NCBI Conserved Domain Search

Conserved domains on [gi|896581323|ref|WP_049470132|]

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MULTISPECIES: DEAD/DEAH box helicase [Stenotrophomonas]

Protein Classification

ATP-dependent RNA helicase DeaD( domain architecture ID 1001512)

ATP-dependent RNA helicase DeaD is DEAD-box RNA helicase involved in various cellular processes at low temperature, including ribosome biogenesis, mRNA degradation and translation initiation

EC: 3.6.4.13

Gene Ontology: GO:0033592|GO:0003724|GO:0016887|GO:0005524

PubMed: 34680866|21779027

Graphical summary

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List of domain hits

Name

Accession

Description

Interval

E-value

SrmB

COG0513

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

11-398

0e+00

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

Pssm-ID: 440279 [Multi-domain] Cd Length: 420 Bit Score: 634.49 E-value: 0e+00

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  11 FAQLGLSEPVMQAVTAIGYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSNIDLQQIK-PQALILAPTREL 89
Cdd:COG0513    4 FADLGLSPPLLKALAELGYTTPTPIQAQAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQRLDPSRPRaPQALILAPTREL 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  90 AIQVAEAFQSYSSKIpGFRVLPVYGGQPYGQQLSALRRGVHIVVGTPGRVIDHLDRSTLDLSELKTLVLDEADEMLRMGF 169
Cdd:COG0513   84 ALQVAEELRKLAKYL-GLRVATVYGGVSIGRQIRALKRGVDIVVATPGRLLDLIERGALDLSGVETLVLDEADRMLDMGF 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 170 IDDVEAVLKKLPEQRQVALFSATMPPQIRRIAQTYLQDPVEVTIAAKTTTSANIRQRYWWVSGMHKLDALTRILEVEPFD 249
Cdd:COG0513  163 IEDIERILKLLPKERQTLLFSATMPPEIRKLAKRYLKNPVRIEVAPENATAETIEQRYYLVDKRDKLELLRRLLRDEDPE 242

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 250 AMIIFARTKAGTEELASKLQARGLAAAAINGDMQQAQRERTIAMLKEGKLDILVATDVAARGLDVERISHVLNYDIPYDT 329
Cdd:COG0513  243 RAIVFCNTKRGADRLAEKLQKRGISAAALHGDLSQGQRERALDAFRNGKIRVLVATDVAARGIDIDDVSHVINYDLPEDP 322

                        330       340       350       360       370       380
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 896581323 330 ESYVHRIGRTGRAGRSGEAILFATPREKGMLRQIERATRQPIEEMQLPSVEAVNDTRINKFTSRISETL 398
Cdd:COG0513  323 EDYVHRIGRTGRAGAEGTAISLVTPDERRLLRAIEKLIGQKIEEEELPGFEPVEEKRLERLKPKIKEKL 391

RRM_EcCsdA_like

cd12499

RNA recognition motif (RRM) found in Escherichia coli cold-shock DEAD box protein A (CsdA) and ...

511-581

1.60e-38

RNA recognition motif (RRM) found in Escherichia coli cold-shock DEAD box protein A (CsdA) and similar proteins; This subgroup corresponds to the C-terminal RRM homology domain of E. coli CsdA, also termed ATP-dependent RNA helicase deaD, or translation factor W2, a member of the DbpA subfamily of prokaryotic DEAD-box rRNA helicases that have been implicated in ribosome biogenesis. CsdA may be involved in translation initiation, gene regulation after cold-shock, mRNA decay and biogenesis of the large or small ribosomal subunit. It contains two N-terminal ATPase catalytic domains and a C-terminal RNA binding domain, an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain). The catalytic domains bind to nearby regions of RNA to stimulate ATP hydrolysis and disrupt RNA structures. The C-terminal domain is responsible for the high-affinity RNA binding.

Pssm-ID: 409922 [Multi-domain] Cd Length: 73 Bit Score: 136.55 E-value: 1.60e-38

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 896581323 511 TYRISVGHQHGVKPANIVGAIANEAGLESRFIGRIDIHDDFSLLDLPAQMPPDVLSHLQKVWVSGQQLQMR 581
Cdd:cd12499    1 RYRIEVGRKDGVKPGNIVGAIANEAGIDSRFIGRIKIFDDHSTVELPKGMPKDVLQHLKKVRVCGQPLNIK 71

Name

Accession

Description

Interval

E-value

SrmB

COG0513

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

11-398

0e+00

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

Pssm-ID: 440279 [Multi-domain] Cd Length: 420 Bit Score: 634.49 E-value: 0e+00

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  11 FAQLGLSEPVMQAVTAIGYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSNIDLQQIK-PQALILAPTREL 89
Cdd:COG0513    4 FADLGLSPPLLKALAELGYTTPTPIQAQAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQRLDPSRPRaPQALILAPTREL 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  90 AIQVAEAFQSYSSKIpGFRVLPVYGGQPYGQQLSALRRGVHIVVGTPGRVIDHLDRSTLDLSELKTLVLDEADEMLRMGF 169
Cdd:COG0513   84 ALQVAEELRKLAKYL-GLRVATVYGGVSIGRQIRALKRGVDIVVATPGRLLDLIERGALDLSGVETLVLDEADRMLDMGF 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 170 IDDVEAVLKKLPEQRQVALFSATMPPQIRRIAQTYLQDPVEVTIAAKTTTSANIRQRYWWVSGMHKLDALTRILEVEPFD 249
Cdd:COG0513  163 IEDIERILKLLPKERQTLLFSATMPPEIRKLAKRYLKNPVRIEVAPENATAETIEQRYYLVDKRDKLELLRRLLRDEDPE 242

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 250 AMIIFARTKAGTEELASKLQARGLAAAAINGDMQQAQRERTIAMLKEGKLDILVATDVAARGLDVERISHVLNYDIPYDT 329
Cdd:COG0513  243 RAIVFCNTKRGADRLAEKLQKRGISAAALHGDLSQGQRERALDAFRNGKIRVLVATDVAARGIDIDDVSHVINYDLPEDP 322

                        330       340       350       360       370       380
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 896581323 330 ESYVHRIGRTGRAGRSGEAILFATPREKGMLRQIERATRQPIEEMQLPSVEAVNDTRINKFTSRISETL 398
Cdd:COG0513  323 EDYVHRIGRTGRAGAEGTAISLVTPDERRLLRAIEKLIGQKIEEEELPGFEPVEEKRLERLKPKIKEKL 391

PRK11634

ATP-dependent RNA helicase DeaD; Provisional

11-640

0e+00

ATP-dependent RNA helicase DeaD; Provisional

Pssm-ID: 236941 [Multi-domain] Cd Length: 629 Bit Score: 616.09 E-value: 0e+00

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  11 FAQLGLSEPVMQAVTAIGYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSNIDLQQIKPQALILAPTRELA 90
Cdd:PRK11634   8 FADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHNLDPELKAPQILVLAPTRELA 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  91 IQVAEAFQSYSSKIPGFRVLPVYGGQPYGQQLSALRRGVHIVVGTPGRVIDHLDRSTLDLSELKTLVLDEADEMLRMGFI 170
Cdd:PRK11634  88 VQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRALRQGPQIVVGTPGRLLDHLKRGTLDLSKLSGLVLDEADEMLRMGFI 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 171 DDVEAVLKKLPEQRQVALFSATMPPQIRRIAQTYLQDPVEVTIAAKTTTSANIRQRYWWVSGMHKLDALTRILEVEPFDA 250
Cdd:PRK11634 168 EDVETIMAQIPEGHQTALFSATMPEAIRRITRRFMKEPQEVRIQSSVTTRPDISQSYWTVWGMRKNEALVRFLEAEDFDA 247

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 251 MIIFARTKAGTEELASKLQARGLAAAAINGDMQQAQRERTIAMLKEGKLDILVATDVAARGLDVERISHVLNYDIPYDTE 330
Cdd:PRK11634 248 AIIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAARGLDVERISLVVNYDIPMDSE 327

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 331 SYVHRIGRTGRAGRSGEAILFATPREKGMLRQIERATRQPIEEMQLPSVEAVNDTRINKFTSRISETLGAGGLDFYRQLL 410
Cdd:PRK11634 328 SYVHRIGRTGRAGRAGRALLFVENRERRLLRNIERTMKLTIPEVELPNAELLGKRRLEKFAAKVQQQLESSDLDQYRALL 407

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 411 ERFENEQNVPAIEI---AAALAKLLQGDTPFLLQP-PVRAPREERAPRERFDRGDRPERGDRFERNDRgPRFErgpRRDD 486
Cdd:PRK11634 408 AKIQPTAEGEELDLetlAAALLKMAQGERPLILPPdAPMRPKREFRDRDDRGPRDRNDRGPRGDREDR-PRRE---RRDV 483

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 487 AEggfeprprrevpprgapeqgMETYRISVGHQHGVKPANIVGAIANEAGLESRFIGRIDIHDDFSLLDLPAQMPPDVLS 566
Cdd:PRK11634 484 GD--------------------MQLYRIEVGRDDGVEVRHIVGAIANEGDISSRYIGNIKLFASHSTIELPKGMPGEVLQ 543

                        570       580       590       600       610       620       630
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 896581323 567 HLQKVWVSGQQLQMRALA-----PGEDTNPAPRPFKPRFDKRGPGGPGGPRRSGPGGPAGDRGGDRDSRPPRRDGFKPR 640
Cdd:PRK11634 544 HFTRTRILNKPMNMQLLGdaqphTGGERRGGGRGFGGERREGGRNFSGERREGGRGDGRRFSGERREGRAPRRDDSTGR 622

DEADc

cd00268

DEAD-box helicase domain of DEAD box helicases; DEAD-box helicases comprise a diverse family ...

20-212

8.35e-103

DEAD-box helicase domain of DEAD box helicases; DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.

Pssm-ID: 350669 [Multi-domain] Cd Length: 196 Bit Score: 310.53 E-value: 8.35e-103

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  20 VMQAVTAIGYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSNIDLQQIK----PQALILAPTRELAIQVAE 95
Cdd:cd00268    1 LLKALKKLGFEKPTPIQAQAIPLILSGRDVIGQAQTGSGKTLAFLLPILEKLLPEPKKkgrgPQALVLAPTRELAMQIAE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  96 AFQSYSsKIPGFRVLPVYGGQPYGQQLSALRRGVHIVVGTPGRVIDHLDRSTLDLSELKTLVLDEADEMLRMGFIDDVEA 175
Cdd:cd00268   81 VARKLG-KGTGLKVAAIYGGAPIKKQIEALKKGPDIVVGTPGRLLDLIERGKLDLSNVKYLVLDEADRMLDMGFEEDVEK 159

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 896581323 176 VLKKLPEQRQVALFSATMPPQIRRIAQTYLQDPVEVT 212
Cdd:cd00268  160 ILSALPKDRQTLLFSATLPEEVKELAKKFLKNPVRIE 196

DEAD

pfam00270

DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...

33-200

5.56e-65

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: 210.95 E-value: 5.56e-65

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323   33 SPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSNIDLQQIKPQALILAPTRELAIQVAEAFQSYSSKIpGFRVLPV 112
Cdd:pfam00270   1 TPIQAEAIPAILEGRDVLVQAPTGSGKTLAFLLPALEALDKLDNGPQALVLAPTRELAEQIYEELKKLGKGL-GLKVASL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  113 YGGQPYGQQLSALrRGVHIVVGTPGRVIDHLDRSTLdLSELKTLVLDEADEMLRMGFIDDVEAVLKKLPEQRQVALFSAT 192
Cdd:pfam00270  80 LGGDSRKEQLEKL-KGPDILVGTPGRLLDLLQERKL-LKNLKLLVLDEAHRLLDMGFGPDLEEILRRLPKKRQILLLSAT 157


                  ....*...
gi 896581323  193 MPPQIRRI 200
Cdd:pfam00270 158 LPRNLEDL 165

DEXDc

smart00487

DEAD-like helicases superfamily;

28-226

4.07e-55

DEAD-like helicases superfamily;

Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 186.16 E-value: 4.07e-55

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323    28 GYETPSPIQAATIPAMLEG-RDVLGQAQTGTGKTAAFALPVLSNIdLQQIKPQALILAPTRELAIQVAEAFQSYSSKIPG 106
Cdd:smart00487   5 GFEPLRPYQKEAIEALLSGlRDVILAAPTGSGKTLAALLPALEAL-KRGKGGRVLVLVPTRELAEQWAEELKKLGPSLGL 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323   107 fRVLPVYGGQPYGQQLSALRRGV-HIVVGTPGRVIDHLDRSTLDLSELKTLVLDEADEMLRMGFIDDVEAVLKKLPEQRQ 185
Cdd:smart00487  84 -KVVGLYGGDSKREQLRKLESGKtDILVTTPGRLLDLLENDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQ 162

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|.
gi 896581323   186 VALFSATMPPQIRRIAQTYLQDPVEVTIaaKTTTSANIRQR 226
Cdd:smart00487 163 LLLLSATPPEEIENLLELFLNDPVFIDV--GFTPLEPIEQF 201

RRM_EcCsdA_like

cd12499

RNA recognition motif (RRM) found in Escherichia coli cold-shock DEAD box protein A (CsdA) and ...

511-581

1.60e-38

Pssm-ID: 409922 [Multi-domain] Cd Length: 73 Bit Score: 136.55 E-value: 1.60e-38

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 896581323 511 TYRISVGHQHGVKPANIVGAIANEAGLESRFIGRIDIHDDFSLLDLPAQMPPDVLSHLQKVWVSGQQLQMR 581
Cdd:cd12499    1 RYRIEVGRKDGVKPGNIVGAIANEAGIDSRFIGRIKIFDDHSTVELPKGMPKDVLQHLKKVRVCGQPLNIK 71

DbpA

pfam03880

DbpA RNA binding domain; This RNA binding domain is found at the C-terminus of a number of ...

511-581

1.12e-25

DbpA RNA binding domain; This RNA binding domain is found at the C-terminus of a number of DEAD helicase proteins. It is sufficient to confer specificity for hairpin 92 of 23S rRNA, which is part of the ribosomal A-site. However, several members of this family lack specificity for 23S rRNA. These can proteins can generally be distinguished by a basic region that extends beyond this domain [Karl Kossen, unpublished data].

Pssm-ID: 461082 [Multi-domain] Cd Length: 72 Bit Score: 100.53 E-value: 1.12e-25

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 896581323  511 TYRISVGHQHGVKPANIVGAIANEAGLESRFIGRIDIHDDFSLLDLPAQMPPDVLSHLQKVWVSGQQLQMR 581
Cdd:pfam03880   1 RLFINVGKKDGVRPGDIVGALANEAGLPGDDIGKIDIFDNFSFVEVPAEKAEKVLKALKGTKIKGRKVRVE 71

Name

Accession

Description

Interval

E-value

SrmB

COG0513

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

11-398

0e+00

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

Pssm-ID: 440279 [Multi-domain] Cd Length: 420 Bit Score: 634.49 E-value: 0e+00

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  11 FAQLGLSEPVMQAVTAIGYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSNIDLQQIK-PQALILAPTREL 89
Cdd:COG0513    4 FADLGLSPPLLKALAELGYTTPTPIQAQAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQRLDPSRPRaPQALILAPTREL 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  90 AIQVAEAFQSYSSKIpGFRVLPVYGGQPYGQQLSALRRGVHIVVGTPGRVIDHLDRSTLDLSELKTLVLDEADEMLRMGF 169
Cdd:COG0513   84 ALQVAEELRKLAKYL-GLRVATVYGGVSIGRQIRALKRGVDIVVATPGRLLDLIERGALDLSGVETLVLDEADRMLDMGF 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 170 IDDVEAVLKKLPEQRQVALFSATMPPQIRRIAQTYLQDPVEVTIAAKTTTSANIRQRYWWVSGMHKLDALTRILEVEPFD 249
Cdd:COG0513  163 IEDIERILKLLPKERQTLLFSATMPPEIRKLAKRYLKNPVRIEVAPENATAETIEQRYYLVDKRDKLELLRRLLRDEDPE 242

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 250 AMIIFARTKAGTEELASKLQARGLAAAAINGDMQQAQRERTIAMLKEGKLDILVATDVAARGLDVERISHVLNYDIPYDT 329
Cdd:COG0513  243 RAIVFCNTKRGADRLAEKLQKRGISAAALHGDLSQGQRERALDAFRNGKIRVLVATDVAARGIDIDDVSHVINYDLPEDP 322

                        330       340       350       360       370       380
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 896581323 330 ESYVHRIGRTGRAGRSGEAILFATPREKGMLRQIERATRQPIEEMQLPSVEAVNDTRINKFTSRISETL 398
Cdd:COG0513  323 EDYVHRIGRTGRAGAEGTAISLVTPDERRLLRAIEKLIGQKIEEEELPGFEPVEEKRLERLKPKIKEKL 391

PRK11634

ATP-dependent RNA helicase DeaD; Provisional

11-640

0e+00

ATP-dependent RNA helicase DeaD; Provisional

Pssm-ID: 236941 [Multi-domain] Cd Length: 629 Bit Score: 616.09 E-value: 0e+00

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  11 FAQLGLSEPVMQAVTAIGYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSNIDLQQIKPQALILAPTRELA 90
Cdd:PRK11634   8 FADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHNLDPELKAPQILVLAPTRELA 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  91 IQVAEAFQSYSSKIPGFRVLPVYGGQPYGQQLSALRRGVHIVVGTPGRVIDHLDRSTLDLSELKTLVLDEADEMLRMGFI 170
Cdd:PRK11634  88 VQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRALRQGPQIVVGTPGRLLDHLKRGTLDLSKLSGLVLDEADEMLRMGFI 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 171 DDVEAVLKKLPEQRQVALFSATMPPQIRRIAQTYLQDPVEVTIAAKTTTSANIRQRYWWVSGMHKLDALTRILEVEPFDA 250
Cdd:PRK11634 168 EDVETIMAQIPEGHQTALFSATMPEAIRRITRRFMKEPQEVRIQSSVTTRPDISQSYWTVWGMRKNEALVRFLEAEDFDA 247

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 251 MIIFARTKAGTEELASKLQARGLAAAAINGDMQQAQRERTIAMLKEGKLDILVATDVAARGLDVERISHVLNYDIPYDTE 330
Cdd:PRK11634 248 AIIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAARGLDVERISLVVNYDIPMDSE 327

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 331 SYVHRIGRTGRAGRSGEAILFATPREKGMLRQIERATRQPIEEMQLPSVEAVNDTRINKFTSRISETLGAGGLDFYRQLL 410
Cdd:PRK11634 328 SYVHRIGRTGRAGRAGRALLFVENRERRLLRNIERTMKLTIPEVELPNAELLGKRRLEKFAAKVQQQLESSDLDQYRALL 407

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 411 ERFENEQNVPAIEI---AAALAKLLQGDTPFLLQP-PVRAPREERAPRERFDRGDRPERGDRFERNDRgPRFErgpRRDD 486
Cdd:PRK11634 408 AKIQPTAEGEELDLetlAAALLKMAQGERPLILPPdAPMRPKREFRDRDDRGPRDRNDRGPRGDREDR-PRRE---RRDV 483

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 487 AEggfeprprrevpprgapeqgMETYRISVGHQHGVKPANIVGAIANEAGLESRFIGRIDIHDDFSLLDLPAQMPPDVLS 566
Cdd:PRK11634 484 GD--------------------MQLYRIEVGRDDGVEVRHIVGAIANEGDISSRYIGNIKLFASHSTIELPKGMPGEVLQ 543

                        570       580       590       600       610       620       630
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 896581323 567 HLQKVWVSGQQLQMRALA-----PGEDTNPAPRPFKPRFDKRGPGGPGGPRRSGPGGPAGDRGGDRDSRPPRRDGFKPR 640
Cdd:PRK11634 544 HFTRTRILNKPMNMQLLGdaqphTGGERRGGGRGFGGERREGGRNFSGERREGGRGDGRRFSGERREGRAPRRDDSTGR 622

PRK11776

ATP-dependent RNA helicase DbpA; Provisional

11-386

3.54e-148

ATP-dependent RNA helicase DbpA; Provisional

Pssm-ID: 236977 [Multi-domain] Cd Length: 460 Bit Score: 436.93 E-value: 3.54e-148

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  11 FAQLGLSEPVMQAVTAIGYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSNIDLQQIKPQALILAPTRELA 90
Cdd:PRK11776   6 FSTLPLPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQKLDVKRFRVQALVLCPTRELA 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  91 IQVAEAFQSYSSKIPGFRVLPVYGGQPYGQQLSALRRGVHIVVGTPGRVIDHLDRSTLDLSELKTLVLDEADEMLRMGFI 170
Cdd:PRK11776  86 DQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLEHGAHIIVGTPGRILDHLRKGTLDLDALNTLVLDEADRMLDMGFQ 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 171 DDVEAVLKKLPEQRQVALFSATMPPQIRRIAQTYLQDPVEVTIAAKTTTSAnIRQRYWWVSGMHKLDALTRILEVEPFDA 250
Cdd:PRK11776 166 DAIDAIIRQAPARRQTLLFSATYPEGIAAISQRFQRDPVEVKVESTHDLPA-IEQRFYEVSPDERLPALQRLLLHHQPES 244

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 251 MIIFARTKAGTEELASKLQARGLAAAAINGDMQQAQRERTIAMLKEGKLDILVATDVAARGLDVERISHVLNYDIPYDTE 330
Cdd:PRK11776 245 CVVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSVLVATDVAARGLDIKALEAVINYELARDPE 324

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 896581323 331 SYVHRIGRTGRAGRSGEAILFATPREKGMLRQIERATRQPIEEMQLPSVEAVNDTR 386
Cdd:PRK11776 325 VHVHRIGRTGRAGSKGLALSLVAPEEMQRANAIEDYLGRKLNWEPLPSLSPLSGVP 380

PRK11192

ATP-dependent RNA helicase SrmB; Provisional

10-373

1.10e-106

ATP-dependent RNA helicase SrmB; Provisional

Pssm-ID: 236877 [Multi-domain] Cd Length: 434 Bit Score: 329.60 E-value: 1.10e-106

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  10 QFAQLGLSEPVMQAVTAIGYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSN-IDLQQIKPQA---LILAP 85
Cdd:PRK11192   2 TFSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQHlLDFPRRKSGPpriLILTP 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  86 TRELAIQVAEAFQSYSSKIpGFRVLPVYGGQPYGQQLSALRRGVHIVVGTPGRVIDHLDRSTLDLSELKTLVLDEADEML 165
Cdd:PRK11192  82 TRELAMQVADQARELAKHT-HLDIATITGGVAYMNHAEVFSENQDIVVATPGRLLQYIKEENFDCRAVETLILDEADRML 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 166 RMGFIDDVEAVLKKLPEQRQVALFSATMP-PQIRRIAQTYLQDPVEVTIAAKTTTSANIRQRYWWVSGM-HKLDALTRIL 243
Cdd:PRK11192 161 DMGFAQDIETIAAETRWRKQTLLFSATLEgDAVQDFAERLLNDPVEVEAEPSRRERKKIHQWYYRADDLeHKTALLCHLL 240

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 244 EVEPFDAMIIFARTKAGTEELASKLQARGLAAAAINGDMQQAQRERTIAMLKEGKLDILVATDVAARGLDVERISHVLNY 323
Cdd:PRK11192 241 KQPEVTRSIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAARGIDIDDVSHVINF 320

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|
gi 896581323 324 DIPYDTESYVHRIGRTGRAGRSGEAILFATPREKGMLRQIERATRQPIEE 373
Cdd:PRK11192 321 DMPRSADTYLHRIGRTGRAGRKGTAISLVEAHDHLLLGKIERYIEEPLKA 370

PRK10590

ATP-dependent RNA helicase RhlE; Provisional

9-380

1.14e-104

ATP-dependent RNA helicase RhlE; Provisional

Pssm-ID: 236722 [Multi-domain] Cd Length: 456 Bit Score: 325.22 E-value: 1.14e-104

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323   9 LQFAQLGLSEPVMQAVTAIGYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSNIDLQQIKPQ------ALI 82
Cdd:PRK10590   1 MSFDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHLITRQPHAKgrrpvrALI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  83 LAPTRELAIQVAEAFQSYSsKIPGFRVLPVYGGQPYGQQLSALRRGVHIVVGTPGRVIDHLDRSTLDLSELKTLVLDEAD 162
Cdd:PRK10590  81 LTPTRELAAQIGENVRDYS-KYLNIRSLVVFGGVSINPQMMKLRGGVDVLVATPGRLLDLEHQNAVKLDQVEILVLDEAD 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 163 EMLRMGFIDDVEAVLKKLPEQRQVALFSATMPPQIRRIAQTYLQDPVEVTIAAKTTTSANIRQRYWWVSGMHKLDALTRI 242
Cdd:PRK10590 160 RMLDMGFIHDIRRVLAKLPAKRQNLLFSATFSDDIKALAEKLLHNPLEIEVARRNTASEQVTQHVHFVDKKRKRELLSQM 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 243 LEVEPFDAMIIFARTKAGTEELASKLQARGLAAAAINGDMQQAQRERTIAMLKEGKLDILVATDVAARGLDVERISHVLN 322
Cdd:PRK10590 240 IGKGNWQQVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRVLVATDIAARGLDIEELPHVVN 319

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 896581323 323 YDIPYDTESYVHRIGRTGRAGRSGEAILFATPREKGMLRQIERATRQPIEEMQLPSVE 380
Cdd:PRK10590 320 YELPNVPEDYVHRIGRTGRAAATGEALSLVCVDEHKLLRDIEKLLKKEIPRIAIPGYE 377

PRK04837

ATP-dependent RNA helicase RhlB; Provisional

11-352

1.99e-103

ATP-dependent RNA helicase RhlB; Provisional

Pssm-ID: 235314 [Multi-domain] Cd Length: 423 Bit Score: 320.76 E-value: 1.99e-103

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  11 FAQLGLSEPVMQAVTAIGYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFA-------LPVLSNIDLQQIKPQALIL 83
Cdd:PRK04837  10 FSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLtatfhylLSHPAPEDRKVNQPRALIM 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  84 APTRELAIQV---AEAFqsysSKIPGFRVLPVYGGQPYGQQLSALRRGVHIVVGTPGRVIDHLDRSTLDLSELKTLVLDE 160
Cdd:PRK04837  90 APTRELAVQIhadAEPL----AQATGLKLGLAYGGDGYDKQLKVLESGVDILIGTTGRLIDYAKQNHINLGAIQVVVLDE 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 161 ADEMLRMGFIDDVEAVLKKLPE--QRQVALFSATMPPQIRRIAQTYLQDPVEVTIAAKTTTSANIRQRYWWVSGMHKLDA 238
Cdd:PRK04837 166 ADRMFDLGFIKDIRWLFRRMPPanQRLNMLFSATLSYRVRELAFEHMNNPEYVEVEPEQKTGHRIKEELFYPSNEEKMRL 245

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 239 LTRILEVEPFDAMIIFARTKAGTEELASKLQARGLAAAAINGDMQQAQRERTIAMLKEGKLDILVATDVAARGLDVERIS 318
Cdd:PRK04837 246 LQTLIEEEWPDRAIIFANTKHRCEEIWGHLAADGHRVGLLTGDVAQKKRLRILEEFTRGDLDILVATDVAARGLHIPAVT 325

                        330       340       350
                 ....*....|....*....|....*....|....
gi 896581323 319 HVLNYDIPYDTESYVHRIGRTGRAGRSGEAILFA 352
Cdd:PRK04837 326 HVFNYDLPDDCEDYVHRIGRTGRAGASGHSISLA 359

DEADc

cd00268

DEAD-box helicase domain of DEAD box helicases; DEAD-box helicases comprise a diverse family ...

20-212

8.35e-103

Pssm-ID: 350669 [Multi-domain] Cd Length: 196 Bit Score: 310.53 E-value: 8.35e-103

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  20 VMQAVTAIGYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSNIDLQQIK----PQALILAPTRELAIQVAE 95
Cdd:cd00268    1 LLKALKKLGFEKPTPIQAQAIPLILSGRDVIGQAQTGSGKTLAFLLPILEKLLPEPKKkgrgPQALVLAPTRELAMQIAE 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  96 AFQSYSsKIPGFRVLPVYGGQPYGQQLSALRRGVHIVVGTPGRVIDHLDRSTLDLSELKTLVLDEADEMLRMGFIDDVEA 175
Cdd:cd00268   81 VARKLG-KGTGLKVAAIYGGAPIKKQIEALKKGPDIVVGTPGRLLDLIERGKLDLSNVKYLVLDEADRMLDMGFEEDVEK 159

                        170       180       190
                 ....*....|....*....|....*....|....*..
gi 896581323 176 VLKKLPEQRQVALFSATMPPQIRRIAQTYLQDPVEVT 212
Cdd:cd00268  160 ILSALPKDRQTLLFSATLPEEVKELAKKFLKNPVRIE 196

PTZ00424

helicase 45; Provisional

11-374

9.65e-93

helicase 45; Provisional

Pssm-ID: 185609 [Multi-domain] Cd Length: 401 Bit Score: 292.12 E-value: 9.65e-93

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  11 FAQLGLSEPVMQAVTAIGYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSNIDLQQIKPQALILAPTRELA 90
Cdd:PTZ00424  30 FDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQLIDYDLNACQALILAPTRELA 109

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  91 IQ---VAEAFQSYSSkipgFRVLPVYGGQPYGQQLSALRRGVHIVVGTPGRVIDHLDRSTLDLSELKTLVLDEADEMLRM 167
Cdd:PTZ00424 110 QQiqkVVLALGDYLK----VRCHACVGGTVVRDDINKLKAGVHMVVGTPGRVYDMIDKRHLRVDDLKLFILDEADEMLSR 185

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 168 GFIDDVEAVLKKLPEQRQVALFSATMPPQIRRIAQTYLQDPVEVTIAAKTTTSANIRQRYWWV-SGMHKLDALTRILEVE 246
Cdd:PTZ00424 186 GFKGQIYDVFKKLPPDVQVALFSATMPNEILELTTKFMRDPKRILVKKDELTLEGIRQFYVAVeKEEWKFDTLCDLYETL 265

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 247 PFDAMIIFARTKAGTEELASKLQARGLAAAAINGDMQQAQRERTIAMLKEGKLDILVATDVAARGLDVERISHVLNYDIP 326
Cdd:PTZ00424 266 TITQAIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLP 345

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....*...
gi 896581323 327 YDTESYVHRIGRTGRAGRSGEAILFATPREKGMLRQIERATRQPIEEM 374
Cdd:PTZ00424 346 ASPENYIHRIGRSGRFGRKGVAINFVTPDDIEQLKEIERHYNTQIEEM 393

PRK04537

ATP-dependent RNA helicase RhlB; Provisional

1-484

3.75e-86

ATP-dependent RNA helicase RhlB; Provisional

Pssm-ID: 235307 [Multi-domain] Cd Length: 572 Bit Score: 280.68 E-value: 3.75e-86

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323   1 MSQDSQAPLQFAQLGLSEPVMQAVTAIGYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSNI-------DL 73
Cdd:PRK04537   1 MSDKPLTDLTFSSFDLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMNRLlsrpalaDR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  74 QQIKPQALILAPTRELAIQVAEAFQSYSSKIpGFRVLPVYGGQPYGQQLSALRRGVHIVVGTPGRVIDHLDR-STLDLSE 152
Cdd:PRK04537  81 KPEDPRALILAPTRELAIQIHKDAVKFGADL-GLRFALVYGGVDYDKQRELLQQGVDVIIATPGRLIDYVKQhKVVSLHA 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 153 LKTLVLDEADEMLRMGFIDDVEAVLKKLPEQ--RQVALFSATMPPQIRRIAQTYLQDPVEVTIAAKTTTSANIRQRYWWV 230
Cdd:PRK04537 160 CEICVLDEADRMFDLGFIKDIRFLLRRMPERgtRQTLLFSATLSHRVLELAYEHMNEPEKLVVETETITAARVRQRIYFP 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 231 SGMHKLDALTRILEVEPFDAMIIFARTKAGTEELASKLQARGLAAAAINGDMQQAQRERTIAMLKEGKLDILVATDVAAR 310
Cdd:PRK04537 240 ADEEKQTLLLGLLSRSEGARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATDVAAR 319

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 311 GLDVERISHVLNYDIPYDTESYVHRIGRTGRAGRSGEAILFATPREKgmlrqieratrqpieeMQLPSVEAVNDTRINkf 390
Cdd:PRK04537 320 GLHIDGVKYVYNYDLPFDAEDYVHRIGRTARLGEEGDAISFACERYA----------------MSLPDIEAYIEQKIP-- 381

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 391 tsriSETLGAggldfyrQLLERFENEQNVPAieiAAALAKLLQGDTPFLLQPPVRAPREERAPRERFDRGDrPERGDRFE 470
Cdd:PRK04537 382 ----VEPVTA-------ELLTPLPRPPRVPV---EGEEADDEAGDSVGTIFREAREQRAAEEQRRGGGRSG-PGGGSRSG 446

                        490
                 ....*....|....*....
gi 896581323 471 RNDRGPR-----FERGPRR 484
Cdd:PRK04537 447 SVGGGGRrdgagADGKPRP 465

PTZ00110

helicase; Provisional

11-392

1.79e-83

helicase; Provisional

Pssm-ID: 240273 [Multi-domain] Cd Length: 545 Bit Score: 272.80 E-value: 1.79e-83

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  11 FAQLGLSEPVMQAVTAIGYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSNIDLQQI-----KPQALILAP 85
Cdd:PTZ00110 132 FEYTSFPDYILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAIVHINAQPLlrygdGPIVLVLAP 211

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  86 TRELAIQV-AEAFQ-SYSSKIpgfRVLPVYGGQPYGQQLSALRRGVHIVVGTPGRVIDHLDRSTLDLSELKTLVLDEADE 163
Cdd:PTZ00110 212 TRELAEQIrEQCNKfGASSKI---RNTVAYGGVPKRGQIYALRRGVEILIACPGRLIDFLESNVTNLRRVTYLVLDEADR 288

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 164 MLRMGFiddvEAVLKKLPEQ----RQVALFSATMPPQIRRIAQTYL-QDPVEVTIAAKT-TTSANIRQRYWWVSGMHKLD 237
Cdd:PTZ00110 289 MLDMGF----EPQIRKIVSQirpdRQTLMWSATWPKEVQSLARDLCkEEPVHVNVGSLDlTACHNIKQEVFVVEEHEKRG 364

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 238 ALTRILE--VEPFDAMIIFARTKAGTEELASKLQARGLAAAAINGDMQQAQRERTIAMLKEGKLDILVATDVAARGLDVE 315
Cdd:PTZ00110 365 KLKMLLQriMRDGDKILIFVETKKGADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVK 444

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 316 RISHVLNYDIPYDTESYVHRIGRTGRAGRSGEAILFATPREKGMLR---QIERATRQPIE-EMQLPSVEAVNDTRINKFT 391
Cdd:PTZ00110 445 DVKYVINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLTPDKYRLARdlvKVLREAKQPVPpELEKLSNERSNGTERRRWG 524


                 .
gi 896581323 392 S 392
Cdd:PTZ00110 525 G 525

PRK01297

ATP-dependent RNA helicase RhlB; Provisional

10-378

5.00e-83

ATP-dependent RNA helicase RhlB; Provisional

Pssm-ID: 234938 [Multi-domain] Cd Length: 475 Bit Score: 269.47 E-value: 5.00e-83

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  10 QFAQLGLSEPVMQAVTAIGYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSniDLQQIKPQ---------A 80
Cdd:PRK01297  88 RFHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIIN--QLLQTPPPkerymgeprA 165

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  81 LILAPTRELAIQVAEAFQSYSsKIPGFRVLPVYGGQPYGQQLSALR-RGVHIVVGTPGRVIDHLDRSTLDLSELKTLVLD 159
Cdd:PRK01297 166 LIIAPTRELVVQIAKDAAALT-KYTGLNVMTFVGGMDFDKQLKQLEaRFCDILVATPGRLLDFNQRGEVHLDMVEVMVLD 244

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 160 EADEMLRMGFIDDVEAVLKKLP--EQRQVALFSATMPPQIRRIAQTYLQDPVEVTIAAKTTTSANIRQRYWWVSGMHKLD 237
Cdd:PRK01297 245 EADRMLDMGFIPQVRQIIRQTPrkEERQTLLFSATFTDDVMNLAKQWTTDPAIVEIEPENVASDTVEQHVYAVAGSDKYK 324

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 238 ALTRILEVEPFDAMIIFARTKAGTEELASKLQARGLAAAAINGDMQQAQRERTIAMLKEGKLDILVATDVAARGLDVERI 317
Cdd:PRK01297 325 LLYNLVTQNPWERVMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATDVAGRGIHIDGI 404

                        330       340       350       360       370       380
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 896581323 318 SHVLNYDIPYDTESYVHRIGRTGRAGRSGEAILFATPREKGMLRQIERATRQPIEEMQLPS 378
Cdd:PRK01297 405 SHVINFTLPEDPDDYVHRIGRTGRAGASGVSISFAGEDDAFQLPEIEELLGRKISCEMPPA 465

PLN00206

DEAD-box ATP-dependent RNA helicase; Provisional

9-371

2.53e-72

DEAD-box ATP-dependent RNA helicase; Provisional

Pssm-ID: 215103 [Multi-domain] Cd Length: 518 Bit Score: 242.39 E-value: 2.53e-72

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323   9 LQFAQLGLSEPVMQAVTAIGYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLS--------NIDLQQiKPQA 80
Cdd:PLN00206 121 LSFSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIISrcctirsgHPSEQR-NPLA 199

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  81 LILAPTRELAIQVAEAFQSYSSKIPgFRVLPVYGGQPYGQQLSALRRGVHIVVGTPGRVIDHLDRSTLDLSELKTLVLDE 160
Cdd:PLN00206 200 MVLTPTRELCVQVEDQAKVLGKGLP-FKTALVVGGDAMPQQLYRIQQGVELIVGTPGRLIDLLSKHDIELDNVSVLVLDE 278

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 161 ADEMLRMGFIDDVEAVLKKLPeQRQVALFSATMPPQIRRIAQTYLQDPVEVTIAAKTTTSANIRQRYWWVSGMHKLDALT 240
Cdd:PLN00206 279 VDCMLERGFRDQVMQIFQALS-QPQVLLFSATVSPEVEKFASSLAKDIILISIGNPNRPNKAVKQLAIWVETKQKKQKLF 357

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 241 RIL--EVEPFDAMIIFARTKAGTEELASKLQ-ARGLAAAAINGDMQQAQRERTIAMLKEGKLDILVATDVAARGLDVERI 317
Cdd:PLN00206 358 DILksKQHFKPPAVVFVSSRLGADLLANAITvVTGLKALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRV 437

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 896581323 318 SHVLNYDIPYDTESYVHRIGRTGRAGRSGEAILFATPREKGM---LRQIERATRQPI 371
Cdd:PLN00206 438 RQVIIFDMPNTIKEYIHQIGRASRMGEKGTAIVFVNEEDRNLfpeLVALLKSSGAAI 494

DEADc_EIF4A

cd17939

DEAD-box helicase domain of eukaryotic initiation factor 4A; The eukaryotic initiation ...

14-211

3.95e-67

DEAD-box helicase domain of eukaryotic initiation factor 4A; The eukaryotic initiation factor-4A (eIF4A) family consists of 3 proteins EIF4A1, EIF4A2, and EIF4A3. These factors are required for the binding of mRNA to 40S ribosomal subunits. In addition these proteins are helicases that function to unwind double-stranded RNA. EIF4A proteins are members of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.

Pssm-ID: 350697 [Multi-domain] Cd Length: 199 Bit Score: 217.96 E-value: 3.95e-67

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  14 LGLSEPVMQAVTAIGYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSNIDLQQIKPQALILAPTRELAIQV 93
Cdd:cd17939    2 MGLSEDLLRGIYAYGFEKPSAIQQRAIVPIIKGRDVIAQAQSGTGKTATFSIGALQRIDTTVRETQALVLAPTRELAQQI 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  94 AEAFQSYSSKIpGFRVLPVYGGQPYGQQLSALRRGVHIVVGTPGRVIDHLDRSTLDLSELKTLVLDEADEMLRMGFIDDV 173
Cdd:cd17939   82 QKVVKALGDYM-GVKVHACIGGTSVREDRRKLQYGPHIVVGTPGRVFDMLQRRSLRTDKIKMFVLDEADEMLSRGFKDQI 160

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 896581323 174 EAVLKKLPEQRQVALFSATMPPQIRRIAQTYLQDPVEV 211
Cdd:cd17939  161 YDIFQFLPPETQVVLFSATMPHEVLEVTKKFMRDPVRI 198

DEADc_DDX3_DDX4

cd17967

DEAD-box helicase domain of ATP-dependent RNA helicases DDX3 and DDX4; This subfamily includes ...

10-213

5.11e-66

DEAD-box helicase domain of ATP-dependent RNA helicases DDX3 and DDX4; This subfamily includes Drosophila melanogaster Vasa, which is essential for development. DEAD box protein 3 (DDX3) has been reported to display a high level of RNA-independent ATPase activity stimulated by both RNA and DNA. DEAD box protein 4 (DDX4, also known as VASA homolog) is an ATP-dependent RNA helicase required during spermatogenesis and is essential for the germline integrity. DDX3 and DDX4 are members of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.

Pssm-ID: 350725 [Multi-domain] Cd Length: 221 Bit Score: 215.81 E-value: 5.11e-66

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  10 QFAQLGLSEPVMQAVTAIGYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSNI----------DLQQIKPQ 79
Cdd:cd17967    1 SFEEAGLRELLLENIKRAGYTKPTPVQKYAIPIILAGRDLMACAQTGSGKTAAFLLPIISKLledgppsvgrGRRKAYPS 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  80 ALILAPTRELAIQ---VAEAFqSYSSKIpgfRVLPVYGGQPYGQQLSALRRGVHIVVGTPGRVIDHLDRSTLDLSELKTL 156
Cdd:cd17967   81 ALILAPTRELAIQiyeEARKF-SYRSGV---RSVVVYGGADVVHQQLQLLRGCDILVATPGRLVDFIERGRISLSSIKFL 156

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 896581323 157 VLDEADEMLRMGFIDDVEAVLKK----LPEQRQVALFSATMPPQIRRIAQTYLQDPVEVTI 213
Cdd:cd17967  157 VLDEADRMLDMGFEPQIRKIVEHpdmpPKGERQTLMFSATFPREIQRLAADFLKNYIFLTV 217

DEADc_DDX47

cd17954

DEAD-box helicase domain of DEAD box protein 47; DDX47 (also called E4-DEAD box protein) can ...

10-211

7.34e-66

DEAD-box helicase domain of DEAD box protein 47; DDX47 (also called E4-DEAD box protein) can shuttle between the nucleus and the cytoplasm, and has an RNA-independent ATPase activity. DX47 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.

Pssm-ID: 350712 [Multi-domain] Cd Length: 203 Bit Score: 214.87 E-value: 7.34e-66

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  10 QFAQLGLSEPVMQAVTAIGYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSNIdLQQIKP-QALILAPTRE 88
Cdd:cd17954    1 TFKELGVCEELCEACEKLGWKKPTKIQEEAIPVALQGRDIIGLAETGSGKTAAFALPILQAL-LENPQRfFALVLAPTRE 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  89 LAIQVAEAFQSYSSKIpGFRVLPVYGGQPYGQQLSALRRGVHIVVGTPGRVIDHLDRST-LDLSELKTLVLDEADEMLRM 167
Cdd:cd17954   80 LAQQISEQFEALGSSI-GLKSAVLVGGMDMMAQAIALAKKPHVIVATPGRLVDHLENTKgFSLKSLKFLVMDEADRLLNM 158

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 896581323 168 GFIDDVEAVLKKLPEQRQVALFSATMPPQIRRIAQTYLQDPVEV 211
Cdd:cd17954  159 DFEPEIDKILKVIPRERTTYLFSATMTTKVAKLQRASLKNPVKI 202

DEAD

pfam00270

DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...

33-200

5.56e-65

Pssm-ID: 425570 [Multi-domain] Cd Length: 165 Bit Score: 210.95 E-value: 5.56e-65

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323   33 SPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSNIDLQQIKPQALILAPTRELAIQVAEAFQSYSSKIpGFRVLPV 112
Cdd:pfam00270   1 TPIQAEAIPAILEGRDVLVQAPTGSGKTLAFLLPALEALDKLDNGPQALVLAPTRELAEQIYEELKKLGKGL-GLKVASL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  113 YGGQPYGQQLSALrRGVHIVVGTPGRVIDHLDRSTLdLSELKTLVLDEADEMLRMGFIDDVEAVLKKLPEQRQVALFSAT 192
Cdd:pfam00270  80 LGGDSRKEQLEKL-KGPDILVGTPGRLLDLLQERKL-LKNLKLLVLDEAHRLLDMGFGPDLEEILRRLPKKRQILLLSAT 157


                  ....*...
gi 896581323  193 MPPQIRRI 200
Cdd:pfam00270 158 LPRNLEDL 165

DEADc_DDX23

cd17945

DEAD-box helicase domain of DEAD box protein 23; DDX23 (also called U5 snRNP 100kD protein and ...

20-212

2.80e-64

DEAD-box helicase domain of DEAD box protein 23; DDX23 (also called U5 snRNP 100kD protein and PRP28 homolog) is involved in pre-mRNA splicing and its phosphorylated form (by SRPK2) is required for spliceosomal B complex formation. Diseases associated with DDX23 include distal hereditary motor neuropathy, type II. DDX23 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.

Pssm-ID: 350703 [Multi-domain] Cd Length: 220 Bit Score: 211.41 E-value: 2.80e-64

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  20 VMQAVTAIGYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSNI------DLQQIK--PQALILAPTRELAI 91
Cdd:cd17945    1 LLRVIRKLGYKEPTPIQRQAIPIGLQNRDIIGIAETGSGKTAAFLIPLLVYIsrlpplDEETKDdgPYALILAPTRELAQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  92 QVAEAFQSYSSKiPGFRVLPVYGGQPYGQQLSALRRGVHIVVGTPGRVIDHLDRSTLDLSELKTLVLDEADEMLRMGFID 171
Cdd:cd17945   81 QIEEETQKFAKP-LGIRVVSIVGGHSIEEQAFSLRNGCEILIATPGRLLDCLERRLLVLNQCTYVVLDEADRMIDMGFEP 159

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 896581323 172 DVEAVLKKLP--------------------EQRQVALFSATMPPQIRRIAQTYLQDPVEVT 212
Cdd:cd17945  160 QVTKILDAMPvsnkkpdteeaeklaasgkhRYRQTMMFTATMPPAVEKIAKGYLRRPVVVT 220

DEADc_DDX49

cd17955

DEAD-box helicase domain of DEAD box protein 49; DDX49 (also called Dbp8) is a member of the ...

11-210

5.93e-64

DEAD-box helicase domain of DEAD box protein 49; DDX49 (also called Dbp8) is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.

Pssm-ID: 350713 [Multi-domain] Cd Length: 204 Bit Score: 209.77 E-value: 5.93e-64

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  11 FAQLGLSEPVMQAVTAIGYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSNIDLQQIKPQALILAPTRELA 90
Cdd:cd17955    1 FEDLGLSSWLVKQCASLGIKEPTPIQKLCIPEILAGRDVIGGAKTGSGKTAAFALPILQRLSEDPYGIFALVLTPTRELA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  91 IQVAEAFQSYSSKIpGFRVLPVYGGQPYGQQLSALRRGVHIVVGTPGRVIDHL---DRSTLDLSELKTLVLDEADEMLRM 167
Cdd:cd17955   81 YQIAEQFRALGAPL-GLRCCVIVGGMDMVKQALELSKRPHIVVATPGRLADHLrssDDTTKVLSRVKFLVLDEADRLLTG 159

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 896581323 168 GFIDDVEAVLKKLPEQRQVALFSATMPPQIRRIAQTYLQDPVE 210
Cdd:cd17955  160 SFEDDLATILSALPPKRQTLLFSATLTDALKALKELFGNKPFF 202

DEADc_DDX6

cd17940

DEAD-box helicase domain of DEAD box protein 6; DEAD box protein 6 (DDX6, also known as Rck or ...

11-211

3.49e-62

DEAD-box helicase domain of DEAD box protein 6; DEAD box protein 6 (DDX6, also known as Rck or p54) participates in mRNA regulation mediated by miRNA-mediated silencing. It also plays a role in global and transcript-specific messenger RNA (mRNA) storage, translational repression, and decay. It is a member of the DEAD-box helicase family, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.

Pssm-ID: 350698 [Multi-domain] Cd Length: 201 Bit Score: 205.22 E-value: 3.49e-62

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  11 FAQLGLSEPVMQAVTAIGYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSNIDLQQIKPQALILAPTRELA 90
Cdd:cd17940    1 FEDYGLKRELLMGIFEKGFEKPSPIQEESIPIALSGRDILARAKNGTGKTGAYLIPILEKIDPKKDVIQALILVPTRELA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  91 IQVAEAFQSYSsKIPGFRVLPVYGGQPYGQQLSALRRGVHIVVGTPGRVIDHLDRSTLDLSELKTLVLDEADEMLRMGFI 170
Cdd:cd17940   81 LQTSQVCKELG-KHMGVKVMVTTGGTSLRDDIMRLYQTVHVLVGTPGRILDLAKKGVADLSHCKTLVLDEADKLLSQDFQ 159

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 896581323 171 DDVEAVLKKLPEQRQVALFSATMPPQIRRIAQTYLQDPVEV 211
Cdd:cd17940  160 PIIEKILNFLPKERQILLFSATFPLTVKNFMDRHMHNPYEI 200

DEADc_MSS116

cd17964

DEAD-box helicase domain of DEAD-box helicase Mss116; Mss116 is an RNA chaperone important for ...

16-205

1.24e-60

DEAD-box helicase domain of DEAD-box helicase Mss116; Mss116 is an RNA chaperone important for mitochondrial group I and II intron splicing, translational activation, and RNA end processing. Mss116 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.

Pssm-ID: 350722 [Multi-domain] Cd Length: 211 Bit Score: 201.27 E-value: 1.24e-60

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  16 LSEPVMQAVTAIGYETPSPIQAATIPAMLE-GRDVLGQAQTGTGKTAAFALPVL-----SNIDLQQIKPQALILAPTREL 89
Cdd:cd17964    1 LDPSLLKALTRMGFETMTPVQQKTLKPILStGDDVLARAKTGTGKTLAFLLPAIqsllnTKPAGRRSGVSALIISPTREL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  90 AIQVAEAFQSYSSKIPGFRVLPVYGGQPYGQQLSALRR-GVHIVVGTPGRVIDHLDRSTL--DLSELKTLVLDEADEMLR 166
Cdd:cd17964   81 ALQIAAEAKKLLQGLRKLRVQSAVGGTSRRAELNRLRRgRPDILVATPGRLIDHLENPGVakAFTDLDYLVLDEADRLLD 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 896581323 167 MGFIDDVEAVLKKLP----EQRQVALFSATMPPQIRRIAQTYL 205
Cdd:cd17964  161 MGFRPDLEQILRHLPeknaDPRQTLLFSATVPDEVQQIARLTL 203

DEADc_DDX27

cd17947

DEAD-box helicase domain of DEAD box protein 27; DDX27 (also called RHLP, deficiency of ...

20-211

7.40e-60

DEAD-box helicase domain of DEAD box protein 27; DDX27 (also called RHLP, deficiency of ribosomal subunits protein 1 homolog, and probable ATP-dependent RNA helicase DDX27) is involved in the processing of 5.8S and 28S ribosomal RNAs. More specifically, the encoded protein localizes to the nucleolus, where it interacts with the PeBoW complex to ensure proper 3' end formation of 47S rRNA. DDX27 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.

Pssm-ID: 350705 [Multi-domain] Cd Length: 196 Bit Score: 198.63 E-value: 7.40e-60

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  20 VMQAVTAIGYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSNI---DLQQIKPQALILAPTRELAIQVAEA 96
Cdd:cd17947    1 LLRALSSLGFTKPTPIQAAAIPLALLGKDICASAVTGSGKTAAFLLPILERLlyrPKKKAATRVLVLVPTRELAMQCFSV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  97 FQSYsSKIPGFRVLPVYGGQPYGQQLSALRRGVHIVVGTPGRVIDHLDRS-TLDLSELKTLVLDEADEMLRMGFIDDVEA 175
Cdd:cd17947   81 LQQL-AQFTDITFALAVGGLSLKAQEAALRARPDIVIATPGRLIDHLRNSpSFDLDSIEILVLDEADRMLEEGFADELKE 159

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 896581323 176 VLKKLPEQRQVALFSATMPPQIRRIAQTYLQDPVEV 211
Cdd:cd17947  160 ILRLCPRTRQTMLFSATMTDEVKDLAKLSLNKPVRV 195

DEADc_DDX4

cd18052

DEAD-box helicase domain of DEAD box protein 4; DEAD box protein 4 (DDX4, also known as VASA ...

6-205

1.15e-59

DEAD-box helicase domain of DEAD box protein 4; DEAD box protein 4 (DDX4, also known as VASA homolog) is an ATP-dependent RNA helicase required during spermatogenesis and is essential for the germline integrity. DEAD-box helicases are a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.

Pssm-ID: 350810 [Multi-domain] Cd Length: 264 Bit Score: 200.58 E-value: 1.15e-59

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323   6 QAPLQFAQLGLSEPVMQAVTAIGYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSNIDLQQIK-------- 77
Cdd:cd18052   40 PAILTFEEANLCETLLKNIRKAGYEKPTPVQKYAIPIILAGRDLMACAQTGSGKTAAFLLPVLTGMMKEGLTassfsevq 119

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  78 -PQALILAPTRELAIQV---AEAFqSYSSKIpgfRVLPVYGGQPYGQQLSALRRGVHIVVGTPGRVIDHLDRSTLDLSEL 153
Cdd:cd18052  120 ePQALIVAPTRELANQIfleARKF-SYGTCI---RPVVVYGGVSVGHQIRQIEKGCHILVATPGRLLDFIGRGKISLSKL 195

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 896581323 154 KTLVLDEADEMLRMGFIDDVEAVLKKL----PEQRQVALFSATMPPQIRRIAQTYL 205
Cdd:cd18052  196 KYLILDEADRMLDMGFGPEIRKLVSEPgmpsKEDRQTLMFSATFPEEIQRLAAEFL 251

DEADc_DDX46

cd17953

DEAD-box helicase domain of DEAD box protein 46; DDX46 (also called Prp5-like DEAD-box protein) ...

8-212

7.17e-59

DEAD-box helicase domain of DEAD box protein 46; DDX46 (also called Prp5-like DEAD-box protein) is a component of the 17S U2 snRNP complex. It plays an important role in pre-mRNA splicing and has a role in antiviral innate immunity. DDX46 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.

Pssm-ID: 350711 [Multi-domain] Cd Length: 222 Bit Score: 197.21 E-value: 7.17e-59

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323   8 PLQF-AQLGLSEPVMQAVTAIGYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSNI-DLQQIK----PQAL 81
Cdd:cd17953   10 PIQKwSQCGLSEKVLDLIKKLGYEKPTPIQAQALPAIMSGRDVIGIAKTGSGKTLAFLLPMFRHIkDQRPVKpgegPIGL 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  82 ILAPTRELAIQVAEAFQSYsSKIPGFRVLPVYGGQPYGQQLSALRRGVHIVVGTPGRVIDHL---DRSTLDLSELKTLVL 158
Cdd:cd17953   90 IMAPTRELALQIYVECKKF-SKALGLRVVCVYGGSGISEQIAELKRGAEIVVCTPGRMIDILtanNGRVTNLRRVTYVVL 168

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 896581323 159 DEADEMLRMGFIDDVEAVLKKLPEQRQVALFSATMPPQIRRIAQTYLQDPVEVT 212
Cdd:cd17953  169 DEADRMFDMGFEPQIMKIVNNIRPDRQTVLFSATFPRKVEALARKVLHKPIEIT 222

DEADc_EIF4AII_EIF4AI_DDX2

cd18046

DEAD-box helicase domain of eukaryotic initiation factor 4A-I and 4-II; Eukaryotic initiation ...

11-211

3.05e-56

DEAD-box helicase domain of eukaryotic initiation factor 4A-I and 4-II; Eukaryotic initiation factor 4A-I (DDX2A) and eukaryotic initiation factor 4A-II (DDX2B) are involved in cap recognition and are required for mRNA binding to ribosome. They are DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.

Pssm-ID: 350804 [Multi-domain] Cd Length: 201 Bit Score: 189.19 E-value: 3.05e-56

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  11 FAQLGLSEPVMQAVTAIGYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSNIDLQQIKPQALILAPTRELA 90
Cdd:cd18046    1 FDDMNLKESLLRGIYAYGFEKPSAIQQRAIMPCIKGYDVIAQAQSGTGKTATFSISILQQIDTSLKATQALVLAPTRELA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  91 IQ---VAEAFQSYSskipGFRVLPVYGGQPYGQQLSALRRGVHIVVGTPGRVIDHLDRSTLDLSELKTLVLDEADEMLRM 167
Cdd:cd18046   81 QQiqkVVMALGDYM----GIKCHACIGGTSVRDDAQKLQAGPHIVVGTPGRVFDMINRRYLRTDYIKMFVLDEADEMLSR 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 896581323 168 GFIDDVEAVLKKLPEQRQVALFSATMPPQIRRIAQTYLQDPVEV 211
Cdd:cd18046  157 GFKDQIYDIFQKLPPDTQVVLLSATMPNDVLEVTTKFMRDPIRI 200

DEADc_DDX54

cd17959

DEAD-box helicase domain of DEAD box protein 54; DDX54 interacts in a hormone-dependent manner ...

11-209

5.25e-56

DEAD-box helicase domain of DEAD box protein 54; DDX54 interacts in a hormone-dependent manner with nuclear receptors, and represses their transcriptional activity. DDX54 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.

Pssm-ID: 350717 [Multi-domain] Cd Length: 205 Bit Score: 188.67 E-value: 5.25e-56

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  11 FAQLGLSEPVMQAVTAIGYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSNID--LQQIKPQALILAPTRE 88
Cdd:cd17959    3 FQSMGLSPPLLRAIKKKGYKVPTPIQRKTIPLILDGRDVVAMARTGSGKTAAFLIPMIEKLKahSPTVGARALILSPTRE 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  89 LAIQVAEAFQSYSsKIPGFRVLPVYGGQPYGQQLSALRRGVHIVVGTPGRVIDHLDRSTLDLSELKTLVLDEADEMLRMG 168
Cdd:cd17959   83 LALQTLKVTKELG-KFTDLRTALLVGGDSLEEQFEALASNPDIIIATPGRLLHLLVEMNLKLSSVEYVVFDEADRLFEMG 161

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 896581323 169 FIDDVEAVLKKLPEQRQVALFSATMPPQIRRIAQTYLQDPV 209
Cdd:cd17959  162 FAEQLHEILSRLPENRQTLLFSATLPKLLVEFAKAGLNEPV 202

DEADc_DDX5_DDX17

cd17966

DEAD-box helicase domain of ATP-dependent RNA helicases DDX5 and DDX17; DDX5 and DDX17 are ...

20-212

2.25e-55

DEAD-box helicase domain of ATP-dependent RNA helicases DDX5 and DDX17; DDX5 and DDX17 are members of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.

Pssm-ID: 350724 [Multi-domain] Cd Length: 197 Bit Score: 186.81 E-value: 2.25e-55

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  20 VMQAVTAIGYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSNIDLQQIK-----PQALILAPTRELAIQVA 94
Cdd:cd17966    1 VMDELKRQGFTEPTAIQAQGWPMALSGRDMVGIAQTGSGKTLAFLLPAIVHINAQPPLergdgPIVLVLAPTRELAQQIQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  95 EAFQSY--SSKIpgfRVLPVYGGQPYGQQLSALRRGVHIVVGTPGRVIDHLDRSTLDLSELKTLVLDEADEMLRMGFIDD 172
Cdd:cd17966   81 QEANKFggSSRL---RNTCVYGGAPKGPQIRDLRRGVEICIATPGRLIDFLDQGKTNLRRVTYLVLDEADRMLDMGFEPQ 157

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 896581323 173 VEAVLKKLPEQRQVALFSATMPPQIRRIAQTYLQDPVEVT 212
Cdd:cd17966  158 IRKIVDQIRPDRQTLMWSATWPKEVRRLAEDFLKDYIQVN 197

SF2_C_DEAD

cd18787

C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...

223-351

2.55e-55

C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis, and RNA degradation. They are superfamily (SF)2 helicases that, similar to SF1, 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: 350174 [Multi-domain] Cd Length: 131 Bit Score: 184.25 E-value: 2.55e-55

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 223 IRQRYWWVSGMHKLDAL-TRILEVEPFDAMIIFARTKAGTEELASKLQARGLAAAAINGDMQQAQRERTIAMLKEGKLDI 301
Cdd:cd18787    1 IKQLYVVVEEEEKKLLLlLLLLEKLKPGKAIIFVNTKKRVDRLAELLEELGIKVAALHGDLSQEERERALKKFRSGKVRV 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 896581323 302 LVATDVAARGLDVERISHVLNYDIPYDTESYVHRIGRTGRAGRSGEAILF 351
Cdd:cd18787   81 LVATDVAARGLDIPGVDHVINYDLPRDAEDYVHRIGRTGRAGRKGTAITF 130

DEXDc

smart00487

DEAD-like helicases superfamily;

28-226

4.07e-55

DEAD-like helicases superfamily;

Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 186.16 E-value: 4.07e-55

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323    28 GYETPSPIQAATIPAMLEG-RDVLGQAQTGTGKTAAFALPVLSNIdLQQIKPQALILAPTRELAIQVAEAFQSYSSKIPG 106
Cdd:smart00487   5 GFEPLRPYQKEAIEALLSGlRDVILAAPTGSGKTLAALLPALEAL-KRGKGGRVLVLVPTRELAEQWAEELKKLGPSLGL 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323   107 fRVLPVYGGQPYGQQLSALRRGV-HIVVGTPGRVIDHLDRSTLDLSELKTLVLDEADEMLRMGFIDDVEAVLKKLPEQRQ 185
Cdd:smart00487  84 -KVVGLYGGDSKREQLRKLESGKtDILVTTPGRLLDLLENDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQ 162

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|.
gi 896581323   186 VALFSATMPPQIRRIAQTYLQDPVEVTIaaKTTTSANIRQR 226
Cdd:smart00487 163 LLLLSATPPEEIENLLELFLNDPVFIDV--GFTPLEPIEQF 201

DEADc_DDX19_DDX25

cd17963

DEAD-box helicase domain of ATP-dependent RNA helicases DDX19 and DDX25; DDX19 (also called ...

16-212

4.50e-54

DEAD-box helicase domain of ATP-dependent RNA helicases DDX19 and DDX25; DDX19 (also called DEAD box RNA helicase DEAD5) and DDX25 (also called gonadotropin-regulated testicular RNA helicase (GRTH)) are members of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.

Pssm-ID: 350721 [Multi-domain] Cd Length: 196 Bit Score: 183.16 E-value: 4.50e-54

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  16 LSEPVMQAVTAIGYETPSPIQAATIPAMLEG--RDVLGQAQTGTGKTAAFALPVLSNIDLQQIKPQALILAPTRELAIQ- 92
Cdd:cd17963    1 LKPELLKGLYAMGFNKPSKIQETALPLILSDppENLIAQSQSGTGKTAAFVLAMLSRVDPTLKSPQALCLAPTRELARQi 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  93 --VAEAFQSYSSKIPGFRV--LPVYGGQPYGQQlsalrrgvhIVVGTPGRVIDHLDRSTLDLSELKTLVLDEADEMLRM- 167
Cdd:cd17963   81 geVVEKMGKFTGVKVALAVpgNDVPRGKKITAQ---------IVIGTPGTVLDWLKKRQLDLKKIKILVLDEADVMLDTq 151

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 896581323 168 GFIDDVEAVLKKLPEQRQVALFSATMPPQIRRIAQTYLQDPVEVT 212
Cdd:cd17963  152 GHGDQSIRIKRMLPRNCQILLFSATFPDSVRKFAEKIAPNANTIK 196

DEADc_DDX42

cd17952

DEAD-box helicase domain of DEAD box protein 42; DDX42 (also called Splicing Factor ...

20-212

5.82e-54

DEAD-box helicase domain of DEAD box protein 42; DDX42 (also called Splicing Factor 3B-Associated 125 kDa Protein, RHELP, or RNAHP) is an NTPase with a preference for ATP, the hydrolysis of which is enhanced by various RNA substrates. It acts as a non-processive RNA helicase with protein displacement and RNA annealing activities. DDX42 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.

Pssm-ID: 350710 [Multi-domain] Cd Length: 197 Bit Score: 183.00 E-value: 5.82e-54

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  20 VMQAVTAIGYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSNI-DLQQIKPQ----ALILAPTRELAIQVA 94
Cdd:cd17952    1 LLNAIRKQEYEQPTPIQAQALPVALSGRDMIGIAKTGSGKTAAFIWPMLVHImDQRELEKGegpiAVIVAPTRELAQQIY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  95 EAFQSYSsKIPGFRVLPVYGGQPYGQQLSALRRGVHIVVGTPGRVIDHLDRSTLDLSELKTLVLDEADEMLRMGFIDDVE 174
Cdd:cd17952   81 LEAKKFG-KAYNLRVVAVYGGGSKWEQAKALQEGAEIVVATPGRLIDMVKKKATNLQRVTYLVLDEADRMFDMGFEYQVR 159

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 896581323 175 AVLKKLPEQRQVALFSATMPPQIRRIAQTYLQDPVEVT 212
Cdd:cd17952  160 SIVGHVRPDRQTLLFSATFKKKIEQLARDILSDPIRVV 197

DEADc_DDX59

cd17962

DEAD-box helicase domain of DEAD box protein 59; DDX59 plays an important role in lung cancer ...

28-212

9.96e-54

DEAD-box helicase domain of DEAD box protein 59; DDX59 plays an important role in lung cancer development by promoting DNA replication. DDX59 knockdown mice showed reduced cell proliferation, anchorage-independent cell growth, and reduction of tumor formation. Recent work shows that EGFR and Ras regulate DDX59 during lung cancer development. Diseases associated with DDX59 (also called zinc finger HIT domain-containing protein 5) include orofaciodigital syndrome V and orofaciodigital syndrome. DDX59 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.

Pssm-ID: 350720 [Multi-domain] Cd Length: 193 Bit Score: 182.36 E-value: 9.96e-54

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  28 GYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSNIDLQQIKPQALILAPTRELAIQVAEAFQSYSSKIPGF 107
Cdd:cd17962    9 GYEVPTPIQMQMIPVGLLGRDILASADTGSGKTAAFLLPVIIRCLTEHRNPSALILTPTRELAVQIEDQAKELMKGLPPM 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 108 RVLPVYGGQPYGQQLSALRRGVHIVVGTPGRVIDHLDRSTLDLSELKTLVLDEADEMLRMGFIDDVEAVLKKLPEQRQVA 187
Cdd:cd17962   89 KTALLVGGLPLPPQLYRLQQGVKVIIATPGRLLDILKQSSVELDNIKIVVVDEADTMLKMGFQQQVLDILENISHDHQTI 168

                        170       180
                 ....*....|....*....|....*
gi 896581323 188 LFSATMPPQIRRIAQTYLQDPVEVT 212
Cdd:cd17962  169 LVSATIPRGIEQLAGQLLQNPVRIT 193

DEADc_DDX20

cd17943

DEAD-box helicase domain of DEAD box protein 20; DDX20 (also called DEAD Box Protein DP 103, ...

20-211

2.19e-53

DEAD-box helicase domain of DEAD box protein 20; DDX20 (also called DEAD Box Protein DP 103, Component Of Gems 3, Gemin-3, and SMN-Interacting Protein) interacts directly with SMN (survival of motor neurons), the spinal muscular atrophy gene product, and may play a catalytic role in the function of the SMN complex on ribonucleoproteins. Diseases associated with DDX20 include spinal muscular atrophy and muscular atrophy. DDX20 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.

Pssm-ID: 350701 [Multi-domain] Cd Length: 192 Bit Score: 181.31 E-value: 2.19e-53

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  20 VMQAVTAIGYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSNIDLQQIKPQALILAPTRELAIQVAEAFQS 99
Cdd:cd17943    1 VLEGLKAAGFQRPSPIQLAAIPLGLAGHDLIVQAKSGTGKTLVFVVIALESLDLERRHPQVLILAPTREIAVQIHDVFKK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 100 YSSKIPGFRVLPVYGGQPYGQQLSALRRgVHIVVGTPGRVIDHLDRSTLDLSELKTLVLDEADEMLRMGFIDDVEAVLKK 179
Cdd:cd17943   81 IGKKLEGLKCEVFIGGTPVKEDKKKLKG-CHIAVGTPGRIKQLIELGALNVSHVRLFVLDEADKLMEGSFQKDVNWIFSS 159

                        170       180       190
                 ....*....|....*....|....*....|..
gi 896581323 180 LPEQRQVALFSATMPPQIRRIAQTYLQDPVEV 211
Cdd:cd17943  160 LPKNKQVIAFSATYPKNLDNLLARYMRKPVLV 191

DEADc_DDX39

cd17950

DEAD-box helicase domain of DEAD box protein 39; DDX39A is involved in pre-mRNA splicing and ...

10-213

4.49e-52

DEAD-box helicase domain of DEAD box protein 39; DDX39A is involved in pre-mRNA splicing and is required for the export of mRNA out of the nucleus. DDX39B is an essential splicing factor required for association of U2 small nuclear ribonucleoprotein with pre-mRNA, and it also plays an important role in mRNA export from the nucleus to the cytoplasm. Diseases associated with DDX39A (also called UAP56-Related Helicase, 49 kDa) include gastrointestinal stromal tumor and inflammatory bowel disease 6, while diseases associated with DDX39B (also called 56 kDa U2AF65-Associated Protein) include Plasmodium vivax malaria. DDX39 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.

Pssm-ID: 350708 [Multi-domain] Cd Length: 208 Bit Score: 178.31 E-value: 4.49e-52

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  10 QFAQLGLSEPVMQAVTAIGYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVlsnidLQQIKP-----QALILA 84
Cdd:cd17950    3 GFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLST-----LQQLEPvdgqvSVLVIC 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  85 PTRELAIQVAEAFQSYSSKIPGFRVLPVYGGQPYGQQLSALRRGV-HIVVGTPGRVIDHLDRSTLDLSELKTLVLDEADE 163
Cdd:cd17950   78 HTRELAFQISNEYERFSKYMPNVKTAVFFGGVPIKKDIEVLKNKCpHIVVGTPGRILALVREKKLKLSHVKHFVLDECDK 157

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 896581323 164 MLRMgfID---DVEAVLKKLPEQRQVALFSATMPPQIRRIAQTYLQDPVEVTI 213
Cdd:cd17950  158 MLEQ--LDmrrDVQEIFRATPHDKQVMMFSATLSKEIRPVCKKFMQDPLEIFV 208

DEADc_DDX43_DDX53

cd17958

DEAD-box helicase domain of DEAD box proteins 43 and 53; DDX43 (also called cancer/testis ...

20-212

3.45e-51

DEAD-box helicase domain of DEAD box proteins 43 and 53; DDX43 (also called cancer/testis antigen 13 or helical antigen) displays tumor-specific expression. Diseases associated with DDX43 include rheumatoid lung disease. DDX53 is also called cancer/testis antigen 26 or DEAD-Box Protein CAGE. Both DDX46 and DDX53 are members of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.

Pssm-ID: 350716 [Multi-domain] Cd Length: 197 Bit Score: 175.73 E-value: 3.45e-51

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  20 VMQAVTAIGYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSNIDLQ------QIKPQALILAPTRELAIQV 93
Cdd:cd17958    1 IMKEIKKQGFEKPSPIQSQAWPIILQGIDLIGVAQTGTGKTLAYLLPGFIHLDLQpipreqRNGPGVLVLTPTRELALQI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  94 AEAFQSYSSKipGFRVLPVYGGQPYGQQLSALRRGVHIVVGTPGRVIDHLDRSTLDLSELKTLVLDEADEMLRMGFIDDV 173
Cdd:cd17958   81 EAECSKYSYK--GLKSVCVYGGGNRNEQIEDLSKGVDIIIATPGRLNDLQMNNVINLKSITYLVLDEADRMLDMGFEPQI 158

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 896581323 174 EAVLKKLPEQRQVALFSATMPPQIRRIAQTYLQDPVEVT 212
Cdd:cd17958  159 RKILLDIRPDRQTIMTSATWPDGVRRLAQSYLKDPMIVY 197

DEADc_EIF4AIII_DDX48

cd18045

DEAD-box helicase domain of eukaryotic initiation factor 4A-III; Eukaryotic initiation factor ...

11-211

2.26e-50

DEAD-box helicase domain of eukaryotic initiation factor 4A-III; Eukaryotic initiation factor 4A-III (EIF4AIII, also known as DDX48) is part of the exon junction complex (EJC) that plays a major role in posttranscriptional regulation of mRNA. EJC consists of four proteins (eIF4AIII, Barentsz [Btz], Mago, and Y14), mRNA, and ATP. DDX48 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.

Pssm-ID: 350803 [Multi-domain] Cd Length: 201 Bit Score: 173.42 E-value: 2.26e-50

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  11 FAQLGLSEPVMQAVTAIGYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSNIDLQQIKPQALILAPTRELA 90
Cdd:cd18045    1 FETMGLREDLLRGIYAYGFEKPSAIQQRAIKPIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQVRETQALILSPTRELA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  91 IQVAEAFQSYsSKIPGFRVLPVYGGQPYGQQLSALRRGVHIVVGTPGRVIDHLDRSTLDLSELKTLVLDEADEMLRMGFI 170
Cdd:cd18045   81 VQIQKVLLAL-GDYMNVQCHACIGGTSVGDDIRKLDYGQHIVSGTPGRVFDMIRRRSLRTRHIKMLVLDEADEMLNKGFK 159

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 896581323 171 DDVEAVLKKLPEQRQVALFSATMPPQIRRIAQTYLQDPVEV 211
Cdd:cd18045  160 EQIYDVYRYLPPATQVVLVSATLPQDILEMTNKFMTDPIRI 200

DEADc_DDX41

cd17951

DEAD-box helicase domain of DEAD box protein 41; DDX41 (also called ABS and MPLPF) interacts ...

20-211

3.47e-50

DEAD-box helicase domain of DEAD box protein 41; DDX41 (also called ABS and MPLPF) interacts with several spliceosomal proteins and may recognize the bacterial second messengers cyclic di-GMP and cyclic di-AMP, resulting in the induction of genes involved in the innate immune response. Diseases associated with DDX41 include "myeloproliferative/lymphoproliferative neoplasms, familial" and "Ddx41-related susceptibility to familial myeloproliferative/lymphoproliferative neoplasms". DDX41 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.

Pssm-ID: 350709 [Multi-domain] Cd Length: 206 Bit Score: 173.29 E-value: 3.47e-50

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  20 VMQAVTAIGYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSNIDLQQIK--------PQALILAPTRELAI 91
Cdd:cd17951    1 ILKGLKKKGIKKPTPIQMQGLPTILSGRDMIGIAFTGSGKTLVFTLPLIMFALEQEKKlpfikgegPYGLIVCPSRELAR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  92 QVAEAFQSYSSKI-----PGFRVLPVYGGQPYGQQLSALRRGVHIVVGTPGRVIDHLDRSTLDLSELKTLVLDEADEMLR 166
Cdd:cd17951   81 QTHEVIEYYCKALqeggyPQLRCLLCIGGMSVKEQLEVIRKGVHIVVATPGRLMDMLNKKKINLDICRYLCLDEADRMID 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 896581323 167 MGFIDDVEAVLKKLPEQRQVALFSATMPPQIRRIAQTYLQDPVEV 211
Cdd:cd17951  161 MGFEEDIRTIFSYFKGQRQTLLFSATMPKKIQNFAKSALVKPVTV 205

DEADc_DDX31

cd17949

DEAD-box helicase domain of DEAD box protein 31; DDX31 (also called helicain or G2 helicase) ...

28-212

3.69e-50

DEAD-box helicase domain of DEAD box protein 31; DDX31 (also called helicain or G2 helicase) plays a role in ribosome biogenesis and TP53/p53 regulation through its interaction with NPM1. DDX31 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.

Pssm-ID: 350707 [Multi-domain] Cd Length: 214 Bit Score: 173.54 E-value: 3.69e-50

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  28 GYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSniDLQQIKPQ--------ALILAPTRELAIQVAEAFQS 99
Cdd:cd17949   10 GIEKPTAIQKLAIPVLLQGRDVLVRSQTGSGKTLAYLLPIIQ--RLLSLEPRvdrsdgtlALVLVPTRELALQIYEVLEK 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 100 YSSK----IPGFrvlpVYGGQPYGQQLSALRRGVHIVVGTPGRVIDHLDR-STLDLSELKTLVLDEADEMLRMGFIDDVE 174
Cdd:cd17949   88 LLKPfhwiVPGY----LIGGEKRKSEKARLRKGVNILIATPGRLLDHLKNtQSFDVSNLRWLVLDEADRLLDMGFEKDIT 163

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 896581323 175 AVLKKL-------------PEQRQVALFSATMPPQIRRIAQTYLQDPVEVT 212
Cdd:cd17949  164 KILELLddkrskaggekskPSRRQTVLVSATLTDGVKRLAGLSLKDPVYID 214

DEADc_DDX21_DDX50

cd17944

DEAD-box helicase domain of DEAD box proteins 21 and 50; DDX21 (also called Gu-Alpha and ...

34-210

4.50e-50

DEAD-box helicase domain of DEAD box proteins 21 and 50; DDX21 (also called Gu-Alpha and nucleolar RNA helicase 2) is an RNA helicase that acts as a sensor of the transcriptional status of both RNA polymerase (Pol) I and II. It promotes ribosomal RNA (rRNA) processing and transcription from polymerase II (Pol II) and binds various RNAs, such as rRNAs, snoRNAs, 7SK and, at lower extent, mRNAs. DDX50 (also called Gu-Beta, Nucleolar Protein Gu2, and malignant cell derived RNA helicase). DDX21 and DDX50 have similar genomic structures and are in tandem orientation on chromosome 10, suggesting that the two genes arose by gene duplication in evolution. Diseases associated with DDX21 include stomach disease and cerebral creatine deficiency syndrome 3. Diseases associated with DDX50 include rectal disease. Both are members of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. Their name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP- binding region.

Pssm-ID: 350702 [Multi-domain] Cd Length: 202 Bit Score: 172.72 E-value: 4.50e-50

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  34 PIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSNI--DLQQIK----PQALILAPTRELAIQVAEAFQSYSSKIpgf 107
Cdd:cd17944   15 PIQVKTFHPVYSGKDLIAQARTGTGKTFSFAIPLIEKLqeDQQPRKrgraPKVLVLAPTRELANQVTKDFKDITRKL--- 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 108 RVLPVYGGQPYGQQLSALRRGVHIVVGTPGRVIDHLDRSTLDLSELKTLVLDEADEMLRMGFIDDVEAVL----KKLPEQ 183
Cdd:cd17944   92 SVACFYGGTPYQQQIFAIRNGIDILVGTPGRIKDHLQNGRLDLTKLKHVVLDEVDQMLDMGFAEQVEEILsvsyKKDSED 171

                        170       180
                 ....*....|....*....|....*...
gi 896581323 184 R-QVALFSATMPPQIRRIAQTYLQDPVE 210
Cdd:cd17944  172 NpQTLLFSATCPDWVYNVAKKYMKSQYE 199

DEADc_DDX52

cd17957

DEAD-box helicase domain of DEAD box protein 52; DDX52 (also called ROK1 and HUSSY19) is ...

20-213

2.32e-49

DEAD-box helicase domain of DEAD box protein 52; DDX52 (also called ROK1 and HUSSY19) is ubiquitously expressed in testis, endometrium, and other tissues in humans. DDX52 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.

Pssm-ID: 350715 [Multi-domain] Cd Length: 198 Bit Score: 170.85 E-value: 2.32e-49

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  20 VMQAVTAIGYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSNI--DLQQIKPQALILAPTRELAIQVAEAF 97
Cdd:cd17957    1 LLNNLEESGYREPTPIQMQAIPILLHGRDLLACAPTGSGKTLAFLIPILQKLgkPRKKKGLRALILAPTRELASQIYREL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  98 QSYsSKIPGFRVLPVYGG----QPYGQQLSalrRGVHIVVGTPGRVIDHLDRSTLDLSELKTLVLDEADEMLRMGFIDDV 173
Cdd:cd17957   81 LKL-SKGTGLRIVLLSKSleakAKDGPKSI---TKYDILVSTPLRLVFLLKQGPIDLSSVEYLVLDEADKLFEPGFREQT 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 896581323 174 EAVLKKLPEQR-QVALFSATMPPQIRRIAQTYLQDPVEVTI 213
Cdd:cd17957  157 DEILAACTNPNlQRSLFSATIPSEVEELARSVMKDPIRIIV 197

DEADc_DDX1

cd17938

DEAD-box helicase domain of DEAD box protein 1; DEAD box protein 1 (DDX1) acts as an ...

11-211

4.81e-49

DEAD-box helicase domain of DEAD box protein 1; DEAD box protein 1 (DDX1) acts as an ATP-dependent RNA helicase, able to unwind both RNA-RNA and RNA-DNA duplexes. It possesses 5' single-stranded RNA overhang nuclease activity as well as ATPase activity on various RNA, but not DNA polynucleotides. DDX1 may play a role in RNA clearance at DNA double-strand breaks (DSBs), thereby facilitating the template-guided repair of transcriptionally active regions of the genome. It may also be involved in 3'-end cleavage and polyadenylation of pre-mRNAs. DDX1 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.

Pssm-ID: 350696 [Multi-domain] Cd Length: 204 Bit Score: 170.19 E-value: 4.81e-49

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  11 FAQLGLSEPVMQAVTAIGYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLsnidlqQIKpQALILAPTRELA 90
Cdd:cd17938    1 FEELGVMPELIKAVEELDWLLPTDIQAEAIPLILGGGDVLMAAETGSGKTGAFCLPVL------QIV-VALILEPSRELA 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  91 IQVAEAFQSYSSKI--PGFRVLPVYGGQPYGQQLSALRRGVHIVVGTPGRVIDHLDRSTLDLSELKTLVLDEADEMLRMG 168
Cdd:cd17938   74 EQTYNCIENFKKYLdnPKLRVALLIGGVKAREQLKRLESGVDIVVGTPGRLEDLIKTGKLDLSSVRFFVLDEADRLLSQG 153

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 896581323 169 FIDDVEAVLKKLP-----EQR-QVALFSATM-PPQIRRIAQTYLQDPVEV 211
Cdd:cd17938  154 NLETINRIYNRIPkitsdGKRlQVIVCSATLhSFEVKKLADKIMHFPTWV 203

DEADc_DDX55

cd17960

DEAD-box helicase domain of DEAD box protein 55; DDX55 is a member of the DEAD-box helicases, ...

20-212

8.78e-49

DEAD-box helicase domain of DEAD box protein 55; DDX55 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.

Pssm-ID: 350718 [Multi-domain] Cd Length: 202 Bit Score: 169.29 E-value: 8.78e-49

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  20 VMQAVTAIGYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSNI--DLQQIKP---QALILAPTRELAIQVA 94
Cdd:cd17960    1 ILDVVAELGFTSMTPVQAATIPLFLSNKDVVVEAVTGSGKTLAFLIPVLEILlkRKANLKKgqvGALIISPTRELATQIY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  95 EAFQSYSSKI-PGFRVLPVYGGQPYGQQLSALRR-GVHIVVGTPGRVIDHLDRST--LDLSELKTLVLDEADEMLRMGFI 170
Cdd:cd17960   81 EVLQSFLEHHlPKLKCQLLIGGTNVEEDVKKFKRnGPNILVGTPGRLEELLSRKAdkVKVKSLEVLVLDEADRLLDLGFE 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 896581323 171 DDVEAVLKKLPEQRQVALFSATMPPQIRRIAQTYLQDPVEVT 212
Cdd:cd17960  161 ADLNRILSKLPKQRRTGLFSATQTDAVEELIKAGLRNPVRVV 202

DEADc_DDX10

cd17941

DEAD-box helicase domain of DEAD box protein 10; Fusion of the DDX10 gene and the nucleoporin ...

28-211

8.91e-49

DEAD-box helicase domain of DEAD box protein 10; Fusion of the DDX10 gene and the nucleoporin gene, NUP98, by inversion 11 (p15q22) chromosome translocation is found in the patients with de novo or therapy-related myeloid malignancies. Diseases associated with DDX10 (also known as DDX10-NUP98 Fusion Protein Type 2) include myelodysplastic syndrome and leukemia, acute myeloid. DDX10 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.

Pssm-ID: 350699 [Multi-domain] Cd Length: 198 Bit Score: 169.01 E-value: 8.91e-49

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  28 GYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSNIDLQQIKPQ----ALILAPTRELAIQVAEAFQsyssK 103
Cdd:cd17941    9 GFIKMTEIQRDSIPHALQGRDILGAAKTGSGKTLAFLVPLLEKLYRERWTPEdglgALIISPTRELAMQIFEVLR----K 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 104 IPGFRVLP---VYGGQPYGQQLSALRRgVHIVVGTPGRVIDHLDRS-TLDLSELKTLVLDEADEMLRMGFIDDVEAVLKK 179
Cdd:cd17941   85 VGKYHSFSaglIIGGKDVKEEKERINR-MNILVCTPGRLLQHMDETpGFDTSNLQMLVLDEADRILDMGFKETLDAIVEN 163

                        170       180       190
                 ....*....|....*....|....*....|..
gi 896581323 180 LPEQRQVALFSATMPPQIRRIAQTYLQDPVEV 211
Cdd:cd17941  164 LPKSRQTLLFSATQTKSVKDLARLSLKNPEYI 195

DEADc_DDX3

cd18051

DEAD-box helicase domain of DEAD box protein 3; DDX3 (also called helicase-like protein, DEAD ...

11-207

1.38e-48

DEAD-box helicase domain of DEAD box protein 3; DDX3 (also called helicase-like protein, DEAD box, X isoform, or DDX14) has been reported to display a high level of RNA-independent ATPase activity stimulated by both RNA and DNA. This protein has multiple conserved domains and is thought to play roles in both the nucleus and cytoplasm. Nuclear roles include transcriptional regulation, mRNP assembly, pre-mRNA splicing, and mRNA export. In the cytoplasm, this protein is thought to be involved in translation, cellular signaling, and viral replication. Misregulation of this gene has been implicated in tumorigenesis. Diseases associated with DDX3 include mental retardation, X-linked 102 and agenesis of the corpus callosum, with facial anomalies and robin sequence. DDX3 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.

Pssm-ID: 350809 [Multi-domain] Cd Length: 249 Bit Score: 170.22 E-value: 1.38e-48

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  11 FAQLGLSEPVMQAVTAIGYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSNI----------------DLQ 74
Cdd:cd18051   23 FSDLDLGEIIRNNIELARYTKPTPVQKHAIPIIKSKRDLMACAQTGSGKTAAFLLPILSQIyeqgpgeslpsesgyyGRR 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  75 QIKPQALILAPTRELAIQV---AEAFqSYSSKIpgfRVLPVYGGQPYGQQLSALRRGVHIVVGTPGRVIDHLDRSTLDLS 151
Cdd:cd18051  103 KQYPLALVLAPTRELASQIydeARKF-AYRSRV---RPCVVYGGADIGQQMRDLERGCHLLVATPGRLVDMLERGKIGLD 178

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 152 ELKTLVLDEADEMLRMGFIDDVEAVLKK--LPE--QRQVALFSATMPPQIRRIAQTYLQD 207
Cdd:cd18051  179 YCKYLVLDEADRMLDMGFEPQIRRIVEQdtMPPtgERQTLMFSATFPKEIQMLARDFLDN 238

DEADc_DDX56

cd17961

DEAD-box helicase domain of DEAD box protein 56; DDX56 is a helicase required for assembly of ...

22-209

5.48e-47

DEAD-box helicase domain of DEAD box protein 56; DDX56 is a helicase required for assembly of infectious West Nile virus particles. New research suggests that DDX56 relocalizes to the site of virus assembly during WNV infection and that its interaction with WNV capsid in the cytoplasm may occur transiently during virion morphogenesis. DDX56 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.

Pssm-ID: 350719 [Multi-domain] Cd Length: 206 Bit Score: 164.68 E-value: 5.48e-47

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  22 QAVTAIGYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSNI-DLQQIK-----PQALILAPTRELAIQVAE 95
Cdd:cd17961    7 KAIAKLGWEKPTLIQSKAIPLALEGKDILARARTGSGKTAAYALPIIQKIlKAKAESgeeqgTRALILVPTRELAQQVSK 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  96 AFQSYSSKI-PGFRVLPVYGGQPYGQQLSALRRGVHIVVGTPGRVIDHLDR-STLDLSELKTLVLDEADEMLRMGFIDDV 173
Cdd:cd17961   87 VLEQLTAYCrKDVRVVNLSASSSDSVQRALLAEKPDIVVSTPARLLSHLESgSLLLLSTLKYLVIDEADLVLSYGYEEDL 166

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 896581323 174 EAVLKKLPEQRQVALFSATMPPQIRRIAQTYLQDPV 209
Cdd:cd17961  167 KSLLSYLPKNYQTFLMSATLSEDVEALKKLVLHNPA 202

DEADc_DDX5

cd18049

DEAD-box helicase domain of DEAD box protein 5; DDX5 (also called RNA helicase P68, HLR1, ...

9-215

3.11e-45

DEAD-box helicase domain of DEAD box protein 5; DDX5 (also called RNA helicase P68, HLR1, G17P1, or HUMP68) is involved in pathways that include the alteration of RNA structures, plays a role as a coregulator of transcription, a regulator of splicing, and in the processing of small noncoding RNAs. It synergizes with DDX17 and SRA1 RNA to activate MYOD1 transcriptional activity and is involved in skeletal muscle differentiation. Dysregulation of this gene may play a role in cancer development. DDX5 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.

Pssm-ID: 350807 [Multi-domain] Cd Length: 234 Bit Score: 160.95 E-value: 3.11e-45

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323   9 LQFAQLGLSEPVMQAVTAIGYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSNIDLQQI-----KPQALIL 83
Cdd:cd18049   24 LNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPFlergdGPICLVL 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  84 APTRELAIQVAEAFQSYSsKIPGFRVLPVYGGQPYGQQLSALRRGVHIVVGTPGRVIDHLDRSTLDLSELKTLVLDEADE 163
Cdd:cd18049  104 APTRELAQQVQQVAAEYG-RACRLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLEAGKTNLRRCTYLVLDEADR 182

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|..
gi 896581323 164 MLRMGFIDDVEAVLKKLPEQRQVALFSATMPPQIRRIAQTYLQDPVEVTIAA 215
Cdd:cd18049  183 MLDMGFEPQIRKIVDQIRPDRQTLMWSATWPKEVRQLAEDFLKDYIHINIGA 234

DEADc_DDX24

cd17946

DEAD-box helicase domain of DEAD box protein 24; The human DDX24 gene encodes a DEAD box ...

20-193

2.95e-43

DEAD-box helicase domain of DEAD box protein 24; The human DDX24 gene encodes a DEAD box protein, which shows little similarity to any of the other known human DEAD box proteins, but shows a high similarity to mouse Ddx24 at the amino acid level. MDM2 mediates nonproteolytic polyubiquitylation of the DEAD-Box RNA helicase DDX24. DDX24 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP- binding region.

Pssm-ID: 350704 [Multi-domain] Cd Length: 235 Bit Score: 155.47 E-value: 2.95e-43

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  20 VMQAVTAIGYETPSPIQAATIP-AMLEGRDVLGQAQTGTGKTAAFALPVLSNIdLQQ----------IKPQALILAPTRE 88
Cdd:cd17946    1 ILRALADLGFSEPTPIQALALPaAIRDGKDVIGAAETGSGKTLAFGIPILERL-LSQkssngvggkqKPLRALILTPTRE 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  89 LAIQVAEAFQSySSKIPGFRVLPVYGGQPYGQQLSALRRGVHIVVGTPGR---VI----DHLDRstldLSELKTLVLDEA 161
Cdd:cd17946   80 LAVQVKDHLKA-IAKYTNIKIASIVGGLAVQKQERLLKKRPEIVVATPGRlweLIqegnEHLAN----LKSLRFLVLDEA 154

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 896581323 162 DEMLRMGFIDDVEAVLKKLP-------EQRQVALFSATM 193
Cdd:cd17946  155 DRMLEKGHFAELEKILELLNkdragkkRKRQTFVFSATL 193

DEADc_DDX17

cd18050

DEAD-box helicase domain of DEAD box protein 17; DDX17 (also called DEAD Box Protein P72 or ...

11-214

1.32e-42

DEAD-box helicase domain of DEAD box protein 17; DDX17 (also called DEAD Box Protein P72 or DEAD Box Protein P82) has a wide variety of functions including regulating the alternative splicing of exons exhibiting specific features such as the inclusion of AC-rich alternative exons in CD44 transcripts, playing a role in innate immunity, and promoting mRNA degradation mediated by the antiviral zinc-finger protein ZC3HAV1 in an ATPase-dependent manner. DDX17 synergizes with DDX5 and SRA1 RNA to activate MYOD1 transcriptional activity and is involved in skeletal muscle differentiation. DDX17 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.

Pssm-ID: 350808 [Multi-domain] Cd Length: 271 Bit Score: 154.78 E-value: 1.32e-42

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  11 FAQLGLSEPVMQAVTAIGYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSNIDLQQI-----KPQALILAP 85
Cdd:cd18050   64 FHQANFPQYVMDVLLDQNFKEPTPIQCQGFPLALSGRDMVGIAQTGSGKTLAYLLPAIVHINHQPYlergdGPICLVLAP 143

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  86 TRELAIQVAEAFQSYSsKIPGFRVLPVYGGQPYGQQLSALRRGVHIVVGTPGRVIDHLDRSTLDLSELKTLVLDEADEML 165
Cdd:cd18050  144 TRELAQQVQQVADDYG-KSSRLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLEAGKTNLRRCTYLVLDEADRML 222

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 896581323 166 RMGFIDDVEAVLKKLPEQRQVALFSATMPPQIRRIAQTYLQDPVEVTIA 214
Cdd:cd18050  223 DMGFEPQIRKIVDQIRPDRQTLMWSATWPKEVRQLAEDFLRDYVQINIG 271

DEADc_DDX18

cd17942

DEAD-box helicase domain of DEAD box protein 18; This DDX18 gene encodes a DEAD box protein ...

21-200

2.86e-41

DEAD-box helicase domain of DEAD box protein 18; This DDX18 gene encodes a DEAD box protein and is activated by Myc protein. DDX18 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.

Pssm-ID: 350700 [Multi-domain] Cd Length: 198 Bit Score: 148.66 E-value: 2.86e-41

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  21 MQAVTAIGYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSNIDLQQIKPQ----ALILAPTRELAIQ---V 93
Cdd:cd17942    2 LKAIEEMGFTKMTEIQAKSIPPLLEGRDVLGAAKTGSGKTLAFLIPAIELLYKLKFKPRngtgVIIISPTRELALQiygV 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  94 AEAFQSYSSKIPGFrvlpVYGGQPYGQQLSALRRGVHIVVGTPGRVIDHLDRST-LDLSELKTLVLDEADEMLRMGFIDD 172
Cdd:cd17942   82 AKELLKYHSQTFGI----VIGGANRKAEAEKLGKGVNILVATPGRLLDHLQNTKgFLYKNLQCLIIDEADRILEIGFEEE 157

                        170       180
                 ....*....|....*....|....*...
gi 896581323 173 VEAVLKKLPEQRQVALFSATmppQIRRI 200
Cdd:cd17942  158 MRQIIKLLPKRRQTMLFSAT---QTRKV 182

RRM_EcCsdA_like

cd12499

RNA recognition motif (RRM) found in Escherichia coli cold-shock DEAD box protein A (CsdA) and ...

511-581

1.60e-38

Pssm-ID: 409922 [Multi-domain] Cd Length: 73 Bit Score: 136.55 E-value: 1.60e-38

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 896581323 511 TYRISVGHQHGVKPANIVGAIANEAGLESRFIGRIDIHDDFSLLDLPAQMPPDVLSHLQKVWVSGQQLQMR 581
Cdd:cd12499    1 RYRIEVGRKDGVKPGNIVGAIANEAGIDSRFIGRIKIFDDHSTVELPKGMPKDVLQHLKKVRVCGQPLNIK 71

DEADc_DDX25

cd18048

DEAD-box helicase domain of DEAD box protein 25; DDX25 (also called gonadotropin-regulated ...

1-208

7.58e-34

DEAD-box helicase domain of DEAD box protein 25; DDX25 (also called gonadotropin-regulated testicular RNA helicase (GRTH) is a testis-specific protein essential for completion of spermatogenesis. DDX25 is also a novel negative regulator of IFN pathway and facilitates RNA virus infection. Diseases associated with DDX25 include hydrolethalus syndrome, an autosomal recessive lethal malformation syndrome characterized by multiple developmental defects of fetus.. DDX25 (also called gonadotropin-regulated testicular RNA helicase) is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.

Pssm-ID: 350806 [Multi-domain] Cd Length: 229 Bit Score: 128.99 E-value: 7.58e-34

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323   1 MSQDSQAPL----QFAQLGLSEPVMQAVTAIGYETPSPIQAATIPAMLEG--RDVLGQAQTGTGKTAAFALPVLSNIDLQ 74
Cdd:cd18048    6 LQRDPTSPLfsvkSFEELHLKEELLRGIYAMGFNRPSKIQENALPMMLADppQNLIAQSQSGTGKTAAFVLAMLSRVDAL 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  75 QIKPQALILAPTRELAIQVAEAFQSYSSKIPGFRVLPVYGGQ--PYGQQLSAlrrgvHIVVGTPGRVIDHLDRSTL-DLS 151
Cdd:cd18048   86 KLYPQCLCLSPTFELALQTGKVVEEMGKFCVGIQVIYAIRGNrpGKGTDIEA-----QIVIGTPGTVLDWCFKLRLiDVT 160

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 896581323 152 ELKTLVLDEADEMLRM-GFIDDVEAVLKKLPEQRQVALFSATMPPQIRRIAQTYLQDP 208
Cdd:cd18048  161 NISVFVLDEADVMINVqGHSDHSVRVKRSMPKECQMLLFSATFEDSVWAFAERIVPDP 218

Helicase_C

pfam00271

Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...

235-343

5.77e-32

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: 119.62 E-value: 5.77e-32

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  235 KLDALTRILEVEPFDAMIIFARTKagtEELASK--LQARGLAAAAINGDMQQAQRERTIAMLKEGKLDILVATDVAARGL 312
Cdd:pfam00271   2 KLEALLELLKKERGGKVLIFSQTK---KTLEAEllLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGL 78

                          90       100       110
                  ....*....|....*....|....*....|.
gi 896581323  313 DVERISHVLNYDIPYDTESYVHRIGRTGRAG 343
Cdd:pfam00271  79 DLPDVDLVINYDLPWNPASYIQRIGRAGRAG 109

DEADc_DDX51

cd17956

DEAD-box helicase domain of DEAD box protein 51; DDX51 aids cell cancer proliferation by ...

20-193

1.52e-30

DEAD-box helicase domain of DEAD box protein 51; DDX51 aids cell cancer proliferation by regulating multiple signalling pathways. Mammalian DEAD box protein Ddx51 acts in 3' end maturation of 28S rRNA by promoting the release of U8 snoRNA.It is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.

Pssm-ID: 350714 [Multi-domain] Cd Length: 231 Bit Score: 119.66 E-value: 1.52e-30

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  20 VMQAVTAIGYETPSPIQAATIPAMLEG---------RDVLGQAQTGTGKTAAFALPVLSNIdLQQIKPQ--ALILAPTRE 88
Cdd:cd17956    1 LLKNLQNNGITSAFPVQAAVIPWLLPSskstppyrpGDLCVSAPTGSGKTLAYVLPIVQAL-SKRVVPRlrALIVVPTKE 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  89 LAIQVAEAFQSYSSKIpGFRVLPVyGGQPY----GQQLSALRRG-----VHIVVGTPGRVIDHLDRST-LDLSELKTLVL 158
Cdd:cd17956   80 LVQQVYKVFESLCKGT-GLKVVSL-SGQKSfkkeQKLLLVDTSGrylsrVDILVATPGRLVDHLNSTPgFTLKHLRFLVI 157

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 896581323 159 DEADEMLRMGFIDDVEAVLKKL--------------------PEQRQVALFSATM 193
Cdd:cd17956  158 DEADRLLNQSFQDWLETVMKALgrptapdlgsfgdanllersVRPLQKLLFSATL 212

HELICc

smart00490

helicase superfamily c-terminal domain;

262-343

2.07e-26

helicase superfamily c-terminal domain;

Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 102.68 E-value: 2.07e-26

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323   262 EELASKLQARGLAAAAINGDMQQAQRERTIAMLKEGKLDILVATDVAARGLDVERISHVLNYDIPYDTESYVHRIGRTGR 341
Cdd:smart00490   1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGR 80


                   ..
gi 896581323   342 AG 343
Cdd:smart00490  81 AG 82

DEADc_DDX28

cd17948

DEAD-box helicase domain of DEAD box protein 28; DDX28 (also called mitochondrial DEAD-box ...

32-194

7.37e-26

DEAD-box helicase domain of DEAD box protein 28; DDX28 (also called mitochondrial DEAD-box polypeptide 28) plays an essential role in facilitating the proper assembly of the mitochondrial large ribosomal subunit and its helicase activity is essential for this function. DDX28 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.

Pssm-ID: 350706 [Multi-domain] Cd Length: 231 Bit Score: 106.30 E-value: 7.37e-26

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  32 PSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSNIDLQQIK-------PQALILAPTRELAIQVAEAFQSYSSKI 104
Cdd:cd17948   13 PTTVQKQGIPSILRGRNTLCAAETGSGKTLTYLLPIIQRLLRYKLLaegpfnaPRGLVITPSRELAEQIGSVAQSLTEGL 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 105 pGFRVLPVYGGQPYGQQLSALRRGVHIVVGTPGRVIDHLDRSTLDLSELKTLVLDEADEMLRMGFIDDVEAVLKKLPEQR 184
Cdd:cd17948   93 -GLKVKVITGGRTKRQIRNPHFEEVDILVATPGALSKLLTSRIYSLEQLRHLVLDEADTLLDDSFNEKLSHFLRRFPLAS 171

                        170       180
                 ....*....|....*....|...
gi 896581323 185 -------------QVALFSATMP 194
Cdd:cd17948  172 rrsentdgldpgtQLVLVSATMP 194

DbpA

pfam03880

DbpA RNA binding domain; This RNA binding domain is found at the C-terminus of a number of ...

511-581

1.12e-25

Pssm-ID: 461082 [Multi-domain] Cd Length: 72 Bit Score: 100.53 E-value: 1.12e-25

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 896581323  511 TYRISVGHQHGVKPANIVGAIANEAGLESRFIGRIDIHDDFSLLDLPAQMPPDVLSHLQKVWVSGQQLQMR 581
Cdd:pfam03880   1 RLFINVGKKDGVRPGDIVGALANEAGLPGDDIGKIDIFDNFSFVEVPAEKAEKVLKALKGTKIKGRKVRVE 71

DEADc_DDX19

cd18047

DEAD-box helicase domain of DEAD box protein 19; DDX19 is an RNA helicase involved in both ...

11-208

7.13e-25

DEAD-box helicase domain of DEAD box protein 19; DDX19 is an RNA helicase involved in both mRNA (mRNA) export from the nucleus into the cytoplasm and in mRNA translation. DDX19 functions in the nucleus in resolving RNA:DNA hybrids (R-loops). Activation of a DNA damage response pathway dependent upon the ATR kinase, a major regulator of replication fork progression, stimulates translocation of DDX19 from the cytoplasm into the nucleus. Only nuclear Ddx19 is competent to resolve R-loops. DDX19 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.

Pssm-ID: 350805 [Multi-domain] Cd Length: 205 Bit Score: 102.88 E-value: 7.13e-25

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  11 FAQLGLSEPVMQAVTAIGYETPSPIQAATIPAMLEG--RDVLGQAQTGTGKTAAFALPVLSNIDLQQIKPQALILAPTRE 88
Cdd:cd18047    3 FEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEppQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQCLCLSPTYE 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  89 LAIQVAEAFQSYSSKIPGFRVlpvyggqPYGQQLSALRRGV----HIVVGTPGRVIDH-LDRSTLDLSELKTLVLDEADE 163
Cdd:cd18047   83 LALQTGKVIEQMGKFYPELKL-------AYAVRGNKLERGQkiseQIVIGTPGTVLDWcSKLKFIDPKKIKVFVLDEADV 155

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 896581323 164 ML-RMGFIDDVEAVLKKLPEQRQVALFSATMPPQIRRIAQTYLQDP 208
Cdd:cd18047  156 MIaTQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDP 201

DEADc_MRH4

cd17965

DEAD-box helicase domain of ATP-dependent RNA helicase MRH4; Mitochondrial RNA helicase 4 ...

32-201

5.94e-21

DEAD-box helicase domain of ATP-dependent RNA helicase MRH4; Mitochondrial RNA helicase 4 (MRH4) plays an essential role during the late stages of mitochondrial ribosome or mitoribosome assembly by promoting remodeling of the 21S rRNA-protein interactions. MRH4 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.

Pssm-ID: 350723 [Multi-domain] Cd Length: 251 Bit Score: 92.82 E-value: 5.94e-21

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  32 PSPIQAATIPAMLEGR----------DVLGQ------AQTGTGKTAAFALPVLSNIDLQQI-----------------KP 78
Cdd:cd17965   31 PSPIQTLAIKKLLKTLmrkvtkqtsnEEPKLevfllaAETGSGKTLAYLAPLLDYLKRQEQepfeeaeeeyesakdtgRP 110

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  79 QALILAPTRELAIQVAEAFQSYSsKIPGFRVLPVYG--GQPYGQQLSALRRGVHIVVGTPGRVIDHLDRSTLDLSELKTL 156
Cdd:cd17965  111 RSVILVPTHELVEQVYSVLKKLS-HTVKLGIKTFSSgfGPSYQRLQLAFKGRIDILVTTPGKLASLAKSRPKILSRVTHL 189

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 896581323 157 VLDEADEMLRMGFIDDVEAVLKKLPEQRQVALFSATMP-----------PQIRRIA 201
Cdd:cd17965  190 VVDEADTLFDRSFLQDTTSIIKRAPKLKHLILCSATIPkefdktlrklfPDVVRIA 245

SSL2

COG1061

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

45-487

9.13e-19

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

Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 90.08 E-value: 9.13e-19

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  45 EGRDVLGQAQTGTGKT--AAFAlpvlsnIDLQQIKPQALILAPTRELAIQVAEAFQSYsskipgFRVLPVYGGQPygqql 122
Cdd:COG1061   99 GGGRGLVVAPTGTGKTvlALAL------AAELLRGKRVLVLVPRRELLEQWAEELRRF------LGDPLAGGGKK----- 161

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 123 salRRGVHIVVGTPGRVIDHLDRSTLDlSELKTLVLDEADEMLRMGFiddvEAVLKKLPEQRQVALfSAT------MPPQ 196
Cdd:COG1061  162 ---DSDAPITVATYQSLARRAHLDELG-DRFGLVIIDEAHHAGAPSY----RRILEAFPAAYRLGL-TATpfrsdgREIL 232

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 197 IRR-------------IAQTYLQDP----VEVTIAAKTTTSANIRQRYWWV---SGMHKLDALTRILEVEPFD-AMIIFA 255
Cdd:COG1061  233 LFLfdgivyeyslkeaIEDGYLAPPeyygIRVDLTDERAEYDALSERLREAlaaDAERKDKILRELLREHPDDrKTLVFC 312

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 256 RTKAGTEELASKLQARGLAAAAINGDMQQAQRERTIAMLKEGKLDILVATDVAARGLDVERISHVLnydIPYDTES---Y 332
Cdd:COG1061  313 SSVDHAEALAELLNEAGIRAAVVTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDVPRLDVAI---LLRPTGSpreF 389

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 333 VHRIGRTGRAGRSGEAILF------ATPREKGMLRQIERATRQPIEEM--QLPSVEAVNDTRINKFTSRISETLGAGGLD 404
Cdd:COG1061  390 IQRLGRGLRPAPGKEDALVydfvgnDVPVLEELAKDLRDLAGYRVEFLdeEESEELALLIAVKPALEVKGELEEELLEEL 469

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 405 FYRQLLERFENEQNVPAIEIAAALAKLLQGDTPFLLQPPVRAPREERAPRERFDRGDRPERGDRFERNDRGPRFERGPRR 484
Cdd:COG1061  470 ELLEDALLLVLAELLLLELLALALELLELAKAEGKAEEEEEEKELLLLLALAKLLKLLLLLLLLLLLELLELLAALLRLE 549


                 ...
gi 896581323 485 DDA 487
Cdd:COG1061  550 ELA 552

RecQ

COG0514

Superfamily II DNA helicase RecQ [Replication, recombination and repair];

28-376

1.46e-18

Superfamily II DNA helicase RecQ [Replication, recombination and repair];

Pssm-ID: 440280 [Multi-domain] Cd Length: 489 Bit Score: 89.04 E-value: 1.46e-18

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  28 GYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPvlsnidlqqikpqALILA-PTreLAI---------QVAEAF 97
Cdd:COG0514   14 GYDSFRPGQEEIIEAVLAGRDALVVMPTGGGKSLCYQLP-------------ALLLPgLT--LVVsplialmkdQVDALR 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  98 QSysskipGFRVLPVYGGQPYGQQ---LSALRRG-VHIVVGTP-----GRVIDHLDRSTLDLselktLVLDEA------- 161
Cdd:COG0514   79 AA------GIRAAFLNSSLSAEERrevLRALRAGeLKLLYVAPerllnPRFLELLRRLKISL-----FAIDEAhcisqwg 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 162 -D---EMLRMGfiddveAVLKKLPeQRQVALFSATMPPQIRR--IAQTYLQDPVEVTiaakttTS---ANIRQRYWWVSG 232
Cdd:COG0514  148 hDfrpDYRRLG------ELRERLP-NVPVLALTATATPRVRAdiAEQLGLEDPRVFV------GSfdrPNLRLEVVPKPP 214

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 233 MHKLDALTRILEVEPFDAMIIFARTKAGTEELASKLQARGLAAAAINGDMQQAQRERTIAMLKEGKLDILVAT------- 305
Cdd:COG0514  215 DDKLAQLLDFLKEHPGGSGIVYCLSRKKVEELAEWLREAGIRAAAYHAGLDAEEREANQDRFLRDEVDVIVATiafgmgi 294

                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 896581323 306 ---DVaargldveRIshVLNYDIPYDTESYVHRIGRTGRAGRSGEAILFATPREKGMLRQ-IERAT----RQPIEEMQL 376
Cdd:COG0514  295 dkpDV--------RF--VIHYDLPKSIEAYYQEIGRAGRDGLPAEALLLYGPEDVAIQRFfIEQSPpdeeRKRVERAKL 363

SF2-N

cd00046

N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...

46-192

2.44e-18

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: 82.07 E-value: 2.44e-18

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  46 GRDVLGQAQTGTGKTAAFALPVLSNIDLQqiKPQALILAPTRELAIQVAEAFQSYSSkiPGFRVLPVYGGQPYGQQLSAL 125
Cdd:cd00046    1 GENVLITAPTGSGKTLAALLAALLLLLKK--GKKVLVLVPTKALALQTAERLRELFG--PGIRVAVLVGGSSAEEREKNK 76

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 126 RRGVHIVVGTPGRVIDHLDRST-LDLSELKTLVLDEADEML-RMGFID-DVEAVLKKLPEQRQVALFSAT 192
Cdd:cd00046   77 LGDADIIIATPDMLLNLLLREDrLFLKDLKLIIVDEAHALLiDSRGALiLDLAVRKAGLKNAQVILLSAT 146

PRK11057

ATP-dependent DNA helicase RecQ; Provisional

13-365

3.83e-18

ATP-dependent DNA helicase RecQ; Provisional

Pssm-ID: 182933 [Multi-domain] Cd Length: 607 Bit Score: 88.23 E-value: 3.83e-18

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  13 QLGLSEPVMQAVtaIGYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSNIDLqqikpqALILAPTRELAIQ 92
Cdd:PRK11057   9 LESLAKQVLQET--FGYQQFRPGQQEIIDAVLSGRDCLVVMPTGGGKSLCYQIPALVLDGL------TLVVSPLISLMKD 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  93 VAEAFQSYsskipGFRVLPVYGGQPYGQQLS---ALRRG-VHIVVGTPGRVI--DHLDRstLDLSELKTLVLDEADEMLR 166
Cdd:PRK11057  81 QVDQLLAN-----GVAAACLNSTQTREQQLEvmaGCRTGqIKLLYIAPERLMmdNFLEH--LAHWNPALLAVDEAHCISQ 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 167 MG--FIDDVEAV--LK-KLPEQRQVALfSATMPPQIRR--IAQTYLQDPVevtIAAKTTTSANIRqrYWWVSGMHKLDAL 239
Cdd:PRK11057 154 WGhdFRPEYAALgqLRqRFPTLPFMAL-TATADDTTRQdiVRLLGLNDPL---IQISSFDRPNIR--YTLVEKFKPLDQL 227

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 240 TRILEVEPFDAMIIFARTKAGTEELASKLQARGLAAAAINGDMQQAQRERTIAMLKEGKLDILVATDVAARGLDVERISH 319
Cdd:PRK11057 228 MRYVQEQRGKSGIIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRF 307

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 896581323 320 VLNYDIPYDTESYVHRIGRTGRAGRSGEAILFATP------------REKGMLRQIER 365
Cdd:PRK11057 308 VVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDPadmawlrrcleeKPAGQQQDIER 365

SF2_C_RecQ

cd18794

C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ...

235-351

4.17e-14

C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an evolutionarily conserved class of enzymes, dedicated to preserving genomic integrity by operating in telomere maintenance, DNA repair, and replication. They 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: 350181 [Multi-domain] Cd Length: 134 Bit Score: 69.54 E-value: 4.17e-14

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 235 KLDALTRILEVEPFDAMIIFARTKAGTEELASKLQARGLAAAAINGDMQQAQRERTIAMLKEGKLDILVATDVAARGLDV 314
Cdd:cd18794   17 KLDLLKRIKVEHLGGSGIIYCLSRKECEQVAARLQSKGISAAAYHAGLEPSDRRDVQRKWLRDKIQVIVATVAFGMGIDK 96

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 896581323 315 ERISHVLNYDIPYDTESYVHRIGRTGRAGRSGEAILF 351
Cdd:cd18794   97 PDVRFVIHYSLPKSMESYYQESGRAGRDGLPSECILF 133

YprA

COG1205

ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, ...

15-350

1.81e-13

ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, recombination and repair];

Pssm-ID: 440818 [Multi-domain] Cd Length: 758 Bit Score: 73.72 E-value: 1.81e-13

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  15 GLSEPVMQAVTAIGYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSNIdLQQIKPQALILAPTRELAIQVA 94
Cdd:COG1205   40 WLPPELRAALKKRGIERLYSHQAEAIEAARAGKNVVIATPTASGKSLAYLLPVLEAL-LEDPGATALYLYPTKALARDQL 118

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  95 EAFQSYSSKI-PGFRVLPVYGGQPyGQQLSALRRGVHIVVGTPgrviDHLDRSTLD--------LSELKTLVLDEAdEML 165
Cdd:COG1205  119 RRLRELAEALgLGVRVATYDGDTP-PEERRWIREHPDIVLTNP----DMLHYGLLPhhtrwarfFRNLRYVVIDEA-HTY 192

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 166 RMGFIDDVEAVLKKLpeqrqvalfsatmppqiRRIAQTYLQDPVEV----TIAAKTTTSANI-----------------R 224
Cdd:COG1205  193 RGVFGSHVANVLRRL-----------------RRICRHYGSDPQFIlasaTIGNPAEHAERLtgrpvtvvdedgsprgeR 255

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 225 QRYWW----VSGMHKLDALT---RILEvepfDAM------IIFARTKAGTEELASKLQAR------GLAAAAINGDMQQA 285
Cdd:COG1205  256 TFVLWnpplVDDGIRRSALAeaaRLLA----DLVreglrtLVFTRSRRGAELLARYARRAlrepdlADRVAAYRAGYLPE 331

                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 896581323 286 QRERTIAMLKEGKLDILVAT-------DVAarGLDVerishVLNYDIPYDTESYVHRIGRTGRAGRSGEAIL 350
Cdd:COG1205  332 ERREIERGLRSGELLGVVSTnalelgiDIG--GLDA-----VVLAGYPGTRASFWQQAGRAGRRGQDSLVVL 396

MPH1

COG1111

ERCC4-related helicase [Replication, recombination and repair];

239-480

1.02e-12

ERCC4-related helicase [Replication, recombination and repair];

Pssm-ID: 440728 [Multi-domain] Cd Length: 718 Bit Score: 71.30 E-value: 1.02e-12

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 239 LTRILEVEPFDAMIIFARTKAGTEELASKLQARGLAA------AAINGD--MQQAQRERTIAMLKEGKLDILVATDVAAR 310
Cdd:COG1111  344 LKEQLGTNPDSRIIVFTQYRDTAEMIVEFLSEPGIKAgrfvgqASKEGDkgLTQKEQIEILERFRAGEFNVLVATSVAEE 423

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 311 GLDVERISHVLNYDiPYDTE-SYVHRIGRTGRAGRSGEAILFA--TPREK--GMLRQIERATRQPIEEMQlpsveavndT 385
Cdd:COG1111  424 GLDIPEVDLVIFYE-PVPSEiRSIQRKGRTGRKREGRVVVLIAkgTRDEAyyWSSRRKEKKMKSILKKLK---------K 493

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 386 RINKFTSRISETLGAGGLDFYRQLLERFENEQNVPAIEIAAALAKLLQGDT--PFLLQPPVRAPREERAPRERFDRGDRP 463
Cdd:COG1111  494 LLDKQEKEKLKESAQATLDEFESIKELAEDEINEKDLDEIESSENGAHVDWrePVLLQVIVSTLAESLELRELGEKVDDE 573

                        250
                 ....*....|....*..
gi 896581323 464 ERGDRFERNDRGPRFER 480
Cdd:COG1111  574 VNLILEIDRVDVVDDGS 590

RRM_DbpA

cd12252

RNA recognition motif (RRM) found in the DbpA subfamily of prokaryotic DEAD-box rRNA helicases; ...

511-581

1.63e-12

RNA recognition motif (RRM) found in the DbpA subfamily of prokaryotic DEAD-box rRNA helicases; This subfamily corresponds to the C-terminal RRM homology domain of dbpA proteins implicated in ribosome biogenesis. They bind with high affinity and specificity to RNA substrates containing hairpin 92 of 23S rRNA (HP92), which is part of the ribosomal A-site. The majority of dbpA proteins contain two N-terminal ATPase catalytic domains and a C-terminal RNA binding domain, an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain). The catalytic domains bind to nearby regions of RNA to stimulate ATP hydrolysis and disrupt RNA structures. The C-terminal domain is responsible for the high-affinity RNA binding. Several members of this family lack specificity for 23S rRNA. These proteins can generally be distinguished by a basic region that extends beyond the C-terminal domain.

Pssm-ID: 409698 [Multi-domain] Cd Length: 71 Bit Score: 62.95 E-value: 1.63e-12

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 896581323 511 TYRISVGHQHGVKPANIVGAIANEAGLESRFIGRIDIHDDFSLLDLPAQMPPDVLSHLQKVWVSGQQLQMR 581
Cdd:cd12252    1 RLFINVGRKDGIDPRDLLGAICRAGGISRDDIGAIRIFDNFSFVEVPEAEAERVIEALNGKKIKGKKLRVE 71

DEXHc_Hrq1-like

cd17923

DEAH-box helicase domain of Hrq1 and similar proteins; Yeast Hrq1, similar to RecQ4, plays a ...

36-225

6.27e-10

DEAH-box helicase domain of Hrq1 and similar proteins; Yeast Hrq1, similar to RecQ4, plays a role in DNA inter-strand crosslink (ICL) repair and in telomere maintenance. Hrq1 lacks the Sld2-like domain found in RecQ4. Hrq1 belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

Pssm-ID: 350681 [Multi-domain] Cd Length: 182 Bit Score: 58.75 E-value: 6.27e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  36 QAATIPAMLEGRDVLGQAQTGTGKTAAFALPVLSNIdLQQIKPQALILAPTRELAIQVAEAFQSYSSKI-PGFRVLPVYG 114
Cdd:cd17923    5 QAEAIEAARAGRSVVVTTGTASGKSLCYQLPILEAL-LRDPGSRALYLYPTKALAQDQLRSLRELLEQLgLGIRVATYDG 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 115 GQPYGQQLSALRRGVHIVVGTPgrviDHLDRSTLD--------LSELKTLVLDEAdEMLRMGFIDDVEAVLKKLpeqrqv 186
Cdd:cd17923   84 DTPREERRAIIRNPPRILLTNP----DMLHYALLPhhdrwarfLRNLRYVVLDEA-HTYRGVFGSHVALLLRRL------ 152

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 896581323 187 alfsatmppqiRRIAQTYLQDPveVTIAAkTTTSANIRQ 225
Cdd:cd17923  153 -----------RRLCRRYGADP--QFILT-SATIGNPAE 177

SF2_C

cd18785

C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...

252-351

9.07e-10

C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases include DEAD-box helicases, UvrB, RecG, Ski2, Sucrose Non-Fermenting (SNF) family helicases, and dicer proteins, among others. Similar to SF1 helicases, they do not form toroidal structures like SF3-6 helicases. SF2 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.

Pssm-ID: 350172 [Multi-domain] Cd Length: 77 Bit Score: 55.40 E-value: 9.07e-10

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 252 IIFARTKAGTEELASKLQarglaaaaingdmqqaqrertiamlkegkldILVATDVAARGLDVERISHVLNYDIPYDTES 331
Cdd:cd18785    7 IVFTNSIEHAEEIASSLE-------------------------------ILVATNVLGEGIDVPSLDTVIFFDPPSSAAS 55

                         90       100
                 ....*....|....*....|.
gi 896581323 332 YVHRIGRTGRAG-RSGEAILF 351
Cdd:cd18785   56 YIQRVGRAGRGGkDEGEVILF 76

SF2_C_SNF

cd18793

C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...

230-337

1.29e-09

C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) family includes chromatin-remodeling factors, such as CHD proteins and SMARCA proteins, recombination proteins Rad54, and many others. They 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: 350180 [Multi-domain] Cd Length: 135 Bit Score: 56.72 E-value: 1.29e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 230 VSGmhKLDALTRILE--VEPFDAMIIFARTKAGTEELASKLQARGLAAAAINGDMQQAQRERTIAMLKEGK--LDILVAT 305
Cdd:cd18793    9 VSG--KLEALLELLEelREPGEKVLIFSQFTDTLDILEEALRERGIKYLRLDGSTSSKERQKLVDRFNEDPdiRVFLLST 86

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 896581323 306 DVAARGLDVERISHVLNYDIPYDT------ESYVHRIG 337
Cdd:cd18793   87 KAGGVGLNLTAANRVILYDPWWNPaveeqaIDRAHRIG 124

DEXHc_dicer

cd18034

DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ...

55-161

1.88e-08

DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicers exist throughout eukaryotes, and a subset have an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

Pssm-ID: 350792 [Multi-domain] Cd Length: 200 Bit Score: 54.97 E-value: 1.88e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  55 TGTGKT--AAFALPVLS--NIDLQQIKPQALILAPTRELAIQVAEAFQSYSskipGFRVLPVYGGQ----PYGQQLSALR 126
Cdd:cd18034   25 TGSGKTliAVMLIKEMGelNRKEKNPKKRAVFLVPTVPLVAQQAEAIRSHT----DLKVGEYSGEMgvdkWTKERWKEEL 100

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 896581323 127 RGVHIVVGTPGRVIDHLDRSTLDLSELKTLVLDEA 161
Cdd:cd18034  101 EKYDVLVMTAQILLDALRHGFLSLSDINLLIFDEC 135

SF2_C_dicer

cd18802

C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...

281-342

3.15e-08

C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicer exists throughout eukaryotes, and a subset has an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer helicase domains 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: 350189 [Multi-domain] Cd Length: 142 Bit Score: 52.98 E-value: 3.15e-08

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 896581323 281 DMQQAQRERTIAMLKEGKLDILVATDVAARGLDVERISHVLNYDIPYDTESYVHRIGRtGRA 342
Cdd:cd18802   73 LMTQRKQKETLDKFRDGELNLLIATSVLEEGIDVPACNLVIRFDLPKTLRSYIQSRGR-ARA 133

SF2_C_LHR

cd18796

C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ...

236-351

4.01e-08

C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a DNA damage-inducible helicase that uses ATP hydrolysis to drive unidirectional 3'-to-5' translocation along single-stranded DNA (ssDNA) and to unwind RNA:DNA duplexes. This group also includes related bacterial and archaeal helicases. LHR family helicases 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: 350183 [Multi-domain] Cd Length: 150 Bit Score: 52.65 E-value: 4.01e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 236 LDALTRIL-EVEPFDAMIIFARTKAGTEELASKLQAR------GLAAAAINGDMQQAQRERTIAMLKEGKLDILVATDVA 308
Cdd:cd18796   25 ADAYAEVIfLLERHKSTLVFTNTRSQAERLAQRLRELcpdrvpPDFIALHHGSLSRELREEVEAALKRGDLKVVVATSSL 104

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 896581323 309 ARGLDVERISHVLNYDIPYDTESYVHRIGRTGRagRSGEAILF 351
Cdd:cd18796  105 ELGIDIGDVDLVIQIGSPKSVARLLQRLGRSGH--RPGAASKG 145

PRK13766

Hef nuclease; Provisional

235-365

5.14e-08

Hef nuclease; Provisional

Pssm-ID: 237496 [Multi-domain] Cd Length: 773 Bit Score: 56.04 E-value: 5.14e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 235 KLDALTRI----LEVEPFDAMIIFARTKAGTEELASKLQARGLAA------AAINGD--MQQAQRERTIAMLKEGKLDIL 302
Cdd:PRK13766 348 KLEKLREIvkeqLGKNPDSRIIVFTQYRDTAEKIVDLLEKEGIKAvrfvgqASKDGDkgMSQKEQIEILDKFRAGEFNVL 427

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 896581323 303 VATDVAARGLDVERISHVLNYD-IPYDTESyVHRIGRTGRaGRSGEAILFATP-------------REKGMLRQIER 365
Cdd:PRK13766 428 VSTSVAEEGLDIPSVDLVIFYEpVPSEIRS-IQRKGRTGR-QEEGRVVVLIAKgtrdeayywssrrKEKKMKEELKN 502

PLN03137

ATP-dependent DNA helicase; Q4-like; Provisional

34-362

6.19e-07

ATP-dependent DNA helicase; Q4-like; Provisional

Pssm-ID: 215597 [Multi-domain] Cd Length: 1195 Bit Score: 52.98 E-value: 6.19e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323   34 PIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPVL-------------SNI-----DLQQIKPQALILAPTRELAIQVaE 95
Cdd:PLN03137  463 PNQREIINATMSGYDVFVLMPTGGGKSLTYQLPALicpgitlvisplvSLIqdqimNLLQANIPAASLSAGMEWAEQL-E 541

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323   96 AFQSYSSKIPGFRVLPVyggqpygqqlsalrrgvhivvgTPGRVI--DHLDRSTLDL---SELKTLVLDEADEMLRMG-- 168
Cdd:PLN03137  542 ILQELSSEYSKYKLLYV----------------------TPEKVAksDSLLRHLENLnsrGLLARFVIDEAHCVSQWGhd 599

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  169 FIDDVE--AVLKKLPEQRQVALFSATMPPQIRRiaqtylqdpvEVTIAAKTTTSANIRQRY----WWVSGMHK----LDA 238
Cdd:PLN03137  600 FRPDYQglGILKQKFPNIPVLALTATATASVKE----------DVVQALGLVNCVVFRQSFnrpnLWYSVVPKtkkcLED 669

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  239 LTRILEVEPFDAM-IIFARTKAGTEELASKLQARGLAAAAINGDMQQAQRERTIAMLKEGKLDILVATDVAARGLDVERI 317
Cdd:PLN03137  670 IDKFIKENHFDECgIIYCLSRMDCEKVAERLQEFGHKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPDV 749

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*....
gi 896581323  318 SHVLNYDIPYDTESYVHRIGRTGRAGRSGEAILFAT----PREKGMLRQ 362
Cdd:PLN03137  750 RFVIHHSLPKSIEGYHQECGRAGRDGQRSSCVLYYSysdyIRVKHMISQ 798

HepA

COG0553

Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...

235-339

1.20e-06

Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair];

Pssm-ID: 440319 [Multi-domain] Cd Length: 682 Bit Score: 51.76 E-value: 1.20e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 235 KLDALTRILE--VEPFDAMIIFARTKAGTEELASKLQARGLAAAAINGDMQQAQRERTIAMLKEGK--LDILVATDVAAR 310
Cdd:COG0553  534 KLEALLELLEelLAEGEKVLVFSQFTDTLDLLEERLEERGIEYAYLHGGTSAEERDELVDRFQEGPeaPVFLISLKAGGE 613

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 896581323 311 GLDVERISHVLNYDIPY--DTESY----VHRIGRT 339
Cdd:COG0553  614 GLNLTAADHVIHYDLWWnpAVEEQaidrAHRIGQT 648

DEXHc_LHR-like

cd17922

DEXH-box helicase domain of LHR; Large helicase-related protein (LHR) is a DNA ...

46-166

2.79e-06

DEXH-box helicase domain of LHR; Large helicase-related protein (LHR) is a DNA damage-inducible helicase that uses ATP hydrolysis to drive unidirectional 3'-to-5' translocation along single-stranded DNA (ssDNA) and to unwind RNA:DNA duplexes. This group also includes related bacterial and archaeal helicases from the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

Pssm-ID: 350680 [Multi-domain] Cd Length: 166 Bit Score: 47.96 E-value: 2.79e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  46 GRDVLGQAQTGTGKTAAFALPVLSNIDLQQIKP-QALILAPTRELAIQVAEAFQSYSSKI-PGFRVLPVYGGQPYGQQLS 123
Cdd:cd17922    1 GRNVLIAAPTGSGKTEAAFLPALSSLADEPEKGvQVLYISPLKALINDQERRLEEPLDEIdLEIPVAVRHGDTSQSEKAK 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 896581323 124 ALRRGVHIVVGTP--------GRVIDHLdrstldLSELKTLVLDEADEMLR 166
Cdd:cd17922   81 QLKNPPGILITTPeslelllvNKKLREL------FAGLRYVVVDEIHALLG 125

SF2_C_FANCM_Hef

cd18801

C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ...

235-350

1.77e-05

C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex. It is required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. FANCM and Hef 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: 350188 [Multi-domain] Cd Length: 143 Bit Score: 45.04 E-value: 1.77e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 235 KLDALTRILeVEPFDAM--------IIFARTKAGTEELASKLQAR----------GLAAAAINGDMQQAQRERTIAMLKE 296
Cdd:cd18801   10 KLEKLEEIV-KEHFKKKqegsdtrvIIFSEFRDSAEEIVNFLSKIrpgiratrfiGQASGKSSKGMSQKEQKEVIEQFRK 88

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 896581323 297 GKLDILVATDVAARGLDVERISHVLNYDIPYDTESYVHRIGRTGRaGRSGEAIL 350
Cdd:cd18801   89 GGYNVLVATSIGEEGLDIGEVDLIICYDASPSPIRMIQRMGRTGR-KRQGRVVV 141

DEXHc_RecG

cd17918

DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ...

31-168

3.83e-05

DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase RecG family is part of the DEAD-like helicases superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

Pssm-ID: 350676 [Multi-domain] Cd Length: 180 Bit Score: 44.71 E-value: 3.83e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  31 TPSPIQAATIPAML------EGRDVLGQAQTGTGKTAAFALPVLSNIDLQQikpQALILAPTRELAIQVAEAFQSYsskI 104
Cdd:cd17918   15 SLTKDQAQAIKDIEkdlhspEPMDRLLSGDVGSGKTLVALGAALLAYKNGK---QVAILVPTEILAHQHYEEARKF---L 88

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 896581323 105 PGFRVLPVYGGQPygQQLSAlrrGVHIVVGTpgRVIDHLDRSTLDlselktLVLDEADEMLRMG 168
Cdd:cd17918   89 PFINVELVTGGTK--AQILS---GISLLVGT--HALLHLDVKFKN------LDLVIVDEQHRFG 139

SF2_C_UvrB

cd18790

C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) ...

257-368

3.95e-05

C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) plays a central role in nucleotide excision repair (NER). Together with other components of the NER system, like UvrA, UvrC, UvrD (helicase II), and DNA polymerase I, it recognizes and cleaves damaged DNA in a multistep ATP-dependent reaction. UvrB is critical for the second phase of damage recognition by verifying the nature of the damage and forming the pre-incision complex. Its ATPase site becomes activated in the presence of UvrA and damaged DNA. Its activity is strand destabilization via distortion of the DNA at lesion site, with very limited DNA unwinding. UvrB is a DEAD-like helicase 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: 350177 [Multi-domain] Cd Length: 171 Bit Score: 44.54 E-value: 3.95e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 257 TKAGTEELASKLQARGLAAAAINGDMQQAQRERTIAMLKEGKLDILVATDVAARGLDVERISHV--LNYDIP---YDTES 331
Cdd:cd18790   36 TKRMAEDLTEYLQELGVKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVaiLDADKEgflRSETS 115

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 896581323 332 YVHRIGRTGRaGRSGEAILFATPREKGMLRQIERATR 368
Cdd:cd18790  116 LIQTIGRAAR-NVNGKVILYADKITDSMQKAIEETER 151

DEXHc_RecQ

cd17920

DEXH-box helicase domain of RecQ family proteins; The RecQ family of the type II DEAD box ...

28-211

4.14e-05

DEXH-box helicase domain of RecQ family proteins; The RecQ family of the type II DEAD box helicase superfamily is a family of highly conserved DNA repair helicases. This domain contains the ATP-binding region.

Pssm-ID: 350678 [Multi-domain] Cd Length: 200 Bit Score: 44.83 E-value: 4.14e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  28 GYETPSPIQAATIPAMLEGRDVLGQAQTGTGKTAAFALPvlsnidlqqikpqALILAPTrelAI-----------QVAEA 96
Cdd:cd17920    9 GYDEFRPGQLEAINAVLAGRDVLVVMPTGGGKSLCYQLP-------------ALLLDGV---TLvvsplislmqdQVDRL 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  97 FQSysskipGFRVLPVYGGQPYGQQLSALRR----GVHIVVGTP-----GRVIDHLDRSTLdLSELKTLVLDEA------ 161
Cdd:cd17920   73 QQL------GIRAAALNSTLSPEEKREVLLRikngQYKLLYVTPerllsPDFLELLQRLPE-RKRLALIVVDEAhcvsqw 145

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 896581323 162 -----DEMLRMGfiddveAVLKKLPeQRQVALFSATMPPQIRR--IAQTYLQDPVEV 211
Cdd:cd17920  146 ghdfrPDYLRLG------RLRRALP-GVPILALTATATPEVREdiLKRLGLRNPVIF 195

SF2_C_XPB

cd18789

C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex ...

234-314

4.97e-05

C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex helicase XPB (xeroderma pigmentosum type B) subunit (also known as DNA excision repair protein ERCC-3 or TFIIH 89 kDa subunit) is the ATP-dependent 3'-5' DNA helicase component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. XPB is a DEAD-like helicase 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: 350176 [Multi-domain] Cd Length: 153 Bit Score: 43.78 E-value: 4.97e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 234 HKLDALTRILEV-EPFDAMIIFARTKAGTEELASKLQArglaaAAINGDMQQAQRERTIAMLKEGKLDILVATDVAARGL 312
Cdd:cd18789   34 NKLRALEELLKRhEQGDKIIVFTDNVEALYRYAKRLLK-----PFITGETPQSEREEILQNFREGEYNTLVVSKVGDEGI 108


                 ..
gi 896581323 313 DV 314
Cdd:cd18789  109 DL 110

SF2_C_RecG

cd18811

C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ...

240-354

7.28e-05

C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a critical role in recombination and DNA repair. RecG helps process Holliday junction intermediates to mature products by catalyzing branch migration. It is a DEAD-like helicase 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: 350198 [Multi-domain] Cd Length: 159 Bit Score: 43.49 E-value: 7.28e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 240 TRILEVEPFDAmiifARTKAGTEELASKLQARgLAAAAINGDMQQAQRERTIAMLKEGKLDILVATDVAARGLDVERISH 319
Cdd:cd18811   34 PLIEESEKLDL----KAAVAMYEYLKERFRPE-LNVGLLHGRLKSDEKDAVMAEFREGEVDILVSTTVIEVGVDVPNATV 108

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 896581323 320 VLNYDIPYDTESYVHRI-GRTGRAGRSGEAILFATP 354
Cdd:cd18811  109 MVIEDAERFGLSQLHQLrGRVGRGDHQSYCLLVYKD 144

RRM_EcDbpA_like

cd12501

RNA recognition motif (RRM) found in Escherichia coli RNA helicase dbpA and similar proteins; ...

511-583

8.73e-05

RNA recognition motif (RRM) found in Escherichia coli RNA helicase dbpA and similar proteins; This subgroup corresponds to the C-terminal RRM homology domain of dbpA. E. coli dbpA is a member of the DbpA subfamily of prokaryotic DEAD-box rRNA helicases that have been implicated in ribosome biogenesis. It binds with high affinity and specificity for RNA substrates containing hairpin 92 of 23S rRNA (HP92) with either 3' or 5' extensions. As a non-processive ATP-dependent helicase, DbpA destabilizes and unwinds short <9bp (base pairs) RNA duplexes as well as long duplex RNA stretches. It disrupts RNA helices exclusively in a 3'- 5' direction and requires a single-stranded loading site 3' of the substrate helix. dbpA contains two N-terminal ATPase catalytic domains and a C-terminal RNA binding domain, an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain). The catalytic domains bind to nearby regions of RNA to stimulate ATP hydrolysis and disrupt RNA structures. The C-terminal domain binds specifically to hairpin 92.

Pssm-ID: 409924 [Multi-domain] Cd Length: 73 Bit Score: 41.07 E-value: 8.73e-05

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 896581323 511 TYRISVGHQHGVKPANIVGAIANEAGLESRFIGRIDIHDDFSLLDLPAQMPPDVLSHLQKVWVSGQQLQMRAL 583
Cdd:cd12501    1 TIQIDGGKKQKLRPGDILGALTGDNGIDGEDIGKINITDFVSYVAVKRSVAKDALKKLREGKIKGRKFRVRLL 73

Cas3_I

cd09639

CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short ...

48-374

9.72e-05

CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; DEAD/DEAH box helicase DNA helicase cas3'; Often but not always is fused to HD nuclease domain; signature gene for Type I

Pssm-ID: 187770 [Multi-domain] Cd Length: 353 Bit Score: 45.11 E-value: 9.72e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  48 DVLGQAQTGTGKTAAFALPVLSNIDlQQIKPQALILAPTR----ELAIQVAEAFQS--YSSKIPGFRVLPVYGGQPYGQQ 121
Cdd:cd09639    1 LLVIEAPTGYGKTEAALLWALHSLK-SQKADRVIIALPTRatinAMYRRAKEAFGEtgLYHSSILSSRIKEMGDSEEFEH 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 122 LSAL-RRGVHIVVGTPGRV--IDHLDRS----------TLDLSELKTLVLDEAD--EMLRMGFIddvEAVLKKLPEQRQ- 185
Cdd:cd09639   80 LFPLyIHSNDTLFLDPITVctIDQVLKSvfgefghyefTLASIANSLLIFDEVHfyDEYTLALI---LAVLEVLKDNDVp 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 186 VALFSATMPPQIRRIAQTYlqDPVEVTIAAKTttSANIRQRYW-----WVSgmhKLDALTRILEVEP-FDAMIIFARTKA 259
Cdd:cd09639  157 ILLMSATLPKFLKEYAEKI--GYVEENEPLDL--KPNERAPFIkiesdKVG---EISSLERLLEFIKkGGSVAIIVNTVD 229

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 260 GTEELASKLQARGLAAAAI--NGDMQQAQRERTIAMLKE----GKLDILVATDVAARGLDVEriSHVLNYDI-PYDteSY 332
Cdd:cd09639  230 RAQEFYQQLKEKGPEEEIMliHSRFTEKDRAKKEAELLLefkkSEKFVIVATQVIEASLDIS--VDVMITELaPID--SL 305

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....*....
gi 896581323 333 VHRIGRTGRAGRSGEAILFAT---PREKGML----RQIERaTRQPIEEM 374
Cdd:cd09639  306 IQRLGRLHRYGEKNGEEVYIItdaPDGKGQKpypyDLVER-TIELLEEG 353

Cas3

COG1203

CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ...

53-358

2.50e-04

CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; CRISPR-Cas type I system-associated endonuclease/helicase Cas3 is part of the Pathway/BioSystem: CRISPR-Cas system

Pssm-ID: 440816 [Multi-domain] Cd Length: 535 Bit Score: 43.92 E-value: 2.50e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  53 AQTGTGKT---AAFALpvlsnIDLQQIKPQALILA-PTRELAIQVAEAFQsyssKIPGFRVLPVYG------------GQ 116
Cdd:COG1203  154 APTGGGKTeaaLLFAL-----RLAAKHGGRRIIYAlPFTSIINQTYDRLR----DLFGEDVLLHHSladldlleeeeeYE 224

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 117 PYGQQLSALRRGVH--IVVGTpgrvIDHLDRSTLD--------LSEL--KTLVLDEAD----EMLRMgfiddVEAVLKKL 180
Cdd:COG1203  225 SEARWLKLLKELWDapVVVTT----IDQLFESLFSnrkgqerrLHNLanSVIILDEVQayppYMLAL-----LLRLLEWL 295

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 181 PE-QRQVALFSATMPPQIRRIaqtyLQDPVEV----TIAAKTTTSANIRQRYWWVSGMHKLDALTRILEVEPFD---AMI 252
Cdd:COG1203  296 KNlGGSVILMTATLPPLLREE----LLEAYELipdePEELPEYFRAFVRKRVELKEGPLSDEELAELILEALHKgksVLV 371

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 253 IFArTKAGTEELASKLQARGLAAAAI--NGDMQQAQRERTIAMLKE----GKLDILVATDVAARGLDverishvLNYDI- 325
Cdd:COG1203  372 IVN-TVKDAQELYEALKEKLPDEEVYllHSRFCPADRSEIEKEIKErlerGKPCILVSTQVVEAGVD-------IDFDVv 443

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|.
gi 896581323 326 -----PYDteSYVHRIGRT---GRAGRSGEAILFATPREKG 358
Cdd:COG1203  444 irdlaPLD--SLIQRAGRCnrhGRKEEEGNVYVFDPEDEGG 482

RRM_BsYxiN_like

cd12500

RNA recognition motif (RRM) found in Bacillus subtilis ATP-dependent RNA helicase YxiN and ...

514-581

3.75e-04

RNA recognition motif (RRM) found in Bacillus subtilis ATP-dependent RNA helicase YxiN and similar proteins; This subgroup corresponds to the C-terminal RRM homology domain of YxiN. B. subtilis YxiN is a member of the DbpA subfamily of prokaryotic DEAD-box rRNA helicases that have been implicated in ribosome biogenesis. It binds with high affinity and specificity to RNA substrates containing hairpin 92 of 23S rRNA (HP92) with either 3' or 5' extensions in an ATP-dependent manner. YxiN contains two N-terminal ATPase catalytic domains and a C-terminal RNA binding domain, an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain). The catalytic domains bind to nearby regions of RNA to stimulate ATP hydrolysis and disrupt RNA structures. The C-terminal domain is responsible for the high-affinity RNA binding.

Pssm-ID: 409923 [Multi-domain] Cd Length: 73 Bit Score: 39.37 E-value: 3.75e-04

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 896581323 514 ISVGHQHGVKPANIVGAIANEAGLESRFIGRIDIHDDFSLLDLPAQMPPDVLSHLQKVWVSGQQLQMR 581
Cdd:cd12500    4 FNGGKKKKIRAVDIVGAISNIDGVTGDDIGIITVQDNCSYVDILNGKGDHVLKVMKNTTIKGKQVKVN 71

DEXHc_HFM1

cd18023

DEXH-box helicase domain of ATP-dependent DNA helicase HFM1; HFM1 is a type II DEAD box ...

35-200

4.04e-04

DEXH-box helicase domain of ATP-dependent DNA helicase HFM1; HFM1 is a type II DEAD box helicase, required for crossover formation and complete synapsis of homologous chromosomes during meiosis. HFM1 belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

Pssm-ID: 350781 [Multi-domain] Cd Length: 206 Bit Score: 41.96 E-value: 4.04e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  35 IQAATIPAMLEG-RDVLGQAQTGTGKTAAFALPVLSNI----DLQQIKPQALILAPTRELaiqVAEAFQSYSSKIP--GF 107
Cdd:cd18023    5 IQSEVFPDLLYSdKNFVVSAPTGSGKTVLFELAILRLLkernPLPWGNRKVVYIAPIKAL---CSEKYDDWKEKFGplGL 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 108 RVLPVYGGQPYGQQLSAlrRGVHIVVGTPGRvidhLDRSTLDLSELKTLVldeadEMLRMGFIDDV-----------EAV 176
Cdd:cd18023   82 SCAELTGDTEMDDTFEI--QDADIILTTPEK----WDSMTRRWRDNGNLV-----QLVALVLIDEVhiikenrgatlEVV 150

                        170       180
                 ....*....|....*....|....
gi 896581323 177 LKKLpeqRQVALFSATMPPQIRRI 200
Cdd:cd18023  151 VSRM---KTLSSSSELRGSTVRPM 171

DEXHc_archSki2

cd18028

DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ...

34-194

4.34e-04

DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type 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: 350786 [Multi-domain] Cd Length: 177 Bit Score: 41.55 E-value: 4.34e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  34 PIQAATIPA-MLEGRDVLGQAQTGTGKTAAFALPVLSNIDLQQikpQALILAPTRELAIQVAEAFQSYSSkiPGFRVLPV 112
Cdd:cd18028    4 PPQAEAVRAgLLKGENLLISIPTASGKTLIAEMAMVNTLLEGG---KALYLVPLRALASEKYEEFKKLEE--IGLKVGIS 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 113 YGGqpYGQQLSALRRgVHIVVGTPGRvIDHLDRSTLD-LSELKTLVLDE---ADEMLRMGFIDDVEAVLKKLPEQRQVAL 188
Cdd:cd18028   79 TGD--YDEDDEWLGD-YDIIVATYEK-FDSLLRHSPSwLRDVGVVVVDEihlISDEERGPTLESIVARLRRLNPNTQIIG 154


                 ....*.
gi 896581323 189 FSATMP 194
Cdd:cd18028  155 LSATIG 160

CMS1

pfam14617

U3-containing 90S pre-ribosomal complex subunit; This is a family of fungal and plant ...

78-159

4.61e-04

U3-containing 90S pre-ribosomal complex subunit; This is a family of fungal and plant CMS1-like proteins. The family has similarity to the DEAD-box helicases.

Pssm-ID: 373164 Cd Length: 250 Bit Score: 42.54 E-value: 4.61e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323   78 PQALILAPTRELAIQVAEAFQSYSSKipGFRVLPVYGGQ-PYGQQLSALRRG-VHIVVGTPGRVIDHLDRSTLDLSELKT 155
Cdd:pfam14617 125 PHTLVLTIAALRAADVLRPLKKLQTK--GFKVAKLFAKHiKLEEHITYCKASrIGIGVGTPGRIADLLENESLSVDNLKY 202


                  ....
gi 896581323  156 LVLD 159
Cdd:pfam14617 203 IILD 206

SF2_C_Hrq

cd18797

C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role ...

252-352

9.28e-04

C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role in DNA inter-strand crosslink (ICL) repair and in telomere maintenance. Hrq1 lacks the Sld2-like domain found in RecQ4. HrQ family helicases 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: 350184 [Multi-domain] Cd Length: 146 Bit Score: 39.93 E-value: 9.28e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 252 IIFARTKAGTEELASKLQARGLAAAAINGDMQ-------QAQRERTIAMLKEGKLDILVATDVAARGLDVERISHVLNYD 324
Cdd:cd18797   39 IVFCRSRKLAELLLRYLKARLVEEGPLASKVAsyragylAEDRREIEAELFNGELLGVVATNALELGIDIGGLDAVVLAG 118

                         90       100
                 ....*....|....*....|....*...
gi 896581323 325 IPYDTESYVHRIGRTGRAGRSGEAILFA 352
Cdd:cd18797  119 YPGSLASLWQQAGRAGRRGKDSLVILVA 146

ResIII

pfam04851

Type III restriction enzyme, res subunit;

55-192

9.80e-04

Type III restriction enzyme, res subunit;

Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 40.35 E-value: 9.80e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323   55 TGTGKT---AAFALpvlsNIDLQQIKPQALILAPTRELAIQVAEAFQSYSS---KIPGFRvlpvyggqpYGQQLSALRRG 128
Cdd:pfam04851  32 TGSGKTltaAKLIA----RLFKKGPIKKVLFLVPRKDLLEQALEEFKKFLPnyvEIGEII---------SGDKKDESVDD 98

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 896581323  129 VHIVVGTPGRVIDHLDRSTLDLSELKTLVL--DEADEmlrmGFIDDVEAVLKKLPEQRQVAlFSAT 192
Cdd:pfam04851  99 NKIVVTTIQSLYKALELASLELLPDFFDVIiiDEAHR----SGASSYRNILEYFKPAFLLG-LTAT 159

DDXDc_reverse_gyrase

cd17924

DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of ...

25-178

1.05e-03

DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of DNA by introducing positive supercoils in an ATP-dependent process. Reverse gyrase belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

Pssm-ID: 350682 [Multi-domain] Cd Length: 189 Bit Score: 40.77 E-value: 1.05e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  25 TAIGYETPSPiQAATIPAMLEGRDVLGQAQTGTGKTAaFALpvLSNIDLQQIKPQALILAPTRELAIQVAEAFQSYSSKI 104
Cdd:cd17924   12 KKTGFPPWGA-QRTWAKRLLRGKSFAIIAPTGVGKTT-FGL--ATSLYLASKGKRSYLIFPTKSLVKQAYERLSKYAEKA 87

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 896581323 105 PG-FRVLPVYGGQPYGQQLSALRR----GVHIVVGTPGRVIDHLDRstldLSELKtlvldeademLRMGFIDDVEAVLK 178
Cdd:cd17924   88 GVeVKILVYHSRLKKKEKEELLEKiekgDFDILVTTNQFLSKNFDL----LSNKK----------FDFVFVDDVDAVLK 152

DEXHc_Hef

cd18035

DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ...

35-161

1.18e-03

DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. All archaea encode a protein of the XPF/MUS81/FANCM family of endonucleases. It exists in two forms: a long form, referred as Hef which consists of an N-terminal helicase fused to a C-terminal nuclease and is specific to euryarchaea and a short form, referred as XPF which lacks the helicase domain and is specific to crenarchaea and thaumarchaea. Hef has the unique feature of having both active helicase and nuclease domains. This domain configuration is highly similar with the human FANCM, a possible ortholog of archaeal Hef proteins. Hef is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

Pssm-ID: 350793 [Multi-domain] Cd Length: 181 Bit Score: 40.19 E-value: 1.18e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  35 IQAATIPAMLEGRDVLGQAQTGTGKTAaFALPVLSNIdLQQIKPQALILAPTRELAIQVAEAF-QSYSSKIPgfrVLPVY 113
Cdd:cd18035    5 LYQVLIAAVALNGNTLIVLPTGLGKTI-IAILVAADR-LTKKGGKVLILAPSRPLVEQHAENLkRVLNIPDK---ITSLT 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 896581323 114 GGQPYGQQLSALRRGvHIVVGTPGRVIDHLDRSTLDLSELKTLVLDEA 161
Cdd:cd18035   80 GEVKPEERAERWDAS-KIIVATPQVIENDLLAGRITLDDVSLLIFDEA 126

DEXHc_Ski2

cd17921

DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ...

34-194

1.28e-03

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

Pssm-ID: 350679 [Multi-domain] Cd Length: 181 Bit Score: 40.32 E-value: 1.28e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323  34 PIQAATI-PAMLEGRDVLGQAQTGTGKTAAFALPVLSNidLQQIKPQALILAPTRELAIQVAEAFQSySSKIPGFRVLPV 112
Cdd:cd17921    4 PIQREALrALYLSGDSVLVSAPTSSGKTLIAELAILRA--LATSGGKAVYIAPTRALVNQKEADLRE-RFGPLGKNVGLL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 113 YGGQPYGQQLSALRrgvHIVVGTPGRvIDHL--DRSTLDLSELKTLVLDEADemlrmgFIDD------VEAVLKKLP--- 181
Cdd:cd17921   81 TGDPSVNKLLLAEA---DILVATPEK-LDLLlrNGGERLIQDVRLVVVDEAH------LIGDgergvvLELLLSRLLrin 150

                        170
                 ....*....|...
gi 896581323 182 EQRQVALFSATMP 194
Cdd:cd17921  151 KNARFVGLSATLP 163

SF2_C_EcoAI-like

cd18799

C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ...

252-314

1.70e-03

C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family is composed of helicase restriction enzymes, including the HsdR subunit of restriction-modification enzymes such as Escherichia coli type I restriction enzyme EcoAI R protein (R.EcoAI). The EcoAI enzyme recognizes 5'-GAGN(7)GTCA-3'. The HsdR or R subunit is required for both nuclease and ATPase activities, but not for modification. These proteins 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: 350186 [Multi-domain] Cd Length: 116 Bit Score: 38.69 E-value: 1.70e-03

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 896581323 252 IIFARTKAGTEELASKLQARGLAAAAINGDmqQAQRERTIAMLK-----EGKLDILVATDVAARGLDV 314
Cdd:cd18799   10 LIFCVSIEHAEFMAEAFNEAGIDAVALNSD--YSDRERGDEALIllffgELKPPILVTVDLLTTGVDI 75

ComFA

COG4098

Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ...

286-374

7.34e-03

Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, recombination and repair];

Pssm-ID: 443274 [Multi-domain] Cd Length: 451 Bit Score: 39.09 E-value: 7.34e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896581323 286 QRERTIAMLKEGKLDILVATDVAARGLDVERIS-HVLNYDIP-YDTESYVhRIGrtGRAGRS-----GEAILFATprekG 358
Cdd:COG4098  357 ERKEKVQAFRDGEIPILVTTTILERGVTFPNVDvAVLGADHPvFTEAALV-QIA--GRVGRSadyptGEVIFFHH----G 429

                         90
                 ....*....|....*.
gi 896581323 359 MLRQIERATRQpIEEM 374
Cdd:COG4098  430 KTRAMKRAIRE-IKRM 444

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