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Conserved domains on  [gi|822088693|gb|KLD59278|]
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hypothetical protein WP50_19740, partial [Lactiplantibacillus plantarum]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
AAA_19 pfam13245
AAA domain;
34-176 5.95e-46

AAA domain;


:

Pssm-ID: 433059 [Multi-domain]  Cd Length: 136  Bit Score: 150.45  E-value: 5.95e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822088693   34 QTEALKAAITAPVFLLTGGPGTGKTTIIRGLVALYAELHDValdinqykdkPFPILLAAPTGRAAKRMAETTGLPASTIH 113
Cdd:pfam13245   1 QREAVRTALPSKVVLLTGGPGTGKTTTIRHIVALLVALGGV----------SFPILLAAPTGRAAKRLSERTGLPASTIH 70

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 822088693  114 RLLGLTGREDGP--EEPSKELDGGLLIIDEMSMVDTVLFQQLLTAIPSHMQVILVGDKDQLPSVG 176
Cdd:pfam13245  71 RLLGFDDLEAGGflRDEEEPLDGDLLIVDEFSMVDLPLAYRLLKALPDGAQLLLVGDPDQLPSVG 135
RecD super family cl33920
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 165-257 1.01e-11

ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair];


The actual alignment was detected with superfamily member COG0507:

Pssm-ID: 440273 [Multi-domain]  Cd Length: 514  Bit Score: 64.23  E-value: 1.01e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822088693 165 LVGDKDQLPSVGYEAEWRVAEHLQRLlaadNDEKLSERAVDHAIEHVGRASNITYDESQTEALK-AAITAPVFLLTGGPG 243
Cdd:COG0507   75 LVLDGRRYLTRLLEAEQRLARRLRRL----ARPALDEADVEAALAALEPRAGITLSDEQREAVAlALTTRRVSVLTGGAG 150

                         90
                 ....*....|....*.
gi 822088693 244 TGKT--IRCLLLNIRK 257
Cdd:COG0507  151 TGKTttLRALLAALEA 166
 
Name Accession Description Interval E-value
AAA_19 pfam13245
AAA domain;
34-176 5.95e-46

AAA domain;


Pssm-ID: 433059 [Multi-domain]  Cd Length: 136  Bit Score: 150.45  E-value: 5.95e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822088693   34 QTEALKAAITAPVFLLTGGPGTGKTTIIRGLVALYAELHDValdinqykdkPFPILLAAPTGRAAKRMAETTGLPASTIH 113
Cdd:pfam13245   1 QREAVRTALPSKVVLLTGGPGTGKTTTIRHIVALLVALGGV----------SFPILLAAPTGRAAKRLSERTGLPASTIH 70

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 822088693  114 RLLGLTGREDGP--EEPSKELDGGLLIIDEMSMVDTVLFQQLLTAIPSHMQVILVGDKDQLPSVG 176
Cdd:pfam13245  71 RLLGFDDLEAGGflRDEEEPLDGDLLIVDEFSMVDLPLAYRLLKALPDGAQLLLVGDPDQLPSVG 135
recD_rel TIGR01448
helicase, putative, RecD/TraA family; This model describes a family similar to RecD, the ...
 16-176 4.87e-45

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: 160.72  E-value: 4.87e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822088693   16 DHAIEHVGRASNITYDESQTEALKAAITAPVFLLTGGPGTGKTTIIRGLVALYAELHDvaldinqykdkPFPILLAAPTG 95
Cdd:TIGR01448 310 QEHIWEVEKKLRKGLSEEQKQALDTAIQHKVVILTGGPGTGKTTITRAIIELAEELGG-----------LLPVGLAAPTG 378

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822088693   96 RAAKRMAETTGLPASTIHRLLGLTGREDGPEEPSKELDGGLLIIDEMSMVDTVLFQQLLTAIPSHMQVILVGDKDQLPSV 175
Cdd:TIGR01448 379 RAAKRLGEVTGLTASTIHRLLGYGPDTFRHNHLEDPIDCDLLIVDESSMMDTWLALSLLAALPDHARLLLVGDTDQLPSV 458


                  .
gi 822088693  176 G 176
Cdd:TIGR01448 459 G 459
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 2-176 1.05e-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: 141.27  E-value: 1.05e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822088693   2 LAADNDEKLSERAVDHAIEHVGRASNITYDESQTEALK-AAITAPVFLLtggpgtgkttIIRGLVALYAELHdvaldinq 80
Cdd:COG0507   97 LRRLARPALDEADVEAALAALEPRAGITLSDEQREAVAlALTTRRVSVLtggagtgkttTLRALLAALEALG-------- 168

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822088693  81 ykdkpFPILLAAPTGRAAKRMAETTGLPASTIHRLLGLTGRED----GPEEPSKELDggLLIIDEMSMVDTVLFQQLLTA 156
Cdd:COG0507  169 -----LRVALAAPTGKAAKRLSESTGIEARTIHRLLGLRPDSGrfrhNRDNPLTPAD--LLVVDEASMVDTRLMAALLEA 241

                        170       180
                 ....*....|....*....|.
gi 822088693 157 IPS-HMQVILVGDKDQLPSVG 176
Cdd:COG0507  242 LPRaGARLILVGDPDQLPSVG 262
DEXSc_RecD-like cd17933
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ...
 78-176 1.62e-38

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: 131.91  E-value: 1.62e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822088693  78 INQYKDKPFPILLAAPTGRAAKRMAETTGLPASTIHRLLGLTGREDGPEEPSKE-LDGGLLIIDEMSMVDTVLFQQLLTA 156
Cdd:cd17933   33 LAALEAEGKRVVLAAPTGKAAKRLSESTGIEASTIHRLLGINPGGGGFYYNEENpLDADLLIVDEASMVDTRLMAALLSA 112

                         90       100
                 ....*....|....*....|
gi 822088693 157 IPSHMQVILVGDKDQLPSVG 176
Cdd:cd17933  113 IPAGARLILVGDPDQLPSVG 132
recD PRK10875
exodeoxyribonuclease V subunit alpha;
78-190 4.43e-17

exodeoxyribonuclease V subunit alpha;


Pssm-ID: 236783 [Multi-domain]  Cd Length: 615  Bit Score: 80.37  E-value: 4.43e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822088693  78 INQYKDKPFPILLAAPTGRAAKRMAETTG-----LP------------ASTIHRLLG-------LTGREDGPeepskeLD 133
Cdd:PRK10875 192 IQLADGERCRIRLAAPTGKAAARLTESLGkalrqLPltdeqkkripeeASTLHRLLGaqpgsqrLRYHAGNP------LH 265

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 822088693 134 GGLLIIDEMSMVDTVLFQQLLTAIPSHMQVILVGDKDQLPSV---------------GYEAEwRvAEHLQRL 190
Cdd:PRK10875 266 LDVLVVDEASMVDLPMMARLIDALPPHARVIFLGDRDQLASVeagavlgdicrfaeaGYSAE-R-AQQLSRL 335
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 165-257 1.01e-11

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: 64.23  E-value: 1.01e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822088693 165 LVGDKDQLPSVGYEAEWRVAEHLQRLlaadNDEKLSERAVDHAIEHVGRASNITYDESQTEALK-AAITAPVFLLTGGPG 243
Cdd:COG0507   75 LVLDGRRYLTRLLEAEQRLARRLRRL----ARPALDEADVEAALAALEPRAGITLSDEQREAVAlALTTRRVSVLTGGAG 150

                         90
                 ....*....|....*.
gi 822088693 244 TGKT--IRCLLLNIRK 257
Cdd:COG0507  151 TGKTttLRALLAALEA 166
AAA_19 pfam13245
AAA domain;
223-247 1.32e-05

AAA domain;


Pssm-ID: 433059 [Multi-domain]  Cd Length: 136  Bit Score: 43.75  E-value: 1.32e-05
                          10        20
                  ....*....|....*....|....*
gi 822088693  223 QTEALKAAITAPVFLLTGGPGTGKT 247
Cdd:pfam13245   1 QREAVRTALPSKVVLLTGGPGTGKT 25
EEXXEc_NFX1 cd17936
EEXXE-box helicase domain of NFX1; Human NFX1 protein was identified as a protein that ...
 218-254 6.64e-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: 42.53  E-value: 6.64e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 822088693 218 TYDESQTEALKAAITAPVFLLTGGPGTGKT------IRCLLLN 254
Cdd:cd17936    1 TLDPSQLEALKHALTSELALIQGPPGTGKTflgvklVRALLQN 43
recD TIGR01447
exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha ...
 177-247 6.64e-04

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: 40.90  E-value: 6.64e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 822088693  177 YEAEWRVAEHLQRLLAADNDEklserAVDHAIEHVGRASNItyDESQTEALKAAITAPVFLLTGGPGTGKT 247
Cdd:TIGR01447 110 WREEEKLAAKLRTLLEARKRT-----APSAILENLFPLLNE--QNWRKTAVALALKSNFSLITGGPGTGKT 173
 
Name Accession Description Interval E-value
AAA_19 pfam13245
AAA domain;
34-176 5.95e-46

AAA domain;


Pssm-ID: 433059 [Multi-domain]  Cd Length: 136  Bit Score: 150.45  E-value: 5.95e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822088693   34 QTEALKAAITAPVFLLTGGPGTGKTTIIRGLVALYAELHDValdinqykdkPFPILLAAPTGRAAKRMAETTGLPASTIH 113
Cdd:pfam13245   1 QREAVRTALPSKVVLLTGGPGTGKTTTIRHIVALLVALGGV----------SFPILLAAPTGRAAKRLSERTGLPASTIH 70

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 822088693  114 RLLGLTGREDGP--EEPSKELDGGLLIIDEMSMVDTVLFQQLLTAIPSHMQVILVGDKDQLPSVG 176
Cdd:pfam13245  71 RLLGFDDLEAGGflRDEEEPLDGDLLIVDEFSMVDLPLAYRLLKALPDGAQLLLVGDPDQLPSVG 135
recD_rel TIGR01448
helicase, putative, RecD/TraA family; This model describes a family similar to RecD, the ...
 16-176 4.87e-45

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: 160.72  E-value: 4.87e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822088693   16 DHAIEHVGRASNITYDESQTEALKAAITAPVFLLTGGPGTGKTTIIRGLVALYAELHDvaldinqykdkPFPILLAAPTG 95
Cdd:TIGR01448 310 QEHIWEVEKKLRKGLSEEQKQALDTAIQHKVVILTGGPGTGKTTITRAIIELAEELGG-----------LLPVGLAAPTG 378

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822088693   96 RAAKRMAETTGLPASTIHRLLGLTGREDGPEEPSKELDGGLLIIDEMSMVDTVLFQQLLTAIPSHMQVILVGDKDQLPSV 175
Cdd:TIGR01448 379 RAAKRLGEVTGLTASTIHRLLGYGPDTFRHNHLEDPIDCDLLIVDESSMMDTWLALSLLAALPDHARLLLVGDTDQLPSV 458


                  .
gi 822088693  176 G 176
Cdd:TIGR01448 459 G 459
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 2-176 1.05e-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: 141.27  E-value: 1.05e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822088693   2 LAADNDEKLSERAVDHAIEHVGRASNITYDESQTEALK-AAITAPVFLLtggpgtgkttIIRGLVALYAELHdvaldinq 80
Cdd:COG0507   97 LRRLARPALDEADVEAALAALEPRAGITLSDEQREAVAlALTTRRVSVLtggagtgkttTLRALLAALEALG-------- 168

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822088693  81 ykdkpFPILLAAPTGRAAKRMAETTGLPASTIHRLLGLTGRED----GPEEPSKELDggLLIIDEMSMVDTVLFQQLLTA 156
Cdd:COG0507  169 -----LRVALAAPTGKAAKRLSESTGIEARTIHRLLGLRPDSGrfrhNRDNPLTPAD--LLVVDEASMVDTRLMAALLEA 241

                        170       180
                 ....*....|....*....|.
gi 822088693 157 IPS-HMQVILVGDKDQLPSVG 176
Cdd:COG0507  242 LPRaGARLILVGDPDQLPSVG 262
DEXSc_RecD-like cd17933
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ...
 78-176 1.62e-38

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: 131.91  E-value: 1.62e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822088693  78 INQYKDKPFPILLAAPTGRAAKRMAETTGLPASTIHRLLGLTGREDGPEEPSKE-LDGGLLIIDEMSMVDTVLFQQLLTA 156
Cdd:cd17933   33 LAALEAEGKRVVLAAPTGKAAKRLSESTGIEASTIHRLLGINPGGGGFYYNEENpLDADLLIVDEASMVDTRLMAALLSA 112

                         90       100
                 ....*....|....*....|
gi 822088693 157 IPSHMQVILVGDKDQLPSVG 176
Cdd:cd17933  113 IPAGARLILVGDPDQLPSVG 132
AAA_30 pfam13604
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 29-176 7.63e-24

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: 94.94  E-value: 7.63e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822088693   29 TYDESQTEALKAAITAP--VFLLTGGPGTGKTTIIRGLVALYAELhdvaldinqykdkPFPILLAAPTGRAAKRMAETTG 106
Cdd:pfam13604   1 TLNAEQAAAVRALLTSGdrVAVLVGPAGTGKTTALKALREAWEAA-------------GYRVIGLAPTGRAAKVLGEELG 67

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 822088693  107 LPASTIHRLLGLTGREDGPEepskelDGGLLIIDEMSMVDTVLFQQLLTAIPSH-MQVILVGDKDQLPSVG 176
Cdd:pfam13604  68 IPADTIAKLLHRLGGRAGLD------PGTLLIVDEAGMVGTRQMARLLKLAEDAgARVILVGDPRQLPSVE 132
recD TIGR01447
exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha ...
 88-176 6.61e-19

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: 85.58  E-value: 6.61e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822088693   88 ILLAAPTGRAAKRMAETTG---------------LP--ASTIHRLLGLT-GREDGPEEPSKELDGGLLIIDEMSMVDTVL 149
Cdd:TIGR01447 195 IALAAPTGKAAARLAESLRkavknlaaaealiaaLPseAVTIHRLLGIKpDTKRFRHHERNPLPLDVLVVDEASMVDLPL 274

                          90       100
                  ....*....|....*....|....*..
gi 822088693  150 FQQLLTAIPSHMQVILVGDKDQLPSVG 176
Cdd:TIGR01447 275 MAKLLKALPPNTKLILLGDKNQLPSVE 301
recD PRK10875
exodeoxyribonuclease V subunit alpha;
78-190 4.43e-17

exodeoxyribonuclease V subunit alpha;


Pssm-ID: 236783 [Multi-domain]  Cd Length: 615  Bit Score: 80.37  E-value: 4.43e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822088693  78 INQYKDKPFPILLAAPTGRAAKRMAETTG-----LP------------ASTIHRLLG-------LTGREDGPeepskeLD 133
Cdd:PRK10875 192 IQLADGERCRIRLAAPTGKAAARLTESLGkalrqLPltdeqkkripeeASTLHRLLGaqpgsqrLRYHAGNP------LH 265

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 822088693 134 GGLLIIDEMSMVDTVLFQQLLTAIPSHMQVILVGDKDQLPSV---------------GYEAEwRvAEHLQRL 190
Cdd:PRK10875 266 LDVLVVDEASMVDLPMMARLIDALPPHARVIFLGDRDQLASVeagavlgdicrfaeaGYSAE-R-AQQLSRL 335
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 165-257 1.01e-11

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: 64.23  E-value: 1.01e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822088693 165 LVGDKDQLPSVGYEAEWRVAEHLQRLlaadNDEKLSERAVDHAIEHVGRASNITYDESQTEALK-AAITAPVFLLTGGPG 243
Cdd:COG0507   75 LVLDGRRYLTRLLEAEQRLARRLRRL----ARPALDEADVEAALAALEPRAGITLSDEQREAVAlALTTRRVSVLTGGAG 150

                         90
                 ....*....|....*.
gi 822088693 244 TGKT--IRCLLLNIRK 257
Cdd:COG0507  151 TGKTttLRALLAALEA 166
recD_rel TIGR01448
helicase, putative, RecD/TraA family; This model describes a family similar to RecD, the ...
 105-247 3.30e-11

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: 62.88  E-value: 3.30e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822088693  105 TGLPASTIHRLLGLTGREDGPEEpskeldggllIIDEMSMVDTVLFqqLLTAIPshmqVILVGDKDQLPSVgYEAEWRVA 184
Cdd:TIGR01448 229 TYLPRNRFIKQVVHLLNVQPQER----------LLVPEAVELERLY--LDEEPK----LAAEDGRIYLPSL-FRAEKQIA 291

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 822088693  185 EHLQRLLAADNdeKLSERAVDHAIEHVGRASNITYDESQTEALKAAITAPVFLLTGGPGTGKT 247
Cdd:TIGR01448 292 SHIRRLLATSP--AIGAINDQEHIWEVEKKLRKGLSEEQKQALDTAIQHKVVILTGGPGTGKT 352
DExxQc_SF1-N cd17914
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ...
 71-209 7.11e-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: 49.79  E-value: 7.11e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822088693  71 LHDVALDINQYKDKPFPILLAAPTGRAAKRMAETtglpastihrllgltgredgpeepskeldggllIIDEMSMVDTVLF 150
Cdd:cd17914   17 VKIVAALMQNKNGEPGRILLVTPTNKAAAQLDNI---------------------------------LVDEAAQILEPET 63

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 822088693 151 QQLLTAIPSHMQVILVGDKDQLPSVgyeaeWRVAEhlqrLLAADNDEKLSERAVDHAIE 209
Cdd:cd17914   64 SRLIDLALDQGRVILVGDHDQLGPV-----WRGAV----LAKICNEQSLFTRLVRLGVS 113
AAA_19 pfam13245
AAA domain;
223-247 1.32e-05

AAA domain;


Pssm-ID: 433059 [Multi-domain]  Cd Length: 136  Bit Score: 43.75  E-value: 1.32e-05
                          10        20
                  ....*....|....*....|....*
gi 822088693  223 QTEALKAAITAPVFLLTGGPGTGKT 247
Cdd:pfam13245   1 QREAVRTALPSKVVLLTGGPGTGKT 25
EEXXEc_NFX1 cd17936
EEXXE-box helicase domain of NFX1; Human NFX1 protein was identified as a protein that ...
 218-254 6.64e-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: 42.53  E-value: 6.64e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 822088693 218 TYDESQTEALKAAITAPVFLLTGGPGTGKT------IRCLLLN 254
Cdd:cd17936    1 TLDPSQLEALKHALTSELALIQGPPGTGKTflgvklVRALLQN 43
DEXSc_RecD-like cd17933
DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ...
 223-257 7.13e-05

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: 42.16  E-value: 7.13e-05
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 822088693 223 QTEALKAAITAPVFLLTGGPGTGKT--IRCLLLNIRK 257
Cdd:cd17933    2 QKAAVRLVLRNRVSVLTGGAGTGKTttLKALLAALEA 38
DEXSc_Pif1_like cd18037
DEAD-box helicase domain of Pif1; Pif1 and other members of this family are RecD-like ...
 55-175 1.20e-04

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: 41.85  E-value: 1.20e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822088693  55 TGKTTIIRGLvalyaelhdvaldINQYKDKPFPILLAAPTGRAAkrmaetTGLPASTIHRLLGLTGREDGPEEP------ 128
Cdd:cd18037   23 TGKSYLLRRI-------------IRALPSRPKRVAVTASTGIAA------CNIGGTTLHSFAGIGLGSEPAEDLlervkr 83

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 822088693 129 SKELDGGL-----LIIDEMSMVDTVLFQQL---LTAI-PSH-----MQVILVGDKDQLPSV 175
Cdd:cd18037   84 SPYLVQRWrkcdvLIIDEISMLDADLFDKLdrvAREVrGSDkpfggIQLILCGDFLQLPPV 144
TraA_Ti TIGR02768
Ti-type conjugative transfer relaxase TraA; This protein contains domains distinctive of a ...
 91-226 1.20e-04

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: 43.26  E-value: 1.20e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822088693   91 AAPTGRAAKRMAETTGLPASTIHRL-LGLTGREDGPEepskelDGGLLIIDEMSMVDTVLFQQLL-TAIPSHMQVILVGD 168
Cdd:TIGR02768 402 AALSGKAAEGLQAESGIESRTLASLeYAWANGRDLLS------DKDVLVIDEAGMVGSRQMARVLkEAEEAGAKVVLVGD 475

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 822088693  169 KDQLPSVGYEAEWR-VAEHL----------QRLLAADNDEKLSERA-VDHAIEHVGRASNITYDESQTEA 226
Cdd:TIGR02768 476 PEQLQPIEAGAAFRaIAERIgyaeletirrQREAWARQASLELARGdVEKALAAYRDHGHITIHDTREEA 545
recD TIGR01447
exodeoxyribonuclease V, alpha subunit; This family describes the exodeoxyribonuclease V alpha ...
 177-247 6.64e-04

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: 40.90  E-value: 6.64e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 822088693  177 YEAEWRVAEHLQRLLAADNDEklserAVDHAIEHVGRASNItyDESQTEALKAAITAPVFLLTGGPGTGKT 247
Cdd:TIGR01447 110 WREEEKLAAKLRTLLEARKRT-----APSAILENLFPLLNE--QNWRKTAVALALKSNFSLITGGPGTGKT 173
DEXXQc_SF1 cd18043
DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are ...
 220-247 4.73e-03

DEXXQ-box helicase domain of Superfamily 1 helicases; Superfamily 1 (SF1) helicases are nucleic acid motor proteins that couple ATP hydrolysis to translocation along with the concomitant unwinding of DNA or RNA. This is central to many aspects of cellular DNA and RNA metabolism and accordingly, they are implicated in a wide range of nucleic acid processing events including DNA replication, recombination, and repair as well as many aspects of RNA metabolism. Superfamily 1 helicases are members 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: 350801 [Multi-domain]  Cd Length: 127  Bit Score: 36.41  E-value: 4.73e-03
                         10        20
                 ....*....|....*....|....*...
gi 822088693 220 DESQTEALKAAITAPVFLLTGGPGTGKT 247
Cdd:cd18043    1 DSSQEAAIISARNGKNVVIQGPPGTGKS 28
DEXXQc_UPF1 cd18039
DEXXQ-box helicase domain of UPF1; UPF1 (also called RNA Helicase And ATPase, Regulator Of ...
 221-247 5.94e-03

DEXXQ-box helicase domain of UPF1; UPF1 (also called RNA Helicase And ATPase, Regulator Of Nonsense Transcripts, or ATP-Dependent Helicase RENT1) is an RNA-dependent helicase and ATPase required for nonsense-mediated decay (NMD) of mRNAs containing premature stop codons. It is recruited to mRNAs upon translation termination and undergoes a cycle of phosphorylation and dephosphorylation; its phosphorylation appears to be a key step in NMD. It is recruited by release factors to stalled ribosomes together with the SMG1C protein kinase complex to form the transient SURF (SMG1-UPF1-eRF1-eRF3) complex. In EJC-dependent NMD, the SURF complex associates with the exon junction complex (EJC) located downstream from the termination codon through UPF2 and allows the formation of an UPF1-UPF2-UPF3 surveillance complex which is believed to activate NMD. Diseases associated with UPF1 include juvenile amyotrophic lateral sclerosis and epidermolysis bullosa, junctional, non-Herlitz type. UPF1 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: 350797 [Multi-domain]  Cd Length: 234  Bit Score: 37.23  E-value: 5.94e-03
                         10        20
                 ....*....|....*....|....*..
gi 822088693 221 ESQTEALKAAITAPVFLLTGGPGTGKT 247
Cdd:cd18039    4 HSQVDAVKTALQRPLSLIQGPPGTGKT 30
 
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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