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Conserved domains on  [gi|2462533313|ref|XP_054228679|]
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ATP-dependent RNA helicase DDX55 isoform X11 [Homo sapiens]

Protein Classification

DEADc_DDX55 and SF2_C_DEAD domain-containing protein( domain architecture ID 13028868)

protein containing domains DEADc_DDX55, SF2_C_DEAD, and DUF4217

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DEADc_DDX55 cd17960
DEAD-box helicase domain of DEAD box protein 55; DDX55 is a member of the DEAD-box helicases, ...
 1-181 1.35e-109

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: 320.29  E-value: 1.35e-109
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   1 MRNKDVAAEAVTGSGKTLAFVIPILEILLRREEKLKKSQVGAIIITPTRELAIQIDEVLSHFTK-HFPEFSQILWIGGRN 79
Cdd:cd17960    25 LSNKDVVVEAVTGSGKTLAFLIPVLEILLKRKANLKKGQVGALIISPTRELATQIYEVLQSFLEhHLPKLKCQLLIGGTN 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  80 PGEDVERFKQQGGNIIVATPGRLEDMFRRKAEgldlASCVRSLDVLVLDEADRLLDMGFEASINTILEFLPKQRRTGLFS 159
Cdd:cd17960   105 VEEDVKKFKRNGPNILVGTPGRLEELLSRKAD----KVKVKSLEVLVLDEADRLLDLGFEADLNRILSKLPKQRRTGLFS 180

                         170       180
                  ....*....|....*....|..
gi 2462533313 160 ATQTQEVENLVRAGLRNPVRVS 181
Cdd:cd17960   181 ATQTDAVEELIKAGLRNPVRVV 202
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
1-377 6.39e-109

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


:

Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 326.72  E-value: 6.39e-109
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   1 MRNKDVAAEAVTGSGKTLAFVIPILEILLRREEKlkksQVGAIIITPTRELAIQIDEVLSHFTKHFPEFSQILwIGGRNP 80
Cdd:COG0513    37 LAGRDVLGQAQTGTGKTAAFLLPLLQRLDPSRPR----APQALILAPTRELALQVAEELRKLAKYLGLRVATV-YGGVSI 111

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  81 GEDVERFKQqGGNIIVATPGRLEDMFRRKAegLDLascvRSLDVLVLDEADRLLDMGFEASINTILEFLPKQRRTGLFSA 160
Cdd:COG0513   112 GRQIRALKR-GVDIVVATPGRLLDLIERGA--LDL----SGVETLVLDEADRMLDMGFIEDIERILKLLPKERQTLLFSA 184

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 161 TQTQEVENLVRAGLRNPVRVSVKEKgvaassaQKTPSRLENYYMVCKADEKFNQLVHFLRNHKQEKHLVFFSTCACVEYY 240
Cdd:COG0513   185 TMPPEIRKLAKRYLKNPVRIEVAPE-------NATAETIEQRYYLVDKRDKLELLRRLLRDEDPERAIVFCNTKRGADRL 257

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 241 GKALEVlvKGVKIMCIHGKM-KYKRNKIFMEFRKLQSGILVCTDVMARGIDIPEVNWVLQYDPPSNASAFVHRCGRTARI 319
Cdd:COG0513   258 AEKLQK--RGISAAALHGDLsQGQRERALDAFRNGKIRVLVATDVAARGIDIDDVSHVINYDLPEDPEDYVHRIGRTGRA 335

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462533313 320 GHGGSALVFLLPMEESYINFL--AINQKCPLQEMKP-----QRNTADLLPKLKSMALADRAVFEK 377
Cdd:COG0513   336 GAEGTAISLVTPDERRLLRAIekLIGQKIEEEELPGfepveEKRLERLKPKIKEKLKGKKAGRGG 400
DUF4217 pfam13959
Domain of unknown function (DUF4217); This short domain is found at the C-terminus of many ...
 362-403 8.99e-13

Domain of unknown function (DUF4217); This short domain is found at the C-terminus of many helicase proteins.


:

Pssm-ID: 464056 [Multi-domain]  Cd Length: 59  Bit Score: 62.80  E-value: 8.99e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 2462533313 362 PKLKSMALADRAVFEKGMKAFVSYVQAYAKHECNLIFRLKAL 403
Cdd:pfam13959   2 LQLEKLVLKDRELKELAQKAFVSYVRAYSKHLAKSIFNVKKL 43
 
Name Accession Description Interval E-value
DEADc_DDX55 cd17960
DEAD-box helicase domain of DEAD box protein 55; DDX55 is a member of the DEAD-box helicases, ...
 1-181 1.35e-109

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: 320.29  E-value: 1.35e-109
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   1 MRNKDVAAEAVTGSGKTLAFVIPILEILLRREEKLKKSQVGAIIITPTRELAIQIDEVLSHFTK-HFPEFSQILWIGGRN 79
Cdd:cd17960    25 LSNKDVVVEAVTGSGKTLAFLIPVLEILLKRKANLKKGQVGALIISPTRELATQIYEVLQSFLEhHLPKLKCQLLIGGTN 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  80 PGEDVERFKQQGGNIIVATPGRLEDMFRRKAEgldlASCVRSLDVLVLDEADRLLDMGFEASINTILEFLPKQRRTGLFS 159
Cdd:cd17960   105 VEEDVKKFKRNGPNILVGTPGRLEELLSRKAD----KVKVKSLEVLVLDEADRLLDLGFEADLNRILSKLPKQRRTGLFS 180

                         170       180
                  ....*....|....*....|..
gi 2462533313 160 ATQTQEVENLVRAGLRNPVRVS 181
Cdd:cd17960   181 ATQTDAVEELIKAGLRNPVRVV 202
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
1-377 6.39e-109

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 326.72  E-value: 6.39e-109
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   1 MRNKDVAAEAVTGSGKTLAFVIPILEILLRREEKlkksQVGAIIITPTRELAIQIDEVLSHFTKHFPEFSQILwIGGRNP 80
Cdd:COG0513    37 LAGRDVLGQAQTGTGKTAAFLLPLLQRLDPSRPR----APQALILAPTRELALQVAEELRKLAKYLGLRVATV-YGGVSI 111

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  81 GEDVERFKQqGGNIIVATPGRLEDMFRRKAegLDLascvRSLDVLVLDEADRLLDMGFEASINTILEFLPKQRRTGLFSA 160
Cdd:COG0513   112 GRQIRALKR-GVDIVVATPGRLLDLIERGA--LDL----SGVETLVLDEADRMLDMGFIEDIERILKLLPKERQTLLFSA 184

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 161 TQTQEVENLVRAGLRNPVRVSVKEKgvaassaQKTPSRLENYYMVCKADEKFNQLVHFLRNHKQEKHLVFFSTCACVEYY 240
Cdd:COG0513   185 TMPPEIRKLAKRYLKNPVRIEVAPE-------NATAETIEQRYYLVDKRDKLELLRRLLRDEDPERAIVFCNTKRGADRL 257

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 241 GKALEVlvKGVKIMCIHGKM-KYKRNKIFMEFRKLQSGILVCTDVMARGIDIPEVNWVLQYDPPSNASAFVHRCGRTARI 319
Cdd:COG0513   258 AEKLQK--RGISAAALHGDLsQGQRERALDAFRNGKIRVLVATDVAARGIDIDDVSHVINYDLPEDPEDYVHRIGRTGRA 335

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462533313 320 GHGGSALVFLLPMEESYINFL--AINQKCPLQEMKP-----QRNTADLLPKLKSMALADRAVFEK 377
Cdd:COG0513   336 GAEGTAISLVTPDERRLLRAIekLIGQKIEEEELPGfepveEKRLERLKPKIKEKLKGKKAGRGG 400
PRK11776 PRK11776
ATP-dependent RNA helicase DbpA; Provisional
 3-364 1.17e-57

ATP-dependent RNA helicase DbpA; Provisional


Pssm-ID: 236977 [Multi-domain]  Cd Length: 460  Bit Score: 195.41  E-value: 1.17e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   3 NKDVAAEAVTGSGKTLAFVIPILEILlrreeKLKKSQVGAIIITPTRELAIQI-DEV--LSHFTKHFpefsQILWIGGRN 79
Cdd:PRK11776   41 GKDVIAQAKTGSGKTAAFGLGLLQKL-----DVKRFRVQALVLCPTRELADQVaKEIrrLARFIPNI----KVLTLCGGV 111

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  80 PgedverFKQQ------GGNIIVATPGRLEDMFRRkaEGLDLAScvrsLDVLVLDEADRLLDMGFEASINTILEFLPKQR 153
Cdd:PRK11776  112 P------MGPQidslehGAHIIVGTPGRILDHLRK--GTLDLDA----LNTLVLDEADRMLDMGFQDAIDAIIRQAPARR 179

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 154 RTGLFSATQTQEVENLVRAGLRNPVRVSVKEKGVAassaqktpSRLENYYMVCKADEKFNQLVHFLRNHKQEKHLVFFST 233
Cdd:PRK11776  180 QTLLFSATYPEGIAAISQRFQRDPVEVKVESTHDL--------PAIEQRFYEVSPDERLPALQRLLLHHQPESCVVFCNT 251

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 234 CA-CVEYYgKALEvlVKGVKIMCIHGKM-KYKRNKIFMEFRKLQSGILVCTDVMARGIDIPEVNWVLQYDPPSNASAFVH 311
Cdd:PRK11776  252 KKeCQEVA-DALN--AQGFSALALHGDLeQRDRDQVLVRFANRSCSVLVATDVAARGLDIKALEAVINYELARDPEVHVH 328

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462533313 312 RCGRTARIGHGGSALVFLLPMEESYINFLAINQKCPLQ-----EMKPqRNTADLLPKL 364
Cdd:PRK11776  329 RIGRTGRAGSKGLALSLVAPEEMQRANAIEDYLGRKLNweplpSLSP-LSGVPLLPEM 385
PRK11192 PRK11192
ATP-dependent RNA helicase SrmB; Provisional
 1-365 7.70e-57

ATP-dependent RNA helicase SrmB; Provisional


Pssm-ID: 236877 [Multi-domain]  Cd Length: 434  Bit Score: 192.46  E-value: 7.70e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   1 MRNKDVAAEAVTGSGKTLAFVIPILEILL---RReeklKKSQVGAIIITPTRELAIQIDEVLSHFTKHfpefsQILWI-- 75
Cdd:PRK11192   36 LDGRDVLGSAPTGTGKTAAFLLPALQHLLdfpRR----KSGPPRILILTPTRELAMQVADQARELAKH-----THLDIat 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  76 --GGRNPGEDVERF-KQQggNIIVATPGRLedMFRRKAEGLDLascvRSLDVLVLDEADRLLDMGFEASINTILEFLPKQ 152
Cdd:PRK11192  107 itGGVAYMNHAEVFsENQ--DIVVATPGRL--LQYIKEENFDC----RAVETLILDEADRMLDMGFAQDIETIAAETRWR 178

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 153 RRTGLFSATQTQE-VENLVRAGLRNPVRVSVKekgvaassaqktPSRLEN------YYMVCKADEKFNQLVHFLRNHKQE 225
Cdd:PRK11192  179 KQTLLFSATLEGDaVQDFAERLLNDPVEVEAE------------PSRRERkkihqwYYRADDLEHKTALLCHLLKQPEVT 246

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 226 KHLVFFSTCACVEYYGKALEVlvKGVKIMCIHGKM-KYKRNKIFMEFRKLQSGILVCTDVMARGIDIPEVNWVLQYDPPS 304
Cdd:PRK11192  247 RSIVFVRTRERVHELAGWLRK--AGINCCYLEGEMvQAKRNEAIKRLTDGRVNVLVATDVAARGIDIDDVSHVINFDMPR 324

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462533313 305 NASAFVHRCGRTARIGHGGSALVF-------LLPMEESYINflainqkcplQEMKPqRNTADLLPKLK 365
Cdd:PRK11192  325 SADTYLHRIGRTGRAGRKGTAISLveahdhlLLGKIERYIE----------EPLKA-RVIDELRPKTK 381
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 199-329 1.67e-50

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: 166.53  E-value: 1.67e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 199 LENYYMVCKADEKFNQL-VHFLRNHKQEKHLVFFSTCACVEYYGKALEVLvkGVKIMCIHGKMKYK-RNKIFMEFRKLQS 276
Cdd:cd18787     1 IKQLYVVVEEEEKKLLLlLLLLEKLKPGKAIIFVNTKKRVDRLAELLEEL--GIKVAALHGDLSQEeRERALKKFRSGKV 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2462533313 277 GILVCTDVMARGIDIPEVNWVLQYDPPSNASAFVHRCGRTARIGHGGSALVFL 329
Cdd:cd18787    79 RVLVATDVAARGLDIPGVDHVINYDLPRDAEDYVHRIGRTGRAGRKGTAITFV 131
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 1-169 4.95e-45

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: 153.17  E-value: 4.95e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   1 MRNKDVAAEAVTGSGKTLAFVIPILEILLRREEKLKksqvgAIIITPTRELAIQIDEVLSHFTKHFpEFSQILWIGGRNP 80
Cdd:pfam00270  12 LEGRDVLVQAPTGSGKTLAFLLPALEALDKLDNGPQ-----ALVLAPTRELAEQIYEELKKLGKGL-GLKVASLLGGDSR 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  81 GEDVERFKqqGGNIIVATPGRLEDMFRRKAEgldlascVRSLDVLVLDEADRLLDMGFEASINTILEFLPKQRRTGLFSA 160
Cdd:pfam00270  86 KEQLEKLK--GPDILVGTPGRLLDLLQERKL-------LKNLKLLVLDEAHRLLDMGFGPDLEEILRRLPKKRQILLLSA 156


                  ....*....
gi 2462533313 161 TQTQEVENL 169
Cdd:pfam00270 157 TLPRNLEDL 165
DEXDc smart00487
DEAD-like helicases superfamily;
2-185 2.56e-40

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 142.25  E-value: 2.56e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313    2 RNKDVAAEAVTGSGKTLAFVIPILEILLRREEKlkksqvGAIIITPTRELAIQIDEVLSHFTKHFPeFSQILWIGGRNPG 81
Cdd:smart00487  23 GLRDVILAAPTGSGKTLAALLPALEALKRGKGG------RVLVLVPTRELAEQWAEELKKLGPSLG-LKVVGLYGGDSKR 95

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   82 EDVERFKQQGGNIIVATPGRLEDMFRRKAEGLdlascvRSLDVLVLDEADRLLDMGFEASINTILEFLPKQRRTGLFSAT 161
Cdd:smart00487  96 EQLRKLESGKTDILVTTPGRLLDLLENDKLSL------SNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLLLLSAT 169

                          170       180
                   ....*....|....*....|....
gi 2462533313  162 QTQEVENLVRAGLRNPVRVSVKEK 185
Cdd:smart00487 170 PPEEIENLLELFLNDPVFIDVGFT 193
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 210-320 2.12e-28

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: 107.30  E-value: 2.12e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 210 EKFNQLVHFLRNHKQEKHLVFFSTCACVEYygKALEVLvKGVKIMCIHGKMKYK-RNKIFMEFRKLQSGILVCTDVMARG 288
Cdd:pfam00271   1 EKLEALLELLKKERGGKVLIFSQTKKTLEA--ELLLEK-EGIKVARLHGDLSQEeREEILEDFRKGKIDVLVATDVAERG 77

                          90       100       110
                  ....*....|....*....|....*....|..
gi 2462533313 289 IDIPEVNWVLQYDPPSNASAFVHRCGRTARIG 320
Cdd:pfam00271  78 LDLPDVDLVINYDLPWNPASYIQRIGRAGRAG 109
HELICc smart00490
helicase superfamily c-terminal domain;
249-320 6.13e-23

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 91.89  E-value: 6.13e-23
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462533313  249 KGVKIMCIHGKMKYK-RNKIFMEFRKLQSGILVCTDVMARGIDIPEVNWVLQYDPPSNASAFVHRCGRTARIG 320
Cdd:smart00490  10 LGIKVARLHGGLSQEeREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGRAG 82
DUF4217 pfam13959
Domain of unknown function (DUF4217); This short domain is found at the C-terminus of many ...
 362-403 8.99e-13

Domain of unknown function (DUF4217); This short domain is found at the C-terminus of many helicase proteins.


Pssm-ID: 464056 [Multi-domain]  Cd Length: 59  Bit Score: 62.80  E-value: 8.99e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 2462533313 362 PKLKSMALADRAVFEKGMKAFVSYVQAYAKHECNLIFRLKAL 403
Cdd:pfam13959   2 LQLEKLVLKDRELKELAQKAFVSYVRAYSKHLAKSIFNVKKL 43
ComFA COG4098
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ...
 10-317 2.17e-09

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: 59.12  E-value: 2.17e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  10 AVTGSGKT-LAFviPILEILLRReeklkKSQVGaiIITPTRELAIqidEVLSHFTKHFPEFSQILWIGGrnpGEDVERFK 88
Cdd:COG4098   136 AVCGAGKTeMLF--PAIAEALKQ-----GGRVC--IATPRVDVVL---ELAPRLQQAFPGVDIAALYGG---SEEKYRYA 200

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  89 QqggnIIVATPG---RLEDMFrrkaegldlascvrslDVLVLDEADrlldmGFEASINTILEFLPKQ-RRTG----LFSA 160
Cdd:COG4098   201 Q----LVIATTHqllRFYQAF----------------DLLIIDEVD-----AFPYSGDPMLQYAVKRaRKPDgkliYLTA 255

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 161 TQTQEVENLVRAGLRN-------------PVRVSVKEKGVAASSAQKTPSRlenyymvckadekfnQLVHFLRNHKQEKH 227
Cdd:COG4098   256 TPSKALQRQVKRGKLKvvklparyhghplPVPKFKWLGNWKKRLRRGKLPR---------------KLLKWLKKRLKEGR 320

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 228 --LVFFSTCACVEYYGKALEVLVKGVKIMCIHGKMKYKRNKIfMEFRKLQSGILVCTDVMARGIDIPEVN-WVLQYDPPS 304
Cdd:COG4098   321 qlLIFVPTIELLEQLVALLQKLFPEERIAGVHAEDPERKEKV-QAFRDGEIPILVTTTILERGVTFPNVDvAVLGADHPV 399

                         330
                  ....*....|....*..
gi 2462533313 305 -NASAFVH---RCGRTA 317
Cdd:COG4098   400 fTEAALVQiagRVGRSA 416
mfd TIGR00580
transcription-repair coupling factor (mfd); All proteins in this family for which functions ...
 237-295 4.54e-06

transcription-repair coupling factor (mfd); All proteins in this family for which functions are known are DNA-dependent ATPases that function in the process of transcription-coupled DNA repair in which the repair of the transcribed strand of actively transcribed genes is repaired at a higher rate than the repair of non-transcribed regions of the genome and than the non-transcribed strand of the same gene. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is closely related to the RecG and UvrB families. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273152 [Multi-domain]  Cd Length: 926  Bit Score: 48.89  E-value: 4.54e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 237 VEYYGKALEVLVKGVKIMCIHGKM-KYKRNKIFMEFRKLQSGILVCTDVMARGIDIPEVN 295
Cdd:TIGR00580 673 IEKLATQLRELVPEARIAIAHGQMtENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNAN 732
 
Name Accession Description Interval E-value
DEADc_DDX55 cd17960
DEAD-box helicase domain of DEAD box protein 55; DDX55 is a member of the DEAD-box helicases, ...
 1-181 1.35e-109

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: 320.29  E-value: 1.35e-109
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   1 MRNKDVAAEAVTGSGKTLAFVIPILEILLRREEKLKKSQVGAIIITPTRELAIQIDEVLSHFTK-HFPEFSQILWIGGRN 79
Cdd:cd17960    25 LSNKDVVVEAVTGSGKTLAFLIPVLEILLKRKANLKKGQVGALIISPTRELATQIYEVLQSFLEhHLPKLKCQLLIGGTN 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  80 PGEDVERFKQQGGNIIVATPGRLEDMFRRKAEgldlASCVRSLDVLVLDEADRLLDMGFEASINTILEFLPKQRRTGLFS 159
Cdd:cd17960   105 VEEDVKKFKRNGPNILVGTPGRLEELLSRKAD----KVKVKSLEVLVLDEADRLLDLGFEADLNRILSKLPKQRRTGLFS 180

                         170       180
                  ....*....|....*....|..
gi 2462533313 160 ATQTQEVENLVRAGLRNPVRVS 181
Cdd:cd17960   181 ATQTDAVEELIKAGLRNPVRVV 202
SrmB COG0513
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
1-377 6.39e-109

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


Pssm-ID: 440279 [Multi-domain]  Cd Length: 420  Bit Score: 326.72  E-value: 6.39e-109
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   1 MRNKDVAAEAVTGSGKTLAFVIPILEILLRREEKlkksQVGAIIITPTRELAIQIDEVLSHFTKHFPEFSQILwIGGRNP 80
Cdd:COG0513    37 LAGRDVLGQAQTGTGKTAAFLLPLLQRLDPSRPR----APQALILAPTRELALQVAEELRKLAKYLGLRVATV-YGGVSI 111

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  81 GEDVERFKQqGGNIIVATPGRLEDMFRRKAegLDLascvRSLDVLVLDEADRLLDMGFEASINTILEFLPKQRRTGLFSA 160
Cdd:COG0513   112 GRQIRALKR-GVDIVVATPGRLLDLIERGA--LDL----SGVETLVLDEADRMLDMGFIEDIERILKLLPKERQTLLFSA 184

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 161 TQTQEVENLVRAGLRNPVRVSVKEKgvaassaQKTPSRLENYYMVCKADEKFNQLVHFLRNHKQEKHLVFFSTCACVEYY 240
Cdd:COG0513   185 TMPPEIRKLAKRYLKNPVRIEVAPE-------NATAETIEQRYYLVDKRDKLELLRRLLRDEDPERAIVFCNTKRGADRL 257

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 241 GKALEVlvKGVKIMCIHGKM-KYKRNKIFMEFRKLQSGILVCTDVMARGIDIPEVNWVLQYDPPSNASAFVHRCGRTARI 319
Cdd:COG0513   258 AEKLQK--RGISAAALHGDLsQGQRERALDAFRNGKIRVLVATDVAARGIDIDDVSHVINYDLPEDPEDYVHRIGRTGRA 335

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462533313 320 GHGGSALVFLLPMEESYINFL--AINQKCPLQEMKP-----QRNTADLLPKLKSMALADRAVFEK 377
Cdd:COG0513   336 GAEGTAISLVTPDERRLLRAIekLIGQKIEEEELPGfepveEKRLERLKPKIKEKLKGKKAGRGG 400
DEADc cd00268
DEAD-box helicase domain of DEAD box helicases; DEAD-box helicases comprise a diverse family ...
 1-181 1.80e-65

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: 207.29  E-value: 1.80e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   1 MRNKDVAAEAVTGSGKTLAFVIPILEILLRREEKlKKSQVGAIIITPTRELAIQIDEVLSHFTKHfPEFSQILWIGGRNP 80
Cdd:cd00268    25 LSGRDVIGQAQTGSGKTLAFLLPILEKLLPEPKK-KGRGPQALVLAPTRELAMQIAEVARKLGKG-TGLKVAAIYGGAPI 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  81 GEDVERFKQqGGNIIVATPGRLEDMFRRKAegLDLascvRSLDVLVLDEADRLLDMGFEASINTILEFLPKQRRTGLFSA 160
Cdd:cd00268   103 KKQIEALKK-GPDIVVGTPGRLLDLIERGK--LDL----SNVKYLVLDEADRMLDMGFEEDVEKILSALPKDRQTLLFSA 175

                         170       180
                  ....*....|....*....|.
gi 2462533313 161 TQTQEVENLVRAGLRNPVRVS 181
Cdd:cd00268   176 TLPEEVKELAKKFLKNPVRIE 196
PRK11776 PRK11776
ATP-dependent RNA helicase DbpA; Provisional
 3-364 1.17e-57

ATP-dependent RNA helicase DbpA; Provisional


Pssm-ID: 236977 [Multi-domain]  Cd Length: 460  Bit Score: 195.41  E-value: 1.17e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   3 NKDVAAEAVTGSGKTLAFVIPILEILlrreeKLKKSQVGAIIITPTRELAIQI-DEV--LSHFTKHFpefsQILWIGGRN 79
Cdd:PRK11776   41 GKDVIAQAKTGSGKTAAFGLGLLQKL-----DVKRFRVQALVLCPTRELADQVaKEIrrLARFIPNI----KVLTLCGGV 111

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  80 PgedverFKQQ------GGNIIVATPGRLEDMFRRkaEGLDLAScvrsLDVLVLDEADRLLDMGFEASINTILEFLPKQR 153
Cdd:PRK11776  112 P------MGPQidslehGAHIIVGTPGRILDHLRK--GTLDLDA----LNTLVLDEADRMLDMGFQDAIDAIIRQAPARR 179

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 154 RTGLFSATQTQEVENLVRAGLRNPVRVSVKEKGVAassaqktpSRLENYYMVCKADEKFNQLVHFLRNHKQEKHLVFFST 233
Cdd:PRK11776  180 QTLLFSATYPEGIAAISQRFQRDPVEVKVESTHDL--------PAIEQRFYEVSPDERLPALQRLLLHHQPESCVVFCNT 251

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 234 CA-CVEYYgKALEvlVKGVKIMCIHGKM-KYKRNKIFMEFRKLQSGILVCTDVMARGIDIPEVNWVLQYDPPSNASAFVH 311
Cdd:PRK11776  252 KKeCQEVA-DALN--AQGFSALALHGDLeQRDRDQVLVRFANRSCSVLVATDVAARGLDIKALEAVINYELARDPEVHVH 328

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462533313 312 RCGRTARIGHGGSALVFLLPMEESYINFLAINQKCPLQ-----EMKPqRNTADLLPKL 364
Cdd:PRK11776  329 RIGRTGRAGSKGLALSLVAPEEMQRANAIEDYLGRKLNweplpSLSP-LSGVPLLPEM 385
PRK11192 PRK11192
ATP-dependent RNA helicase SrmB; Provisional
 1-365 7.70e-57

ATP-dependent RNA helicase SrmB; Provisional


Pssm-ID: 236877 [Multi-domain]  Cd Length: 434  Bit Score: 192.46  E-value: 7.70e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   1 MRNKDVAAEAVTGSGKTLAFVIPILEILL---RReeklKKSQVGAIIITPTRELAIQIDEVLSHFTKHfpefsQILWI-- 75
Cdd:PRK11192   36 LDGRDVLGSAPTGTGKTAAFLLPALQHLLdfpRR----KSGPPRILILTPTRELAMQVADQARELAKH-----THLDIat 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  76 --GGRNPGEDVERF-KQQggNIIVATPGRLedMFRRKAEGLDLascvRSLDVLVLDEADRLLDMGFEASINTILEFLPKQ 152
Cdd:PRK11192  107 itGGVAYMNHAEVFsENQ--DIVVATPGRL--LQYIKEENFDC----RAVETLILDEADRMLDMGFAQDIETIAAETRWR 178

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 153 RRTGLFSATQTQE-VENLVRAGLRNPVRVSVKekgvaassaqktPSRLEN------YYMVCKADEKFNQLVHFLRNHKQE 225
Cdd:PRK11192  179 KQTLLFSATLEGDaVQDFAERLLNDPVEVEAE------------PSRRERkkihqwYYRADDLEHKTALLCHLLKQPEVT 246

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 226 KHLVFFSTCACVEYYGKALEVlvKGVKIMCIHGKM-KYKRNKIFMEFRKLQSGILVCTDVMARGIDIPEVNWVLQYDPPS 304
Cdd:PRK11192  247 RSIVFVRTRERVHELAGWLRK--AGINCCYLEGEMvQAKRNEAIKRLTDGRVNVLVATDVAARGIDIDDVSHVINFDMPR 324

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462533313 305 NASAFVHRCGRTARIGHGGSALVF-------LLPMEESYINflainqkcplQEMKPqRNTADLLPKLK 365
Cdd:PRK11192  325 SADTYLHRIGRTGRAGRKGTAISLveahdhlLLGKIERYIE----------EPLKA-RVIDELRPKTK 381
DEADc_DDX10 cd17941
DEAD-box helicase domain of DEAD box protein 10; Fusion of the DDX10 gene and the nucleoporin ...
 4-182 9.08e-57

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: 185.19  E-value: 9.08e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   4 KDVAAEAVTGSGKTLAFVIPILEiLLRREEKLKKSQVGAIIITPTRELAIQIDEVLSHFTKHFpEFSQILWIGGRNPGED 83
Cdd:cd17941    28 RDILGAAKTGSGKTLAFLVPLLE-KLYRERWTPEDGLGALIISPTRELAMQIFEVLRKVGKYH-SFSAGLIIGGKDVKEE 105

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  84 VERFKQQggNIIVATPGR-LEDMfrRKAEGLDLAScvrsLDVLVLDEADRLLDMGFEASINTILEFLPKQRRTGLFSATQ 162
Cdd:cd17941   106 KERINRM--NILVCTPGRlLQHM--DETPGFDTSN----LQMLVLDEADRILDMGFKETLDAIVENLPKSRQTLLFSATQ 177

                         170       180
                  ....*....|....*....|
gi 2462533313 163 TQEVENLVRAGLRNPVRVSV 182
Cdd:cd17941   178 TKSVKDLARLSLKNPEYISV 197
DEADc_MSS116 cd17964
DEAD-box helicase domain of DEAD-box helicase Mss116; Mss116 is an RNA chaperone important for ...
 4-175 6.86e-56

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: 183.17  E-value: 6.86e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   4 KDVAAEAVTGSGKTLAFVIPILEILLRREEKLKKSQVGAIIITPTRELAIQIDEVLSHFTKHFPEFSQILWIGGRNPGED 83
Cdd:cd17964    33 DDVLARAKTGTGKTLAFLLPAIQSLLNTKPAGRRSGVSALIISPTRELALQIAAEAKKLLQGLRKLRVQSAVGGTSRRAE 112

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  84 VERFKQQGGNIIVATPGRLEDMFRRKAEGLDLascvRSLDVLVLDEADRLLDMGFEASINTILEFLPK----QRRTGLFS 159
Cdd:cd17964   113 LNRLRRGRPDILVATPGRLIDHLENPGVAKAF----TDLDYLVLDEADRLLDMGFRPDLEQILRHLPEknadPRQTLLFS 188

                         170
                  ....*....|....*.
gi 2462533313 160 ATQTQEVENLVRAGLR 175
Cdd:cd17964   189 ATVPDEVQQIARLTLK 204
PRK04537 PRK04537
ATP-dependent RNA helicase RhlB; Provisional
 4-364 2.33e-53

ATP-dependent RNA helicase RhlB; Provisional


Pssm-ID: 235307 [Multi-domain]  Cd Length: 572  Bit Score: 186.69  E-value: 2.33e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   4 KDVAAEAVTGSGKTLAFVIPILEILLRREE--KLKKSQVGAIIITPTRELAIQIDEVLSHFTKHFP-EFSqiLWIGGRNP 80
Cdd:PRK04537   47 GDVAGQAQTGTGKTLAFLVAVMNRLLSRPAlaDRKPEDPRALILAPTRELAIQIHKDAVKFGADLGlRFA--LVYGGVDY 124

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  81 GEDVERFkQQGGNIIVATPGRLEDmFRRKAEGLDLASCvrslDVLVLDEADRLLDMGFEASINTILEFLPKQ--RRTGLF 158
Cdd:PRK04537  125 DKQRELL-QQGVDVIIATPGRLID-YVKQHKVVSLHAC----EICVLDEADRMFDLGFIKDIRFLLRRMPERgtRQTLLF 198

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 159 SATQTQEVENLVRAGLRNPVRVSVKEKGVaassaqkTPSRLENYYMVCKADEKFNQLVHFLRNHKQEKHLVFFSTCACVE 238
Cdd:PRK04537  199 SATLSHRVLELAYEHMNEPEKLVVETETI-------TAARVRQRIYFPADEEKQTLLLGLLSRSEGARTMVFVNTKAFVE 271

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 239 YYGKALEVlvKGVKIMCIHGKM-KYKRNKIFMEFRKLQSGILVCTDVMARGIDIPEVNWVLQYDPPSNASAFVHRCGRTA 317
Cdd:PRK04537  272 RVARTLER--HGYRVGVLSGDVpQKKRESLLNRFQKGQLEILVATDVAARGLHIDGVKYVYNYDLPFDAEDYVHRIGRTA 349

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2462533313 318 RIGHGGSALVFL-------LPMEESYinflaINQKCPLQEMkpqrnTADLLPKL 364
Cdd:PRK04537  350 RLGEEGDAISFAceryamsLPDIEAY-----IEQKIPVEPV-----TAELLTPL 393
PRK01297 PRK01297
ATP-dependent RNA helicase RhlB; Provisional
 1-329 8.67e-53

ATP-dependent RNA helicase RhlB; Provisional


Pssm-ID: 234938 [Multi-domain]  Cd Length: 475  Bit Score: 182.80  E-value: 8.67e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   1 MRNKDVAAEAVTGSGKTLAFVIPILEILLRR--EEKLKKSQVGAIIITPTRELAIQIDEVLSHFTKhFPEFSQILWIGGR 78
Cdd:PRK01297  122 LAGHDAIGRAQTGTGKTAAFLISIINQLLQTppPKERYMGEPRALIIAPTRELVVQIAKDAAALTK-YTGLNVMTFVGGM 200

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  79 NPGEDVERFKQQGGNIIVATPGRLEDMFRRKAEGLDLascvrsLDVLVLDEADRLLDMGFEASINTILEFLPK--QRRTG 156
Cdd:PRK01297  201 DFDKQLKQLEARFCDILVATPGRLLDFNQRGEVHLDM------VEVMVLDEADRMLDMGFIPQVRQIIRQTPRkeERQTL 274

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 157 LFSATQTQEVENLVRAGLRNPVRVSVKEKGVAASSAQktpsrlENYYMVCKADeKFNQLVHFLRNHKQEKHLVFFSTCAC 236
Cdd:PRK01297  275 LFSATFTDDVMNLAKQWTTDPAIVEIEPENVASDTVE------QHVYAVAGSD-KYKLLYNLVTQNPWERVMVFANRKDE 347

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 237 VEyygKALEVLVK-GVKIMCIHGKM-KYKRNKIFMEFRKLQSGILVCTDVMARGIDIPEVNWVLQYDPPSNASAFVHRCG 314
Cdd:PRK01297  348 VR---RIEERLVKdGINAAQLSGDVpQHKRIKTLEGFREGKIRVLVATDVAGRGIHIDGISHVINFTLPEDPDDYVHRIG 424

                         330
                  ....*....|....*
gi 2462533313 315 RTARIGHGGSALVFL 329
Cdd:PRK01297  425 RTGRAGASGVSISFA 439
DEADc_DDX27 cd17947
DEAD-box helicase domain of DEAD box protein 27; DDX27 (also called RHLP, deficiency of ...
 4-181 1.59e-52

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: 173.98  E-value: 1.59e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   4 KDVAAEAVTGSGKTLAFVIPILEILLRREEKLKKSQVgaIIITPTRELAIQIDEVLSHFTKhfpeFSQI---LWIGGRNP 80
Cdd:cd17947    28 KDICASAVTGSGKTAAFLLPILERLLYRPKKKAATRV--LVLVPTRELAMQCFSVLQQLAQ----FTDItfaLAVGGLSL 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  81 GEDvERFKQQGGNIIVATPGRLEDMFRrKAEGLDLAScvrsLDVLVLDEADRLLDMGFEASINTILEFLPKQRRTGLFSA 160
Cdd:cd17947   102 KAQ-EAALRARPDIVIATPGRLIDHLR-NSPSFDLDS----IEILVLDEADRMLEEGFADELKEILRLCPRTRQTMLFSA 175

                         170       180
                  ....*....|....*....|.
gi 2462533313 161 TQTQEVENLVRAGLRNPVRVS 181
Cdd:cd17947   176 TMTDEVKDLAKLSLNKPVRVF 196
PRK10590 PRK10590
ATP-dependent RNA helicase RhlE; Provisional
 4-326 2.03e-51

ATP-dependent RNA helicase RhlE; Provisional


Pssm-ID: 236722 [Multi-domain]  Cd Length: 456  Bit Score: 178.85  E-value: 2.03e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   4 KDVAAEAVTGSGKTLAFVIPILEILLRREEKLK-KSQVGAIIITPTRELAIQIDEVLSHFTKHFPEFSQILWIG-GRNPg 81
Cdd:PRK10590   39 RDLMASAQTGTGKTAGFTLPLLQHLITRQPHAKgRRPVRALILTPTRELAAQIGENVRDYSKYLNIRSLVVFGGvSINP- 117

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  82 edvERFKQQGG-NIIVATPGRLEDMFRRKAEGLDlascvrSLDVLVLDEADRLLDMGFEASINTILEFLPKQRRTGLFSA 160
Cdd:PRK10590  118 ---QMMKLRGGvDVLVATPGRLLDLEHQNAVKLD------QVEILVLDEADRMLDMGFIHDIRRVLAKLPAKRQNLLFSA 188

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 161 TQTQEVENLVRAGLRNPVRVSVKEKGVAAssaqktpsrlenyymvckadEKFNQLVHFL-RNHKQE------------KH 227
Cdd:PRK10590  189 TFSDDIKALAEKLLHNPLEIEVARRNTAS--------------------EQVTQHVHFVdKKRKREllsqmigkgnwqQV 248

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 228 LVFFSTCACVEYYGKALEvlVKGVKIMCIHG-KMKYKRNKIFMEFRKLQSGILVCTDVMARGIDIPEVNWVLQYDPPSNA 306
Cdd:PRK10590  249 LVFTRTKHGANHLAEQLN--KDGIRSAAIHGnKSQGARTRALADFKSGDIRVLVATDIAARGLDIEELPHVVNYELPNVP 326

                         330       340
                  ....*....|....*....|
gi 2462533313 307 SAFVHRCGRTARIGHGGSAL 326
Cdd:PRK10590  327 EDYVHRIGRTGRAAATGEAL 346
PTZ00110 PTZ00110
helicase; Provisional
 4-331 2.13e-51

helicase; Provisional


Pssm-ID: 240273 [Multi-domain]  Cd Length: 545  Bit Score: 180.74  E-value: 2.13e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   4 KDVAAEAVTGSGKTLAFVIPILeILLRREEKLKKSQvGAI--IITPTRELAIQIDEVLSHFTKHFPEFSQILWIGGRNPG 81
Cdd:PTZ00110  168 RDMIGIAETGSGKTLAFLLPAI-VHINAQPLLRYGD-GPIvlVLAPTRELAEQIREQCNKFGASSKIRNTVAYGGVPKRG 245

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  82 EDVERfkQQGGNIIVATPGRLEDMFRRKAEGLdlascvRSLDVLVLDEADRLLDMGFEASINTILEFLPKQRRTGLFSAT 161
Cdd:PTZ00110  246 QIYAL--RRGVEILIACPGRLIDFLESNVTNL------RRVTYLVLDEADRMLDMGFEPQIRKIVSQIRPDRQTLMWSAT 317

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 162 QTQEVENLVRAGLRN-PVRVSVkekgvaASSAQKTPSRLENYYMVCKADEKFNQLVHFLRN--HKQEKHLVFFSTCACVE 238
Cdd:PTZ00110  318 WPKEVQSLARDLCKEePVHVNV------GSLDLTACHNIKQEVFVVEEHEKRGKLKMLLQRimRDGDKILIFVETKKGAD 391

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 239 YYGKALEVlvKGVKIMCIHG-KMKYKRNKIFMEFRKLQSGILVCTDVMARGIDIPEVNWVLQYDPPSNASAFVHRCGRTA 317
Cdd:PTZ00110  392 FLTKELRL--DGWPALCIHGdKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTG 469

                         330
                  ....*....|....
gi 2462533313 318 RIGHGGSALVFLLP 331
Cdd:PTZ00110  470 RAGAKGASYTFLTP 483
PRK11634 PRK11634
ATP-dependent RNA helicase DeaD; Provisional
 4-329 4.35e-51

ATP-dependent RNA helicase DeaD; Provisional


Pssm-ID: 236941 [Multi-domain]  Cd Length: 629  Bit Score: 181.20  E-value: 4.35e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   4 KDVAAEAVTGSGKTLAFVIPILEILlrrEEKLKKSQVgaIIITPTRELAIQIDEVLSHFTKHFPEFSQILWIGGRNpgED 83
Cdd:PRK11634   44 RDVLGMAQTGSGKTAAFSLPLLHNL---DPELKAPQI--LVLAPTRELAVQVAEAMTDFSKHMRGVNVVALYGGQR--YD 116

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  84 VE-RFKQQGGNIIVATPGRLEDMFRRKAegLDLAScvrsLDVLVLDEADRLLDMGFEASINTILEFLPKQRRTGLFSATQ 162
Cdd:PRK11634  117 VQlRALRQGPQIVVGTPGRLLDHLKRGT--LDLSK----LSGLVLDEADEMLRMGFIEDVETIMAQIPEGHQTALFSATM 190

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 163 TQEVENLVRAGLRNPVRVSVKekgvaaSSAQKTPSRLENYYMVcKADEKFNQLVHFLRNHKQEKHLVFFSTCACVEYYGK 242
Cdd:PRK11634  191 PEAIRRITRRFMKEPQEVRIQ------SSVTTRPDISQSYWTV-WGMRKNEALVRFLEAEDFDAAIIFVRTKNATLEVAE 263

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 243 ALEVlvKGVKIMCIHGKMkykrNKIFME--FRKLQSG---ILVCTDVMARGIDIPEVNWVLQYDPPSNASAFVHRCGRTA 317
Cdd:PRK11634  264 ALER--NGYNSAALNGDM----NQALREqtLERLKDGrldILIATDVAARGLDVERISLVVNYDIPMDSESYVHRIGRTG 337

                         330
                  ....*....|..
gi 2462533313 318 RIGHGGSALVFL 329
Cdd:PRK11634  338 RAGRAGRALLFV 349
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 199-329 1.67e-50

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: 166.53  E-value: 1.67e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 199 LENYYMVCKADEKFNQL-VHFLRNHKQEKHLVFFSTCACVEYYGKALEVLvkGVKIMCIHGKMKYK-RNKIFMEFRKLQS 276
Cdd:cd18787     1 IKQLYVVVEEEEKKLLLlLLLLEKLKPGKAIIFVNTKKRVDRLAELLEEL--GIKVAALHGDLSQEeRERALKKFRSGKV 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2462533313 277 GILVCTDVMARGIDIPEVNWVLQYDPPSNASAFVHRCGRTARIGHGGSALVFL 329
Cdd:cd18787    79 RVLVATDVAARGLDIPGVDHVINYDLPRDAEDYVHRIGRTGRAGRKGTAITFV 131
DEADc_DDX18 cd17942
DEAD-box helicase domain of DEAD box protein 18; This DDX18 gene encodes a DEAD box protein ...
 1-177 1.69e-48

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: 163.69  E-value: 1.69e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   1 MRNKDVAAEAVTGSGKTLAFVIPILEILLRREEKlKKSQVGAIIITPTRELAIQIDEVLSHFTKHFPEFSQILwIGGRNP 80
Cdd:cd17942    25 LEGRDVLGAAKTGSGKTLAFLIPAIELLYKLKFK-PRNGTGVIIISPTRELALQIYGVAKELLKYHSQTFGIV-IGGANR 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  81 GEDVERFKQqGGNIIVATPGRLEDMFRRKAEGLdlascVRSLDVLVLDEADRLLDMGFEASINTILEFLPKQRRTGLFSA 160
Cdd:cd17942   103 KAEAEKLGK-GVNILVATPGRLLDHLQNTKGFL-----YKNLQCLIIDEADRILEIGFEEEMRQIIKLLPKRRQTMLFSA 176

                         170
                  ....*....|....*..
gi 2462533313 161 TQTQEVENLVRAGLRNP 177
Cdd:cd17942   177 TQTRKVEDLARISLKKK 193
PTZ00424 PTZ00424
helicase 45; Provisional
 3-333 5.52e-47

helicase 45; Provisional


Pssm-ID: 185609 [Multi-domain]  Cd Length: 401  Bit Score: 165.77  E-value: 5.52e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   3 NKDVAAEAVTGSGKTLAFVIPILEILlrrEEKLKKSQVgaIIITPTRELAIQIDEVlshfTKHFPEFSQI---LWIGGRN 79
Cdd:PTZ00424   65 GYDTIGQAQSGTGKTATFVIAALQLI---DYDLNACQA--LILAPTRELAQQIQKV----VLALGDYLKVrchACVGGTV 135

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  80 PGEDVERFKQqGGNIIVATPGRLEDMFRRKAEGLDlascvrSLDVLVLDEADRLLDMGFEASINTILEFLPKQRRTGLFS 159
Cdd:PTZ00424  136 VRDDINKLKA-GVHMVVGTPGRVYDMIDKRHLRVD------DLKLFILDEADEMLSRGFKGQIYDVFKKLPPDVQVALFS 208

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 160 ATQTQEVENLVRAGLRNPVRVSVKEKgvaassaQKTPSRLENYYMVCKADE-KFNQLVHFLRNHKQEKHLVFFSTCACVE 238
Cdd:PTZ00424  209 ATMPNEILELTTKFMRDPKRILVKKD-------ELTLEGIRQFYVAVEKEEwKFDTLCDLYETLTITQAIIYCNTRRKVD 281

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 239 YYGKALEVlvKGVKIMCIHGKMKYK-RNKIFMEFRKLQSGILVCTDVMARGIDIPEVNWVLQYDPPSNASAFVHRCGRTA 317
Cdd:PTZ00424  282 YLTKKMHE--RDFTVSCMHGDMDQKdRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSG 359

                         330
                  ....*....|....*.
gi 2462533313 318 RIGHGGSALVFLLPME 333
Cdd:PTZ00424  360 RFGRKGVAINFVTPDD 375
DEADc_DDX47 cd17954
DEAD-box helicase domain of DEAD box protein 47; DDX47 (also called E4-DEAD box protein) can ...
 3-181 5.30e-46

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: 157.09  E-value: 5.30e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   3 NKDVAAEAVTGSGKTLAFVIPILEILLRREEKLKksqvgAIIITPTRELAIQIDEVLSHFTKHFPEFSQILwIGGRNPGE 82
Cdd:cd17954    37 GRDIIGLAETGSGKTAAFALPILQALLENPQRFF-----ALVLAPTRELAQQISEQFEALGSSIGLKSAVL-VGGMDMMA 110

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  83 DVERFKQQgGNIIVATPGRLEDMFRRkAEGLDLascvRSLDVLVLDEADRLLDMGFEASINTILEFLPKQRRTGLFSATQ 162
Cdd:cd17954   111 QAIALAKK-PHVIVATPGRLVDHLEN-TKGFSL----KSLKFLVMDEADRLLNMDFEPEIDKILKVIPRERTTYLFSATM 184

                         170
                  ....*....|....*....
gi 2462533313 163 TQEVENLVRAGLRNPVRVS 181
Cdd:cd17954   185 TTKVAKLQRASLKNPVKIE 203
PRK04837 PRK04837
ATP-dependent RNA helicase RhlB; Provisional
 4-338 2.73e-45

ATP-dependent RNA helicase RhlB; Provisional


Pssm-ID: 235314 [Multi-domain]  Cd Length: 423  Bit Score: 161.68  E-value: 2.73e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   4 KDVAAEAVTGSGKTLAFVIPILEILLRRE--EKLKKSQVGAIIITPTRELAIQID---EVLSHFTKhfpeFSQILWIGGR 78
Cdd:PRK04837   46 RDVAGQAQTGTGKTMAFLTATFHYLLSHPapEDRKVNQPRALIMAPTRELAVQIHadaEPLAQATG----LKLGLAYGGD 121

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  79 npGEDVERFK-QQGGNIIVATPGRLEDMFRRKAEGLDlascvrSLDVLVLDEADRLLDMGFEASINTILEFLP--KQRRT 155
Cdd:PRK04837  122 --GYDKQLKVlESGVDILIGTTGRLIDYAKQNHINLG------AIQVVVLDEADRMFDLGFIKDIRWLFRRMPpaNQRLN 193

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 156 GLFSATQTQEVENLVRAGLRNPVRVSVKEKgvaassaQKTPSRL--ENYYMvcKADEKFNQLVHFLRNHKQEKHLVFFST 233
Cdd:PRK04837  194 MLFSATLSYRVRELAFEHMNNPEYVEVEPE-------QKTGHRIkeELFYP--SNEEKMRLLQTLIEEEWPDRAIIFANT 264

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 234 ---CACVEYYGKAlevlvKGVKIMCIHGKM-KYKRNKIFMEFRKLQSGILVCTDVMARGIDIPEVNWVLQYDPPSNASAF 309
Cdd:PRK04837  265 khrCEEIWGHLAA-----DGHRVGLLTGDVaQKKRLRILEEFTRGDLDILVATDVAARGLHIPAVTHVFNYDLPDDCEDY 339

                         330       340       350
                  ....*....|....*....|....*....|....*.
gi 2462533313 310 VHRCGRTARIGHGGSALVFL-------LPMEESYIN 338
Cdd:PRK04837  340 VHRIGRTGRAGASGHSISLAceeyalnLPAIETYIG 375
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 1-169 4.95e-45

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: 153.17  E-value: 4.95e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   1 MRNKDVAAEAVTGSGKTLAFVIPILEILLRREEKLKksqvgAIIITPTRELAIQIDEVLSHFTKHFpEFSQILWIGGRNP 80
Cdd:pfam00270  12 LEGRDVLVQAPTGSGKTLAFLLPALEALDKLDNGPQ-----ALVLAPTRELAEQIYEELKKLGKGL-GLKVASLLGGDSR 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  81 GEDVERFKqqGGNIIVATPGRLEDMFRRKAEgldlascVRSLDVLVLDEADRLLDMGFEASINTILEFLPKQRRTGLFSA 160
Cdd:pfam00270  86 KEQLEKLK--GPDILVGTPGRLLDLLQERKL-------LKNLKLLVLDEAHRLLDMGFGPDLEEILRRLPKKRQILLLSA 156


                  ....*....
gi 2462533313 161 TQTQEVENL 169
Cdd:pfam00270 157 TLPRNLEDL 165
DEADc_DDX41 cd17951
DEAD-box helicase domain of DEAD box protein 41; DDX41 (also called ABS and MPLPF) interacts ...
 4-180 3.19e-42

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: 147.49  E-value: 3.19e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   4 KDVAAEAVTGSGKTLAFVIPILEILLRREEKLKKSQVG---AIIITPTRELAIQIDEVLSHFTKH-----FPEFSQILWI 75
Cdd:cd17951    28 RDMIGIAFTGSGKTLVFTLPLIMFALEQEKKLPFIKGEgpyGLIVCPSRELARQTHEVIEYYCKAlqeggYPQLRCLLCI 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  76 GGRNPGEDVERFKQqGGNIIVATPGRLEDMFRRKAEGLDLasCvrslDVLVLDEADRLLDMGFEASINTILEFLPKQRRT 155
Cdd:cd17951   108 GGMSVKEQLEVIRK-GVHIVVATPGRLMDMLNKKKINLDI--C----RYLCLDEADRMIDMGFEEDIRTIFSYFKGQRQT 180

                         170       180
                  ....*....|....*....|....*
gi 2462533313 156 GLFSATQTQEVENLVRAGLRNPVRV 180
Cdd:cd17951   181 LLFSATMPKKIQNFAKSALVKPVTV 205
DEADc_DDX31 cd17949
DEAD-box helicase domain of DEAD box protein 31; DDX31 (also called helicain or G2 helicase) ...
 3-181 7.65e-42

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: 146.58  E-value: 7.65e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   3 NKDVAAEAVTGSGKTLAFVIPILEILLRREEKLKKSQ-VGAIIITPTRELAIQIDEVLSHFTKHFPefsqilWI------ 75
Cdd:cd17949    28 GRDVLVRSQTGSGKTLAYLLPIIQRLLSLEPRVDRSDgTLALVLVPTRELALQIYEVLEKLLKPFH------WIvpgyli 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  76 GGRNPGEDVERFKQqGGNIIVATPGRLEDMFRrKAEGLDLAScvrsLDVLVLDEADRLLDMGFEASINTILEFL------ 149
Cdd:cd17949   102 GGEKRKSEKARLRK-GVNILIATPGRLLDHLK-NTQSFDVSN----LRWLVLDEADRLLDMGFEKDITKILELLddkrsk 175

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 2462533313 150 -------PKQRRTGLFSATQTQEVENLVRAGLRNPVRVS 181
Cdd:cd17949   176 aggekskPSRRQTVLVSATLTDGVKRLAGLSLKDPVYID 214
PLN00206 PLN00206
DEAD-box ATP-dependent RNA helicase; Provisional
 1-329 9.77e-42

DEAD-box ATP-dependent RNA helicase; Provisional


Pssm-ID: 215103 [Multi-domain]  Cd Length: 518  Bit Score: 154.18  E-value: 9.77e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   1 MRNKDVAAEAVTGSGKTLAFVIPILE--ILLRREEKLKKSQVGAIIITPTRELAIQIDEVLSHFTKHFPeFSQILWIGGR 78
Cdd:PLN00206  156 LSGRSLLVSADTGSGKTASFLVPIISrcCTIRSGHPSEQRNPLAMVLTPTRELCVQVEDQAKVLGKGLP-FKTALVVGGD 234

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  79 NPGEDVERFkQQGGNIIVATPGRLEDMFRRKAEGLDLAScvrsldVLVLDEADRLLDMGFEASINTILEFLPkQRRTGLF 158
Cdd:PLN00206  235 AMPQQLYRI-QQGVELIVGTPGRLIDLLSKHDIELDNVS------VLVLDEVDCMLERGFRDQVMQIFQALS-QPQVLLF 306

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 159 SATQTQEVENLVRAGLRNPVRVSVKEKGVAASSAQKTPSRLEnyymvckADEKFNQLVHFL--RNHKQEKHLVFFSTCAC 236
Cdd:PLN00206  307 SATVSPEVEKFASSLAKDIILISIGNPNRPNKAVKQLAIWVE-------TKQKKQKLFDILksKQHFKPPAVVFVSSRLG 379

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 237 VEYYGKALEVlVKGVKIMCIHGK--MKyKRNKIFMEFRKLQSGILVCTDVMARGIDIPEVNWVLQYDPPSNASAFVHRCG 314
Cdd:PLN00206  380 ADLLANAITV-VTGLKALSIHGEksMK-ERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIG 457

                         330
                  ....*....|....*
gi 2462533313 315 RTARIGHGGSALVFL 329
Cdd:PLN00206  458 RASRMGEKGTAIVFV 472
DEADc_DDX23 cd17945
DEAD-box helicase domain of DEAD box protein 23; DDX23 (also called U5 snRNP 100kD protein and ...
 3-181 2.74e-41

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: 145.54  E-value: 2.74e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   3 NKDVAAEAVTGSGKTLAFVIPILEILLR---REEKLKKSQVGAIIITPTRELAIQIDEVLSHFTKHFPeFSQILWIGGRN 79
Cdd:cd17945    27 NRDIIGIAETGSGKTAAFLIPLLVYISRlppLDEETKDDGPYALILAPTRELAQQIEEETQKFAKPLG-IRVVSIVGGHS 105

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  80 PgEDVERFKQQGGNIIVATPGRLEDMFRRKAegLDLASCvrslDVLVLDEADRLLDMGFEASINTILEFLP--------- 150
Cdd:cd17945   106 I-EEQAFSLRNGCEILIATPGRLLDCLERRL--LVLNQC----TYVVLDEADRMIDMGFEPQVTKILDAMPvsnkkpdte 178

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2462533313 151 -----------KQRRTGLFSATQTQEVENLVRAGLRNPVRVS 181
Cdd:cd17945   179 eaeklaasgkhRYRQTMMFTATMPPAVEKIAKGYLRRPVVVT 220
DEADc_DDX3_DDX4 cd17967
DEAD-box helicase domain of ATP-dependent RNA helicases DDX3 and DDX4; This subfamily includes ...
 1-182 6.11e-41

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: 144.55  E-value: 6.11e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   1 MRNKDVAAEAVTGSGKTLAFVIPILEILLRREEKL-----KKSQVGAIIITPTRELAIQIDEVLSHFTKHFPEFSQILWi 75
Cdd:cd17967    35 LAGRDLMACAQTGSGKTAAFLLPIISKLLEDGPPSvgrgrRKAYPSALILAPTRELAIQIYEEARKFSYRSGVRSVVVY- 113

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  76 GGRNPGEDVERFkQQGGNIIVATPGRLEDMFRRKAEGLDlascvrSLDVLVLDEADRLLDMGFEASINTILEF--LPK-- 151
Cdd:cd17967   114 GGADVVHQQLQL-LRGCDILVATPGRLVDFIERGRISLS------SIKFLVLDEADRMLDMGFEPQIRKIVEHpdMPPkg 186

                         170       180       190
                  ....*....|....*....|....*....|.
gi 2462533313 152 QRRTGLFSATQTQEVENLVRAGLRNPVRVSV 182
Cdd:cd17967   187 ERQTLMFSATFPREIQRLAADFLKNYIFLTV 217
DEXDc smart00487
DEAD-like helicases superfamily;
2-185 2.56e-40

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 142.25  E-value: 2.56e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313    2 RNKDVAAEAVTGSGKTLAFVIPILEILLRREEKlkksqvGAIIITPTRELAIQIDEVLSHFTKHFPeFSQILWIGGRNPG 81
Cdd:smart00487  23 GLRDVILAAPTGSGKTLAALLPALEALKRGKGG------RVLVLVPTRELAEQWAEELKKLGPSLG-LKVVGLYGGDSKR 95

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   82 EDVERFKQQGGNIIVATPGRLEDMFRRKAEGLdlascvRSLDVLVLDEADRLLDMGFEASINTILEFLPKQRRTGLFSAT 161
Cdd:smart00487  96 EQLRKLESGKTDILVTTPGRLLDLLENDKLSL------SNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLLLLSAT 169

                          170       180
                   ....*....|....*....|....
gi 2462533313  162 QTQEVENLVRAGLRNPVRVSVKEK 185
Cdd:smart00487 170 PPEEIENLLELFLNDPVFIDVGFT 193
DEADc_DDX54 cd17959
DEAD-box helicase domain of DEAD box protein 54; DDX54 interacts in a hormone-dependent manner ...
 1-180 5.82e-39

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: 138.59  E-value: 5.82e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   1 MRNKDVAAEAVTGSGKTLAFVIPILEILLRREeklKKSQVGAIIITPTRELAIQIdevlSHFTKHFPEFSQILWI---GG 77
Cdd:cd17959    36 LDGRDVVAMARTGSGKTAAFLIPMIEKLKAHS---PTVGARALILSPTRELALQT----LKVTKELGKFTDLRTAllvGG 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  78 rnpgedvERFKQQGG------NIIVATPGRLedmFRRKAE-GLDLascvRSLDVLVLDEADRLLDMGFEASINTILEFLP 150
Cdd:cd17959   109 -------DSLEEQFEalasnpDIIIATPGRL---LHLLVEmNLKL----SSVEYVVFDEADRLFEMGFAEQLHEILSRLP 174

                         170       180       190
                  ....*....|....*....|....*....|
gi 2462533313 151 KQRRTGLFSATQTQEVENLVRAGLRNPVRV 180
Cdd:cd17959   175 ENRQTLLFSATLPKLLVEFAKAGLNEPVLI 204
DEADc_DDX49 cd17955
DEAD-box helicase domain of DEAD box protein 49; DDX49 (also called Dbp8) is a member of the ...
 4-178 2.27e-38

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: 136.97  E-value: 2.27e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   4 KDVAAEAVTGSGKTLAFVIPILEILlrREEKlkkSQVGAIIITPTRELAIQIDEVLSHFTKhFPEFSQILWIGGRNPGED 83
Cdd:cd17955    37 RDVIGGAKTGSGKTAAFALPILQRL--SEDP---YGIFALVLTPTRELAYQIAEQFRALGA-PLGLRCCVIVGGMDMVKQ 110

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  84 VERFKQQGgNIIVATPGRLEDMFRrkaEGLDLASCVRSLDVLVLDEADRLLDMGFEASINTILEFLPKQRRTGLFSATQT 163
Cdd:cd17955   111 ALELSKRP-HIVVATPGRLADHLR---SSDDTTKVLSRVKFLVLDEADRLLTGSFEDDLATILSALPPKRQTLLFSATLT 186

                         170
                  ....*....|....*
gi 2462533313 164 QEVENLVRAGLRNPV 178
Cdd:cd17955   187 DALKALKELFGNKPF 201
DEADc_EIF4A cd17939
DEAD-box helicase domain of eukaryotic initiation factor 4A; The eukaryotic initiation ...
 4-180 2.63e-37

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: 134.37  E-value: 2.63e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   4 KDVAAEAVTGSGKTLAFVIPILEILLRREEKLKksqvgAIIITPTRELAIQIDEVLSHFTKHFPEFSQILwIGGRNPGED 83
Cdd:cd17939    35 RDVIAQAQSGTGKTATFSIGALQRIDTTVRETQ-----ALVLAPTRELAQQIQKVVKALGDYMGVKVHAC-IGGTSVRED 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  84 VERFkQQGGNIIVATPGRLEDMFRRKAegldlaSCVRSLDVLVLDEADRLLDMGFEASINTILEFLPKQRRTGLFSATQT 163
Cdd:cd17939   109 RRKL-QYGPHIVVGTPGRVFDMLQRRS------LRTDKIKMFVLDEADEMLSRGFKDQIYDIFQFLPPETQVVLFSATMP 181

                         170
                  ....*....|....*..
gi 2462533313 164 QEVENLVRAGLRNPVRV 180
Cdd:cd17939   182 HEVLEVTKKFMRDPVRI 198
DEADc_DDX52 cd17957
DEAD-box helicase domain of DEAD box protein 52; DDX52 (also called ROK1 and HUSSY19) is ...
 2-182 3.76e-36

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: 131.17  E-value: 3.76e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   2 RNKDVAAEAVTGSGKTLAFVIPILEILLRREeklKKSQVGAIIITPTRELAIQIDEVLSHFTKHFPeFSQILWIGGRNPG 81
Cdd:cd17957    26 HGRDLLACAPTGSGKTLAFLIPILQKLGKPR---KKKGLRALILAPTRELASQIYRELLKLSKGTG-LRIVLLSKSLEAK 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  82 EDVERFKQQGGNIIVATPGRLEDMFRRKAegLDLAscvrSLDVLVLDEADRLLDMGFEASINTILEFLP-KQRRTGLFSA 160
Cdd:cd17957   102 AKDGPKSITKYDILVSTPLRLVFLLKQGP--IDLS----SVEYLVLDEADKLFEPGFREQTDEILAACTnPNLQRSLFSA 175

                         170       180
                  ....*....|....*....|..
gi 2462533313 161 TQTQEVENLVRAGLRNPVRVSV 182
Cdd:cd17957   176 TIPSEVEELARSVMKDPIRIIV 197
DEADc_DDX42 cd17952
DEAD-box helicase domain of DEAD box protein 42; DDX42 (also called Splicing Factor ...
 1-181 5.32e-36

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: 130.61  E-value: 5.32e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   1 MRNKDVAAEAVTGSGKTLAFVIPILEILLRREEKLKKSQVGAIIITPTRELAIQIDEVLSHFTKHFpEFSQILWIGGRNP 80
Cdd:cd17952    25 LSGRDMIGIAKTGSGKTAAFIWPMLVHIMDQRELEKGEGPIAVIVAPTRELAQQIYLEAKKFGKAY-NLRVVAVYGGGSK 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  81 GEDVERFKQqGGNIIVATPGRLEDMFRRKAEGLDLAScvrsldVLVLDEADRLLDMGFEASINTILEFLPKQRRTGLFSA 160
Cdd:cd17952   104 WEQAKALQE-GAEIVVATPGRLIDMVKKKATNLQRVT------YLVLDEADRMFDMGFEYQVRSIVGHVRPDRQTLLFSA 176

                         170       180
                  ....*....|....*....|.
gi 2462533313 161 TQTQEVENLVRAGLRNPVRVS 181
Cdd:cd17952   177 TFKKKIEQLARDILSDPIRVV 197
DEADc_DDX24 cd17946
DEAD-box helicase domain of DEAD box protein 24; The human DDX24 gene encodes a DEAD box ...
 4-223 7.45e-36

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: 131.59  E-value: 7.45e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   4 KDVAAEAVTGSGKTLAFVIPILEILLRREEKLKKSQ----VGAIIITPTRELAIQIDEVLSHFTKHfPEFSQILWIGGRN 79
Cdd:cd17946    29 KDVIGAAETGSGKTLAFGIPILERLLSQKSSNGVGGkqkpLRALILTPTRELAVQVKDHLKAIAKY-TNIKIASIVGGLA 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  80 PgEDVERFKQQGGNIIVATPGRLEDMFrrkAEGLDLASCVRSLDVLVLDEADRLLDMGFEASINTILEFLP-------KQ 152
Cdd:cd17946   108 V-QKQERLLKKRPEIVVATPGRLWELI---QEGNEHLANLKSLRFLVLDEADRMLEKGHFAELEKILELLNkdragkkRK 183

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462533313 153 RRTGLFSATQTQEvenlvragLRNPVRVSVKEKgvaaSSAQKTPSRLENyymvckadekFNQLVHFLRNHK 223
Cdd:cd17946   184 RQTFVFSATLTLD--------HQLPLKLNSKKK----KKKKEKKQKLEL----------LIEKVGFRKKPK 232
DEADc_DDX56 cd17961
DEAD-box helicase domain of DEAD box protein 56; DDX56 is a helicase required for assembly of ...
 4-178 1.24e-35

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: 130.01  E-value: 1.24e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   4 KDVAAEAVTGSGKTLAFVIPILE-ILLRREEKLKKSQVGAIIITPTRELAIQIDEVLSHFTKHFPEFSQILWIGGrNPGE 82
Cdd:cd17961    32 KDILARARTGSGKTAAYALPIIQkILKAKAESGEEQGTRALILVPTRELAQQVSKVLEQLTAYCRKDVRVVNLSA-SSSD 110

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  83 DVERFKQQGG-NIIVATPGRLEDMFRRKAEGLdlascVRSLDVLVLDEADRLLDMGFEASINTILEFLPKQRRTGLFSAT 161
Cdd:cd17961   111 SVQRALLAEKpDIVVSTPARLLSHLESGSLLL-----LSTLKYLVIDEADLVLSYGYEEDLKSLLSYLPKNYQTFLMSAT 185

                         170
                  ....*....|....*..
gi 2462533313 162 QTQEVENLVRAGLRNPV 178
Cdd:cd17961   186 LSEDVEALKKLVLHNPA 202
DEADc_DDX6 cd17940
DEAD-box helicase domain of DEAD box protein 6; DEAD box protein 6 (DDX6, also known as Rck or ...
 3-180 1.83e-35

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: 129.34  E-value: 1.83e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   3 NKDVAAEAVTGSGKTLAFVIPILEILlrreeKLKKSQVGAIIITPTRELAIQIDEVLSHFTKHfPEFSQILWIGGRNPGE 82
Cdd:cd17940    36 GRDILARAKNGTGKTGAYLIPILEKI-----DPKKDVIQALILVPTRELALQTSQVCKELGKH-MGVKVMVTTGGTSLRD 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  83 DVERFkQQGGNIIVATPGRLEDMFRRKAegLDLASCVrsldVLVLDEADRLLDMGFEASINTILEFLPKQRRTGLFSATQ 162
Cdd:cd17940   110 DIMRL-YQTVHVLVGTPGRILDLAKKGV--ADLSHCK----TLVLDEADKLLSQDFQPIIEKILNFLPKERQILLFSATF 182

                         170
                  ....*....|....*...
gi 2462533313 163 TQEVENLVRAGLRNPVRV 180
Cdd:cd17940   183 PLTVKNFMDRHMHNPYEI 200
DEADc_DDX4 cd18052
DEAD-box helicase domain of DEAD box protein 4; DEAD box protein 4 (DDX4, also known as VASA ...
 1-175 2.35e-35

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: 130.86  E-value: 2.35e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   1 MRNKDVAAEAVTGSGKTLAFVIPILEILLRreEKLKKSQVG------AIIITPTRELAIQIDEVLSHFTKHFPEFSQILW 74
Cdd:cd18052    78 LAGRDLMACAQTGSGKTAAFLLPVLTGMMK--EGLTASSFSevqepqALIVAPTRELANQIFLEARKFSYGTCIRPVVVY 155

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  75 iGGRNPGEDVERFkQQGGNIIVATPGRLEDMFRRKAEGLDlascvrSLDVLVLDEADRLLDMGFEASINTILEFL---PK 151
Cdd:cd18052   156 -GGVSVGHQIRQI-EKGCHILVATPGRLLDFIGRGKISLS------KLKYLILDEADRMLDMGFGPEIRKLVSEPgmpSK 227

                         170       180
                  ....*....|....*....|....*
gi 2462533313 152 QRR-TGLFSATQTQEVENLVRAGLR 175
Cdd:cd18052   228 EDRqTLMFSATFPEEIQRLAAEFLK 252
DEADc_DDX20 cd17943
DEAD-box helicase domain of DEAD box protein 20; DDX20 (also called DEAD Box Protein DP 103, ...
 5-181 1.94e-34

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: 126.22  E-value: 1.94e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   5 DVAAEAVTGSGKTLAFVIPILEILLRReeklkKSQVGAIIITPTRELAIQIDEVLSHFTKHFPEFSQILWIGGRNPGEDV 84
Cdd:cd17943    29 DLIVQAKSGTGKTLVFVVIALESLDLE-----RRHPQVLILAPTREIAVQIHDVFKKIGKKLEGLKCEVFIGGTPVKEDK 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  85 ERFKqqGGNIIVATPGRLEDMFRrkaeglDLASCVRSLDVLVLDEADRLLDMGFEASINTILEFLPKQRRTGLFSATQTQ 164
Cdd:cd17943   104 KKLK--GCHIAVGTPGRIKQLIE------LGALNVSHVRLFVLDEADKLMEGSFQKDVNWIFSSLPKNKQVIAFSATYPK 175

                         170
                  ....*....|....*..
gi 2462533313 165 EVENLVRAGLRNPVRVS 181
Cdd:cd17943   176 NLDNLLARYMRKPVLVR 192
DEADc_DDX1 cd17938
DEAD-box helicase domain of DEAD box protein 1; DEAD box protein 1 (DDX1) acts as an ...
 5-180 2.00e-33

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: 123.97  E-value: 2.00e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   5 DVAAEAVTGSGKTLAFVIPILEIllrreeklkksqVGAIIITPTRELAIQIDEVLSHFTKHF--PEFSQILWIGGRNPGE 82
Cdd:cd17938    38 DVLMAAETGSGKTGAFCLPVLQI------------VVALILEPSRELAEQTYNCIENFKKYLdnPKLRVALLIGGVKARE 105

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  83 DVERFkQQGGNIIVATPGRLEDMFRRkaeGLDLASCVRsldVLVLDEADRLLDMGFEASINTILEFLPKQRRTG------ 156
Cdd:cd17938   106 QLKRL-ESGVDIVVGTPGRLEDLIKT---GKLDLSSVR---FFVLDEADRLLSQGNLETINRIYNRIPKITSDGkrlqvi 178

                         170       180
                  ....*....|....*....|....*
gi 2462533313 157 LFSAT-QTQEVENLVRAGLRNPVRV 180
Cdd:cd17938   179 VCSATlHSFEVKKLADKIMHFPTWV 203
DEADc_DDX3 cd18051
DEAD-box helicase domain of DEAD box protein 3; DDX3 (also called helicase-like protein, DEAD ...
 3-176 7.79e-33

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: 124.00  E-value: 7.79e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   3 NKDVAAEAVTGSGKTLAFVIPIL-EILLRREEKLKKSQVG----------AIIITPTRELAIQI-DEvlshfTKHFPEFS 70
Cdd:cd18051    58 KRDLMACAQTGSGKTAAFLLPILsQIYEQGPGESLPSESGyygrrkqyplALVLAPTRELASQIyDE-----ARKFAYRS 132

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  71 QI---LWIGGRNPGE---DVERfkqqGGNIIVATPGRLEDMFRRKAEGLDlasCVRsldVLVLDEADRLLDMGFEASINT 144
Cdd:cd18051   133 RVrpcVVYGGADIGQqmrDLER----GCHLLVATPGRLVDMLERGKIGLD---YCK---YLVLDEADRMLDMGFEPQIRR 202

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 2462533313 145 ILE--FLPK--QRRTGLFSATQTQEVENLVRAGLRN 176
Cdd:cd18051   203 IVEqdTMPPtgERQTLMFSATFPKEIQMLARDFLDN 238
DEADc_DDX46 cd17953
DEAD-box helicase domain of DEAD box protein 46; DDX46 (also called Prp5-like DEAD-box protein) ...
 1-180 9.21e-33

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: 122.87  E-value: 9.21e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   1 MRNKDVAAEAVTGSGKTLAFVIPIL-EILLRREEKLKKSQVGaIIITPTRELAIQIdevlshfTKHFPEFSQILWI---- 75
Cdd:cd17953    47 MSGRDVIGIAKTGSGKTLAFLLPMFrHIKDQRPVKPGEGPIG-LIMAPTRELALQI-------YVECKKFSKALGLrvvc 118

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  76 --GGRNPGEDVERFKQqGGNIIVATPGRLEDMFrrKAEGLDLAScVRSLDVLVLDEADRLLDMGFEASINTILEFLPKQR 153
Cdd:cd17953   119 vyGGSGISEQIAELKR-GAEIVVCTPGRMIDIL--TANNGRVTN-LRRVTYVVLDEADRMFDMGFEPQIMKIVNNIRPDR 194

                         170       180
                  ....*....|....*....|....*..
gi 2462533313 154 RTGLFSATQTQEVENLVRAGLRNPVRV 180
Cdd:cd17953   195 QTVLFSATFPRKVEALARKVLHKPIEI 221
DEADc_DDX5_DDX17 cd17966
DEAD-box helicase domain of ATP-dependent RNA helicases DDX5 and DDX17; DDX5 and DDX17 are ...
 1-181 3.14e-32

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: 120.55  E-value: 3.14e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   1 MRNKDVAAEAVTGSGKTLAFVIP-ILEI----LLRREEklkksqvGAI--IITPTRELAIQIDEVLSHFTKHFPEFSQIL 73
Cdd:cd17966    25 LSGRDMVGIAQTGSGKTLAFLLPaIVHInaqpPLERGD-------GPIvlVLAPTRELAQQIQQEANKFGGSSRLRNTCV 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  74 WiGGRNPGEDVeRFKQQGGNIIVATPGRLEDMFRRKAEGLdlascvRSLDVLVLDEADRLLDMGFEASINTILEFLPKQR 153
Cdd:cd17966    98 Y-GGAPKGPQI-RDLRRGVEICIATPGRLIDFLDQGKTNL------RRVTYLVLDEADRMLDMGFEPQIRKIVDQIRPDR 169

                         170       180
                  ....*....|....*....|....*...
gi 2462533313 154 RTGLFSATQTQEVENLVRAGLRNPVRVS 181
Cdd:cd17966   170 QTLMWSATWPKEVRRLAEDFLKDYIQVN 197
DEADc_DDX59 cd17962
DEAD-box helicase domain of DEAD box protein 59; DDX59 plays an important role in lung cancer ...
 4-181 4.94e-32

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: 119.96  E-value: 4.94e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   4 KDVAAEAVTGSGKTLAFVIPILEILLRreeklKKSQVGAIIITPTRELAIQIDEVLSHFTKHFPEFSQILWIGGRNPGED 83
Cdd:cd17962    28 RDILASADTGSGKTAAFLLPVIIRCLT-----EHRNPSALILTPTRELAVQIEDQAKELMKGLPPMKTALLVGGLPLPPQ 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  84 VERFkQQGGNIIVATPGRLEDMFRRKAEGLDlascvrSLDVLVLDEADRLLDMGFEASINTILEFLPKQRRTGLFSATQT 163
Cdd:cd17962   103 LYRL-QQGVKVIIATPGRLLDILKQSSVELD------NIKIVVVDEADTMLKMGFQQQVLDILENISHDHQTILVSATIP 175

                         170
                  ....*....|....*...
gi 2462533313 164 QEVENLVRAGLRNPVRVS 181
Cdd:cd17962   176 RGIEQLAGQLLQNPVRIT 193
DEADc_DDX51 cd17956
DEAD-box helicase domain of DEAD box protein 51; DDX51 aids cell cancer proliferation by ...
 2-177 1.73e-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: 116.96  E-value: 1.73e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   2 RNKDVAAEAVTGSGKTLAFVIPILEILLRReeklKKSQVGAIIITPTRELAIQIDEVLSHFTKHFPefSQILWIGGRN-- 79
Cdd:cd17956    35 RPGDLCVSAPTGSGKTLAYVLPIVQALSKR----VVPRLRALIVVPTKELVQQVYKVFESLCKGTG--LKVVSLSGQKsf 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  80 PGEDVERFKQQGGN------IIVATPGRLEDMFRRKaEGLDLascvRSLDVLVLDEADRLLDMGFE-------------- 139
Cdd:cd17956   109 KKEQKLLLVDTSGRylsrvdILVATPGRLVDHLNST-PGFTL----KHLRFLVIDEADRLLNQSFQdwletvmkalgrpt 183

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 2462533313 140 ------ASINTILEFLPKQRRTGLFSATQTQEVENLVRAGLRNP 177
Cdd:cd17956   184 apdlgsFGDANLLERSVRPLQKLLFSATLTRDPEKLSSLKLHRP 227
DEADc_DDX43_DDX53 cd17958
DEAD-box helicase domain of DEAD box proteins 43 and 53; DDX43 (also called cancer/testis ...
 1-180 3.04e-30

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: 115.25  E-value: 3.04e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   1 MRNKDVAAEAVTGSGKTLAFVIP-ILEILLRREEKLKKSQVGAIIITPTRELAIQIDEVLSHFTkhFPEFSQILWIGGRN 79
Cdd:cd17958    25 LQGIDLIGVAQTGTGKTLAYLLPgFIHLDLQPIPREQRNGPGVLVLTPTRELALQIEAECSKYS--YKGLKSVCVYGGGN 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  80 PGEDVERFKQqGGNIIVATPGRLEDMFRRKAEGLDlascvrSLDVLVLDEADRLLDMGFEASINTILEFLPKQRRTGLFS 159
Cdd:cd17958   103 RNEQIEDLSK-GVDIIIATPGRLNDLQMNNVINLK------SITYLVLDEADRMLDMGFEPQIRKILLDIRPDRQTIMTS 175

                         170       180
                  ....*....|....*....|.
gi 2462533313 160 ATQTQEVENLVRAGLRNPVRV 180
Cdd:cd17958   176 ATWPDGVRRLAQSYLKDPMIV 196
DEADc_EIF4AIII_DDX48 cd18045
DEAD-box helicase domain of eukaryotic initiation factor 4A-III; Eukaryotic initiation factor ...
 1-180 5.08e-30

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: 114.87  E-value: 5.08e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   1 MRNKDVAAEAVTGSGKTLAFVIPILEILlrrEEKLKKSQVgaIIITPTRELAIQIDEVLSHFTkHFPEFSQILWIGGRNP 80
Cdd:cd18045    34 IKGRDVIAQSQSGTGKTATFSISVLQCL---DIQVRETQA--LILSPTRELAVQIQKVLLALG-DYMNVQCHACIGGTSV 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  81 GEDVERFkQQGGNIIVATPGRLEDMFRRKAEGldlascVRSLDVLVLDEADRLLDMGFEASINTILEFLPKQRRTGLFSA 160
Cdd:cd18045   108 GDDIRKL-DYGQHIVSGTPGRVFDMIRRRSLR------TRHIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLVSA 180

                         170       180
                  ....*....|....*....|
gi 2462533313 161 TQTQEVENLVRAGLRNPVRV 180
Cdd:cd18045   181 TLPQDILEMTNKFMTDPIRI 200
DEADc_EIF4AII_EIF4AI_DDX2 cd18046
DEAD-box helicase domain of eukaryotic initiation factor 4A-I and 4-II; Eukaryotic initiation ...
 1-180 8.36e-30

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: 114.08  E-value: 8.36e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   1 MRNKDVAAEAVTGSGKTLAFVIPILEillRREEKLKKSQvgAIIITPTRELAIQIDEVLSHFTKHFpEFSQILWIGGRNP 80
Cdd:cd18046    34 IKGYDVIAQAQSGTGKTATFSISILQ---QIDTSLKATQ--ALVLAPTRELAQQIQKVVMALGDYM-GIKCHACIGGTSV 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  81 GEDVERFkQQGGNIIVATPGRLEDMFRRKAEGLDlascvrSLDVLVLDEADRLLDMGFEASINTILEFLPKQRRTGLFSA 160
Cdd:cd18046   108 RDDAQKL-QAGPHIVVGTPGRVFDMINRRYLRTD------YIKMFVLDEADEMLSRGFKDQIYDIFQKLPPDTQVVLLSA 180

                         170       180
                  ....*....|....*....|
gi 2462533313 161 TQTQEVENLVRAGLRNPVRV 180
Cdd:cd18046   181 TMPNDVLEVTTKFMRDPIRI 200
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 210-320 2.12e-28

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: 107.30  E-value: 2.12e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 210 EKFNQLVHFLRNHKQEKHLVFFSTCACVEYygKALEVLvKGVKIMCIHGKMKYK-RNKIFMEFRKLQSGILVCTDVMARG 288
Cdd:pfam00271   1 EKLEALLELLKKERGGKVLIFSQTKKTLEA--ELLLEK-EGIKVARLHGDLSQEeREEILEDFRKGKIDVLVATDVAERG 77

                          90       100       110
                  ....*....|....*....|....*....|..
gi 2462533313 289 IDIPEVNWVLQYDPPSNASAFVHRCGRTARIG 320
Cdd:pfam00271  78 LDLPDVDLVINYDLPWNPASYIQRIGRAGRAG 109
DEADc_DDX39 cd17950
DEAD-box helicase domain of DEAD box protein 39; DDX39A is involved in pre-mRNA splicing and ...
 1-182 4.92e-27

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: 107.05  E-value: 4.92e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   1 MRNKDVAAEAVTGSGKTLAFVIPILEILlrreeKLKKSQVGAIIITPTRELAIQIDEVLSHFTKHFPEFSQILWIGGRNP 80
Cdd:cd17950    37 ILGMDVLCQAKSGMGKTAVFVLSTLQQL-----EPVDGQVSVLVICHTRELAFQISNEYERFSKYMPNVKTAVFFGGVPI 111

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  81 GEDVERFKQQGGNIIVATPGRLEDMFRRKAegLDLascvRSLDVLVLDEADRLL-DMGFEASINTILEFLPKQRRTGLFS 159
Cdd:cd17950   112 KKDIEVLKNKCPHIVVGTPGRILALVREKK--LKL----SHVKHFVLDECDKMLeQLDMRRDVQEIFRATPHDKQVMMFS 185

                         170       180
                  ....*....|....*....|...
gi 2462533313 160 ATQTQEVENLVRAGLRNPVRVSV 182
Cdd:cd17950   186 ATLSKEIRPVCKKFMQDPLEIFV 208
DEADc_DDX19_DDX25 cd17963
DEAD-box helicase domain of ATP-dependent RNA helicases DDX19 and DDX25; DDX19 (also called ...
 8-171 7.37e-25

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: 100.73  E-value: 7.37e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   8 AEAVTGSGKTLAFVIPILEillRREEKLKKSQvgAIIITPTRELAIQIDEVLSHFTKhFPEFSQILWIggrnPGEDVERF 87
Cdd:cd17963    38 AQSQSGTGKTAAFVLAMLS---RVDPTLKSPQ--ALCLAPTRELARQIGEVVEKMGK-FTGVKVALAV----PGNDVPRG 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  88 KQQGGNIIVATPGRLEDMFRRKAegLDLascvRSLDVLVLDEADRLLDM-GFEASINTILEFLPKQRRTGLFSATQTQEV 166
Cdd:cd17963   108 KKITAQIVIGTPGTVLDWLKKRQ--LDL----KKIKILVLDEADVMLDTqGHGDQSIRIKRMLPRNCQILLFSATFPDSV 181


                  ....*
gi 2462533313 167 ENLVR 171
Cdd:cd17963   182 RKFAE 186
DEADc_DDX5 cd18049
DEAD-box helicase domain of DEAD box protein 5; DDX5 (also called RNA helicase P68, HLR1, ...
 1-182 9.59e-24

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: 98.54  E-value: 9.59e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   1 MRNKDVAAEAVTGSGKTLAFVIPILeILLRREEKLKKSQvGAI--IITPTRELAIQIDEVLSHFTKHFPEFSQILWiGGR 78
Cdd:cd18049    59 LSGLDMVGVAQTGSGKTLSYLLPAI-VHINHQPFLERGD-GPIclVLAPTRELAQQVQQVAAEYGRACRLKSTCIY-GGA 135

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  79 NPGEDVeRFKQQGGNIIVATPGRLEDMFrrKAEGLDLASCVrsldVLVLDEADRLLDMGFEASINTILEFLPKQRRTGLF 158
Cdd:cd18049   136 PKGPQI-RDLERGVEICIATPGRLIDFL--EAGKTNLRRCT----YLVLDEADRMLDMGFEPQIRKIVDQIRPDRQTLMW 208

                         170       180
                  ....*....|....*....|....
gi 2462533313 159 SATQTQEVENLVRAGLRNPVRVSV 182
Cdd:cd18049   209 SATWPKEVRQLAEDFLKDYIHINI 232
DEADc_DDX21_DDX50 cd17944
DEAD-box helicase domain of DEAD box proteins 21 and 50; DDX21 (also called Gu-Alpha and ...
 4-175 1.14e-23

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: 97.61  E-value: 1.14e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   4 KDVAAEAVTGSGKTLAFVIPILEILLRREEKLKKSQV-GAIIITPTRELAIQIDEVLSHFTKhfpEFSQILWIGGRNPGE 82
Cdd:cd17944    28 KDLIAQARTGTGKTFSFAIPLIEKLQEDQQPRKRGRApKVLVLAPTRELANQVTKDFKDITR---KLSVACFYGGTPYQQ 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  83 DVERFKqQGGNIIVATPGRLEDMFRRKAegLDLAscvrSLDVLVLDEADRLLDMGFEASINTILEFLPKQR-----RTGL 157
Cdd:cd17944   105 QIFAIR-NGIDILVGTPGRIKDHLQNGR--LDLT----KLKHVVLDEVDQMLDMGFAEQVEEILSVSYKKDsednpQTLL 177

                         170
                  ....*....|....*...
gi 2462533313 158 FSATQTQEVENLVRAGLR 175
Cdd:cd17944   178 FSATCPDWVYNVAKKYMK 195
DEADc_DDX17 cd18050
DEAD-box helicase domain of DEAD box protein 17; DDX17 (also called DEAD Box Protein P72 or ...
 1-182 1.98e-23

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: 98.54  E-value: 1.98e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   1 MRNKDVAAEAVTGSGKTLAFVIPILeILLRREEKLKKSQvGAI--IITPTRELAIQIDEVLSHFTKHFPEFSQILWiGGR 78
Cdd:cd18050    97 LSGRDMVGIAQTGSGKTLAYLLPAI-VHINHQPYLERGD-GPIclVLAPTRELAQQVQQVADDYGKSSRLKSTCIY-GGA 173

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  79 NPGEDVeRFKQQGGNIIVATPGRLEDMFRRKAEGLdlascvRSLDVLVLDEADRLLDMGFEASINTILEFLPKQRRTGLF 158
Cdd:cd18050   174 PKGPQI-RDLERGVEICIATPGRLIDFLEAGKTNL------RRCTYLVLDEADRMLDMGFEPQIRKIVDQIRPDRQTLMW 246

                         170       180
                  ....*....|....*....|....
gi 2462533313 159 SATQTQEVENLVRAGLRNPVRVSV 182
Cdd:cd18050   247 SATWPKEVRQLAEDFLRDYVQINI 270
HELICc smart00490
helicase superfamily c-terminal domain;
249-320 6.13e-23

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 91.89  E-value: 6.13e-23
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462533313  249 KGVKIMCIHGKMKYK-RNKIFMEFRKLQSGILVCTDVMARGIDIPEVNWVLQYDPPSNASAFVHRCGRTARIG 320
Cdd:smart00490  10 LGIKVARLHGGLSQEeREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGRAG 82
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
2-377 7.15e-21

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


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 94.71  E-value: 7.15e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   2 RNKDVAAEAVTGSGKTLAFVIPILEILLRREeklkksqvgAIIITPTRELAIQIdevLSHFTKHFPEFsqilwiggrnpg 81
Cdd:COG1061    99 GGGRGLVVAPTGTGKTVLALALAAELLRGKR---------VLVLVPRRELLEQW---AEELRRFLGDP------------ 154

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  82 EDVERFKQQGGNIIVATPgrleDMFRRKAEgldLASCVRSLDVLVLDEADRLLDMGFEAsintILEFLPKQRRTGLfSAT 161
Cdd:COG1061   155 LAGGGKKDSDAPITVATY----QSLARRAH---LDELGDRFGLVIIDEAHHAGAPSYRR----ILEAFPAAYRLGL-TAT 222

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 162 ------QTQEVEN------------LVRAG-LRNPVRVSVKEKGVAASSAQKTPSRLENYYMVCKADEKFNQLVHFLRNH 222
Cdd:COG1061   223 pfrsdgREILLFLfdgivyeyslkeAIEDGyLAPPEYYGIRVDLTDERAEYDALSERLREALAADAERKDKILRELLREH 302

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 223 KQEKH-LVFFSTCACVEYYGKALEVlvKGVKIMCIHGKMKYK-RNKIFMEFRKLQSGILVCTDVMARGIDIPEVNWVLQY 300
Cdd:COG1061   303 PDDRKtLVFCSSVDHAEALAELLNE--AGIRAAVVTGDTPKKeREEILEAFRDGELRILVTVDVLNEGVDVPRLDVAILL 380

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 301 DPPSNASAFVHRCGRTARIGHGGSALVFL------LPMEESYINFLAINQKCPLQEMKPQRNTADLLPKLKSMALADRAV 374
Cdd:COG1061   381 RPTGSPREFIQRLGRGLRPAPGKEDALVYdfvgndVPVLEELAKDLRDLAGYRVEFLDEEESEELALLIAVKPALEVKGE 460


                  ...
gi 2462533313 375 FEK 377
Cdd:COG1061   461 LEE 463
DEADc_DDX28 cd17948
DEAD-box helicase domain of DEAD box protein 28; DDX28 (also called mitochondrial DEAD-box ...
 2-181 4.06e-20

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: 88.58  E-value: 4.06e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   2 RNKDVAAEavTGSGKTLAFVIPILEILLRREEKLKKSQVG--AIIITPTRELAIQIDEVLSHFTKHFPEFSQILwIGGRN 79
Cdd:cd17948    28 RNTLCAAE--TGSGKTLTYLLPIIQRLLRYKLLAEGPFNAprGLVITPSRELAEQIGSVAQSLTEGLGLKVKVI-TGGRT 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  80 PGeDVERFKQQGGNIIVATPGRLEDMFRRKAEGLDLASCvrsldvLVLDEADRLLDMGFEASINTILE-----FLPKQRR 154
Cdd:cd17948   105 KR-QIRNPHFEEVDILVATPGALSKLLTSRIYSLEQLRH------LVLDEADTLLDDSFNEKLSHFLRrfplaSRRSENT 177

                         170       180
                  ....*....|....*....|....*..
gi 2462533313 155 TGLFSATQtqevenLVRAGLRNPVRVS 181
Cdd:cd17948   178 DGLDPGTQ------LVLVSATMPSGVG 198
DEADc_MRH4 cd17965
DEAD-box helicase domain of ATP-dependent RNA helicase MRH4; Mitochondrial RNA helicase 4 ...
 6-171 3.31e-17

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: 80.50  E-value: 3.31e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   6 VAAEavTGSGKTLAFVIPILEILLRRE-----------EKLKK-SQVGAIIITPTRELAIQIDEVLSHFtKHFPEFS--Q 71
Cdd:cd17965    66 LAAE--TGSGKTLAYLAPLLDYLKRQEqepfeeaeeeyESAKDtGRPRSVILVPTHELVEQVYSVLKKL-SHTVKLGikT 142

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  72 ILWIGGRNPGEDVERFKqQGGNIIVATPGRLEDMFrrKAEGLDLASCvrslDVLVLDEADRLLDMGFEASINTILEFLPK 151
Cdd:cd17965   143 FSSGFGPSYQRLQLAFK-GRIDILVTTPGKLASLA--KSRPKILSRV----THLVVDEADTLFDRSFLQDTTSIIKRAPK 215

                         170       180
                  ....*....|....*....|
gi 2462533313 152 QRRTGLFSATQTQEVENLVR 171
Cdd:cd17965   216 LKHLILCSATIPKEFDKTLR 235
SF2-N cd00046
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ...
 3-161 2.11e-16

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: 75.52  E-value: 2.11e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   3 NKDVAAEAVTGSGKTLAFVIPILEILLRREEKlkksqvgAIIITPTRELAIQIDEVLShftkhfPEFSQILWIGGRNPGE 82
Cdd:cd00046     1 GENVLITAPTGSGKTLAALLAALLLLLKKGKK-------VLVLVPTKALALQTAERLR------ELFGPGIRVAVLVGGS 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  83 DV-ERFKQQGGN--IIVATPGRLEDMFRRkaeglDLASCVRSLDVLVLDEADRLLDMGFEASIN--TILEFLPKQRRTGL 157
Cdd:cd00046    68 SAeEREKNKLGDadIIIATPDMLLNLLLR-----EDRLFLKDLKLIIVDEAHALLIDSRGALILdlAVRKAGLKNAQVIL 142


                  ....
gi 2462533313 158 FSAT 161
Cdd:cd00046   143 LSAT 146
DUF4217 pfam13959
Domain of unknown function (DUF4217); This short domain is found at the C-terminus of many ...
 362-403 8.99e-13

Domain of unknown function (DUF4217); This short domain is found at the C-terminus of many helicase proteins.


Pssm-ID: 464056 [Multi-domain]  Cd Length: 59  Bit Score: 62.80  E-value: 8.99e-13
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 2462533313 362 PKLKSMALADRAVFEKGMKAFVSYVQAYAKHECNLIFRLKAL 403
Cdd:pfam13959   2 LQLEKLVLKDRELKELAQKAFVSYVRAYSKHLAKSIFNVKKL 43
DEADc_DDX25 cd18048
DEAD-box helicase domain of DEAD box protein 25; DDX25 (also called gonadotropin-regulated ...
 4-161 5.11e-11

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: 62.35  E-value: 5.11e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   4 KDVAAEAVTGSGKTLAFVipiLEILLRREEKLKKSQvgAIIITPTRELAIQIDEVLSHFTKHFPEFSQILWIGGRNPGED 83
Cdd:cd18048    58 QNLIAQSQSGTGKTAAFV---LAMLSRVDALKLYPQ--CLCLSPTFELALQTGKVVEEMGKFCVGIQVIYAIRGNRPGKG 132

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  84 VERFKQqggnIIVATPGRLED-MFRrkaegLDLAScVRSLDVLVLDEADRLLDM-GFEASINTILEFLPKQRRTGLFSAT 161
Cdd:cd18048   133 TDIEAQ----IVIGTPGTVLDwCFK-----LRLID-VTNISVFVLDEADVMINVqGHSDHSVRVKRSMPKECQMLLFSAT 202
DEXHc_Hrq1-like cd17923
DEAH-box helicase domain of Hrq1 and similar proteins; Yeast Hrq1, similar to RecQ4, plays a ...
 12-130 3.55e-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: 3.55e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  12 TGSGKTLAFVIPILEILLRReeklkkSQVGAIIITPTRELAI-QidevLSHFTKHFPEFSQILWIG---GRNPGEDVERF 87
Cdd:cd17923    24 TASGKSLCYQLPILEALLRD------PGSRALYLYPTKALAQdQ----LRSLRELLEQLGLGIRVAtydGDTPREERRAI 93

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2462533313  88 KQQGGNIIVATPGRLEDMFRRKAEGldLASCVRSLDVLVLDEA 130
Cdd:cd17923    94 IRNPPRILLTNPDMLHYALLPHHDR--WARFLRNLRYVVLDEA 134
DEADc_DDX19 cd18047
DEAD-box helicase domain of DEAD box protein 19; DDX19 is an RNA helicase involved in both ...
 4-161 9.24e-10

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: 58.19  E-value: 9.24e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   4 KDVAAEAVTGSGKTLAFVIPILEILlrrEEKLKKSQvgAIIITPTRELAIQIDEVLSHFTKHFPEFSQILWIGGRNPGED 83
Cdd:cd18047    41 QNLIAQSQSGTGKTAAFVLAMLSQV---EPANKYPQ--CLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERG 115

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462533313  84 VeRFKQQggnIIVATPGRLEDmFRRKAEGLDlascVRSLDVLVLDEADRLL-DMGFEASINTILEFLPKQRRTGLFSAT 161
Cdd:cd18047   116 Q-KISEQ---IVIGTPGTVLD-WCSKLKFID----PKKIKVFVLDEADVMIaTQGHQDQSIRIQRMLPRNCQMLLFSAT 185
ComFA COG4098
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ...
 10-317 2.17e-09

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: 59.12  E-value: 2.17e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  10 AVTGSGKT-LAFviPILEILLRReeklkKSQVGaiIITPTRELAIqidEVLSHFTKHFPEFSQILWIGGrnpGEDVERFK 88
Cdd:COG4098   136 AVCGAGKTeMLF--PAIAEALKQ-----GGRVC--IATPRVDVVL---ELAPRLQQAFPGVDIAALYGG---SEEKYRYA 200

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  89 QqggnIIVATPG---RLEDMFrrkaegldlascvrslDVLVLDEADrlldmGFEASINTILEFLPKQ-RRTG----LFSA 160
Cdd:COG4098   201 Q----LVIATTHqllRFYQAF----------------DLLIIDEVD-----AFPYSGDPMLQYAVKRaRKPDgkliYLTA 255

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 161 TQTQEVENLVRAGLRN-------------PVRVSVKEKGVAASSAQKTPSRlenyymvckadekfnQLVHFLRNHKQEKH 227
Cdd:COG4098   256 TPSKALQRQVKRGKLKvvklparyhghplPVPKFKWLGNWKKRLRRGKLPR---------------KLLKWLKKRLKEGR 320

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 228 --LVFFSTCACVEYYGKALEVLVKGVKIMCIHGKMKYKRNKIfMEFRKLQSGILVCTDVMARGIDIPEVN-WVLQYDPPS 304
Cdd:COG4098   321 qlLIFVPTIELLEQLVALLQKLFPEERIAGVHAEDPERKEKV-QAFRDGEIPILVTTTILERGVTFPNVDvAVLGADHPV 399

                         330
                  ....*....|....*..
gi 2462533313 305 -NASAFVH---RCGRTA 317
Cdd:COG4098   400 fTEAALVQiagRVGRSA 416
Cas3_I cd09639
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short ...
 5-320 5.67e-09

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: 57.44  E-value: 5.67e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   5 DVAAEAVTGSGKT-LAFVIPILEILLRREEKLkksqvgaIIITPTRELAIQIDEVLSHFTKHFPEFSQILWIGGRNPGED 83
Cdd:cd09639     1 LLVIEAPTGYGKTeAALLWALHSLKSQKADRV-------IIALPTRATINAMYRRAKEAFGETGLYHSSILSSRIKEMGD 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  84 VERFKQ-----QGGN-------IIVATPGRLEDMFRRKAEGLDLASCVRSLDVLVLDEADrLLDMGFEASINTILEFLpk 151
Cdd:cd09639    74 SEEFEHlfplyIHSNdtlfldpITVCTIDQVLKSVFGEFGHYEFTLASIANSLLIFDEVH-FYDEYTLALILAVLEVL-- 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 152 qRRTG----LFSATQTqevENLVRAGLRN-PVrvsVKEKGVAASSAQKTPSRLEnyymVCKADEKFNQLVHFLRNHKQE- 225
Cdd:cd09639   151 -KDNDvpilLMSATLP---KFLKEYAEKIgYV---EENEPLDLKPNERAPFIKI----ESDKVGEISSLERLLEFIKKGg 219

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 226 KHLVFFSTC-ACVEYYGKALEvLVKGVKIMCIHGKMKY-----KRNKIFMEFRKLQSGILVCTDVMARGIDIpEVNWVlq 299
Cdd:cd09639   220 SVAIIVNTVdRAQEFYQQLKE-KGPEEEIMLIHSRFTEkdrakKEAELLLEFKKSEKFVIVATQVIEASLDI-SVDVM-- 295

                         330       340
                  ....*....|....*....|.
gi 2462533313 300 YDPPSNASAFVHRCGRTARIG 320
Cdd:cd09639   296 ITELAPIDSLIQRLGRLHRYG 316
BRR2 COG1204
Replicative superfamily II helicase [Replication, recombination and repair];
3-161 1.63e-08

Replicative superfamily II helicase [Replication, recombination and repair];


Pssm-ID: 440817 [Multi-domain]  Cd Length: 529  Bit Score: 56.44  E-value: 1.63e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   3 NKDVAAEAVTGSGKTLafvipILEILLRREEKLKKSqvgAIIITPTRELAiqiDEVLSHFTKHFPEFSQILWI--GGRNP 80
Cdd:COG1204    38 GKNLVVSAPTASGKTL-----IAELAILKALLNGGK---ALYIVPLRALA---SEKYREFKRDFEELGIKVGVstGDYDS 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  81 G-EDVERFkqqggNIIVATPGRLEDMFRRKAEGLDlascvrSLDVLVLDEAdRLLD-----MGFEASINTILEFLPKQRR 154
Cdd:COG1204   107 DdEWLGRY-----DILVATPEKLDSLLRNGPSWLR------DVDLVVVDEA-HLIDdesrgPTLEVLLARLRRLNPEAQI 174


                  ....*..
gi 2462533313 155 TGLfSAT 161
Cdd:COG1204   175 VAL-SAT 180
SF2_C_LHR cd18796
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ...
 213-329 6.85e-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: 51.50  E-value: 6.85e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 213 NQLVHFLRNHKqeKHLVFFSTCACVEYYGKAL----EVLVKGVKIMCIHGKM-KYKRNKIfmEfRKLQSG---ILVCTDV 284
Cdd:cd18796    29 AEVIFLLERHK--STLVFTNTRSQAERLAQRLrelcPDRVPPDFIALHHGSLsRELREEV--E-AALKRGdlkVVVATSS 103

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 2462533313 285 MARGIDIPEVNWVLQYDPPSNASAFVHRCGRTARIGHGGSALVFL 329
Cdd:cd18796   104 LELGIDIGDVDLVIQIGSPKSVARLLQRLGRSGHRPGAASKGRLV 148
SF2_C_FANCM_Hef cd18801
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ...
 207-318 7.73e-08

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: 51.20  E-value: 7.73e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 207 KADEKFNQLVHFLRNH-------KQEKHLVFFSTCACVEYYGKALEVLVKGVKIMCIHGKMKYKRNK---------IFME 270
Cdd:cd18801     6 KIHPKLEKLEEIVKEHfkkkqegSDTRVIIFSEFRDSAEEIVNFLSKIRPGIRATRFIGQASGKSSKgmsqkeqkeVIEQ 85

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 2462533313 271 FRKLQSGILVCTDVMARGIDIPEVNWVLQYDPPSNASAFVHRCGRTAR 318
Cdd:cd18801    86 FRKGGYNVLVATSIGEEGLDIGEVDLIICYDASPSPIRMIQRMGRTGR 133
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 278-331 1.31e-07

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: 48.47  E-value: 1.31e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2462533313 278 ILVCTDVMARGIDIPEVNWVLQYDPPSNASAFVHRCGRTARiGHGGSALVFLLP 331
Cdd:cd18785    25 ILVATNVLGEGIDVPSLDTVIFFDPPSSAASYIQRVGRAGR-GGKDEGEVILFV 77
DEXHc_Ski2 cd17921
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ...
 2-161 1.72e-07

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: 51.11  E-value: 1.72e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   2 RNKDVAAEAVTGSGKTLAFVIPILEILLRREEKlkksqvgAIIITPTRELAiqiDEVLSHFTKHF-PEFSQilwIGGRNP 80
Cdd:cd17921    16 SGDSVLVSAPTSSGKTLIAELAILRALATSGGK-------AVYIAPTRALV---NQKEADLRERFgPLGKN---VGLLTG 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  81 GEDVERFKQQGGNIIVATPGRLEDMFRRKAEGLdlascVRSLDVLVLDEAdRLLDMG-----FEASINTILEFLPKQRRT 155
Cdd:cd17921    83 DPSVNKLLLAEADILVATPEKLDLLLRNGGERL-----IQDVRLVVVDEA-HLIGDGergvvLELLLSRLLRINKNARFV 156


                  ....*.
gi 2462533313 156 GLfSAT 161
Cdd:cd17921   157 GL-SAT 161
MPH1 COG1111
ERCC4-related helicase [Replication, recombination and repair];
278-322 2.08e-07

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


Pssm-ID: 440728 [Multi-domain]  Cd Length: 718  Bit Score: 53.20  E-value: 2.08e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 2462533313 278 ILVCTDVMARGIDIPEVNWVLQYDPPSNASAFVHRCGRTARIGHG 322
Cdd:COG1111   414 VLVATSVAEEGLDIPEVDLVIFYEPVPSEIRSIQRKGRTGRKREG 458
DEXHc_LHR-like cd17922
DEXH-box helicase domain of LHR; Large helicase-related protein (LHR) is a DNA ...
 3-172 4.72e-07

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: 49.50  E-value: 4.72e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   3 NKDVAAEAVTGSGKTLAFVIPILEILLRREEKlkksQVGAIIITPTRELA--IQ--IDEVLSHFTkhfPEFSQILWIGGR 78
Cdd:cd17922     1 GRNVLIAAPTGSGKTEAAFLPALSSLADEPEK----GVQVLYISPLKALIndQErrLEEPLDEID---LEIPVAVRHGDT 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  79 NPGEDvERFKQQGGNIIVATPGRLEDMF-RRKAEGLdlascVRSLDVLVLDEADRLLD----MGFEASINTILEFL-PKQ 152
Cdd:cd17922    74 SQSEK-AKQLKNPPGILITTPESLELLLvNKKLREL-----FAGLRYVVVDEIHALLGskrgVQLELLLERLRKLTgRPL 147

                         170       180
                  ....*....|....*....|
gi 2462533313 153 RRTGLfSATqtqeVENLVRA 172
Cdd:cd17922   148 RRIGL-SAT----LGNLEEA 162
SF2_C_TRCF cd18810
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ...
 237-295 2.00e-06

C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair coupling factor (TrcF) dissociates transcription elongation complexes blocked at nonpairing lesions and mediates recruitment of DNA repair proteins. TrcF 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: 350197 [Multi-domain]  Cd Length: 151  Bit Score: 47.34  E-value: 2.00e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 237 VEYYGKALEVLVKGVKIMCIHGKM-KYKRNKIFMEFRKLQSGILVCTDVMARGIDIPEVN 295
Cdd:cd18810    38 IEKLATQLRQLVPEARIAIAHGQMtENELEEVMLEFAKGEYDILVCTTIIESGIDIPNAN 97
mfd TIGR00580
transcription-repair coupling factor (mfd); All proteins in this family for which functions ...
 237-295 4.54e-06

transcription-repair coupling factor (mfd); All proteins in this family for which functions are known are DNA-dependent ATPases that function in the process of transcription-coupled DNA repair in which the repair of the transcribed strand of actively transcribed genes is repaired at a higher rate than the repair of non-transcribed regions of the genome and than the non-transcribed strand of the same gene. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is closely related to the RecG and UvrB families. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273152 [Multi-domain]  Cd Length: 926  Bit Score: 48.89  E-value: 4.54e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 237 VEYYGKALEVLVKGVKIMCIHGKM-KYKRNKIFMEFRKLQSGILVCTDVMARGIDIPEVN 295
Cdd:TIGR00580 673 IEKLATQLRELVPEARIAIAHGQMtENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNAN 732
SF2_C_dicer cd18802
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ...
 272-318 4.99e-06

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: 46.05  E-value: 4.99e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2462533313 272 RKLQSG---ILVCTDVMARGIDIPEVNWVLQYDPPSNASAFVHRCGRtAR 318
Cdd:cd18802    84 DKFRDGelnLLIATSVLEEGIDVPACNLVIRFDLPKTLRSYIQSRGR-AR 132
RecQ COG0514
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
202-315 9.94e-06

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


Pssm-ID: 440280 [Multi-domain]  Cd Length: 489  Bit Score: 47.44  E-value: 9.94e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 202 YYMV--CKADEKFNQLVHFLRNHKQEKHLVFFSTCACVEYYGKALEVlvKGVKIMCIHGKMKYK-RNKIFMEFRKLQSGI 278
Cdd:COG0514   206 RLEVvpKPPDDKLAQLLDFLKEHPGGSGIVYCLSRKKVEELAEWLRE--AGIRAAAYHAGLDAEeREANQDRFLRDEVDV 283

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2462533313 279 LVCTdV---MarGIDIPEVNWVLQYDPPSNASAF---VHRCGR 315
Cdd:COG0514   284 IVAT-IafgM--GIDKPDVRFVIHYDLPKSIEAYyqeIGRAGR 323
DEXHc_HFM1 cd18023
DEXH-box helicase domain of ATP-dependent DNA helicase HFM1; HFM1 is a type II DEAD box ...
 3-129 1.10e-05

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: 46.20  E-value: 1.10e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   3 NKDVAAEAVTGSGKTLAFVIPILEILLRREEKlKKSQVGAIIITPTRELAIQidevlsHFTKHFPEFSQI----LWIGGR 78
Cdd:cd18023    17 DKNFVVSAPTGSGKTVLFELAILRLLKERNPL-PWGNRKVVYIAPIKALCSE------KYDDWKEKFGPLglscAELTGD 89

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2462533313  79 NPGEDVerFKQQGGNIIVATPGRLEDMFRRKAEGLDLASCVRsldvLVL-DE 129
Cdd:cd18023    90 TEMDDT--FEIQDADIILTTPEKWDSMTRRWRDNGNLVQLVA----LVLiDE 135
SF2_C_RecG_TRCF cd18792
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ...
 237-295 1.69e-05

C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family contains recombination factor RecG and transcription-repair coupling factor TrcF. 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: 350179 [Multi-domain]  Cd Length: 160  Bit Score: 44.57  E-value: 1.69e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 237 VEYYGKALEVLVKGVKIMCIHGKMKY-KRNKIFMEFRKLQSGILVCTDVMARGIDIPEVN 295
Cdd:cd18792    47 IEALAEELKELVPEARVALLHGKMTEdEKEAVMLEFREGEYDILVSTTVIEVGIDVPNAN 106
ResIII pfam04851
Type III restriction enzyme, res subunit;
12-161 3.92e-05

Type III restriction enzyme, res subunit;


Pssm-ID: 398492 [Multi-domain]  Cd Length: 162  Bit Score: 43.81  E-value: 3.92e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  12 TGSGKTL--AFVIpileILLRREEKLKKsqvgAIIITPTRELAIQIdevLSHFTKHFPE-FSQILWIGGRNpgedvERFK 88
Cdd:pfam04851  32 TGSGKTLtaAKLI----ARLFKKGPIKK----VLFLVPRKDLLEQA---LEEFKKFLPNyVEIGEIISGDK-----KDES 95

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462533313  89 QQGGNIIVATPGRLedmFRRKAEGLDLAScVRSLDVLVLDEADRLLDMGFEAsintILEFLPKQRRTGlFSAT 161
Cdd:pfam04851  96 VDDNKIVVTTIQSL---YKALELASLELL-PDFFDVIIIDEAHRSGASSYRN----ILEYFKPAFLLG-LTAT 159
PRK13766 PRK13766
Hef nuclease; Provisional
 270-327 8.39e-05

Hef nuclease; Provisional


Pssm-ID: 237496 [Multi-domain]  Cd Length: 773  Bit Score: 44.86  E-value: 8.39e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2462533313 270 EFRKLQSGILVCTDVMARGIDIPEVNWVLQYDP-PSnASAFVHRCGRTARiGHGGSALV 327
Cdd:PRK13766  418 KFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEPvPS-EIRSIQRKGRTGR-QEEGRVVV 474
SF2_C_XPB cd18789
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex ...
 211-330 9.20e-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: 42.24  E-value: 9.20e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 211 KFNQLVHFLRNHKQ-EKHLVFFSTCACVEYYGKALEVLVkgvkimcIHGKM-KYKRNKIFMEFRKLQSGILVCTDVMARG 288
Cdd:cd18789    35 KLRALEELLKRHEQgDKIIVFTDNVEALYRYAKRLLKPF-------ITGETpQSEREEILQNFREGEYNTLVVSKVGDEG 107

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 2462533313 289 IDIPEVNWVLQYDpPSNASA--FVHRCGRTARIGHGGSALVFLL 330
Cdd:cd18789   108 IDLPEANVAIQIS-GHGGSRrqEAQRLGRILRPKKGGGKNAFFY 150
SF2_C_RecG cd18811
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ...
 235-330 1.47e-04

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: 41.95  E-value: 1.47e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 235 ACVEYYGKALEVLVKGVKIMCIHGKMKYK-RNKIFMEFRKLQSGILVCTDVMARGIDIPEVNWVLQYDPpsnasafvHRC 313
Cdd:cd18811    46 AAVAMYEYLKERFRPELNVGLLHGRLKSDeKDAVMAEFREGEVDILVSTTVIEVGVDVPNATVMVIEDA--------ERF 117

                          90       100
                  ....*....|....*....|...
gi 2462533313 314 GRTA------RIGHGGSALVFLL 330
Cdd:cd18811   118 GLSQlhqlrgRVGRGDHQSYCLL 140
YprA COG1205
ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, ...
 4-130 1.82e-04

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: 43.67  E-value: 1.82e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   4 KDVAAEAVTGSGKTLAFVIPILEILLRreeklkKSQVGAIIITPTRELAI-QIDEVLshftkhfpEFSQILWIG------ 76
Cdd:COG1205    72 KNVVIATPTASGKSLAYLLPVLEALLE------DPGATALYLYPTKALARdQLRRLR--------ELAEALGLGvrvaty 137

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462533313  77 -GRNPGEDVERFKQQgGNIIVATPgrleDM-----------FRRkaegldlasCVRSLDVLVLDEA 130
Cdd:COG1205   138 dGDTPPEERRWIREH-PDIVLTNP----DMlhygllphhtrWAR---------FFRNLRYVVIDEA 189
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
 211-320 3.17e-04

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: 40.54  E-value: 3.17e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 211 KFNQLVHFLRNHKQEKH-LVFFStcacveYYGKALEVL-----VKGVKIMCIHGKMK-YKRNKIFMEFRKLQSG--ILVC 281
Cdd:cd18793    12 KLEALLELLEELREPGEkVLIFS------QFTDTLDILeealrERGIKYLRLDGSTSsKERQKLVDRFNEDPDIrvFLLS 85

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 2462533313 282 TDVMARGIDIPEVNWVLQYDPPSNASAFVHRCGRTARIG 320
Cdd:cd18793    86 TKAGGVGLNLTAANRVILYDPWWNPAVEEQAIDRAHRIG 124
DEXHc_RE cd17926
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ...
 10-161 4.59e-04

DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family is composed of helicase restriction enzymes and similar proteins such as TFIIH basal transcription factor complex helicase XPB subunit. These proteins are part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350684 [Multi-domain]  Cd Length: 146  Bit Score: 40.37  E-value: 4.59e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  10 AVTGSGKTLafvIPILEILLRREEKLkksqvgaIIITPTRELAIQIdevlshfTKHFPEFSQILWIgGRNPGEDVERFKq 89
Cdd:cd17926    25 LPTGSGKTL---TALALIAYLKELRT-------LIVVPTDALLDQW-------KERFEDFLGDSSI-GLIGGGKKKDFD- 85

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462533313  90 qGGNIIVATPGRLEdmFRRKAEGLDLASCvrslDVLVLDEADRLLDMGFEAsintILEFLPKQRRTGlFSAT 161
Cdd:cd17926    86 -DANVVVATYQSLS--NLAEEEKDLFDQF----GLLIVDEAHHLPAKTFSE----ILKELNAKYRLG-LTAT 145
TrwB_TraG_TraD_VirD4 cd01127
TrwB/TraG/TraD/VirD4 family of bacterial conjugation proteins; The TraG/TraD/VirD4 family are ...
 12-73 1.71e-03

TrwB/TraG/TraD/VirD4 family of bacterial conjugation proteins; The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion (T4S) systems, versatile bacterial secretion systems mediating transport of protein and/or DNA. They are present in gram-negative and gram-positive bacteria, as well as archaea. They form hexameric rings and belong to the RecA-like NTPases superfamily, which also includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases.


Pssm-ID: 410871 [Multi-domain]  Cd Length: 144  Bit Score: 38.74  E-value: 1.71e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462533313  12 TGSGKTLAFVIPILEILLRREeklkksqvGAIIITPTRELAIQIDEVLSHFTKHFPEFSQIL 73
Cdd:cd01127     8 TGSGKTTSIVIPLLDQAARGG--------SVIITDPKGELFLVIPDRDDSFAALRALFFNQL 61
DDXDc_reverse_gyrase cd17924
DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of ...
 2-149 2.23e-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: 38.85  E-value: 2.23e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313   2 RNKDVAAEAVTGSGKTLAFVIPILEILLRReeklKKSqvgaIIITPTRELAIQIDEVLSHFTKHFPEFSQILWIGGRNP- 80
Cdd:cd17924    31 RGKSFAIIAPTGVGKTTFGLATSLYLASKG----KRS----YLIFPTKSLVKQAYERLSKYAEKAGVEVKILVYHSRLKk 102

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462533313  81 ---GEDVERFKQQGGNIIVATpgrleDMFRRKaeGLDLASCVRsLDVLVLDEADRLLDMGfeASINTILEFL 149
Cdd:cd17924   103 kekEELLEKIEKGDFDILVTT-----NQFLSK--NFDLLSNKK-FDFVFVDDVDAVLKSS--KNIDRLLKLL 164
DEXHc_Hef cd18035
DEXH-box helicase domain of Hef; Hef (helicase-associated endonuclease fork-structure) belongs ...
 12-132 4.01e-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: 37.88  E-value: 4.01e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313  12 TGSGKTLafvIPILEILLRREEKlkKSQVgaIIITPTRELAIQIDEVLSHFTKHFPEFSQIlwIGGRNPGEDVERFKQqg 91
Cdd:cd18035    25 TGLGKTI---IAILVAADRLTKK--GGKV--LILAPSRPLVEQHAENLKRVLNIPDKITSL--TGEVKPEERAERWDA-- 93

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 2462533313  92 GNIIVATPGRLEDmfrrkaeglDLASCVRSLD---VLVLDEADR 132
Cdd:cd18035    94 SKIIVATPQVIEN---------DLLAGRITLDdvsLLIFDEAHH 128
PRK11057 PRK11057
ATP-dependent DNA helicase RecQ; Provisional
 210-331 9.29e-03

ATP-dependent DNA helicase RecQ; Provisional


Pssm-ID: 182933 [Multi-domain]  Cd Length: 607  Bit Score: 38.16  E-value: 9.29e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462533313 210 EKF---NQLVHFLRNHKQEKHLVFFSTCACVEYYGKALEVlvKGVKIMCIHGKMKY-KRNKIFMEFRKLQSGILVCTDVM 285
Cdd:PRK11057  219 EKFkplDQLMRYVQEQRGKSGIIYCNSRAKVEDTAARLQS--RGISAAAYHAGLDNdVRADVQEAFQRDDLQIVVATVAF 296

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2462533313 286 ARGIDIPEVNWVLQYDPPSNASAFVHRCGRTARIGHGGSALVFLLP 331
Cdd:PRK11057  297 GMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDP 342
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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