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Conserved domains on  [gi|446629519|ref|WP_000706865|]
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MULTISPECIES: YqaJ viral recombinase family protein [Gammaproteobacteria]

Protein Classification

YqaJ viral recombinase family protein( domain architecture ID 10009228)

YqaJ viral recombinase family protein similar to Escherichia virus Lambda exonuclease that facilitates phage DNA recombination through the double-strand break repair (DSBR) and single-strand annealing pathways

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
COG5377 COG5377
Phage-related protein, predicted endonuclease [Mobilome: prophages, transposons];
1-305 4.66e-86

Phage-related protein, predicted endonuclease [Mobilome: prophages, transposons];


:

Pssm-ID: 444142 [Multi-domain]  Cd Length: 313  Bit Score: 261.86  E-value: 4.66e-86
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446629519   1 MKIVN---LSQREEDWLDWRRQGVTATDAAILLNRSPYKTRWRLWAEKTGYAREvDLSLNPLVRRGIENEDAARRAFEEK 77
Cdd:COG5377    1 MKLVNtkdLSQSREEWLALRRKGIGASDAAAILGLSPYKSPLDLWLEKTGGLPP-DLEENEAMYWGNLLEPVVAREFEKR 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446629519  78 YDDMLLP--ACVESVQYPLMRASLDGLRDNGEPV-ELKSPSATVWEDVCAEkansKAYQLYYPQVQHQLLVTGAKQGWLV 154
Cdd:COG5377   80 TGLKVRRvnAILQHPEYPFMLANLDRLVVGENGVlEIKTASAYLADEWGED----EVPDYYLCQVQHQLAVTGASWAYVA 155
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446629519 155 FYFEGQ-IQEFPILRDEAMIQEILAEAKKFWQQVVDKKEPDKDPERDLYI------PQ--GEEVNrwiAAAEEYRLYDAE 225
Cdd:COG5377  156 VLIGGNeFRWFRIERDEELIEELIEAEKDFWEHVEKGVPPPPDGSDDAEEalkalyPEddGSSID---LLDEELAELIEE 232
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446629519 226 IQELKQRLSELQERQKPHLDTMKSLMGEYFHADYCGVMVTRY-KAAGRVDYKKLLADkasgvKPEDVDQYR-EKSSERCR 303
Cdd:COG5377  233 LEELKAEIKELEERKKALENQLKAAMGDAETALFGGGRVTWKtKRRGRVDSKKLKKE-----QPEIYEKYTkTSSSRRFR 307

                 ..
gi 446629519 304 VT 305
Cdd:COG5377  308 IK 309
 
Name Accession Description Interval E-value
COG5377 COG5377
Phage-related protein, predicted endonuclease [Mobilome: prophages, transposons];
1-305 4.66e-86

Phage-related protein, predicted endonuclease [Mobilome: prophages, transposons];


Pssm-ID: 444142 [Multi-domain]  Cd Length: 313  Bit Score: 261.86  E-value: 4.66e-86
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446629519   1 MKIVN---LSQREEDWLDWRRQGVTATDAAILLNRSPYKTRWRLWAEKTGYAREvDLSLNPLVRRGIENEDAARRAFEEK 77
Cdd:COG5377    1 MKLVNtkdLSQSREEWLALRRKGIGASDAAAILGLSPYKSPLDLWLEKTGGLPP-DLEENEAMYWGNLLEPVVAREFEKR 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446629519  78 YDDMLLP--ACVESVQYPLMRASLDGLRDNGEPV-ELKSPSATVWEDVCAEkansKAYQLYYPQVQHQLLVTGAKQGWLV 154
Cdd:COG5377   80 TGLKVRRvnAILQHPEYPFMLANLDRLVVGENGVlEIKTASAYLADEWGED----EVPDYYLCQVQHQLAVTGASWAYVA 155
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446629519 155 FYFEGQ-IQEFPILRDEAMIQEILAEAKKFWQQVVDKKEPDKDPERDLYI------PQ--GEEVNrwiAAAEEYRLYDAE 225
Cdd:COG5377  156 VLIGGNeFRWFRIERDEELIEELIEAEKDFWEHVEKGVPPPPDGSDDAEEalkalyPEddGSSID---LLDEELAELIEE 232
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446629519 226 IQELKQRLSELQERQKPHLDTMKSLMGEYFHADYCGVMVTRY-KAAGRVDYKKLLADkasgvKPEDVDQYR-EKSSERCR 303
Cdd:COG5377  233 LEELKAEIKELEERKKALENQLKAAMGDAETALFGGGRVTWKtKRRGRVDSKKLKKE-----QPEIYEKYTkTSSSRRFR 307

                 ..
gi 446629519 304 VT 305
Cdd:COG5377  308 IK 309
phage_rel_nuc TIGR03033
putative phage-type endonuclease; Members of this protein family are found often in phage ...
6-159 1.33e-41

putative phage-type endonuclease; Members of this protein family are found often in phage genomes and in prokaryotic genomes in uncharacterized regions that resemble integrated prophage regions.


Pssm-ID: 200235 [Multi-domain]  Cd Length: 153  Bit Score: 142.18  E-value: 1.33e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446629519    6 LSQREEDWLDWRRQGVTATDAAILLNRSPYKTRWRLWAEKTGYAREVDlsLNPLVRRGIENEDAARRAFEEKYDDMLLPA 85
Cdd:TIGR03033   2 LVQRTEEWHAWRKGGITASDIAAIMGLNPYKTPEELWKEKTGFVEPED--MNEAMYHGVKLEPEAREAFRDKYGIMAEPF 79
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446629519   86 CVESVQYPLMRASLDGL-RDNGEPVELKSPS---ATVWedVCAEKANSKAYqlYYPQVQHQLLVTGAKQGWLVFYFEG 159
Cdd:TIGR03033  80 CLEHDEYPWMAASLDGLvADDKQILEIKCPServSKLW--VSELSGEVPAY--YQAQVQWQLYVSGSQAAYFAVYLGG 153
YqaJ pfam09588
YqaJ-like viral recombinase domain; This protein family is found in many different bacterial ...
12-149 1.57e-26

YqaJ-like viral recombinase domain; This protein family is found in many different bacterial species but is of viral origin. The protein forms an oligomer and functions as a processive alkaline exonuclease that digests linear double-stranded DNA in a Mg(2+)-dependent reaction, It has a preference for 5'-phosphorylated DNA ends. It thus forms part of the two-component SynExo viral recombinase functional unit.


Pssm-ID: 430702 [Multi-domain]  Cd Length: 142  Bit Score: 102.45  E-value: 1.57e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446629519   12 DWLDWRRQGVTATDAAILLNRSPYKTRWRLWAEKTGyaREVDLSLNPLVRRGIENEDAARRAFEEKYDD--MLLPACVES 89
Cdd:pfam09588   1 EWLEARRGGITASDAAAALGTNPYKSSVSLWLEKTG--QVEPFKDKKAMAWGTELEPIARAEYEFRTGVkvRRVNGLLQH 78
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446629519   90 VQYPLMRASLDGL-----RDNGEPVELKSPSATVWEDVCAEKANsKAYQLYYPQVQHQLLVTGAK 149
Cdd:pfam09588  79 PEDPFLLASPDGIvvgarDGDRGILEIKCPFSATFGASLWGGAD-GIPEEYMLQVQHQLAVTGAE 142
PDDEXK_lambda_exonuclease-like cd22343
Uncharacterized nucleases similar to lambda phage exonuclease; This model characterizes a ...
8-184 5.01e-21

Uncharacterized nucleases similar to lambda phage exonuclease; This model characterizes a diverse set of nucleases such as alkaline exonuclease from Laribacter hongkongensis, lambda phage exonuclease, or a Cas4-like protein from the Mimivirus virophage resistance element system. They belong to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI.


Pssm-ID: 411747 [Multi-domain]  Cd Length: 182  Bit Score: 88.55  E-value: 5.01e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446629519   8 QREEDWLDWRRQGVTATDA--AILLNRSPYKTRWRLWAEKTGYAREVDlslNPLVRRGIENEDAARRAFEEKYDDMLLPa 85
Cdd:cd22343    2 QRSPEWFEARKGRITASNFgrVLTTVENKKAPPASLLKRILGPRPFKS---TAATRWGIENEPEAREAYEELTGVKVKE- 77
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446629519  86 C--VESVQYPLMRASLDGL-RDNGEP---VELKSPsatvWEDVCAEKANSKAYQL----YYPQVQHQLLVTGAKQGWLVF 155
Cdd:cd22343   78 CglVIHPEHPWLGASPDGLvTCDCCGkglLEIKCP----YSKDRKLKENFKLDKLethpYYYQVQGQMAVTGREWCDFVV 153
                        170       180
                 ....*....|....*....|....*....
gi 446629519 156 YFEGQIQEFPILRDEAMIQEILAEAKKFW 184
Cdd:cd22343  154 YTPKGSHIERIKRDEEFWAEILPKLEEFY 182
 
Name Accession Description Interval E-value
COG5377 COG5377
Phage-related protein, predicted endonuclease [Mobilome: prophages, transposons];
1-305 4.66e-86

Phage-related protein, predicted endonuclease [Mobilome: prophages, transposons];


Pssm-ID: 444142 [Multi-domain]  Cd Length: 313  Bit Score: 261.86  E-value: 4.66e-86
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446629519   1 MKIVN---LSQREEDWLDWRRQGVTATDAAILLNRSPYKTRWRLWAEKTGYAREvDLSLNPLVRRGIENEDAARRAFEEK 77
Cdd:COG5377    1 MKLVNtkdLSQSREEWLALRRKGIGASDAAAILGLSPYKSPLDLWLEKTGGLPP-DLEENEAMYWGNLLEPVVAREFEKR 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446629519  78 YDDMLLP--ACVESVQYPLMRASLDGLRDNGEPV-ELKSPSATVWEDVCAEkansKAYQLYYPQVQHQLLVTGAKQGWLV 154
Cdd:COG5377   80 TGLKVRRvnAILQHPEYPFMLANLDRLVVGENGVlEIKTASAYLADEWGED----EVPDYYLCQVQHQLAVTGASWAYVA 155
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446629519 155 FYFEGQ-IQEFPILRDEAMIQEILAEAKKFWQQVVDKKEPDKDPERDLYI------PQ--GEEVNrwiAAAEEYRLYDAE 225
Cdd:COG5377  156 VLIGGNeFRWFRIERDEELIEELIEAEKDFWEHVEKGVPPPPDGSDDAEEalkalyPEddGSSID---LLDEELAELIEE 232
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446629519 226 IQELKQRLSELQERQKPHLDTMKSLMGEYFHADYCGVMVTRY-KAAGRVDYKKLLADkasgvKPEDVDQYR-EKSSERCR 303
Cdd:COG5377  233 LEELKAEIKELEERKKALENQLKAAMGDAETALFGGGRVTWKtKRRGRVDSKKLKKE-----QPEIYEKYTkTSSSRRFR 307

                 ..
gi 446629519 304 VT 305
Cdd:COG5377  308 IK 309
phage_rel_nuc TIGR03033
putative phage-type endonuclease; Members of this protein family are found often in phage ...
6-159 1.33e-41

putative phage-type endonuclease; Members of this protein family are found often in phage genomes and in prokaryotic genomes in uncharacterized regions that resemble integrated prophage regions.


Pssm-ID: 200235 [Multi-domain]  Cd Length: 153  Bit Score: 142.18  E-value: 1.33e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446629519    6 LSQREEDWLDWRRQGVTATDAAILLNRSPYKTRWRLWAEKTGYAREVDlsLNPLVRRGIENEDAARRAFEEKYDDMLLPA 85
Cdd:TIGR03033   2 LVQRTEEWHAWRKGGITASDIAAIMGLNPYKTPEELWKEKTGFVEPED--MNEAMYHGVKLEPEAREAFRDKYGIMAEPF 79
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446629519   86 CVESVQYPLMRASLDGL-RDNGEPVELKSPS---ATVWedVCAEKANSKAYqlYYPQVQHQLLVTGAKQGWLVFYFEG 159
Cdd:TIGR03033  80 CLEHDEYPWMAASLDGLvADDKQILEIKCPServSKLW--VSELSGEVPAY--YQAQVQWQLYVSGSQAAYFAVYLGG 153
YqaJ pfam09588
YqaJ-like viral recombinase domain; This protein family is found in many different bacterial ...
12-149 1.57e-26

YqaJ-like viral recombinase domain; This protein family is found in many different bacterial species but is of viral origin. The protein forms an oligomer and functions as a processive alkaline exonuclease that digests linear double-stranded DNA in a Mg(2+)-dependent reaction, It has a preference for 5'-phosphorylated DNA ends. It thus forms part of the two-component SynExo viral recombinase functional unit.


Pssm-ID: 430702 [Multi-domain]  Cd Length: 142  Bit Score: 102.45  E-value: 1.57e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446629519   12 DWLDWRRQGVTATDAAILLNRSPYKTRWRLWAEKTGyaREVDLSLNPLVRRGIENEDAARRAFEEKYDD--MLLPACVES 89
Cdd:pfam09588   1 EWLEARRGGITASDAAAALGTNPYKSSVSLWLEKTG--QVEPFKDKKAMAWGTELEPIARAEYEFRTGVkvRRVNGLLQH 78
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446629519   90 VQYPLMRASLDGL-----RDNGEPVELKSPSATVWEDVCAEKANsKAYQLYYPQVQHQLLVTGAK 149
Cdd:pfam09588  79 PEDPFLLASPDGIvvgarDGDRGILEIKCPFSATFGASLWGGAD-GIPEEYMLQVQHQLAVTGAE 142
PDDEXK_lambda_exonuclease-like cd22343
Uncharacterized nucleases similar to lambda phage exonuclease; This model characterizes a ...
8-184 5.01e-21

Uncharacterized nucleases similar to lambda phage exonuclease; This model characterizes a diverse set of nucleases such as alkaline exonuclease from Laribacter hongkongensis, lambda phage exonuclease, or a Cas4-like protein from the Mimivirus virophage resistance element system. They belong to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI.


Pssm-ID: 411747 [Multi-domain]  Cd Length: 182  Bit Score: 88.55  E-value: 5.01e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446629519   8 QREEDWLDWRRQGVTATDA--AILLNRSPYKTRWRLWAEKTGYAREVDlslNPLVRRGIENEDAARRAFEEKYDDMLLPa 85
Cdd:cd22343    2 QRSPEWFEARKGRITASNFgrVLTTVENKKAPPASLLKRILGPRPFKS---TAATRWGIENEPEAREAYEELTGVKVKE- 77
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446629519  86 C--VESVQYPLMRASLDGL-RDNGEP---VELKSPsatvWEDVCAEKANSKAYQL----YYPQVQHQLLVTGAKQGWLVF 155
Cdd:cd22343   78 CglVIHPEHPWLGASPDGLvTCDCCGkglLEIKCP----YSKDRKLKENFKLDKLethpYYYQVQGQMAVTGREWCDFVV 153
                        170       180
                 ....*....|....*....|....*....
gi 446629519 156 YFEGQIQEFPILRDEAMIQEILAEAKKFW 184
Cdd:cd22343  154 YTPKGSHIERIKRDEEFWAEILPKLEEFY 182
 
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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