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Conserved domains on  [gi|529144051|ref|WP_020934035|]
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exodeoxyribonuclease III [Corynebacterium maris]

Protein Classification

exonuclease/endonuclease/phosphatase family protein( domain architecture ID 662)

exonuclease/endonuclease/phosphatase (EEP) family protein may cleave phosphodiester bonds

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
EEP super family cl00490
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 3-297 7.95e-96

Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.


The actual alignment was detected with superfamily member cd10281:

Pssm-ID: 469791 [Multi-domain]  Cd Length: 253  Bit Score: 282.96  E-value: 7.95e-96
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051   3 ITIASVNVNGIRAATKirhednPGMHAWLRQTPAEVVLLQEVRATVDESIKALQPALdaGWHYVGAPAAAKGRAGVGILS 82
Cdd:cd10281    1 MRVISVNVNGIRAAAK------KGFLEWLAAQDADVVCLQEVRAQEEQLDDDFFEPE--GYNAYFFDAEKKGYAGVAIYS 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051  83 RAPLDDVTVGFG--SFLDSGRWLEGTYQGVRVASLYLPSGAVDSEKLDEKYVFLDEFSGVLDELADTHDKMVVGGDWNIC 160
Cdd:cd10281   73 RTQPKAVIYGLGfeEFDDEGRYIEADFDNVSVASLYVPSGSSGDERQEAKMAFLDAFLEHLKELRRKRREFIVCGDFNIA 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051 161 HREQDLKNSKPNRKKSGHLPDERAWMDSVFGsfpdaevqekpglgeffgvvdyeprpirgaaqDPKWFDVARRLHPEDAA 240
Cdd:cd10281  153 HTEIDIKNWKANQKNSGFLPEERAWLDQVFG--------------------------------ELGYVDAFRELNPDEGQ 200

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 529144051 241 YTWWTYRGQAFNNNAGWRIDYQAATRSMLDAATRTWVDRaatvEERWSDHSPMLVEY 297
Cdd:cd10281  201 YTWWSNRGQARANNVGWRIDYQIATPGLASKVVSAWIYR----EERFSDHAPLIVDY 253
 
Name Accession Description Interval E-value
Nape_like_AP-endo cd10281
Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) ...
 3-297 7.95e-96

Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.


Pssm-ID: 197336 [Multi-domain]  Cd Length: 253  Bit Score: 282.96  E-value: 7.95e-96
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051   3 ITIASVNVNGIRAATKirhednPGMHAWLRQTPAEVVLLQEVRATVDESIKALQPALdaGWHYVGAPAAAKGRAGVGILS 82
Cdd:cd10281    1 MRVISVNVNGIRAAAK------KGFLEWLAAQDADVVCLQEVRAQEEQLDDDFFEPE--GYNAYFFDAEKKGYAGVAIYS 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051  83 RAPLDDVTVGFG--SFLDSGRWLEGTYQGVRVASLYLPSGAVDSEKLDEKYVFLDEFSGVLDELADTHDKMVVGGDWNIC 160
Cdd:cd10281   73 RTQPKAVIYGLGfeEFDDEGRYIEADFDNVSVASLYVPSGSSGDERQEAKMAFLDAFLEHLKELRRKRREFIVCGDFNIA 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051 161 HREQDLKNSKPNRKKSGHLPDERAWMDSVFGsfpdaevqekpglgeffgvvdyeprpirgaaqDPKWFDVARRLHPEDAA 240
Cdd:cd10281  153 HTEIDIKNWKANQKNSGFLPEERAWLDQVFG--------------------------------ELGYVDAFRELNPDEGQ 200

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 529144051 241 YTWWTYRGQAFNNNAGWRIDYQAATRSMLDAATRTWVDRaatvEERWSDHSPMLVEY 297
Cdd:cd10281  201 YTWWSNRGQARANNVGWRIDYQIATPGLASKVVSAWIYR----EERFSDHAPLIVDY 253
XthA COG0708
Exonuclease III [Replication, recombination and repair];
4-298 4.54e-95

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 281.19  E-value: 4.54e-95
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051   4 TIASVNVNGIRAATKIrhednpgMHAWLRQTPAEVVLLQEVRATVDE-SIKALQPAldaGWHYVGAPAaaKGRAGVGILS 82
Cdd:COG0708    2 KIASWNVNGIRARLPK-------LLDWLAEEDPDVLCLQETKAQDEQfPLEAFEAA---GYHVYFHGQ--KGYNGVAILS 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051  83 RAPLDDVTVGFG--SFLDSGRWLEGTYQGVRVASLYLPSG-AVDSEKLDEKYVFLDEFSGVLDELADTHDKMVVGGDWNI 159
Cdd:COG0708   70 RLPPEDVRRGLGgdEFDAEGRYIEADFGGVRVVSLYVPNGgSVGSEKFDYKLRFLDALRAYLAELLAPGRPLILCGDFNI 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051 160 CHREQDLKNSKPNRKKSGHLPDERAWMDSVFgsfpdaevqekpGLGeffgvvdyeprpirgaaqdpkWFDVARRLHPEDA 239
Cdd:COG0708  150 APTEIDVKNPKANLKNAGFLPEERAWFDRLL------------ELG---------------------LVDAFRALHPDVE 196

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051 240 -AYTWWTYRGQAFNNNAGWRIDYQAATRSMLDAATRTWVDRAATVEERWSDHSPMLVEYD 298
Cdd:COG0708  197 gQYTWWSYRAGAFARNRGWRIDYILASPALADRLKDAGIDREPRGDERPSDHAPVVVELD 256
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 5-298 4.73e-57

exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273186 [Multi-domain]  Cd Length: 254  Bit Score: 184.02  E-value: 4.73e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051    5 IASVNVNGIRAATKIRHEDnpgmhaWLRQTPAEVVLLQEVRATVDESIKALQPALDAGWHYVGAPaaaKGRAGVGILSRA 84
Cdd:TIGR00633   3 IISWNVNGLRARLHKLFLD------WLKEEQPDVLCLQETKVADEQFPAELFEELGYHVFFHGAK---KGYSGVAILSKV 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051   85 PLDDVTVGFGS--FLDSGRWLEGTYQGVRVASLYLP-SGAVDSEKLDEKYVFLDEFSGVLDELADTHDKMVVGGDWNICH 161
Cdd:TIGR00633  74 EPLDVRYGFGGepHDEEGRVITAEFDGFTVVNVYVPnGGSRDLERLEYKLQFWDALFQYLEKELDAGKPVVICGDMNVAH 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051  162 REQDLKNSKPNRKKSGHLPDERAWMDSVFGSfpdaevqekpglgeffGVVdyeprpirgaaqdpkwfDVARRLHPEDA-A 240
Cdd:TIGR00633 154 TEIDLGNPKENKGNAGFTPEEREWFDELLEA----------------GFV-----------------DTFRHFNPDTGdA 200

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 529144051  241 YTWWTYRGQAFNNNAGWRIDYQAATRSMLDAATRTWVDRaatvEERWSDHSPMLVEYD 298
Cdd:TIGR00633 201 YTWWDYRSGARDRNRGWRIDYFLVSEPLAERVVDSYIDS----EIRGSDHCPIVLELD 254
PRK11756 PRK11756
exonuclease III; Provisional
 5-299 6.80e-20

exonuclease III; Provisional


Pssm-ID: 236970 [Multi-domain]  Cd Length: 268  Bit Score: 86.87  E-value: 6.80e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051   5 IASVNVNGIRAatkiRhednpgMH---AWLRQTPAEVVLLQEVRATVD----ESIKALqpaldaGWH--YVGapaaAKGR 75
Cdd:PRK11756   3 FVSFNINGLRA----R------PHqleAIIEKHQPDVIGLQETKVHDEmfplEEVEAL------GYHvfYHG----QKGH 62

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051  76 AGVGILSRAPLDDVTVGF-GSFLDSG-RWLEGTY---QG-VRVASLYLPSGavDSEKLDEKY----VFLDEFSGVLDELA 145
Cdd:PRK11756  63 YGVALLSKQTPIAVRKGFpTDDEEAQrRIIMATIptpNGnLTVINGYFPQG--ESRDHPTKFpakrQFYQDLQNYLETEL 140

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051 146 DTHDKMVVGGDWNICHREQDLKNSKPNRK---KSGH---LPDERAWMDSVFGsfpdaevqekpglgefFGVVdyeprpir 219
Cdd:PRK11756 141 SPDNPLLIMGDMNISPTDLDIGIGEENRKrwlRTGKcsfLPEEREWLDRLMD----------------WGLV-------- 196

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051 220 gaaqdpkwfDVARRLHPE-DAAYTWWTYRGQAFNNNAGWRIDYQAATRSMLDAATRTWVD---RAAtveERWSDHSPMLV 295
Cdd:PRK11756 197 ---------DTFRQLNPDvNDRFSWFDYRSKGFDDNRGLRIDLILATQPLAERCVETGIDydiRGM---EKPSDHAPIWA 264


                 ....
gi 529144051 296 EYDI 299
Cdd:PRK11756 265 TFKL 268
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 6-159 1.17e-15

Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12 and Nocturnin.


Pssm-ID: 460902 [Multi-domain]  Cd Length: 183  Bit Score: 73.41  E-value: 1.17e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051    6 ASVNVNGIRAATKIRHEDNPGMHAWLRQTPAEVVLLQEVRATVDESIKALQPALDAGWHYVGaPAAAKGRAGVGILSRAP 85
Cdd:pfam03372   1 LTWNVNGGNADAAGDDRKLDALAALIRAYDPDVVALQETDDDDASRLLLALLAYGGFLSYGG-PGGGGGGGGVAILSRYP 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 529144051   86 LDDVTVGFGSFLD--SGRWLEGTYQGVRVASLYLPSGAVDSEKLDEKYVFLDEFSGVLDELADTHDKMVVGGDWNI 159
Cdd:pfam03372  80 LSSVILVDLGEFGdpALRGAIAPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALLAPRSEPVILAGDFNA 155
 
Name Accession Description Interval E-value
Nape_like_AP-endo cd10281
Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) ...
 3-297 7.95e-96

Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities.


Pssm-ID: 197336 [Multi-domain]  Cd Length: 253  Bit Score: 282.96  E-value: 7.95e-96
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051   3 ITIASVNVNGIRAATKirhednPGMHAWLRQTPAEVVLLQEVRATVDESIKALQPALdaGWHYVGAPAAAKGRAGVGILS 82
Cdd:cd10281    1 MRVISVNVNGIRAAAK------KGFLEWLAAQDADVVCLQEVRAQEEQLDDDFFEPE--GYNAYFFDAEKKGYAGVAIYS 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051  83 RAPLDDVTVGFG--SFLDSGRWLEGTYQGVRVASLYLPSGAVDSEKLDEKYVFLDEFSGVLDELADTHDKMVVGGDWNIC 160
Cdd:cd10281   73 RTQPKAVIYGLGfeEFDDEGRYIEADFDNVSVASLYVPSGSSGDERQEAKMAFLDAFLEHLKELRRKRREFIVCGDFNIA 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051 161 HREQDLKNSKPNRKKSGHLPDERAWMDSVFGsfpdaevqekpglgeffgvvdyeprpirgaaqDPKWFDVARRLHPEDAA 240
Cdd:cd10281  153 HTEIDIKNWKANQKNSGFLPEERAWLDQVFG--------------------------------ELGYVDAFRELNPDEGQ 200

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 529144051 241 YTWWTYRGQAFNNNAGWRIDYQAATRSMLDAATRTWVDRaatvEERWSDHSPMLVEY 297
Cdd:cd10281  201 YTWWSNRGQARANNVGWRIDYQIATPGLASKVVSAWIYR----EERFSDHAPLIVDY 253
XthA COG0708
Exonuclease III [Replication, recombination and repair];
4-298 4.54e-95

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 281.19  E-value: 4.54e-95
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051   4 TIASVNVNGIRAATKIrhednpgMHAWLRQTPAEVVLLQEVRATVDE-SIKALQPAldaGWHYVGAPAaaKGRAGVGILS 82
Cdd:COG0708    2 KIASWNVNGIRARLPK-------LLDWLAEEDPDVLCLQETKAQDEQfPLEAFEAA---GYHVYFHGQ--KGYNGVAILS 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051  83 RAPLDDVTVGFG--SFLDSGRWLEGTYQGVRVASLYLPSG-AVDSEKLDEKYVFLDEFSGVLDELADTHDKMVVGGDWNI 159
Cdd:COG0708   70 RLPPEDVRRGLGgdEFDAEGRYIEADFGGVRVVSLYVPNGgSVGSEKFDYKLRFLDALRAYLAELLAPGRPLILCGDFNI 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051 160 CHREQDLKNSKPNRKKSGHLPDERAWMDSVFgsfpdaevqekpGLGeffgvvdyeprpirgaaqdpkWFDVARRLHPEDA 239
Cdd:COG0708  150 APTEIDVKNPKANLKNAGFLPEERAWFDRLL------------ELG---------------------LVDAFRALHPDVE 196

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051 240 -AYTWWTYRGQAFNNNAGWRIDYQAATRSMLDAATRTWVDRAATVEERWSDHSPMLVEYD 298
Cdd:COG0708  197 gQYTWWSYRAGAFARNRGWRIDYILASPALADRLKDAGIDREPRGDERPSDHAPVVVELD 256
ExoIII_AP-endo cd09073
Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ...
 5-297 4.70e-67

Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily.


Pssm-ID: 197307 [Multi-domain]  Cd Length: 251  Bit Score: 209.84  E-value: 4.70e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051   5 IASVNVNGIRAATKirhednPGMHAWLRQTPAEVVLLQEVRATVDESIKALQPALdaGWHYVGAPAAAKGRAGVGILSRA 84
Cdd:cd09073    2 IISWNVNGLRARLK------KGVLKWLKEEKPDILCLQETKADEDKLPEELQHVE--GYHSYWSPARKKGYSGVATLSKE 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051  85 PLDDVTVGFGS--FLDSGRWLEGTYQGVRVASLYLPSGAVDSEKLDEKYVFLDEFSGVLDELADTHDKMVVGGDWNICHR 162
Cdd:cd09073   74 EPLDVSYGIGGeeFDSEGRVITAEFDDFYLINVYFPNGGRGLERLDYKLRFYEAFLEFLEKLRKRGKPVVICGDFNVAHE 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051 163 EQDLKNSKPNRKKSGHLPDERAWMDsvfgsfpdaEVQEKPglgeffgvvdyeprpirgaaqdpkWFDVARRLHPEDAAYT 242
Cdd:cd09073  154 EIDLARPKKNEKNAGFTPEERAWFD---------KLLSLG------------------------YVDTFRHFHPEPGAYT 200

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 529144051 243 WWTYRGQAFNNNAGWRIDYQAATRSMLDAATRTWVDRaatvEERWSDHSPMLVEY 297
Cdd:cd09073  201 WWSYRGNARERNVGWRIDYFLVSEELAEKVKDSGILS----KVKGSDHAPVTLEL 251
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 5-298 4.73e-57

exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273186 [Multi-domain]  Cd Length: 254  Bit Score: 184.02  E-value: 4.73e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051    5 IASVNVNGIRAATKIRHEDnpgmhaWLRQTPAEVVLLQEVRATVDESIKALQPALDAGWHYVGAPaaaKGRAGVGILSRA 84
Cdd:TIGR00633   3 IISWNVNGLRARLHKLFLD------WLKEEQPDVLCLQETKVADEQFPAELFEELGYHVFFHGAK---KGYSGVAILSKV 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051   85 PLDDVTVGFGS--FLDSGRWLEGTYQGVRVASLYLP-SGAVDSEKLDEKYVFLDEFSGVLDELADTHDKMVVGGDWNICH 161
Cdd:TIGR00633  74 EPLDVRYGFGGepHDEEGRVITAEFDGFTVVNVYVPnGGSRDLERLEYKLQFWDALFQYLEKELDAGKPVVICGDMNVAH 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051  162 REQDLKNSKPNRKKSGHLPDERAWMDSVFGSfpdaevqekpglgeffGVVdyeprpirgaaqdpkwfDVARRLHPEDA-A 240
Cdd:TIGR00633 154 TEIDLGNPKENKGNAGFTPEEREWFDELLEA----------------GFV-----------------DTFRHFNPDTGdA 200

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 529144051  241 YTWWTYRGQAFNNNAGWRIDYQAATRSMLDAATRTWVDRaatvEERWSDHSPMLVEYD 298
Cdd:TIGR00633 201 YTWWDYRSGARDRNRGWRIDYFLVSEPLAERVVDSYIDS----EIRGSDHCPIVLELD 254
ExoIII-like_AP-endo cd09086
Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of ...
 4-296 3.62e-56

Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and 3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.


Pssm-ID: 197320 [Multi-domain]  Cd Length: 254  Bit Score: 181.94  E-value: 3.62e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051   4 TIASVNVNGIRAatkiRHEDnpgMHAWLRQTPAEVVLLQEVRATvDESIkALQPALDAGWH--YVGApaaaKGRAGVGIL 81
Cdd:cd09086    2 KIATWNVNSIRA----RLEQ---VLDWLKEEDPDVLCLQETKVE-DDQF-PADAFEALGYHvaVHGQ----KAYNGVAIL 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051  82 SRAPLDDVTVGFGSFLDSG--RWLEGTYQGVRVASLYLPSG-AVDSEKLDEKYVFLDEFSGVLDELADTHDKMVVGGDWN 158
Cdd:cd09086   69 SRLPLEDVRTGFPGDPDDDqaRLIAARVGGVRVINLYVPNGgDIGSPKFAYKLDWLDRLIRYLQKLLKPDDPLVLVGDFN 148

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051 159 ICHREQDLKNSKPNRKKSGHLPDERAWMDSVFgsfpdaevqekpGLGeffgvvdyeprpirgaaqdpkWFDVARRLHPED 238
Cdd:cd09086  149 IAPEDIDVWDPKQLLGKVLFTPEEREALRALL------------DLG---------------------FVDAFRALHPDE 195

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 529144051 239 AAYTWWTYRGQAFNNNAGWRIDYQAATRSMLDAATRTWVDRAATVEERWSDHSPMLVE 296
Cdd:cd09086  196 KLFTWWDYRAGAFERNRGLRIDHILASPALADRLKDVGIDREPRGWEKPSDHAPVVAE 253
Mth212-like_AP-endo cd09085
Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic ...
 4-297 4.86e-52

Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues.


Pssm-ID: 197319 [Multi-domain]  Cd Length: 252  Bit Score: 171.31  E-value: 4.86e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051   4 TIASVNVNGIRAATKirhednPGMHAWLRQTPAEVVLLQEVRAT---VDESIKALqpaldAGWHYVGAPAAAKGRAGVGI 80
Cdd:cd09085    2 KIISWNVNGLRAVHK------KGFLDWFKEEKPDILCLQETKAQpeqLPEDLRNI-----EGYHSYFNSAERKGYSGVAL 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051  81 LSRAPLDDVTVGFGS--FLDSGRWLEGTYQGVRVASLYLPSGAVDSEKLDEKYVFLDEFSGVLDELADTHDKMVVGGDWN 158
Cdd:cd09085   71 YSKIEPDSVREGLGVeeFDNEGRILIADFDDFTLFNIYFPNGQMSEERLDYKLEFYDAFLEYLNELRDSGKNVIICGDFN 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051 159 ICHREQDLKNSKPNRKKSGHLPDERAWMDSVFgsfpdaevqekpglgeffgvvdyeprpirgaaqDPKWFDVARRLHPED 238
Cdd:cd09085  151 TAHKEIDLARPKENEKVSGFLPEERAWMDKFI---------------------------------ENGYVDTFRMFNKEP 197

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 529144051 239 AAYTWWTYRGQAFNNNAGWRIDY----QAATRSMLDAATRTWVdraatveeRWSDHSPMLVEY 297
Cdd:cd09085  198 GQYTWWSYRTRARERNVGWRIDYffvnEEFKPKVKDAGILPDV--------MGSDHCPVSLEL 252
exoDNase_III TIGR00195
exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model ...
 5-296 1.42e-51

exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 272954 [Multi-domain]  Cd Length: 254  Bit Score: 169.87  E-value: 1.42e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051    5 IASVNVNGIRAATKIrhednpgMHAWLRQTPAEVVLLQEVRAtVDESIkALQPALDAGWHYVGAPAaaKGRAGVGILSRA 84
Cdd:TIGR00195   3 IISWNVNGLRARPHK-------GLAWLKENQPDVLCLQETKV-QDEQF-PLEPFHKEGYHVFFSGQ--KGYSGVAIFSKE 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051   85 PLDDVTVGFGS--FLDSGRWLEGTYQGVRVASLYLPSG-AVDSEKLDEKYVFLDEFSGVLDELADTHDKMVVGGDWNICH 161
Cdd:TIGR00195  72 EPISVRRGFGVeeEDAEGRIIMAEFDSFLVINGYFPNGsRDDSEKLPYKLQWLEALQNYLEKLVDKDKPVLICGDMNIAP 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051  162 REQDLKNSKPNRKKSGHLPDERAWMDSVFGsfpdaevqekpglgefFGVVDyeprpirgaaqdpkwfdVARRLHPEDAAY 241
Cdd:TIGR00195 152 TEIDLHIPDENRNHTGFLPEEREWLDRLLE----------------AGLVD-----------------TFRKFNPDEGAY 198

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 529144051  242 TWWTYRGQAFNNNAGWRIDYQAATRSMLDAATRTWVDRAATVEERWSDHSPMLVE 296
Cdd:TIGR00195 199 SWWDYRTKARDRNRGWRIDYFLVSEPLKERCVDCGIDYDIRGSEKPSDHCPVVLE 253
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This ...
 3-296 2.17e-34

Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.


Pssm-ID: 197321 [Multi-domain]  Cd Length: 253  Bit Score: 125.36  E-value: 2.17e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051   3 ITIASVNVNGIRAATKirhednPGMHAWLRQTPAEVVLLQEVRATVDESIKALQPALDaGWHYVGAPAAAKGRAGVGILS 82
Cdd:cd09087    1 LKIISWNVNGLRALLK------KGLLDYVKKEDPDILCLQETKLQEGDVPKELKELLK-GYHQYWNAAEKKGYSGTAILS 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051  83 RAPLDDVTVGFGSFL--DSGRWLEGTYQGVRVASLYLP-SGAvDSEKLDEKYVFLDEFSGVLDELADTHdKMVVGGDWNI 159
Cdd:cd09087   74 KKKPLSVTYGIGIEEhdQEGRVITAEFENFYLVNTYVPnSGR-GLERLDRRKEWDVDFRAYLKKLDSKK-PVIWCGDLNV 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051 160 CHREQDLKNSKPNRKKSGHLPDERAWMDSVFGSfpdaevqekpglgeffgvvdyeprpirgaaqdpKWFDVARRLHPEDA 239
Cdd:cd09087  152 AHEEIDLANPKTNKKSAGFTPEERESFTELLEA---------------------------------GFVDTFRHLHPDKE 198

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 529144051 240 -AYTWWTYRGQAFNNNAGWRIDYQAATRSML----DAATRTWVDRaatveerwSDHSPMLVE 296
Cdd:cd09087  199 gAYTFWSYRGNARAKNVGWRLDYFLVSERLKdrvvDSFIRSDIMG--------SDHCPIGLE 252
PRK11756 PRK11756
exonuclease III; Provisional
 5-299 6.80e-20

exonuclease III; Provisional


Pssm-ID: 236970 [Multi-domain]  Cd Length: 268  Bit Score: 86.87  E-value: 6.80e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051   5 IASVNVNGIRAatkiRhednpgMH---AWLRQTPAEVVLLQEVRATVD----ESIKALqpaldaGWH--YVGapaaAKGR 75
Cdd:PRK11756   3 FVSFNINGLRA----R------PHqleAIIEKHQPDVIGLQETKVHDEmfplEEVEAL------GYHvfYHG----QKGH 62

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051  76 AGVGILSRAPLDDVTVGF-GSFLDSG-RWLEGTY---QG-VRVASLYLPSGavDSEKLDEKY----VFLDEFSGVLDELA 145
Cdd:PRK11756  63 YGVALLSKQTPIAVRKGFpTDDEEAQrRIIMATIptpNGnLTVINGYFPQG--ESRDHPTKFpakrQFYQDLQNYLETEL 140

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051 146 DTHDKMVVGGDWNICHREQDLKNSKPNRK---KSGH---LPDERAWMDSVFGsfpdaevqekpglgefFGVVdyeprpir 219
Cdd:PRK11756 141 SPDNPLLIMGDMNISPTDLDIGIGEENRKrwlRTGKcsfLPEEREWLDRLMD----------------WGLV-------- 196

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051 220 gaaqdpkwfDVARRLHPE-DAAYTWWTYRGQAFNNNAGWRIDYQAATRSMLDAATRTWVD---RAAtveERWSDHSPMLV 295
Cdd:PRK11756 197 ---------DTFRQLNPDvNDRFSWFDYRSKGFDDNRGLRIDLILATQPLAERCVETGIDydiRGM---EKPSDHAPIWA 264


                 ....
gi 529144051 296 EYDI 299
Cdd:PRK11756 265 TFKL 268
Ape2-like_AP-endo cd09088
Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This ...
 5-292 1.74e-17

Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily.


Pssm-ID: 197322 [Multi-domain]  Cd Length: 309  Bit Score: 80.82  E-value: 1.74e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051   5 IASVNVNGIRAaTKIRHEDN--PGMHAWLRQTPAEVVLLQEVRATVDESIKALqpALDAGWH-YVGAPAAAKGRAGV--- 78
Cdd:cd09088    2 IVTWNVNGIRT-RLQYQPWNkeNSLKSFLDSLDADIICLQETKLTRDELDEPS--AIVEGYDsFFSFSRGRKGYSGVaty 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051  79 ----------------GILS------RAPLDDVTVGFGS---FLDSGRWL----EG-----TYQGVRVASLYLPSGAVDS 124
Cdd:cd09088   79 crdsaatpvaaeegltGVLSspnqknELSENDDIGCYGEmleFTDSKELLeldsEGrcvltDHGTFVLINVYCPRADPEK 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051 125 EkldEKYVFLDEFSGVLDELADTHDKM----VVGGDWNICHREQDLKNSKPNRKKSGHLPDE---RAWMDSVFGsfpdae 197
Cdd:cd09088  159 E---ERLEFKLDFYRLLEERVEALLKAgrrvILVGDVNVSHRPIDHCDPDDSEDFGGESFEDnpsRQWLDQLLG------ 229

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051 198 vqekpglgeffgvvdyePRPIRGAAQDPKWFDVARRLHPE-DAAYTWWTYRGQAFNNNAGWRIDYQAATRSMLDaatrtW 276
Cdd:cd09088  230 -----------------DSGEGGGSPGGLLIDSFRYFHPTrKGAYTCWNTLTGARPTNYGTRIDYILADRGLLP-----W 287

                        330
                 ....*....|....*..
gi 529144051 277 VDRAATVEERW-SDHSP 292
Cdd:cd09088  288 VKAADILPEVEgSDHCP 304
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 3-261 8.47e-16

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 75.50  E-value: 8.47e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051   3 ITIASVNVNGIRAATkirhedNPGMHAWLRQTPAEVVLLQEVRATVDESIKALQPALDAgWHYvgapAAAKGRAGVGILS 82
Cdd:PRK13911   1 MKLISWNVNGLRACM------TKGFMDFFNSVDADVFCIQESKMQQEQNTFEFKGYFDF-WNC----AIKKGYSGVVTFT 69

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051  83 RAplDDVTVGFGSFLDS----GRWLEGTYQGVRVASLYLPSGAVDSEKLDEKYVFLDEFSGVLDELaDTHDKMVVGGDWN 158
Cdd:PRK13911  70 KK--EPLSVSYGINIEEhdkeGRVITCEFESFYLVNVYTPNSQQALSRLSYRMSWEVEFKKFLKAL-ELKKPVIVCGDLN 146

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051 159 ICHREQDLKNSKPNRKKSGHLPDERAWMDSVFGSfpdaevqekpglgeffgvvdyeprpirgaaqdpKWFDVARRLHP-E 237
Cdd:PRK13911 147 VAHNEIDLENPKTNRKNAGFSDEERGKFSELLNA---------------------------------GFIDTFRYFYPnK 193

                        250       260
                 ....*....|....*....|....
gi 529144051 238 DAAYTWWTYRGQAFNNNAGWRIDY 261
Cdd:PRK13911 194 EKAYTWWSYMQQARDKNIGWRIDY 217
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 6-159 1.17e-15

Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12 and Nocturnin.


Pssm-ID: 460902 [Multi-domain]  Cd Length: 183  Bit Score: 73.41  E-value: 1.17e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051    6 ASVNVNGIRAATKIRHEDNPGMHAWLRQTPAEVVLLQEVRATVDESIKALQPALDAGWHYVGaPAAAKGRAGVGILSRAP 85
Cdd:pfam03372   1 LTWNVNGGNADAAGDDRKLDALAALIRAYDPDVVALQETDDDDASRLLLALLAYGGFLSYGG-PGGGGGGGGVAILSRYP 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 529144051   86 LDDVTVGFGSFLD--SGRWLEGTYQGVRVASLYLPSGAVDSEKLDEKYVFLDEFSGVLDELADTHDKMVVGGDWNI 159
Cdd:pfam03372  80 LSSVILVDLGEFGdpALRGAIAPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALLAPRSEPVILAGDFNA 155
EEP cd08372
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 5-297 1.14e-14

Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins.


Pssm-ID: 197306 [Multi-domain]  Cd Length: 241  Bit Score: 72.13  E-value: 1.14e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051   5 IASVNVNGIRAATKIRhednpGMHAWLRQTPAEVVLLQEVRATvdESIKALQPALDAGWHYVGAPAA--AKGRAGVGILS 82
Cdd:cd08372    1 VASYNVNGLNAATRAS-----GIARWVRELDPDIVCLQEVKDS--QYSAVALNQLLPEGYHQYQSGPsrKEGYEGVAILS 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051  83 RAPLDDVTVGFGSFLDSGRWLEGTYQGVR---------VASLYLPSGavdSEKLDEKYVFLDEFSGVLDELADTHDKMVV 153
Cdd:cd08372   74 KTPKFKIVEKHQYKFGEGDSGERRAVVVKfdvhdkelcVVNAHLQAG---GTRADVRDAQLKEVLEFLKRLRQPNSAPVV 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051 154 -GGDWNICHREQDLKNskpnrkksghlpdeRAWMDSVFgsfpdaevqekpglgeffgvvdyeprpIRGAAQDpkwfdvar 232
Cdd:cd08372  151 iCGDFNVRPSEVDSEN--------------PSSMLRLF---------------------------VALNLVD-------- 181

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 529144051 233 rlHPEDA--AYTWWTYRgqafnNNAGWRIDYQAATRSMLDAATRTWVDRAATVEERWSDHSPMLVEY 297
Cdd:cd08372  182 --SFETLphAYTFDTYM-----HNVKSRLDYIFVSKSLLPSVKSSKILSDAARARIPSDHYPIEVTL 241
L1-EN cd09076
Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; ...
 5-297 2.78e-12

Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.


Pssm-ID: 197310 [Multi-domain]  Cd Length: 236  Bit Score: 65.07  E-value: 2.78e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051   5 IASVNVNGIRAATKiRHEDNpgmhAWLRQTPAEVVLLQEVRATVDESIKALqpalDAGWHYVGAPAAAKGRAGVGILSRA 84
Cdd:cd09076    1 IGTLNVRGLRSPGK-RAQLL----EELKRKKLDILGLQETHWTGEGELKKK----REGGTILYSGSDSGKSRGVAILLSK 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051  85 PLDDVTVGFgSFLDSGRWL--EGTYQGVR--VASLYLPSGAVDSEKLDekyvFLDEFSGVLDELADtHDKMVVGGDWNic 160
Cdd:cd09076   72 TAANKLLEY-TKVVSGRIImvRFKIKGKRltIINVYAPTARDEEEKEE----FYDQLQDVLDKVPR-HDTLIIGGDFN-- 143

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051 161 HREqdlknSKPNRKKSGHlpderawmdsvfgsfpdaevQEKPGLGEffgvvdyepRPIRGAAQDPKWFDVARRLHPEDAA 240
Cdd:cd09076  144 AVL-----GPKDDGRKGL--------------------DKRNENGE---------RALSALIEEHDLVDVWRENNPKTRE 189

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 529144051 241 YTWWTYRGQAFNnnagwRIDYQAATRSMLDAATRTwvdraATVEERWSDHSPMLVEY 297
Cdd:cd09076  190 YTWRSPDHGSRS-----RIDRILVSKRLRVKVKKT-----KITPGAGSDHRLVTLKL 236
TDP2 cd09080
Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related ...
 3-172 6.27e-03

Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains; Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.


Pssm-ID: 197314 [Multi-domain]  Cd Length: 248  Bit Score: 37.32  E-value: 6.27e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051   3 ITIASVNVNGIRA-ATKIRHEdnpgmHAW--LRQTPAEVVLLQEVratVDESIKAL--QPALDAGWHYVGAPAAAKGRA- 76
Cdd:cd09080    1 LKVLTWNVDFLDDvNLAERMR-----AILklLEELDPDVIFLQEV---TPPFLAYLlsQPWVRKNYYFSEGPPSPAVDPy 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 529144051  77 GVGILSRAPLDDVTVGF-GSFLDSGRwLEGTYQG-----VRVASLYLPSGAVDSEkldEKYVFLDEFSGVLDELADTHDK 150
Cdd:cd09080   73 GVLILSKKSLVVRRVPFtSTRMGRNL-LAAEINLgsgepLRLATTHLESLKSHSS---ERTAQLEEIAKKLKKPPGAANV 148

                        170       180
                 ....*....|....*....|..
gi 529144051 151 mVVGGDWNICHREQDLKNSKPN 172
Cdd:cd09080  149 -ILGGDFNLRDKEDDTGGLPNG 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.
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