NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1515054357|gb|ROK32946|]
View 

exonuclease [Escherichia coli]

Protein Classification

lambda exonuclease family protein( domain architecture ID 16909715)

lambda exonuclease family protein similar to Escherichia phage Lambda exonuclease, which facilitates phage DNA recombination through the double-strand break repair (DSBR) and single-strand annealing pathways; also important for the late, rolling-circle mode of lambda DNA replication

CATH:  3.90.320.10
EC:  3.1.11.3
Gene Ontology:  GO:0046872|GO:0004527
PubMed:  22638584

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

Name Accession Description Interval E-value
PDDEXK_lambda_exonuclease-like cd22343
Uncharacterized nucleases similar to lambda phage exonuclease; This model characterizes a ...
18-207 1.56e-41

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: 139.39  E-value: 1.56e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515054357  18 EQGDDAWHKLRLGVITASEVHNVIAKPRSGKKWPDmkmsyfhTLLAEVCTGvAPEVNAKALAWGKQYENDARTLFEFTSG 97
Cdd:cd22343     1 QQRSPEWFEARKGRITASNFGRVLTTVENKKAPPA-------SLLKRILGP-RPFKSTAATRWGIENEPEAREAYEELTG 72
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515054357  98 VNVTESPIIYRDESMRTACSPDGL----CSDGNGLELKCPFTSRDFMKFRLGGFEAIKSAYMAQVQYSMWVTRKDAWYFA 173
Cdd:cd22343    73 VKVKECGLVIHPEHPWLGASPDGLvtcdCCGKGLLEIKCPYSKDRKLKENFKLDKLETHPYYYQVQGQMAVTGREWCDFV 152
                         170       180       190
                  ....*....|....*....|....*....|....
gi 1515054357 174 NYDPRmkreGLHYVVVERDEKYMASFDEMVPEFI 207
Cdd:cd22343   153 VYTPK----GSHIERIKRDEEFWAEILPKLEEFY 182
 
Name Accession Description Interval E-value
PDDEXK_lambda_exonuclease-like cd22343
Uncharacterized nucleases similar to lambda phage exonuclease; This model characterizes a ...
18-207 1.56e-41

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: 139.39  E-value: 1.56e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515054357  18 EQGDDAWHKLRLGVITASEVHNVIAKPRSGKKWPDmkmsyfhTLLAEVCTGvAPEVNAKALAWGKQYENDARTLFEFTSG 97
Cdd:cd22343     1 QQRSPEWFEARKGRITASNFGRVLTTVENKKAPPA-------SLLKRILGP-RPFKSTAATRWGIENEPEAREAYEELTG 72
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515054357  98 VNVTESPIIYRDESMRTACSPDGL----CSDGNGLELKCPFTSRDFMKFRLGGFEAIKSAYMAQVQYSMWVTRKDAWYFA 173
Cdd:cd22343    73 VKVKECGLVIHPEHPWLGASPDGLvtcdCCGKGLLEIKCPYSKDRKLKENFKLDKLETHPYYYQVQGQMAVTGREWCDFV 152
                         170       180       190
                  ....*....|....*....|....*....|....
gi 1515054357 174 NYDPRmkreGLHYVVVERDEKYMASFDEMVPEFI 207
Cdd:cd22343   153 VYTPK----GSHIERIKRDEEFWAEILPKLEEFY 182
YqaJ pfam09588
YqaJ-like viral recombinase domain; This protein family is found in many different bacterial ...
24-168 1.47e-33

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: 117.47  E-value: 1.47e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515054357  24 WHKLRLGVITASEVHNVIakprSGKKWpdmkmSYFHTLLAEVCTGVAPEVNAKALAWGKQYENDARTLFEFTSGVNVTES 103
Cdd:pfam09588   2 WLEARRGGITASDAAAAL----GTNPY-----KSSVSLWLEKTGQVEPFKDKKAMAWGTELEPIARAEYEFRTGVKVRRV 72
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1515054357 104 PIIYRD-ESMRTACSPDGLCSDGN-----GLELKCPFtSRDFMKFRLGGFEAIKSAYMAQVQYSMWVTRKD 168
Cdd:pfam09588  73 NGLLQHpEDPFLLASPDGIVVGARdgdrgILEIKCPF-SATFGASLWGGADGIPEEYMLQVQHQLAVTGAE 142
COG5377 COG5377
Phage-related protein, predicted endonuclease [Mobilome: prophages, transposons];
12-213 2.53e-12

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


Pssm-ID: 444142 [Multi-domain]  Cd Length: 313  Bit Score: 64.64  E-value: 2.53e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515054357  12 IDVRAVEQGDDAWHKLRLGVITASEVHNVIAkpRSGKKWPDmkmsyfhTLLAEVCTGVAPEVNAK-ALAWGKQYENDART 90
Cdd:COG5377     4 VNTKDLSQSREEWLALRRKGIGASDAAAILG--LSPYKSPL-------DLWLEKTGGLPPDLEENeAMYWGNLLEPVVAR 74
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515054357  91 LFEFTSGVNVTESPIIYRDES---MRtaCSPDGLCSDGNG-LELKCP--FTSRDFMKfrlggfEAIKSAYMAQVQYSMWV 164
Cdd:COG5377    75 EFEKRTGLKVRRVNAILQHPEypfML--ANLDRLVVGENGvLEIKTAsaYLADEWGE------DEVPDYYLCQVQHQLAV 146
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1515054357 165 TRKDAWYFANYDprmkrEGLHYVV--VERDEkymasfdemvpEFIEKMDEA 213
Cdd:COG5377   147 TGASWAYVAVLI-----GGNEFRWfrIERDE-----------ELIEELIEA 181
phage_rel_nuc TIGR03033
putative phage-type endonuclease; Members of this protein family are found often in phage ...
18-177 8.01e-12

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: 60.90  E-value: 8.01e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515054357  18 EQGDDAWHKLRLGVITASEVHNViakprsgkkwpdMKMSYFHT---LLAEVCTGVAPEVNAKALAWGKQYENDARTLFEF 94
Cdd:TIGR03033   3 VQRTEEWHAWRKGGITASDIAAI------------MGLNPYKTpeeLWKEKTGFVEPEDMNEAMYHGVKLEPEAREAFRD 70
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515054357  95 TSGVNvTESPIIYRDESMRTACSPDGL-CSDGNGLELKCP--FTSRDFMKFRLGGfeaIKSAYMAQVQYSMWVTRKDAWY 171
Cdd:TIGR03033  71 KYGIM-AEPFCLEHDEYPWMAASLDGLvADDKQILEIKCPseRVSKLWVSELSGE---VPAYYQAQVQWQLYVSGSQAAY 146

                  ....*.
gi 1515054357 172 FANYDP 177
Cdd:TIGR03033 147 FAVYLG 152
 
Name Accession Description Interval E-value
PDDEXK_lambda_exonuclease-like cd22343
Uncharacterized nucleases similar to lambda phage exonuclease; This model characterizes a ...
18-207 1.56e-41

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: 139.39  E-value: 1.56e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515054357  18 EQGDDAWHKLRLGVITASEVHNVIAKPRSGKKWPDmkmsyfhTLLAEVCTGvAPEVNAKALAWGKQYENDARTLFEFTSG 97
Cdd:cd22343     1 QQRSPEWFEARKGRITASNFGRVLTTVENKKAPPA-------SLLKRILGP-RPFKSTAATRWGIENEPEAREAYEELTG 72
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515054357  98 VNVTESPIIYRDESMRTACSPDGL----CSDGNGLELKCPFTSRDFMKFRLGGFEAIKSAYMAQVQYSMWVTRKDAWYFA 173
Cdd:cd22343    73 VKVKECGLVIHPEHPWLGASPDGLvtcdCCGKGLLEIKCPYSKDRKLKENFKLDKLETHPYYYQVQGQMAVTGREWCDFV 152
                         170       180       190
                  ....*....|....*....|....*....|....
gi 1515054357 174 NYDPRmkreGLHYVVVERDEKYMASFDEMVPEFI 207
Cdd:cd22343   153 VYTPK----GSHIERIKRDEEFWAEILPKLEEFY 182
YqaJ pfam09588
YqaJ-like viral recombinase domain; This protein family is found in many different bacterial ...
24-168 1.47e-33

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: 117.47  E-value: 1.47e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515054357  24 WHKLRLGVITASEVHNVIakprSGKKWpdmkmSYFHTLLAEVCTGVAPEVNAKALAWGKQYENDARTLFEFTSGVNVTES 103
Cdd:pfam09588   2 WLEARRGGITASDAAAAL----GTNPY-----KSSVSLWLEKTGQVEPFKDKKAMAWGTELEPIARAEYEFRTGVKVRRV 72
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1515054357 104 PIIYRD-ESMRTACSPDGLCSDGN-----GLELKCPFtSRDFMKFRLGGFEAIKSAYMAQVQYSMWVTRKD 168
Cdd:pfam09588  73 NGLLQHpEDPFLLASPDGIVVGARdgdrgILEIKCPF-SATFGASLWGGADGIPEEYMLQVQHQLAVTGAE 142
COG5377 COG5377
Phage-related protein, predicted endonuclease [Mobilome: prophages, transposons];
12-213 2.53e-12

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


Pssm-ID: 444142 [Multi-domain]  Cd Length: 313  Bit Score: 64.64  E-value: 2.53e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515054357  12 IDVRAVEQGDDAWHKLRLGVITASEVHNVIAkpRSGKKWPDmkmsyfhTLLAEVCTGVAPEVNAK-ALAWGKQYENDART 90
Cdd:COG5377     4 VNTKDLSQSREEWLALRRKGIGASDAAAILG--LSPYKSPL-------DLWLEKTGGLPPDLEENeAMYWGNLLEPVVAR 74
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515054357  91 LFEFTSGVNVTESPIIYRDES---MRtaCSPDGLCSDGNG-LELKCP--FTSRDFMKfrlggfEAIKSAYMAQVQYSMWV 164
Cdd:COG5377    75 EFEKRTGLKVRRVNAILQHPEypfML--ANLDRLVVGENGvLEIKTAsaYLADEWGE------DEVPDYYLCQVQHQLAV 146
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1515054357 165 TRKDAWYFANYDprmkrEGLHYVV--VERDEkymasfdemvpEFIEKMDEA 213
Cdd:COG5377   147 TGASWAYVAVLI-----GGNEFRWfrIERDE-----------ELIEELIEA 181
phage_rel_nuc TIGR03033
putative phage-type endonuclease; Members of this protein family are found often in phage ...
18-177 8.01e-12

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: 60.90  E-value: 8.01e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515054357  18 EQGDDAWHKLRLGVITASEVHNViakprsgkkwpdMKMSYFHT---LLAEVCTGVAPEVNAKALAWGKQYENDARTLFEF 94
Cdd:TIGR03033   3 VQRTEEWHAWRKGGITASDIAAI------------MGLNPYKTpeeLWKEKTGFVEPEDMNEAMYHGVKLEPEAREAFRD 70
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1515054357  95 TSGVNvTESPIIYRDESMRTACSPDGL-CSDGNGLELKCP--FTSRDFMKFRLGGfeaIKSAYMAQVQYSMWVTRKDAWY 171
Cdd:TIGR03033  71 KYGIM-AEPFCLEHDEYPWMAASLDGLvADDKQILEIKCPseRVSKLWVSELSGE---VPAYYQAQVQWQLYVSGSQAAY 146

                  ....*.
gi 1515054357 172 FANYDP 177
Cdd:TIGR03033 147 FAVYLG 152
Viral_alk_exo pfam01771
Viral alkaline exonuclease; This family includes various alkaline exonucleases from members of ...
19-93 2.46e-03

Viral alkaline exonuclease; This family includes various alkaline exonucleases from members of the Herpesviridae and Baculoviridae. Alkaline exonuclease appears to have an important role in the replication of herpes simplex virus.


Pssm-ID: 396366  Cd Length: 460  Bit Score: 38.50  E-value: 2.46e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1515054357  19 QGDDA-WHKLRLGVITASEVHNVIAKPRSGKKWpdmkmsyfhtllAEVCTGVAPEVNAKALAWGKQYENDARTLFE 93
Cdd:pfam01771 106 QSENPlWDLLRDGTISASKLYWAVKQQNPSKKI------------FEPWPITNNHYVASPVAFGLRCEPVVKTLVA 169
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH