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Conserved domains on  [gi|292397824|ref|YP_003517890|]
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alkaline exonuclease [Lymantria xylina nucleopolyhedrovirus]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
YqaJ super family cl09232
YqaJ-like viral recombinase domain; This protein family is found in many different bacterial ...
39-261 2.83e-14

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.


The actual alignment was detected with superfamily member pfam01771:

Pssm-ID: 447697  Cd Length: 460  Bit Score: 74.33  E-value: 2.83e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292397824   39 LHVERQTRGQSKNALWNALRLDRRTAS-------GSSPD----QHAPRQN-----AAMTFGLRQEEqlkldetVVselRD 102
Cdd:pfam01771  97 LLIERETRGQSENPLWDLLRDGTISASklywavkQQNPSkkifEPWPITNnhyvaSPVAFGLRCEP-------VV---KT 166
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292397824  103 LVElTLSPARATTAVLDCGLFFS-RRGLNSASPDAYF--VMSTGGFVPV-------EIKCPFSYrdttveqmrsglgarr 172
Cdd:pfam01771 167 LVA-ELVVTPDGEVVHDCGFLIDpTDGIFGASLDLCVnvSTGTDNPLPFkpdaeiyEIKCRFKY---------------- 229
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292397824  173 aryrvkhtalsvnvrgppLFAVEKTDPHYRQMQRqmyVLEAPMCVYLVKFKGSHVSVAVrrdEDFCRRENASE-ERLLTM 251
Cdd:pfam01771 230 ------------------LFDKEECDPLYQAYTE---LYNRPTKAALIDFIYSIPKPAV---EYVGPGRLPSErEYLLTY 285
                         250
                  ....*....|
gi 292397824  252 YVARNLNRKR 261
Cdd:pfam01771 286 DQAWDLAPKR 295
 
Name Accession Description Interval E-value
Viral_alk_exo pfam01771
Viral alkaline exonuclease; This family includes various alkaline exonucleases from members of ...
39-261 2.83e-14

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: 74.33  E-value: 2.83e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292397824   39 LHVERQTRGQSKNALWNALRLDRRTAS-------GSSPD----QHAPRQN-----AAMTFGLRQEEqlkldetVVselRD 102
Cdd:pfam01771  97 LLIERETRGQSENPLWDLLRDGTISASklywavkQQNPSkkifEPWPITNnhyvaSPVAFGLRCEP-------VV---KT 166
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292397824  103 LVElTLSPARATTAVLDCGLFFS-RRGLNSASPDAYF--VMSTGGFVPV-------EIKCPFSYrdttveqmrsglgarr 172
Cdd:pfam01771 167 LVA-ELVVTPDGEVVHDCGFLIDpTDGIFGASLDLCVnvSTGTDNPLPFkpdaeiyEIKCRFKY---------------- 229
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292397824  173 aryrvkhtalsvnvrgppLFAVEKTDPHYRQMQRqmyVLEAPMCVYLVKFKGSHVSVAVrrdEDFCRRENASE-ERLLTM 251
Cdd:pfam01771 230 ------------------LFDKEECDPLYQAYTE---LYNRPTKAALIDFIYSIPKPAV---EYVGPGRLPSErEYLLTY 285
                         250
                  ....*....|
gi 292397824  252 YVARNLNRKR 261
Cdd:pfam01771 286 DQAWDLAPKR 295
PDDEXK_lambda_exonuclease-like cd22343
Uncharacterized nucleases similar to lambda phage exonuclease; This model characterizes a ...
48-238 2.87e-10

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: 58.89  E-value: 2.87e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292397824  48 QSKNALWNALRLDRRTAS--------GSSPDQH------------APRQNAAMTFGLRQEEQ-LKLDETVVselrdlvel 106
Cdd:cd22343    1 QQRSPEWFEARKGRITASnfgrvlttVENKKAPpasllkrilgprPFKSTAATRWGIENEPEaREAYEELT--------- 71
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292397824 107 tlsparaTTAVLDCGLF----FSRRGlnsASPDAYFVMSTGGFVPVEIKCPFSYRDTTVEQMRSGLgarraryrvkhtal 182
Cdd:cd22343   72 -------GVKVKECGLVihpeHPWLG---ASPDGLVTCDCCGKGLLEIKCPYSKDRKLKENFKLDK-------------- 127
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 292397824 183 svnvrgpplfavEKTDPHYRQMQRQMYVLEAPMCvYLVKF--KGSHVSVaVRRDEDFC 238
Cdd:cd22343  128 ------------LETHPYYYQVQGQMAVTGREWC-DFVVYtpKGSHIER-IKRDEEFW 171
 
Name Accession Description Interval E-value
Viral_alk_exo pfam01771
Viral alkaline exonuclease; This family includes various alkaline exonucleases from members of ...
39-261 2.83e-14

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: 74.33  E-value: 2.83e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292397824   39 LHVERQTRGQSKNALWNALRLDRRTAS-------GSSPD----QHAPRQN-----AAMTFGLRQEEqlkldetVVselRD 102
Cdd:pfam01771  97 LLIERETRGQSENPLWDLLRDGTISASklywavkQQNPSkkifEPWPITNnhyvaSPVAFGLRCEP-------VV---KT 166
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292397824  103 LVElTLSPARATTAVLDCGLFFS-RRGLNSASPDAYF--VMSTGGFVPV-------EIKCPFSYrdttveqmrsglgarr 172
Cdd:pfam01771 167 LVA-ELVVTPDGEVVHDCGFLIDpTDGIFGASLDLCVnvSTGTDNPLPFkpdaeiyEIKCRFKY---------------- 229
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292397824  173 aryrvkhtalsvnvrgppLFAVEKTDPHYRQMQRqmyVLEAPMCVYLVKFKGSHVSVAVrrdEDFCRRENASE-ERLLTM 251
Cdd:pfam01771 230 ------------------LFDKEECDPLYQAYTE---LYNRPTKAALIDFIYSIPKPAV---EYVGPGRLPSErEYLLTY 285
                         250
                  ....*....|
gi 292397824  252 YVARNLNRKR 261
Cdd:pfam01771 286 DQAWDLAPKR 295
PDDEXK_lambda_exonuclease-like cd22343
Uncharacterized nucleases similar to lambda phage exonuclease; This model characterizes a ...
48-238 2.87e-10

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: 58.89  E-value: 2.87e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292397824  48 QSKNALWNALRLDRRTAS--------GSSPDQH------------APRQNAAMTFGLRQEEQ-LKLDETVVselrdlvel 106
Cdd:cd22343    1 QQRSPEWFEARKGRITASnfgrvlttVENKKAPpasllkrilgprPFKSTAATRWGIENEPEaREAYEELT--------- 71
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 292397824 107 tlsparaTTAVLDCGLF----FSRRGlnsASPDAYFVMSTGGFVPVEIKCPFSYRDTTVEQMRSGLgarraryrvkhtal 182
Cdd:cd22343   72 -------GVKVKECGLVihpeHPWLG---ASPDGLVTCDCCGKGLLEIKCPYSKDRKLKENFKLDK-------------- 127
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 292397824 183 svnvrgpplfavEKTDPHYRQMQRQMYVLEAPMCvYLVKF--KGSHVSVaVRRDEDFC 238
Cdd:cd22343  128 ------------LETHPYYYQVQGQMAVTGREWC-DFVVYtpKGSHIER-IKRDEEFW 171
 
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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