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Conserved domains on  [gi|100913206|ref|NP_001348|]
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ATP-dependent RNA helicase A [Homo sapiens]

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 ...
 330-563 6.58e-169

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: 500.52  E-value: 6.58e-169
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  330 VPWSPPQSNWNPWTSSNIDEGPLAFATPEQISMDLKNELMYQLEQDHDLQAILQERELLPVKKFESEILEAISQNSVVII 409
Cdd:cd17972     1 VPWSPPQSNWNPWTSSNIDEGPLAFATPEQISMDLKNELMYQREQDHNLQQILQERELLPVKKFREEILEAISNNPVVII 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  410 RGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEPGKSCGYSVRFESILPRPHASIMFC 489
Cdd:cd17972    81 RGATGCGKTTQVPQYILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEVGKSCGYSVRFESVLPRPHASILFC 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 100913206  490 TVGVLLRKLEAGIRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPEVRIVLMSATIDTSMFCEYFFNCPIIEV 563
Cdd:cd17972   161 TVGVLLRKLEAGIRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPDLRVILMSATIDTSMFCEYFFNCPVIEV 234
HrpA super family cl34328
HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];
388-886 2.30e-115

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: 380.58  E-value: 2.30e-115
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  388 LPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDdfiqNDRAAECNIVVTQPRRISAVSVAERVAFERGEEPGK 467
Cdd:COG1643    10 LPVSAVLPELLAALRAHQVVVLAAPPGAGKTTQLPLALLE----LGWGAGGRIGMLEPRRLAARAAAERMAEELGEPVGE 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  468 SCGYSVRFESilpR--PHASIMFCTVGVLLRKLEA--GIRGISHVIVDEIHERDINTDFLLVVLRDVVQAY-PEVRIVLM 542
Cdd:COG1643    86 TVGYRVRFED---KvsAATRIEVVTEGILLRELQRdpELEGVDTVIFDEFHERSLNADLLLALLLDLQPALrPDLKLLVM 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  543 SATIDTSMFCEYFFNCPIIEVYGRTYPVQeyfledciqmTHFVPPPKDKKkkdkdddggedddancnlicgdeygpetrl 622
Cdd:COG1643   163 SATLDAERFARLLGDAPVIESSGRTYPVE----------VRYRPLPADER------------------------------ 202

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  623 smsqlneketpfELIEALLKYIETL--NVPGAVLVFLPGWNLIYTMQKHLEmnPHFGSHrYQILPLHSQIPREEQRKVFD 700
Cdd:COG1643   203 ------------DLEDAVADAVREAlaEEPGDILVFLPGEREIRRTAEALR--GRLPPD-TEILPLYGRLSAAEQDRAFA 267

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  701 PVPVGVTKVILSTNIAETSITINDVVYVIDSCKQKVKLFTAHNNMTNYATVWASKTNLEQRKGRAGRVRPGFCFHLCSRA 780
Cdd:COG1643   268 PAPHGRRRIVLATNIAETSLTVPGIRYVIDSGLARIPRYDPRSGVTRLPTERISQASANQRAGRAGRLAPGICYRLWSEE 347

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  781 RFERLETHMTPEMFRTPLHEIALSIKLLRLGGIGQFlaKAIEPPPLDAVIEAEHTLRELDALDANDELTPLGRILAKLPI 860
Cdd:COG1643   348 DFARRPAFTDPEILRADLASLILELAAWGLGDPEDL--PFLDPPPARAIADARALLQELGALDADGRLTPLGRALARLPL 425

                         490       500
                  ....*....|....*....|....*.
gi 100913206  861 EPRFGKMMIMGCIFYVGDAICTIAAA 886
Cdd:COG1643   426 DPRLARMLLAAAELGCLREAAILAAL 451
DSRM_DHX9_rpt2 cd19855
second double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; ...
 178-252 1.85e-44

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: 155.07  E-value: 1.85e-44
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 100913206  178 LENAKARLNQYFQKEKIQGEYKYTQVGPDHNRSFIAEMTIYIKQLGRRIFAREHGSNKKLAAQSCALSLVRQLYH 252
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 4.08e-40

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: 142.41  E-value: 4.08e-40
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 100913206    3 DVKNFLYAWCGKRKMTPSYEIRAVGNKNRQKFMCEVQVEGYNYTGMGNSTNKKDAQSNAARDFVNYLVR 71
Cdd:cd19854     1 EIKAFLYAWCGKKKLTPEYDIKEAGNKHRQRFKCEVRVEGFDYVGTGNATNKKDAQTNAARDFLNYLVR 69
OB_NTP_bind pfam07717
Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus ...
 994-1073 1.78e-19

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: 83.84  E-value: 1.78e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206   994 LLAFGVYPNVCYHKEKRKILTT--EGRNALIHKSSVNCpfssQDMKYPSPFFVFGEKIRTRAISAKGMTLVTPLQLLLFA 1071
Cdd:pfam07717    4 ALAAGLYPNVARRDPKGKGYTTlsDNQRVFIHPSSVLF----NEKTFPPEWVVYQELVETTKVYIRTVTAISPEWLLLFA 79


                   ..
gi 100913206  1072 SK 1073
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 ...
 330-563 6.58e-169

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: 500.52  E-value: 6.58e-169
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  330 VPWSPPQSNWNPWTSSNIDEGPLAFATPEQISMDLKNELMYQLEQDHDLQAILQERELLPVKKFESEILEAISQNSVVII 409
Cdd:cd17972     1 VPWSPPQSNWNPWTSSNIDEGPLAFATPEQISMDLKNELMYQREQDHNLQQILQERELLPVKKFREEILEAISNNPVVII 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  410 RGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEPGKSCGYSVRFESILPRPHASIMFC 489
Cdd:cd17972    81 RGATGCGKTTQVPQYILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEVGKSCGYSVRFESVLPRPHASILFC 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 100913206  490 TVGVLLRKLEAGIRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPEVRIVLMSATIDTSMFCEYFFNCPIIEV 563
Cdd:cd17972   161 TVGVLLRKLEAGIRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPDLRVILMSATIDTSMFCEYFFNCPVIEV 234
HrpA COG1643
HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];
388-886 2.30e-115

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


Pssm-ID: 441249 [Multi-domain]  Cd Length: 836  Bit Score: 380.58  E-value: 2.30e-115
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  388 LPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDdfiqNDRAAECNIVVTQPRRISAVSVAERVAFERGEEPGK 467
Cdd:COG1643    10 LPVSAVLPELLAALRAHQVVVLAAPPGAGKTTQLPLALLE----LGWGAGGRIGMLEPRRLAARAAAERMAEELGEPVGE 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  468 SCGYSVRFESilpR--PHASIMFCTVGVLLRKLEA--GIRGISHVIVDEIHERDINTDFLLVVLRDVVQAY-PEVRIVLM 542
Cdd:COG1643    86 TVGYRVRFED---KvsAATRIEVVTEGILLRELQRdpELEGVDTVIFDEFHERSLNADLLLALLLDLQPALrPDLKLLVM 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  543 SATIDTSMFCEYFFNCPIIEVYGRTYPVQeyfledciqmTHFVPPPKDKKkkdkdddggedddancnlicgdeygpetrl 622
Cdd:COG1643   163 SATLDAERFARLLGDAPVIESSGRTYPVE----------VRYRPLPADER------------------------------ 202

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  623 smsqlneketpfELIEALLKYIETL--NVPGAVLVFLPGWNLIYTMQKHLEmnPHFGSHrYQILPLHSQIPREEQRKVFD 700
Cdd:COG1643   203 ------------DLEDAVADAVREAlaEEPGDILVFLPGEREIRRTAEALR--GRLPPD-TEILPLYGRLSAAEQDRAFA 267

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  701 PVPVGVTKVILSTNIAETSITINDVVYVIDSCKQKVKLFTAHNNMTNYATVWASKTNLEQRKGRAGRVRPGFCFHLCSRA 780
Cdd:COG1643   268 PAPHGRRRIVLATNIAETSLTVPGIRYVIDSGLARIPRYDPRSGVTRLPTERISQASANQRAGRAGRLAPGICYRLWSEE 347

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  781 RFERLETHMTPEMFRTPLHEIALSIKLLRLGGIGQFlaKAIEPPPLDAVIEAEHTLRELDALDANDELTPLGRILAKLPI 860
Cdd:COG1643   348 DFARRPAFTDPEILRADLASLILELAAWGLGDPEDL--PFLDPPPARAIADARALLQELGALDADGRLTPLGRALARLPL 425

                         490       500
                  ....*....|....*....|....*.
gi 100913206  861 EPRFGKMMIMGCIFYVGDAICTIAAA 886
Cdd:COG1643   426 DPRLARMLLAAAELGCLREAAILAAL 451
DEAH_box_HrpA TIGR01967
RNA helicase HrpA; This model represents HrpA, one of two related but uncharacterized DEAH-box ...
 388-1026 5.82e-84

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: 300.53  E-value: 5.82e-84
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206   388 LPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILddfiQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEPGK 467
Cdd:TIGR01967   66 LPVSAKREDIAEAIAENQVVIIAGETGSGKTTQLPKICL----ELGRGSHGLIGHTQPRRLAARTVAQRIAEELGTPLGE 141

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206   468 SCGYSVRFESILpRPHASIMFCTVGVLLRKLEAGiRGISH---VIVDEIHERDINTDFLLVVLRDVVQAYPEVRIVLMSA 544
Cdd:TIGR01967  142 KVGYKVRFHDQV-SSNTLVKLMTDGILLAETQQD-RFLSRydtIIIDEAHERSLNIDFLLGYLKQLLPRRPDLKIIITSA 219

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206   545 TIDTSMFCEYFFNCPIIEVYGRTYPVQEYfledciqmthfvpppkdkkkkdkdddggedddancnlicgdeYGPetrlsm 624
Cdd:TIGR01967  220 TIDPERFSRHFNNAPIIEVSGRTYPVEVR------------------------------------------YRP------ 251

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206   625 sqLNEKETPFEL--IEALLKYIETL--NVPGAVLVFLPGWNLIYTMQKHLEmnphfgSHRY---QILPLHSQIPREEQRK 697
Cdd:TIGR01967  252 --LVEEQEDDDLdqLEAILDAVDELfaEGPGDILIFLPGEREIRDAAEILR------KRNLrhtEILPLYARLSNKEQQR 323

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206   698 VFDpvPVGVTKVILSTNIAETSITINDVVYVIDSCKQKVKLFTAHNNMTNYATVWASKTNLEQRKGRAGRVRPGFCFHLC 777
Cdd:TIGR01967  324 VFQ--PHSGRRIVLATNVAETSLTVPGIHYVIDTGTARISRYSYRTKVQRLPIEPISQASANQRKGRCGRVAPGICIRLY 401

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206   778 SRARFERLETHMTPEMFRTPLHEIALSIKLLRLGGIGQFlaKAIEPPPLDAVIEAEHTLRELDALD---ANDELTPLGRI 854
Cdd:TIGR01967  402 SEEDFNSRPEFTDPEILRTNLASVILQMLALRLGDIAAF--PFIEAPDPRAIRDGFRLLEELGALDddeAEPQLTPIGRQ 479

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206   855 LAKLPIEPRFGKMMIMGCIFYVGDAICTIAAATC------FPEPFINEGKRlgyIHRNFAGNRfSDHVALLSVFQAWDDA 928
Cdd:TIGR01967  480 LAQLPVDPRLARMLLEAHRLGCLQEVLIIASALSiqdpreRPMEKQQAADQ---AHARFKDPR-SDFLSRVNLWRHIEEQ 555

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206   929 RMGGEEAEIR-FCEHKRLNMATLRMTWEAKVQLKEILINSGFPedclltqvfTNTGPDNNLDVVISLLAfGVYPNVCYHK 1007
Cdd:TIGR01967  556 RQALSANQFRnACRKQYLNYLRVREWQDIYRQLTQVVKELGLK---------LNEEPADYDAIHKALLS-GLLSQIGMKD 625

                          650
                   ....*....|....*....
gi 100913206  1008 EKRKILTTEGRNALIHKSS 1026
Cdd:TIGR01967  626 EKHEYDGARGRKFHIFPGS 644
SF2_C_RHA cd18791
C-terminal helicase domain of the RNA helicase A (RHA) family helicases; The RNA helicase A ...
 568-777 3.91e-73

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: 240.51  E-value: 3.91e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  568 YPVQEYFLEDCIQMTHfvpppkdkkkkdkdddggedddancnlicgdeygpetrlsMSQLNEKETPFELIEALLKYIETL 647
Cdd:cd18791     1 FPVEVYYLEDILELLG----------------------------------------ISSEKEDPDYVDAAVRLILQIHRT 40

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  648 NVPGAVLVFLPGWNLIYTMQKHLEMNPHFGS-HRYQILPLHSQIPREEQRKVFDPVPVGVTKVILSTNIAETSITINDVV 726
Cdd:cd18791    41 EEPGDILVFLPGQEEIERLCELLREELLSPDlGKLLVLPLHSSLPPEEQQRVFEPPPPGVRKVVLATNIAETSITIPGVV 120

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 100913206  727 YVIDSCKQKVKLFTAHNNMTNYATVWASKTNLEQRKGRAGRVRPGFCFHLC 777
Cdd:cd18791   121 YVIDSGLVKEKVYDPRTGLSSLVTVWISKASAEQRAGRAGRTRPGKCYRLY 171
PRK11664 PRK11664
ATP-dependent RNA helicase HrpB; Provisional
 387-869 5.53e-69

ATP-dependent RNA helicase HrpB; Provisional


Pssm-ID: 236950 [Multi-domain]  Cd Length: 812  Bit Score: 249.07  E-value: 5.53e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  387 LLPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDRaaecnIVVTQPRRISAVSVAERVAFERGEEPG 466
Cdd:PRK11664    3 SLPVAAVLPELLTALKTAPQVLLKAPTGAGKSTWLPLQLLQHGGINGK-----IIMLEPRRLAARNVAQRLAEQLGEKPG 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  467 KSCGYSVRFESILPrPHASIMFCTVGVLLRKLE--AGIRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPE-VRIVLMS 543
Cdd:PRK11664   78 ETVGYRMRAESKVG-PNTRLEVVTEGILTRMIQrdPELSGVGLVILDEFHERSLQADLALALLLDVQQGLRDdLKLLIMS 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  544 ATIDTSMFCEYFFNCPIIEVYGRTYPVQeyfledciqmTHFVPppkdkkkkdkdddggedddancnlicgdeygpetrLS 623
Cdd:PRK11664  157 ATLDNDRLQQLLPDAPVIVSEGRSFPVE----------RRYQP-----------------------------------LP 191

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  624 MSQlneketPFEliEALLKYIETL--NVPGAVLVFLPGWNLIYTMQKHLEmnpHFGSHRYQILPLHSQIPREEQRKVFDP 701
Cdd:PRK11664  192 AHQ------RFD--EAVARATAELlrQESGSLLLFLPGVGEIQRVQEQLA---SRVASDVLLCPLYGALSLAEQQKAILP 260

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  702 VPVGVTKVILSTNIAETSITINDVVYVIDSCKQKVKLFTAHNNMTNYATVWASKTNLEQRKGRAGRVRPGFCFHLCSRAR 781
Cdd:PRK11664  261 APAGRRKVVLATNIAETSLTIEGIRLVVDSGLERVARFDPKTGLTRLVTQRISQASMTQRAGRAGRLEPGICLHLYSKEQ 340

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  782 FERLETHMTPEMFRTPLHEIALSikLLRLG--GIGQFlaKAIEPPPLDAVIEAEHTLRELDALDANDELTPLGRILAKLP 859
Cdd:PRK11664  341 AERAAAQSEPEILHSDLSGLLLE--LLQWGchDPAQL--SWLDQPPAAALAAAKRLLQQLGALDGQGRLTARGRKMAALG 416

                         490
                  ....*....|
gi 100913206  860 IEPRFGKMMI 869
Cdd:PRK11664  417 NDPRLAAMLV 426
DSRM_DHX9_rpt2 cd19855
second double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; ...
 178-252 1.85e-44

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: 155.07  E-value: 1.85e-44
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 100913206  178 LENAKARLNQYFQKEKIQGEYKYTQVGPDHNRSFIAEMTIYIKQLGRRIFAREHGSNKKLAAQSCALSLVRQLYH 252
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 4.08e-40

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: 142.41  E-value: 4.08e-40
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 100913206    3 DVKNFLYAWCGKRKMTPSYEIRAVGNKNRQKFMCEVQVEGYNYTGMGNSTNKKDAQSNAARDFVNYLVR 71
Cdd:cd19854     1 EIKAFLYAWCGKKKLTPEYDIKEAGNKHRQRFKCEVRVEGFDYVGTGNATNKKDAQTNAARDFLNYLVR 69
DEXDc smart00487
DEAD-like helicases superfamily;
396-569 8.05e-23

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 97.56  E-value: 8.05e-23
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206    396 EILEAISQN-SVVIIRGATGCGKTTQVPQFILDDFIQNDRaaeCNIVVTQPRRISAVSVAERVAFERGEEPGKSCGYSVR 474
Cdd:smart00487   15 EAIEALLSGlRDVILAAPTGSGKTLAALLPALEALKRGKG---GRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGG 91

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206    475 FESI-----LPRPHASIMFCTVGVLLRKLEAG---IRGISHVIVDEIHERDiNTDFLLVVLRDVVQAYPEVRIVLMSATI 546
Cdd:smart00487   92 DSKReqlrkLESGKTDILVTTPGRLLDLLENDklsLSNVDLVILDEAHRLL-DGGFGDQLEKLLKLLPKNVQLLLLSATP 170

                           170       180
                    ....*....|....*....|....*
gi 100913206    547 --DTSMFCEYFFNCPIIEVYGRTYP 569
Cdd:smart00487  171 peEIENLLELFLNDPVFIDVGFTPL 195
HA2 smart00847
Helicase associated domain (HA2) Add an annotation; This presumed domain is about 90 amino ...
 838-919 8.58e-22

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: 90.41  E-value: 8.58e-22
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206    838 ELDALDANDELTPLGRILAKLPIEPRFGKMMIMGCIFYVGDAICTIAAATCFPEPFINE-GKRLGYIHRNFAGNRfSDHV 916
Cdd:smart00847    1 ELGALDDDGRLTPLGRKMAELPLDPRLAKMLLAAAEFGCLDEILTIVAMLSVGDPRPKEkREDADAARRRFADPE-SDHL 79


                    ...
gi 100913206    917 ALL 919
Cdd:smart00847   80 TLL 82
HA2 pfam04408
Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in ...
 832-918 5.10e-21

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: 89.22  E-value: 5.10e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206   832 AEHTLRELDALDANDELTPLGRILAKLPIEPRFGKMMIMGCIFYVGDAICTIAAATCFPEPFINEG-------------- 897
Cdd:pfam04408    1 ALELLYYLGALDEDGELTPLGRKMAELPLDPRLAKMLLAAAELGCLDEVLTIVAALSVRDPFVQPNfldprsaakaarrr 80

                           90       100
                   ....*....|....*....|....
gi 100913206   898 --KRLGYIHRNFAGNRF-SDHVAL 918
Cdd:pfam04408   81 rrAADEKARAKFARLDLeGDHLTL 104
OB_NTP_bind pfam07717
Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus ...
 994-1073 1.78e-19

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: 83.84  E-value: 1.78e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206   994 LLAFGVYPNVCYHKEKRKILTT--EGRNALIHKSSVNCpfssQDMKYPSPFFVFGEKIRTRAISAKGMTLVTPLQLLLFA 1071
Cdd:pfam07717    4 ALAAGLYPNVARRDPKGKGYTTlsDNQRVFIHPSSVLF----NEKTFPPEWVVYQELVETTKVYIRTVTAISPEWLLLFA 79


                   ..
gi 100913206  1072 SK 1073
Cdd:pfam07717   80 PH 81
DSRM smart00358
Double-stranded RNA binding motif;
5-69 3.72e-16

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 73.84  E-value: 3.72e-16
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 100913206      5 KNFLYAWCGKRKMTPSYE-IRAVGNKNRQKFMCEVQVEGYnYTGMGNSTNKKDAQSNAARDFVNYL 69
Cdd:smart00358    2 KSLLQELAQKRKLPPEYElVKEEGPDHAPRFTVTVKVGGK-RTGEGEGSSKKEAKQRAAEAALRSL 66
DSRM smart00358
Double-stranded RNA binding motif;
181-251 2.31e-14

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 68.83  E-value: 2.31e-14
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 100913206    181 AKARLNQYFQKEKIQGEYKYT-QVGPDHNRSFIAEMTIyikqlGRRIFAREHGSNKKLAAQSCALSLVRQLY 251
Cdd:smart00358    1 PKSLLQELAQKRKLPPEYELVkEEGPDHAPRFTVTVKV-----GGKRTGEGEGSSKKEAKQRAAEAALRSLK 67
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 181-250 5.17e-13

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: 64.94  E-value: 5.17e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 100913206   181 AKARLNQYFQKEKIQGEYKYT-QVGPDHNRSFIAEMTIyikqlGRRIFAREHGSNKKLAAQSCALSLVRQL 250
Cdd:pfam00035    1 PKSLLQEYAQKNGKPPPYEYVsEEGPPHSPKFTVTVKV-----DGKLYGSGTGSSKKEAEQLAAEKALEKL 66
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 5-69 3.11e-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: 62.63  E-value: 3.11e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 100913206     5 KNFLYAWCGKRKMTPSYEIRAV-GNKNRQKFMCEVQVEGYNYtGMGNSTNKKDAQSNAARDFVNYL 69
Cdd:pfam00035    2 KSLLQEYAQKNGKPPPYEYVSEeGPPHSPKFTVTVKVDGKLY-GSGTGSSKKEAEQLAAEKALEKL 66
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 395-547 2.00e-06

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


Pssm-ID: 425570 [Multi-domain]  Cd Length: 165  Bit Score: 49.16  E-value: 2.00e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206   395 SEILEAISQNSVVIIRGATGCGKTT--QVPqfILDDFIQNDRAAECnIVVTqPRRISAVSVAERVafergEEPGKSCGYS 472
Cdd:pfam00270    5 AEAIPAILEGRDVLVQAPTGSGKTLafLLP--ALEALDKLDNGPQA-LVLA-PTRELAEQIYEEL-----KKLGKGLGLK 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206   473 VRFE----------SILPRPHasIMFCTVGVLLR--KLEAGIRGISHVIVDEIHErdINTDFLLVVLRDVV-QAYPEVRI 539
Cdd:pfam00270   76 VASLlggdsrkeqlEKLKGPD--ILVGTPGRLLDllQERKLLKNLKLLVLDEAHR--LLDMGFGPDLEEILrRLPKKRQI 151


                   ....*...
gi 100913206   540 VLMSATID 547
Cdd:pfam00270  152 LLLSATLP 159
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
180-250 9.34e-04

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 42.39  E-value: 9.34e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 100913206  180 NAKARLNQYFQKEKIQG-EYKYTQV-GPDHNRSFIAEMTIyikqlGRRIFAREHGSNKKLAAQSCALSLVRQL 250
Cdd:COG0571   158 DYKTALQEWLQARGLPLpEYEVVEEeGPDHAKTFTVEVLV-----GGKVLGEGTGRSKKEAEQAAAKAALEKL 225
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
13-69 3.98e-03

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 40.47  E-value: 3.98e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 100913206   13 GKRKMTPSYEIRAV-GNKNRQKFMCEVQVEGYNY-TGMGNStnKKDAQSNAARDFVNYL 69
Cdd:COG0571   169 ARGLPLPEYEVVEEeGPDHAKTFTVEVLVGGKVLgEGTGRS--KKEAEQAAAKAALEKL 225
 
Name Accession Description Interval E-value
DEXHc_DHX9 cd17972
DEXH-box helicase domain of DEAH-box helicase 9; DEAH-box helicase 9 (DHX9, also known as ...
 330-563 6.58e-169

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: 500.52  E-value: 6.58e-169
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  330 VPWSPPQSNWNPWTSSNIDEGPLAFATPEQISMDLKNELMYQLEQDHDLQAILQERELLPVKKFESEILEAISQNSVVII 409
Cdd:cd17972     1 VPWSPPQSNWNPWTSSNIDEGPLAFATPEQISMDLKNELMYQREQDHNLQQILQERELLPVKKFREEILEAISNNPVVII 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  410 RGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEPGKSCGYSVRFESILPRPHASIMFC 489
Cdd:cd17972    81 RGATGCGKTTQVPQYILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEVGKSCGYSVRFESVLPRPHASILFC 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 100913206  490 TVGVLLRKLEAGIRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPEVRIVLMSATIDTSMFCEYFFNCPIIEV 563
Cdd:cd17972   161 TVGVLLRKLEAGIRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPDLRVILMSATIDTSMFCEYFFNCPVIEV 234
HrpA COG1643
HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis];
388-886 2.30e-115

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


Pssm-ID: 441249 [Multi-domain]  Cd Length: 836  Bit Score: 380.58  E-value: 2.30e-115
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  388 LPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDdfiqNDRAAECNIVVTQPRRISAVSVAERVAFERGEEPGK 467
Cdd:COG1643    10 LPVSAVLPELLAALRAHQVVVLAAPPGAGKTTQLPLALLE----LGWGAGGRIGMLEPRRLAARAAAERMAEELGEPVGE 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  468 SCGYSVRFESilpR--PHASIMFCTVGVLLRKLEA--GIRGISHVIVDEIHERDINTDFLLVVLRDVVQAY-PEVRIVLM 542
Cdd:COG1643    86 TVGYRVRFED---KvsAATRIEVVTEGILLRELQRdpELEGVDTVIFDEFHERSLNADLLLALLLDLQPALrPDLKLLVM 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  543 SATIDTSMFCEYFFNCPIIEVYGRTYPVQeyfledciqmTHFVPPPKDKKkkdkdddggedddancnlicgdeygpetrl 622
Cdd:COG1643   163 SATLDAERFARLLGDAPVIESSGRTYPVE----------VRYRPLPADER------------------------------ 202

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  623 smsqlneketpfELIEALLKYIETL--NVPGAVLVFLPGWNLIYTMQKHLEmnPHFGSHrYQILPLHSQIPREEQRKVFD 700
Cdd:COG1643   203 ------------DLEDAVADAVREAlaEEPGDILVFLPGEREIRRTAEALR--GRLPPD-TEILPLYGRLSAAEQDRAFA 267

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  701 PVPVGVTKVILSTNIAETSITINDVVYVIDSCKQKVKLFTAHNNMTNYATVWASKTNLEQRKGRAGRVRPGFCFHLCSRA 780
Cdd:COG1643   268 PAPHGRRRIVLATNIAETSLTVPGIRYVIDSGLARIPRYDPRSGVTRLPTERISQASANQRAGRAGRLAPGICYRLWSEE 347

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  781 RFERLETHMTPEMFRTPLHEIALSIKLLRLGGIGQFlaKAIEPPPLDAVIEAEHTLRELDALDANDELTPLGRILAKLPI 860
Cdd:COG1643   348 DFARRPAFTDPEILRADLASLILELAAWGLGDPEDL--PFLDPPPARAIADARALLQELGALDADGRLTPLGRALARLPL 425

                         490       500
                  ....*....|....*....|....*.
gi 100913206  861 EPRFGKMMIMGCIFYVGDAICTIAAA 886
Cdd:COG1643   426 DPRLARMLLAAAELGCLREAAILAAL 451
DEAH_box_HrpA TIGR01967
RNA helicase HrpA; This model represents HrpA, one of two related but uncharacterized DEAH-box ...
 388-1026 5.82e-84

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: 300.53  E-value: 5.82e-84
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206   388 LPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILddfiQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEPGK 467
Cdd:TIGR01967   66 LPVSAKREDIAEAIAENQVVIIAGETGSGKTTQLPKICL----ELGRGSHGLIGHTQPRRLAARTVAQRIAEELGTPLGE 141

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206   468 SCGYSVRFESILpRPHASIMFCTVGVLLRKLEAGiRGISH---VIVDEIHERDINTDFLLVVLRDVVQAYPEVRIVLMSA 544
Cdd:TIGR01967  142 KVGYKVRFHDQV-SSNTLVKLMTDGILLAETQQD-RFLSRydtIIIDEAHERSLNIDFLLGYLKQLLPRRPDLKIIITSA 219

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206   545 TIDTSMFCEYFFNCPIIEVYGRTYPVQEYfledciqmthfvpppkdkkkkdkdddggedddancnlicgdeYGPetrlsm 624
Cdd:TIGR01967  220 TIDPERFSRHFNNAPIIEVSGRTYPVEVR------------------------------------------YRP------ 251

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206   625 sqLNEKETPFEL--IEALLKYIETL--NVPGAVLVFLPGWNLIYTMQKHLEmnphfgSHRY---QILPLHSQIPREEQRK 697
Cdd:TIGR01967  252 --LVEEQEDDDLdqLEAILDAVDELfaEGPGDILIFLPGEREIRDAAEILR------KRNLrhtEILPLYARLSNKEQQR 323

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206   698 VFDpvPVGVTKVILSTNIAETSITINDVVYVIDSCKQKVKLFTAHNNMTNYATVWASKTNLEQRKGRAGRVRPGFCFHLC 777
Cdd:TIGR01967  324 VFQ--PHSGRRIVLATNVAETSLTVPGIHYVIDTGTARISRYSYRTKVQRLPIEPISQASANQRKGRCGRVAPGICIRLY 401

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206   778 SRARFERLETHMTPEMFRTPLHEIALSIKLLRLGGIGQFlaKAIEPPPLDAVIEAEHTLRELDALD---ANDELTPLGRI 854
Cdd:TIGR01967  402 SEEDFNSRPEFTDPEILRTNLASVILQMLALRLGDIAAF--PFIEAPDPRAIRDGFRLLEELGALDddeAEPQLTPIGRQ 479

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206   855 LAKLPIEPRFGKMMIMGCIFYVGDAICTIAAATC------FPEPFINEGKRlgyIHRNFAGNRfSDHVALLSVFQAWDDA 928
Cdd:TIGR01967  480 LAQLPVDPRLARMLLEAHRLGCLQEVLIIASALSiqdpreRPMEKQQAADQ---AHARFKDPR-SDFLSRVNLWRHIEEQ 555

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206   929 RMGGEEAEIR-FCEHKRLNMATLRMTWEAKVQLKEILINSGFPedclltqvfTNTGPDNNLDVVISLLAfGVYPNVCYHK 1007
Cdd:TIGR01967  556 RQALSANQFRnACRKQYLNYLRVREWQDIYRQLTQVVKELGLK---------LNEEPADYDAIHKALLS-GLLSQIGMKD 625

                          650
                   ....*....|....*....
gi 100913206  1008 EKRKILTTEGRNALIHKSS 1026
Cdd:TIGR01967  626 EKHEYDGARGRKFHIFPGS 644
DEXHc_RHA-like cd17917
DEXH-box helicase domain of DEAD-like helicase RHA family proteins; The RNA helicase A (RHA) ...
 404-563 9.77e-82

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: 264.32  E-value: 9.77e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  404 NSVVIIRGATGCGKTTQVPQFILDDFIQNDRaaECNIVVTQPRRISAVSVAERVAFERGEEPGKSCGYSVRFESILPrPH 483
Cdd:cd17917     1 NQVVVIVGETGSGKTTQVPQFLLEDGLAKGG--KGRIVCTQPRRIAAISVAERVAEERGEKLGEEVGYQIRFESKTS-SK 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  484 ASIMFCTVGVLLRKLEAG--IRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPEVRIVLMSATIDTSMFCEYFFNCPII 561
Cdd:cd17917    78 TRIKFCTDGILLRELLSDplLSGYSHVILDEAHERSLDTDFLLGLLKDLLRKRPDLKVILMSATLDAEKFSSYFGGAPVI 157


                  ..
gi 100913206  562 EV 563
Cdd:cd17917   158 HI 159
SF2_C_RHA cd18791
C-terminal helicase domain of the RNA helicase A (RHA) family helicases; The RNA helicase A ...
 568-777 3.91e-73

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: 240.51  E-value: 3.91e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  568 YPVQEYFLEDCIQMTHfvpppkdkkkkdkdddggedddancnlicgdeygpetrlsMSQLNEKETPFELIEALLKYIETL 647
Cdd:cd18791     1 FPVEVYYLEDILELLG----------------------------------------ISSEKEDPDYVDAAVRLILQIHRT 40

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  648 NVPGAVLVFLPGWNLIYTMQKHLEMNPHFGS-HRYQILPLHSQIPREEQRKVFDPVPVGVTKVILSTNIAETSITINDVV 726
Cdd:cd18791    41 EEPGDILVFLPGQEEIERLCELLREELLSPDlGKLLVLPLHSSLPPEEQQRVFEPPPPGVRKVVLATNIAETSITIPGVV 120

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 100913206  727 YVIDSCKQKVKLFTAHNNMTNYATVWASKTNLEQRKGRAGRVRPGFCFHLC 777
Cdd:cd18791   121 YVIDSGLVKEKVYDPRTGLSSLVTVWISKASAEQRAGRAGRTRPGKCYRLY 171
DEXHc_DHX30 cd17976
DEXH-box helicase domain of DEAH-box helicase 30; DEAH-box helicase 30 (DHX30) plays an ...
 388-563 5.37e-73

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: 240.46  E-value: 5.37e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  388 LPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEPGK 467
Cdd:cd17976     1 LPVDSHKESILSAIEQNPVVVISGDTGCGKTTRIPQFILEDYVLRGRGARCNVVITQPRRISAVSVAQRVAHELGPNLRR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  468 SCGYSVRFESILPRPHASIMFCTVGVLLRKLE--AGIRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPEVRIVLMSAT 545
Cdd:cd17976    81 NVGYQVRLESRPPPRGGALLFCTVGVLLKKLQsnPRLEGVSHVIVDEVHERDVNTDFLLILLKGVLQLNPELRVVLMSAT 160

                         170
                  ....*....|....*...
gi 100913206  546 IDTSMFCEYFFNCPIIEV 563
Cdd:cd17976   161 GDNQRLSRYFGGCPVVRV 178
PRK11664 PRK11664
ATP-dependent RNA helicase HrpB; Provisional
 387-869 5.53e-69

ATP-dependent RNA helicase HrpB; Provisional


Pssm-ID: 236950 [Multi-domain]  Cd Length: 812  Bit Score: 249.07  E-value: 5.53e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  387 LLPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDRaaecnIVVTQPRRISAVSVAERVAFERGEEPG 466
Cdd:PRK11664    3 SLPVAAVLPELLTALKTAPQVLLKAPTGAGKSTWLPLQLLQHGGINGK-----IIMLEPRRLAARNVAQRLAEQLGEKPG 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  467 KSCGYSVRFESILPrPHASIMFCTVGVLLRKLE--AGIRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPE-VRIVLMS 543
Cdd:PRK11664   78 ETVGYRMRAESKVG-PNTRLEVVTEGILTRMIQrdPELSGVGLVILDEFHERSLQADLALALLLDVQQGLRDdLKLLIMS 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  544 ATIDTSMFCEYFFNCPIIEVYGRTYPVQeyfledciqmTHFVPppkdkkkkdkdddggedddancnlicgdeygpetrLS 623
Cdd:PRK11664  157 ATLDNDRLQQLLPDAPVIVSEGRSFPVE----------RRYQP-----------------------------------LP 191

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  624 MSQlneketPFEliEALLKYIETL--NVPGAVLVFLPGWNLIYTMQKHLEmnpHFGSHRYQILPLHSQIPREEQRKVFDP 701
Cdd:PRK11664  192 AHQ------RFD--EAVARATAELlrQESGSLLLFLPGVGEIQRVQEQLA---SRVASDVLLCPLYGALSLAEQQKAILP 260

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  702 VPVGVTKVILSTNIAETSITINDVVYVIDSCKQKVKLFTAHNNMTNYATVWASKTNLEQRKGRAGRVRPGFCFHLCSRAR 781
Cdd:PRK11664  261 APAGRRKVVLATNIAETSLTIEGIRLVVDSGLERVARFDPKTGLTRLVTQRISQASMTQRAGRAGRLEPGICLHLYSKEQ 340

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  782 FERLETHMTPEMFRTPLHEIALSikLLRLG--GIGQFlaKAIEPPPLDAVIEAEHTLRELDALDANDELTPLGRILAKLP 859
Cdd:PRK11664  341 AERAAAQSEPEILHSDLSGLLLE--LLQWGchDPAQL--SWLDQPPAAALAAAKRLLQQLGALDGQGRLTARGRKMAALG 416

                         490
                  ....*....|
gi 100913206  860 IEPRFGKMMI 869
Cdd:PRK11664  417 NDPRLAAMLV 426
DEXHc_DHX36 cd17981
DEXH-box helicase domain of DEAH-box helicase 36; DEAH-box helicase 36 (DHX36, also known as ...
 388-563 1.18e-67

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


Pssm-ID: 350739 [Multi-domain]  Cd Length: 180  Bit Score: 225.49  E-value: 1.18e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  388 LPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEP-- 465
Cdd:cd17981     1 LPSYGMKQEIINMIDNNQVTVISGETGCGKTTQVTQFILDDAIERGKGSSCRIVCTQPRRISAISVAERVAAERAESCgl 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  466 GKSCGYSVRFESILPRPHASIMFCTVGVLLRKLEAG--IRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPEVRIVLMS 543
Cdd:cd17981    81 GNSTGYQIRLESRKPRKQGSILYCTTGIVLQWLQSDphLSNVSHLVLDEIHERNLQSDVLMGIVKDLLPFRSDLKVILMS 160

                         170       180
                  ....*....|....*....|
gi 100913206  544 ATIDTSMFCEYFFNCPIIEV 563
Cdd:cd17981   161 ATLNAEKFSDYFNNCPMIHI 180
PRK11131 PRK11131
ATP-dependent RNA helicase HrpA; Provisional
 355-892 1.23e-65

ATP-dependent RNA helicase HrpA; Provisional


Pssm-ID: 182986 [Multi-domain]  Cd Length: 1294  Bit Score: 244.20  E-value: 1.23e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  355 ATPEQISMDLKNELMYQLEQDHDLQAIlQERELLPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILddfiQNDR 434
Cdd:PRK11131   41 AIFQEIAKEIAQAAQRVLLREAARPEI-TYPENLPVSQKKQDILEAIRDHQVVIVAGETGSGKTTQLPKICL----ELGR 115

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  435 AAECNIVVTQPRRISAVSVAERVAFERGEEPGKSCGYSVRF-ESILPRPHASIMfcTVGVLLRKLEAGiRGISH---VIV 510
Cdd:PRK11131  116 GVKGLIGHTQPRRLAARTVANRIAEELETELGGCVGYKVRFnDQVSDNTMVKLM--TDGILLAEIQQD-RLLMQydtIII 192

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  511 DEIHERDINTDFLLVVLRDVVQAYPEVRIVLMSATIDTSMFCEYFFNCPIIEVYGRTYPVqeyfledciqmthfvpppkd 590
Cdd:PRK11131  193 DEAHERSLNIDFILGYLKELLPRRPDLKVIITSATIDPERFSRHFNNAPIIEVSGRTYPV-------------------- 252

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  591 kkkkdkdddggedddancnlicgdeygpETRLSMSQLNEKETPFELIEALLKYIETLNV--PGAVLVFLPGWNLIYTMQK 668
Cdd:PRK11131  253 ----------------------------EVRYRPIVEEADDTERDQLQAIFDAVDELGRegPGDILIFMSGEREIRDTAD 304

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  669 HLEMN--PHfgshrYQILPLHSQIPREEQRKVFDpvPVGVTKVILSTNIAETSITINDVVYVIDSCKQKVKLFTAHNNMT 746
Cdd:PRK11131  305 ALNKLnlRH-----TEILPLYARLSNSEQNRVFQ--SHSGRRIVLATNVAETSLTVPGIKYVIDPGTARISRYSYRTKVQ 377

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  747 NYATVWASKTNLEQRKGRAGRVRPGFCFHLCSRARFERLETHMTPEMFRTPLHEIALSIKLLRLGGIGQFlaKAIEPPPL 826
Cdd:PRK11131  378 RLPIEPISQASANQRKGRCGRVSEGICIRLYSEDDFLSRPEFTDPEILRTNLASVILQMTALGLGDIAAF--PFVEAPDK 455

                         490       500       510       520       530       540       550
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 100913206  827 DAVIEAEHTLRELDALDAND-----ELTPLGRILAKLPIEPRFGKMMI----MGCIFYVgdaiCTIAAATCFPEP 892
Cdd:PRK11131  456 RNIQDGVRLLEELGAITTDEqasayKLTPLGRQLAQLPVDPRLARMVLeaqkHGCVREV----MIITSALSIQDP 526
DEXHc_DHX57 cd17985
DEXH-box helicase domain of DEAH-box helicase 57; DEAH-box helicase 57 (DHX57) belongs to the ...
 388-563 4.03e-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: 206.62  E-value: 4.03e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  388 LPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEPGK 467
Cdd:cd17985     1 LPAWQERETILELLEKHQVLVISGMTGCGKTTQIPQFILDNSLQGPPLPVANIICTQPRRISAISVAERVAQERAERVGQ 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  468 SCGYSVRFESILPRPhASIMFCTVGVLLRKLEAG--IRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPEVRIVLMSAT 545
Cdd:cd17985    81 SVGYQIRLESVKSSA-TRLLYCTTGVLLRRLEGDptLQGVTHVIVDEVHERTEESDFLLLVLKDLMVQRPDLKVILMSAT 159

                         170
                  ....*....|....*...
gi 100913206  546 IDTSMFCEYFFNCPIIEV 563
Cdd:cd17985   160 LNAELFSDYFNSCPVIHI 177
DEXHc_YTHDC2 cd17987
DEXH-box helicase domain of YTH domain containing 2; YTH domain containing 2 (YTHDC2) ...
 388-563 1.43e-59

DEXH-box helicase domain of YTH domain containing 2; YTH domain containing 2 (YTHDC2) regulates mRNA translation and stability via binding to N6-methyladenosine, a modified RNA nucleotide enriched in the stop codons and 3' UTRs of eukaryotic messenger RNAs. YTHDC2 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350745 [Multi-domain]  Cd Length: 176  Bit Score: 202.37  E-value: 1.43e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  388 LPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNdrAAECNIVVTQPRRISAVSVAERVAFERGEEPGK 467
Cdd:cd17987     1 LPVFEKQEQIVRIIKENKVVLIVGETGSGKTTQIPQFLLDDCYAN--GIPCRIFCTQPRRLAAIAVAERVAAERGEKIGQ 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  468 SCGYSVRFESILpRPHASIMFCTVGVLLRKLEAG---IRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPEVRIVLMSA 544
Cdd:cd17987    79 TVGYQIRLESRV-SPKTLLTFCTNGVLLRTLMAGdsaLSTVTHVIVDEVHERDRFSDFLLTKLRDILQKHPNLKLILSSA 157

                         170
                  ....*....|....*....
gi 100913206  545 TIDTSMFCEYFFNCPIIEV 563
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 ...
 388-563 1.13e-56

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: 194.36  E-value: 1.13e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  388 LPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQN-DRAAECNIVVTQPRRISAVSVAERVAFERGEEPG 466
Cdd:cd17975     1 LPVFKHRESILETLKRHRVVVVAGETGSGKSTQVPQFLLEDLLLNgGTAQKCNIVCTQPRRISAMSLATRVCEELGCESG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  467 KS-----CGYSVRFESilpRPHAS--IMFCTVGVLLRKLEAG--IRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPEV 537
Cdd:cd17975    81 PGgknslCGYQIRMES---RTGEAtrLLYCTTGVLLRKLQEDglLSSISHIIVDEVHERSVQSDFLLIILKEILHKRSDL 157

                         170       180
                  ....*....|....*....|....*.
gi 100913206  538 RIVLMSATIDTSMFCEYFFNCPIIEV 563
Cdd:cd17975   158 HLILMSATVDCEKFSSYFTHCPILRI 183
DEXHc_TDRD9 cd17988
DEXH-box helicase domain of tudor domain containing 9; Tudor domain containing 9 (TDRD9, also ...
 388-555 1.14e-52

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: 182.70  E-value: 1.14e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  388 LPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQndRAAECNIVVTQPRRISAVSVAERVAFERGEEPGK 467
Cdd:cd17988     1 LPIYAKREEILSLIEANSVVIIKGATGCGKTTQLPQFILDHYYK--RGKYCNIVVTQPRRIAAISIARRVSQEREWTLGS 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  468 SCGYSVRFESILPRpHASIMFCTVGVLLRKL--EAGIRGISHVIVDEIHERDINTDFLLVVLRDVVQAYP-EVRIVLMSA 544
Cdd:cd17988    79 LVGYQVGLERPASE-ETRLIYCTTGVLLQKLinNKTLTEYTHIILDEVHERDQELDFLLLVVRRLLRTNSrHVKIILMSA 157

                         170
                  ....*....|.
gi 100913206  545 TIDTSMFCEYF 555
Cdd:cd17988   158 TISCKEFADYF 168
DEXHc_DHX33 cd17978
DEXH-box helicase domain of DEAH-box helicase 33; DEAH-box helicase 33 (DHX33) stimulates RNA ...
 388-561 2.66e-48

DEXH-box helicase domain of DEAH-box helicase 33; DEAH-box helicase 33 (DHX33) stimulates RNA polymerase I transcription of the 47S precursor rRNA. DHX33 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438710 [Multi-domain]  Cd Length: 178  Bit Score: 169.84  E-value: 2.66e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  388 LPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDRAaecnIVVTQPRRISAVSVAERVAFERGEEPGK 467
Cdd:cd17978     1 LPIYSARKRLLEELRKHDTVIIIGETGSGKTTQIPQYLYEAGFARGGM----IGITQPRRVAAVSVAKRVAEEMGVELGQ 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  468 SCGYSVRFESIlPRPHASIMFCTVGVLLRK--LEAGIRGISHVIVDEIHERDINTDFLLVVLRDV-----VQAYPEVRIV 540
Cdd:cd17978    77 LVGYSVRFDDV-TSEETRIKYMTDGMLLREaiGDPLLSKYSVIILDEAHERTVHTDVLFGLVKSAqrrrkEQKLSPLKVI 155

                         170       180
                  ....*....|....*....|.
gi 100913206  541 LMSATIDTSMFCEYFFNCPII 561
Cdd:cd17978   156 IMSATLDADLFSEYFNGAPVL 176
DEXHc_DHX34 cd17979
DEXH-box helicase domain of DEAH-box helicase 34; DEAH-box helicase 34 (DHX34) plays a role in ...
 388-563 4.69e-48

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: 169.16  E-value: 4.69e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  388 LPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDdfiqndrAAECNIVVTQPRRISAVSVAERVAFERGEEPGK 467
Cdd:cd17979     1 LPIAQYREKIIELLKTHQVVIVAGDTGCGKSTQVPQYLLA-------AGFRHIACTQPRRIACISLAKRVAFESLNQYGS 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  468 SCGYSVRFESIlPRPHASIMFCTVGVLLRKLE--AGIRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPEVRIVLMSAT 545
Cdd:cd17979    74 KVAYQIRFERT-RTLATKLLFLTEGLLLRQIQrdASLPQYNVLILDEVHERHLHGDFLLGVLRCLLRLRPDLKLILMSAT 152

                         170
                  ....*....|....*...
gi 100913206  546 IDTSMFCEYFFNCPIIEV 563
Cdd:cd17979   153 INIELFSGYFEGAPVVQV 170
DSRM_DHX9_rpt2 cd19855
second double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; ...
 178-252 1.85e-44

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: 155.07  E-value: 1.85e-44
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 100913206  178 LENAKARLNQYFQKEKIQGEYKYTQVGPDHNRSFIAEMTIYIKQLGRRIFAREHGSNKKLAAQSCALSLVRQLYH 252
Cdd:cd19855     1 LDNAKSRLNEFLQKNKIPAEYKYTSVGPDHNRSFIAELSIFVKQLGKTIYARETGSNKKLASQSCALSLVRQLYH 75
DEXHc_DHX15 cd17973
DEXH-box helicase domain of DEAH-box helicase 15; DEAH-box helicase 15 (DHX15) is a pre-mRNA ...
 379-563 4.83e-44

DEXH-box helicase domain of DEAH-box helicase 15; DEAH-box helicase 15 (DHX15) is a pre-mRNA processing factor involved in disassembly of spliceosomes after the release of mature mRNA. DHX15 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 438709 [Multi-domain]  Cd Length: 187  Bit Score: 157.96  E-value: 4.83e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  379 QAILQERELLPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDRAAEcnIVVTQPRRISAVSVAERVA 458
Cdd:cd17973     4 FEILEKRRELPVWEQKEDFLKLLKNNQILVLVGETGSGKTTQIPQFVLDDELPHQPKKL--VACTQPRRVAAMSVAQRVA 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  459 FERGEEPGKSCGYSVRFESiLPRPHASIMFCTVGVLLRKLEAG--IRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPE 536
Cdd:cd17973    82 EEMDVKLGEEVGYSIRFED-CSSAKTILKYMTDGMLLREAMSDplLSRYSVIILDEAHERTLATDILMGLLKEVVRRRPD 160

                         170       180
                  ....*....|....*....|....*..
gi 100913206  537 VRIVLMSATIDTSMFCEYFFNCPIIEV 563
Cdd:cd17973   161 LKLIVMSATLDAGKFQKYFDNAPLLKV 187
DEXHc_DHX8 cd17971
DEXH-box helicase domain of DEAH-box helicase 8; DEAH-box helicase 8 (DHX8 ,also known as ...
 383-563 7.94e-44

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: 157.26  E-value: 7.94e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  383 QERELLPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDRAAECnivvTQPRRISAVSVAERVAFERG 462
Cdd:cd17971     1 EQRESLPIYKLKEQLIQAVHDNQILVVIGETGSGKTTQITQYLAEAGYTSRGKIGC----TQPRRVAAMSVAKRVAEEFG 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  463 EEPGKSCGYSVRFESIlPRPHASIMFCTVGVLLRK--LEAGIRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPEVRIV 540
Cdd:cd17971    77 CCLGQEVGYTIRFEDC-TSPETVIKYMTDGMLLREclIDPDLSQYSVIMLDEAHERTIHTDVLFGLLKKTVQKRPDLKLI 155

                         170       180
                  ....*....|....*....|...
gi 100913206  541 LMSATIDTSMFCEYFFNCPIIEV 563
Cdd:cd17971   156 VTSATLDAVKFSQYFYEAPIFTI 178
DEXHc_HrpA cd17989
DEXH-box helicase domain of ATP-dependent RNA helicase HrpA; HrpA is part of the HrpB-HrpA ...
 388-563 4.56e-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: 4.56e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  388 LPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDdfiqNDRAAECNIVVTQPRRISAVSVAERVAFERGEEPGK 467
Cdd:cd17989     1 LPVSQKRDEIAKAIAENQVVIIAGETGSGKTTQLPKICLE----LGRGIRGLIGHTQPRRLAARSVAERIAEELKTELGG 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  468 SCGYSVRFESILpRPHASIMFCTVGVLLRKLEAG--IRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPEVRIVLMSAT 545
Cdd:cd17989    77 AVGYKVRFTDQT-SDETCVKLMTDGILLAETQTDryLRAYDTIIIDEAHERSLNIDFLLGYLKQLLPRRPDLKVIITSAT 155

                         170
                  ....*....|....*...
gi 100913206  546 IDTSMFCEYFFNCPIIEV 563
Cdd:cd17989   156 IDAERFSRHFNNAPIIEV 173
DEXHc_DHX37 cd17982
DEXH-box helicase domain of DEAH-box helicase 37; DHX37 plays a role in the development of the ...
 388-553 2.11e-41

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: 150.58  E-value: 2.11e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  388 LPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILD-DFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGeEPG 466
Cdd:cd17982     1 LPILAEEQEIMEAINENPVVIICGETGSGKTTQVPQFLYEaGFGSPESDNPGMIGITQPRRVAAVSMAKRVAEELN-VFG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  467 KSCGYSVRFESILpRPHASIMFCTVGVLLRKLEAG--IRGISHVIVDEIHERDINTDFLLVVLRDVV-----------QA 533
Cdd:cd17982    80 KEVSYQIRYDSTV-SENTKIKFMTDGVLLKEIQTDflLRKYSVIIIDEAHERSVNTDILIGMLSRIVplraklylqdqTV 158

                         170       180
                  ....*....|....*....|
gi 100913206  534 YPeVRIVLMSATIDTSMFCE 553
Cdd:cd17982   159 KP-LKLVIMSATLRVEDFTE 177
DEXHc_DHX35 cd17980
DEXH-box helicase domain of DEAH-box helicase 35; DHX35 plays a role in colorectal cancers and ...
 388-555 3.32e-41

DEXH-box helicase domain of DEAH-box helicase 35; DHX35 plays a role in colorectal cancers and seems to be associated with risk to thyroid cancers. It also has been shown to positively regulate poxviruses, such as Myxoma virus. DEAH-box helicase 35 (DHX35) belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350738 [Multi-domain]  Cd Length: 185  Bit Score: 149.93  E-value: 3.32e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  388 LPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILD-DFIQNDRAaecnIVVTQPRRISAVSVAERVAFERGEEPG 466
Cdd:cd17980     1 LPVFKLRNHILYLVENYQTIVIVGETGCGKSTQIPQYLAEaGWTAGGRV----VGCTQPRRVAAVTVAGRVAEEMGAVLG 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  467 KSCGYSVRFESILPRPHASIMFCTVGVLLRKLEAG--IRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPEVRIVLMSA 544
Cdd:cd17980    77 HEVGYCIRFDDCTDPQATRIKFLTDGMLVREMMLDplLTKYSVIMLDEAHERTLYTDILIGLLKKIQKKRGDLRLIVASA 156

                         170
                  ....*....|.
gi 100913206  545 TIDTSMFCEYF 555
Cdd:cd17980   157 TLDAEKFRDFF 167
DEXHc_HrpB cd17990
DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA ...
 388-563 8.89e-41

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


Pssm-ID: 438711 [Multi-domain]  Cd Length: 174  Bit Score: 148.25  E-value: 8.89e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  388 LPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDRaaecNIVVTQPRRISAVSVAERVAFERGEEPGK 467
Cdd:cd17990     1 LPIAAVLPALRAALDAGGQVVLEAPPGAGKTTRVPLALLAELWIAGG----KIIVLEPRRVAARAAARRLATLLGEAPGE 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  468 SCGYSVRFESILPRpHASIMFCTVGVLLRKLEA--GIRGISHVIVDEIHERDINTDFLLVVLRDVVQAY-PEVRIVLMSA 544
Cdd:cd17990    77 TVGYRVRGESRVGR-RTRVEVVTEGVLLRRLQRdpELSGVGAVILDEFHERSLDADLALALLLEVQQLLrDDLRLLAMSA 155

                         170
                  ....*....|....*....
gi 100913206  545 TIDTSMFCEYFFNCPIIEV 563
Cdd:cd17990   156 TLDGDGLAALLPEAPVVES 174
DSRM_DHX9_rpt1 cd19854
first double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins; ...
 3-71 4.08e-40

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: 142.41  E-value: 4.08e-40
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 100913206    3 DVKNFLYAWCGKRKMTPSYEIRAVGNKNRQKFMCEVQVEGYNYTGMGNSTNKKDAQSNAARDFVNYLVR 71
Cdd:cd19854     1 EIKAFLYAWCGKKKLTPEYDIKEAGNKHRQRFKCEVRVEGFDYVGTGNATNKKDAQTNAARDFLNYLVR 69
DEXHc_DHX38 cd17983
DEXH-box helicase domain of DEAH-box helicase 38; DEAH-box helicase 38 (DHX38, also known as ...
 388-563 9.10e-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: 145.30  E-value: 9.10e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  388 LPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDRAAECnivvTQPRRISAVSVAERVAFERGEEPGK 467
Cdd:cd17983     1 LPIFAVRQELLNVIRDNNVVIVVGETGSGKTTQLTQYLHEDGYTDYGMIGC----TQPRRVAAMSVAKRVSEEMGVELGE 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  468 SCGYSVRFESIlPRPHASIMFCTVGVLLRK--LEAGIRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPEVRIVLMSAT 545
Cdd:cd17983    77 EVGYAIRFEDC-TSENTVIKYMTDGILLREslRDPDLDKYSAIIMDEAHERSLNTDVLFGLLREVVARRRDLKLIVTSAT 155

                         170
                  ....*....|....*...
gi 100913206  546 IDTSMFCEYFFNCPIIEV 563
Cdd:cd17983   156 MDADKFADFFGNVPIFTI 173
DEXHc_DHX16 cd17974
DEXH-box helicase domain of DEAH-box helicase 16; DEAH-box helicase 16 (DHX16) is probably ...
 388-563 1.01e-39

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: 145.34  E-value: 1.01e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  388 LPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDRAaecNIVVTQPRRISAVSVAERVAFERGEEPGK 467
Cdd:cd17974     1 LPVYPYRDDLLAAVKEHQVLIIVGETGSGKTTQIPQYLHEAGYTKGGG---KIGCTQPRRVAAMSVAARVAEEMGVKLGN 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  468 SCGYSVRFESIlPRPHASIMFCTVGVLLRKL--EAGIRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPEVRIVLMSAT 545
Cdd:cd17974    78 EVGYSIRFEDC-TSEKTVLKYMTDGMLLREFltEPDLASYSVMIIDEAHERTLHTDILFGLVKDIARFRPDLKLLISSAT 156

                         170
                  ....*....|....*...
gi 100913206  546 IDTSMFCEYFFNCPIIEV 563
Cdd:cd17974   157 MDAEKFSAFFDDAPIFRI 174
DEXHc_DHX40 cd17984
DEXH-box helicase domain of DEAH-box helicase 40; DEAH-box helicase 40 (DHX40) belongs to the ...
 388-563 2.53e-33

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: 127.28  E-value: 2.53e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  388 LPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILD-DFIQNDRaaecnIVVTQPRRISAVSVAERVAFERGEEPG 466
Cdd:cd17984     1 LPIQKQRKKLVQAVRDNSFLIVTGNTGSGKTTQLPKYLYEaGFSQHGM-----IGVTQPRRVAAISVAQRVAEEMKCTLG 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  467 KSCGYSVRFESILPRPHAsIMFCTVGVLLRKLEA--GIRGISHVIVDEIHERDINTDFLLVVLRDVVQAYP-----EVRI 539
Cdd:cd17984    76 SKVGYQVRFDDCSSKETA-IKYMTDGCLLRHILAdpNLTKYSVIILDEAHERSLTTDILFGLLKKLFQEKSpnrkeHLKV 154

                         170       180
                  ....*....|....*....|....
gi 100913206  540 VLMSATIDTSMFCEYFFNCPIIEV 563
Cdd:cd17984   155 VVMSATLELAKLSAFFGNCPVFDI 178
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 404-545 1.68e-26

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: 106.33  E-value: 1.68e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  404 NSVVIIRGATGCGKTTQVPQFILDDFIQndraAECNIVVTQPRRISAVSVAERVAFERGeePGKSCGYSVRFESILPR-- 481
Cdd:cd00046     1 GENVLITAPTGSGKTLAALLAALLLLLK----KGKKVLVLVPTKALALQTAERLRELFG--PGIRVAVLVGGSSAEERek 74

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 100913206  482 ---PHASIMFCTVGVLLRKLEA----GIRGISHVIVDEIHERDINTDFLLVVLRDVVQA-YPEVRIVLMSAT 545
Cdd:cd00046    75 nklGDADIIIATPDMLLNLLLRedrlFLKDLKLIIVDEAHALLIDSRGALILDLAVRKAgLKNAQVILLSAT 146
DEXHc_DHX32 cd17977
DEXH-box helicase domain of DEAH-box helicase 32; DEAH-box helicase 32 (DHX32) belongs to the ...
 388-563 1.97e-24

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


Pssm-ID: 350735 [Multi-domain]  Cd Length: 176  Bit Score: 101.44  E-value: 1.97e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  388 LPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQ----FILDDFIQNDraaecNIVVTQPRRISAVSVAERVAFERGE 463
Cdd:cd17977     1 LPVWEAKYEFMESLAHNQIVIVSGDAKTGKSSQIPQwcaeYCLSAHYQHG-----VVVCTQVHKQTAVWLALRVADEMDV 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  464 EPGKSCGYSVRFESILPRpHASIMFCTVGVLLRKLEA----GIRGIshVIVDEIHERDINTDFLLVVLRDVVQAYPEVRI 539
Cdd:cd17977    76 NIGHEVGYVIPFENCCTN-ETILRYCTDDMLLREMMSdpllESYGV--IILDDAHERTVSTDVLLGLLKDVLLSRPELKL 152

                         170       180
                  ....*....|....*....|....
gi 100913206  540 VLMSATIDTSMFCEYFFNCPIIEV 563
Cdd:cd17977   153 VIITCPHLSSKLLSYYGNVPLIEV 176
DEXDc smart00487
DEAD-like helicases superfamily;
396-569 8.05e-23

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 97.56  E-value: 8.05e-23
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206    396 EILEAISQN-SVVIIRGATGCGKTTQVPQFILDDFIQNDRaaeCNIVVTQPRRISAVSVAERVAFERGEEPGKSCGYSVR 474
Cdd:smart00487   15 EAIEALLSGlRDVILAAPTGSGKTLAALLPALEALKRGKG---GRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGG 91

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206    475 FESI-----LPRPHASIMFCTVGVLLRKLEAG---IRGISHVIVDEIHERDiNTDFLLVVLRDVVQAYPEVRIVLMSATI 546
Cdd:smart00487   92 DSKReqlrkLESGKTDILVTTPGRLLDLLENDklsLSNVDLVILDEAHRLL-DGGFGDQLEKLLKLLPKNVQLLLLSATP 170

                           170       180
                    ....*....|....*....|....*
gi 100913206    547 --DTSMFCEYFFNCPIIEVYGRTYP 569
Cdd:smart00487  171 peEIENLLELFLNDPVFIDVGFTPL 195
HA2 smart00847
Helicase associated domain (HA2) Add an annotation; This presumed domain is about 90 amino ...
 838-919 8.58e-22

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: 90.41  E-value: 8.58e-22
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206    838 ELDALDANDELTPLGRILAKLPIEPRFGKMMIMGCIFYVGDAICTIAAATCFPEPFINE-GKRLGYIHRNFAGNRfSDHV 916
Cdd:smart00847    1 ELGALDDDGRLTPLGRKMAELPLDPRLAKMLLAAAEFGCLDEILTIVAMLSVGDPRPKEkREDADAARRRFADPE-SDHL 79


                    ...
gi 100913206    917 ALL 919
Cdd:smart00847   80 TLL 82
HA2 pfam04408
Helicase associated domain (HA2); This presumed domain is about 90 amino acid residues in ...
 832-918 5.10e-21

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: 89.22  E-value: 5.10e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206   832 AEHTLRELDALDANDELTPLGRILAKLPIEPRFGKMMIMGCIFYVGDAICTIAAATCFPEPFINEG-------------- 897
Cdd:pfam04408    1 ALELLYYLGALDEDGELTPLGRKMAELPLDPRLAKMLLAAAELGCLDEVLTIVAALSVRDPFVQPNfldprsaakaarrr 80

                           90       100
                   ....*....|....*....|....
gi 100913206   898 --KRLGYIHRNFAGNRF-SDHVAL 918
Cdd:pfam04408   81 rrAADEKARAKFARLDLeGDHLTL 104
DEXQc_DQX1 cd17986
DEXQ-box helicase domain of DEAQ-box RNA dependent ATPase 1; DEAQ-box RNA dependent ATPase 1 ...
 388-563 1.51e-19

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: 87.65  E-value: 1.51e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  388 LPVKKFESEILEAI-SQNSVVIIRGATGCGKTTQVPQFILdDFIQNDRAAECNIVVTQPRRISAVSVAERVAFERGEEPG 466
Cdd:cd17986     1 LPIWAAKFTFLEQLeSPSGIVLVSGEPGSGKSTQVPQWCA-EFALSRGFQKGQVTVTQPHPLAARSLALRVADEMDLNLG 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  467 KSCGYSVRFESILPrPHASIMFCTVGVLLRKLEA--GIRGISHVIVDEIHERDINTDFLLVVLRDVVQAYPEVRIVLMSA 544
Cdd:cd17986    80 HEVGYSIPQEDCTG-PNTILRFCWDRLLLQEMTStpLLGAWGVVVLDEAQERSVASDSLLGLLKDVRLQRPELRVVVVTS 158

                         170
                  ....*....|....*....
gi 100913206  545 TIDTSMFCEYFFNCPIIEV 563
Cdd:cd17986   159 PALEPKLRAFWGNPPVVHV 177
OB_NTP_bind pfam07717
Oligonucleotide/oligosaccharide-binding (OB)-fold; This family is found towards the C-terminus ...
 994-1073 1.78e-19

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: 83.84  E-value: 1.78e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206   994 LLAFGVYPNVCYHKEKRKILTT--EGRNALIHKSSVNCpfssQDMKYPSPFFVFGEKIRTRAISAKGMTLVTPLQLLLFA 1071
Cdd:pfam07717    4 ALAAGLYPNVARRDPKGKGYTTlsDNQRVFIHPSSVLF----NEKTFPPEWVVYQELVETTKVYIRTVTAISPEWLLLFA 79


                   ..
gi 100913206  1072 SK 1073
Cdd:pfam07717   80 PH 81
PHA02653 PHA02653
RNA helicase NPH-II; Provisional
 396-771 2.97e-17

RNA helicase NPH-II; Provisional


Pssm-ID: 177443 [Multi-domain]  Cd Length: 675  Bit Score: 87.34  E-value: 2.97e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  396 EILEAISQNSVVIIRGATGCGKTTQVPQFI------------LDDFIQNdrAAECNIVVTQPRrisavsvaerVAFER-- 461
Cdd:PHA02653  171 KIFEAWISRKPVVLTGGTGVGKTSQVPKLLlwfnylfggfdnLDKIDPN--FIERPIVLSLPR----------VALVRlh 238

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  462 GEEPGKSCGY--------SVRFESIL-------PRPHAsIMFCTVGVLLRKLeagiRGISHVIVDEIHERDINTDFLLVV 526
Cdd:PHA02653  239 SITLLKSLGFdeidgspiSLKYGSIPdelintnPKPYG-LVFSTHKLTLNKL----FDYGTVIIDEVHEHDQIGDIIIAV 313

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  527 LRdvvQAYPEVR-IVLMSATI--DTSMFCEYFFNCPIIEVYGRT-YPVQEYFLEDCIQmthfvpPPKDKkkkdkdddgge 602
Cdd:PHA02653  314 AR---KHIDKIRsLFLMTATLedDRDRIKEFFPNPAFVHIPGGTlFPISEVYVKNKYN------PKNKR----------- 373

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  603 dddancnlicgdEYGPETRLSMSQlneketpfelieALLKYieTLNVPGAVLVFLPGWNLIYTMQKHLE-MNPHfgshrY 681
Cdd:PHA02653  374 ------------AYIEEEKKNIVT------------ALKKY--TPPKGSSGIVFVASVSQCEEYKKYLEkRLPI-----Y 422

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  682 QILPLHSQIPREEQ--RKVFD-PVPVgvtkVILSTNIAETSITINDVVYVIDSCKQKVKLFTAHNNMtnyatvWASKTNL 758
Cdd:PHA02653  423 DFYIIHGKVPNIDEilEKVYSsKNPS----IIISTPYLESSVTIRNATHVYDTGRVYVPEPFGGKEM------FISKSMR 492

                         410
                  ....*....|...
gi 100913206  759 EQRKGRAGRVRPG 771
Cdd:PHA02653  493 TQRKGRVGRVSPG 505
DSRM smart00358
Double-stranded RNA binding motif;
5-69 3.72e-16

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 73.84  E-value: 3.72e-16
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 100913206      5 KNFLYAWCGKRKMTPSYE-IRAVGNKNRQKFMCEVQVEGYnYTGMGNSTNKKDAQSNAARDFVNYL 69
Cdd:smart00358    2 KSLLQELAQKRKLPPEYElVKEEGPDHAPRFTVTVKVGGK-RTGEGEGSSKKEAKQRAAEAALRSL 66
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 635-768 1.76e-15

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: 73.40  E-value: 1.76e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206   635 ELIEALLKYIETLNvPGAVLVFLPgwnliytMQKHLEMNPHFGSHRYQILPLHSQIPREEQRKVFDPVPVGVTKVILSTN 714
Cdd:pfam00271    1 EKLEALLELLKKER-GGKVLIFSQ-------TKKTLEAELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATD 72

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 100913206   715 IAETSITINDVVYVIDsckqkvklFTAHNNMTNYatvwasktnlEQRKGRAGRV 768
Cdd:pfam00271   73 VAERGLDLPDVDLVIN--------YDLPWNPASY----------IQRIGRAGRA 108
DSRM smart00358
Double-stranded RNA binding motif;
181-251 2.31e-14

Double-stranded RNA binding motif;


Pssm-ID: 214634 [Multi-domain]  Cd Length: 67  Bit Score: 68.83  E-value: 2.31e-14
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 100913206    181 AKARLNQYFQKEKIQGEYKYT-QVGPDHNRSFIAEMTIyikqlGRRIFAREHGSNKKLAAQSCALSLVRQLY 251
Cdd:smart00358    1 PKSLLQELAQKRKLPPEYELVkEEGPDHAPRFTVTVKV-----GGKRTGEGEGSSKKEAKQRAAEAALRSLK 67
HELICc smart00490
helicase superfamily c-terminal domain;
671-767 7.99e-14

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 68.01  E-value: 7.99e-14
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206    671 EMNPHFGSHRYQILPLHSQIPREEQRKVFDPVPVGVTKVILSTNIAETSITINDVVYVIDSCkqkvklftahnnmtnyat 750
Cdd:smart00490    2 ELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYD------------------ 63

                            90
                    ....*....|....*..
gi 100913206    751 VWASKTNLEQRKGRAGR 767
Cdd:smart00490   64 LPWSPASYIQRIGRAGR 80
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 181-250 5.17e-13

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: 64.94  E-value: 5.17e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 100913206   181 AKARLNQYFQKEKIQGEYKYT-QVGPDHNRSFIAEMTIyikqlGRRIFAREHGSNKKLAAQSCALSLVRQL 250
Cdd:pfam00035    1 PKSLLQEYAQKNGKPPPYEYVsEEGPPHSPKFTVTVKV-----DGKLYGSGTGSSKKEAEQLAAEKALEKL 66
dsrm pfam00035
Double-stranded RNA binding motif; Sequences gathered for seed by HMM_iterative_training ...
 5-69 3.11e-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: 62.63  E-value: 3.11e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 100913206     5 KNFLYAWCGKRKMTPSYEIRAV-GNKNRQKFMCEVQVEGYNYtGMGNSTNKKDAQSNAARDFVNYL 69
Cdd:pfam00035    2 KSLLQEYAQKNGKPPPYEYVSEeGPPHSPKFTVTVKVDGKLY-GSGTGSSKKEAEQLAAEKALEKL 66
DSRM_EIF2AK2-like cd19875
double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...
 185-250 1.12e-08

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: 52.65  E-value: 1.12e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 100913206  185 LNQYFQKEKIQGEYKYTQVGPDHNRSFIAEMTIyikqlGRRIFAREHGSNKKLAAQSCALSLVRQL 250
Cdd:cd19875     7 LNEYCQKRGLSLEFVDVSVGPDHCPGFTASATI-----DGIVFASATGTSKKEAKRAAAKLALKKL 67
DSRM_SF cd00048
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
 11-63 6.12e-08

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


Pssm-ID: 380679 [Multi-domain]  Cd Length: 57  Bit Score: 50.36  E-value: 6.12e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 100913206   11 WCGKRKM-TPSYEIRAVGNKNRQKFMCEVQVEGYNYTGMGNStnKKDAQSNAAR 63
Cdd:cd00048     3 LCQKNKWpPPEYETVEEGGPHNPRFTCTVTVNGQTFEGEGKS--KKEAKQAAAE 54
DSRM_RNAse_III_family cd10845
double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...
 180-250 8.95e-07

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


Pssm-ID: 380682 [Multi-domain]  Cd Length: 69  Bit Score: 47.49  E-value: 8.95e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 100913206  180 NAKARLNQYFQKEKIQG-EYKYT-QVGPDHNRSFIAEMTIyikqlGRRIFAREHGSNKKLAAQSCALSLVRQL 250
Cdd:cd10845     2 DYKTALQEYLQKRGLPLpEYELVeEEGPDHNKTFTVEVKV-----NGKVIGEGTGRSKKEAEQAAAKAALEKL 69
DSRM_SF cd00048
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ...
 186-243 9.24e-07

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: 46.89  E-value: 9.24e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 100913206  186 NQYFQKEKIQG-EYKYTQVGPDHNRSFIAEMTIYIkqlgrrIFAREHGSNKKLAAQSCA 243
Cdd:cd00048     1 NELCQKNKWPPpEYETVEEGGPHNPRFTCTVTVNG------QTFEGEGKSKKEAKQAAA 53
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 395-547 2.00e-06

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


Pssm-ID: 425570 [Multi-domain]  Cd Length: 165  Bit Score: 49.16  E-value: 2.00e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206   395 SEILEAISQNSVVIIRGATGCGKTT--QVPqfILDDFIQNDRAAECnIVVTqPRRISAVSVAERVafergEEPGKSCGYS 472
Cdd:pfam00270    5 AEAIPAILEGRDVLVQAPTGSGKTLafLLP--ALEALDKLDNGPQA-LVLA-PTRELAEQIYEEL-----KKLGKGLGLK 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206   473 VRFE----------SILPRPHasIMFCTVGVLLR--KLEAGIRGISHVIVDEIHErdINTDFLLVVLRDVV-QAYPEVRI 539
Cdd:pfam00270   76 VASLlggdsrkeqlEKLKGPD--ILVGTPGRLLDllQERKLLKNLKLLVLDEAHR--LLDMGFGPDLEEILrRLPKKRQI 151


                   ....*...
gi 100913206   540 VLMSATID 547
Cdd:pfam00270  152 LLLSATLP 159
DEXHc_Ski2 cd17921
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ...
 392-547 4.25e-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: 48.41  E-value: 4.25e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  392 KFESEILEAI--SQNSVVIirGA-TGCGKTTQVPQFILDDFIQNDRaaecNIVVTQPRRisAVsVAERVA-F-ERGEEPG 466
Cdd:cd17921     4 PIQREALRALylSGDSVLV--SApTSSGKTLIAELAILRALATSGG----KAVYIAPTR--AL-VNQKEAdLrERFGPLG 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  467 KSCG--YSVRFESILPRPHASIMFCT---VGVLLRKL-EAGIRGISHVIVDEIH-----ERDIntdFLLVVLRDVVQAYP 535
Cdd:cd17921    75 KNVGllTGDPSVNKLLLAEADILVATpekLDLLLRNGgERLIQDVRLVVVDEAHligdgERGV---VLELLLSRLLRINK 151

                         170
                  ....*....|..
gi 100913206  536 EVRIVLMSATID 547
Cdd:cd17921   152 NARFVGLSATLP 163
DSRM_RNAse_III_family cd10845
double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins; RNase ...
 3-69 4.42e-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: 45.56  E-value: 4.42e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 100913206    3 DVKNFLYAWCGKRKM-TPSYE-IRAVGNKNRQKFMCEVQVEGyNYTGMGNSTNKKDAQSNAARDFVNYL 69
Cdd:cd10845     2 DYKTALQEYLQKRGLpLPEYElVEEEGPDHNKTFTVEVKVNG-KVIGEGTGRSKKEAEQAAAKAALEKL 69
DSRM_SON-like cd19870
double-stranded RNA binding motif of protein SON and similar proteins; Protein SON (also known ...
 12-63 3.35e-05

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: 43.04  E-value: 3.35e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 100913206   12 CGKRK-MTPSYE-IRAVGNKNRQKFMCEVQVEGYNYTGMGNSTNKKDAQSNAAR 63
Cdd:cd19870    12 CNKRKwGPPEFRlVEESGPPHRKHFLFKVVVNGVEYQPSVASGNKKDAKAQAAT 65
DSRM_Kanadaptin cd19856
double-stranded RNA binding motif of Kanadaptin and similar proteins; Kanadaptin (also known ...
 178-255 3.84e-04

double-stranded RNA binding motif of Kanadaptin and similar proteins; Kanadaptin (also known as human lung cancer oncogene 3 protein (HLC-3), kidney anion exchanger adapter protein, or solute carrier family 4 anion exchanger member 1 adapter protein (SLC4A1AP)) is a nuclear protein widely expressed in mammalian tissues. It was originally isolated as a kidney Cl-/HCO3- anion exchanger 1 (kAE1)-binding protein. It is a highly mobile nucleocytoplasmic shuttling and multilocalizing protein. Its role in mammalian cells remains unclear. The double-stranded RNA binding motif (DSRM) is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380685  Cd Length: 86  Bit Score: 40.68  E-value: 3.84e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 100913206  178 LENAKARLNQYFQKEKIQGEYKYTQVGPDHNRSFIA--EMTIYIkQLGRRIFAREHGSNKKLAAQ-SCALSLVRQLYHLG 254
Cdd:cd19856     5 LKDPKKALKGFFDREGEELEYEVEEQGSGRTRKYVCriELPLDD-ASGGPIVAEASVSGKKKEAVvACALEACRILDRHG 83


                  .
gi 100913206  255 V 255
Cdd:cd19856    84 L 84
DSRM_AtDRB-like cd19878
double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding proteins ...
 182-243 4.11e-04

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


Pssm-ID: 380707 [Multi-domain]  Cd Length: 67  Bit Score: 39.81  E-value: 4.11e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 100913206  182 KARLNQYFQKEKIQ-GEYKYTQVGPDHNRSFIAEMTIyikqLGRRiFAREHGSNKKLAAQSCA 243
Cdd:cd19878     2 KNLLQEYAQKKKIPlPKYESAKSGPSHQPTFVSTVIV----LGVR-FSSEGAKNKKQAEQSAA 59
DSRM_EIF2AK2-like cd19875
double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 ...
 8-69 7.84e-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: 7.84e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 100913206    8 LYAWCGKRKMTPSYEIRAVGNKNRQKFMCEVQVEGyNYTGMGNSTNKKDAQSNAARDFVNYL 69
Cdd:cd19875     7 LNEYCQKRGLSLEFVDVSVGPDHCPGFTASATIDG-IVFASATGTSKKEAKRAAAKLALKKL 67
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
180-250 9.34e-04

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 42.39  E-value: 9.34e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 100913206  180 NAKARLNQYFQKEKIQG-EYKYTQV-GPDHNRSFIAEMTIyikqlGRRIFAREHGSNKKLAAQSCALSLVRQL 250
Cdd:COG0571   158 DYKTALQEWLQARGLPLpEYEVVEEeGPDHAKTFTVEVLV-----GGKVLGEGTGRSKKEAEQAAAKAALEKL 225
DSRM_DUS2L cd19871
double-stranded RNA binding motif of tRNA-dihydrouridine(20) synthase [NAD(P)+]-like (DUS2L) ...
 5-62 3.27e-03

double-stranded RNA binding motif of tRNA-dihydrouridine(20) synthase [NAD(P)+]-like (DUS2L) and similar proteins; DUS2L (also known as dihydrouridine synthase 2 (DUS2), up-regulated in lung cancer protein 8 (URLC8), or tRNA-dihydrouridine synthase 2-like) catalyzes the synthesis of dihydrouridine, a modified base found in the D-loop of most tRNAs. It negatively regulates the activation of EIF2AK2/PKR. DUS2L contains an N-terminal FMN-binding domain and a C-terminal double-stranded RNA binding motif (DSRM) that is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380700  Cd Length: 68  Bit Score: 37.25  E-value: 3.27e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 100913206    5 KNFLYAWCGKRKMT-PSYEirAVGNKNRQKFMCEVQVEGYNYTGMGNSTNKKDAQSNAA 62
Cdd:cd19871     3 KMILNEWCRKNKLPqPVYE--TVQRPSDRLFQSVVTVDGKKYTSSLWEKSKKLAEQAAA 59
Rnc COG0571
dsRNA-specific ribonuclease [Transcription];
13-69 3.98e-03

dsRNA-specific ribonuclease [Transcription];


Pssm-ID: 440336 [Multi-domain]  Cd Length: 229  Bit Score: 40.47  E-value: 3.98e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 100913206   13 GKRKMTPSYEIRAV-GNKNRQKFMCEVQVEGYNY-TGMGNStnKKDAQSNAARDFVNYL 69
Cdd:COG0571   169 ARGLPLPEYEVVEEeGPDHAKTFTVEVLVGGKVLgEGTGRS--KKEAEQAAAKAALEKL 225
DSRM_PRKRA-like_rpt1 cd19862
first double-stranded RNA binding motif of protein activator of the interferon-induced protein ...
 8-72 5.03e-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: 5.03e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 100913206    8 LYAWCGKRKMTPSYEIRAVGNKNRQK-FMCEVQVEGYNYTGMGNStnKKDAQSNAARDFVNYLVRI 72
Cdd:cd19862     7 LQELCAKRGITPKYELISSEGAVHEPtFTFRVTVGDITATGSGTS--KKKAKHAAAENALEQLKGS 70
 
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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