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Conserved domains on  [gi|157883966]
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Chain A, EXODEOXYRIBONUCLEASE

Protein Classification

exodeoxyribonuclease III( domain architecture ID 10178908)

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:0006281|GO:0008311
PubMed:  7885481|10838565
SCOP:  4002213

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Nape_like_AP-endo cd10281
Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) ...
 2-254 4.66e-157

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: 436.27  E-value: 4.66e-157
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966   2 LKIISANVNGIRSAYKKGFYEYIAASGADIVCVQELKAQEADLSADMKNPHGMHGHWHCAEKRGYSGVAVYSKRKPDNVQ 81
Cdd:cd10281    1 MRVISVNVNGIRAAAKKGFLEWLAAQDADVVCLQEVRAQEEQLDDDFFEPEGYNAYFFDAEKKGYAGVAIYSRTQPKAVI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966  82 IGMGIEEFDREGRFVRCDFGRLSVISLYLPSGSSAEERQQVKYRFLDAFYPMLEAMKNEGRDIVVCGDWNIAHQNIDLKN 161
Cdd:cd10281   81 YGLGFEEFDDEGRYIEADFDNVSVASLYVPSGSSGDERQEAKMAFLDAFLEHLKELRRKRREFIVCGDFNIAHTEIDIKN 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966 162 WKGNQKNSGFLPEEREWIGKVIHKLGWTDMWRTLYPDVPGYTWWSNRGQAYAKDVGWRIDYQMVTPELAAKAVSAHVYKD 241
Cdd:cd10281  161 WKANQKNSGFLPEERAWLDQVFGELGYVDAFRELNPDEGQYTWWSNRGQARANNVGWRIDYQIATPGLASKVVSAWIYRE 240

                        250
                 ....*....|...
gi 157883966 242 EKFSDHAPLVVEY 254
Cdd:cd10281  241 ERFSDHAPLIVDY 253
 
Name Accession Description Interval E-value
Nape_like_AP-endo cd10281
Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) ...
 2-254 4.66e-157

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: 436.27  E-value: 4.66e-157
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966   2 LKIISANVNGIRSAYKKGFYEYIAASGADIVCVQELKAQEADLSADMKNPHGMHGHWHCAEKRGYSGVAVYSKRKPDNVQ 81
Cdd:cd10281    1 MRVISVNVNGIRAAAKKGFLEWLAAQDADVVCLQEVRAQEEQLDDDFFEPEGYNAYFFDAEKKGYAGVAIYSRTQPKAVI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966  82 IGMGIEEFDREGRFVRCDFGRLSVISLYLPSGSSAEERQQVKYRFLDAFYPMLEAMKNEGRDIVVCGDWNIAHQNIDLKN 161
Cdd:cd10281   81 YGLGFEEFDDEGRYIEADFDNVSVASLYVPSGSSGDERQEAKMAFLDAFLEHLKELRRKRREFIVCGDFNIAHTEIDIKN 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966 162 WKGNQKNSGFLPEEREWIGKVIHKLGWTDMWRTLYPDVPGYTWWSNRGQAYAKDVGWRIDYQMVTPELAAKAVSAHVYKD 241
Cdd:cd10281  161 WKANQKNSGFLPEERAWLDQVFGELGYVDAFRELNPDEGQYTWWSNRGQARANNVGWRIDYQIATPGLASKVVSAWIYRE 240

                        250
                 ....*....|...
gi 157883966 242 EKFSDHAPLVVEY 254
Cdd:cd10281  241 ERFSDHAPLIVDY 253
XthA COG0708
Exonuclease III [Replication, recombination and repair];
2-255 1.94e-131

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 371.72  E-value: 1.94e-131
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966   2 LKIISANVNGIRSAYKKgFYEYIAASGADIVCVQELKAQEADLSADMKNPHGMHGHWHCaeKRGYSGVAVYSKRKPDNVQ 81
Cdd:COG0708    1 MKIASWNVNGIRARLPK-LLDWLAEEDPDVLCLQETKAQDEQFPLEAFEAAGYHVYFHG--QKGYNGVAILSRLPPEDVR 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966  82 IGMGIEEFDREGRFVRCDFGRLSVISLYLPSGSSAE-ERQQVKYRFLDAFYPMLEAMKNEGRDIVVCGDWNIAHQNIDLK 160
Cdd:COG0708   78 RGLGGDEFDAEGRYIEADFGGVRVVSLYVPNGGSVGsEKFDYKLRFLDALRAYLAELLAPGRPLILCGDFNIAPTEIDVK 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966 161 NWKGNQKNSGFLPEEREWIGKVIHkLGWTDMWRTLYPDVPG-YTWWSNRGQAYAKDVGWRIDYQMVTPELAAKAVSAHVY 239
Cdd:COG0708  158 NPKANLKNAGFLPEERAWFDRLLE-LGLVDAFRALHPDVEGqYTWWSYRAGAFARNRGWRIDYILASPALADRLKDAGID 236

                        250       260
                 ....*....|....*....|
gi 157883966 240 K----DEKFSDHAPLVVEYD 255
Cdd:COG0708  237 ReprgDERPSDHAPVVVELD 256
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 2-255 2.61e-91

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: 269.92  E-value: 2.61e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966    2 LKIISANVNGIRSAYKKGFYEYIAASGADIVCVQELKAQEADLSADMKNPHGMHGHWHCAeKRGYSGVAVYSKRKPDNVQ 81
Cdd:TIGR00633   1 MKIISWNVNGLRARLHKLFLDWLKEEQPDVLCLQETKVADEQFPAELFEELGYHVFFHGA-KKGYSGVAILSKVEPLDVR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966   82 IGMGIEEFDREGRFVRCDFGRLSVISLYLPSGSS-AEERQQVKYRFLDAFYPMLEAMKNEGRDIVVCGDWNIAHQNIDLK 160
Cdd:TIGR00633  80 YGFGGEPHDEEGRVITAEFDGFTVVNVYVPNGGSrDLERLEYKLQFWDALFQYLEKELDAGKPVVICGDMNVAHTEIDLG 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966  161 NWKGNQKNSGFLPEEREWIGKVIHkLGWTDMWRTLYPDVPG-YTWWSNRGQAYAKDVGWRIDYQMVTPELAAKAVSAHVY 239
Cdd:TIGR00633 160 NPKENKGNAGFTPEEREWFDELLE-AGFVDTFRHFNPDTGDaYTWWDYRSGARDRNRGWRIDYFLVSEPLAERVVDSYID 238

                         250
                  ....*....|....*.
gi 157883966  240 KDEKFSDHAPLVVEYD 255
Cdd:TIGR00633 239 SEIRGSDHCPIVLELD 254
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 2-253 4.99e-60

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 190.29  E-value: 4.99e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966   2 LKIISANVNGIRSAYKKGFYEYIAASGADIVCVQELKAQEADLSADMKnphGMHGHWHCAEKRGYSGVAVYSKRKPDNVQ 81
Cdd:PRK13911   1 MKLISWNVNGLRACMTKGFMDFFNSVDADVFCIQESKMQQEQNTFEFK---GYFDFWNCAIKKGYSGVVTFTKKEPLSVS 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966  82 IGMGIEEFDREGRFVRCDFGRLSVISLYLPSGSSAEERQQVKYRFLDAFYPMLEAMKNEgRDIVVCGDWNIAHQNIDLKN 161
Cdd:PRK13911  78 YGINIEEHDKEGRVITCEFESFYLVNVYTPNSQQALSRLSYRMSWEVEFKKFLKALELK-KPVIVCGDLNVAHNEIDLEN 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966 162 WKGNQKNSGFLPEEREWIGKVIHKlGWTDMWRTLYPDV-PGYTWWSNRGQAYAKDVGWRIDYQMVTPELAAKAVSAHVYK 240
Cdd:PRK13911 157 PKTNRKNAGFSDEERGKFSELLNA-GFIDTFRYFYPNKeKAYTWWSYMQQARDKNIGWRIDYFLCSNPLKTRLKDALIYK 235

                        250
                 ....*....|...
gi 157883966 241 DEKFSDHAPLVVE 253
Cdd:PRK13911 236 DILGSDHCPVGLE 248
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 5-152 1.16e-17

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: 78.42  E-value: 1.16e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966    5 ISANVNGIRS------AYKKGFYEYIAASGADIVCVQELKA-QEADLSADMKNPHGMHGHWHCAEKRGYSGVAVYSKRKP 77
Cdd:pfam03372   1 LTWNVNGGNAdaagddRKLDALAALIRAYDPDVVALQETDDdDASRLLLALLAYGGFLSYGGPGGGGGGGGVAILSRYPL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 157883966   78 DNVQIGMGIEEFDREGRFVRCDFGRLSVISLYLPSGSSAEERQQVKYRFLDAFYPMLEAMKNEGRDIVVCGDWNI 152
Cdd:pfam03372  81 SSVILVDLGEFGDPALRGAIAPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALLAPRSEPVILAGDFNA 155
 
Name Accession Description Interval E-value
Nape_like_AP-endo cd10281
Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) ...
 2-254 4.66e-157

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: 436.27  E-value: 4.66e-157
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966   2 LKIISANVNGIRSAYKKGFYEYIAASGADIVCVQELKAQEADLSADMKNPHGMHGHWHCAEKRGYSGVAVYSKRKPDNVQ 81
Cdd:cd10281    1 MRVISVNVNGIRAAAKKGFLEWLAAQDADVVCLQEVRAQEEQLDDDFFEPEGYNAYFFDAEKKGYAGVAIYSRTQPKAVI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966  82 IGMGIEEFDREGRFVRCDFGRLSVISLYLPSGSSAEERQQVKYRFLDAFYPMLEAMKNEGRDIVVCGDWNIAHQNIDLKN 161
Cdd:cd10281   81 YGLGFEEFDDEGRYIEADFDNVSVASLYVPSGSSGDERQEAKMAFLDAFLEHLKELRRKRREFIVCGDFNIAHTEIDIKN 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966 162 WKGNQKNSGFLPEEREWIGKVIHKLGWTDMWRTLYPDVPGYTWWSNRGQAYAKDVGWRIDYQMVTPELAAKAVSAHVYKD 241
Cdd:cd10281  161 WKANQKNSGFLPEERAWLDQVFGELGYVDAFRELNPDEGQYTWWSNRGQARANNVGWRIDYQIATPGLASKVVSAWIYRE 240

                        250
                 ....*....|...
gi 157883966 242 EKFSDHAPLVVEY 254
Cdd:cd10281  241 ERFSDHAPLIVDY 253
ExoIII_AP-endo cd09073
Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ...
 3-254 6.54e-138

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: 387.80  E-value: 6.54e-138
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966   3 KIISANVNGIRSAYKKGFYEYIAASGADIVCVQELKAQEADLSADMKNPHGMHGHWHCAEKRGYSGVAVYSKRKPDNVQI 82
Cdd:cd09073    1 KIISWNVNGLRARLKKGVLKWLKEEKPDILCLQETKADEDKLPEELQHVEGYHSYWSPARKKGYSGVATLSKEEPLDVSY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966  83 GMGIEEFDREGRFVRCDFGRLSVISLYLPSGSSAEERQQVKYRFLDAFYPMLEAMKNEGRDIVVCGDWNIAHQNIDLKNW 162
Cdd:cd09073   81 GIGGEEFDSEGRVITAEFDDFYLINVYFPNGGRGLERLDYKLRFYEAFLEFLEKLRKRGKPVVICGDFNVAHEEIDLARP 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966 163 KGNQKNSGFLPEEREWIGKVIHKlGWTDMWRTLYPDVPGYTWWSNRGQAYAKDVGWRIDYQMVTPELAAKAVSAHVYKDE 242
Cdd:cd09073  161 KKNEKNAGFTPEERAWFDKLLSL-GYVDTFRHFHPEPGAYTWWSYRGNARERNVGWRIDYFLVSEELAEKVKDSGILSKV 239

                        250
                 ....*....|..
gi 157883966 243 KFSDHAPLVVEY 254
Cdd:cd09073  240 KGSDHAPVTLEL 251
XthA COG0708
Exonuclease III [Replication, recombination and repair];
2-255 1.94e-131

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 371.72  E-value: 1.94e-131
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966   2 LKIISANVNGIRSAYKKgFYEYIAASGADIVCVQELKAQEADLSADMKNPHGMHGHWHCaeKRGYSGVAVYSKRKPDNVQ 81
Cdd:COG0708    1 MKIASWNVNGIRARLPK-LLDWLAEEDPDVLCLQETKAQDEQFPLEAFEAAGYHVYFHG--QKGYNGVAILSRLPPEDVR 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966  82 IGMGIEEFDREGRFVRCDFGRLSVISLYLPSGSSAE-ERQQVKYRFLDAFYPMLEAMKNEGRDIVVCGDWNIAHQNIDLK 160
Cdd:COG0708   78 RGLGGDEFDAEGRYIEADFGGVRVVSLYVPNGGSVGsEKFDYKLRFLDALRAYLAELLAPGRPLILCGDFNIAPTEIDVK 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966 161 NWKGNQKNSGFLPEEREWIGKVIHkLGWTDMWRTLYPDVPG-YTWWSNRGQAYAKDVGWRIDYQMVTPELAAKAVSAHVY 239
Cdd:COG0708  158 NPKANLKNAGFLPEERAWFDRLLE-LGLVDAFRALHPDVEGqYTWWSYRAGAFARNRGWRIDYILASPALADRLKDAGID 236

                        250       260
                 ....*....|....*....|
gi 157883966 240 K----DEKFSDHAPLVVEYD 255
Cdd:COG0708  237 ReprgDERPSDHAPVVVELD 256
Mth212-like_AP-endo cd09085
Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic ...
 2-254 4.60e-105

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: 304.97  E-value: 4.60e-105
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966   2 LKIISANVNGIRSAYKKGFYEYIAASGADIVCVQELKAQEADLSADMKNPHGMHGHWHCAEKRGYSGVAVYSKRKPDNVQ 81
Cdd:cd09085    1 MKIISWNVNGLRAVHKKGFLDWFKEEKPDILCLQETKAQPEQLPEDLRNIEGYHSYFNSAERKGYSGVALYSKIEPDSVR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966  82 IGMGIEEFDREGRFVRCDFGRLSVISLYLPSGSSAEERQQVKYRFLDAFYPMLEAMKNEGRDIVVCGDWNIAHQNIDLKN 161
Cdd:cd09085   81 EGLGVEEFDNEGRILIADFDDFTLFNIYFPNGQMSEERLDYKLEFYDAFLEYLNELRDSGKNVIICGDFNTAHKEIDLAR 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966 162 WKGNQKNSGFLPEEREWIGKVIHKlGWTDMWRTLYPDVPGYTWWSNRGQAYAKDVGWRIDYQMVTPELAAKAVSAHVYKD 241
Cdd:cd09085  161 PKENEKVSGFLPEERAWMDKFIEN-GYVDTFRMFNKEPGQYTWWSYRTRARERNVGWRIDYFFVNEEFKPKVKDAGILPD 239

                        250
                 ....*....|...
gi 157883966 242 EKFSDHAPLVVEY 254
Cdd:cd09085  240 VMGSDHCPVSLEL 252
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 2-255 2.61e-91

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: 269.92  E-value: 2.61e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966    2 LKIISANVNGIRSAYKKGFYEYIAASGADIVCVQELKAQEADLSADMKNPHGMHGHWHCAeKRGYSGVAVYSKRKPDNVQ 81
Cdd:TIGR00633   1 MKIISWNVNGLRARLHKLFLDWLKEEQPDVLCLQETKVADEQFPAELFEELGYHVFFHGA-KKGYSGVAILSKVEPLDVR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966   82 IGMGIEEFDREGRFVRCDFGRLSVISLYLPSGSS-AEERQQVKYRFLDAFYPMLEAMKNEGRDIVVCGDWNIAHQNIDLK 160
Cdd:TIGR00633  80 YGFGGEPHDEEGRVITAEFDGFTVVNVYVPNGGSrDLERLEYKLQFWDALFQYLEKELDAGKPVVICGDMNVAHTEIDLG 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966  161 NWKGNQKNSGFLPEEREWIGKVIHkLGWTDMWRTLYPDVPG-YTWWSNRGQAYAKDVGWRIDYQMVTPELAAKAVSAHVY 239
Cdd:TIGR00633 160 NPKENKGNAGFTPEEREWFDELLE-AGFVDTFRHFNPDTGDaYTWWDYRSGARDRNRGWRIDYFLVSEPLAERVVDSYID 238

                         250
                  ....*....|....*.
gi 157883966  240 KDEKFSDHAPLVVEYD 255
Cdd:TIGR00633 239 SEIRGSDHCPIVLELD 254
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This ...
 2-253 5.84e-84

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: 251.32  E-value: 5.84e-84
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966   2 LKIISANVNGIRSAYKKGFYEYIAASGADIVCVQELKAQEADLSADMKN-PHGMHGHWHCAEKRGYSGVAVYSKRKPDNV 80
Cdd:cd09087    1 LKIISWNVNGLRALLKKGLLDYVKKEDPDILCLQETKLQEGDVPKELKElLKGYHQYWNAAEKKGYSGTAILSKKKPLSV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966  81 QIGMGIEEFDREGRFVRCDFGRLSVISLYLP-SG---SSAEERQQ--VKYRfldAFYPMLEAMKNegrdIVVCGDWNIAH 154
Cdd:cd09087   81 TYGIGIEEHDQEGRVITAEFENFYLVNTYVPnSGrglERLDRRKEwdVDFR---AYLKKLDSKKP----VIWCGDLNVAH 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966 155 QNIDLKNWKGNQKNSGFLPEEREWIGKvIHKLGWTDMWRTLYPDVPG-YTWWSNRGQAYAKDVGWRIDYQMVTPELAAKA 233
Cdd:cd09087  154 EEIDLANPKTNKKSAGFTPEERESFTE-LLEAGFVDTFRHLHPDKEGaYTFWSYRGNARAKNVGWRLDYFLVSERLKDRV 232

                        250       260
                 ....*....|....*....|
gi 157883966 234 VSAHVYKDEKFSDHAPLVVE 253
Cdd:cd09087  233 VDSFIRSDIMGSDHCPIGLE 252
exoDNase_III TIGR00195
exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model ...
 2-253 5.45e-81

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: 243.83  E-value: 5.45e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966    2 LKIISANVNGIRSAYKKGFyEYIAASGADIVCVQELKAQEADLSADMKNPHGMHGHWHCAekRGYSGVAVYSKRKPDNVQ 81
Cdd:TIGR00195   1 MKIISWNVNGLRARPHKGL-AWLKENQPDVLCLQETKVQDEQFPLEPFHKEGYHVFFSGQ--KGYSGVAIFSKEEPISVR 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966   82 IGMGIEEFDREGRFVRCDFGRLSVISLYLPSGSS-AEERQQVKYRFLDAFYPMLEAMKNEGRDIVVCGDWNIAHQNIDLK 160
Cdd:TIGR00195  78 RGFGVEEEDAEGRIIMAEFDSFLVINGYFPNGSRdDSEKLPYKLQWLEALQNYLEKLVDKDKPVLICGDMNIAPTEIDLH 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966  161 NWKGNQKNSGFLPEEREWIGKVIhKLGWTDMWRTLYPDVPGYTWWSNRGQAYAKDVGWRIDYQMVTPELAAKAVSAHVYK 240
Cdd:TIGR00195 158 IPDENRNHTGFLPEEREWLDRLL-EAGLVDTFRKFNPDEGAYSWWDYRTKARDRNRGWRIDYFLVSEPLKERCVDCGIDY 236

                         250
                  ....*....|....*..
gi 157883966  241 D----EKFSDHAPLVVE 253
Cdd:TIGR00195 237 DirgsEKPSDHCPVVLE 253
ExoIII-like_AP-endo cd09086
Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of ...
 2-253 4.00e-67

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: 208.52  E-value: 4.00e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966   2 LKIISANVNGIRsAYKKGFYEYIAASGADIVCVQELKAQEADLSADMKNPHGMHGHWHCaeKRGYSGVAVYSKRKPDNVQ 81
Cdd:cd09086    1 MKIATWNVNSIR-ARLEQVLDWLKEEDPDVLCLQETKVEDDQFPADAFEALGYHVAVHG--QKAYNGVAILSRLPLEDVR 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966  82 IGMGIEEFDREGRFVRCDFGRLSVISLYLPSGSSA-EERQQVKYRFLDAFYPMLEAMKNEGRDIVVCGDWNIAHQNIDLK 160
Cdd:cd09086   78 TGFPGDPDDDQARLIAARVGGVRVINLYVPNGGDIgSPKFAYKLDWLDRLIRYLQKLLKPDDPLVLVGDFNIAPEDIDVW 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966 161 NWKGNQKNSGFLPEEREWIGKVIhKLGWTDMWRTLYPDVPGYTWWSNRGQAYAKDVGWRIDYQMVTPELAAKAVSAHVYK 240
Cdd:cd09086  158 DPKQLLGKVLFTPEEREALRALL-DLGFVDAFRALHPDEKLFTWWDYRAGAFERNRGLRIDHILASPALADRLKDVGIDR 236

                        250
                 ....*....|....*..
gi 157883966 241 D----EKFSDHAPLVVE 253
Cdd:cd09086  237 EprgwEKPSDHAPVVAE 253
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 2-253 4.99e-60

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 190.29  E-value: 4.99e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966   2 LKIISANVNGIRSAYKKGFYEYIAASGADIVCVQELKAQEADLSADMKnphGMHGHWHCAEKRGYSGVAVYSKRKPDNVQ 81
Cdd:PRK13911   1 MKLISWNVNGLRACMTKGFMDFFNSVDADVFCIQESKMQQEQNTFEFK---GYFDFWNCAIKKGYSGVVTFTKKEPLSVS 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966  82 IGMGIEEFDREGRFVRCDFGRLSVISLYLPSGSSAEERQQVKYRFLDAFYPMLEAMKNEgRDIVVCGDWNIAHQNIDLKN 161
Cdd:PRK13911  78 YGINIEEHDKEGRVITCEFESFYLVNVYTPNSQQALSRLSYRMSWEVEFKKFLKALELK-KPVIVCGDLNVAHNEIDLEN 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966 162 WKGNQKNSGFLPEEREWIGKVIHKlGWTDMWRTLYPDV-PGYTWWSNRGQAYAKDVGWRIDYQMVTPELAAKAVSAHVYK 240
Cdd:PRK13911 157 PKTNRKNAGFSDEERGKFSELLNA-GFIDTFRYFYPNKeKAYTWWSYMQQARDKNIGWRIDYFLCSNPLKTRLKDALIYK 235

                        250
                 ....*....|...
gi 157883966 241 DEKFSDHAPLVVE 253
Cdd:PRK13911 236 DILGSDHCPVGLE 248
PRK11756 PRK11756
exonuclease III; Provisional
 2-255 4.00e-41

exonuclease III; Provisional


Pssm-ID: 236970 [Multi-domain]  Cd Length: 268  Bit Score: 141.96  E-value: 4.00e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966   2 LKIISANVNGIRSAYKKgFYEYIAASGADIVCVQELKAQEADLSADMKNPHGMHGHWHcaEKRGYSGVAVYSKRKPDNVQ 81
Cdd:PRK11756   1 MKFVSFNINGLRARPHQ-LEAIIEKHQPDVIGLQETKVHDEMFPLEEVEALGYHVFYH--GQKGHYGVALLSKQTPIAVR 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966  82 IGMGIEEFDREGRFVRCDF----GRLSVISLYLPSGssaEERQQ-VKYRFLDAFYP----MLEAMKNEGRDIVVCGDWNI 152
Cdd:PRK11756  78 KGFPTDDEEAQRRIIMATIptpnGNLTVINGYFPQG---ESRDHpTKFPAKRQFYQdlqnYLETELSPDNPLLIMGDMNI 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966 153 AHQNIDL-------KNWKGNQKNSgFLPEEREWIGKvIHKLGWTDMWRTLYPDVPG-YTWWSNRGQAYAKDVGWRIDYQM 224
Cdd:PRK11756 155 SPTDLDIgigeenrKRWLRTGKCS-FLPEEREWLDR-LMDWGLVDTFRQLNPDVNDrFSWFDYRSKGFDDNRGLRIDLIL 232

                        250       260       270
                 ....*....|....*....|....*....|....*
gi 157883966 225 VTPELAAKAVSAHVYKD----EKFSDHAPLVVEYD 255
Cdd:PRK11756 233 ATQPLAERCVETGIDYDirgmEKPSDHAPIWATFK 267
Ape2-like_AP-endo cd09088
Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This ...
 3-253 3.38e-36

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: 130.51  E-value: 3.38e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966   3 KIISANVNGIRS------AYKKGFYEYIAAS-GADIVCVQELKAQEADLSADMKNPHGMHGHWHCAEKR-GYSGVAVYSK 74
Cdd:cd09088    1 RIVTWNVNGIRTrlqyqpWNKENSLKSFLDSlDADIICLQETKLTRDELDEPSAIVEGYDSFFSFSRGRkGYSGVATYCR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966  75 ------------------------RKPDNVQIGM--GIEEF---------DREGRFVRCDFGRLSVISLYLPS-GSSAEE 118
Cdd:cd09088   81 dsaatpvaaeegltgvlsspnqknELSENDDIGCygEMLEFtdskellelDSEGRCVLTDHGTFVLINVYCPRaDPEKEE 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966 119 RQQVKYRFLDAFYPMLEAMKNEGRDIVVCGDWNIAHQNID--------LKNWKGNQKNSG------FLPEEREWIGKVIH 184
Cdd:cd09088  161 RLEFKLDFYRLLEERVEALLKAGRRVILVGDVNVSHRPIDhcdpddseDFGGESFEDNPSrqwldqLLGDSGEGGGSPGG 240

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966 185 KLgwTDMWRTLYPDVPG-YTWWSNRGQAYAKDVGWRIDYQMVTPELAAKAVSAHVYKDEKFSDHAPLVVE 253
Cdd:cd09088  241 LL--IDSFRYFHPTRKGaYTCWNTLTGARPTNYGTRIDYILADRGLLPWVKAADILPEVEGSDHCPVYAD 308
EEP cd08372
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 4-254 2.15e-24

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: 97.55  E-value: 2.15e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966   4 IISANVNGIRSAYK-KGFYEYIAASGADIVCVQELK-AQEADLSADMKNPHGMHGHW-HCAEKRGYSGVAVYSKR---KP 77
Cdd:cd08372    1 VASYNVNGLNAATRaSGIARWVRELDPDIVCLQEVKdSQYSAVALNQLLPEGYHQYQsGPSRKEGYEGVAILSKTpkfKI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966  78 DNVQIGMGIEEFDREGRFVRCDFGR----LSVISLYLPSGssaEERQQVKYRFLDAFYP-MLEAMKNEGRDIVVCGDWNI 152
Cdd:cd08372   81 VEKHQYKFGEGDSGERRAVVVKFDVhdkeLCVVNAHLQAG---GTRADVRDAQLKEVLEfLKRLRQPNSAPVVICGDFNV 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966 153 AHQNIDLKNWKGnqknsgflpeerewIGKVIHKLGWTDMWRTLypdVPGYTWWSNRgqayaKDVGWRIDYQMVTPELAAK 232
Cdd:cd08372  158 RPSEVDSENPSS--------------MLRLFVALNLVDSFETL---PHAYTFDTYM-----HNVKSRLDYIFVSKSLLPS 215

                        250       260
                 ....*....|....*....|....*.
gi 157883966 233 AVSAHVYKDEKF----SDHAPLVVEY 254
Cdd:cd08372  216 VKSSKILSDAARaripSDHYPIEVTL 241
L1-EN cd09076
Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; ...
 4-254 3.42e-22

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: 91.64  E-value: 3.42e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966   4 IISANVNGIRSAYK-KGFYEYIAASGADIVCVQELKaqEADLSADMKNPHGMHGHWHCAEKRGYSGVAVYSKRKPDNVQI 82
Cdd:cd09076    1 IGTLNVRGLRSPGKrAQLLEELKRKKLDILGLQETH--WTGEGELKKKREGGTILYSGSDSGKSRGVAILLSKTAANKLL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966  83 GMgieEFDREGRFVRCDF----GRLSVISLYLPSGSSAEERQQvkyrfldaFYPMLEA-MKNEGRD--IVVCGDWNiAHQ 155
Cdd:cd09076   79 EY---TKVVSGRIIMVRFkikgKRLTIINVYAPTARDEEEKEE--------FYDQLQDvLDKVPRHdtLIIGGDFN-AVL 146

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966 156 NIDLKNWKGNQKNSGflPEEREWiGKVIHKLGWTDMWRTLYPDVPGYTWWSNRGQAYAkdvgwRIDYQMVTPELAAKAVS 235
Cdd:cd09076  147 GPKDDGRKGLDKRNE--NGERAL-SALIEEHDLVDVWRENNPKTREYTWRSPDHGSRS-----RIDRILVSKRLRVKVKK 218

                        250
                 ....*....|....*....
gi 157883966 236 AhVYKDEKFSDHAPLVVEY 254
Cdd:cd09076  219 T-KITPGAGSDHRLVTLKL 236
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 5-152 1.16e-17

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: 78.42  E-value: 1.16e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966    5 ISANVNGIRS------AYKKGFYEYIAASGADIVCVQELKA-QEADLSADMKNPHGMHGHWHCAEKRGYSGVAVYSKRKP 77
Cdd:pfam03372   1 LTWNVNGGNAdaagddRKLDALAALIRAYDPDVVALQETDDdDASRLLLALLAYGGFLSYGGPGGGGGGGGVAILSRYPL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 157883966   78 DNVQIGMGIEEFDREGRFVRCDFGRLSVISLYLPSGSSAEERQQVKYRFLDAFYPMLEAMKNEGRDIVVCGDWNI 152
Cdd:pfam03372  81 SSVILVDLGEFGDPALRGAIAPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALLAPRSEPVILAGDFNA 155
YafD COG3021
Uncharacterized conserved protein YafD, endonuclease/exonuclease/phosphatase (EEP) superfamily ...
 2-257 8.25e-13

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


Pssm-ID: 442257 [Multi-domain]  Cd Length: 310  Bit Score: 66.94  E-value: 8.25e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966   2 LKIISANVNGIRSAYKKgFYEYIAASGADIVCVQELKAQEAD----LSADMknPHGMhghwHCAEKRGYsGVAVYSKRKP 77
Cdd:COG3021   95 LRVLTANVLFGNADAEA-LAALVREEDPDVLVLQETTPAWEEalaaLEADY--PYRV----LCPLDNAY-GMALLSRLPL 166

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966  78 DNVQIGMGIEEfdrEGRFVRCDF----GRLSVISLYL--PSGSSAEERQQvkyrfLDAfypMLEAMKNEGRDIVVCGDWN 151
Cdd:COG3021  167 TEAEVVYLVGD---DIPSIRATVelpgGPVRLVAVHPapPVGGSAERDAE-----LAA---LAKAVAALDGPVIVAGDFN 235

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966 152 IA--HQNIDLKnwkgnQKNSGFLPEEREWigkvihklGWTDMWRTLYPdvpgytwwsnrgqayakDVGWRIDYQMVTPEL 229
Cdd:COG3021  236 ATpwSPTLRRL-----LRASGLRDARAGR--------GLGPTWPANLP-----------------FLRLPIDHVLVSRGL 285

                        250       260
                 ....*....|....*....|....*...
gi 157883966 230 AAKAVSAHvykDEKFSDHAPLVVEYDYA 257
Cdd:COG3021  286 TVVDVRVL---PVIGSDHRPLLAELALP 310
EEP-2 cd09084
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This ...
 4-254 6.62e-12

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: 63.47  E-value: 6.62e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966   4 IISANVNG----IRSAYKKGFYEYIAASGADIVCVQELKAQEADLSADMKN--PHGMHGHWHCAEKRGYSGVAVYSKRKP 77
Cdd:cd09084    1 VMSYNVRSfnryKWKDDPDKILDFIKKQDPDILCLQEYYGSEGDKDDDLRLllKGYPYYYVVYKSDSGGTGLAIFSKYPI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966  78 DNVQIgmgIEEFDREGRFVRCDF---GR-LSVISLYLPS----------GSSAEERQQVKYRFLDAFYP----------- 132
Cdd:cd09084   81 LNSGS---IDFPNTNNNAIFADIrvgGDtIRVYNVHLESfritpsdkelYKEEKKAKELSRNLLRKLAEafkrraaqadl 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966 133 MLEAMKNEGRDIVVCGDWN-----IAHQNI--DLKNwkgnqknsgflpeerewigkvihklGWTDMWRtlypdVPGYTWW 205
Cdd:cd09084  158 LAADIAASPYPVIVCGDFNdtpasYVYRTLkkGLTD-------------------------AFVEAGS-----GFGYTFN 207

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*....
gi 157883966 206 SNRGqayakdvGWRIDYQMVTPELaaKAVSAHVYKDeKFSDHAPLVVEY 254
Cdd:cd09084  208 GLFF-------PLRIDYILTSKGF--KVLRYRVDPG-KYSDHYPIVATL 246
TDP2 cd09080
Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related ...
 2-204 2.38e-08

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: 53.50  E-value: 2.38e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966   2 LKIISANVNGIRSAYKKGFYE----YIAASGADIVCVQELkaQEADLSADMKNPHgMHGHWHCAE-----KRGYSGVAVY 72
Cdd:cd09080    1 LKVLTWNVDFLDDVNLAERMRailkLLEELDPDVIFLQEV--TPPFLAYLLSQPW-VRKNYYFSEgppspAVDPYGVLIL 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966  73 SKRKPDNVQI-----GMGieefdREGRFVRCDFG---RLSVISLYLPSGSS-AEERQ-QVKYrfldafypMLEAMK--NE 140
Cdd:cd09080   78 SKKSLVVRRVpftstRMG-----RNLLAAEINLGsgePLRLATTHLESLKShSSERTaQLEE--------IAKKLKkpPG 144

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 157883966 141 GRDIVVCGDWNIAHQNIDLknwkgnqknsgflpeerewigkVIHKLGWTDMWRTLYPDV-PGYTW 204
Cdd:cd09080  145 AANVILGGDFNLRDKEDDT----------------------GGLPNGFVDAWEELGPPGePGYTW 187
R1-I-EN cd09077
Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat ...
 2-253 9.67e-07

Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-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. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-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: 197311 [Multi-domain]  Cd Length: 205  Bit Score: 48.06  E-value: 9.67e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966   2 LKIISANVNGIRSAYKkGFYEYIAASGADIVCVQElkaqeadlsaDMKNPHGMhGHWHCAEKRGysgVAVYSKRKPDNVQ 81
Cdd:cd09077    1 LRILQINLNRCKAAQD-LLLQTAREEGADIALIQE----------PYLVPVNN-PNWVTDESGR---AAIVVSDRLPRKP 65

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966  82 IgmgiEEFDREGRFVRCDFGRLSVISLYLPSGSSAEErqqvkyrfldaFYPMLEAMKNE----GRDIVVCGDWNIAHQni 157
Cdd:cd09077   66 I----QRLSLGLGIVAARVGGITVVSCYAPPSESLEE-----------FEEYLENLVRIvrglSRPVIIGGDFNAWSP-- 128

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966 158 dlkNWKGNQKNS-GFLPEerEWIGkvihKLGWTDMWRtlyPDVPgyTWWSNRGQAYakdvgwrIDYQMVTPELAAKAVSA 236
Cdd:cd09077  129 ---AWGSKRTDRrGRLLE--DWIA----NLGLVLLND---GNSP--TFVRPRGTSI-------IDVTFCSPSLARRISNW 187

                        250
                 ....*....|....*..
gi 157883966 237 HVYKDEKFSDHAPLVVE 253
Cdd:cd09077  188 RVLEDETLSDHRYIRFT 204
ElsH COG3568
Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function ...
 1-255 1.69e-06

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


Pssm-ID: 442789 [Multi-domain]  Cd Length: 167  Bit Score: 46.83  E-value: 1.69e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966   1 MLKIISANV-NGI---RSAYKKGFYEYIAASGADIVCVQElkaqeadlsadmknphgmhghwhcaekrgysgVAVYSKRK 76
Cdd:COG3568    7 TLRVMTYNIrYGLgtdGRADLERIARVIRALDPDVVALQE--------------------------------NAILSRYP 54

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966  77 PDNVQIgMGIEEFDREGR-FVRCDF----GRLSVISLYLPSGSSAEERQQVKYrfldafypMLEAMKNEGRD--IVVCGD 149
Cdd:COG3568   55 IVSSGT-FDLPDPGGEPRgALWADVdvpgKPLRVVNTHLDLRSAAARRRQARA--------LAELLAELPAGapVILAGD 125

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966 150 WNIahqnidlknwkgnqknsgflpeerewigkvihklgwtdmwrtlypdvpgytwwsnrgqayakdvgwrIDYQMVTPEL 229
Cdd:COG3568  126 FND-------------------------------------------------------------------IDYILVSPGL 138

                        250       260
                 ....*....|....*....|....*....
gi 157883966 230 aaKAVSAHVYKDE---KFSDHAPLVVEYD 255
Cdd:COG3568  139 --RVLSAEVLDSPlgrAASDHLPVVADLE 165
COG2374 COG2374
Predicted extracellular nuclease [General function prediction only];
24-252 7.83e-05

Predicted extracellular nuclease [General function prediction only];


Pssm-ID: 441941 [Multi-domain]  Cd Length: 362  Bit Score: 43.09  E-value: 7.83e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966  24 IAASGADIVCVQELKAQEA---DLsADMKNPHGmhGHW---HCAEKRGYSGVAV---YskrKPDNVQI------------ 82
Cdd:COG2374  110 IAALDADIVGLQEVENNGSalqDL-VAALNLAG--GTYafvHPPDGPDGDGIRVallY---RPDRVTLvgsatiadlpds 183

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966  83 GMGIEEFDR---EGRFVRCDFGRLSVISLYLPS----------GSSAEER-QQVKY--RFLDAfypmlEAMKNEGRDIVV 146
Cdd:COG2374  184 PGNPDRFSRpplAVTFELANGEPFTVIVNHFKSkgsddpgdgqGASEAKRtAQAEAlrAFVDS-----LLAADPDAPVIV 258

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966 147 CGDWNiAHqnidlknwkgnqknsgflPEEREwIGKVIHKLGWTDMWRTLYPDVPG-YTWWSNRGQayakdvgwrIDYQMV 225
Cdd:COG2374  259 LGDFN-DY------------------PFEDP-LRALLGAGGLTNLAEKLPAAERYsYVYDGNSGL---------LDHILV 309

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*..
gi 157883966 226 TPELAAKAVS-------AHVYKDE-------------KFSDHAPLVV 252
Cdd:COG2374  310 SPALAARVTGadiwhinADIYNDDfkpdfrtyaddpgRASDHDPVVV 356
MnuA_DNase1-like cd10283
Mycoplasma pulmonis MnuA nuclease-like; This subfamily includes Mycoplasma pulmonis MnuA, a ...
 2-254 3.04e-03

Mycoplasma pulmonis MnuA nuclease-like; This subfamily includes Mycoplasma pulmonis MnuA, a membrane-associated nuclease related to Deoxyribonuclease 1 (DNase1 or DNase I, EC 3.1.21.1). The in vivo role of MnuA is as yet undetermined. This subfamily 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: 197338 [Multi-domain]  Cd Length: 266  Bit Score: 38.15  E-value: 3.04e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966   2 LKIISANV----NGIRSAYKKGFYEYIAASGADIVCVQELKAQEADLSA--DMKNPH-GMHGHWHCA---EKRGYSGVA- 70
Cdd:cd10283    1 LRIASWNIlnfgNSKGKEKNPAIAEIISAFDLDLIALQEVMDNGGGLDAlaKLVNELnKPGGTWKYIvsdKTGGSSGDKe 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966  71 ----VYSKRKPDNVQiGMGIE------EFDREGRFVRCDFGR----LSVISLYLPSGSSAEERQQVKY----RFLDAFYP 132
Cdd:cd10283   81 ryafLYKSSKVRKVG-KAVLEkdsntdGFARPPYAAKFKSGGtgfdFTLVNVHLKSGGSSKSGQGAKRvaeaQALAEYLK 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966 133 MLEAMKnEGRDIVVCGDWNIAhqnidlknwkgnQKNSGFlpeerewigKVIHKLGWTDmwrtLYPDVPGYtwwSNRGQAY 212
Cdd:cd10283  160 ELADED-PDDDVILLGDFNIP------------ADEDAF---------KALTKAGFKS----LLPDSTNL---STSFKGY 210

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 157883966 213 AKdvgwRIDYQMVTPELAAKAVSAHVYKD------------------EKFSDHAPLVVEY 254
Cdd:cd10283  211 AN----SYDNIFVSGNLKEKFSNSGVFDFnilvdeageedldyskwrKQISDHDPVWVEF 266
 
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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