|
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 ... |
235-414 |
1.08e-79 |
|
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: 252.17 E-value: 1.08e-79
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321820 235 EQERVVNLIVKKRtNVFYTGSAGTGKSVILQTIIRQLSSlyGKESIAITASTGLAAVTIGGSTLHKWSGIGIGNKTIDQL 314
Cdd:cd18037 1 EQRRVLDLVLDGK-NVFFTGSAGTGKSYLLRRIIRALPS--RPKRVAVTASTGIAACNIGGTTLHSFAGIGLGSEPAEDL 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321820 315 VKKIQSQKDLLAAWRYTKVLIIDEISMVDGNLLDKLEQIARRIRKNDDPFGGIQLVLTGDFFQLPPVAKKDE------HN 388
Cdd:cd18037 78 LERVKRSPYLVQRWRKCDVLIIDEISMLDADLFDKLDRVAREVRGSDKPFGGIQLILCGDFLQLPPVTKNSErqafffRG 157
|
170 180
....*....|....*....|....*.
gi 6321820 389 VVKFCFESEMWKRCIQKTILLTKVFR 414
Cdd:cd18037 158 DQQFCFEAKSWERCIFLTVELTKVFR 183
|
|
| PIF1 |
pfam05970 |
PIF1-like helicase; This family includes homologs of the PIF1 helicase, which inhibits ... |
232-534 |
2.72e-55 |
|
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: 193.37 E-value: 2.72e-55
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321820 232 LTMEQERVVNLIV-----KKRTNVFYTGSAGTGKSVILQTIIRQLSSlyGKESIAITASTGLAAVTI-GGSTLHKWSGIG 305
Cdd:pfam05970 1 LNDEQKKVFDAIIesvinNKGGVFFVYGYGGTGKTFLWKAIITSLRS--EGKIVLAVASSGVAALLLpGGRTAHSRFGIP 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321820 306 IGnktIDQLVK-KIQSQKDLLAAWRYTKVLIIDEISMVDGNLLDKLEQIARRIRKNDD--PFGGIQLVLTGDFFQLPPVA 382
Cdd:pfam05970 79 LD---IDELSTcKIKRGSKLAELLEKTSLIVWDEAPMTHRHCFEALDRTLRDILSETDdkPFGGKTVVLGGDFRQILPVI 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321820 383 KK--DEHNVVKFCFESEMWKRCiqKTILLTKVFRQQDNKL-----------IDILNAIRYG--------ELTVDIAKTIR 441
Cdd:pfam05970 156 PKgsRPEIVNASITNSYLWKHV--KVLELTKNMRLLADSLdqteakelqdfSDWLLAIGDGkindenerEQLIDIPIDIL 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321820 442 nLNRDID---------YADGIAP----------TELYATRREVELSNVKKLQSLPGDLYEFKAVD-------------NA 489
Cdd:pfam05970 234 -LNTGGDpieaivsevYPDILQNstdpnyleerAILCPTNEDVDEINNYRLSQLPGEEKEYLSSDsisksdndseidaLY 312
|
330 340 350 360
....*....|....*....|....*....|....*....|....*.
gi 6321820 490 PERYQAILDSSLMVEKVVALKEDAQVMMLKN-KPDVELVNGSLGKV 534
Cdd:pfam05970 313 PTEFLNSLNANGLPNHVLKLKVGAPVMLLRNlDQSRGLCNGTRLIV 358
|
|
| RecD |
COG0507 |
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ... |
232-696 |
4.19e-38 |
|
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: 148.97 E-value: 4.19e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321820 232 LTMEQERVVNLIVKKRTNVFYTGSAGTGKSVILQTIIRQLSSLYGKesIAITASTGLAA------VTIGGSTLHKWSGIG 305
Cdd:COG0507 125 LSDEQREAVALALTTRRVSVLTGGAGTGKTTTLRALLAALEALGLR--VALAAPTGKAAkrlsesTGIEARTIHRLLGLR 202
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321820 306 IGNKTIDQLVKKIQSQKDllaawrytkVLIIDEISMVDGNLLDKLEQIARRirknddpfGGIQLVLTGDFFQLPPVAKKd 385
Cdd:COG0507 203 PDSGRFRHNRDNPLTPAD---------LLVVDEASMVDTRLMAALLEALPR--------AGARLILVGDPDQLPSVGAG- 264
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321820 386 ehNVVKfcfesEMWKRCIQKTILLTKVFRQ-QDNKLIDILNAIRYGeltvDIAKTIRNLNRDIDYadgiAPTELYATRRE 464
Cdd:COG0507 265 --AVLR-----DLIESGTVPVVELTEVYRQaDDSRIIELAHAIREG----DAPEALNARYADVVF----VEAEDAEEAAE 329
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321820 465 VELSNVKKLQSLPGDLY-----EFKAVD-NapERYQAILDSSLMVEKVVA------LKEDAQVMMLKNKPDVELVNGSLG 532
Cdd:COG0507 330 AIVELYADRPAGGEDIQvlaptNAGVDAlN--QAIREALNPAGELERELAedgeleLYVGDRVMFTRNDYDLGVFNGDIG 407
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321820 533 KVLffvteslvvkmkeiyKIVDDEvvmdmrlvsrvignpllkeskefrqdlnARPLARLERlkilinyavkisphkekfp 612
Cdd:COG0507 408 TVL---------------SIDEDE----------------------------GRLTVRFDG------------------- 425
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321820 613 yvrwtvgknkyihelmvperfpidipRENVGLERTQIP-LMLCWALSIHKAQGQTIQRLKVDL----RRIFEAGQVYVAL 687
Cdd:COG0507 426 --------------------------REIVTYDPSELDqLELAYAITVHKSQGSTFDRVILVLpsehSPLLSRELLYTAL 479
|
....*....
gi 6321820 688 SRAVTMDTL 696
Cdd:COG0507 480 TRARELLTL 488
|
|
| SF1_C_RecD |
cd18809 |
C-terminal helicase domain of RecD family helicases; RecD is a member of the RecBCD (EC 3.1.11. ... |
652-690 |
1.05e-09 |
|
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: 55.26 E-value: 1.05e-09
10 20 30 40
....*....|....*....|....*....|....*....|..
gi 6321820 652 MLCWALSIHKAQGQTIQRLKVDL---RRIFEAGQVYVALSRA 690
Cdd:cd18809 31 LQAYAMTIHKSQGSEFDRVIVVLptsHPMLSRGLLYTALTRA 72
|
|
| recD |
TIGR01447 |
exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha ... |
253-381 |
9.35e-09 |
|
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: 58.62 E-value: 9.35e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321820 253 TGSAGTGKSVILQTIIRQL---SSLYGKESIAITASTGLAAVTIGGS----------TLHKWSGIGIGNKTIDQLVKKIQ 319
Cdd:TIGR01447 165 TGGPGTGKTTTVARLLLALvkqSPKQGKLRIALAAPTGKAAARLAESlrkavknlaaAEALIAALPSEAVTIHRLLGIKP 244
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 6321820 320 SQKDllaaWRYTK-------VLIIDEISMVDGNLLDKLEQIARrirknddpfGGIQLVLTGDFFQLPPV 381
Cdd:TIGR01447 245 DTKR----FRHHErnplpldVLVVDEASMVDLPLMAKLLKALP---------PNTKLILLGDKNQLPSV 300
|
|
| AAA |
smart00382 |
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ... |
246-372 |
6.00e-06 |
|
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: 46.60 E-value: 6.00e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321820 246 KRTNVFYTGSAGTGKSVILQTIIRQLSSLYGK-ESIAITASTGLAAVTIGGSTLHKWSGIGIGNKTIDQLVKKIQSQKdl 324
Cdd:smart00382 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGvIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALALARKLK-- 78
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|
gi 6321820 325 laawryTKVLIIDEISMVDGNLLDKLEQIARRIR--KNDDPFGGIQLVLT 372
Cdd:smart00382 79 ------PDVLILDEITSLLDAEQEALLLLLEELRllLLLKSEKNLTVILT 122
|
|
| PRK13889 |
PRK13889 |
conjugal transfer relaxase TraA; Provisional |
224-378 |
2.49e-03 |
|
conjugal transfer relaxase TraA; Provisional
Pssm-ID: 237546 [Multi-domain] Cd Length: 988 Bit Score: 41.21 E-value: 2.49e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321820 224 RSASSPVVLTMEQERVVNLIVKKRTNVFYTGSAGTGKSVILqTIIRQLSSLYGKEsIAITASTGLAAVTI-GGStlhkws 302
Cdd:PRK13889 339 RAEARGLVLSGEQADALAHVTDGRDLGVVVGYAGTGKSAML-GVAREAWEAAGYE-VRGAALSGIAAENLeGGS------ 410
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 6321820 303 giGIGNKTIDQLVKKIQSQKDLLAAwryTKVLIIDEISMVDGNLLDKLEQIARRirknddpfGGIQLVLTGDFFQL 378
Cdd:PRK13889 411 --GIASRTIASLEHGWGQGRDLLTS---RDVLVIDEAGMVGTRQLERVLSHAAD--------AGAKVVLVGDPQQL 473
|
|
| |
|
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 ... |
235-414 |
1.08e-79 |
|
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: 252.17 E-value: 1.08e-79
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321820 235 EQERVVNLIVKKRtNVFYTGSAGTGKSVILQTIIRQLSSlyGKESIAITASTGLAAVTIGGSTLHKWSGIGIGNKTIDQL 314
Cdd:cd18037 1 EQRRVLDLVLDGK-NVFFTGSAGTGKSYLLRRIIRALPS--RPKRVAVTASTGIAACNIGGTTLHSFAGIGLGSEPAEDL 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321820 315 VKKIQSQKDLLAAWRYTKVLIIDEISMVDGNLLDKLEQIARRIRKNDDPFGGIQLVLTGDFFQLPPVAKKDE------HN 388
Cdd:cd18037 78 LERVKRSPYLVQRWRKCDVLIIDEISMLDADLFDKLDRVAREVRGSDKPFGGIQLILCGDFLQLPPVTKNSErqafffRG 157
|
170 180
....*....|....*....|....*.
gi 6321820 389 VVKFCFESEMWKRCIQKTILLTKVFR 414
Cdd:cd18037 158 DQQFCFEAKSWERCIFLTVELTKVFR 183
|
|
| PIF1 |
pfam05970 |
PIF1-like helicase; This family includes homologs of the PIF1 helicase, which inhibits ... |
232-534 |
2.72e-55 |
|
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: 193.37 E-value: 2.72e-55
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321820 232 LTMEQERVVNLIV-----KKRTNVFYTGSAGTGKSVILQTIIRQLSSlyGKESIAITASTGLAAVTI-GGSTLHKWSGIG 305
Cdd:pfam05970 1 LNDEQKKVFDAIIesvinNKGGVFFVYGYGGTGKTFLWKAIITSLRS--EGKIVLAVASSGVAALLLpGGRTAHSRFGIP 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321820 306 IGnktIDQLVK-KIQSQKDLLAAWRYTKVLIIDEISMVDGNLLDKLEQIARRIRKNDD--PFGGIQLVLTGDFFQLPPVA 382
Cdd:pfam05970 79 LD---IDELSTcKIKRGSKLAELLEKTSLIVWDEAPMTHRHCFEALDRTLRDILSETDdkPFGGKTVVLGGDFRQILPVI 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321820 383 KK--DEHNVVKFCFESEMWKRCiqKTILLTKVFRQQDNKL-----------IDILNAIRYG--------ELTVDIAKTIR 441
Cdd:pfam05970 156 PKgsRPEIVNASITNSYLWKHV--KVLELTKNMRLLADSLdqteakelqdfSDWLLAIGDGkindenerEQLIDIPIDIL 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321820 442 nLNRDID---------YADGIAP----------TELYATRREVELSNVKKLQSLPGDLYEFKAVD-------------NA 489
Cdd:pfam05970 234 -LNTGGDpieaivsevYPDILQNstdpnyleerAILCPTNEDVDEINNYRLSQLPGEEKEYLSSDsisksdndseidaLY 312
|
330 340 350 360
....*....|....*....|....*....|....*....|....*.
gi 6321820 490 PERYQAILDSSLMVEKVVALKEDAQVMMLKN-KPDVELVNGSLGKV 534
Cdd:pfam05970 313 PTEFLNSLNANGLPNHVLKLKVGAPVMLLRNlDQSRGLCNGTRLIV 358
|
|
| RecD |
COG0507 |
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ... |
232-696 |
4.19e-38 |
|
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: 148.97 E-value: 4.19e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321820 232 LTMEQERVVNLIVKKRTNVFYTGSAGTGKSVILQTIIRQLSSLYGKesIAITASTGLAA------VTIGGSTLHKWSGIG 305
Cdd:COG0507 125 LSDEQREAVALALTTRRVSVLTGGAGTGKTTTLRALLAALEALGLR--VALAAPTGKAAkrlsesTGIEARTIHRLLGLR 202
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321820 306 IGNKTIDQLVKKIQSQKDllaawrytkVLIIDEISMVDGNLLDKLEQIARRirknddpfGGIQLVLTGDFFQLPPVAKKd 385
Cdd:COG0507 203 PDSGRFRHNRDNPLTPAD---------LLVVDEASMVDTRLMAALLEALPR--------AGARLILVGDPDQLPSVGAG- 264
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321820 386 ehNVVKfcfesEMWKRCIQKTILLTKVFRQ-QDNKLIDILNAIRYGeltvDIAKTIRNLNRDIDYadgiAPTELYATRRE 464
Cdd:COG0507 265 --AVLR-----DLIESGTVPVVELTEVYRQaDDSRIIELAHAIREG----DAPEALNARYADVVF----VEAEDAEEAAE 329
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321820 465 VELSNVKKLQSLPGDLY-----EFKAVD-NapERYQAILDSSLMVEKVVA------LKEDAQVMMLKNKPDVELVNGSLG 532
Cdd:COG0507 330 AIVELYADRPAGGEDIQvlaptNAGVDAlN--QAIREALNPAGELERELAedgeleLYVGDRVMFTRNDYDLGVFNGDIG 407
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321820 533 KVLffvteslvvkmkeiyKIVDDEvvmdmrlvsrvignpllkeskefrqdlnARPLARLERlkilinyavkisphkekfp 612
Cdd:COG0507 408 TVL---------------SIDEDE----------------------------GRLTVRFDG------------------- 425
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321820 613 yvrwtvgknkyihelmvperfpidipRENVGLERTQIP-LMLCWALSIHKAQGQTIQRLKVDL----RRIFEAGQVYVAL 687
Cdd:COG0507 426 --------------------------REIVTYDPSELDqLELAYAITVHKSQGSTFDRVILVLpsehSPLLSRELLYTAL 479
|
....*....
gi 6321820 688 SRAVTMDTL 696
Cdd:COG0507 480 TRARELLTL 488
|
|
| DEXSc_RecD-like |
cd17933 |
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ... |
235-413 |
2.62e-22 |
|
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: 93.77 E-value: 2.62e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321820 235 EQERVVNLIVKKRTNVFyTGSAGTGKSVILQTIIRQLSSlyGKESIAITASTGLAAVTIGGSTlhkwsgiGIGNKTIDQL 314
Cdd:cd17933 1 EQKAAVRLVLRNRVSVL-TGGAGTGKTTTLKALLAALEA--EGKRVVLAAPTGKAAKRLSEST-------GIEASTIHRL 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321820 315 VKkIQSQKDLLAAWRYTK----VLIIDEISMVDGNLLDKLEQIARRirknddpfgGIQLVLTGDFFQLPPVAKKdehNVV 390
Cdd:cd17933 71 LG-INPGGGGFYYNEENPldadLLIVDEASMVDTRLMAALLSAIPA---------GARLILVGDPDQLPSVGAG---NVL 137
|
170 180
....*....|....*....|...
gi 6321820 391 KFcfeseMWKRCIQKTILLTKVF 413
Cdd:cd17933 138 RD-----LIASKGVPTVELTEVF 155
|
|
| AAA_30 |
pfam13604 |
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ... |
232-445 |
5.60e-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: 82.61 E-value: 5.60e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321820 232 LTMEQERVVNLIVKKRTNVF-YTGSAGTGKSVILQTIIRQLSSLyGKESIAItASTGLAAVTIGGSTlhkwsgiGIGNKT 310
Cdd:pfam13604 2 LNAEQAAAVRALLTSGDRVAvLVGPAGTGKTTALKALREAWEAA-GYRVIGL-APTGRAAKVLGEEL-------GIPADT 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321820 311 IDQLVKKIQSQKDLLAAwrytKVLIIDEISMVDgnlLDKLEQIARRIRKNddpfgGIQLVLTGDFFQLPPVAKKDehnVV 390
Cdd:pfam13604 73 IAKLLHRLGGRAGLDPG----TLLIVDEAGMVG---TRQMARLLKLAEDA-----GARVILVGDPRQLPSVEAGG---AF 137
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*
gi 6321820 391 KFCFESEMwkrciqKTILLTKVFRQQDNKLIDILNAIRYGeltvDIAKTIRNLNR 445
Cdd:pfam13604 138 RDLLAAGI------GTAELTEIVRQRDPWQRAASLALRDG----DPAEALDALAD 182
|
|
| AAA_19 |
pfam13245 |
AAA domain; |
236-381 |
3.92e-11 |
|
AAA domain;
Pssm-ID: 433059 [Multi-domain] Cd Length: 136 Bit Score: 61.08 E-value: 3.92e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321820 236 QERVVNLIVKKRtNVFYTGSAGTGKSVILQTIIRQLSSLYG-KESIAITASTGLAAVTIG------GSTLHKWsgigIGN 308
Cdd:pfam13245 1 QREAVRTALPSK-VVLLTGGPGTGKTTTIRHIVALLVALGGvSFPILLAAPTGRAAKRLSertglpASTIHRL----LGF 75
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 6321820 309 KTIDQLVKKIQSQKDLLAAWrytkvLIIDEISMVDGNLLDKL-EQIARrirknddpfgGIQLVLTGDFFQLPPV 381
Cdd:pfam13245 76 DDLEAGGFLRDEEEPLDGDL-----LIVDEFSMVDLPLAYRLlKALPD----------GAQLLLVGDPDQLPSV 134
|
|
| SF1_C_RecD |
cd18809 |
C-terminal helicase domain of RecD family helicases; RecD is a member of the RecBCD (EC 3.1.11. ... |
652-690 |
1.05e-09 |
|
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: 55.26 E-value: 1.05e-09
10 20 30 40
....*....|....*....|....*....|....*....|..
gi 6321820 652 MLCWALSIHKAQGQTIQRLKVDL---RRIFEAGQVYVALSRA 690
Cdd:cd18809 31 LQAYAMTIHKSQGSEFDRVIVVLptsHPMLSRGLLYTALTRA 72
|
|
| recD |
TIGR01447 |
exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha ... |
253-381 |
9.35e-09 |
|
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: 58.62 E-value: 9.35e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321820 253 TGSAGTGKSVILQTIIRQL---SSLYGKESIAITASTGLAAVTIGGS----------TLHKWSGIGIGNKTIDQLVKKIQ 319
Cdd:TIGR01447 165 TGGPGTGKTTTVARLLLALvkqSPKQGKLRIALAAPTGKAAARLAESlrkavknlaaAEALIAALPSEAVTIHRLLGIKP 244
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 6321820 320 SQKDllaaWRYTK-------VLIIDEISMVDGNLLDKLEQIARrirknddpfGGIQLVLTGDFFQLPPV 381
Cdd:TIGR01447 245 DTKR----FRHHErnplpldVLVVDEASMVDLPLMAKLLKALP---------PNTKLILLGDKNQLPSV 300
|
|
| AAA |
smart00382 |
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ... |
246-372 |
6.00e-06 |
|
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: 46.60 E-value: 6.00e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321820 246 KRTNVFYTGSAGTGKSVILQTIIRQLSSLYGK-ESIAITASTGLAAVTIGGSTLHKWSGIGIGNKTIDQLVKKIQSQKdl 324
Cdd:smart00382 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGvIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALALARKLK-- 78
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|
gi 6321820 325 laawryTKVLIIDEISMVDGNLLDKLEQIARRIR--KNDDPFGGIQLVLT 372
Cdd:smart00382 79 ------PDVLILDEITSLLDAEQEALLLLLEELRllLLLKSEKNLTVILT 122
|
|
| TraA_Ti |
TIGR02768 |
Ti-type conjugative transfer relaxase TraA; This protein contains domains distinctive of a ... |
232-383 |
7.71e-05 |
|
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: 45.95 E-value: 7.71e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321820 232 LTMEQERVVNLIVKKRTNVFYTGSAGTGKSVILqTIIRQLSSLYGKESIAiTASTGLAAVTIGGSTlhkwsgiGIGNKTI 311
Cdd:TIGR02768 353 LSEEQYEAVRHVTGSGDIAVVVGRAGTGKSTML-KAAREAWEAAGYRVIG-AALSGKAAEGLQAES-------GIESRTL 423
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 6321820 312 DQLVKKIQSQKDLLAAwryTKVLIIDEISMVDGNLLDKLEQIARRirknddpfGGIQLVLTGDFFQLPPVAK 383
Cdd:TIGR02768 424 ASLEYAWANGRDLLSD---KDVLVIDEAGMVGSRQMARVLKEAEE--------AGAKVVLVGDPEQLQPIEA 484
|
|
| AAA_22 |
pfam13401 |
AAA domain; |
253-373 |
1.88e-04 |
|
AAA domain;
Pssm-ID: 379165 [Multi-domain] Cd Length: 129 Bit Score: 41.94 E-value: 1.88e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321820 253 TGSAGTGKSVILQTIIRQLSSlYGKESIAITASTGLAAVTIGGSTLHKWSGIGIGNKTIDQLVKKIQsqkDLLAAWRYTK 332
Cdd:pfam13401 11 TGESGTGKTTLLRRLLEQLPE-VRDSVVFVDLPSGTSPKDLLRALLRALGLPLSGRLSKEELLAALQ---QLLLALAVAV 86
|
90 100 110 120
....*....|....*....|....*....|....*....|.
gi 6321820 333 VLIIDEISMVDGNLLDKLeqiaRRIRknDDPFGGIQLVLTG 373
Cdd:pfam13401 87 VLIIDEAQHLSLEALEEL----RDLL--NLSSKLLQLILVG 121
|
|
| AAA_7 |
pfam12775 |
P-loop containing dynein motor region; This domain is found in human cytoplasmic dynein-2 ... |
230-273 |
2.55e-04 |
|
P-loop containing dynein motor region; This domain is found in human cytoplasmic dynein-2 proteins. Cytoplasmic dynein-2 (dynein-2) performs intraflagellar transport and is associated with human skeletal ciliopathies. Dyneins share a conserved motor domain that couples cycles of ATP hydrolysis with conformational changes to produce movement. Structural analysis reveal that the motor's ring consists of six AAA+ domains (ATPases associated with various cellular activities (AAA1-AAA6). This is the third nucleotide binding sites in the dynein motor. However, AAA3 has lost the catalytic residues necessary for ATP hydrolysis (the Walker B glutamate, the arginine finger, sensor-I and sensor-II motifs).
Pssm-ID: 463698 [Multi-domain] Cd Length: 179 Bit Score: 42.38 E-value: 2.55e-04
10 20 30 40
....*....|....*....|....*....|....*....|....*..
gi 6321820 230 VVLTMEQER---VVNLIVKKRTNVFYTGSAGTGKSVILQTIIRQLSS 273
Cdd:pfam12775 11 LVPTVDTVRytyLLDLLLKNGKPVLLVGPTGTGKTVIIQNLLRKLDK 57
|
|
| SF1_C |
cd18786 |
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ... |
643-692 |
1.60e-03 |
|
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: 38.19 E-value: 1.60e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|..
gi 6321820 643 GLERTQIPLMLCWALSIHKAQGQTIQR--LKVDLRRIFEAGQVYVALSRAVT 692
Cdd:cd18786 32 GLSLDEFDLQLVGAITIDSSQGLTFDVvtLYLPTANSLTPRRLYVALTRARK 83
|
|
| TraI_TIGR |
TIGR02760 |
conjugative transfer relaxase protein TraI; This protein is a component of the relaxosome ... |
232-445 |
2.28e-03 |
|
conjugative transfer relaxase protein TraI; This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.
Pssm-ID: 274285 [Multi-domain] Cd Length: 1960 Bit Score: 41.43 E-value: 2.28e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321820 232 LTMEQERVVNLIVK-KRTNVFYTGSAGTGKSVILQTIIRQLSSLYGKESIAItasTGLAAVTIGGSTLHKwsgIGIGNKT 310
Cdd:TIGR02760 1020 LTHGQKQAIHLIIStKDRFVAVQGLAGVGKTTMLESRYKPVLQAFESEQLQV---IGLAPTHEAVGELKS---AGVQAQT 1093
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321820 311 IDQLVKKIQSQKDLLAAWRYTkVLIIDEISMVDGnlldklEQIARRIRKNDDPfgGIQLVLTGDFFQLPPVAKKDEhnvv 390
Cdd:TIGR02760 1094 LDSFLTDISLYRNSGGDFRNT-LFILDESSMVSN------FQLTHATELVQKS--GSRAVSLGDIAQLQSLAAGKP---- 1160
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*
gi 6321820 391 kfcFESEMwKRCIQKTILLTKVFRQQDNKLidiLNAIRYGELTVDIAKTIRNLNR 445
Cdd:TIGR02760 1161 ---FELAI-TFDIIDTAIMKEIVRQNNSAE---LKAAHNSLDKRSNPKALELLKN 1208
|
|
| PRK13889 |
PRK13889 |
conjugal transfer relaxase TraA; Provisional |
224-378 |
2.49e-03 |
|
conjugal transfer relaxase TraA; Provisional
Pssm-ID: 237546 [Multi-domain] Cd Length: 988 Bit Score: 41.21 E-value: 2.49e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321820 224 RSASSPVVLTMEQERVVNLIVKKRTNVFYTGSAGTGKSVILqTIIRQLSSLYGKEsIAITASTGLAAVTI-GGStlhkws 302
Cdd:PRK13889 339 RAEARGLVLSGEQADALAHVTDGRDLGVVVGYAGTGKSAML-GVAREAWEAAGYE-VRGAALSGIAAENLeGGS------ 410
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 6321820 303 giGIGNKTIDQLVKKIQSQKDLLAAwryTKVLIIDEISMVDGNLLDKLEQIARRirknddpfGGIQLVLTGDFFQL 378
Cdd:PRK13889 411 --GIASRTIASLEHGWGQGRDLLTS---RDVLVIDEAGMVGTRQLERVLSHAAD--------AGAKVVLVGDPQQL 473
|
|
| AAA |
cd00009 |
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ... |
249-372 |
6.15e-03 |
|
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.
Pssm-ID: 99707 [Multi-domain] Cd Length: 151 Bit Score: 37.90 E-value: 6.15e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6321820 249 NVFYTGSAGTGKSVILQTIIRQLSsLYGKESIAITASTGLAavtiggstlhKWSGIGIGNKTIDQLVKKIQSQKDLlaaw 328
Cdd:cd00009 21 NLLLYGPPGTGKTTLARAIANELF-RPGAPFLYLNASDLLE----------GLVVAELFGHFLVRLLFELAEKAKP---- 85
|
90 100 110 120
....*....|....*....|....*....|....*....|....
gi 6321820 329 rytKVLIIDEISMVDGNLLDKLEQIARRIRKNDDPFGGIQLVLT 372
Cdd:cd00009 86 ---GVLFIDEIDSLSRGAQNALLRVLETLNDLRIDRENVRVIGA 126
|
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