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Conserved domains on  [gi|1861233131|ref|WP_176072149|]
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exodeoxyribonuclease III, partial [Paraburkholderia phenazinium]

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) ...
 2-212 9.84e-121

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: 342.67  E-value: 9.84e-121
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131   2 LRVITANLNGIRSAAKKGFFDWLGDQKADCVCVQEIKVSADDLPPEFAAPHGFTGHFHHAEKKGYSGAGLYTRREPDDLI 81
Cdd:cd10281     1 MRVISVNVNGIRAAAKKGFLEWLAAQDADVVCLQEVRAQEEQLDDDFFEPEGYNAYFFDAEKKGYAGVAIYSRTQPKAVI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131  82 IGYGSSEFDSEGRYVEARYGKLSVISVYVPSGSSGEERQQAKFRFMAEFMPHLAELKAKKREVILCGDVNIVHKEIDIRN 161
Cdd:cd10281    81 YGLGFEEFDDEGRYIEADFDNVSVASLYVPSGSSGDERQEAKMAFLDAFLEHLKELRRKRREFIVCGDFNIAHTEIDIKN 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1861233131 162 WKSNQKNSGCLPEERAWLTQLFDEVGYVDVFRTLDPRPDQYTWWSNRGQAY 212
Cdd:cd10281   161 WKANQKNSGFLPEERAWLDQVFGELGYVDAFRELNPDEGQYTWWSNRGQAR 211
 
Name Accession Description Interval E-value
Nape_like_AP-endo cd10281
Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) ...
 2-212 9.84e-121

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: 342.67  E-value: 9.84e-121
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131   2 LRVITANLNGIRSAAKKGFFDWLGDQKADCVCVQEIKVSADDLPPEFAAPHGFTGHFHHAEKKGYSGAGLYTRREPDDLI 81
Cdd:cd10281     1 MRVISVNVNGIRAAAKKGFLEWLAAQDADVVCLQEVRAQEEQLDDDFFEPEGYNAYFFDAEKKGYAGVAIYSRTQPKAVI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131  82 IGYGSSEFDSEGRYVEARYGKLSVISVYVPSGSSGEERQQAKFRFMAEFMPHLAELKAKKREVILCGDVNIVHKEIDIRN 161
Cdd:cd10281    81 YGLGFEEFDDEGRYIEADFDNVSVASLYVPSGSSGDERQEAKMAFLDAFLEHLKELRRKRREFIVCGDFNIAHTEIDIKN 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1861233131 162 WKSNQKNSGCLPEERAWLTQLFDEVGYVDVFRTLDPRPDQYTWWSNRGQAY 212
Cdd:cd10281   161 WKANQKNSGFLPEERAWLDQVFGELGYVDAFRELNPDEGQYTWWSNRGQAR 211
XthA COG0708
Exonuclease III [Replication, recombination and repair];
2-212 5.79e-104

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 300.07  E-value: 5.79e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131   2 LRVITANLNGIRSAAKKgFFDWLGDQKADCVCVQEIKVSADDLPPEFAAPHGFtgHFHHAEKKGYSGAGLYTRREPDDLI 81
Cdd:COG0708     1 MKIASWNVNGIRARLPK-LLDWLAEEDPDVLCLQETKAQDEQFPLEAFEAAGY--HVYFHGQKGYNGVAILSRLPPEDVR 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131  82 IGYGSSEFDSEGRYVEARYGKLSVISVYVPSGSS-GEERQQAKFRFMAEFMPHLAELKAKKREVILCGDVNIVHKEIDIR 160
Cdd:COG0708    78 RGLGGDEFDAEGRYIEADFGGVRVVSLYVPNGGSvGSEKFDYKLRFLDALRAYLAELLAPGRPLILCGDFNIAPTEIDVK 157

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1861233131 161 NWKSNQKNSGCLPEERAWLTQLFDeVGYVDVFRTLDP-RPDQYTWWSNRGQAY 212
Cdd:COG0708   158 NPKANLKNAGFLPEERAWFDRLLE-LGLVDAFRALHPdVEGQYTWWSYRAGAF 209
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 2-211 1.83e-69

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: 212.52  E-value: 1.83e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131   2 LRVITANLNGIRSAAKKGFFDWLGDQKADCVCVQEIKVSADDLPPEFAAPHGFTgHFHHAEKKGYSGAGLYTRREPDDLI 81
Cdd:TIGR00633   1 MKIISWNVNGLRARLHKLFLDWLKEEQPDVLCLQETKVADEQFPAELFEELGYH-VFFHGAKKGYSGVAILSKVEPLDVR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131  82 IGYGSSEFDSEGRYVEARYGKLSVISVYVP-SGSSGEERQQAKFRFMAEFMPHLAELKAKKREVILCGDVNIVHKEIDIR 160
Cdd:TIGR00633  80 YGFGGEPHDEEGRVITAEFDGFTVVNVYVPnGGSRDLERLEYKLQFWDALFQYLEKELDAGKPVVICGDMNVAHTEIDLG 159

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1861233131 161 NWKSNQKNSGCLPEERAWLTQLFDEvGYVDVFRTLDP-RPDQYTWWSNRGQA 211
Cdd:TIGR00633 160 NPKENKGNAGFTPEEREWFDELLEA-GFVDTFRHFNPdTGDAYTWWDYRSGA 210
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 2-211 8.84e-41

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 139.06  E-value: 8.84e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131   2 LRVITANLNGIRSAAKKGFFDWLGDQKADCVCVQEIKVSADDLPPEFaapHGFTGHFHHAEKKGYSGAGLYTRREPDDLI 81
Cdd:PRK13911    1 MKLISWNVNGLRACMTKGFMDFFNSVDADVFCIQESKMQQEQNTFEF---KGYFDFWNCAIKKGYSGVVTFTKKEPLSVS 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131  82 IGYGSSEFDSEGRYVEARYGKLSVISVYVPSGSSGEERQQAKFRFMAEFMPHLAELKAKKrEVILCGDVNIVHKEIDIRN 161
Cdd:PRK13911   78 YGINIEEHDKEGRVITCEFESFYLVNVYTPNSQQALSRLSYRMSWEVEFKKFLKALELKK-PVIVCGDLNVAHNEIDLEN 156

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1861233131 162 WKSNQKNSGCLPEERAWLTQLFDeVGYVDVFRTLDPRPDQ-YTWWSNRGQA 211
Cdd:PRK13911  157 PKTNRKNAGFSDEERGKFSELLN-AGFIDTFRYFYPNKEKaYTWWSYMQQA 206
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 5-152 7.55e-15

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


Pssm-ID: 460902 [Multi-domain]  Cd Length: 183  Bit Score: 69.56  E-value: 7.55e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131   5 ITANLNGIRSAA------KKGFFDWLGDQKADCVCVQEIKVSADDLPPE-FAAPHGFTGHFHHAEKKGYSGAGLYTRREP 77
Cdd:pfam03372   1 LTWNVNGGNADAagddrkLDALAALIRAYDPDVVALQETDDDDASRLLLaLLAYGGFLSYGGPGGGGGGGGVAILSRYPL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1861233131  78 DDLIIGYGSSEFDSEGRYVEARYGKLSVISVYVPSGSSGEERQQAKFRFMAEFMPHLAELKAKKREVILCGDVNI 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) ...
 2-212 9.84e-121

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: 342.67  E-value: 9.84e-121
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131   2 LRVITANLNGIRSAAKKGFFDWLGDQKADCVCVQEIKVSADDLPPEFAAPHGFTGHFHHAEKKGYSGAGLYTRREPDDLI 81
Cdd:cd10281     1 MRVISVNVNGIRAAAKKGFLEWLAAQDADVVCLQEVRAQEEQLDDDFFEPEGYNAYFFDAEKKGYAGVAIYSRTQPKAVI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131  82 IGYGSSEFDSEGRYVEARYGKLSVISVYVPSGSSGEERQQAKFRFMAEFMPHLAELKAKKREVILCGDVNIVHKEIDIRN 161
Cdd:cd10281    81 YGLGFEEFDDEGRYIEADFDNVSVASLYVPSGSSGDERQEAKMAFLDAFLEHLKELRRKRREFIVCGDFNIAHTEIDIKN 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1861233131 162 WKSNQKNSGCLPEERAWLTQLFDEVGYVDVFRTLDPRPDQYTWWSNRGQAY 212
Cdd:cd10281   161 WKANQKNSGFLPEERAWLDQVFGELGYVDAFRELNPDEGQYTWWSNRGQAR 211
XthA COG0708
Exonuclease III [Replication, recombination and repair];
2-212 5.79e-104

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 300.07  E-value: 5.79e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131   2 LRVITANLNGIRSAAKKgFFDWLGDQKADCVCVQEIKVSADDLPPEFAAPHGFtgHFHHAEKKGYSGAGLYTRREPDDLI 81
Cdd:COG0708     1 MKIASWNVNGIRARLPK-LLDWLAEEDPDVLCLQETKAQDEQFPLEAFEAAGY--HVYFHGQKGYNGVAILSRLPPEDVR 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131  82 IGYGSSEFDSEGRYVEARYGKLSVISVYVPSGSS-GEERQQAKFRFMAEFMPHLAELKAKKREVILCGDVNIVHKEIDIR 160
Cdd:COG0708    78 RGLGGDEFDAEGRYIEADFGGVRVVSLYVPNGGSvGSEKFDYKLRFLDALRAYLAELLAPGRPLILCGDFNIAPTEIDVK 157

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1861233131 161 NWKSNQKNSGCLPEERAWLTQLFDeVGYVDVFRTLDP-RPDQYTWWSNRGQAY 212
Cdd:COG0708   158 NPKANLKNAGFLPEERAWFDRLLE-LGLVDAFRALHPdVEGQYTWWSYRAGAF 209
Mth212-like_AP-endo cd09085
Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic ...
 2-211 1.69e-92

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: 271.07  E-value: 1.69e-92
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131   2 LRVITANLNGIRSAAKKGFFDWLGDQKADCVCVQEIKVSADDLPPEFAAPHGFTGHFHHAEKKGYSGAGLYTRREPDDLI 81
Cdd:cd09085     1 MKIISWNVNGLRAVHKKGFLDWFKEEKPDILCLQETKAQPEQLPEDLRNIEGYHSYFNSAERKGYSGVALYSKIEPDSVR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131  82 IGYGSSEFDSEGRYVEARYGKLSVISVYVPSGSSGEERQQAKFRFMAEFMPHLAELKAKKREVILCGDVNIVHKEIDIRN 161
Cdd:cd09085    81 EGLGVEEFDNEGRILIADFDDFTLFNIYFPNGQMSEERLDYKLEFYDAFLEYLNELRDSGKNVIICGDFNTAHKEIDLAR 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 1861233131 162 WKSNQKNSGCLPEERAWLTQLFdEVGYVDVFRTLDPRPDQYTWWSNRGQA 211
Cdd:cd09085   161 PKENEKVSGFLPEERAWMDKFI-ENGYVDTFRMFNKEPGQYTWWSYRTRA 209
ExoIII_AP-endo cd09073
Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ...
 3-212 8.63e-90

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: 264.15  E-value: 8.63e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131   3 RVITANLNGIRSAAKKGFFDWLGDQKADCVCVQEIKVSADDLPPEFAAPHGFTGHFHHAEKKGYSGAGLYTRREPDDLII 82
Cdd:cd09073     1 KIISWNVNGLRARLKKGVLKWLKEEKPDILCLQETKADEDKLPEELQHVEGYHSYWSPARKKGYSGVATLSKEEPLDVSY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131  83 GYGSSEFDSEGRYVEARYGKLSVISVYVPSGSSGEERQQAKFRFMAEFMPHLAELKAKKREVILCGDVNIVHKEIDIRNW 162
Cdd:cd09073    81 GIGGEEFDSEGRVITAEFDDFYLINVYFPNGGRGLERLDYKLRFYEAFLEFLEKLRKRGKPVVICGDFNVAHEEIDLARP 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 1861233131 163 KSNQKNSGCLPEERAWLTQLFDEvGYVDVFRTLDPRPDQYTWWSNRGQAY 212
Cdd:cd09073   161 KKNEKNAGFTPEERAWFDKLLSL-GYVDTFRHFHPEPGAYTWWSYRGNAR 209
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 2-211 1.83e-69

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: 212.52  E-value: 1.83e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131   2 LRVITANLNGIRSAAKKGFFDWLGDQKADCVCVQEIKVSADDLPPEFAAPHGFTgHFHHAEKKGYSGAGLYTRREPDDLI 81
Cdd:TIGR00633   1 MKIISWNVNGLRARLHKLFLDWLKEEQPDVLCLQETKVADEQFPAELFEELGYH-VFFHGAKKGYSGVAILSKVEPLDVR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131  82 IGYGSSEFDSEGRYVEARYGKLSVISVYVP-SGSSGEERQQAKFRFMAEFMPHLAELKAKKREVILCGDVNIVHKEIDIR 160
Cdd:TIGR00633  80 YGFGGEPHDEEGRVITAEFDGFTVVNVYVPnGGSRDLERLEYKLQFWDALFQYLEKELDAGKPVVICGDMNVAHTEIDLG 159

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1861233131 161 NWKSNQKNSGCLPEERAWLTQLFDEvGYVDVFRTLDP-RPDQYTWWSNRGQA 211
Cdd:TIGR00633 160 NPKENKGNAGFTPEEREWFDELLEA-GFVDTFRHFNPdTGDAYTWWDYRSGA 210
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This ...
 2-211 3.06e-68

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: 209.33  E-value: 3.06e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131   2 LRVITANLNGIRSAAKKGFFDWLGDQKADCVCVQEIKVSADDLPPEFAA-PHGFTGHFHHAEKKGYSGAGLYTRREPDDL 80
Cdd:cd09087     1 LKIISWNVNGLRALLKKGLLDYVKKEDPDILCLQETKLQEGDVPKELKElLKGYHQYWNAAEKKGYSGTAILSKKKPLSV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131  81 IIGYGSSEFDSEGRYVEARYGKLSVISVYVPSGSSGEERQQAKFRFMAEFMPHLAELKAKKReVILCGDVNIVHKEIDIR 160
Cdd:cd09087    81 TYGIGIEEHDQEGRVITAEFENFYLVNTYVPNSGRGLERLDRRKEWDVDFRAYLKKLDSKKP-VIWCGDLNVAHEEIDLA 159

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1861233131 161 NWKSNQKNSGCLPEERAWLTQLFDEvGYVDVFRTLDP-RPDQYTWWSNRGQA 211
Cdd:cd09087   160 NPKTNKKSAGFTPEERESFTELLEA-GFVDTFRHLHPdKEGAYTFWSYRGNA 210
exoDNase_III TIGR00195
exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model ...
 2-211 1.62e-64

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: 199.92  E-value: 1.62e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131   2 LRVITANLNGIRSAAKKGFfDWLGDQKADCVCVQEIKVSADDLPPEFAAPHGFTGHFHHAekKGYSGAGLYTRREPDDLI 81
Cdd:TIGR00195   1 MKIISWNVNGLRARPHKGL-AWLKENQPDVLCLQETKVQDEQFPLEPFHKEGYHVFFSGQ--KGYSGVAIFSKEEPISVR 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131  82 IGYGSSEFDSEGRYVEARYGKLSVISVYVPSGSS-GEERQQAKFRFMAEFMPHLAELKAKKREVILCGDVNIVHKEIDIR 160
Cdd:TIGR00195  78 RGFGVEEEDAEGRIIMAEFDSFLVINGYFPNGSRdDSEKLPYKLQWLEALQNYLEKLVDKDKPVLICGDMNIAPTEIDLH 157

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1861233131 161 NWKSNQKNSGCLPEERAWLTQLFdEVGYVDVFRTLDPRPDQYTWWSNRGQA 211
Cdd:TIGR00195 158 IPDENRNHTGFLPEEREWLDRLL-EAGLVDTFRKFNPDEGAYSWWDYRTKA 207
ExoIII-like_AP-endo cd09086
Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of ...
 2-212 4.63e-49

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: 160.37  E-value: 4.63e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131   2 LRVITANLNGIRsaAKKGF-FDWLGDQKADCVCVQEIKVSADDLPPEFAAPHGFtgHFHHAEKKGYSGAGLYTRREPDDL 80
Cdd:cd09086     1 MKIATWNVNSIR--ARLEQvLDWLKEEDPDVLCLQETKVEDDQFPADAFEALGY--HVAVHGQKAYNGVAILSRLPLEDV 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131  81 IIGYGSSEFDSEGRYVEARYGKLSVISVYVPSGSS-GEERQQAKFRFMAEFMPHLAELKAKKREVILCGDVNIVHKEIDI 159
Cdd:cd09086    77 RTGFPGDPDDDQARLIAARVGGVRVINLYVPNGGDiGSPKFAYKLDWLDRLIRYLQKLLKPDDPLVLVGDFNIAPEDIDV 156

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1861233131 160 RNWKSNQKNSGCLPEERAWLTQLFDeVGYVDVFRTLDPRPDQYTWWSNRGQAY 212
Cdd:cd09086   157 WDPKQLLGKVLFTPEEREALRALLD-LGFVDAFRALHPDEKLFTWWDYRAGAF 208
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 2-211 8.84e-41

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 139.06  E-value: 8.84e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131   2 LRVITANLNGIRSAAKKGFFDWLGDQKADCVCVQEIKVSADDLPPEFaapHGFTGHFHHAEKKGYSGAGLYTRREPDDLI 81
Cdd:PRK13911    1 MKLISWNVNGLRACMTKGFMDFFNSVDADVFCIQESKMQQEQNTFEF---KGYFDFWNCAIKKGYSGVVTFTKKEPLSVS 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131  82 IGYGSSEFDSEGRYVEARYGKLSVISVYVPSGSSGEERQQAKFRFMAEFMPHLAELKAKKrEVILCGDVNIVHKEIDIRN 161
Cdd:PRK13911   78 YGINIEEHDKEGRVITCEFESFYLVNVYTPNSQQALSRLSYRMSWEVEFKKFLKALELKK-PVIVCGDLNVAHNEIDLEN 156

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1861233131 162 WKSNQKNSGCLPEERAWLTQLFDeVGYVDVFRTLDPRPDQ-YTWWSNRGQA 211
Cdd:PRK13911  157 PKTNRKNAGFSDEERGKFSELLN-AGFIDTFRYFYPNKEKaYTWWSYMQQA 206
Ape2-like_AP-endo cd09088
Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This ...
 3-206 7.85e-31

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: 114.72  E-value: 7.85e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131   3 RVITANLNGIRS----------AAKKGFFDWLgdqKADCVCVQEIKVSADDLPPEFAAPHGFTGHFH-HAEKKGYSGAGL 71
Cdd:cd09088     1 RIVTWNVNGIRTrlqyqpwnkeNSLKSFLDSL---DADIICLQETKLTRDELDEPSAIVEGYDSFFSfSRGRKGYSGVAT 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131  72 YTRR-------------------------EPDDLIIGYGS----------SEFDSEGRYVEARYGKLSVISVYVPS-GSS 115
Cdd:cd09088    78 YCRDsaatpvaaeegltgvlsspnqknelSENDDIGCYGEmleftdskelLELDSEGRCVLTDHGTFVLINVYCPRaDPE 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131 116 GEERQQAKFRF------MAEfmphlAELKAkKREVILCGDVNIVHKEIDIRNWKSNQKNSGCLPEE---RAWLTQ-LFDE 185
Cdd:cd09088   158 KEERLEFKLDFyrlleeRVE-----ALLKA-GRRVILVGDVNVSHRPIDHCDPDDSEDFGGESFEDnpsRQWLDQlLGDS 231

                         250       260       270
                  ....*....|....*....|....*....|
gi 1861233131 186 VG--------YVDVFRTLDP-RPDQYTWWS 206
Cdd:cd09088   232 GEgggspgglLIDSFRYFHPtRKGAYTCWN 261
PRK11756 PRK11756
exonuclease III; Provisional
 2-208 8.65e-29

exonuclease III; Provisional


Pssm-ID: 236970 [Multi-domain]  Cd Length: 268  Bit Score: 108.44  E-value: 8.65e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131   2 LRVITANLNGIRS-----AAkkgffdwLGDQ-KADCVCVQEIKVSADDLPPEFAAPHGFTGHFHHaeKKGYSGAGLYTRR 75
Cdd:PRK11756    1 MKFVSFNINGLRArphqlEA-------IIEKhQPDVIGLQETKVHDEMFPLEEVEALGYHVFYHG--QKGHYGVALLSKQ 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131  76 EPDDLIIGYGSSEFDSEGRYVEARY----GKLSVISVYVPSGSS--GEERQQAKFRFMAEFMPHLAELKAKKREVILCGD 149
Cdd:PRK11756   72 TPIAVRKGFPTDDEEAQRRIIMATIptpnGNLTVINGYFPQGESrdHPTKFPAKRQFYQDLQNYLETELSPDNPLLIMGD 151

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1861233131 150 VNIVHKEIDI-------RNWKSNQKNSgCLPEERAWLTQLFDeVGYVDVFRTLDP-RPDQYTWWSNR 208
Cdd:PRK11756  152 MNISPTDLDIgigeenrKRWLRTGKCS-FLPEEREWLDRLMD-WGLVDTFRQLNPdVNDRFSWFDYR 216
EEP cd08372
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 4-208 1.26e-18

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: 80.99  E-value: 1.26e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131   4 VITANLNGIRSA-AKKGFFDWLGDQKADCVCVQEIKVSADDLPPE-FAAPHGFTGHFHHAE-KKGYSGAGLYTRR---EP 77
Cdd:cd08372     1 VASYNVNGLNAAtRASGIARWVRELDPDIVCLQEVKDSQYSAVALnQLLPEGYHQYQSGPSrKEGYEGVAILSKTpkfKI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131  78 DDLIIGYGSSEFDSEGRYVEARYGK----LSVISVYVPSGSSGEERQQAKFRFMAEFMphLAELKAKKREVILCGDVNIV 153
Cdd:cd08372    81 VEKHQYKFGEGDSGERRAVVVKFDVhdkeLCVVNAHLQAGGTRADVRDAQLKEVLEFL--KRLRQPNSAPVVICGDFNVR 158

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1861233131 154 HKEIDIRNWKSnqknSGCLPEERAwltqlfdevgYVDVFRTLdprPDQYTWWSNR 208
Cdd:cd08372   159 PSEVDSENPSS----MLRLFVALN----------LVDSFETL---PHAYTFDTYM 196
L1-EN cd09076
Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; ...
 4-212 2.63e-17

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: 77.39  E-value: 2.63e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131   4 VITANLNGIRSAAK-KGFFDWLGDQKADCVCVQEIKVSADDLPPEfaAPHGFTGHFHHAEKKGYSGAGLYTRREPDDLII 82
Cdd:cd09076     1 IGTLNVRGLRSPGKrAQLLEELKRKKLDILGLQETHWTGEGELKK--KREGGTILYSGSDSGKSRGVAILLSKTAANKLL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131  83 GYgssEFDSEGRYVEAR----YGKLSVISVYVPSGSSGEERQQakfrFMAEFMPHLAELKAKKrEVILCGDVNIVHKEID 158
Cdd:cd09076    79 EY---TKVVSGRIIMVRfkikGKRLTIINVYAPTARDEEEKEE----FYDQLQDVLDKVPRHD-TLIIGGDFNAVLGPKD 150

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1861233131 159 IRNWKSNQKNSGclpEERAwLTQLFDEVGYVDVFRTLDPRPDQYTWWSNRGQAY 212
Cdd:cd09076   151 DGRKGLDKRNEN---GERA-LSALIEEHDLVDVWRENNPKTREYTWRSPDHGSR 200
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 5-152 7.55e-15

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


Pssm-ID: 460902 [Multi-domain]  Cd Length: 183  Bit Score: 69.56  E-value: 7.55e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131   5 ITANLNGIRSAA------KKGFFDWLGDQKADCVCVQEIKVSADDLPPE-FAAPHGFTGHFHHAEKKGYSGAGLYTRREP 77
Cdd:pfam03372   1 LTWNVNGGNADAagddrkLDALAALIRAYDPDVVALQETDDDDASRLLLaLLAYGGFLSYGGPGGGGGGGGVAILSRYPL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1861233131  78 DDLIIGYGSSEFDSEGRYVEARYGKLSVISVYVPSGSSGEERQQAKFRFMAEFMPHLAELKAKKREVILCGDVNI 152
Cdd:pfam03372  81 SSVILVDLGEFGDPALRGAIAPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALLAPRSEPVILAGDFNA 155
YafD COG3021
Uncharacterized conserved protein YafD, endonuclease/exonuclease/phosphatase (EEP) superfamily ...
 2-153 2.63e-06

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


Pssm-ID: 442257 [Multi-domain]  Cd Length: 310  Bit Score: 46.91  E-value: 2.63e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131   2 LRVITANLNGiRSAAKKGFFDWLGDQKADCVCVQEIKVSADDLPPEFAA--PHgftgHFHHAEKKGYsGAGLYTRREpdd 79
Cdd:COG3021    95 LRVLTANVLF-GNADAEALAALVREEDPDVLVLQETTPAWEEALAALEAdyPY----RVLCPLDNAY-GMALLSRLP--- 165

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1861233131  80 lIIGYGSSEFDSEGRY-----VEARYGKLSVISVYVPSGSSGEERQQAKFRFMAEfmphlaELKAKKREVILCGDVNIV 153
Cdd:COG3021   166 -LTEAEVVYLVGDDIPsiratVELPGGPVRLVAVHPAPPVGGSAERDAELAALAK------AVAALDGPVIVAGDFNAT 237
TDP2 cd09080
Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related ...
 2-204 6.55e-06

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: 45.41  E-value: 6.55e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131   2 LRVITANLNG---IRSAAK-KGFFDWLGDQKADCVCVQEikVSADDLPPEFAAPH-----GFTGHFHHAEKKGYsGAGLY 72
Cdd:cd09080     1 LKVLTWNVDFlddVNLAERmRAILKLLEELDPDVIFLQE--VTPPFLAYLLSQPWvrknyYFSEGPPSPAVDPY-GVLIL 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131  73 TRREPDDLIIGYGSSEFDSEGRYVEARYG---KLSVISVYVPSGSSGEERQQAKFRFMAEFMPHLAelkaKKREVILCGD 149
Cdd:cd09080    78 SKKSLVVRRVPFTSTRMGRNLLAAEINLGsgePLRLATTHLESLKSHSSERTAQLEEIAKKLKKPP----GAANVILGGD 153

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1861233131 150 VNIVHKEIDIrnwksnqknsgclpeerawltqLFDEVGYVDVFRTLDPRPDQ-YTW 204
Cdd:cd09080   154 FNLRDKEDDT----------------------GGLPNGFVDAWEELGPPGEPgYTW 187
R1-I-EN cd09077
Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat ...
 2-210 7.12e-04

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: 39.20  E-value: 7.12e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131   2 LRVITANLNGIRSAakkgfFDWLGD----QKADCVCVQEIKVsaddlppefaaPHGFTGHFHHAEKKGysgAGLYTRREP 77
Cdd:cd09077     1 LRILQINLNRCKAA-----QDLLLQtareEGADIALIQEPYL-----------VPVNNPNWVTDESGR---AAIVVSDRL 61

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131  78 DDLIIgygsSEFDSEGRYVEARYGKLSVISVYVPSGSSgeerqqakfrfMAEFMPHLAELKAKK----REVILCGDVNIV 153
Cdd:cd09077    62 PRKPI----QRLSLGLGIVAARVGGITVVSCYAPPSES-----------LEEFEEYLENLVRIVrglsRPVIIGGDFNAW 126

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1861233131 154 HKEidirnWKSNQKNS-GCLpeerawLTQLFDEVGYVdvfrtLDPRPDQYTWWSNRGQ 210
Cdd:cd09077   127 SPA-----WGSKRTDRrGRL------LEDWIANLGLV-----LLNDGNSPTFVRPRGT 168
EEP-2 cd09084
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This ...
 17-151 4.11e-03

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: 37.28  E-value: 4.11e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131  17 KKGFFDWLGDQKADCVCVQEIKVSADDLPPEFAA-----PHGFtghFHHAEKKGYSGAGLYTRREpddlIIGYGSSEFDS 91
Cdd:cd09084    18 PDKILDFIKKQDPDILCLQEYYGSEGDKDDDLRLllkgyPYYY---VVYKSDSGGTGLAIFSKYP----ILNSGSIDFPN 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1861233131  92 EGR---YVEARYGK--LSVISVYVPS----------GSSGEERQQAKFRFMAEFMPH-----------LAELKAKKREVI 145
Cdd:cd09084    91 TNNnaiFADIRVGGdtIRVYNVHLESfritpsdkelYKEEKKAKELSRNLLRKLAEAfkrraaqadllAADIAASPYPVI 170


                  ....*.
gi 1861233131 146 LCGDVN 151
Cdd:cd09084   171 VCGDFN 176
 
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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