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Conserved domains on  [gi|642905958|ref|YP_009037489|]
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Dda-like helicase [Escherichia phage vB_EcoM_JS09]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SH3_14 super family cl39689
Dda helicase SH3 domain; This is a Src homology-3 (SH3) like beta-barrel domain which can be ...
 257-387 2.15e-51

Dda helicase SH3 domain; This is a Src homology-3 (SH3) like beta-barrel domain which can be found in Dda enzyme. Dda is a phage T4 SF1B helicase. The Dda SH3 domain contains two insertions (compared to RecD2), a second beta-ribbon that is referred to as the hook and a beta-ribbon/two-helix substructure that is referred to as the tower. The tower region within the domain is rigidly connected to domain 2A in Dda and appears to be specifically designed for the task of supporting the extended pin. Hence, it is suggested that 2A and this SH3 domain move as one unit during the ATP-driven translocation of ssDNA while maintaining contact with the pin. In this scenario, the pin-tower interaction can be considered as an additional transmission site that serves to more efficiently couple the energy from ATP binding and hydrolysis to the unwinding of dsDNA.


The actual alignment was detected with superfamily member pfam18343:

Pssm-ID: 408149  Cd Length: 134  Bit Score: 169.49  E-value: 2.15e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958  257 EKPFIKDEVIVLQEPFTKTYKLDGKN-MTEMLFNNGQFVRIRDAVETSTFVKARGVSGEYMI---RYWNLTVETYGDDEE 332
Cdd:pfam18343   1 DEDFIPGEIIVTQEPLFKSYKIDGKYpVCEIIFENGELVKIIDAEYTSTFVKAKGIDGELLIvdnEAFDLAVETVEDDDG 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 642905958  333 YiREDIKVISSEEELYKFNLFLAKTAETYKFWNKGGKAPWSEFWDAKRMFTKVKA 387
Cdd:pfam18343  81 N-REEFKIISDDEEKEKFALFLGKAAETYKNMNGGGKAPWRAFWDAKEQFIETKA 134
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 5-437 1.70e-43

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: 159.37  E-value: 1.70e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958   5 DLTEGQKNAFnvvmEAIKEKKHHVTINGPAGTGKTTLTRFIVEALISSGESgIILAAPTHAAKKVLSKLAGQEASTIHSI 84
Cdd:COG0507  124 TLSDEQREAV----ALALTTRRVSVLTGGAGTGKTTTLRALLAALEALGLR-VALAAPTGKAAKRLSESTGIEARTIHRL 198

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958  85 LKINPttyeENVLFEQKKVPDLALCRVLLFDEASMCDRSLFKIMLASIPKW-CTVIGIGDRCQIRPVDPGestAYLSPFF 163
Cdd:COG0507  199 LGLRP----DSGRFRHNRDNPLTPADLLVVDEASMVDTRLMAALLEALPRAgARLILVGDPDQLPSVGAG---AVLRDLI 271

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958 164 THKDFVQCNLTEVKR--SNAPIIDVATDIRNGKwiYDKVVDGhgvhGYTDLksymmnYFNVVKTPEDLFEN--------- 232
Cdd:COG0507  272 ESGTVPVVELTEVYRqaDDSRIIELAHAIREGD--APEALNA----RYADV------VFVEAEDAEEAAEAivelyadrp 339

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958 233 ------RMMAFTNKSVDKLNSIIRRKLL---ETEKPFIKDE---------VIVLqepftktykldgKNMTEMLFNNGQFV 294
Cdd:COG0507  340 aggediQVLAPTNAGVDALNQAIREALNpagELERELAEDGelelyvgdrVMFT------------RNDYDLGVFNGDIG 407

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958 295 RIRDAVETSTFVKARgVSGEYMIRYwnltvetygDDEEYiredikvisseEELykfnlflaKTAetYkfwnkggkapwse 374
Cdd:COG0507  408 TVLSIDEDEGRLTVR-FDGREIVTY---------DPSEL-----------DQL--------ELA--Y------------- 443

                        410       420       430       440       450       460
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 642905958 375 fwdakrmftkvkalpVSTFHKAQGMSVDTAFVYTPCIHYAdsELAKQLLYVGTTRGRFDVHFI 437
Cdd:COG0507  444 ---------------AITVHKSQGSTFDRVILVLPSEHSP--LLSRELLYTALTRARELLTLV 489
 
Name Accession Description Interval E-value
SH3_14 pfam18343
Dda helicase SH3 domain; This is a Src homology-3 (SH3) like beta-barrel domain which can be ...
 257-387 2.15e-51

Dda helicase SH3 domain; This is a Src homology-3 (SH3) like beta-barrel domain which can be found in Dda enzyme. Dda is a phage T4 SF1B helicase. The Dda SH3 domain contains two insertions (compared to RecD2), a second beta-ribbon that is referred to as the hook and a beta-ribbon/two-helix substructure that is referred to as the tower. The tower region within the domain is rigidly connected to domain 2A in Dda and appears to be specifically designed for the task of supporting the extended pin. Hence, it is suggested that 2A and this SH3 domain move as one unit during the ATP-driven translocation of ssDNA while maintaining contact with the pin. In this scenario, the pin-tower interaction can be considered as an additional transmission site that serves to more efficiently couple the energy from ATP binding and hydrolysis to the unwinding of dsDNA.


Pssm-ID: 408149  Cd Length: 134  Bit Score: 169.49  E-value: 2.15e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958  257 EKPFIKDEVIVLQEPFTKTYKLDGKN-MTEMLFNNGQFVRIRDAVETSTFVKARGVSGEYMI---RYWNLTVETYGDDEE 332
Cdd:pfam18343   1 DEDFIPGEIIVTQEPLFKSYKIDGKYpVCEIIFENGELVKIIDAEYTSTFVKAKGIDGELLIvdnEAFDLAVETVEDDDG 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 642905958  333 YiREDIKVISSEEELYKFNLFLAKTAETYKFWNKGGKAPWSEFWDAKRMFTKVKA 387
Cdd:pfam18343  81 N-REEFKIISDDEEKEKFALFLGKAAETYKNMNGGGKAPWRAFWDAKEQFIETKA 134
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 5-437 1.70e-43

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: 159.37  E-value: 1.70e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958   5 DLTEGQKNAFnvvmEAIKEKKHHVTINGPAGTGKTTLTRFIVEALISSGESgIILAAPTHAAKKVLSKLAGQEASTIHSI 84
Cdd:COG0507  124 TLSDEQREAV----ALALTTRRVSVLTGGAGTGKTTTLRALLAALEALGLR-VALAAPTGKAAKRLSESTGIEARTIHRL 198

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958  85 LKINPttyeENVLFEQKKVPDLALCRVLLFDEASMCDRSLFKIMLASIPKW-CTVIGIGDRCQIRPVDPGestAYLSPFF 163
Cdd:COG0507  199 LGLRP----DSGRFRHNRDNPLTPADLLVVDEASMVDTRLMAALLEALPRAgARLILVGDPDQLPSVGAG---AVLRDLI 271

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958 164 THKDFVQCNLTEVKR--SNAPIIDVATDIRNGKwiYDKVVDGhgvhGYTDLksymmnYFNVVKTPEDLFEN--------- 232
Cdd:COG0507  272 ESGTVPVVELTEVYRqaDDSRIIELAHAIREGD--APEALNA----RYADV------VFVEAEDAEEAAEAivelyadrp 339

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958 233 ------RMMAFTNKSVDKLNSIIRRKLL---ETEKPFIKDE---------VIVLqepftktykldgKNMTEMLFNNGQFV 294
Cdd:COG0507  340 aggediQVLAPTNAGVDALNQAIREALNpagELERELAEDGelelyvgdrVMFT------------RNDYDLGVFNGDIG 407

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958 295 RIRDAVETSTFVKARgVSGEYMIRYwnltvetygDDEEYiredikvisseEELykfnlflaKTAetYkfwnkggkapwse 374
Cdd:COG0507  408 TVLSIDEDEGRLTVR-FDGREIVTY---------DPSEL-----------DQL--------ELA--Y------------- 443

                        410       420       430       440       450       460
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 642905958 375 fwdakrmftkvkalpVSTFHKAQGMSVDTAFVYTPCIHYAdsELAKQLLYVGTTRGRFDVHFI 437
Cdd:COG0507  444 ---------------AITVHKSQGSTFDRVILVLPSEHSP--LLSRELLYTALTRARELLTLV 489
DEXSc_RecD-like cd17933
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ...
 9-176 9.64e-41

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: 142.31  E-value: 9.64e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958   9 GQKNAFNVVMeaikeKKHHVTINGPAGTGKTTLTRFIVEALISSGESgIILAAPTHAAKKVLSKLAGQEASTIHSILKIN 88
Cdd:cd17933    1 EQKAAVRLVL-----RNRVSVLTGGAGTGKTTTLKALLAALEAEGKR-VVLAAPTGKAAKRLSESTGIEASTIHRLLGIN 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958  89 PTTYEENvlfeqKKVPDLALCRVLLFDEASMCDRSLFKIMLASIPKWCTVIGIGDRCQIRPVDPGESTAYLspfFTHKDF 168
Cdd:cd17933   75 PGGGGFY-----YNEENPLDADLLIVDEASMVDTRLMAALLSAIPAGARLILVGDPDQLPSVGAGNVLRDL---IASKGV 146


                 ....*...
gi 642905958 169 VQCNLTEV 176
Cdd:cd17933  147 PTVELTEV 154
recD_rel TIGR01448
helicase, putative, RecD/TraA family; This model describes a family similar to RecD, the ...
 6-193 9.34e-25

helicase, putative, RecD/TraA family; This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 273632 [Multi-domain]  Cd Length: 720  Bit Score: 107.18  E-value: 9.34e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958    6 LTEGQKNAfnvvMEAIKEKKHHVTINGPaGTGKTTLTRFIVE--ALISSGESgIILAAPTHAAKKVLSKLAGQEASTIHS 83
Cdd:TIGR01448 324 LSEEQKQA----LDTAIQHKVVILTGGP-GTGKTTITRAIIElaEELGGLLP-VGLAAPTGRAAKRLGEVTGLTASTIHR 397

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958   84 ILKINPTTYEENVLfeQKKVPdlalCRVLLFDEASMCDRSLFKIMLASIPKWCTVIGIGDRCQIRPVDPGEStayLSPFF 163
Cdd:TIGR01448 398 LLGYGPDTFRHNHL--EDPID----CDLLIVDESSMMDTWLALSLLAALPDHARLLLVGDTDQLPSVGPGQV---LKDLI 468

                         170       180       190
                  ....*....|....*....|....*....|..
gi 642905958  164 THKDFVQCNLTEVKR--SNAPIIDVATDIRNG 193
Cdd:TIGR01448 469 LSQAIPVTRLTKVYRqaAGSPIITLAHGILHG 500
AAA_30 pfam13604
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 6-194 3.36e-23

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: 96.09  E-value: 3.36e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958    6 LTEGQKNAfnvVMEAIKEKKHHVTINGPAGTGKTTLTRFIVEALISSGESgIILAAPTHAAKKVLSKLAGQEASTIHSil 85
Cdd:pfam13604   2 LNAEQAAA---VRALLTSGDRVAVLVGPAGTGKTTALKALREAWEAAGYR-VIGLAPTGRAAKVLGEELGIPADTIAK-- 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958   86 kinpttyeenVLFEQKKVPDLALCRVLLFDEASMCDRSLFKIMLASIPKWCT-VIGIGDRCQIRPVDPGestaylSPF-- 162
Cdd:pfam13604  76 ----------LLHRLGGRAGLDPGTLLIVDEAGMVGTRQMARLLKLAEDAGArVILVGDPRQLPSVEAG------GAFrd 139

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 642905958  163 --FTHKDFVQcnLTEVKR-SNAPIIDVATDIRNGK 194
Cdd:pfam13604 140 llAAGIGTAE--LTEIVRqRDPWQRAASLALRDGD 172
recD PRK10875
exodeoxyribonuclease V subunit alpha;
30-153 6.73e-09

exodeoxyribonuclease V subunit alpha;


Pssm-ID: 236783 [Multi-domain]  Cd Length: 615  Bit Score: 58.03  E-value: 6.73e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958  30 INGPAGTGKTTLTRFIVEALI--SSGESGII-LAAPT--HAAK------KVLSKLA---------GQEASTIHSILKINP 89
Cdd:PRK10875 172 ISGGPGTGKTTTVAKLLAALIqlADGERCRIrLAAPTgkAAARlteslgKALRQLPltdeqkkriPEEASTLHRLLGAQP 251

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 642905958  90 TT-----YEENVLfeqkkvpDLalcRVLLFDEASMCDRSLFKIMLASIPKWCTVIGIGDRCQIRPVDPG 153
Cdd:PRK10875 252 GSqrlryHAGNPL-------HL---DVLVVDEASMVDLPMMARLIDALPPHARVIFLGDRDQLASVEAG 310
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 24-132 6.87e-05

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: 42.75  E-value: 6.87e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958    24 KKHHVTINGPAGTGKTTLTRFIVEALISSGESGIILAAPTHAAKKVLSKLAGQEASTIHSILKINpttyEENVLFEQKKV 103
Cdd:smart00382   1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGEL----RLRLALALARK 76

                           90       100       110
                   ....*....|....*....|....*....|
gi 642905958   104 PDLalcRVLLFDEA-SMCDRSLFKIMLASI 132
Cdd:smart00382  77 LKP---DVLILDEItSLLDAEQEALLLLLE 103
 
Name Accession Description Interval E-value
SH3_14 pfam18343
Dda helicase SH3 domain; This is a Src homology-3 (SH3) like beta-barrel domain which can be ...
 257-387 2.15e-51

Dda helicase SH3 domain; This is a Src homology-3 (SH3) like beta-barrel domain which can be found in Dda enzyme. Dda is a phage T4 SF1B helicase. The Dda SH3 domain contains two insertions (compared to RecD2), a second beta-ribbon that is referred to as the hook and a beta-ribbon/two-helix substructure that is referred to as the tower. The tower region within the domain is rigidly connected to domain 2A in Dda and appears to be specifically designed for the task of supporting the extended pin. Hence, it is suggested that 2A and this SH3 domain move as one unit during the ATP-driven translocation of ssDNA while maintaining contact with the pin. In this scenario, the pin-tower interaction can be considered as an additional transmission site that serves to more efficiently couple the energy from ATP binding and hydrolysis to the unwinding of dsDNA.


Pssm-ID: 408149  Cd Length: 134  Bit Score: 169.49  E-value: 2.15e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958  257 EKPFIKDEVIVLQEPFTKTYKLDGKN-MTEMLFNNGQFVRIRDAVETSTFVKARGVSGEYMI---RYWNLTVETYGDDEE 332
Cdd:pfam18343   1 DEDFIPGEIIVTQEPLFKSYKIDGKYpVCEIIFENGELVKIIDAEYTSTFVKAKGIDGELLIvdnEAFDLAVETVEDDDG 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 642905958  333 YiREDIKVISSEEELYKFNLFLAKTAETYKFWNKGGKAPWSEFWDAKRMFTKVKA 387
Cdd:pfam18343  81 N-REEFKIISDDEEKEKFALFLGKAAETYKNMNGGGKAPWRAFWDAKEQFIETKA 134
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 5-437 1.70e-43

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: 159.37  E-value: 1.70e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958   5 DLTEGQKNAFnvvmEAIKEKKHHVTINGPAGTGKTTLTRFIVEALISSGESgIILAAPTHAAKKVLSKLAGQEASTIHSI 84
Cdd:COG0507  124 TLSDEQREAV----ALALTTRRVSVLTGGAGTGKTTTLRALLAALEALGLR-VALAAPTGKAAKRLSESTGIEARTIHRL 198

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958  85 LKINPttyeENVLFEQKKVPDLALCRVLLFDEASMCDRSLFKIMLASIPKW-CTVIGIGDRCQIRPVDPGestAYLSPFF 163
Cdd:COG0507  199 LGLRP----DSGRFRHNRDNPLTPADLLVVDEASMVDTRLMAALLEALPRAgARLILVGDPDQLPSVGAG---AVLRDLI 271

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958 164 THKDFVQCNLTEVKR--SNAPIIDVATDIRNGKwiYDKVVDGhgvhGYTDLksymmnYFNVVKTPEDLFEN--------- 232
Cdd:COG0507  272 ESGTVPVVELTEVYRqaDDSRIIELAHAIREGD--APEALNA----RYADV------VFVEAEDAEEAAEAivelyadrp 339

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958 233 ------RMMAFTNKSVDKLNSIIRRKLL---ETEKPFIKDE---------VIVLqepftktykldgKNMTEMLFNNGQFV 294
Cdd:COG0507  340 aggediQVLAPTNAGVDALNQAIREALNpagELERELAEDGelelyvgdrVMFT------------RNDYDLGVFNGDIG 407

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958 295 RIRDAVETSTFVKARgVSGEYMIRYwnltvetygDDEEYiredikvisseEELykfnlflaKTAetYkfwnkggkapwse 374
Cdd:COG0507  408 TVLSIDEDEGRLTVR-FDGREIVTY---------DPSEL-----------DQL--------ELA--Y------------- 443

                        410       420       430       440       450       460
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 642905958 375 fwdakrmftkvkalpVSTFHKAQGMSVDTAFVYTPCIHYAdsELAKQLLYVGTTRGRFDVHFI 437
Cdd:COG0507  444 ---------------AITVHKSQGSTFDRVILVLPSEHSP--LLSRELLYTALTRARELLTLV 489
DEXSc_RecD-like cd17933
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ...
 9-176 9.64e-41

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: 142.31  E-value: 9.64e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958   9 GQKNAFNVVMeaikeKKHHVTINGPAGTGKTTLTRFIVEALISSGESgIILAAPTHAAKKVLSKLAGQEASTIHSILKIN 88
Cdd:cd17933    1 EQKAAVRLVL-----RNRVSVLTGGAGTGKTTTLKALLAALEAEGKR-VVLAAPTGKAAKRLSESTGIEASTIHRLLGIN 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958  89 PTTYEENvlfeqKKVPDLALCRVLLFDEASMCDRSLFKIMLASIPKWCTVIGIGDRCQIRPVDPGESTAYLspfFTHKDF 168
Cdd:cd17933   75 PGGGGFY-----YNEENPLDADLLIVDEASMVDTRLMAALLSAIPAGARLILVGDPDQLPSVGAGNVLRDL---IASKGV 146


                 ....*...
gi 642905958 169 VQCNLTEV 176
Cdd:cd17933  147 PTVELTEV 154
recD_rel TIGR01448
helicase, putative, RecD/TraA family; This model describes a family similar to RecD, the ...
 6-193 9.34e-25

helicase, putative, RecD/TraA family; This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 273632 [Multi-domain]  Cd Length: 720  Bit Score: 107.18  E-value: 9.34e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958    6 LTEGQKNAfnvvMEAIKEKKHHVTINGPaGTGKTTLTRFIVE--ALISSGESgIILAAPTHAAKKVLSKLAGQEASTIHS 83
Cdd:TIGR01448 324 LSEEQKQA----LDTAIQHKVVILTGGP-GTGKTTITRAIIElaEELGGLLP-VGLAAPTGRAAKRLGEVTGLTASTIHR 397

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958   84 ILKINPTTYEENVLfeQKKVPdlalCRVLLFDEASMCDRSLFKIMLASIPKWCTVIGIGDRCQIRPVDPGEStayLSPFF 163
Cdd:TIGR01448 398 LLGYGPDTFRHNHL--EDPID----CDLLIVDESSMMDTWLALSLLAALPDHARLLLVGDTDQLPSVGPGQV---LKDLI 468

                         170       180       190
                  ....*....|....*....|....*....|..
gi 642905958  164 THKDFVQCNLTEVKR--SNAPIIDVATDIRNG 193
Cdd:TIGR01448 469 LSQAIPVTRLTKVYRqaAGSPIITLAHGILHG 500
AAA_30 pfam13604
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 6-194 3.36e-23

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: 96.09  E-value: 3.36e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958    6 LTEGQKNAfnvVMEAIKEKKHHVTINGPAGTGKTTLTRFIVEALISSGESgIILAAPTHAAKKVLSKLAGQEASTIHSil 85
Cdd:pfam13604   2 LNAEQAAA---VRALLTSGDRVAVLVGPAGTGKTTALKALREAWEAAGYR-VIGLAPTGRAAKVLGEELGIPADTIAK-- 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958   86 kinpttyeenVLFEQKKVPDLALCRVLLFDEASMCDRSLFKIMLASIPKWCT-VIGIGDRCQIRPVDPGestaylSPF-- 162
Cdd:pfam13604  76 ----------LLHRLGGRAGLDPGTLLIVDEAGMVGTRQMARLLKLAEDAGArVILVGDPRQLPSVEAG------GAFrd 139

                         170       180       190
                  ....*....|....*....|....*....|....*
gi 642905958  163 --FTHKDFVQcnLTEVKR-SNAPIIDVATDIRNGK 194
Cdd:pfam13604 140 llAAGIGTAE--LTEIVRqRDPWQRAASLALRDGD 172
AAA_19 pfam13245
AAA domain;
17-152 5.01e-21

AAA domain;


Pssm-ID: 433059 [Multi-domain]  Cd Length: 136  Bit Score: 88.43  E-value: 5.01e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958   17 VMEAIKEKkhHVTINGPAGTGKTTLTRFIVEALISSGES--GIILAAPTHAAKKVLSKLAGQEASTIHSILKINPTTYEE 94
Cdd:pfam13245   5 VRTALPSK--VVLLTGGPGTGKTTTIRHIVALLVALGGVsfPILLAAPTGRAAKRLSERTGLPASTIHRLLGFDDLEAGG 82

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 642905958   95 NVLFEQKKVPdlalCRVLLFDEASMCDRSLFKIMLASIPKWCTVIGIGDRCQIRPVDP 152
Cdd:pfam13245  83 FLRDEEEPLD----GDLLIVDEFSMVDLPLAYRLLKALPDGAQLLLVGDPDQLPSVGP 136
recD TIGR01447
exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha ...
 30-437 5.72e-13

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: 70.56  E-value: 5.72e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958   30 INGPAGTGKTTLTRFIVEALIS----SGESGIILAAPTHAA--------KKVLSKLAGQ---------EASTIHSILKIN 88
Cdd:TIGR01447 164 ITGGPGTGKTTTVARLLLALVKqspkQGKLRIALAAPTGKAaarlaeslRKAVKNLAAAealiaalpsEAVTIHRLLGIK 243

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958   89 PTTYEenvlFEQKKVPDLALcRVLLFDEASMCDRSLFKIMLASIPKWCTVIGIGDRCQIRPVdpgESTAYLSPFfthkdf 168
Cdd:TIGR01447 244 PDTKR----FRHHERNPLPL-DVLVVDEASMVDLPLMAKLLKALPPNTKLILLGDKNQLPSV---EAGAVLGDL------ 309

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958  169 vqCNLTEVKRSNAPIIDVATDIRNGKWIYDKVVDGHgvhgytdlKSYMMNYFNVVKTpedLFENRMMAFTNKSVDKLNSI 248
Cdd:TIGR01447 310 --CELASIGKSILYALCKKINSKTRNPLSDNVCFLK--------TSHRFGKDSGIGQ---LAKAINSGDIEAVLNNLRSG 376

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958  249 IRRKLLETekPFIKDEVIVLQEPFTK--TYKLDGKNMTEMLFNNGQFVRIRdaVETSTFVKARGVSGeymiryWNLTVET 326
Cdd:TIGR01447 377 QLIEFEFL--NSKEDAIERLKNLYVKyrTFLQKLAALSDAKEILETFDRLR--LLTALRDGPFGVLG------LNRRIEQ 446

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958  327 -------YGDDEE-YIREDIKVISSEEELYKFN----LFLAKtaetykfwNKGGKAPWSEFWDAKRMFtKVKALP----- 389
Cdd:TIGR01447 447 elqekyfDPDEEGwYIGRPIMVTENDYTLGLFNgdigVLLRD--------PDGILTVWFHFADGSKAV-LPSRLPnyeta 517

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|
gi 642905958  390 -VSTFHKAQGMSVDTAFVYTPcihYADSE-LAKQLLYVGTTRGRFDVHFI 437
Cdd:TIGR01447 518 fAMTVHKSQGSEFDHVILILP---NGNSPvLTRELLYTGITRAKDQLSVW 564
DEXSc_Pif1_like cd18037
DEAD-box helicase domain of Pif1; Pif1 and other members of this family are RecD-like ...
 10-178 8.78e-13

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: 66.50  E-value: 8.78e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958  10 QKNAFNVVmeaikEKKHHVTINGPAGTGKTTLTRFIVEALISSGESgIILAAPTHAAkkvlSKLAGqeASTIHSILKI-- 87
Cdd:cd18037    2 QRRVLDLV-----LDGKNVFFTGSAGTGKSYLLRRIIRALPSRPKR-VAVTASTGIA----ACNIG--GTTLHSFAGIgl 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958  88 ----NPTTYeENVLFEQKKVPDLALCRVLLFDEASMCDRSLFKiMLASIPKWC----------TVIGIGDRCQIRPV-DP 152
Cdd:cd18037   70 gsepAEDLL-ERVKRSPYLVQRWRKCDVLIIDEISMLDADLFD-KLDRVAREVrgsdkpfggiQLILCGDFLQLPPVtKN 147

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 642905958 153 GESTAYLSPFFTHKDFVQ----------CNLTEVKR 178
Cdd:cd18037  148 SERQAFFFRGDQQFCFEAkswercifltVELTKVFR 183
PIF1 pfam05970
PIF1-like helicase; This family includes homologs of the PIF1 helicase, which inhibits ...
 6-260 4.15e-09

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: 57.78  E-value: 4.15e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958    6 LTEGQKNAFNVVMEA-IKEKKHHVTINGPAGTGKTTLTRFIVEALISSGEsgIILA-APTHAAKKVLSKlagqeASTIHS 83
Cdd:pfam05970   1 LNDEQKKVFDAIIESvINNKGGVFFVYGYGGTGKTFLWKAIITSLRSEGK--IVLAvASSGVAALLLPG-----GRTAHS 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958   84 ILKInPTTYEENVLFEQKKVPDLA----LCRVLLFDEASM----C----DRSLFKIMLASIPK---WCTVIGIGDRCQIR 148
Cdd:pfam05970  74 RFGI-PLDIDELSTCKIKRGSKLAelleKTSLIVWDEAPMthrhCfealDRTLRDILSETDDKpfgGKTVVLGGDFRQIL 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958  149 PVDPGES-----TAYLSPFFTHKDFVQCNLTEVKRSNAPIIDVAT------------DIRNGKwIYDKVVDGHGVHGYTD 211
Cdd:pfam05970 153 PVIPKGSrpeivNASITNSYLWKHVKVLELTKNMRLLADSLDQTEakelqdfsdwllAIGDGK-INDENEREQLIDIPID 231

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 642905958  212 L-------------KSYMMNYFNVVKTPEDLFENRMMAFTNKSVDKLNSIIRRKLLETEKPF 260
Cdd:pfam05970 232 IllntggdpieaivSEVYPDILQNSTDPNYLEERAILCPTNEDVDEINNYRLSQLPGEEKEY 293
recD PRK10875
exodeoxyribonuclease V subunit alpha;
30-153 6.73e-09

exodeoxyribonuclease V subunit alpha;


Pssm-ID: 236783 [Multi-domain]  Cd Length: 615  Bit Score: 58.03  E-value: 6.73e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958  30 INGPAGTGKTTLTRFIVEALI--SSGESGII-LAAPT--HAAK------KVLSKLA---------GQEASTIHSILKINP 89
Cdd:PRK10875 172 ISGGPGTGKTTTVAKLLAALIqlADGERCRIrLAAPTgkAAARlteslgKALRQLPltdeqkkriPEEASTLHRLLGAQP 251

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 642905958  90 TT-----YEENVLfeqkkvpDLalcRVLLFDEASMCDRSLFKIMLASIPKWCTVIGIGDRCQIRPVDPG 153
Cdd:PRK10875 252 GSqrlryHAGNPL-------HL---DVLVVDEASMVDLPMMARLIDALPPHARVIFLGDRDQLASVEAG 310
TraI_TIGR TIGR02760
conjugative transfer relaxase protein TraI; This protein is a component of the relaxosome ...
 6-155 9.13e-09

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: 57.99  E-value: 9.13e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958     6 LTEGQKNAFNVVMEAikeKKHHVTINGPAGTGKTTLTRFIVEALISSGESG---IILAAPTHAAKKVLSKlAGQEASTIH 82
Cdd:TIGR02760 1020 LTHGQKQAIHLIIST---KDRFVAVQGLAGVGKTTMLESRYKPVLQAFESEqlqVIGLAPTHEAVGELKS-AGVQAQTLD 1095

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 642905958    83 SILkinpttyeENVLFEQKKVPDLALCRVLLfDEASMCD----RSLFKIMLASIPKWctvIGIGDRCQIRPVDPGES 155
Cdd:TIGR02760 1096 SFL--------TDISLYRNSGGDFRNTLFIL-DESSMVSnfqlTHATELVQKSGSRA---VSLGDIAQLQSLAAGKP 1160
SF1_C_RecD cd18809
C-terminal helicase domain of RecD family helicases; RecD is a member of the RecBCD (EC 3.1.11. ...
 391-437 1.26e-08

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: 51.79  E-value: 1.26e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 642905958 391 STFHKAQGMSVDTAFVYTPcihYADSELAKQLLYVGTTRGRFDVHFI 437
Cdd:cd18809   36 MTIHKSQGSEFDRVIVVLP---TSHPMLSRGLLYTALTRARKLLTLV 79
DExxQc_SF1-N cd17914
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ...
 30-153 1.61e-08

DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members include UvrD/Rep, Pif1-like, and Upf-1-like proteins. Like SF2, they do not form toroidal, predominantly hexameric structures like SF3-6. 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. SF1 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: 438706 [Multi-domain]  Cd Length: 121  Bit Score: 52.49  E-value: 1.61e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958  30 INGPAGTGKTTLTRFIVEALISSGESG---IILAAPTHAAkkvlsklagqeastihsilkinpttyeenvlfeqkkvpdL 106
Cdd:cd17914    4 IQGPPGTGKTRVLVKIVAALMQNKNGEpgrILLVTPTNKA---------------------------------------A 44

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 642905958 107 ALCRVLLFDEASMCDRSLFKIMLASIPKWCTVIGIGDRCQIRPVDPG 153
Cdd:cd17914   45 AQLDNILVDEAAQILEPETSRLIDLALDQGRVILVGDHDQLGPVWRG 91
DEXXQc_Upf1-like cd17934
DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, ...
 30-150 5.14e-08

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: 51.08  E-value: 5.14e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958  30 INGPAGTGKT-TLTRFIVEALISSGESGIILAAPTHAAkkVlsklagqeastihsilkinpttyeENVlfeqkkvpdlal 108
Cdd:cd17934    4 IQGPPGTGKTtTIAAIVLQLLKGLRGKRVLVTAQSNVA--V------------------------DNV------------ 45

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 642905958 109 cRVLLFDEASMCDRSLFKIMLASIPKwctVIGIGDRCQIRPV 150
Cdd:cd17934   46 -DVVIIDEASQITEPELLIALIRAKK---VVLVGDPKQLPPV 83
DEXXQc_DNA2 cd18041
DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses ...
 6-106 3.17e-07

DEXXQ-box helicase domain of DNA2; DNA2 (DNA Replication Helicase/Nuclease 2) possesses different enzymatic activities, such as single-stranded DNA (ssDNA)-dependent ATPase, 5-3 helicase, and endonuclease activities, and is involved in DNA replication and DNA repair in the nucleus and mitochondrion. It is involved in Okazaki fragment processing by cleaving long flaps that escape FEN1: flaps that are longer than 27 nucleotides are coated by replication protein A complex (RPA), leading to recruit DNA2 which cleaves the flap until it is too short to bind RPA and becomes a substrate for FEN1. It is also involved in 5-end resection of DNA during double-strand break (DSB) repair; it is recruited by BLM and mediates the cleavage of 5-ssDNA, while the 3-ssDNA cleavage is prevented by the presence of RPA. DNA2 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: 350799 [Multi-domain]  Cd Length: 203  Bit Score: 50.70  E-value: 3.17e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958   6 LTEGQKNAFNVVMEAikekKHHVTINGPAGTGKTTLTRFIVEALISSGESgIILAAPTHAA-KKVLSKLAGQEAST--IH 82
Cdd:cd18041    2 LNKDQRQAIKKVLNA----KDYALILGMPGTGKTTTIAALVRILVALGKS-VLLTSYTHSAvDNILLKLKKFGVNFlrLG 76

                         90       100
                 ....*....|....*....|....*..
gi 642905958  83 SILKINPTT---YEENVLFEQKKVPDL 106
Cdd:cd18041   77 RLKKIHPDVqefTLEAILKSCKSVEEL 103
PRK13709 PRK13709
conjugal transfer nickase/helicase TraI; Provisional
 5-153 2.90e-06

conjugal transfer nickase/helicase TraI; Provisional


Pssm-ID: 237478 [Multi-domain]  Cd Length: 1747  Bit Score: 49.79  E-value: 2.90e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958    5 DLTEGQKNAFNVVMEAikeKKHHVTINGPAGTGKTTLTRFIVEALISSGESG---IILAAPTHAAKKVLSKlAGQEASTI 81
Cdd:PRK13709  967 GLTSGQRAATRMILES---TDRFTVVQGYAGVGKTTQFRAVMSAVNTLPESErprVVGLGPTHRAVGEMRS-AGVDAQTL 1042

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 642905958   82 HSILkinpttYEENVLFEQKKVPDLAlCRVLLFDEASMCDRS----LFKIMLASIPKwctVIGIGDRCQIRPVDPG 153
Cdd:PRK13709 1043 ASFL------HDTQLQQRSGETPDFS-NTLFLLDESSMVGNTdmarAYALIAAGGGR---AVSSGDTDQLQAIAPG 1108
EEXXEc_NFX1 cd17936
EEXXE-box helicase domain of NFX1; Human NFX1 protein was identified as a protein that ...
 6-149 1.03e-05

EEXXE-box helicase domain of NFX1; Human NFX1 protein was identified as a protein that represses class II MHC (major histocompatibility complex) gene expression. NFX1 binds a conserved cis-acting element, termed the X-box, in promoters of human class II MHC genes. The Cys-rich region contains several NFX1-type zinc finger domains. Frequently, a R3H domain is present in the C-terminus, and a RING finger domain and a PAM2 motif are present in the N-terminus. The lack of R3H and PAM2 motifs in the plant proteins indicates functional differences. Plant NFX1-like proteins are proposed to modulate growth and survival by coordinating reactive oxygen species, salicylic acid, further biotic stress and abscisic acid responses. A common feature of all members may be E3 ubiquitin ligase, due to the presence of a RING finger domain, as well as DNA binding. NFX1 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: 350694 [Multi-domain]  Cd Length: 178  Bit Score: 45.61  E-value: 1.03e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958   6 LTEGQKNAFnvvMEAIKEKkhhVT-INGPAGTGKTTLTRFIVEALI----SSGESGIILAAPT-HAAKKVLSKLAGqeaS 79
Cdd:cd17936    2 LDPSQLEAL---KHALTSE---LAlIQGPPGTGKTFLGVKLVRALLqnqdLSITGPILVVCYTnHALDQFLEGLLD---F 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958  80 TIHSILKIN------PTTY--EENVLFEQKKvpdlalCRVLLFDEASmcdrslfKIM----LASIPKWCT-VIGIGDRCQ 146
Cdd:cd17936   73 GPTKIVRLGarvigmTTTGaaKYRELLQALG------PKVVIVEEAA-------EVLeahiLAALTPSTEhLILIGDHKQ 139


                 ...
gi 642905958 147 IRP 149
Cdd:cd17936  140 LRP 142
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 24-132 6.87e-05

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: 42.75  E-value: 6.87e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958    24 KKHHVTINGPAGTGKTTLTRFIVEALISSGESGIILAAPTHAAKKVLSKLAGQEASTIHSILKINpttyEENVLFEQKKV 103
Cdd:smart00382   1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGEL----RLRLALALARK 76

                           90       100       110
                   ....*....|....*....|....*....|
gi 642905958   104 PDLalcRVLLFDEA-SMCDRSLFKIMLASI 132
Cdd:smart00382  77 LKP---DVLILDEItSLLDAEQEALLLLLE 103
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 9-117 1.52e-04

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: 41.75  E-value: 1.52e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958   9 GQKNAFNVVMEAIK-EKKHHVTINGPAGTGKTTLTRFIVEALISSGESGIILAAPTHAAKKVLSKLAGQEASTIHSILKi 87
Cdd:cd00009    2 GQEEAIEALREALElPPPKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHFLVRLLFELA- 80

                         90       100       110
                 ....*....|....*....|....*....|
gi 642905958  88 npttyeenvlfEQKKVPdlalcrVLLFDEA 117
Cdd:cd00009   81 -----------EKAKPG------VLFIDEI 93
PRK14712 PRK14712
conjugal transfer nickase/helicase TraI; Provisional
 4-154 4.45e-04

conjugal transfer nickase/helicase TraI; Provisional


Pssm-ID: 237796 [Multi-domain]  Cd Length: 1623  Bit Score: 42.93  E-value: 4.45e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958    4 DDLTEGQKNAFNVVMEAikeKKHHVTINGPAGTGKTTLTRFIVEA---LISSGESGIILAAPTHAAKKVLsKLAGQEAST 80
Cdd:PRK14712  834 EKLTSGQRAATRMILET---SDRFTVVQGYAGVGKTTQFRAVMSAvnmLPESERPRVVGLGPTHRAVGEM-RSAGVDAQT 909

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 642905958   81 IHSILkinpttYEENVLFEQKKVPDLAlCRVLLFDEASMCDRSLFKIMLASIPK-WCTVIGIGDRCQIRPVDPGE 154
Cdd:PRK14712  910 LASFL------HDTQLQQRSGETPDFS-NTLFLLDESSMVGNTDMARAYALIAAgGGRAVASGDTDQLQAIAPGQ 977
Helicase_RecD pfam05127
Helicase; This domain contains a P-loop (Walker A) motif, suggesting that it has ATPase ...
 29-121 8.81e-04

Helicase; This domain contains a P-loop (Walker A) motif, suggesting that it has ATPase activity, and a Walker B motif. In tRNA(Met) cytidine acetyltransferase (TmcA) it may function as an RNA helicase motor (driven by ATP hydrolysis) which delivers the wobble base to the active centre of the GCN5-related N-acetyltransferase (GNAT) domain. It is found in the bacterial exodeoxyribonuclease V alpha chain (RecD), which has 5'-3' helicase activity. It is structurally similar to the motor domain 1A in other SF1 helicases.


Pssm-ID: 461555 [Multi-domain]  Cd Length: 171  Bit Score: 39.82  E-value: 8.81e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958   29 TINGPAGTGKTTLTRFIVEALISSGESGIILAAPTHAAKKVLSKLAGQEASTihsiLKINPTTYEENVLFEQKKV----P 104
Cdd:pfam05127   1 VITADRGRGKSAALGLAAAALIAQGYSRIIVTAPSPANVQTLFEFAIKGLDA----LGLTPKFRDGIIRGNGQRIrfiaP 76

                          90       100
                  ....*....|....*....|..
gi 642905958  105 DLAL-----CRVLLFDEASMCD 121
Cdd:pfam05127  77 DELLklpgqADLLVVDEAAAIP 98
DEXDc smart00487
DEAD-like helicases superfamily;
1-140 1.36e-03

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 39.78  E-value: 1.36e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958     1 MTFDDLTEGQKNAFNVVMEAIKekkhHVTINGPAGTGKTT-LTRFIVEALISSGESGIILAAPTHAA--------KKVLS 71
Cdd:smart00487   4 FGFEPLRPYQKEAIEALLSGLR----DVILAAPTGSGKTLaALLPALEALKRGKGGRVLVLVPTRELaeqwaeelKKLGP 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958    72 KLAGQEASTIHS---------ILKINP----TTYEENVLFEQKKVPDLALCRVLLFDEA----SMCDRSLFKIMLASIPK 134
Cdd:smart00487  80 SLGLKVVGLYGGdskreqlrkLESGKTdilvTTPGRLLDLLENDKLSLSNVDLVILDEAhrllDGGFGDQLEKLLKLLPK 159


                   ....*.
gi 642905958   135 WCTVIG 140
Cdd:smart00487 160 NVQLLL 165
ExeA COG3267
Type II secretory pathway ATPase component GspA/ExeA/MshM [Intracellular trafficking, ...
 6-159 3.57e-03

Type II secretory pathway ATPase component GspA/ExeA/MshM [Intracellular trafficking, secretion, and vesicular transport, Extracellular structures];


Pssm-ID: 442498 [Multi-domain]  Cd Length: 261  Bit Score: 39.00  E-value: 3.57e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958   6 LTEGQKNAFNVVMEAIKEKKHHVTINGPAGTGKTTLTRFIVEALISSGESGIIlAAPTHAAKKVLSKLAGQeastihsiL 85
Cdd:COG3267   24 LSPSHREALARLEYALAQGGGFVVLTGEVGTGKTTLLRRLLERLPDDVKVAYI-PNPQLSPAELLRAIADE--------L 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 642905958  86 KINPTTYEENVLFEQ------------KKVpdlalcrVLLFDEASMCDRSLFKI--MLASI----PKWCTVIGIGD---- 143
Cdd:COG3267   95 GLEPKGASKADLLRQlqefllelaaagRRV-------VLIIDEAQNLPPETLEElrLLSNLetdsRKLLQIVLVGQpelr 167

                        170       180       190
                 ....*....|....*....|....*....|...
gi 642905958 144 -----------------RCQIRPVDPGESTAYL 159
Cdd:COG3267  168 erlarpelrqlrqritaRYHLRPLDREETAAYI 200
PRK04182 PRK04182
cytidylate kinase; Provisional
 28-54 5.87e-03

cytidylate kinase; Provisional


Pssm-ID: 235244 [Multi-domain]  Cd Length: 180  Bit Score: 37.48  E-value: 5.87e-03
                         10        20        30
                 ....*....|....*....|....*....|.
gi 642905958  28 VTINGPAGTGKTTLTRFIVEAL----ISSGE 54
Cdd:PRK04182   3 ITISGPPGSGKTTVARLLAEKLglkhVSAGE 33
SF1_C cd18786
C-terminal helicase domain of superfamily 1 DEAD/H-box helicases; Superfamily (SF)1 family ...
 392-436 6.14e-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: 35.88  E-value: 6.14e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 642905958 392 TFHKAQGMSVDTAFVYTPCIHyadsELAKQLLYVGTTRGRFDVHF 436
Cdd:cd18786   47 TIDSSQGLTFDVVTLYLPTAN----SLTPRRLYVALTRARKRLVI 87
CMPK cd02020
Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine ...
 28-54 6.82e-03

Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor.


Pssm-ID: 238978 [Multi-domain]  Cd Length: 147  Bit Score: 37.08  E-value: 6.82e-03
                         10        20        30
                 ....*....|....*....|....*....|.
gi 642905958  28 VTINGPAGTGKTTLTRFIVEAL----ISSGE 54
Cdd:cd02020    2 IAIDGPAGSGKSTVAKLLAKKLglpyLDTGG 32
 
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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