  391 EQLPVKKFEEEIMHTINSNPVVIIRGATGCGKTTQVPQYILDQ-YIRGGRasecnIVVTQPRRISAVSVAERVAYERGED 469
Cdd:COG1643      8 PDLPVSAVLPELLAALRAHQVVVLAAPPGAGKTTQLPLALLELgWGAGGR-----IGMLEPRRLAARAAAERMAEELGEP 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  470 LGKSCGYSVRFESVLpRPHASVLFCTVGVLLRKLEA--GIRGISHVIVDEIHERDINTDFLMVVLRDVIHAF-PDVRVVL 546
Cdd:COG1643     83 VGETVGYRVRFEDKV-SAATRIEVVTEGILLRELQRdpELEGVDTVIFDEFHERSLNADLLLALLLDLQPALrPDLKLLV 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  547 MSATIDTTMFREYFFSCPIIEVFGRTYPVQqyfledciqmTQFVPPPSDKKRkdkdeeggeeevncnlvcgpeygpetkr 626
Cdd:COG1643    162 MSATLDAERFARLLGDAPVIESSGRTYPVE----------VRYRPLPADERD---------------------------- 203

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  627 smaqmneketpfeLIEALLKYVETL--QVAGAVLVFLPGWNLIYSMQKHLEmnAHFGSHrYRILPLHSQIPREEQRLVFE 704
Cdd:COG1643    204 -------------LEDAVADAVREAlaEEPGDILVFLPGEREIRRTAEALR--GRLPPD-TEILPLYGRLSAAEQDRAFA 267

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  705 PVPEGVTKVILSTNIAETSITINDVVYVIDSCKQKVKLFTAHNNMTNYATVWASKTNLEQRKGRAGRVRPGFCFHLCSKA 784
Cdd:COG1643    268 PAPHGRRRIVLATNIAETSLTVPGIRYVIDSGLARIPRYDPRSGVTRLPTERISQASANQRAGRAGRLAPGICYRLWSEE 347

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  785 RFEKLETHMTPEIFRTPLHEVALSIKLLRLGAIGHFlaKAIEPPPLDAVIEAEHTLRELDALDSNDELTPLGRILARLPI 864
Cdd:COG1643    348 DFARRPAFTDPEILRADLASLILELAAWGLGDPEDL--PFLDPPPARAIADARALLQELGALDADGRLTPLGRALARLPL 425

                          490       500
                   ....*....|....*....|....*.
gi 1764642986  865 EPRLGKMMIMGCILNVGDAACTISAA 890
Cdd:COG1643    426 DPRLARMLLAAAELGCLREAAILAAL 451
DSRM_DHX9_rpt2 cd19855
second double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; ...
 185-259 4.91e-45

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: 156.61  E-value: 4.91e-45
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1764642986  185 LDNAKARLNQFFQKEKIQTDYKYNQVGPDHNRSFIAEMTIFVKQLRRNIFAREHGSNKKLAAQSCALSLVRQLYH 259
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 2.63e-43

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: 151.27  E-value: 2.63e-43
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1764642986    3 DIKNFLYAWCGKKKLTPNYDIRAAGNKNRQKFMCEVRVDGFNYIGMGNSTNKKDAQANAARDFVNYLVR 71
Cdd:cd19854      1 EIKAFLYAWCGKKKLTPEYDIKEAGNKHRQRFKCEVRVEGFDYVGTGNATNKKDAQTNAARDFLNYLVR 69
OB_NTP_bind pfam07717
Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus ...
 998-1077 7.57e-20

Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus of the DEAD-box helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. There do seem to be a couple of instances where it occurs by itself -. The structure PDB:3i4u adopts an OB-fold. helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. This C-terminal domain of the yeast helicase contains an oligonucleotide/oligosaccharide-binding (OB)-fold which seems to be placed at the entrance of the putative nucleic acid cavity. It also constitutes the binding site for the G-patch-containing domain of Pfa1p. When found on DEAH/RHA helicases, this domain is central to the regulation of the helicase activity through its binding of both RNA and G-patch domain proteins.


:

Pssm-ID: 400182 [Multi-domain]  Cd Length: 82  Bit Score: 85.00  E-value: 7.57e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  998 LLTYGCYPNVCYHKEKRKILTT--EGRNALIHKSSVNCpfssQDPSYPSPFFVFGEKIRTRAISAKGMTMVSPLQLILFA 1075
Cdd:pfam07717    4 ALAAGLYPNVARRDPKGKGYTTlsDNQRVFIHPSSVLF----NEKTFPPEWVVYQELVETTKVYIRTVTAISPEWLLLFA 79


                   ..
gi 1764642986 1076 AK 1077
Cdd:pfam07717   80 PH 81
 
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 ...
 335-568 1.34e-157

DEXH-box helicase domain of DEAH-box helicase 9; DEAH-box helicase 9 (DHX9, also known as ATP-dependent RNA helicase A or RHA and leukophysin or LKP) plays an important role in many cellular processes, including regulation of DNA replication, transcription, translation, microRNA biogenesis, RNA processing and transport, and maintenance of genomic stability. DHX9 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350730 [Multi-domain]  Cd Length: 234  Bit Score: 469.31  E-value: 1.34e-157
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  335 VQWSPPQVNWNPWTSSNIDEGPLAFCTPEQISSDLQSELHYQIDHDTNLQERLREREQLPVKKFEEEIMHTINSNPVVII 414
Cdd:cd17972      1 VPWSPPQSNWNPWTSSNIDEGPLAFATPEQISMDLKNELMYQREQDHNLQQILQERELLPVKKFREEILEAISNNPVVII 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  415 RGATGCGKTTQVPQYILDQYIRGGRASECNIVVTQPRRISAVSVAERVAYERGEDLGKSCGYSVRFESVLPRPHASVLFC 494
Cdd:cd17972     81 RGATGCGKTTQVPQYILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEVGKSCGYSVRFESVLPRPHASILFC 160

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1764642986  495 TVGVLLRKLEAGIRGISHVIVDEIHERDINTDFLMVVLRDVIHAFPDVRVVLMSATIDTTMFREYFFSCPIIEV 568
Cdd:cd17972    161 TVGVLLRKLEAGIRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPDLRVILMSATIDTSMFCEYFFNCPVIEV 234
HrpA COG1643
HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];
391-890 5.57e-118

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


Pssm-ID: 441249 [Multi-domain]  Cd Length: 836  Bit Score: 386.36  E-value: 5.57e-118
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  391 EQLPVKKFEEEIMHTINSNPVVIIRGATGCGKTTQVPQYILDQ-YIRGGRasecnIVVTQPRRISAVSVAERVAYERGED 469
Cdd:COG1643      8 PDLPVSAVLPELLAALRAHQVVVLAAPPGAGKTTQLPLALLELgWGAGGR-----IGMLEPRRLAARAAAERMAEELGEP 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  470 LGKSCGYSVRFESVLpRPHASVLFCTVGVLLRKLEA--GIRGISHVIVDEIHERDINTDFLMVVLRDVIHAF-PDVRVVL 546
Cdd:COG1643     83 VGETVGYRVRFEDKV-SAATRIEVVTEGILLRELQRdpELEGVDTVIFDEFHERSLNADLLLALLLDLQPALrPDLKLLV 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  547 MSATIDTTMFREYFFSCPIIEVFGRTYPVQqyfledciqmTQFVPPPSDKKRkdkdeeggeeevncnlvcgpeygpetkr 626
Cdd:COG1643    162 MSATLDAERFARLLGDAPVIESSGRTYPVE----------VRYRPLPADERD---------------------------- 203

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  627 smaqmneketpfeLIEALLKYVETL--QVAGAVLVFLPGWNLIYSMQKHLEmnAHFGSHrYRILPLHSQIPREEQRLVFE 704
Cdd:COG1643    204 -------------LEDAVADAVREAlaEEPGDILVFLPGEREIRRTAEALR--GRLPPD-TEILPLYGRLSAAEQDRAFA 267

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  705 PVPEGVTKVILSTNIAETSITINDVVYVIDSCKQKVKLFTAHNNMTNYATVWASKTNLEQRKGRAGRVRPGFCFHLCSKA 784
Cdd:COG1643    268 PAPHGRRRIVLATNIAETSLTVPGIRYVIDSGLARIPRYDPRSGVTRLPTERISQASANQRAGRAGRLAPGICYRLWSEE 347

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  785 RFEKLETHMTPEIFRTPLHEVALSIKLLRLGAIGHFlaKAIEPPPLDAVIEAEHTLRELDALDSNDELTPLGRILARLPI 864
Cdd:COG1643    348 DFARRPAFTDPEILRADLASLILELAAWGLGDPEDL--PFLDPPPARAIADARALLQELGALDADGRLTPLGRALARLPL 425

                          490       500
                   ....*....|....*....|....*.
gi 1764642986  865 EPRLGKMMIMGCILNVGDAACTISAA 890
Cdd:COG1643    426 DPRLARMLLAAAELGCLREAAILAAL 451
DEAH_box_HrpA TIGR01967
RNA helicase HrpA; This model represents HrpA, one of two related but uncharacterized DEAH-box ...
 386-1068 7.42e-86

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: 305.15  E-value: 7.42e-86
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  386 RLREREQLPVKKFEEEIMHTINSNPVVIIRGATGCGKTTQVPQYILDQyirgGRASECNIVVTQPRRISAVSVAERVAYE 465
Cdd:TIGR01967   59 EIRYPDNLPVSAKREDIAEAIAENQVVIIAGETGSGKTTQLPKICLEL----GRGSHGLIGHTQPRRLAARTVAQRIAEE 134

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  466 RGEDLGKSCGYSVRFESVLpRPHASVLFCTVGVLLRKLEAGiRGISH---VIVDEIHERDINTDFLMVVLRDVIHAFPDV 542
Cdd:TIGR01967  135 LGTPLGEKVGYKVRFHDQV-SSNTLVKLMTDGILLAETQQD-RFLSRydtIIIDEAHERSLNIDFLLGYLKQLLPRRPDL 212

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  543 RVVLMSATIDTTMFREYFFSCPIIEVFGRTYPVQQYFledciqmtqfvpppsdkkrkdkdeeggeeevncnlvcgpeygp 622
Cdd:TIGR01967  213 KIIITSATIDPERFSRHFNNAPIIEVSGRTYPVEVRY------------------------------------------- 249

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  623 etkRSMAQMNEkETPFELIEALLKYVETL--QVAGAVLVFLPGWNLIYSMQKHLEmnahfgSHRYR---ILPLHSQIPRE 697
Cdd:TIGR01967  250 ---RPLVEEQE-DDDLDQLEAILDAVDELfaEGPGDILIFLPGEREIRDAAEILR------KRNLRhteILPLYARLSNK 319

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  698 EQRLVFEpvPEGVTKVILSTNIAETSITINDVVYVIDSCKQKVKLFTAHNNMTNYATVWASKTNLEQRKGRAGRVRPGFC 777
Cdd:TIGR01967  320 EQQRVFQ--PHSGRRIVLATNVAETSLTVPGIHYVIDTGTARISRYSYRTKVQRLPIEPISQASANQRKGRCGRVAPGIC 397

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  778 FHLCSKARFEKLETHMTPEIFRTPLHEVALSIKLLRLGAIGHFlaKAIEPPPLDAVIEAEHTLRELDALDSND---ELTP 854
Cdd:TIGR01967  398 IRLYSEEDFNSRPEFTDPEILRTNLASVILQMLALRLGDIAAF--PFIEAPDPRAIRDGFRLLEELGALDDDEaepQLTP 475

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  855 LGRILARLPIEPRLGKMMI----MGCI--LNVGDAACTISAASCFSEPFISEGKRlgfVHRNFAGARfSDHVALLSVFQA 928
Cdd:TIGR01967  476 IGRQLAQLPVDPRLARMLLeahrLGCLqeVLIIASALSIQDPRERPMEKQQAADQ---AHARFKDPR-SDFLSRVNLWRH 551

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  929 WDEVRMGGEEAEAR-FCEHKRLHMSTLRMTWEAKVQLKEILINTGFPeeclmnqvFNNVgPDNNLDVVISLLTyGCYPNV 1007
Cdd:TIGR01967  552 IEEQRQALSANQFRnACRKQYLNYLRVREWQDIYRQLTQVVKELGLK--------LNEE-PADYDAIHKALLS-GLLSQI 621

                          650       660       670       680       690       700
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1764642986 1008 CYHKEKRKILTTEGRNALIHKSSvncPFSSQDPSypspFFVFGEKIRTRAISAKGMTMVSP 1068
Cdd:TIGR01967  622 GMKDEKHEYDGARGRKFHIFPGS---PLFKKPPK----WVMAAELVETSKLYARLVAKIEP 675
SF2_C_RHA cd18791
C-terminal helicase domain of the RNA helicase A (RHA) family helicases; The RNA helicase A ...
 573-781 4.17e-70

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: 231.65  E-value: 4.17e-70
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  573 YPVQQYFLEDCIQMTQfvpppsdkkrkdkdeeggeeevncnlvcgpeygpetkrsMAQMNEKETPFELIEALLKYVETLQ 652
Cdd:cd18791      1 FPVEVYYLEDILELLG---------------------------------------ISSEKEDPDYVDAAVRLILQIHRTE 41

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  653 VAGAVLVFLPGWNLIYSMQKHLEMNAHFGS-HRYRILPLHSQIPREEQRLVFEPVPEGVTKVILSTNIAETSITINDVVY 731
Cdd:cd18791     42 EPGDILVFLPGQEEIERLCELLREELLSPDlGKLLVLPLHSSLPPEEQQRVFEPPPPGVRKVVLATNIAETSITIPGVVY 121

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|
gi 1764642986  732 VIDSCKQKVKLFTAHNNMTNYATVWASKTNLEQRKGRAGRVRPGFCFHLC 781
Cdd:cd18791    122 VIDSGLVKEKVYDPRTGLSSLVTVWISKASAEQRAGRAGRTRPGKCYRLY 171
PRK11664 PRK11664
ATP-dependent RNA helicase HrpB; Provisional
 392-873 8.25e-68

ATP-dependent RNA helicase HrpB; Provisional


Pssm-ID: 236950 [Multi-domain]  Cd Length: 812  Bit Score: 245.22  E-value: 8.25e-68
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  392 QLPVKKFEEEIMHTINSNPVVIIRGATGCGKTTQVPQYILDQYIRGGRasecnIVVTQPRRISAVSVAERVAYERGEDLG 471
Cdd:PRK11664     3 SLPVAAVLPELLTALKTAPQVLLKAPTGAGKSTWLPLQLLQHGGINGK-----IIMLEPRRLAARNVAQRLAEQLGEKPG 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  472 KSCGYSVRFES-VLPRPHASVLfcTVGVLLRKLE--AGIRGISHVIVDEIHERDINTDFLMVVLRDVIHAF-PDVRVVLM 547
Cdd:PRK11664    78 ETVGYRMRAESkVGPNTRLEVV--TEGILTRMIQrdPELSGVGLVILDEFHERSLQADLALALLLDVQQGLrDDLKLLIM 155

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  548 SATIDTTMFREYFFSCPIIEVFGRTYPVQqyfledciqmTQFVPPPSDKKrkdkdeeggeeevncnlvcgpeYGPETKRS 627
Cdd:PRK11664   156 SATLDNDRLQQLLPDAPVIVSEGRSFPVE----------RRYQPLPAHQR----------------------FDEAVARA 203

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  628 MAQMNEKETpfelieallkyvetlqvaGAVLVFLPGWNLIYSMQKHLEmnAHFGSHrYRILPLHSQIPREEQRLVFEPVP 707
Cdd:PRK11664   204 TAELLRQES------------------GSLLLFLPGVGEIQRVQEQLA--SRVASD-VLLCPLYGALSLAEQQKAILPAP 262

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  708 EGVTKVILSTNIAETSITINDVVYVIDSCKQKVKLFTAHNNMTNYATVWASKTNLEQRKGRAGRVRPGFCFHLCSKARFE 787
Cdd:PRK11664   263 AGRRKVVLATNIAETSLTIEGIRLVVDSGLERVARFDPKTGLTRLVTQRISQASMTQRAGRAGRLEPGICLHLYSKEQAE 342

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  788 KLETHMTPEIFRTPLHEVALSikLLRLGAIGHFLAKAIEPPPLDAVIEAEHTLRELDALDSNDELTPLGRILARLPIEPR 867
Cdd:PRK11664   343 RAAAQSEPEILHSDLSGLLLE--LLQWGCHDPAQLSWLDQPPAAALAAAKRLLQQLGALDGQGRLTARGRKMAALGNDPR 420


                   ....*.
gi 1764642986  868 LGKMMI 873
Cdd:PRK11664   421 LAAMLV 426
DSRM_DHX9_rpt2 cd19855
second double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; ...
 185-259 4.91e-45

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: 156.61  E-value: 4.91e-45
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1764642986  185 LDNAKARLNQFFQKEKIQTDYKYNQVGPDHNRSFIAEMTIFVKQLRRNIFAREHGSNKKLAAQSCALSLVRQLYH 259
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 2.63e-43

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: 151.27  E-value: 2.63e-43
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1764642986    3 DIKNFLYAWCGKKKLTPNYDIRAAGNKNRQKFMCEVRVDGFNYIGMGNSTNKKDAQANAARDFVNYLVR 71
Cdd:cd19854      1 EIKAFLYAWCGKKKLTPEYDIKEAGNKHRQRFKCEVRVEGFDYVGTGNATNKKDAQTNAARDFLNYLVR 69
DEXDc smart00487
DEAD-like helicases superfamily;
402-578 2.34e-23

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 99.10  E-value: 2.34e-23
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986   402 IMHTINSNPVVIIRGATGCGKTTQVPQYILDQYIRGGRaseCNIVVTQPRRISAVSVAERVAYERGEDLGKSCGY----- 476
Cdd:smart00487   17 IEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKG---GRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLyggds 93

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986   477 SVRFESVLPRPHASVLFCTVGVLLRKLEAG---IRGISHVIVDEIHERDiNTDFLMVVLRDVIHAFPDVRVVLMSATI-- 551
Cdd:smart00487   94 KREQLRKLESGKTDILVTTPGRLLDLLENDklsLSNVDLVILDEAHRLL-DGGFGDQLEKLLKLLPKNVQLLLLSATPpe 172

                           170       180
                    ....*....|....*....|....*....
gi 1764642986   552 DTTMFREYFFSCPIIEVFGRTYP--VQQY 578
Cdd:smart00487  173 EIENLLELFLNDPVFIDVGFTPLepIEQF 201
HA2 smart00847
Helicase associated domain (HA2) Add an annotation; This presumed domain is about 90 amino ...
 842-923 3.88e-21

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: 88.48  E-value: 3.88e-21
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986   842 ELDALDSNDELTPLGRILARLPIEPRLGKMMIMGCILNVGDAACTISAASCFSEPFISE-GKRLGFVHRNFAGARfSDHV 920
Cdd:smart00847    1 ELGALDDDGRLTPLGRKMAELPLDPRLAKMLLAAAEFGCLDEILTIVAMLSVGDPRPKEkREDADAARRRFADPE-SDHL 79


                    ...
gi 1764642986   921 ALL 923
Cdd:smart00847   80 TLL 82
HA2 pfam04408
Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in ...
 836-922 3.21e-20

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: 86.91  E-value: 3.21e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  836 AEHTLRELDALDSNDELTPLGRILARLPIEPRLGKMMIMGCILNVGDAACTISAASCFSEPFISEG-------------- 901
Cdd:pfam04408    1 ALELLYYLGALDEDGELTPLGRKMAELPLDPRLAKMLLAAAELGCLDEVLTIVAALSVRDPFVQPNfldprsaakaarrr 80

                           90       100
                   ....*....|....*....|....
gi 1764642986  902 KRLGF--VHRNFAGARF-SDHVAL 922
Cdd:pfam04408   81 RRAADekARAKFARLDLeGDHLTL 104
OB_NTP_bind pfam07717
Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus ...
 998-1077 7.57e-20

Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus of the DEAD-box helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. There do seem to be a couple of instances where it occurs by itself -. The structure PDB:3i4u adopts an OB-fold. helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. This C-terminal domain of the yeast helicase contains an oligonucleotide/oligosaccharide-binding (OB)-fold which seems to be placed at the entrance of the putative nucleic acid cavity. It also constitutes the binding site for the G-patch-containing domain of Pfa1p. When found on DEAH/RHA helicases, this domain is central to the regulation of the helicase activity through its binding of both RNA and G-patch domain proteins.


Pssm-ID: 400182 [Multi-domain]  Cd Length: 82  Bit Score: 85.00  E-value: 7.57e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  998 LLTYGCYPNVCYHKEKRKILTT--EGRNALIHKSSVNCpfssQDPSYPSPFFVFGEKIRTRAISAKGMTMVSPLQLILFA 1075
Cdd:pfam07717    4 ALAAGLYPNVARRDPKGKGYTTlsDNQRVFIHPSSVLF----NEKTFPPEWVVYQELVETTKVYIRTVTAISPEWLLLFA 79


                   ..
gi 1764642986 1076 AK 1077
Cdd:pfam07717   80 PH 81
DSRM smart00358
Double-stranded RNA binding motif;
5-69 1.75e-16

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 74.99  E-value: 1.75e-16
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1764642986     5 KNFLYAWCGKKKLTPNYD-IRAAGNKNRQKFMCEVRVDGFnYIGMGNSTNKKDAQANAARDFVNYL 69
Cdd:smart00358    2 KSLLQELAQKRKLPPEYElVKEEGPDHAPRFTVTVKVGGK-RTGEGEGSSKKEAKQRAAEAALRSL 66
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 5-69 1.86e-12

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: 63.40  E-value: 1.86e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1764642986    5 KNFLYAWCGKKKLTPNYD-IRAAGNKNRQKFMCEVRVDGFNYiGMGNSTNKKDAQANAARDFVNYL 69
Cdd:pfam00035    2 KSLLQEYAQKNGKPPPYEyVSEEGPPHSPKFTVTVKVDGKLY-GSGTGSSKKEAEQLAAEKALEKL 66
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 188-257 5.50e-12

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: 61.86  E-value: 5.50e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1764642986  188 AKARLNQFFQKEKIQTDYKYN-QVGPDHNRSFIAEMTIfvkqlRRNIFAREHGSNKKLAAQSCALSLVRQL 257
Cdd:pfam00035    1 PKSLLQEYAQKNGKPPPYEYVsEEGPPHSPKFTVTVKV-----DGKLYGSGTGSSKKEAEQLAAEKALEKL 66
DSRM smart00358
Double-stranded RNA binding motif;
188-258 1.40e-11

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 60.74  E-value: 1.40e-11
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1764642986   188 AKARLNQFFQKEKIQTDYKY-NQVGPDHNRSFIAEMTIfvkqlRRNIFAREHGSNKKLAAQSCALSLVRQLY 258
Cdd:smart00358    1 PKSLLQELAQKRKLPPEYELvKEEGPDHAPRFTVTVKV-----GGKRTGEGEGSSKKEAKQRAAEAALRSLK 67
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 400-554 6.31e-07

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: 50.70  E-value: 6.31e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  400 EEIMHTINSNPVVIIRGATGCGKTT--QVP--QYILDQYiRGGRAsecnIVVTqPRRISAVSVAERVayergEDLGKSCG 475
Cdd:pfam00270    5 AEAIPAILEGRDVLVQAPTGSGKTLafLLPalEALDKLD-NGPQA----LVLA-PTRELAEQIYEEL-----KKLGKGLG 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  476 YSVRFE----------SVLPRPHasVLFCTVGVLLR--KLEAGIRGISHVIVDEIHErdINTDFLMVVLRDVIHAFP-DV 542
Cdd:pfam00270   74 LKVASLlggdsrkeqlEKLKGPD--ILVGTPGRLLDllQERKLLKNLKLLVLDEAHR--LLDMGFGPDLEEILRRLPkKR 149

                          170
                   ....*....|..
gi 1764642986  543 RVVLMSATIDTT 554
Cdd:pfam00270  150 QILLLSATLPRN 161
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
187-257 1.95e-03

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 41.24  E-value: 1.95e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1764642986  187 NAKARLNQFFQKEKIQT-DYK-YNQVGPDHNRSFIAEmtifVKqLRRNIFAREHGSNKKLAAQSCALSLVRQL 257
Cdd:COG0571    158 DYKTALQEWLQARGLPLpEYEvVEEEGPDHAKTFTVE----VL-VGGKVLGEGTGRSKKEAEQAAAKAALEKL 225
Dob10 COG4581
Superfamily II RNA helicase [Replication, recombination and repair];
487-558 5.97e-03

Superfamily II RNA helicase [Replication, recombination and repair];


Pssm-ID: 443638 [Multi-domain]  Cd Length: 751  Bit Score: 40.69  E-value: 5.97e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  487 PHASVLFCTVGVLLRKLEAG---IRGISHVIVDEIHerdintdFL---------MVVLrdvIHAFPDVRVVLMSATI-DT 553
Cdd:COG4581    108 PDAPIVVMTTEILRNMLYREgadLEDVGVVVMDEFH-------YLadpdrgwvwEEPI---IHLPARVQLVLLSATVgNA 177


                   ....*
gi 1764642986  554 TMFRE 558
Cdd:COG4581    178 EEFAE 182
 
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 ...
 335-568 1.34e-157

DEXH-box helicase domain of DEAH-box helicase 9; DEAH-box helicase 9 (DHX9, also known as ATP-dependent RNA helicase A or RHA and leukophysin or LKP) plays an important role in many cellular processes, including regulation of DNA replication, transcription, translation, microRNA biogenesis, RNA processing and transport, and maintenance of genomic stability. DHX9 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350730 [Multi-domain]  Cd Length: 234  Bit Score: 469.31  E-value: 1.34e-157
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  335 VQWSPPQVNWNPWTSSNIDEGPLAFCTPEQISSDLQSELHYQIDHDTNLQERLREREQLPVKKFEEEIMHTINSNPVVII 414
Cdd:cd17972      1 VPWSPPQSNWNPWTSSNIDEGPLAFATPEQISMDLKNELMYQREQDHNLQQILQERELLPVKKFREEILEAISNNPVVII 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  415 RGATGCGKTTQVPQYILDQYIRGGRASECNIVVTQPRRISAVSVAERVAYERGEDLGKSCGYSVRFESVLPRPHASVLFC 494
Cdd:cd17972     81 RGATGCGKTTQVPQYILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEVGKSCGYSVRFESVLPRPHASILFC 160

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1764642986  495 TVGVLLRKLEAGIRGISHVIVDEIHERDINTDFLMVVLRDVIHAFPDVRVVLMSATIDTTMFREYFFSCPIIEV 568
Cdd:cd17972    161 TVGVLLRKLEAGIRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPDLRVILMSATIDTSMFCEYFFNCPVIEV 234
HrpA COG1643
HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];
391-890 5.57e-118

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


Pssm-ID: 441249 [Multi-domain]  Cd Length: 836  Bit Score: 386.36  E-value: 5.57e-118
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  391 EQLPVKKFEEEIMHTINSNPVVIIRGATGCGKTTQVPQYILDQ-YIRGGRasecnIVVTQPRRISAVSVAERVAYERGED 469
Cdd:COG1643      8 PDLPVSAVLPELLAALRAHQVVVLAAPPGAGKTTQLPLALLELgWGAGGR-----IGMLEPRRLAARAAAERMAEELGEP 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  470 LGKSCGYSVRFESVLpRPHASVLFCTVGVLLRKLEA--GIRGISHVIVDEIHERDINTDFLMVVLRDVIHAF-PDVRVVL 546
Cdd:COG1643     83 VGETVGYRVRFEDKV-SAATRIEVVTEGILLRELQRdpELEGVDTVIFDEFHERSLNADLLLALLLDLQPALrPDLKLLV 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  547 MSATIDTTMFREYFFSCPIIEVFGRTYPVQqyfledciqmTQFVPPPSDKKRkdkdeeggeeevncnlvcgpeygpetkr 626
Cdd:COG1643    162 MSATLDAERFARLLGDAPVIESSGRTYPVE----------VRYRPLPADERD---------------------------- 203

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  627 smaqmneketpfeLIEALLKYVETL--QVAGAVLVFLPGWNLIYSMQKHLEmnAHFGSHrYRILPLHSQIPREEQRLVFE 704
Cdd:COG1643    204 -------------LEDAVADAVREAlaEEPGDILVFLPGEREIRRTAEALR--GRLPPD-TEILPLYGRLSAAEQDRAFA 267

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  705 PVPEGVTKVILSTNIAETSITINDVVYVIDSCKQKVKLFTAHNNMTNYATVWASKTNLEQRKGRAGRVRPGFCFHLCSKA 784
Cdd:COG1643    268 PAPHGRRRIVLATNIAETSLTVPGIRYVIDSGLARIPRYDPRSGVTRLPTERISQASANQRAGRAGRLAPGICYRLWSEE 347

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  785 RFEKLETHMTPEIFRTPLHEVALSIKLLRLGAIGHFlaKAIEPPPLDAVIEAEHTLRELDALDSNDELTPLGRILARLPI 864
Cdd:COG1643    348 DFARRPAFTDPEILRADLASLILELAAWGLGDPEDL--PFLDPPPARAIADARALLQELGALDADGRLTPLGRALARLPL 425

                          490       500
                   ....*....|....*....|....*.
gi 1764642986  865 EPRLGKMMIMGCILNVGDAACTISAA 890
Cdd:COG1643    426 DPRLARMLLAAAELGCLREAAILAAL 451
DEAH_box_HrpA TIGR01967
RNA helicase HrpA; This model represents HrpA, one of two related but uncharacterized DEAH-box ...
 386-1068 7.42e-86

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: 305.15  E-value: 7.42e-86
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  386 RLREREQLPVKKFEEEIMHTINSNPVVIIRGATGCGKTTQVPQYILDQyirgGRASECNIVVTQPRRISAVSVAERVAYE 465
Cdd:TIGR01967   59 EIRYPDNLPVSAKREDIAEAIAENQVVIIAGETGSGKTTQLPKICLEL----GRGSHGLIGHTQPRRLAARTVAQRIAEE 134

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  466 RGEDLGKSCGYSVRFESVLpRPHASVLFCTVGVLLRKLEAGiRGISH---VIVDEIHERDINTDFLMVVLRDVIHAFPDV 542
Cdd:TIGR01967  135 LGTPLGEKVGYKVRFHDQV-SSNTLVKLMTDGILLAETQQD-RFLSRydtIIIDEAHERSLNIDFLLGYLKQLLPRRPDL 212

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  543 RVVLMSATIDTTMFREYFFSCPIIEVFGRTYPVQQYFledciqmtqfvpppsdkkrkdkdeeggeeevncnlvcgpeygp 622
Cdd:TIGR01967  213 KIIITSATIDPERFSRHFNNAPIIEVSGRTYPVEVRY------------------------------------------- 249

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  623 etkRSMAQMNEkETPFELIEALLKYVETL--QVAGAVLVFLPGWNLIYSMQKHLEmnahfgSHRYR---ILPLHSQIPRE 697
Cdd:TIGR01967  250 ---RPLVEEQE-DDDLDQLEAILDAVDELfaEGPGDILIFLPGEREIRDAAEILR------KRNLRhteILPLYARLSNK 319

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  698 EQRLVFEpvPEGVTKVILSTNIAETSITINDVVYVIDSCKQKVKLFTAHNNMTNYATVWASKTNLEQRKGRAGRVRPGFC 777
Cdd:TIGR01967  320 EQQRVFQ--PHSGRRIVLATNVAETSLTVPGIHYVIDTGTARISRYSYRTKVQRLPIEPISQASANQRKGRCGRVAPGIC 397

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  778 FHLCSKARFEKLETHMTPEIFRTPLHEVALSIKLLRLGAIGHFlaKAIEPPPLDAVIEAEHTLRELDALDSND---ELTP 854
Cdd:TIGR01967  398 IRLYSEEDFNSRPEFTDPEILRTNLASVILQMLALRLGDIAAF--PFIEAPDPRAIRDGFRLLEELGALDDDEaepQLTP 475

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  855 LGRILARLPIEPRLGKMMI----MGCI--LNVGDAACTISAASCFSEPFISEGKRlgfVHRNFAGARfSDHVALLSVFQA 928
Cdd:TIGR01967  476 IGRQLAQLPVDPRLARMLLeahrLGCLqeVLIIASALSIQDPRERPMEKQQAADQ---AHARFKDPR-SDFLSRVNLWRH 551

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  929 WDEVRMGGEEAEAR-FCEHKRLHMSTLRMTWEAKVQLKEILINTGFPeeclmnqvFNNVgPDNNLDVVISLLTyGCYPNV 1007
Cdd:TIGR01967  552 IEEQRQALSANQFRnACRKQYLNYLRVREWQDIYRQLTQVVKELGLK--------LNEE-PADYDAIHKALLS-GLLSQI 621

                          650       660       670       680       690       700
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1764642986 1008 CYHKEKRKILTTEGRNALIHKSSvncPFSSQDPSypspFFVFGEKIRTRAISAKGMTMVSP 1068
Cdd:TIGR01967  622 GMKDEKHEYDGARGRKFHIFPGS---PLFKKPPK----WVMAAELVETSKLYARLVAKIEP 675
DEXHc_RHA-like cd17917
DEXH-box helicase domain of DEAD-like helicase RHA family proteins; The RNA helicase A (RHA) ...
 409-568 2.23e-79

DEXH-box helicase domain of DEAD-like helicase RHA family proteins; The RNA helicase A (RHA) family includes RHA, also called DEAH-box helicase 9 (DHX9), DHX8, DHX15-16, DHX32-38, and many others. The RHA family belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438707 [Multi-domain]  Cd Length: 159  Bit Score: 257.39  E-value: 2.23e-79
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  409 NPVVIIRGATGCGKTTQVPQYILDQYIRGGRasECNIVVTQPRRISAVSVAERVAYERGEDLGKSCGYSVRFESVLPrPH 488
Cdd:cd17917      1 NQVVVIVGETGSGKTTQVPQFLLEDGLAKGG--KGRIVCTQPRRIAAISVAERVAEERGEKLGEEVGYQIRFESKTS-SK 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  489 ASVLFCTVGVLLRKLEAG--IRGISHVIVDEIHERDINTDFLMVVLRDVIHAFPDVRVVLMSATIDTTMFREYFFSCPII 566
Cdd:cd17917     78 TRIKFCTDGILLRELLSDplLSGYSHVILDEAHERSLDTDFLLGLLKDLLRKRPDLKVILMSATLDAEKFSSYFGGAPVI 157


                   ..
gi 1764642986  567 EV 568
Cdd:cd17917    158 HI 159
DEAH_box_HrpB TIGR01970
ATP-dependent helicase HrpB; This model represents HrpB, one of two related but ...
 393-889 3.18e-75

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: 267.02  E-value: 3.18e-75
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  393 LPVKKFEEEIMHTINSNPVVIIRGATGCGKTTQVPQYILDQYIRGGRasecnIVVTQPRRISAVSVAERVAYERGEDLGK 472
Cdd:TIGR01970    1 LPIHAVLPALRDALAAHPQVVLEAPPGAGKSTAVPLALLDAPGIGGK-----IIMLEPRRLAARSAAQRLASQLGEAVGQ 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  473 SCGYSVRFES-VLPRPHASVLfcTVGVLLRKLEA--GIRGISHVIVDEIHERDINTDFLMVVLRDVIHAF-PDVRVVLMS 548
Cdd:TIGR01970   76 TVGYRVRGENkVSRRTRLEVV--TEGILTRMIQDdpELDGVGALIFDEFHERSLDADLGLALALDVQSSLrEDLKILAMS 153

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  549 ATIDTTMFREYFFSCPIIEVFGRTYPVQqyfledciqmTQFVPPPSDKKrkdkdeeggeeevncnlvcgpeYGPETKRSM 628
Cdd:TIGR01970  154 ATLDGERLSSLLPDAPVVESEGRSFPVE----------IRYLPLRGDQR----------------------LEDAVSRAV 201

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  629 AQMNEKETpfelieallkyvetlqvaGAVLVFLPGWNLIYSMQKHLemNAHFGShRYRILPLHSQIPREEQRLVFEPVPE 708
Cdd:TIGR01970  202 EHALASET------------------GSILVFLPGQAEIRRVQEQL--AERLDS-DVLICPLYGELSLAAQDRAIKPDPQ 260

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  709 GVTKVILSTNIAETSITINDVVYVIDSCKQKVKLFTAHNNMTNYATVWASKTNLEQRKGRAGRVRPGFCFHLCSKARFEK 788
Cdd:TIGR01970  261 GRRKVVLATNIAETSLTIEGIRVVIDSGLARVARFDPKTGITRLETVRISQASATQRAGRAGRLEPGVCYRLWSEEQHQR 340

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  789 LETHMTPEIFRTPLheVALSIKLLRLGAIGHFLAKAIEPPPLDAVIEAEHTLRELDALDSNDELTPLGRILARLPIEPRL 868
Cdd:TIGR01970  341 LPAQDEPEILQADL--SGLALELAQWGAKDPSDLRWLDAPPSVALAAARQLLQRLGALDAQGRLTAHGKAMAALGCHPRL 418

                          490       500
                   ....*....|....*....|.
gi 1764642986  869 GKMMIMGCILNVGDAACTISA 889
Cdd:TIGR01970  419 AAMLLSAHSTGLAALACDLAA 439
DEXHc_DHX30 cd17976
DEXH-box helicase domain of DEAH-box helicase 30; DEAH-box helicase 30 (DHX30) plays an ...
 393-568 3.45e-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: 243.55  E-value: 3.45e-74
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  393 LPVKKFEEEIMHTINSNPVVIIRGATGCGKTTQVPQYILDQYIRGGRASECNIVVTQPRRISAVSVAERVAYERGEDLGK 472
Cdd:cd17976      1 LPVDSHKESILSAIEQNPVVVISGDTGCGKTTRIPQFILEDYVLRGRGARCNVVITQPRRISAVSVAQRVAHELGPNLRR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  473 SCGYSVRFESVLPRPHASVLFCTVGVLLRKLE--AGIRGISHVIVDEIHERDINTDFLMVVLRDVIHAFPDVRVVLMSAT 550
Cdd:cd17976     81 NVGYQVRLESRPPPRGGALLFCTVGVLLKKLQsnPRLEGVSHVIVDEVHERDVNTDFLLILLKGVLQLNPELRVVLMSAT 160

                          170
                   ....*....|....*...
gi 1764642986  551 IDTTMFREYFFSCPIIEV 568
Cdd:cd17976    161 GDNQRLSRYFGGCPVVRV 178
DEXHc_DHX36 cd17981
DEXH-box helicase domain of DEAH-box helicase 36; DEAH-box helicase 36 (DHX36, also known as ...
 393-568 3.37e-70

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: 232.43  E-value: 3.37e-70
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  393 LPVKKFEEEIMHTINSNPVVIIRGATGCGKTTQVPQYILDQYIRGGRASECNIVVTQPRRISAVSVAERVAYERGED--L 470
Cdd:cd17981      1 LPSYGMKQEIINMIDNNQVTVISGETGCGKTTQVTQFILDDAIERGKGSSCRIVCTQPRRISAISVAERVAAERAEScgL 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  471 GKSCGYSVRFESVLPRPHASVLFCTVGVLLRKLEAG--IRGISHVIVDEIHERDINTDFLMVVLRDVIHAFPDVRVVLMS 548
Cdd:cd17981     81 GNSTGYQIRLESRKPRKQGSILYCTTGIVLQWLQSDphLSNVSHLVLDEIHERNLQSDVLMGIVKDLLPFRSDLKVILMS 160

                          170       180
                   ....*....|....*....|
gi 1764642986  549 ATIDTTMFREYFFSCPIIEV 568
Cdd:cd17981    161 ATLNAEKFSDYFNNCPMIHI 180
SF2_C_RHA cd18791
C-terminal helicase domain of the RNA helicase A (RHA) family helicases; The RNA helicase A ...
 573-781 4.17e-70

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: 231.65  E-value: 4.17e-70
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  573 YPVQQYFLEDCIQMTQfvpppsdkkrkdkdeeggeeevncnlvcgpeygpetkrsMAQMNEKETPFELIEALLKYVETLQ 652
Cdd:cd18791      1 FPVEVYYLEDILELLG---------------------------------------ISSEKEDPDYVDAAVRLILQIHRTE 41

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  653 VAGAVLVFLPGWNLIYSMQKHLEMNAHFGS-HRYRILPLHSQIPREEQRLVFEPVPEGVTKVILSTNIAETSITINDVVY 731
Cdd:cd18791     42 EPGDILVFLPGQEEIERLCELLREELLSPDlGKLLVLPLHSSLPPEEQQRVFEPPPPGVRKVVLATNIAETSITIPGVVY 121

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|
gi 1764642986  732 VIDSCKQKVKLFTAHNNMTNYATVWASKTNLEQRKGRAGRVRPGFCFHLC 781
Cdd:cd18791    122 VIDSGLVKEKVYDPRTGLSSLVTVWISKASAEQRAGRAGRTRPGKCYRLY 171
PRK11664 PRK11664
ATP-dependent RNA helicase HrpB; Provisional
 392-873 8.25e-68

ATP-dependent RNA helicase HrpB; Provisional


Pssm-ID: 236950 [Multi-domain]  Cd Length: 812  Bit Score: 245.22  E-value: 8.25e-68
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  392 QLPVKKFEEEIMHTINSNPVVIIRGATGCGKTTQVPQYILDQYIRGGRasecnIVVTQPRRISAVSVAERVAYERGEDLG 471
Cdd:PRK11664     3 SLPVAAVLPELLTALKTAPQVLLKAPTGAGKSTWLPLQLLQHGGINGK-----IIMLEPRRLAARNVAQRLAEQLGEKPG 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  472 KSCGYSVRFES-VLPRPHASVLfcTVGVLLRKLE--AGIRGISHVIVDEIHERDINTDFLMVVLRDVIHAF-PDVRVVLM 547
Cdd:PRK11664    78 ETVGYRMRAESkVGPNTRLEVV--TEGILTRMIQrdPELSGVGLVILDEFHERSLQADLALALLLDVQQGLrDDLKLLIM 155

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  548 SATIDTTMFREYFFSCPIIEVFGRTYPVQqyfledciqmTQFVPPPSDKKrkdkdeeggeeevncnlvcgpeYGPETKRS 627
Cdd:PRK11664   156 SATLDNDRLQQLLPDAPVIVSEGRSFPVE----------RRYQPLPAHQR----------------------FDEAVARA 203

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  628 MAQMNEKETpfelieallkyvetlqvaGAVLVFLPGWNLIYSMQKHLEmnAHFGSHrYRILPLHSQIPREEQRLVFEPVP 707
Cdd:PRK11664   204 TAELLRQES------------------GSLLLFLPGVGEIQRVQEQLA--SRVASD-VLLCPLYGALSLAEQQKAILPAP 262

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  708 EGVTKVILSTNIAETSITINDVVYVIDSCKQKVKLFTAHNNMTNYATVWASKTNLEQRKGRAGRVRPGFCFHLCSKARFE 787
Cdd:PRK11664   263 AGRRKVVLATNIAETSLTIEGIRLVVDSGLERVARFDPKTGLTRLVTQRISQASMTQRAGRAGRLEPGICLHLYSKEQAE 342

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  788 KLETHMTPEIFRTPLHEVALSikLLRLGAIGHFLAKAIEPPPLDAVIEAEHTLRELDALDSNDELTPLGRILARLPIEPR 867
Cdd:PRK11664   343 RAAAQSEPEILHSDLSGLLLE--LLQWGCHDPAQLSWLDQPPAAALAAAKRLLQQLGALDGQGRLTARGRKMAALGNDPR 420


                   ....*.
gi 1764642986  868 LGKMMI 873
Cdd:PRK11664   421 LAAMLV 426
PRK11131 PRK11131
ATP-dependent RNA helicase HrpA; Provisional
 391-933 4.79e-67

ATP-dependent RNA helicase HrpA; Provisional


Pssm-ID: 182986 [Multi-domain]  Cd Length: 1294  Bit Score: 248.05  E-value: 4.79e-67
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  391 EQLPVKKFEEEIMHTINSNPVVIIRGATGCGKTTQVPQYILDQyirgGRASECNIVVTQPRRISAVSVAERVAYERGEDL 470
Cdd:PRK11131    71 ENLPVSQKKQDILEAIRDHQVVIVAGETGSGKTTQLPKICLEL----GRGVKGLIGHTQPRRLAARTVANRIAEELETEL 146

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  471 GKSCGYSVRFESvlprpHAS----VLFCTVGVLLRKLEAGiRGISH---VIVDEIHERDINTDFLMVVLRDVIHAFPDVR 543
Cdd:PRK11131   147 GGCVGYKVRFND-----QVSdntmVKLMTDGILLAEIQQD-RLLMQydtIIIDEAHERSLNIDFILGYLKELLPRRPDLK 220

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  544 VVLMSATIDTTMFREYFFSCPIIEVFGRTYPVQqyfledciqmTQFVPppsdkkrkdkdeeggeeevncnLVcgpEYGPE 623
Cdd:PRK11131   221 VIITSATIDPERFSRHFNNAPIIEVSGRTYPVE----------VRYRP----------------------IV---EEADD 265

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  624 TKRSMaqmneketpfelIEALLKYVETLQV--AGAVLVFLPGWNLIY----SMQK----HLEmnahfgshryrILPLHSQ 693
Cdd:PRK11131   266 TERDQ------------LQAIFDAVDELGRegPGDILIFMSGEREIRdtadALNKlnlrHTE-----------ILPLYAR 322

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  694 IPREEQRLVFEpvPEGVTKVILSTNIAETSITINDVVYVIDSCKQKVKLFTAHNNMTNYATVWASKTNLEQRKGRAGRVR 773
Cdd:PRK11131   323 LSNSEQNRVFQ--SHSGRRIVLATNVAETSLTVPGIKYVIDPGTARISRYSYRTKVQRLPIEPISQASANQRKGRCGRVS 400

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  774 PGFCFHLCSKARFEKLETHMTPEIFRTPLHEVALSIKLLRLGAIGHFlaKAIEPPPLDAVIEAEHTLRELDALDSND--- 850
Cdd:PRK11131   401 EGICIRLYSEDDFLSRPEFTDPEILRTNLASVILQMTALGLGDIAAF--PFVEAPDKRNIQDGVRLLEELGAITTDEqas 478

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  851 --ELTPLGRILARLPIEPRLGKMMI----MGCILNVgdaaCTISAASCFSEPF--------ISEGKrlgfvHRNFAGARf 916
Cdd:PRK11131   479 ayKLTPLGRQLAQLPVDPRLARMVLeaqkHGCVREV----MIITSALSIQDPRerpmdkqqASDEK-----HRRFADKE- 548

                          570
                   ....*....|....*..
gi 1764642986  917 SDHVALLSVfqaWDEVR 933
Cdd:PRK11131   549 SDFLAFVNL---WNYLQ 562
DEXHc_DHX57 cd17985
DEXH-box helicase domain of DEAH-box helicase 57; DEAH-box helicase 57 (DHX57) belongs to the ...
 393-568 3.16e-61

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: 207.00  E-value: 3.16e-61
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  393 LPVKKFEEEIMHTINSNPVVIIRGATGCGKTTQVPQYILDQYIRGGRASECNIVVTQPRRISAVSVAERVAYERGEDLGK 472
Cdd:cd17985      1 LPAWQERETILELLEKHQVLVISGMTGCGKTTQIPQFILDNSLQGPPLPVANIICTQPRRISAISVAERVAQERAERVGQ 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  473 SCGYSVRFESVLPRPhASVLFCTVGVLLRKLEAG--IRGISHVIVDEIHERDINTDFLMVVLRDVIHAFPDVRVVLMSAT 550
Cdd:cd17985     81 SVGYQIRLESVKSSA-TRLLYCTTGVLLRRLEGDptLQGVTHVIVDEVHERTEESDFLLLVLKDLMVQRPDLKVILMSAT 159

                          170
                   ....*....|....*...
gi 1764642986  551 IDTTMFREYFFSCPIIEV 568
Cdd:cd17985    160 LNAELFSDYFNSCPVIHI 177
DEXHc_YTHDC2 cd17987
DEXH-box helicase domain of YTH domain containing 2; YTH domain containing 2 (YTHDC2) ...
 393-568 1.98e-57

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: 195.82  E-value: 1.98e-57
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  393 LPVKKFEEEIMHTINSNPVVIIRGATGCGKTTQVPQYILDQYIRGGraSECNIVVTQPRRISAVSVAERVAYERGEDLGK 472
Cdd:cd17987      1 LPVFEKQEQIVRIIKENKVVLIVGETGSGKTTQIPQFLLDDCYANG--IPCRIFCTQPRRLAAIAVAERVAAERGEKIGQ 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  473 SCGYSVRFESVLpRPHASVLFCTVGVLLRKLEAG---IRGISHVIVDEIHERDINTDFLMVVLRDVIHAFPDVRVVLMSA 549
Cdd:cd17987     79 TVGYQIRLESRV-SPKTLLTFCTNGVLLRTLMAGdsaLSTVTHVIVDEVHERDRFSDFLLTKLRDILQKHPNLKLILSSA 157

                          170
                   ....*....|....*....
gi 1764642986  550 TIDTTMFREYFFSCPIIEV 568
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 ...
 393-568 2.47e-55

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: 190.13  E-value: 2.47e-55
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  393 LPVKKFEEEIMHTINSNPVVIIRGATGCGKTTQVPQYIL-DQYIRGGRASECNIVVTQPRRISAVSVAERVAYERGEDLG 471
Cdd:cd17975      1 LPVFKHRESILETLKRHRVVVVAGETGSGKSTQVPQFLLeDLLLNGGTAQKCNIVCTQPRRISAMSLATRVCEELGCESG 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  472 KS-----CGYSVRFESVLPRPhASVLFCTVGVLLRKLEAG--IRGISHVIVDEIHERDINTDFLMVVLRDVIHAFPDVRV 544
Cdd:cd17975     81 PGgknslCGYQIRMESRTGEA-TRLLYCTTGVLLRKLQEDglLSSISHIIVDEVHERSVQSDFLLIILKEILHKRSDLHL 159

                          170       180
                   ....*....|....*....|....
gi 1764642986  545 VLMSATIDTTMFREYFFSCPIIEV 568
Cdd:cd17975    160 ILMSATVDCEKFSSYFTHCPILRI 183
DEXHc_TDRD9 cd17988
DEXH-box helicase domain of tudor domain containing 9; Tudor domain containing 9 (TDRD9, also ...
 393-560 3.47e-53

DEXH-box helicase domain of tudor domain containing 9; Tudor domain containing 9 (TDRD9, also known as HIG-1or NET54 or C14orf75) is a part of the nuclear PIWI-interacting RNA (piRNA) pathway essential for transposon silencing and male fertility TDRD9 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350746 [Multi-domain]  Cd Length: 180  Bit Score: 183.86  E-value: 3.47e-53
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  393 LPVKKFEEEIMHTINSNPVVIIRGATGCGKTTQVPQYILDQYIRggRASECNIVVTQPRRISAVSVAERVAYERGEDLGK 472
Cdd:cd17988      1 LPIYAKREEILSLIEANSVVIIKGATGCGKTTQLPQFILDHYYK--RGKYCNIVVTQPRRIAAISIARRVSQEREWTLGS 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  473 SCGYSVRFESVLPRpHASVLFCTVGVLLRKL--EAGIRGISHVIVDEIHERDINTDFLMVVLRDVIHAFPD-VRVVLMSA 549
Cdd:cd17988     79 LVGYQVGLERPASE-ETRLIYCTTGVLLQKLinNKTLTEYTHIILDEVHERDQELDFLLLVVRRLLRTNSRhVKIILMSA 157

                          170
                   ....*....|.
gi 1764642986  550 TIDTTMFREYF 560
Cdd:cd17988    158 TISCKEFADYF 168
DEXHc_DHX34 cd17979
DEXH-box helicase domain of DEAH-box helicase 34; DEAH-box helicase 34 (DHX34) plays a role in ...
 393-568 2.80e-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: 172.24  E-value: 2.80e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  393 LPVKKFEEEIMHTINSNPVVIIRGATGCGKTTQVPQYILDQYIRggrasecNIVVTQPRRISAVSVAERVAYERGEDLGK 472
Cdd:cd17979      1 LPIAQYREKIIELLKTHQVVIVAGDTGCGKSTQVPQYLLAAGFR-------HIACTQPRRIACISLAKRVAFESLNQYGS 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  473 SCGYSVRFESVlPRPHASVLFCTVGVLLRKLE--AGIRGISHVIVDEIHERDINTDFLMVVLRDVIHAFPDVRVVLMSAT 550
Cdd:cd17979     74 KVAYQIRFERT-RTLATKLLFLTEGLLLRQIQrdASLPQYNVLILDEVHERHLHGDFLLGVLRCLLRLRPDLKLILMSAT 152

                          170
                   ....*....|....*...
gi 1764642986  551 IDTTMFREYFFSCPIIEV 568
Cdd:cd17979    153 INIELFSGYFEGAPVVQV 170
DEXHc_DHX33 cd17978
DEXH-box helicase domain of DEAH-box helicase 33; DEAH-box helicase 33 (DHX33) stimulates RNA ...
 393-566 2.76e-45

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: 161.37  E-value: 2.76e-45
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  393 LPVKKFEEEIMHTINSNPVVIIRGATGCGKTTQVPQYILDQYIRGGRAsecnIVVTQPRRISAVSVAERVAYERGEDLGK 472
Cdd:cd17978      1 LPIYSARKRLLEELRKHDTVIIIGETGSGKTTQIPQYLYEAGFARGGM----IGITQPRRVAAVSVAKRVAEEMGVELGQ 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  473 SCGYSVRFESVlPRPHASVLFCTVGVLLRK--LEAGIRGISHVIVDEIHERDINTDFLMVVLRDV-----IHAFPDVRVV 545
Cdd:cd17978     77 LVGYSVRFDDV-TSEETRIKYMTDGMLLREaiGDPLLSKYSVIILDEAHERTVHTDVLFGLVKSAqrrrkEQKLSPLKVI 155

                          170       180
                   ....*....|....*....|.
gi 1764642986  546 LMSATIDTTMFREYFFSCPII 566
Cdd:cd17978    156 IMSATLDADLFSEYFNGAPVL 176
DSRM_DHX9_rpt2 cd19855
second double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; ...
 185-259 4.91e-45

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: 156.61  E-value: 4.91e-45
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1764642986  185 LDNAKARLNQFFQKEKIQTDYKYNQVGPDHNRSFIAEMTIFVKQLRRNIFAREHGSNKKLAAQSCALSLVRQLYH 259
Cdd:cd19855      1 LDNAKSRLNEFLQKNKIPAEYKYTSVGPDHNRSFIAELSIFVKQLGKTIYARETGSNKKLASQSCALSLVRQLYH 75
DEXHc_DHX35 cd17980
DEXH-box helicase domain of DEAH-box helicase 35; DHX35 plays a role in colorectal cancers and ...
 393-560 8.92e-45

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: 159.94  E-value: 8.92e-45
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  393 LPVKKFEEEIMHTINSNPVVIIRGATGCGKTTQVPQYILDQ-YIRGGRAsecnIVVTQPRRISAVSVAERVAYERGEDLG 471
Cdd:cd17980      1 LPVFKLRNHILYLVENYQTIVIVGETGCGKSTQIPQYLAEAgWTAGGRV----VGCTQPRRVAAVTVAGRVAEEMGAVLG 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  472 KSCGYSVRFESVLPRPHASVLFCTVGVLLRKLEAG--IRGISHVIVDEIHERDINTDFLMVVLRDVIHAFPDVRVVLMSA 549
Cdd:cd17980     77 HEVGYCIRFDDCTDPQATRIKFLTDGMLVREMMLDplLTKYSVIMLDEAHERTLYTDILIGLLKKIQKKRGDLRLIVASA 156

                          170
                   ....*....|.
gi 1764642986  550 TIDTTMFREYF 560
Cdd:cd17980    157 TLDAEKFRDFF 167
DEXHc_DHX15 cd17973
DEXH-box helicase domain of DEAH-box helicase 15; DEAH-box helicase 15 (DHX15) is a pre-mRNA ...
 384-568 9.30e-45

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: 160.27  E-value: 9.30e-45
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  384 QERLREREQLPVKKFEEEIMHTINSNPVVIIRGATGCGKTTQVPQYILD-QYIRGGRASecnIVVTQPRRISAVSVAERV 462
Cdd:cd17973      4 FEILEKRRELPVWEQKEDFLKLLKNNQILVLVGETGSGKTTQIPQFVLDdELPHQPKKL---VACTQPRRVAAMSVAQRV 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  463 AYERGEDLGKSCGYSVRFESvLPRPHASVLFCTVGVLLRKLEAG--IRGISHVIVDEIHERDINTDFLMVVLRDVIHAFP 540
Cdd:cd17973     81 AEEMDVKLGEEVGYSIRFED-CSSAKTILKYMTDGMLLREAMSDplLSRYSVIILDEAHERTLATDILMGLLKEVVRRRP 159

                          170       180
                   ....*....|....*....|....*...
gi 1764642986  541 DVRVVLMSATIDTTMFREYFFSCPIIEV 568
Cdd:cd17973    160 DLKLIVMSATLDAGKFQKYFDNAPLLKV 187
DSRM_DHX9_rpt1 cd19854
first double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; ...
 3-71 2.63e-43

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: 151.27  E-value: 2.63e-43
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1764642986    3 DIKNFLYAWCGKKKLTPNYDIRAAGNKNRQKFMCEVRVDGFNYIGMGNSTNKKDAQANAARDFVNYLVR 71
Cdd:cd19854      1 EIKAFLYAWCGKKKLTPEYDIKEAGNKHRQRFKCEVRVEGFDYVGTGNATNKKDAQTNAARDFLNYLVR 69
DEXHc_DHX8 cd17971
DEXH-box helicase domain of DEAH-box helicase 8; DEAH-box helicase 8 (DHX8 ,also known as ...
 389-568 1.17e-42

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: 153.79  E-value: 1.17e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  389 EREQLPVKKFEEEIMHTINSNPVVIIRGATGCGKTTQVPQYILDQyirgGRASECNIVVTQPRRISAVSVAERVAYERGE 468
Cdd:cd17971      2 QRESLPIYKLKEQLIQAVHDNQILVVIGETGSGKTTQITQYLAEA----GYTSRGKIGCTQPRRVAAMSVAKRVAEEFGC 77

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  469 DLGKSCGYSVRFESVlPRPHASVLFCTVGVLLRK--LEAGIRGISHVIVDEIHERDINTDFLMVVLRDVIHAFPDVRVVL 546
Cdd:cd17971     78 CLGQEVGYTIRFEDC-TSPETVIKYMTDGMLLREclIDPDLSQYSVIMLDEAHERTIHTDVLFGLLKKTVQKRPDLKLIV 156

                          170       180
                   ....*....|....*....|..
gi 1764642986  547 MSATIDTTMFREYFFSCPIIEV 568
Cdd:cd17971    157 TSATLDAVKFSQYFYEAPIFTI 178
DEXHc_HrpA cd17989
DEXH-box helicase domain of ATP-dependent RNA helicase HrpA; HrpA is part of the HrpB-HrpA ...
 393-568 5.06e-42

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: 151.84  E-value: 5.06e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  393 LPVKKFEEEIMHTINSNPVVIIRGATGCGKTTQVPQYILDQyirgGRASECNIVVTQPRRISAVSVAERVAYERGEDLGK 472
Cdd:cd17989      1 LPVSQKRDEIAKAIAENQVVIIAGETGSGKTTQLPKICLEL----GRGIRGLIGHTQPRRLAARSVAERIAEELKTELGG 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  473 SCGYSVRFESVLpRPHASVLFCTVGVLLRKLEAG--IRGISHVIVDEIHERDINTDFLMVVLRDVIHAFPDVRVVLMSAT 550
Cdd:cd17989     77 AVGYKVRFTDQT-SDETCVKLMTDGILLAETQTDryLRAYDTIIIDEAHERSLNIDFLLGYLKQLLPRRPDLKVIITSAT 155

                          170
                   ....*....|....*...
gi 1764642986  551 IDTTMFREYFFSCPIIEV 568
Cdd:cd17989    156 IDAERFSRHFNNAPIIEV 173
DEXHc_DHX16 cd17974
DEXH-box helicase domain of DEAH-box helicase 16; DEAH-box helicase 16 (DHX16) is probably ...
 393-568 8.68e-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: 148.42  E-value: 8.68e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  393 LPVKKFEEEIMHTINSNPVVIIRGATGCGKTTQVPQYILDQ-YIRGGRASECnivvTQPRRISAVSVAERVAYERGEDLG 471
Cdd:cd17974      1 LPVYPYRDDLLAAVKEHQVLIIVGETGSGKTTQIPQYLHEAgYTKGGGKIGC----TQPRRVAAMSVAARVAEEMGVKLG 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  472 KSCGYSVRFESVlPRPHASVLFCTVGVLLRKL--EAGIRGISHVIVDEIHERDINTDFLMVVLRDVIHAFPDVRVVLMSA 549
Cdd:cd17974     77 NEVGYSIRFEDC-TSEKTVLKYMTDGMLLREFltEPDLASYSVMIIDEAHERTLHTDILFGLVKDIARFRPDLKLLISSA 155

                          170
                   ....*....|....*....
gi 1764642986  550 TIDTTMFREYFFSCPIIEV 568
Cdd:cd17974    156 TMDAEKFSAFFDDAPIFRI 174
DEXHc_DHX37 cd17982
DEXH-box helicase domain of DEAH-box helicase 37; DHX37 plays a role in the development of the ...
 393-568 1.45e-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: 148.27  E-value: 1.45e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  393 LPVKKFEEEIMHTINSNPVVIIRGATGCGKTTQVPQYILD------QYIRGGRasecnIVVTQPRRISAVSVAERVAYER 466
Cdd:cd17982      1 LPILAEEQEIMEAINENPVVIICGETGSGKTTQVPQFLYEagfgspESDNPGM-----IGITQPRRVAAVSMAKRVAEEL 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  467 GeDLGKSCGYSVRFESVLpRPHASVLFCTVGVLLRKLEAG--IRGISHVIVDEIHERDINTDFLM------VVLRDVIHA 538
Cdd:cd17982     76 N-VFGKEVSYQIRYDSTV-SENTKIKFMTDGVLLKEIQTDflLRKYSVIIIDEAHERSVNTDILIgmlsriVPLRAKLYL 153

                          170       180       190
                   ....*....|....*....|....*....|....*...
gi 1764642986  539 FPD----VRVVLMSATIDTTMFRE--YFFSC--PIIEV 568
Cdd:cd17982    154 QDQtvkpLKLVIMSATLRVEDFTEnkLLFPRppPVIKV 191
DEXHc_DHX38 cd17983
DEXH-box helicase domain of DEAH-box helicase 38; DEAH-box helicase 38 (DHX38, also known as ...
 393-568 7.20e-40

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: 145.68  E-value: 7.20e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  393 LPVKKFEEEIMHTINSNPVVIIRGATGCGKTTQVPQYIL-DQYIRGGRasecnIVVTQPRRISAVSVAERVAYERGEDLG 471
Cdd:cd17983      1 LPIFAVRQELLNVIRDNNVVIVVGETGSGKTTQLTQYLHeDGYTDYGM-----IGCTQPRRVAAMSVAKRVSEEMGVELG 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  472 KSCGYSVRFESVlPRPHASVLFCTVGVLLRK--LEAGIRGISHVIVDEIHERDINTDFLMVVLRDVIHAFPDVRVVLMSA 549
Cdd:cd17983     76 EEVGYAIRFEDC-TSENTVIKYMTDGILLREslRDPDLDKYSAIIMDEAHERSLNTDVLFGLLREVVARRRDLKLIVTSA 154

                          170
                   ....*....|....*....
gi 1764642986  550 TIDTTMFREYFFSCPIIEV 568
Cdd:cd17983    155 TMDADKFADFFGNVPIFTI 173
DEXHc_HrpB cd17990
DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA ...
 393-568 3.74e-38

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: 140.54  E-value: 3.74e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  393 LPVKKFEEEIMHTINSNPVVIIRGATGCGKTTQVPQYILDQ-YIRGGRasecnIVVTQPRRISAVSVAERVAYERGEDLG 471
Cdd:cd17990      1 LPIAAVLPALRAALDAGGQVVLEAPPGAGKTTRVPLALLAElWIAGGK-----IIVLEPRRVAARAAARRLATLLGEAPG 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  472 KSCGYSVRFESVLPRpHASVLFCTVGVLLRKLEA--GIRGISHVIVDEIHERDINTDFLMVVLRDVIHAF-PDVRVVLMS 548
Cdd:cd17990     76 ETVGYRVRGESRVGR-RTRVEVVTEGVLLRRLQRdpELSGVGAVILDEFHERSLDADLALALLLEVQQLLrDDLRLLAMS 154

                          170       180
                   ....*....|....*....|
gi 1764642986  549 ATIDTTMFREYFFSCPIIEV 568
Cdd:cd17990    155 ATLDGDGLAALLPEAPVVES 174
DEXHc_DHX40 cd17984
DEXH-box helicase domain of DEAH-box helicase 40; DEAH-box helicase 40 (DHX40) belongs to the ...
 393-568 9.17e-32

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: 122.66  E-value: 9.17e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  393 LPVKKFEEEIMHTINSNPVVIIRGATGCGKTTQVPQYILdqyiRGGRASECNIVVTQPRRISAVSVAERVAYERGEDLGK 472
Cdd:cd17984      1 LPIQKQRKKLVQAVRDNSFLIVTGNTGSGKTTQLPKYLY----EAGFSQHGMIGVTQPRRVAAISVAQRVAEEMKCTLGS 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  473 SCGYSVRFESVLPRPHAsVLFCTVGVLLRKLEA--GIRGISHVIVDEIHERDINTDFLMVVLRDVIHAFP-----DVRVV 545
Cdd:cd17984     77 KVGYQVRFDDCSSKETA-IKYMTDGCLLRHILAdpNLTKYSVIILDEAHERSLTTDILFGLLKKLFQEKSpnrkeHLKVV 155

                          170       180
                   ....*....|....*....|...
gi 1764642986  546 LMSATIDTTMFREYFFSCPIIEV 568
Cdd:cd17984    156 VMSATLELAKLSAFFGNCPVFDI 178
DEXDc smart00487
DEAD-like helicases superfamily;
402-578 2.34e-23

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 99.10  E-value: 2.34e-23
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986   402 IMHTINSNPVVIIRGATGCGKTTQVPQYILDQYIRGGRaseCNIVVTQPRRISAVSVAERVAYERGEDLGKSCGY----- 476
Cdd:smart00487   17 IEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKG---GRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLyggds 93

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986   477 SVRFESVLPRPHASVLFCTVGVLLRKLEAG---IRGISHVIVDEIHERDiNTDFLMVVLRDVIHAFPDVRVVLMSATI-- 551
Cdd:smart00487   94 KREQLRKLESGKTDILVTTPGRLLDLLENDklsLSNVDLVILDEAHRLL-DGGFGDQLEKLLKLLPKNVQLLLLSATPpe 172

                           170       180
                    ....*....|....*....|....*....
gi 1764642986   552 DTTMFREYFFSCPIIEVFGRTYP--VQQY 578
Cdd:smart00487  173 EIENLLELFLNDPVFIDVGFTPLepIEQF 201
DEXHc_DHX32 cd17977
DEXH-box helicase domain of DEAH-box helicase 32; DEAH-box helicase 32 (DHX32) belongs to the ...
 393-568 2.96e-23

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: 97.97  E-value: 2.96e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  393 LPVKKFEEEIMHTINSNPVVIIRGATGCGKTTQVPQY-----ILDQYIRGGrasecnIVVTQPRRISAVSVAERVAYERG 467
Cdd:cd17977      1 LPVWEAKYEFMESLAHNQIVIVSGDAKTGKSSQIPQWcaeycLSAHYQHGV------VVCTQVHKQTAVWLALRVADEMD 74

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  468 EDLGKSCGYSVRFESVLPrpHASVL-FCTVGVLLRKLEA----GIRGIshVIVDEIHERDINTDFLMVVLRDVIHAFPDV 542
Cdd:cd17977     75 VNIGHEVGYVIPFENCCT--NETILrYCTDDMLLREMMSdpllESYGV--IILDDAHERTVSTDVLLGLLKDVLLSRPEL 150

                          170       180
                   ....*....|....*....|....*.
gi 1764642986  543 RVVLMSATIDTTMFREYFFSCPIIEV 568
Cdd:cd17977    151 KLVIITCPHLSSKLLSYYGNVPLIEV 176
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 412-550 3.08e-23

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: 97.09  E-value: 3.08e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  412 VIIRGATGCGKTTQVPQYILDQYIRGGraseCNIVVTQPRRISAVSVAERVAYERgeDLGKSCGYSVRFESVLPR----- 486
Cdd:cd00046      4 VLITAPTGSGKTLAALLAALLLLLKKG----KKVLVLVPTKALALQTAERLRELF--GPGIRVAVLVGGSSAEEReknkl 77

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1764642986  487 PHASVLFCTVGVLLRKLEA----GIRGISHVIVDEIHERDINTDF-LMVVLRDVIHAFPDVRVVLMSAT 550
Cdd:cd00046     78 GDADIIIATPDMLLNLLLRedrlFLKDLKLIIVDEAHALLIDSRGaLILDLAVRKAGLKNAQVILLSAT 146
HA2 smart00847
Helicase associated domain (HA2) Add an annotation; This presumed domain is about 90 amino ...
 842-923 3.88e-21

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: 88.48  E-value: 3.88e-21
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986   842 ELDALDSNDELTPLGRILARLPIEPRLGKMMIMGCILNVGDAACTISAASCFSEPFISE-GKRLGFVHRNFAGARfSDHV 920
Cdd:smart00847    1 ELGALDDDGRLTPLGRKMAELPLDPRLAKMLLAAAEFGCLDEILTIVAMLSVGDPRPKEkREDADAARRRFADPE-SDHL 79


                    ...
gi 1764642986   921 ALL 923
Cdd:smart00847   80 TLL 82
DEXQc_DQX1 cd17986
DEXQ-box helicase domain of DEAQ-box RNA dependent ATPase 1; DEAQ-box RNA dependent ATPase 1 ...
 393-568 1.55e-20

DEXQ-box helicase domain of DEAQ-box RNA dependent ATPase 1; DEAQ-box RNA dependent ATPase 1 (DQX1) belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350744 [Multi-domain]  Cd Length: 177  Bit Score: 90.34  E-value: 1.55e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  393 LPVKKFEEEIMHTINSNP-VVIIRGATGCGKTTQVPQYILdQYIRGGRASECNIVVTQPRRISAVSVAERVAYERGEDLG 471
Cdd:cd17986      1 LPIWAAKFTFLEQLESPSgIVLVSGEPGSGKSTQVPQWCA-EFALSRGFQKGQVTVTQPHPLAARSLALRVADEMDLNLG 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  472 KSCGYSVRFESVLPrPHASVLFCTVGVLLRKLEA--GIRGISHVIVDEIHERDINTDFLMVVLRDVIHAFPDVRVVLMSA 549
Cdd:cd17986     80 HEVGYSIPQEDCTG-PNTILRFCWDRLLLQEMTStpLLGAWGVVVLDEAQERSVASDSLLGLLKDVRLQRPELRVVVVTS 158

                          170
                   ....*....|....*....
gi 1764642986  550 TIDTTMFREYFFSCPIIEV 568
Cdd:cd17986    159 PALEPKLRAFWGNPPVVHV 177
HA2 pfam04408
Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in ...
 836-922 3.21e-20

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: 86.91  E-value: 3.21e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  836 AEHTLRELDALDSNDELTPLGRILARLPIEPRLGKMMIMGCILNVGDAACTISAASCFSEPFISEG-------------- 901
Cdd:pfam04408    1 ALELLYYLGALDEDGELTPLGRKMAELPLDPRLAKMLLAAAELGCLDEVLTIVAALSVRDPFVQPNfldprsaakaarrr 80

                           90       100
                   ....*....|....*....|....
gi 1764642986  902 KRLGF--VHRNFAGARF-SDHVAL 922
Cdd:pfam04408   81 RRAADekARAKFARLDLeGDHLTL 104
OB_NTP_bind pfam07717
Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus ...
 998-1077 7.57e-20

Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus of the DEAD-box helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. There do seem to be a couple of instances where it occurs by itself -. The structure PDB:3i4u adopts an OB-fold. helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. This C-terminal domain of the yeast helicase contains an oligonucleotide/oligosaccharide-binding (OB)-fold which seems to be placed at the entrance of the putative nucleic acid cavity. It also constitutes the binding site for the G-patch-containing domain of Pfa1p. When found on DEAH/RHA helicases, this domain is central to the regulation of the helicase activity through its binding of both RNA and G-patch domain proteins.


Pssm-ID: 400182 [Multi-domain]  Cd Length: 82  Bit Score: 85.00  E-value: 7.57e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  998 LLTYGCYPNVCYHKEKRKILTT--EGRNALIHKSSVNCpfssQDPSYPSPFFVFGEKIRTRAISAKGMTMVSPLQLILFA 1075
Cdd:pfam07717    4 ALAAGLYPNVARRDPKGKGYTTlsDNQRVFIHPSSVLF----NEKTFPPEWVVYQELVETTKVYIRTVTAISPEWLLLFA 79


                   ..
gi 1764642986 1076 AK 1077
Cdd:pfam07717   80 PH 81
PHA02653 PHA02653
RNA helicase NPH-II; Provisional
 408-775 9.14e-19

RNA helicase NPH-II; Provisional


Pssm-ID: 177443 [Multi-domain]  Cd Length: 675  Bit Score: 91.96  E-value: 9.14e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  408 SNPVVIIRGATGCGKTTQVPQYIL-DQYIRGG---------RASECNIVVTQPrrisavsvaeRVAYER--GEDLGKSCG 475
Cdd:PHA02653   178 SRKPVVLTGGTGVGKTSQVPKLLLwFNYLFGGfdnldkidpNFIERPIVLSLP----------RVALVRlhSITLLKSLG 247

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  476 Y--------SVRFESVL-------PRPHASVlFCTVGVLLRKLeagiRGISHVIVDEIHERDINTDFLMVVLR---DVIH 537
Cdd:PHA02653   248 FdeidgspiSLKYGSIPdelintnPKPYGLV-FSTHKLTLNKL----FDYGTVIIDEVHEHDQIGDIIIAVARkhiDKIR 322

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  538 AfpdvrVVLMSATI--DTTMFREYFFSCPIIEVFGRT-YPVQQYFLEDCIQmtqfvppPSDKKrkdkdeeggeeevncnl 614
Cdd:PHA02653   323 S-----LFLMTATLedDRDRIKEFFPNPAFVHIPGGTlFPISEVYVKNKYN-------PKNKR----------------- 373

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  615 vcgpEYGPETKRSMaqmneketpfelIEALLKYveTLQVAGAVLVFLPGWNLIYSMQKHLEmnahfGSH-RYRILPLHSQ 693
Cdd:PHA02653   374 ----AYIEEEKKNI------------VTALKKY--TPPKGSSGIVFVASVSQCEEYKKYLE-----KRLpIYDFYIIHGK 430

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  694 IPREEQRLVFEPVPEGVTkVILSTNIAETSITINDVVYVIDSCKQKVKLFTAHNNMtnyatvWASKTNLEQRKGRAGRVR 773
Cdd:PHA02653   431 VPNIDEILEKVYSSKNPS-IIISTPYLESSVTIRNATHVYDTGRVYVPEPFGGKEM------FISKSMRTQRKGRVGRVS 503


                   ..
gi 1764642986  774 PG 775
Cdd:PHA02653   504 PG 505
DSRM smart00358
Double-stranded RNA binding motif;
5-69 1.75e-16

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 74.99  E-value: 1.75e-16
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1764642986     5 KNFLYAWCGKKKLTPNYD-IRAAGNKNRQKFMCEVRVDGFnYIGMGNSTNKKDAQANAARDFVNYL 69
Cdd:smart00358    2 KSLLQELAQKRKLPPEYElVKEEGPDHAPRFTVTVKVGGK-RTGEGEGSSKKEAKQRAAEAALRSL 66
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 639-772 7.70e-16

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: 74.55  E-value: 7.70e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  639 ELIEALLKYVETLQVaGAVLVFLPgwnliysMQKHLEMNAHFGSHRYRILPLHSQIPREEQRLVFEPVPEGVTKVILSTN 718
Cdd:pfam00271    1 EKLEALLELLKKERG-GKVLIFSQ-------TKKTLEAELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATD 72

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1764642986  719 IAETSITINDVVYVIDsckqkvklFTAHNNMTNYatvwasktnlEQRKGRAGRV 772
Cdd:pfam00271   73 VAERGLDLPDVDLVIN--------YDLPWNPASY----------IQRIGRAGRA 108
HELICc smart00490
helicase superfamily c-terminal domain;
675-771 7.57e-15

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 70.70  E-value: 7.57e-15
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986   675 EMNAHFGSHRYRILPLHSQIPREEQRLVFEPVPEGVTKVILSTNIAETSITINDVVYVIDSCkqkvklftahnnmtnyat 754
Cdd:smart00490    2 ELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYD------------------ 63

                            90
                    ....*....|....*..
gi 1764642986   755 VWASKTNLEQRKGRAGR 771
Cdd:smart00490   64 LPWSPASYIQRIGRAGR 80
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 5-69 1.86e-12

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: 63.40  E-value: 1.86e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1764642986    5 KNFLYAWCGKKKLTPNYD-IRAAGNKNRQKFMCEVRVDGFNYiGMGNSTNKKDAQANAARDFVNYL 69
Cdd:pfam00035    2 KSLLQEYAQKNGKPPPYEyVSEEGPPHSPKFTVTVKVDGKLY-GSGTGSSKKEAEQLAAEKALEKL 66
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 188-257 5.50e-12

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: 61.86  E-value: 5.50e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1764642986  188 AKARLNQFFQKEKIQTDYKYN-QVGPDHNRSFIAEMTIfvkqlRRNIFAREHGSNKKLAAQSCALSLVRQL 257
Cdd:pfam00035    1 PKSLLQEYAQKNGKPPPYEYVsEEGPPHSPKFTVTVKV-----DGKLYGSGTGSSKKEAEQLAAEKALEKL 66
DSRM smart00358
Double-stranded RNA binding motif;
188-258 1.40e-11

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 60.74  E-value: 1.40e-11
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1764642986   188 AKARLNQFFQKEKIQTDYKY-NQVGPDHNRSFIAEMTIfvkqlRRNIFAREHGSNKKLAAQSCALSLVRQLY 258
Cdd:smart00358    1 PKSLLQELAQKRKLPPEYELvKEEGPDHAPRFTVTVKV-----GGKRTGEGEGSSKKEAKQRAAEAALRSLK 67
DSRM_SF cd00048
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
 11-63 7.39e-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: 49.98  E-value: 7.39e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1764642986   11 WCGKKKL-TPNYDIRAAGNKNRQKFMCEVRVDGFNYIGMGNStnKKDAQANAAR 63
Cdd:cd00048      3 LCQKNKWpPPEYETVEEGGPHNPRFTCTVTVNGQTFEGEGKS--KKEAKQAAAE 54
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 400-554 6.31e-07

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: 50.70  E-value: 6.31e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  400 EEIMHTINSNPVVIIRGATGCGKTT--QVP--QYILDQYiRGGRAsecnIVVTqPRRISAVSVAERVayergEDLGKSCG 475
Cdd:pfam00270    5 AEAIPAILEGRDVLVQAPTGSGKTLafLLPalEALDKLD-NGPQA----LVLA-PTRELAEQIYEEL-----KKLGKGLG 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  476 YSVRFE----------SVLPRPHasVLFCTVGVLLR--KLEAGIRGISHVIVDEIHErdINTDFLMVVLRDVIHAFP-DV 542
Cdd:pfam00270   74 LKVASLlggdsrkeqlEKLKGPD--ILVGTPGRLLDllQERKLLKNLKLLVLDEAHR--LLDMGFGPDLEEILRRLPkKR 149

                          170
                   ....*....|..
gi 1764642986  543 RVVLMSATIDTT 554
Cdd:pfam00270  150 QILLLSATLPRN 161
DSRM_RNAse_III_family cd10845
double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...
 187-257 1.80e-06

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: 46.33  E-value: 1.80e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1764642986  187 NAKARLNQFFQKEKIQT-DYKY-NQVGPDHNRSFIAEMTIfvkqlRRNIFAREHGSNKKLAAQSCALSLVRQL 257
Cdd:cd10845      2 DYKTALQEYLQKRGLPLpEYELvEEEGPDHNKTFTVEVKV-----NGKVIGEGTGRSKKEAEQAAAKAALEKL 69
DEXHc_Ski2 cd17921
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ...
 418-552 2.36e-06

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: 49.18  E-value: 2.36e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  418 TGCGKTTqVPQYILdqyIRGGRASECNIVVTQPRRisAVsVAERVAY--ERGEDLGKSCG--YSVRFESVLPRPHASVLF 493
Cdd:cd17921     26 TSSGKTL-IAELAI---LRALATSGGKAVYIAPTR--AL-VNQKEADlrERFGPLGKNVGllTGDPSVNKLLLAEADILV 98

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1764642986  494 CT---VGVLLRKL-EAGIRGISHVIVDEIH-----ERDIntdFLMVVLRDVIHAFPDVRVVLMSATID 552
Cdd:cd17921     99 ATpekLDLLLRNGgERLIQDVRLVVVDEAHligdgERGV---VLELLLSRLLRINKNARFVGLSATLP 163
DSRM_SF cd00048
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
 193-250 2.60e-06

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: 45.74  E-value: 2.60e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1764642986  193 NQFFQKEKIQT-DYKYNQVGPDHNRSFIAEMTIfvkqlrRNIFAREHGSNKKLAAQSCA 250
Cdd:cd00048      1 NELCQKNKWPPpEYETVEEGGPHNPRFTCTVTV------NGQTFEGEGKSKKEAKQAAA 53
DSRM_EIF2AK2-like cd19875
double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...
 192-257 2.86e-06

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: 45.72  E-value: 2.86e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1764642986  192 LNQFFQKEKIQTDYKYNQVGPDHNRSFIAEMTIfvkqlRRNIFAREHGSNKKLAAQSCALSLVRQL 257
Cdd:cd19875      7 LNEYCQKRGLSLEFVDVSVGPDHCPGFTASATI-----DGIVFASATGTSKKEAKRAAAKLALKKL 67
DSRM_SON-like cd19870
double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known ...
 12-63 6.74e-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: 44.96  E-value: 6.74e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1764642986   12 CGKKKL-TPNYD-IRAAGNKNRQKFMCEVRVDGFNYIGMGNSTNKKDAQANAAR 63
Cdd:cd19870     12 CNKRKWgPPEFRlVEESGPPHRKHFLFKVVVNGVEYQPSVASGNKKDAKAQAAT 65
DSRM_RNAse_III_family cd10845
double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...
 3-69 8.06e-06

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: 44.79  E-value: 8.06e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1764642986    3 DIKNFLYAWC-GKKKLTPNYDIRAA-GNKNRQKFMCEVRVDGfNYIGMGNSTNKKDAQANAARDFVNYL 69
Cdd:cd10845      2 DYKTALQEYLqKRGLPLPEYELVEEeGPDHNKTFTVEVKVNG-KVIGEGTGRSKKEAEQAAAKAALEKL 69
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
413-775 1.23e-05

Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 49.25  E-value: 1.23e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  413 IIRGATGCGKTTqVPQYILDQYIRGGRAsecnIVVTqPRRISAVSVAERVAyergEDLGKSCGYSVRFESvlprpHASVL 492
Cdd:COG1061    104 LVVAPTGTGKTV-LALALAAELLRGKRV----LVLV-PRRELLEQWAEELR----RFLGDPLAGGGKKDS-----DAPIT 168

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  493 FCTVGVLLRK--LEAGIRGISHVIVDEIHErdINTDflmvVLRDVIHAFPDVRVVLMSAT---IDTTMFREYFFSCPIIE 567
Cdd:COG1061    169 VATYQSLARRahLDELGDRFGLVIIDEAHH--AGAP----SYRRILEAFPAAYRLGLTATpfrSDGREILLFLFDGIVYE 242

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  568 vfgrtYPVQQYFLEDCIQMTQFVPPPSDKKRKDKdeeggeeevncnlvcgpEYGPETKRSMAQMNEKETpfELIEALLKY 647
Cdd:COG1061    243 -----YSLKEAIEDGYLAPPEYYGIRVDLTDERA-----------------EYDALSERLREALAADAE--RKDKILREL 298

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  648 VETLQVAGAVLVFLPGwnliysmQKHLE-MNAHFGSHRYRILPLHSQIPREEQRLVFEPVPEGVTKVILSTNIAETSITI 726
Cdd:COG1061    299 LREHPDDRKTLVFCSS-------VDHAEaLAELLNEAGIRAAVVTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDV 371

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....*....
gi 1764642986  727 NDVVYVIdsckqkvklftahnnmtnYATVWASKTNLEQRKGRAGRVRPG 775
Cdd:COG1061    372 PRLDVAI------------------LLRPTGSPREFIQRLGRGLRPAPG 402
DSRM_EIF2AK2 cd20314
double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...
 12-63 4.84e-04

double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2) and similar proteins; 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. EIF2AK2 proteins 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: 380746  Cd Length: 68  Bit Score: 39.68  E-value: 4.84e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1764642986   12 CGKKKLTPNYDIRA-AGNKNRQKFMCEVRVDGFNYiGMGNSTNKKDAQANAAR 63
Cdd:cd20314     11 CQKERLTVKYEEEKrSGPTHKPRFFCKYIIDGKEY-PEGEGKSKKEAKQAAAR 62
DEXHc_viral_Ns3 cd17931
DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional ...
 411-550 5.21e-04

DEXH-box helicase domain of NS3 protease-helicase; NS3 is a nonstructural multifunctional protein found in pestiviruses that contains an N-terminal protease and a C-terminal helicase. The N-terminal domain is a chymotrypsin-like serine protease, which is responsible for most of the maturation cleavages of the polyprotein precursor in the cytosolic side of the endoplasmic reticulum membrane. The C-terminal domain, about two-thirds of NS3, is a helicase belonging to superfamily 2 (SF2) thought to be important for unwinding highly structured regions of the RNA genome during replication. NS3 plays an essential role in viral polyprotein processing and genome replication. NS3 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350689 [Multi-domain]  Cd Length: 151  Bit Score: 41.77  E-value: 5.21e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  411 VVIIRGATGCGKTTQV-PQYILDQYIRGGRasecnIVVTQPRRISAVSVAErvaYERGEDlgkscgysVRFE-SVLPRPH 488
Cdd:cd17931      3 LTVLDLHPGAGKTTRVlPQIIREAIKKRLR-----TLVLAPTRVVAAEMYE---ALRGLP--------IRYRtGAVKEEH 66

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  489 ---ASVLFCTVGVLLRKLEAGIRGISH--VIVDEIHerdiNTDFLMVVLRDVIHAF---PDVRVVLMSAT 550
Cdd:cd17931     67 ggnEIVDYMCHGTFTCRLLSPKRVPNYnlIIMDEAH----FTDPASIAARGYIHTRvemGEAAVIFMTAT 132
DSRM_EIF2AK2-like cd19875
double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...
 8-69 6.33e-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: 39.17  E-value: 6.33e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1764642986    8 LYAWCGKKKLTPNYDIRAAGNKNRQKFMCEVRVDGfNYIGMGNSTNKKDAQANAARDFVNYL 69
Cdd:cd19875      7 LNEYCQKRGLSLEFVDVSVGPDHCPGFTASATIDG-IVFASATGTSKKEAKRAAAKLALKKL 67
DEXHc_Mtr4-like cd18024
DEXH-box helicase domain of ATP-dependent RNA helicase Mtr4; Mtr4 (also known as DOB1 or ...
 398-559 8.60e-04

DEXH-box helicase domain of ATP-dependent RNA helicase Mtr4; Mtr4 (also known as DOB1 or SKIV2L2) is a type II DEAD box helicase that plays a role in the processing of structured RNAs, including the maturation of 5.8S ribosomal RNA (rRNA)and is part of the TRAMP complex that is involved in exosome-mediated degradation of aberrant RNAs. Mtr4 belongs 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: 350782 [Multi-domain]  Cd Length: 205  Bit Score: 42.05  E-value: 8.60e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  398 FEEEIMHTINSNPVVIIRGATGCGKTTqVPQYILDQYIRGGRasecNIVVTQPrrISAVSVAE-RVAYERGEDLGKSCGy 476
Cdd:cd18024     36 FQKTAIACIERNESVLVSAHTSAGKTV-VAEYAIAQSLRDKQ----RVIYTSP--IKALSNQKyRELQEEFGDVGLMTG- 107

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  477 svrfeSVLPRPHASVLFCTVGVLLRKLEAG---IRGISHVIVDEIH-----ERDintdflmVVLRDVIHAFPD-VRVVLM 547
Cdd:cd18024    108 -----DVTINPNASCLVMTTEILRSMLYRGseiMREVAWVIFDEIHymrdkERG-------VVWEETIILLPDkVRYVFL 175

                          170
                   ....*....|...
gi 1764642986  548 SATIDTTM-FREY 559
Cdd:cd18024    176 SATIPNARqFAEW 188
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
187-257 1.95e-03

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 41.24  E-value: 1.95e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1764642986  187 NAKARLNQFFQKEKIQT-DYK-YNQVGPDHNRSFIAEmtifVKqLRRNIFAREHGSNKKLAAQSCALSLVRQL 257
Cdd:COG0571    158 DYKTALQEWLQARGLPLpEYEvVEEEGPDHAKTFTVE----VL-VGGKVLGEGTGRSKKEAEQAAAKAALEKL 225
DSRM_PRKRA-like_rpt1 cd19862
first double-stranded RNA binding motif of protein activator of the interferon-induced protein ...
 8-71 5.15e-03

first double-stranded RNA binding motif of protein activator of the interferon-induced protein kinase (PRKRA) and similar proteins; This family includes protein activator of the interferon-induced protein kinase (PRKRA) and the RISC-loading complex subunit TARBP2. PRKRA (also known as interferon-inducible double-stranded RNA-dependent protein kinase activator A, PKR-associated protein X (RAX), PKR-associating protein X, protein kinase, interferon-inducible double-stranded RNA-dependent activator, PACT, or HSD14) is a cellular activator for double-stranded RNA-dependent protein kinase during stress signaling. TARBP2 (also called TAR RNA-binding protein 2, or trans-activation-responsive RNA-binding protein (TRBP)), participates in the formation of the RNA-induced silencing complex (RISC). It is part of the RISC-loading complex (RLC), together with dicer1 and eif2c2/ago2, and is required to process precursor miRNAs. This family also includes Drosophila melanogaster Loquacious and similar proteins. Loquacious (Loqs) is a double-stranded RNA-binding domain (dsRBD) protein, a homolog of human TAR RNA binding protein (TRBP) that is a protein first identified as binding the HIV trans-activator RNA (TAR). Loqs interacts with Dicer1 (dmDcr1) to facilitate miRNA processing. PRKRA family proteins contain three double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380691 [Multi-domain]  Cd Length: 70  Bit Score: 36.85  E-value: 5.15e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1764642986    8 LYAWCGKKKLTPNYD-IRAAGNKNRQKFMCEVRVDGFNYIGMGNStnKKDAQANAARDFVNYLVR 71
Cdd:cd19862      7 LQELCAKRGITPKYElISSEGAVHEPTFTFRVTVGDITATGSGTS--KKKAKHAAAENALEQLKG 69
Dob10 COG4581
Superfamily II RNA helicase [Replication, recombination and repair];
487-558 5.97e-03

Superfamily II RNA helicase [Replication, recombination and repair];


Pssm-ID: 443638 [Multi-domain]  Cd Length: 751  Bit Score: 40.69  E-value: 5.97e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1764642986  487 PHASVLFCTVGVLLRKLEAG---IRGISHVIVDEIHerdintdFL---------MVVLrdvIHAFPDVRVVLMSATI-DT 553
Cdd:COG4581    108 PDAPIVVMTTEILRNMLYREgadLEDVGVVVMDEFH-------YLadpdrgwvwEEPI---IHLPARVQLVLLSATVgNA 177


                   ....*
gi 1764642986  554 TMFRE 558
Cdd:COG4581    178 EEFAE 182
DSRM_RNT1p-like cd19876
double-stranded RNA binding motif of Saccharomyces cerevisiae ribonuclease 3 (RNT1p) and ...
 5-69 6.27e-03

double-stranded RNA binding motif of Saccharomyces cerevisiae ribonuclease 3 (RNT1p) and similar proteins; RNT1p (EC 3.1.26.3; also known as ribonuclease III (RNase III)) is a dsRNA-specific nuclease that cleaves eukaryotic pre-ribosomal RNA at the U3 snoRNP-dependent A0 site in the 5'-external transcribed spacer (ETS) and in the 3'-ETS. RNT1p contains 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: 380705  Cd Length: 69  Bit Score: 36.55  E-value: 6.27e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1764642986    5 KNFLYAWCGKKKLTPNYDIRAAGNKNRQKFMCEVRVDGfNYIGMGNSTNKKDAQANAARDFVNYL 69
Cdd:cd19876      5 KQKLYSLIGPASLKPEYVVVKKEGGNDPNYTVACRING-EVLGTGVGRSIKKAGQRAAMSALSNK 68
 
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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