|
Name |
Accession |
Description |
Interval |
E-value |
| DEXSc_Pif1_like |
cd18037 |
DEAD-box helicase domain of Pif1; Pif1 and other members of this family are RecD-like ... |
208-387 |
1.33e-94 |
|
DEAD-box helicase domain of Pif1; Pif1 and other members of this family are RecD-like helicases involved in maintaining genome stability through unwinding double-stranded DNAs (dsDNAs), DNA/RNA hybrids, and G quadruplex (G4) structures. The members of Pif1 helicase subfamily studied so far all appear to contribute to telomere maintenance. Pif1 is a member of the DEAD-like helicases superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350795 [Multi-domain] Cd Length: 183 Bit Score: 289.53 E-value: 1.33e-94
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 208 EQMEVLRACTSGKSVFFTGSAGTGKSFLLRRIISALP--PDGTVATASTGVAACLIGGTTLHAFAGIGGGDATMQRCLE- 284
Cdd:cd18037 1 EQRRVLDLVLDGKNVFFTGSAGTGKSYLLRRIIRALPsrPKRVAVTASTGIAACNIGGTTLHSFAGIGLGSEPAEDLLEr 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 285 LASRPANAQTWRKCKRLIIDEISMVDGQFFEKIEAVARHIRRNDRPFGGIQLILCGDFLQLPPVIKGDFGAAPTATPQQR 364
Cdd:cd18037 81 VKRSPYLVQRWRKCDVLIIDEISMLDADLFDKLDRVAREVRGSDKPFGGIQLILCGDFLQLPPVTKNSERQAFFFRGDQQ 160
|
170 180
....*....|....*....|...
gi 19920652 365 FCFQSSAWETCIQCVYELKQVHR 387
Cdd:cd18037 161 FCFEAKSWERCIFLTVELTKVFR 183
|
|
| PIF1 |
pfam05970 |
PIF1-like helicase; This family includes homologs of the PIF1 helicase, which inhibits ... |
205-510 |
4.90e-74 |
|
PIF1-like helicase; This family includes homologs of the PIF1 helicase, which inhibits telomerase activity and is cell cycle regulated. This family includes a large number of largely uncharacterized plant proteins. This family includes a P-loop motif that is involved in nucleotide binding.
Pssm-ID: 428699 [Multi-domain] Cd Length: 361 Bit Score: 242.29 E-value: 4.90e-74
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 205 LSEEQMEVLRACT------SGKSVFFTGSAGTGKSFLLRRIISALPPDG--TVATASTGVAACLI-GGTTLHAFAGIGGG 275
Cdd:pfam05970 1 LNDEQKKVFDAIIesvinnKGGVFFVYGYGGTGKTFLWKAIITSLRSEGkiVLAVASSGVAALLLpGGRTAHSRFGIPLD 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 276 DATMQRClELASRPANAQTWRKCKRLIIDEISMVDGQFFEKIEAVARHIRRN--DRPFGGIQLILCGDFLQLPPVIKGdf 353
Cdd:pfam05970 81 IDELSTC-KIKRGSKLAELLEKTSLIVWDEAPMTHRHCFEALDRTLRDILSEtdDKPFGGKTVVLGGDFRQILPVIPK-- 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 354 gaaptATPQQRFCF---QSSAWETCIqcVYELKQVHRQSDP-----------EFVKILNHLRIGHVNDSITSR------- 412
Cdd:pfam05970 158 -----GSRPEIVNAsitNSYLWKHVK--VLELTKNMRLLADsldqteakelqDFSDWLLAIGDGKINDENEREqlidipi 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 413 --LAATSKQKIEG------NGILATQ-----------LCSHTNDANSINESKLENLDGDKILFKADDS-DASMT------ 466
Cdd:pfam05970 231 diLLNTGGDPIEAivsevyPDILQNStdpnyleeraiLCPTNEDVDEINNYRLSQLPGEEKEYLSSDSiSKSDNdseida 310
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|.
gi 19920652 467 -------RTLDQQIQAPSQLYLKVNAQVMLLKNINISNGLVNGARGVVVRM 510
Cdd:pfam05970 311 lypteflNSLNANGLPNHVLKLKVGAPVMLLRNLDQSRGLCNGTRLIVTQL 361
|
|
| RecD |
COG0507 |
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ... |
190-591 |
4.52e-50 |
|
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair];
Pssm-ID: 440273 [Multi-domain] Cd Length: 514 Bit Score: 182.10 E-value: 4.52e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 190 AAKKLYASTTDESLRLSEEQMEVLRACTSGKSVFF-TGSAGTGKSFLLRRIISALPPDG--TVATASTGVAA------CL 260
Cdd:COG0507 110 VEAALAALEPRAGITLSDEQREAVALALTTRRVSVlTGGAGTGKTTTLRALLAALEALGlrVALAAPTGKAAkrlsesTG 189
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 261 IGGTTLHAFAGIGGGDATMQRClelASRPanaqtWRKCKRLIIDEISMVDGQFFEKI-EAVarhirrndrPFGGIQLILC 339
Cdd:COG0507 190 IEARTIHRLLGLRPDSGRFRHN---RDNP-----LTPADLLVVDEASMVDTRLMAALlEAL---------PRAGARLILV 252
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 340 GDFLQLPPVIKGD-FGAaptatpqqrfcFQSSAWETciqcVYELKQVHRQSDP-EFVKILNHLRIGHVNDSITSRLAATS 417
Cdd:COG0507 253 GDPDQLPSVGAGAvLRD-----------LIESGTVP----VVELTEVYRQADDsRIIELAHAIREGDAPEALNARYADVV 317
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 418 KQKIEGNGILATQ-----------------LCSHTNDANSINESKLENLDGDKilfkaddsdasmtrTLDQQIQAPSQLY 480
Cdd:COG0507 318 FVEAEDAEEAAEAivelyadrpaggediqvLAPTNAGVDALNQAIREALNPAG--------------ELERELAEDGELE 383
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 481 LKVNAQVMLLKNiNISNGLVNGARGVVVRMEKDL--PVVRFknnqeyvckhERWIIKTasgnhITRRQVP-LKLAWAFSI 557
Cdd:COG0507 384 LYVGDRVMFTRN-DYDLGVFNGDIGTVLSIDEDEgrLTVRF----------DGREIVT-----YDPSELDqLELAYAITV 447
|
410 420 430
....*....|....*....|....*....|....*...
gi 19920652 558 HKSQGLTLDCV----EMSLSKVFEAGQAYVALSRAKSL 591
Cdd:COG0507 448 HKSQGSTFDRVilvlPSEHSPLLSRELLYTALTRAREL 485
|
|
| TraA_Ti |
TIGR02768 |
Ti-type conjugative transfer relaxase TraA; This protein contains domains distinctive of a ... |
115-626 |
2.08e-15 |
|
Ti-type conjugative transfer relaxase TraA; This protein contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, pfam03389) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, TIGR02760). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer.
Pssm-ID: 274289 [Multi-domain] Cd Length: 744 Bit Score: 79.85 E-value: 2.08e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 115 QPDDATLQKKLREHLMS-------GKPSSFNDVSPVTTAEMIlaRKKAGLLskgsvttpspqgakkRRFEELKEEKERGT 187
Cdd:TIGR02768 276 YIDDPQQFQQLMARVLAspqlvalGDPGTGKEPARFSTREMI--RLEAQMA---------------RSAEALSQSQGHGV 338
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 188 MPAAKKlyaSTTDESLRLSEEQMEVLRACT-SGKSVFFTGSAGTGKSFLLRRIISALPPDG--TVATASTGVAAcliggT 264
Cdd:TIGR02768 339 SPPIVD---AAIDQHYRLSEEQYEAVRHVTgSGDIAVVVGRAGTGKSTMLKAAREAWEAAGyrVIGAALSGKAA-----E 410
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 265 TLHAFAGIgggDATMQRCLELASRPANAQTWRKcKRLIIDEISMVDGQFFEKIEAVARHirrndrpfGGIQLILCGDFLQ 344
Cdd:TIGR02768 411 GLQAESGI---ESRTLASLEYAWANGRDLLSDK-DVLVIDEAGMVGSRQMARVLKEAEE--------AGAKVVLVGDPEQ 478
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 345 LPPVIKGD--------FGAAPTATPQQrfcfQSSAWEtciqcvyelkqvhRQSDPEFVK--ILN---------HLRIGHV 405
Cdd:TIGR02768 479 LQPIEAGAafraiaerIGYAELETIRR----QREAWA-------------RQASLELARgdVEKalaayrdhgHITIHDT 541
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 406 NDSITSRLAATSKQKIEGNGILATQLC-SHTN-DANSINESKLENLDGDKILfkaDDSDASMTRTLDQQIQAPSQLYLKV 483
Cdd:TIGR02768 542 REEAIEQVVADWKQDLREANPAGSQIMlAHTRkDVRALNEAAREALIERGEL---GESILFQTARGERKFAAGDRIVFLE 618
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 484 NAQVMllkninisnGLVNGARGVVVRMEKDLPVVRFKNNqeyvckhERWIIKTASGNHITRrqvplklAWAFSIHKSQGL 563
Cdd:TIGR02768 619 NNRDL---------GVKNGMLGTVEEIEDGRLVVQLDSG-------ELVIIPQAEYDALDH-------GYATTIHKSQGV 675
|
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19920652 564 TLDCVEMSLSKVFEAGQAYVALSRAKslqsirildfDAKQVWANPHVLQFYKGF-----RRKLMDTTM 626
Cdd:TIGR02768 676 TVDRAFVLASKSMDRHLAYVAMTRHR----------ESVQLYAGKEDFTDRGALvktlsRSSTKDTTL 733
|
|
| SF1_C_RecD |
cd18809 |
C-terminal helicase domain of RecD family helicases; RecD is a member of the RecBCD (EC 3.1.11. ... |
550-594 |
3.92e-14 |
|
C-terminal helicase domain of RecD family helicases; RecD is a member of the RecBCD (EC 3.1.11.5, Exonuclease V) complex. It is the alpha chain of the complex and functions as a 3'-5' helicase. The RecBCD enzyme is both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA. RecD family helicases are DEAD-like helicases belonging to superfamily (SF)1, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF2 helicases, SF1 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: 350196 [Multi-domain] Cd Length: 80 Bit Score: 67.97 E-value: 3.92e-14
10 20 30 40
....*....|....*....|....*....|....*....|....*...
gi 19920652 550 KLAWAFSIHKSQGLTLDCVEMSLSKV---FEAGQAYVALSRAKSLQSI 594
Cdd:cd18809 31 LQAYAMTIHKSQGSEFDRVIVVLPTShpmLSRGLLYTALTRARKLLTL 78
|
|
| AAA |
smart00382 |
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ... |
218-338 |
5.72e-04 |
|
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.
Pssm-ID: 214640 [Multi-domain] Cd Length: 148 Bit Score: 40.82 E-value: 5.72e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 218 SGKSVFFTGSAGTGKSFLLRRIISALPPDGTV-----ATASTGVAACLIGGTTLHAFAGIGGGDATMQRCLELASRPana 292
Cdd:smart00382 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGviyidGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALALARKL--- 77
|
90 100 110 120
....*....|....*....|....*....|....*....|....*...
gi 19920652 293 qtwrKCKRLIIDEISMVDGQFFEKIEAVARHIRRNDR--PFGGIQLIL 338
Cdd:smart00382 78 ----KPDVLILDEITSLLDAEQEALLLLLEELRLLLLlkSEKNLTVIL 121
|
|
| UvrD_C_2 |
pfam13538 |
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety ... |
551-589 |
7.92e-03 |
|
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety of helicase enzymes. This domain has a AAA-like structural fold.
Pssm-ID: 463913 [Multi-domain] Cd Length: 52 Bit Score: 34.86 E-value: 7.92e-03
10 20 30 40
....*....|....*....|....*....|....*....|....*.
gi 19920652 551 LAWAFSIHKSQGLTLDCV---EMSLSKVFEAGQA----YVALSRAK 589
Cdd:pfam13538 1 LAYALTVHKAQGSEFPAVflvDPDLTAHYHSMLRrrllYTAVTRAR 46
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| DEXSc_Pif1_like |
cd18037 |
DEAD-box helicase domain of Pif1; Pif1 and other members of this family are RecD-like ... |
208-387 |
1.33e-94 |
|
DEAD-box helicase domain of Pif1; Pif1 and other members of this family are RecD-like helicases involved in maintaining genome stability through unwinding double-stranded DNAs (dsDNAs), DNA/RNA hybrids, and G quadruplex (G4) structures. The members of Pif1 helicase subfamily studied so far all appear to contribute to telomere maintenance. Pif1 is a member of the DEAD-like helicases superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350795 [Multi-domain] Cd Length: 183 Bit Score: 289.53 E-value: 1.33e-94
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 208 EQMEVLRACTSGKSVFFTGSAGTGKSFLLRRIISALP--PDGTVATASTGVAACLIGGTTLHAFAGIGGGDATMQRCLE- 284
Cdd:cd18037 1 EQRRVLDLVLDGKNVFFTGSAGTGKSYLLRRIIRALPsrPKRVAVTASTGIAACNIGGTTLHSFAGIGLGSEPAEDLLEr 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 285 LASRPANAQTWRKCKRLIIDEISMVDGQFFEKIEAVARHIRRNDRPFGGIQLILCGDFLQLPPVIKGDFGAAPTATPQQR 364
Cdd:cd18037 81 VKRSPYLVQRWRKCDVLIIDEISMLDADLFDKLDRVAREVRGSDKPFGGIQLILCGDFLQLPPVTKNSERQAFFFRGDQQ 160
|
170 180
....*....|....*....|...
gi 19920652 365 FCFQSSAWETCIQCVYELKQVHR 387
Cdd:cd18037 161 FCFEAKSWERCIFLTVELTKVFR 183
|
|
| PIF1 |
pfam05970 |
PIF1-like helicase; This family includes homologs of the PIF1 helicase, which inhibits ... |
205-510 |
4.90e-74 |
|
PIF1-like helicase; This family includes homologs of the PIF1 helicase, which inhibits telomerase activity and is cell cycle regulated. This family includes a large number of largely uncharacterized plant proteins. This family includes a P-loop motif that is involved in nucleotide binding.
Pssm-ID: 428699 [Multi-domain] Cd Length: 361 Bit Score: 242.29 E-value: 4.90e-74
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 205 LSEEQMEVLRACT------SGKSVFFTGSAGTGKSFLLRRIISALPPDG--TVATASTGVAACLI-GGTTLHAFAGIGGG 275
Cdd:pfam05970 1 LNDEQKKVFDAIIesvinnKGGVFFVYGYGGTGKTFLWKAIITSLRSEGkiVLAVASSGVAALLLpGGRTAHSRFGIPLD 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 276 DATMQRClELASRPANAQTWRKCKRLIIDEISMVDGQFFEKIEAVARHIRRN--DRPFGGIQLILCGDFLQLPPVIKGdf 353
Cdd:pfam05970 81 IDELSTC-KIKRGSKLAELLEKTSLIVWDEAPMTHRHCFEALDRTLRDILSEtdDKPFGGKTVVLGGDFRQILPVIPK-- 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 354 gaaptATPQQRFCF---QSSAWETCIqcVYELKQVHRQSDP-----------EFVKILNHLRIGHVNDSITSR------- 412
Cdd:pfam05970 158 -----GSRPEIVNAsitNSYLWKHVK--VLELTKNMRLLADsldqteakelqDFSDWLLAIGDGKINDENEREqlidipi 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 413 --LAATSKQKIEG------NGILATQ-----------LCSHTNDANSINESKLENLDGDKILFKADDS-DASMT------ 466
Cdd:pfam05970 231 diLLNTGGDPIEAivsevyPDILQNStdpnyleeraiLCPTNEDVDEINNYRLSQLPGEEKEYLSSDSiSKSDNdseida 310
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|.
gi 19920652 467 -------RTLDQQIQAPSQLYLKVNAQVMLLKNINISNGLVNGARGVVVRM 510
Cdd:pfam05970 311 lypteflNSLNANGLPNHVLKLKVGAPVMLLRNLDQSRGLCNGTRLIVTQL 361
|
|
| RecD |
COG0507 |
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ... |
190-591 |
4.52e-50 |
|
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair];
Pssm-ID: 440273 [Multi-domain] Cd Length: 514 Bit Score: 182.10 E-value: 4.52e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 190 AAKKLYASTTDESLRLSEEQMEVLRACTSGKSVFF-TGSAGTGKSFLLRRIISALPPDG--TVATASTGVAA------CL 260
Cdd:COG0507 110 VEAALAALEPRAGITLSDEQREAVALALTTRRVSVlTGGAGTGKTTTLRALLAALEALGlrVALAAPTGKAAkrlsesTG 189
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 261 IGGTTLHAFAGIGGGDATMQRClelASRPanaqtWRKCKRLIIDEISMVDGQFFEKI-EAVarhirrndrPFGGIQLILC 339
Cdd:COG0507 190 IEARTIHRLLGLRPDSGRFRHN---RDNP-----LTPADLLVVDEASMVDTRLMAALlEAL---------PRAGARLILV 252
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 340 GDFLQLPPVIKGD-FGAaptatpqqrfcFQSSAWETciqcVYELKQVHRQSDP-EFVKILNHLRIGHVNDSITSRLAATS 417
Cdd:COG0507 253 GDPDQLPSVGAGAvLRD-----------LIESGTVP----VVELTEVYRQADDsRIIELAHAIREGDAPEALNARYADVV 317
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 418 KQKIEGNGILATQ-----------------LCSHTNDANSINESKLENLDGDKilfkaddsdasmtrTLDQQIQAPSQLY 480
Cdd:COG0507 318 FVEAEDAEEAAEAivelyadrpaggediqvLAPTNAGVDALNQAIREALNPAG--------------ELERELAEDGELE 383
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 481 LKVNAQVMLLKNiNISNGLVNGARGVVVRMEKDL--PVVRFknnqeyvckhERWIIKTasgnhITRRQVP-LKLAWAFSI 557
Cdd:COG0507 384 LYVGDRVMFTRN-DYDLGVFNGDIGTVLSIDEDEgrLTVRF----------DGREIVT-----YDPSELDqLELAYAITV 447
|
410 420 430
....*....|....*....|....*....|....*...
gi 19920652 558 HKSQGLTLDCV----EMSLSKVFEAGQAYVALSRAKSL 591
Cdd:COG0507 448 HKSQGSTFDRVilvlPSEHSPLLSRELLYTALTRAREL 485
|
|
| DEXSc_RecD-like |
cd17933 |
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ... |
208-348 |
5.32e-26 |
|
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1.11.5, Exonuclease V) complex. It is the alpha chain of the complex and functions as a 3'-5' helicase. The RecBCD enzyme is both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA. RecD 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: 350691 [Multi-domain] Cd Length: 155 Bit Score: 104.17 E-value: 5.32e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 208 EQMEVLRACTSGKSVFFTGSAGTGKSFLLRRIISAL--PPDGTVATASTGVAACLIG------GTTLHAFAGIGGGDATM 279
Cdd:cd17933 1 EQKAAVRLVLRNRVSVLTGGAGTGKTTTLKALLAALeaEGKRVVLAAPTGKAAKRLSestgieASTIHRLLGINPGGGGF 80
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19920652 280 QRclelasrpaNAQTWRKCKRLIIDEISMVDGQFFEKIEAVARHirrndrpfgGIQLILCGDFLQLPPV 348
Cdd:cd17933 81 YY---------NEENPLDADLLIVDEASMVDTRLMAALLSAIPA---------GARLILVGDPDQLPSV 131
|
|
| AAA_30 |
pfam13604 |
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ... |
204-405 |
1.03e-18 |
|
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B.
Pssm-ID: 433343 [Multi-domain] Cd Length: 191 Bit Score: 84.54 E-value: 1.03e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 204 RLSEEQMEVLRA-CTSGKSVFF-TGSAGTGKSFLLRRIISALPPDG--TVATASTGVAACLIGgttlhafAGIGGGDATM 279
Cdd:pfam13604 1 TLNAEQAAAVRAlLTSGDRVAVlVGPAGTGKTTALKALREAWEAAGyrVIGLAPTGRAAKVLG-------EELGIPADTI 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 280 QRcleLASRPANAQTWRKCKRLIIDEISMVDgqfFEKIEAVARHIRRNdrpfgGIQLILCGDFLQLPPVIKGD-FGAAPT 358
Cdd:pfam13604 74 AK---LLHRLGGRAGLDPGTLLIVDEAGMVG---TRQMARLLKLAEDA-----GARVILVGDPRQLPSVEAGGaFRDLLA 142
|
170 180 190 200
....*....|....*....|....*....|....*....|....*..
gi 19920652 359 ATPqqrfcfqssawetciqCVYELKQVHRQSDPEFVKILNHLRIGHV 405
Cdd:pfam13604 143 AGI----------------GTAELTEIVRQRDPWQRAASLALRDGDP 173
|
|
| TraA_Ti |
TIGR02768 |
Ti-type conjugative transfer relaxase TraA; This protein contains domains distinctive of a ... |
115-626 |
2.08e-15 |
|
Ti-type conjugative transfer relaxase TraA; This protein contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, pfam03389) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, TIGR02760). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer.
Pssm-ID: 274289 [Multi-domain] Cd Length: 744 Bit Score: 79.85 E-value: 2.08e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 115 QPDDATLQKKLREHLMS-------GKPSSFNDVSPVTTAEMIlaRKKAGLLskgsvttpspqgakkRRFEELKEEKERGT 187
Cdd:TIGR02768 276 YIDDPQQFQQLMARVLAspqlvalGDPGTGKEPARFSTREMI--RLEAQMA---------------RSAEALSQSQGHGV 338
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 188 MPAAKKlyaSTTDESLRLSEEQMEVLRACT-SGKSVFFTGSAGTGKSFLLRRIISALPPDG--TVATASTGVAAcliggT 264
Cdd:TIGR02768 339 SPPIVD---AAIDQHYRLSEEQYEAVRHVTgSGDIAVVVGRAGTGKSTMLKAAREAWEAAGyrVIGAALSGKAA-----E 410
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 265 TLHAFAGIgggDATMQRCLELASRPANAQTWRKcKRLIIDEISMVDGQFFEKIEAVARHirrndrpfGGIQLILCGDFLQ 344
Cdd:TIGR02768 411 GLQAESGI---ESRTLASLEYAWANGRDLLSDK-DVLVIDEAGMVGSRQMARVLKEAEE--------AGAKVVLVGDPEQ 478
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 345 LPPVIKGD--------FGAAPTATPQQrfcfQSSAWEtciqcvyelkqvhRQSDPEFVK--ILN---------HLRIGHV 405
Cdd:TIGR02768 479 LQPIEAGAafraiaerIGYAELETIRR----QREAWA-------------RQASLELARgdVEKalaayrdhgHITIHDT 541
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 406 NDSITSRLAATSKQKIEGNGILATQLC-SHTN-DANSINESKLENLDGDKILfkaDDSDASMTRTLDQQIQAPSQLYLKV 483
Cdd:TIGR02768 542 REEAIEQVVADWKQDLREANPAGSQIMlAHTRkDVRALNEAAREALIERGEL---GESILFQTARGERKFAAGDRIVFLE 618
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 484 NAQVMllkninisnGLVNGARGVVVRMEKDLPVVRFKNNqeyvckhERWIIKTASGNHITRrqvplklAWAFSIHKSQGL 563
Cdd:TIGR02768 619 NNRDL---------GVKNGMLGTVEEIEDGRLVVQLDSG-------ELVIIPQAEYDALDH-------GYATTIHKSQGV 675
|
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 19920652 564 TLDCVEMSLSKVFEAGQAYVALSRAKslqsirildfDAKQVWANPHVLQFYKGF-----RRKLMDTTM 626
Cdd:TIGR02768 676 TVDRAFVLASKSMDRHLAYVAMTRHR----------ESVQLYAGKEDFTDRGALvktlsRSSTKDTTL 733
|
|
| SF1_C_RecD |
cd18809 |
C-terminal helicase domain of RecD family helicases; RecD is a member of the RecBCD (EC 3.1.11. ... |
550-594 |
3.92e-14 |
|
C-terminal helicase domain of RecD family helicases; RecD is a member of the RecBCD (EC 3.1.11.5, Exonuclease V) complex. It is the alpha chain of the complex and functions as a 3'-5' helicase. The RecBCD enzyme is both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA. RecD family helicases are DEAD-like helicases belonging to superfamily (SF)1, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF2 helicases, SF1 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: 350196 [Multi-domain] Cd Length: 80 Bit Score: 67.97 E-value: 3.92e-14
10 20 30 40
....*....|....*....|....*....|....*....|....*...
gi 19920652 550 KLAWAFSIHKSQGLTLDCVEMSLSKV---FEAGQAYVALSRAKSLQSI 594
Cdd:cd18809 31 LQAYAMTIHKSQGSEFDRVIVVLPTShpmLSRGLLYTALTRARKLLTL 78
|
|
| recD |
TIGR01447 |
exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha ... |
205-620 |
9.20e-14 |
|
exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273631 [Multi-domain] Cd Length: 582 Bit Score: 74.41 E-value: 9.20e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 205 LSEEQMEVLRAC-TSGKSVFF--TGSAGTGKSFLLRRIISAL------PPDGTVA-TASTGVAAC----LIGG------T 264
Cdd:TIGR01447 142 LLNEQNWRKTAVaLALKSNFSliTGGPGTGKTTTVARLLLALvkqspkQGKLRIAlAAPTGKAAArlaeSLRKavknlaA 221
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 265 TLHAFAGIGGGDATMQRCLelASRPANAqTWRKCKR-------LIIDEISMVDGQFFEKI-EAVArhirrndrpfGGIQL 336
Cdd:TIGR01447 222 AEALIAALPSEAVTIHRLL--GIKPDTK-RFRHHERnplpldvLVVDEASMVDLPLMAKLlKALP----------PNTKL 288
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 337 ILCGDFLQLPPVIKGDFGAaptatPQQRFCFQSSAWETCIQCVYELKQVHRQSDPEFVKILNHlRIGHvnDSITSRLAat 416
Cdd:TIGR01447 289 ILLGDKNQLPSVEAGAVLG-----DLCELASIGKSILYALCKKINSKTRNPLSDNVCFLKTSH-RFGK--DSGIGQLA-- 358
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 417 skqkiegNGILATQLCSHTNDANSINESKLENLDGDK---------------------ILFKADDSDASMTR-------- 467
Cdd:TIGR01447 359 -------KAINSGDIEAVLNNLRSGQLIEFEFLNSKEdaierlknlyvkyrtflqklaALSDAKEILETFDRlrlltalr 431
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 468 -------TLDQQIQAPSQ-LYLKVNAQ-------VMLLKNiNISNGLVNGARGVVVRMEKDLPVVRFKNNQeyvckHERW 532
Cdd:TIGR01447 432 dgpfgvlGLNRRIEQELQeKYFDPDEEgwyigrpIMVTEN-DYTLGLFNGDIGVLLRDPDGILTVWFHFAD-----GSKA 505
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 533 IIKTASGNHITrrqvplklAWAFSIHKSQGLTLDCVEMSL----SKVFEAGQAYVALSRAKslqsirildfDAKQVWANP 608
Cdd:TIGR01447 506 VLPSRLPNYET--------AFAMTVHKSQGSEFDHVILILpngnSPVLTRELLYTGITRAK----------DQLSVWSDK 567
|
490
....*....|..
gi 19920652 609 HVLQfyKGFRRK 620
Cdd:TIGR01447 568 ETLN--AAIKRK 577
|
|
| AAA_19 |
pfam13245 |
AAA domain; |
209-348 |
7.76e-10 |
|
AAA domain;
Pssm-ID: 433059 [Multi-domain] Cd Length: 136 Bit Score: 57.23 E-value: 7.76e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 209 QMEVLRACTSGKSVFFTGSAGTGKSFLLRRIISAL-----PPDGTVATASTGVAA------CLIGGTTLHAFAGIGGGDA 277
Cdd:pfam13245 1 QREAVRTALPSKVVLLTGGPGTGKTTTIRHIVALLvalggVSFPILLAAPTGRAAkrlserTGLPASTIHRLLGFDDLEA 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 19920652 278 tmqrcLELASRPANAqtwRKCKRLIIDEISMVDG-QFFEKIEAVARhirrndrpfgGIQLILCGDFLQLPPV 348
Cdd:pfam13245 81 -----GGFLRDEEEP---LDGDLLIVDEFSMVDLpLAYRLLKALPD----------GAQLLLVGDPDQLPSV 134
|
|
| SF1_C |
cd18786 |
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ... |
493-589 |
2.10e-09 |
|
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family members include UvrD/Rep, Pif1-like, and Upf-1-like proteins. Similar to SF2 helicases, they do not form toroidal, predominantly hexameric structures like SF3-6. SF1 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: 350173 [Multi-domain] Cd Length: 89 Bit Score: 54.75 E-value: 2.10e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 493 INISNGLVNGArgVVVRMEKDLPVVRfknnqeyvckherwiiKTASGNHITrrQVPLKLAWAFSIHKSQGLTLDCVEMSL 572
Cdd:cd18786 4 VNAANGLYKGV--VLTPYHRDRAYLN----------------QYLQGLSLD--EFDLQLVGAITIDSSQGLTFDVVTLYL 63
|
90
....*....|....*....
gi 19920652 573 S--KVFEAGQAYVALSRAK 589
Cdd:cd18786 64 PtaNSLTPRRLYVALTRAR 82
|
|
| AAA_22 |
pfam13401 |
AAA domain; |
218-340 |
2.18e-05 |
|
AAA domain;
Pssm-ID: 379165 [Multi-domain] Cd Length: 129 Bit Score: 44.25 E-value: 2.18e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 218 SGKSVFFTGSAGTGKSFLLRRIISALPPDGtvataSTGVAACLIGGTT--------LHAFAGIGGGDATMQRCLELASRP 289
Cdd:pfam13401 4 GAGILVLTGESGTGKTTLLRRLLEQLPEVR-----DSVVFVDLPSGTSpkdllralLRALGLPLSGRLSKEELLAALQQL 78
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|.
gi 19920652 290 ANAQtwRKCKRLIIDEISMVDGQFFEKIeavaRHIRRNDRpfGGIQLILCG 340
Cdd:pfam13401 79 LLAL--AVAVVLIIDEAQHLSLEALEEL----RDLLNLSS--KLLQLILVG 121
|
|
| AAA_16 |
pfam13191 |
AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the ... |
207-331 |
4.43e-04 |
|
AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily.
Pssm-ID: 433025 [Multi-domain] Cd Length: 167 Bit Score: 41.34 E-value: 4.43e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 207 EEQMEVLRAC------TSGKSVFFTGSAGTGKSFLLRRIISALPPDGTVATASTGVAAcliggTTLHAFAGIGGGDATMq 280
Cdd:pfam13191 6 EEELEQLLDAldrvrsGRPPSVLLTGEAGTGKTTLLRELLRALERDGGYFLRGKCDEN-----LPYSPLLEALTREGLL- 79
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*
gi 19920652 281 RCLELASRPANAQTWRKCKRLIIDEISMVDGQ----FFEKIEAVARHIRRNDRPF 331
Cdd:pfam13191 80 RQLLDELESSLLEAWRAALLEALAPVPELPGDlaerLLDLLLRLLDLLARGERPL 134
|
|
| AAA |
smart00382 |
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ... |
218-338 |
5.72e-04 |
|
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.
Pssm-ID: 214640 [Multi-domain] Cd Length: 148 Bit Score: 40.82 E-value: 5.72e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 218 SGKSVFFTGSAGTGKSFLLRRIISALPPDGTV-----ATASTGVAACLIGGTTLHAFAGIGGGDATMQRCLELASRPana 292
Cdd:smart00382 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGviyidGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALALARKL--- 77
|
90 100 110 120
....*....|....*....|....*....|....*....|....*...
gi 19920652 293 qtwrKCKRLIIDEISMVDGQFFEKIEAVARHIRRNDR--PFGGIQLIL 338
Cdd:smart00382 78 ----KPDVLILDEITSLLDAEQEALLLLLEELRLLLLlkSEKNLTVIL 121
|
|
| DEXXQc_Upf1-like |
cd17934 |
DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, ... |
229-352 |
1.06e-03 |
|
DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, HELZ, Mov10L1, Aquarius, IGHMBP2 (SMUBP2), coronavirus Nsp13, and similar proteins. They belong to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 438708 [Multi-domain] Cd Length: 121 Bit Score: 39.53 E-value: 1.06e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920652 229 GTGKSFLLRRIISAL---PPDGTVA-TASTGVAAcliggttlhafagigggdatmqrclelasrpANAQTwrkckrLIID 304
Cdd:cd17934 9 GTGKTTTIAAIVLQLlkgLRGKRVLvTAQSNVAV-------------------------------DNVDV------VIID 51
|
90 100 110 120
....*....|....*....|....*....|....*....|....*...
gi 19920652 305 EISMVDGQffekiEAVArHIRRNDRpfggiqLILCGDFLQLPPVIKGD 352
Cdd:cd17934 52 EASQITEP-----ELLI-ALIRAKK------VVLVGDPKQLPPVVQED 87
|
|
| UvrD_C_2 |
pfam13538 |
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety ... |
551-589 |
7.92e-03 |
|
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety of helicase enzymes. This domain has a AAA-like structural fold.
Pssm-ID: 463913 [Multi-domain] Cd Length: 52 Bit Score: 34.86 E-value: 7.92e-03
10 20 30 40
....*....|....*....|....*....|....*....|....*.
gi 19920652 551 LAWAFSIHKSQGLTLDCV---EMSLSKVFEAGQA----YVALSRAK 589
Cdd:pfam13538 1 LAYALTVHKAQGSEFPAVflvDPDLTAHYHSMLRrrllYTAVTRAR 46
|
|
| |
