NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1092755581|ref|WP_070680980|]
View 

exodeoxyribonuclease III [Rothia sp. HMSC072E10]

Protein Classification

exodeoxyribonuclease III( domain architecture ID 10002229)

exodeoxyribonuclease III is a Mg-dependent 3' to 5' exonuclease acting on dsDNA, which releases 5' phosphomononucleotides as degradation products

CATH:  3.60.10.10
EC:  3.1.11.2
Gene Ontology:  GO:0003677|GO:0046872|GO:0004519|GO:0006281|GO:0008311
PubMed:  7885481|10838565|7661852
SCOP:  4002213

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
XthA COG0708
Exonuclease III [Replication, recombination and repair];
1-265 1.31e-123

Exonuclease III [Replication, recombination and repair];


:

Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 352.07  E-value: 1.31e-123
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581   1 MKIATWNINSIRARENRVEDWLDEHEVDVLALQETKTKDETFPFDLFEFMGYEVAHFGLNQWNGVAIASRVGLEDVQRGF 80
Cdd:COG0708     1 MKIASWNVNGIRARLPKLLDWLAEEDPDVLCLQETKAQDEQFPLEAFEAAGYHVYFHGQKGYNGVAILSRLPPEDVRRGL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581  81 dnqphfgkPGEPEVLEARAIGATCGGVRVWSLYVPNGRGLTDPHMDYKLRWMEALHQNVHNELAANPqsQLALVGDWNVA 160
Cdd:COG0708    81 --------GGDEFDAEGRYIEADFGGVRVVSLYVPNGGSVGSEKFDYKLRFLDALRAYLAELLAPGR--PLILCGDFNIA 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581 161 PEDADVWDIDYFRDNELtpVSEPERRAFAALLKEGMVDVVRPHTP---GEYTYWDYQAGRFAKDEGMRIDFQLFSPELAA 237
Cdd:COG0708   151 PTEIDVKNPKANLKNAG--FLPEERAWFDRLLELGLVDAFRALHPdveGQYTWWSYRAGAFARNRGWRIDYILASPALAD 228

                         250       260
                  ....*....|....*....|....*...
gi 1092755581 238 RVQNAWIDRVERAGEGASDHTPVVVEIA 265
Cdd:COG0708   229 RLKDAGIDREPRGDERPSDHAPVVVELD 256
 
Name Accession Description Interval E-value
XthA COG0708
Exonuclease III [Replication, recombination and repair];
1-265 1.31e-123

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 352.07  E-value: 1.31e-123
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581   1 MKIATWNINSIRARENRVEDWLDEHEVDVLALQETKTKDETFPFDLFEFMGYEVAHFGLNQWNGVAIASRVGLEDVQRGF 80
Cdd:COG0708     1 MKIASWNVNGIRARLPKLLDWLAEEDPDVLCLQETKAQDEQFPLEAFEAAGYHVYFHGQKGYNGVAILSRLPPEDVRRGL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581  81 dnqphfgkPGEPEVLEARAIGATCGGVRVWSLYVPNGRGLTDPHMDYKLRWMEALHQNVHNELAANPqsQLALVGDWNVA 160
Cdd:COG0708    81 --------GGDEFDAEGRYIEADFGGVRVVSLYVPNGGSVGSEKFDYKLRFLDALRAYLAELLAPGR--PLILCGDFNIA 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581 161 PEDADVWDIDYFRDNELtpVSEPERRAFAALLKEGMVDVVRPHTP---GEYTYWDYQAGRFAKDEGMRIDFQLFSPELAA 237
Cdd:COG0708   151 PTEIDVKNPKANLKNAG--FLPEERAWFDRLLELGLVDAFRALHPdveGQYTWWSYRAGAFARNRGWRIDYILASPALAD 228

                         250       260
                  ....*....|....*....|....*...
gi 1092755581 238 RVQNAWIDRVERAGEGASDHTPVVVEIA 265
Cdd:COG0708   229 RLKDAGIDREPRGDERPSDHAPVVVELD 256
ExoIII-like_AP-endo cd09086
Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of ...
 1-264 8.06e-117

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: 334.87  E-value: 8.06e-117
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581   1 MKIATWNINSIRARENRVEDWLDEHEVDVLALQETKTKDETFPFDLFEFMGYEVAHFGLNQWNGVAIASRVGLEDVQRGF 80
Cdd:cd09086     1 MKIATWNVNSIRARLEQVLDWLKEEDPDVLCLQETKVEDDQFPADAFEALGYHVAVHGQKAYNGVAILSRLPLEDVRTGF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581  81 dnqphfgkPGEPEVLEARAIGATCGGVRVWSLYVPNGRGLTDPHMDYKLRWMEALHQNVHNELAANPqsQLALVGDWNVA 160
Cdd:cd09086    81 --------PGDPDDDQARLIAARVGGVRVINLYVPNGGDIGSPKFAYKLDWLDRLIRYLQKLLKPDD--PLVLVGDFNIA 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581 161 PEDADVWDIDYFRDNELTpvSEPERRAFAALLKEGMVDVVRPHTPGE--YTYWDYQAGRFAKDEGMRIDFQLFSPELAAR 238
Cdd:cd09086   151 PEDIDVWDPKQLLGKVLF--TPEEREALRALLDLGFVDAFRALHPDEklFTWWDYRAGAFERNRGLRIDHILASPALADR 228

                         250       260
                  ....*....|....*....|....*.
gi 1092755581 239 VQNAWIDRVERAGEGASDHTPVVVEI 264
Cdd:cd09086   229 LKDVGIDREPRGWEKPSDHAPVVAEL 254
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 1-265 6.36e-93

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: 274.54  E-value: 6.36e-93
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581   1 MKIATWNINSIRARENRV-EDWLDEHEVDVLALQETKTKDETFPFDLFEFMGYEVAHFGL-NQWNGVAIASRVGLEDVQR 78
Cdd:TIGR00633   1 MKIISWNVNGLRARLHKLfLDWLKEEQPDVLCLQETKVADEQFPAELFEELGYHVFFHGAkKGYSGVAILSKVEPLDVRY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581  79 GFDNQPHFgkpgepevLEARAIGATCGGVRVWSLYVPNGRGLTDPHMDYKLRWMEALHQNVHNELAAnpQSQLALVGDWN 158
Cdd:TIGR00633  81 GFGGEPHD--------EEGRVITAEFDGFTVVNVYVPNGGSRDLERLEYKLQFWDALFQYLEKELDA--GKPVVICGDMN 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581 159 VAPEDADVWDIDYFRDNelTPVSEPERRAFAALLKEGMVDVVR---PHTPGEYTYWDYQAGRFAKDEGMRIDFQLFSPEL 235
Cdd:TIGR00633 151 VAHTEIDLGNPKENKGN--AGFTPEEREWFDELLEAGFVDTFRhfnPDTGDAYTWWDYRSGARDRNRGWRIDYFLVSEPL 228

                         250       260       270
                  ....*....|....*....|....*....|
gi 1092755581 236 AARVQNAWIDRVERagegASDHTPVVVEIA 265
Cdd:TIGR00633 229 AERVVDSYIDSEIR----GSDHCPIVLELD 254
PRK11756 PRK11756
exonuclease III; Provisional
 1-263 6.91e-44

exonuclease III; Provisional


Pssm-ID: 236970 [Multi-domain]  Cd Length: 268  Bit Score: 149.66  E-value: 6.91e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581   1 MKIATWNINSIRARENRVEDWLDEHEVDVLALQETKTKDETFPFDLFEFMGYEVAHFGLNQWNGVAIASRVGLEDVQRGF 80
Cdd:PRK11756    1 MKFVSFNINGLRARPHQLEAIIEKHQPDVIGLQETKVHDEMFPLEEVEALGYHVFYHGQKGHYGVALLSKQTPIAVRKGF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581  81 dnqphfgkPGEPEVLEARAIGAT----CGGVRVWSLYVPNGRGLTDP-HMDYKLRWMEALHQNVHNELaaNPQSQLALVG 155
Cdd:PRK11756   81 --------PTDDEEAQRRIIMATiptpNGNLTVINGYFPQGESRDHPtKFPAKRQFYQDLQNYLETEL--SPDNPLLIMG 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581 156 DWNVAPEDADV---------WdidyFRDNELTPVSEpERRAFAALLKEGMVDVVRPHTP---GEYTYWDYQAGRFAKDEG 223
Cdd:PRK11756  151 DMNISPTDLDIgigeenrkrW----LRTGKCSFLPE-EREWLDRLMDWGLVDTFRQLNPdvnDRFSWFDYRSKGFDDNRG 225

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|
gi 1092755581 224 MRIDFQLFSPELAARVQNAWIDRVERAGEGASDHTPVVVE 263
Cdd:PRK11756  226 LRIDLILATQPLAERCVETGIDYDIRGMEKPSDHAPIWAT 265
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 4-159 6.50e-10

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: 57.23  E-value: 6.50e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581   4 ATWNINSIRARENR-------VEDWLDEHEVDVLALQETKTKDETFPFDLFEFMGYEVAHFGLNQ---WNGVAIASRVGL 73
Cdd:pfam03372   1 LTWNVNGGNADAAGddrkldaLAALIRAYDPDVVALQETDDDDASRLLLALLAYGGFLSYGGPGGgggGGGVAILSRYPL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581  74 EDVQRGFDNQPHFGkpgepevlEARAIGATCGGVRVWSLYVPNGRGLTDPHMDYKLRWMEALHqnvHNELAANPQSQLAL 153
Cdd:pfam03372  81 SSVILVDLGEFGDP--------ALRGAIAPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLL---LLALLAPRSEPVIL 149


                  ....*.
gi 1092755581 154 VGDWNV 159
Cdd:pfam03372 150 AGDFNA 155
 
Name Accession Description Interval E-value
XthA COG0708
Exonuclease III [Replication, recombination and repair];
1-265 1.31e-123

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 352.07  E-value: 1.31e-123
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581   1 MKIATWNINSIRARENRVEDWLDEHEVDVLALQETKTKDETFPFDLFEFMGYEVAHFGLNQWNGVAIASRVGLEDVQRGF 80
Cdd:COG0708     1 MKIASWNVNGIRARLPKLLDWLAEEDPDVLCLQETKAQDEQFPLEAFEAAGYHVYFHGQKGYNGVAILSRLPPEDVRRGL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581  81 dnqphfgkPGEPEVLEARAIGATCGGVRVWSLYVPNGRGLTDPHMDYKLRWMEALHQNVHNELAANPqsQLALVGDWNVA 160
Cdd:COG0708    81 --------GGDEFDAEGRYIEADFGGVRVVSLYVPNGGSVGSEKFDYKLRFLDALRAYLAELLAPGR--PLILCGDFNIA 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581 161 PEDADVWDIDYFRDNELtpVSEPERRAFAALLKEGMVDVVRPHTP---GEYTYWDYQAGRFAKDEGMRIDFQLFSPELAA 237
Cdd:COG0708   151 PTEIDVKNPKANLKNAG--FLPEERAWFDRLLELGLVDAFRALHPdveGQYTWWSYRAGAFARNRGWRIDYILASPALAD 228

                         250       260
                  ....*....|....*....|....*...
gi 1092755581 238 RVQNAWIDRVERAGEGASDHTPVVVEIA 265
Cdd:COG0708   229 RLKDAGIDREPRGDERPSDHAPVVVELD 256
ExoIII-like_AP-endo cd09086
Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of ...
 1-264 8.06e-117

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: 334.87  E-value: 8.06e-117
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581   1 MKIATWNINSIRARENRVEDWLDEHEVDVLALQETKTKDETFPFDLFEFMGYEVAHFGLNQWNGVAIASRVGLEDVQRGF 80
Cdd:cd09086     1 MKIATWNVNSIRARLEQVLDWLKEEDPDVLCLQETKVEDDQFPADAFEALGYHVAVHGQKAYNGVAILSRLPLEDVRTGF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581  81 dnqphfgkPGEPEVLEARAIGATCGGVRVWSLYVPNGRGLTDPHMDYKLRWMEALHQNVHNELAANPqsQLALVGDWNVA 160
Cdd:cd09086    81 --------PGDPDDDQARLIAARVGGVRVINLYVPNGGDIGSPKFAYKLDWLDRLIRYLQKLLKPDD--PLVLVGDFNIA 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581 161 PEDADVWDIDYFRDNELTpvSEPERRAFAALLKEGMVDVVRPHTPGE--YTYWDYQAGRFAKDEGMRIDFQLFSPELAAR 238
Cdd:cd09086   151 PEDIDVWDPKQLLGKVLF--TPEEREALRALLDLGFVDAFRALHPDEklFTWWDYRAGAFERNRGLRIDHILASPALADR 228

                         250       260
                  ....*....|....*....|....*.
gi 1092755581 239 VQNAWIDRVERAGEGASDHTPVVVEI 264
Cdd:cd09086   229 LKDVGIDREPRGWEKPSDHAPVVAEL 254
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 1-265 6.36e-93

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: 274.54  E-value: 6.36e-93
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581   1 MKIATWNINSIRARENRV-EDWLDEHEVDVLALQETKTKDETFPFDLFEFMGYEVAHFGL-NQWNGVAIASRVGLEDVQR 78
Cdd:TIGR00633   1 MKIISWNVNGLRARLHKLfLDWLKEEQPDVLCLQETKVADEQFPAELFEELGYHVFFHGAkKGYSGVAILSKVEPLDVRY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581  79 GFDNQPHFgkpgepevLEARAIGATCGGVRVWSLYVPNGRGLTDPHMDYKLRWMEALHQNVHNELAAnpQSQLALVGDWN 158
Cdd:TIGR00633  81 GFGGEPHD--------EEGRVITAEFDGFTVVNVYVPNGGSRDLERLEYKLQFWDALFQYLEKELDA--GKPVVICGDMN 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581 159 VAPEDADVWDIDYFRDNelTPVSEPERRAFAALLKEGMVDVVR---PHTPGEYTYWDYQAGRFAKDEGMRIDFQLFSPEL 235
Cdd:TIGR00633 151 VAHTEIDLGNPKENKGN--AGFTPEEREWFDELLEAGFVDTFRhfnPDTGDAYTWWDYRSGARDRNRGWRIDYFLVSEPL 228

                         250       260       270
                  ....*....|....*....|....*....|
gi 1092755581 236 AARVQNAWIDRVERagegASDHTPVVVEIA 265
Cdd:TIGR00633 229 AERVVDSYIDSEIR----GSDHCPIVLELD 254
exoDNase_III TIGR00195
exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model ...
 1-264 1.83e-68

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: 212.24  E-value: 1.83e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581   1 MKIATWNINSIRARENRVEDWLDEHEVDVLALQETKTKDETFPFDLFEFMGYEVAHFGLNQWNGVAIASRVGLEDVQRGF 80
Cdd:TIGR00195   1 MKIISWNVNGLRARPHKGLAWLKENQPDVLCLQETKVQDEQFPLEPFHKEGYHVFFSGQKGYSGVAIFSKEEPISVRRGF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581  81 dnqphfgkPGEPEVLEARAIGATCGGVRVWSLYVPNGRGLTDPHMDYKLRWMEALHQNVHNEL-AANPqsqLALVGDWNV 159
Cdd:TIGR00195  81 --------GVEEEDAEGRIIMAEFDSFLVINGYFPNGSRDDSEKLPYKLQWLEALQNYLEKLVdKDKP---VLICGDMNI 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581 160 APEDADVWDIDYFRDNelTPVSEPERRAFAALLKEGMVDVVRPHTP--GEYTYWDYQAGRFAKDEGMRIDFQLFSPELAA 237
Cdd:TIGR00195 150 APTEIDLHIPDENRNH--TGFLPEEREWLDRLLEAGLVDTFRKFNPdeGAYSWWDYRTKARDRNRGWRIDYFLVSEPLKE 227

                         250       260
                  ....*....|....*....|....*..
gi 1092755581 238 RVQNAWIDRVERAGEGASDHTPVVVEI 264
Cdd:TIGR00195 228 RCVDCGIDYDIRGSEKPSDHCPVVLEF 254
ExoIII_AP-endo cd09073
Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ...
 2-264 3.56e-61

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: 193.27  E-value: 3.56e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581   2 KIATWNINSIRAR-ENRVEDWLDEHEVDVLALQETKTKDETFPFDLFEFMGYEVAHFGLNQ--WNGVAIASRVGLEDVQR 78
Cdd:cd09073     1 KIISWNVNGLRARlKKGVLKWLKEEKPDILCLQETKADEDKLPEELQHVEGYHSYWSPARKkgYSGVATLSKEEPLDVSY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581  79 GFdnqphfgkPGEPEVLEARAIGATCGGVRVWSLYVPNG-RGLtdPHMDYKLRWMEALHQNVHNELAANpqSQLALVGDW 157
Cdd:cd09073    81 GI--------GGEEFDSEGRVITAEFDDFYLINVYFPNGgRGL--ERLDYKLRFYEAFLEFLEKLRKRG--KPVVICGDF 148

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581 158 NVAPEDADVWDIDYFRDNelTPVSEPERRAFAALLKEGMVDVVRPHTP--GEYTYWDYQAGRFAKDEGMRIDFQLFSPEL 235
Cdd:cd09073   149 NVAHEEIDLARPKKNEKN--AGFTPEERAWFDKLLSLGYVDTFRHFHPepGAYTWWSYRGNARERNVGWRIDYFLVSEEL 226

                         250       260
                  ....*....|....*....|....*....
gi 1092755581 236 AARVQNAWIDRVERagegASDHTPVVVEI 264
Cdd:cd09073   227 AEKVKDSGILSKVK----GSDHAPVTLEL 251
Nape_like_AP-endo cd10281
Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) ...
 1-264 1.67e-48

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: 160.86  E-value: 1.67e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581   1 MKIATWNINSIRARENR-VEDWLDEHEVDVLALQETKTKDETFPFDLFEFMGYEVAHF--GLNQWNGVAIASRVGLEDVQ 77
Cdd:cd10281     1 MRVISVNVNGIRAAAKKgFLEWLAAQDADVVCLQEVRAQEEQLDDDFFEPEGYNAYFFdaEKKGYAGVAIYSRTQPKAVI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581  78 RGFdnqphfgkPGEPEVLEARAIGATCGGVRVWSLYVPNGRGLtDPHMDYKLRWMEALHQNVhNELAANPQsQLALVGDW 157
Cdd:cd10281    81 YGL--------GFEEFDDEGRYIEADFDNVSVASLYVPSGSSG-DERQEAKMAFLDAFLEHL-KELRRKRR-EFIVCGDF 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581 158 NVAPEDADvwdIDYFRDNELTPVSEPERRAF--AALLKEGMVDVVRP--HTPGEYTYWDYQAGRFAKDEGMRIDFQLFSP 233
Cdd:cd10281   150 NIAHTEID---IKNWKANQKNSGFLPEERAWldQVFGELGYVDAFRElnPDEGQYTWWSNRGQARANNVGWRIDYQIATP 226

                         250       260       270
                  ....*....|....*....|....*....|.
gi 1092755581 234 ELAARVQNAWIDRVERagegASDHTPVVVEI 264
Cdd:cd10281   227 GLASKVVSAWIYREER----FSDHAPLIVDY 253
PRK11756 PRK11756
exonuclease III; Provisional
 1-263 6.91e-44

exonuclease III; Provisional


Pssm-ID: 236970 [Multi-domain]  Cd Length: 268  Bit Score: 149.66  E-value: 6.91e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581   1 MKIATWNINSIRARENRVEDWLDEHEVDVLALQETKTKDETFPFDLFEFMGYEVAHFGLNQWNGVAIASRVGLEDVQRGF 80
Cdd:PRK11756    1 MKFVSFNINGLRARPHQLEAIIEKHQPDVIGLQETKVHDEMFPLEEVEALGYHVFYHGQKGHYGVALLSKQTPIAVRKGF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581  81 dnqphfgkPGEPEVLEARAIGAT----CGGVRVWSLYVPNGRGLTDP-HMDYKLRWMEALHQNVHNELaaNPQSQLALVG 155
Cdd:PRK11756   81 --------PTDDEEAQRRIIMATiptpNGNLTVINGYFPQGESRDHPtKFPAKRQFYQDLQNYLETEL--SPDNPLLIMG 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581 156 DWNVAPEDADV---------WdidyFRDNELTPVSEpERRAFAALLKEGMVDVVRPHTP---GEYTYWDYQAGRFAKDEG 223
Cdd:PRK11756  151 DMNISPTDLDIgigeenrkrW----LRTGKCSFLPE-EREWLDRLMDWGLVDTFRQLNPdvnDRFSWFDYRSKGFDDNRG 225

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|
gi 1092755581 224 MRIDFQLFSPELAARVQNAWIDRVERAGEGASDHTPVVVE 263
Cdd:PRK11756  226 LRIDLILATQPLAERCVETGIDYDIRGMEKPSDHAPIWAT 265
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This ...
 1-264 2.76e-41

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: 142.31  E-value: 2.76e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581   1 MKIATWNINSIRAR-ENRVEDWLDEHEVDVLALQETKTKDETFPFDL-FEFMGYEVAHFGLNQ--WNGVAIASRVGLEDV 76
Cdd:cd09087     1 LKIISWNVNGLRALlKKGLLDYVKKEDPDILCLQETKLQEGDVPKELkELLKGYHQYWNAAEKkgYSGTAILSKKKPLSV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581  77 QRGFDNQPHFGkpgepevlEARAIGATCGGVRVWSLYVPN-GRGLTdpHMDYKLRWMEALHQNVHNELAANPqsqLALVG 155
Cdd:cd09087    81 TYGIGIEEHDQ--------EGRVITAEFENFYLVNTYVPNsGRGLE--RLDRRKEWDVDFRAYLKKLDSKKP---VIWCG 147

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581 156 DWNVAPEDADVWDIDYFRDNE-LTPvsePERRAFAALLKEGMVDVVR---PHTPGEYTYWDYQAGRFAKDEGMRIDFQLF 231
Cdd:cd09087   148 DLNVAHEEIDLANPKTNKKSAgFTP---EERESFTELLEAGFVDTFRhlhPDKEGAYTFWSYRGNARAKNVGWRLDYFLV 224

                         250       260       270
                  ....*....|....*....|....*....|...
gi 1092755581 232 SPELAARVQNAWIdrveRAGEGASDHTPVVVEI 264
Cdd:cd09087   225 SERLKDRVVDSFI----RSDIMGSDHCPIGLEL 253
Mth212-like_AP-endo cd09085
Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic ...
 1-264 1.67e-32

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: 119.30  E-value: 1.67e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581   1 MKIATWNINSIRARENRV-EDWLDEHEVDVLALQETKTKDETFPFDLFEFMGYevaHFGLNQ-----WNGVAIASRVGLE 74
Cdd:cd09085     1 MKIISWNVNGLRAVHKKGfLDWFKEEKPDILCLQETKAQPEQLPEDLRNIEGY---HSYFNSaerkgYSGVALYSKIEPD 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581  75 DVQRGFDNqPHFGKpgepevlEARAIGATCGGVRVWSLYVPNGrGLTDPHMDYKLRWMEALHQNVhNELAANPQSqLALV 154
Cdd:cd09085    78 SVREGLGV-EEFDN-------EGRILIADFDDFTLFNIYFPNG-QMSEERLDYKLEFYDAFLEYL-NELRDSGKN-VIIC 146

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581 155 GDWNVAPEDadvwdIDYFR--DNELTPVSEPERRA-FAALLKEGMVDVVRPHT--PGEYTYWDYQAGRFAKDEGMRIDFQ 229
Cdd:cd09085   147 GDFNTAHKE-----IDLARpkENEKVSGFLPEERAwMDKFIENGYVDTFRMFNkePGQYTWWSYRTRARERNVGWRIDYF 221

                         250       260       270
                  ....*....|....*....|....*....|....*.
gi 1092755581 230 LFSPELAARVQNAWI-DRVEragegASDHTPVVVEI 264
Cdd:cd09085   222 FVNEEFKPKVKDAGIlPDVM-----GSDHCPVSLEL 252
Ape2-like_AP-endo cd09088
Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This ...
 2-264 3.55e-24

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: 98.54  E-value: 3.55e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581   2 KIATWNINSIRAR--------ENRVEDWLDEHEVDVLALQETK-TKDE-----TFP--FD-LFEF----MGYE-VAHF-- 57
Cdd:cd09088     1 RIVTWNVNGIRTRlqyqpwnkENSLKSFLDSLDADIICLQETKlTRDEldepsAIVegYDsFFSFsrgrKGYSgVATYcr 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581  58 -----------GL-NQWNGVAIASRVGLEDVQRGFDNQPHFGKPGEPEVL--EARAIGATCGGVRVWSLYVPNGRGLTDP 123
Cdd:cd09088    81 dsaatpvaaeeGLtGVLSSPNQKNELSENDDIGCYGEMLEFTDSKELLELdsEGRCVLTDHGTFVLINVYCPRADPEKEE 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581 124 HMDYKLRWMEALHQNVHNELAANpqSQLALVGDWNVAPEDADVWD-IDYFRDNELTPVSEPERRAFAALLKEG------- 195
Cdd:cd09088   161 RLEFKLDFYRLLEERVEALLKAG--RRVILVGDVNVSHRPIDHCDpDDSEDFGGESFEDNPSRQWLDQLLGDSgegggsp 238

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1092755581 196 ---MVDVVR---PHTPGEYTYWDYQAGRFAKDEGMRIDFQLFSPELAARVQNAWIDRvERAGegaSDHTPVVVEI 264
Cdd:cd09088   239 gglLIDSFRyfhPTRKGAYTCWNTLTGARPTNYGTRIDYILADRGLLPWVKAADILP-EVEG---SDHCPVYADL 309
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 1-264 2.78e-18

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 81.66  E-value: 2.78e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581   1 MKIATWNINSIRARENR-VEDWLDEHEVDVLALQETKTKDETfpfDLFEFMGYevahfgLNQWNgvaIASRVGLEDVQRG 79
Cdd:PRK13911    1 MKLISWNVNGLRACMTKgFMDFFNSVDADVFCIQESKMQQEQ---NTFEFKGY------FDFWN---CAIKKGYSGVVTF 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581  80 FDNQP---HFGKPGEPEVLEARAIGATCGGVRVWSLYVPNGRGLTDpHMDYKLRWMEALHQNVHnelAANPQSQLALVGD 156
Cdd:PRK13911   69 TKKEPlsvSYGINIEEHDKEGRVITCEFESFYLVNVYTPNSQQALS-RLSYRMSWEVEFKKFLK---ALELKKPVIVCGD 144

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581 157 WNVAPEDADVWDIDYFRDNelTPVSEPERRAFAALLKEGMVDVVR---PHTPGEYTYWDYQAGRFAKDEGMRIDFQLFSP 233
Cdd:PRK13911  145 LNVAHNEIDLENPKTNRKN--AGFSDEERGKFSELLNAGFIDTFRyfyPNKEKAYTWWSYMQQARDKNIGWRIDYFLCSN 222

                         250       260       270
                  ....*....|....*....|....*....|.
gi 1092755581 234 ELAARVQNAWIDRvERAGegaSDHTPVVVEI 264
Cdd:PRK13911  223 PLKTRLKDALIYK-DILG---SDHCPVGLEL 249
EEP cd08372
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 3-264 4.86e-16

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: 75.21  E-value: 4.86e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581   3 IATWNINSIRARENRVE--DWLDEHEVDVLALQETKTKDETFPFDLFEFMG----YEVAHFGLNQWNGVAIASRVGLEDV 76
Cdd:cd08372     1 VASYNVNGLNAATRASGiaRWVRELDPDIVCLQEVKDSQYSAVALNQLLPEgyhqYQSGPSRKEGYEGVAILSKTPKFKI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581  77 QRGFDnqphfGKPGEPEVLEARAIGA--TCGG--VRVWSLYVPNGRGltdpHMDYKLRWMEALhQNVHNELAANPQSQLA 152
Cdd:cd08372    81 VEKHQ-----YKFGEGDSGERRAVVVkfDVHDkeLCVVNAHLQAGGT----RADVRDAQLKEV-LEFLKRLRQPNSAPVV 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581 153 LVGDWNVAPEDADvwdidyfrdneltpvsEPERRAFAALLKEGMVDVVRPHTPGEYTYWDYQagrfaKDEGMRIDFQLFS 232
Cdd:cd08372   151 ICGDFNVRPSEVD----------------SENPSSMLRLFVALNLVDSFETLPHAYTFDTYM-----HNVKSRLDYIFVS 209

                         250       260       270
                  ....*....|....*....|....*....|..
gi 1092755581 233 PELAARVQNAWIDRVERAGEGASDHTPVVVEI 264
Cdd:cd08372   210 KSLLPSVKSSKILSDAARARIPSDHYPIEVTL 241
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 4-159 6.50e-10

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: 57.23  E-value: 6.50e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581   4 ATWNINSIRARENR-------VEDWLDEHEVDVLALQETKTKDETFPFDLFEFMGYEVAHFGLNQ---WNGVAIASRVGL 73
Cdd:pfam03372   1 LTWNVNGGNADAAGddrkldaLAALIRAYDPDVVALQETDDDDASRLLLALLAYGGFLSYGGPGGgggGGGVAILSRYPL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581  74 EDVQRGFDNQPHFGkpgepevlEARAIGATCGGVRVWSLYVPNGRGLTDPHMDYKLRWMEALHqnvHNELAANPQSQLAL 153
Cdd:pfam03372  81 SSVILVDLGEFGDP--------ALRGAIAPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLL---LLALLAPRSEPVIL 149


                  ....*.
gi 1092755581 154 VGDWNV 159
Cdd:pfam03372 150 AGDFNA 155
L1-EN cd09076
Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; ...
 3-264 1.09e-08

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: 54.28  E-value: 1.09e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581   3 IATWNINSIRARENR--VEDWLDEHEVDVLALQETKTKDETfpfdlfefMGYEVAHFGLNQWN--------GVAIAsrvg 72
Cdd:cd09076     1 IGTLNVRGLRSPGKRaqLLEELKRKKLDILGLQETHWTGEG--------ELKKKREGGTILYSgsdsgksrGVAIL---- 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581  73 ledvqrgFDNQPHFGKPGEPEVLEARAIGATCGG----VRVWSLYVPNGRgltDPHMdyklrwMEALHQNVHNELAANPQ 148
Cdd:cd09076    69 -------LSKTAANKLLEYTKVVSGRIIMVRFKIkgkrLTIINVYAPTAR---DEEE------KEEFYDQLQDVLDKVPR 132

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581 149 S-QLALVGDWNvAPEDADvwDIDYFRDNELTPVSepERRAFAALLKEGMVDVVRPHTPG--EYTY--WDYQAGRfakdeg 223
Cdd:cd09076   133 HdTLIIGGDFN-AVLGPK--DDGRKGLDKRNENG--ERALSALIEEHDLVDVWRENNPKtrEYTWrsPDHGSRS------ 201

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|.
gi 1092755581 224 mRIDFQLFSPELAARVQnawidRVERAGEGASDHTPVVVEI 264
Cdd:cd09076   202 -RIDRILVSKRLRVKVK-----KTKITPGAGSDHRLVTLKL 236
YafD COG3021
Uncharacterized conserved protein YafD, endonuclease/exonuclease/phosphatase (EEP) superfamily ...
 1-265 1.89e-07

Uncharacterized conserved protein YafD, endonuclease/exonuclease/phosphatase (EEP) superfamily [General function prediction only];


Pssm-ID: 442257 [Multi-domain]  Cd Length: 310  Bit Score: 51.15  E-value: 1.89e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581   1 MKIATWNINSIRARENRVEDWLDEHEVDVLALQET--------KTKDETFPFDLFEfmgyevahfGLNQWNGVAIASRVG 72
Cdd:COG3021    95 LRVLTANVLFGNADAEALAALVREEDPDVLVLQETtpaweealAALEADYPYRVLC---------PLDNAYGMALLSRLP 165

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581  73 LEDVqrgfdnQPHFGKPGEPEVLEARaIGATCGGVRVWSLYVPngrgltdPHMDYKLRWMEALhQNVHNELAANPQSQLa 152
Cdd:COG3021   166 LTEA------EVVYLVGDDIPSIRAT-VELPGGPVRLVAVHPA-------PPVGGSAERDAEL-AALAKAVAALDGPVI- 229

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581 153 LVGDWNVAPedadvWDidyfrdneltpvseperRAFAALLKE-GMVDVVRphtpGEYTYWDYQAGRFAKdeGMRIDFQLF 231
Cdd:COG3021   230 VAGDFNATP-----WS-----------------PTLRRLLRAsGLRDARA----GRGLGPTWPANLPFL--RLPIDHVLV 281

                         250       260       270
                  ....*....|....*....|....*....|....
gi 1092755581 232 SPELAARvqnawidRVERAGEGASDHTPVVVEIA 265
Cdd:COG3021   282 SRGLTVV-------DVRVLPVIGSDHRPLLAELA 308
EEP-1 cd09083
Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of ...
 181-264 1.39e-06

Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, 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: 197317 [Multi-domain]  Cd Length: 252  Bit Score: 48.37  E-value: 1.39e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581 181 SEPERRAFAALLKEGMVD----VVRPHTPGEYTYWDYQAgrfaKDEGMRIDFQLFSPELaaRVQNAWIDRVERAGEGASD 256
Cdd:cd09083   171 AEPDSEPYKTLTSGGLKDardtAATTDGGPEGTFHGFKG----PPGGSRIDYIFVSPGV--KVLSYEILTDRYDGRYPSD 244


                  ....*...
gi 1092755581 257 HTPVVVEI 264
Cdd:cd09083   245 HFPVVADL 252
ElsH COG3568
Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function ...
 1-181 1.92e-04

Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only];


Pssm-ID: 442789 [Multi-domain]  Cd Length: 167  Bit Score: 41.05  E-value: 1.92e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581   1 MKIATWNINSIRARENRVE-----DWLDEHEVDVLALQEtktkdetfpfdlfefmgyevahfglnqwngVAIASRVGLED 75
Cdd:COG3568     8 LRVMTYNIRYGLGTDGRADleriaRVIRALDPDVVALQE------------------------------NAILSRYPIVS 57

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581  76 VQRGFDNQPHFGKPGepeVLEARaIGATCGGVRVWSLyvpngrgltdpHMDYK-----LRWMEALHQNVHNELAANPqsq 150
Cdd:COG3568    58 SGTFDLPDPGGEPRG---ALWAD-VDVPGKPLRVVNT-----------HLDLRsaaarRRQARALAELLAELPAGAP--- 119

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1092755581 151 LALVGDWNvapedadvwDIDY-FRDNELTPVS 181
Cdd:COG3568   120 VILAGDFN---------DIDYiLVSPGLRVLS 142
COG2374 COG2374
Predicted extracellular nuclease [General function prediction only];
133-264 5.95e-04

Predicted extracellular nuclease [General function prediction only];


Pssm-ID: 441941 [Multi-domain]  Cd Length: 362  Bit Score: 40.77  E-value: 5.95e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581 133 EALHQNVHNELAANPQSQLALVGDWNvapedadvwdiDYfrdneltpvsePERRAFAALLKE-GMVDVV-RPHTPGEYTY 210
Cdd:COG2374   238 EALRAFVDSLLAADPDAPVIVLGDFN-----------DY-----------PFEDPLRALLGAgGLTNLAeKLPAAERYSY 295

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581 211 WdYQagrfakDEGMRIDFQLFSPELAARVQNAWI----------------DRVERAGEGASDHTPVVVEI 264
Cdd:COG2374   296 V-YD------GNSGLLDHILVSPALAARVTGADIwhinadiynddfkpdfRTYADDPGRASDHDPVVVGL 358
EEP-2 cd09084
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This ...
 3-264 8.44e-04

Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, 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: 197318 [Multi-domain]  Cd Length: 246  Bit Score: 39.97  E-value: 8.44e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581   3 IATWNINSIRARE-----NRVEDWLDEHEVDVLALQE----TKTKDETFPFDLFEFMGYEVAHFGLNQWNGVAIASRVGL 73
Cdd:cd09084     1 VMSYNVRSFNRYKwkddpDKILDFIKKQDPDILCLQEyygsEGDKDDDLRLLLKGYPYYYVVYKSDSGGTGLAIFSKYPI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581  74 EDVQRgfdnqpHFGKPGEPEVLEA--RAIGATcggVRVWSLYVPNGRGLTDPHMDYKLRWM---------EALHQN---- 138
Cdd:cd09084    81 LNSGS------IDFPNTNNNAIFAdiRVGGDT---IRVYNVHLESFRITPSDKELYKEEKKakelsrnllRKLAEAfkrr 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1092755581 139 ------VHNELAANPQSQLaLVGDWNvapeDadvwdidyfrdnelTPVSEPERRafaalLKEGMVDVVRP--HTPGeYTY 210
Cdd:cd09084   152 aaqadlLAADIAASPYPVI-VCGDFN----D--------------TPASYVYRT-----LKKGLTDAFVEagSGFG-YTF 206

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1092755581 211 WDYqagRFakdeGMRIDFQLFSPELaaRVQNAWIDRVEragegASDHTPVVVEI 264
Cdd:cd09084   207 NGL---FF----PLRIDYILTSKGF--KVLRYRVDPGK-----YSDHYPIVATL 246
 
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