NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|738887299|ref|WP_036774910|]
View 

exodeoxyribonuclease III [Photorhabdus australis]

Protein Classification

exodeoxyribonuclease III( domain architecture ID 10013876)

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

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PRK11756 PRK11756
exonuclease III; Provisional
 1-268 0e+00

exonuclease III; Provisional


:

Pssm-ID: 236970 [Multi-domain]  Cd Length: 268  Bit Score: 611.51  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299   1 MKFISFNINGLRARPHQLAAIVELHQPDVIGLQETKVHDEMFPLEEVSKLGYHVFYYGQKAHYGVALLTRQAPIAVRRGF 80
Cdd:PRK11756   1 MKFVSFNINGLRARPHQLEAIIEKHQPDVIGLQETKVHDEMFPLEEVEALGYHVFYHGQKGHYGVALLSKQTPIAVRKGF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299  81 PGDDEDSQRRIIMADLETPHGLLTVINGYFPQGENRDHPVKFPAKEKFYQDLQSYLEQNLSPQSQVIIMGDMNISPTDLD 160
Cdd:PRK11756  81 PTDDEEAQRRIIMATIPTPNGNLTVINGYFPQGESRDHPTKFPAKRQFYQDLQNYLETELSPDNPLLIMGDMNISPTDLD 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299 161 IGIGDNNQKRWLKTGKCSFLPEERDWMDRLKNWGLVDTFRRLNPECNDQFSWFDYRSKGFDDNRGLRIDLLLASKPLVER 240
Cdd:PRK11756 161 IGIGEENRKRWLRTGKCSFLPEEREWLDRLMDWGLVDTFRQLNPDVNDRFSWFDYRSKGFDDNRGLRIDLILATQPLAER 240

                        250       260
                 ....*....|....*....|....*...
gi 738887299 241 CIATGIDYKIREMEKPSDHAPVWAEFEI 268
Cdd:PRK11756 241 CVETGIDYDIRGMEKPSDHAPIWATFKL 268
 
Name Accession Description Interval E-value
PRK11756 PRK11756
exonuclease III; Provisional
 1-268 0e+00

exonuclease III; Provisional


Pssm-ID: 236970 [Multi-domain]  Cd Length: 268  Bit Score: 611.51  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299   1 MKFISFNINGLRARPHQLAAIVELHQPDVIGLQETKVHDEMFPLEEVSKLGYHVFYYGQKAHYGVALLTRQAPIAVRRGF 80
Cdd:PRK11756   1 MKFVSFNINGLRARPHQLEAIIEKHQPDVIGLQETKVHDEMFPLEEVEALGYHVFYHGQKGHYGVALLSKQTPIAVRKGF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299  81 PGDDEDSQRRIIMADLETPHGLLTVINGYFPQGENRDHPVKFPAKEKFYQDLQSYLEQNLSPQSQVIIMGDMNISPTDLD 160
Cdd:PRK11756  81 PTDDEEAQRRIIMATIPTPNGNLTVINGYFPQGESRDHPTKFPAKRQFYQDLQNYLETELSPDNPLLIMGDMNISPTDLD 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299 161 IGIGDNNQKRWLKTGKCSFLPEERDWMDRLKNWGLVDTFRRLNPECNDQFSWFDYRSKGFDDNRGLRIDLLLASKPLVER 240
Cdd:PRK11756 161 IGIGEENRKRWLRTGKCSFLPEEREWLDRLMDWGLVDTFRQLNPDVNDRFSWFDYRSKGFDDNRGLRIDLILATQPLAER 240

                        250       260
                 ....*....|....*....|....*...
gi 738887299 241 CIATGIDYKIREMEKPSDHAPVWAEFEI 268
Cdd:PRK11756 241 CVETGIDYDIRGMEKPSDHAPIWATFKL 268
XthA COG0708
Exonuclease III [Replication, recombination and repair];
1-267 4.21e-138

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 389.05  E-value: 4.21e-138
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299   1 MKFISFNINGLRARPHQLAAIVELHQPDVIGLQETKVHDEMFPLEEVSKLGYHVFYYGQKAHYGVALLTRQAPIAVRRGF 80
Cdd:COG0708    1 MKIASWNVNGIRARLPKLLDWLAEEDPDVLCLQETKAQDEQFPLEAFEAAGYHVYFHGQKGYNGVAILSRLPPEDVRRGL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299  81 PGDDEDSQRRIIMADLETphglLTVINGYFPQGENRDHPvKFPAKEKFYQDLQSYLEQNLSPQSQVIIMGDMNISPTDLD 160
Cdd:COG0708   81 GGDEFDAEGRYIEADFGG----VRVVSLYVPNGGSVGSE-KFDYKLRFLDALRAYLAELLAPGRPLILCGDFNIAPTEID 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299 161 IgigdNNQKRWLKtgKCSFLPEERDWMDRLKNWGLVDTFRRLNPECNDQFSWFDYRSKGFDDNRGLRIDLLLASKPLVER 240
Cdd:COG0708  156 V----KNPKANLK--NAGFLPEERAWFDRLLELGLVDAFRALHPDVEGQYTWWSYRAGAFARNRGWRIDYILASPALADR 229

                        250       260
                 ....*....|....*....|....*..
gi 738887299 241 CIATGIDYKIREMEKPSDHAPVWAEFE 267
Cdd:COG0708  230 LKDAGIDREPRGDERPSDHAPVVVELD 256
ExoIII-like_AP-endo cd09086
Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of ...
 1-266 7.18e-132

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: 373.00  E-value: 7.18e-132
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299   1 MKFISFNINGLRARPHQLAAIVELHQPDVIGLQETKVHDEMFPLEEVSKLGYHVFYYGQKAHYGVALLTRQAPIAVRRGF 80
Cdd:cd09086    1 MKIATWNVNSIRARLEQVLDWLKEEDPDVLCLQETKVEDDQFPADAFEALGYHVAVHGQKAYNGVAILSRLPLEDVRTGF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299  81 PGDDEDSQRRIIMADLetphGLLTVINGYFPQGENRDHPvKFPAKEKFYQDLQSYLEQNLSPQSQVIIMGDMNISPTDLD 160
Cdd:cd09086   81 PGDPDDDQARLIAARV----GGVRVINLYVPNGGDIGSP-KFAYKLDWLDRLIRYLQKLLKPDDPLVLVGDFNIAPEDID 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299 161 IGIGdnnqKRWLktGKCSFLPEERDWMDRLKNWGLVDTFRRLNPEcNDQFSWFDYRSKGFDDNRGLRIDLLLASKPLVER 240
Cdd:cd09086  156 VWDP----KQLL--GKVLFTPEEREALRALLDLGFVDAFRALHPD-EKLFTWWDYRAGAFERNRGLRIDHILASPALADR 228

                        250       260
                 ....*....|....*....|....*.
gi 738887299 241 CIATGIDYKIREMEKPSDHAPVWAEF 266
Cdd:cd09086  229 LKDVGIDREPRGWEKPSDHAPVVAEL 254
exoDNase_III TIGR00195
exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model ...
 1-266 2.98e-131

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: 371.72  E-value: 2.98e-131
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299    1 MKFISFNINGLRARPHQLAAIVELHQPDVIGLQETKVHDEMFPLEEVSKLGYHVFYYGQKAHYGVALLTRQAPIAVRRGF 80
Cdd:TIGR00195   1 MKIISWNVNGLRARPHKGLAWLKENQPDVLCLQETKVQDEQFPLEPFHKEGYHVFFSGQKGYSGVAIFSKEEPISVRRGF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299   81 PGDDEDSQRRIIMADLETphglLTVINGYFPQGeNRDHPVKFPAKEKFYQDLQSYLEQNLSPQSQVIIMGDMNISPTDLD 160
Cdd:TIGR00195  81 GVEEEDAEGRIIMAEFDS----FLVINGYFPNG-SRDDSEKLPYKLQWLEALQNYLEKLVDKDKPVLICGDMNIAPTEID 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299  161 IGIGDNNQKRwlkTGkcsFLPEERDWMDRLKNWGLVDTFRRLNPEcNDQFSWFDYRSKGFDDNRGLRIDLLLASKPLVER 240
Cdd:TIGR00195 156 LHIPDENRNH---TG---FLPEEREWLDRLLEAGLVDTFRKFNPD-EGAYSWWDYRTKARDRNRGWRIDYFLVSEPLKER 228

                         250       260
                  ....*....|....*....|....*.
gi 738887299  241 CIATGIDYKIREMEKPSDHAPVWAEF 266
Cdd:TIGR00195 229 CVDCGIDYDIRGSEKPSDHCPVVLEF 254
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 4-154 9.39e-20

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: 84.20  E-value: 9.39e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299    4 ISFNINGLRARP-------HQLAAIVELHQPDVIGLQETKVHDEMFPLEEVSKLGYHVFYY---GQKAHYGVALLTRQAP 73
Cdd:pfam03372   1 LTWNVNGGNADAagddrklDALAALIRAYDPDVVALQETDDDDASRLLLALLAYGGFLSYGgpgGGGGGGGVAILSRYPL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299   74 IAVRRGFPGDDEDSQRRIIMADLETPHGLLTVINGyfpqgeNRDHPVKFPAKEKFYQDLQSYLEQNLSPQSQVIIMGDMN 153
Cdd:pfam03372  81 SSVILVDLGEFGDPALRGAIAPFAGVLVVPLVLTL------APHASPRLARDEQRADLLLLLLALLAPRSEPVILAGDFN 154


                  .
gi 738887299  154 I 154
Cdd:pfam03372 155 A 155
 
Name Accession Description Interval E-value
PRK11756 PRK11756
exonuclease III; Provisional
 1-268 0e+00

exonuclease III; Provisional


Pssm-ID: 236970 [Multi-domain]  Cd Length: 268  Bit Score: 611.51  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299   1 MKFISFNINGLRARPHQLAAIVELHQPDVIGLQETKVHDEMFPLEEVSKLGYHVFYYGQKAHYGVALLTRQAPIAVRRGF 80
Cdd:PRK11756   1 MKFVSFNINGLRARPHQLEAIIEKHQPDVIGLQETKVHDEMFPLEEVEALGYHVFYHGQKGHYGVALLSKQTPIAVRKGF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299  81 PGDDEDSQRRIIMADLETPHGLLTVINGYFPQGENRDHPVKFPAKEKFYQDLQSYLEQNLSPQSQVIIMGDMNISPTDLD 160
Cdd:PRK11756  81 PTDDEEAQRRIIMATIPTPNGNLTVINGYFPQGESRDHPTKFPAKRQFYQDLQNYLETELSPDNPLLIMGDMNISPTDLD 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299 161 IGIGDNNQKRWLKTGKCSFLPEERDWMDRLKNWGLVDTFRRLNPECNDQFSWFDYRSKGFDDNRGLRIDLLLASKPLVER 240
Cdd:PRK11756 161 IGIGEENRKRWLRTGKCSFLPEEREWLDRLMDWGLVDTFRQLNPDVNDRFSWFDYRSKGFDDNRGLRIDLILATQPLAER 240

                        250       260
                 ....*....|....*....|....*...
gi 738887299 241 CIATGIDYKIREMEKPSDHAPVWAEFEI 268
Cdd:PRK11756 241 CVETGIDYDIRGMEKPSDHAPIWATFKL 268
XthA COG0708
Exonuclease III [Replication, recombination and repair];
1-267 4.21e-138

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 389.05  E-value: 4.21e-138
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299   1 MKFISFNINGLRARPHQLAAIVELHQPDVIGLQETKVHDEMFPLEEVSKLGYHVFYYGQKAHYGVALLTRQAPIAVRRGF 80
Cdd:COG0708    1 MKIASWNVNGIRARLPKLLDWLAEEDPDVLCLQETKAQDEQFPLEAFEAAGYHVYFHGQKGYNGVAILSRLPPEDVRRGL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299  81 PGDDEDSQRRIIMADLETphglLTVINGYFPQGENRDHPvKFPAKEKFYQDLQSYLEQNLSPQSQVIIMGDMNISPTDLD 160
Cdd:COG0708   81 GGDEFDAEGRYIEADFGG----VRVVSLYVPNGGSVGSE-KFDYKLRFLDALRAYLAELLAPGRPLILCGDFNIAPTEID 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299 161 IgigdNNQKRWLKtgKCSFLPEERDWMDRLKNWGLVDTFRRLNPECNDQFSWFDYRSKGFDDNRGLRIDLLLASKPLVER 240
Cdd:COG0708  156 V----KNPKANLK--NAGFLPEERAWFDRLLELGLVDAFRALHPDVEGQYTWWSYRAGAFARNRGWRIDYILASPALADR 229

                        250       260
                 ....*....|....*....|....*..
gi 738887299 241 CIATGIDYKIREMEKPSDHAPVWAEFE 267
Cdd:COG0708  230 LKDAGIDREPRGDERPSDHAPVVVELD 256
ExoIII-like_AP-endo cd09086
Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of ...
 1-266 7.18e-132

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: 373.00  E-value: 7.18e-132
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299   1 MKFISFNINGLRARPHQLAAIVELHQPDVIGLQETKVHDEMFPLEEVSKLGYHVFYYGQKAHYGVALLTRQAPIAVRRGF 80
Cdd:cd09086    1 MKIATWNVNSIRARLEQVLDWLKEEDPDVLCLQETKVEDDQFPADAFEALGYHVAVHGQKAYNGVAILSRLPLEDVRTGF 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299  81 PGDDEDSQRRIIMADLetphGLLTVINGYFPQGENRDHPvKFPAKEKFYQDLQSYLEQNLSPQSQVIIMGDMNISPTDLD 160
Cdd:cd09086   81 PGDPDDDQARLIAARV----GGVRVINLYVPNGGDIGSP-KFAYKLDWLDRLIRYLQKLLKPDDPLVLVGDFNIAPEDID 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299 161 IGIGdnnqKRWLktGKCSFLPEERDWMDRLKNWGLVDTFRRLNPEcNDQFSWFDYRSKGFDDNRGLRIDLLLASKPLVER 240
Cdd:cd09086  156 VWDP----KQLL--GKVLFTPEEREALRALLDLGFVDAFRALHPD-EKLFTWWDYRAGAFERNRGLRIDHILASPALADR 228

                        250       260
                 ....*....|....*....|....*.
gi 738887299 241 CIATGIDYKIREMEKPSDHAPVWAEF 266
Cdd:cd09086  229 LKDVGIDREPRGWEKPSDHAPVVAEL 254
exoDNase_III TIGR00195
exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model ...
 1-266 2.98e-131

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: 371.72  E-value: 2.98e-131
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299    1 MKFISFNINGLRARPHQLAAIVELHQPDVIGLQETKVHDEMFPLEEVSKLGYHVFYYGQKAHYGVALLTRQAPIAVRRGF 80
Cdd:TIGR00195   1 MKIISWNVNGLRARPHKGLAWLKENQPDVLCLQETKVQDEQFPLEPFHKEGYHVFFSGQKGYSGVAIFSKEEPISVRRGF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299   81 PGDDEDSQRRIIMADLETphglLTVINGYFPQGeNRDHPVKFPAKEKFYQDLQSYLEQNLSPQSQVIIMGDMNISPTDLD 160
Cdd:TIGR00195  81 GVEEEDAEGRIIMAEFDS----FLVINGYFPNG-SRDDSEKLPYKLQWLEALQNYLEKLVDKDKPVLICGDMNIAPTEID 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299  161 IGIGDNNQKRwlkTGkcsFLPEERDWMDRLKNWGLVDTFRRLNPEcNDQFSWFDYRSKGFDDNRGLRIDLLLASKPLVER 240
Cdd:TIGR00195 156 LHIPDENRNH---TG---FLPEEREWLDRLLEAGLVDTFRKFNPD-EGAYSWWDYRTKARDRNRGWRIDYFLVSEPLKER 228

                         250       260
                  ....*....|....*....|....*.
gi 738887299  241 CIATGIDYKIREMEKPSDHAPVWAEF 266
Cdd:TIGR00195 229 CVDCGIDYDIRGSEKPSDHCPVVLEF 254
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 1-267 2.76e-123

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: 351.58  E-value: 2.76e-123
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299    1 MKFISFNINGLRARPHQLA-AIVELHQPDVIGLQETKVHDEMFPLEEVSKLGYHVFYYGQKA-HYGVALLTRQAPIAVRR 78
Cdd:TIGR00633   1 MKIISWNVNGLRARLHKLFlDWLKEEQPDVLCLQETKVADEQFPAELFEELGYHVFFHGAKKgYSGVAILSKVEPLDVRY 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299   79 GFPGDDEDSQRRIIMADLetphGLLTVINGYFPQGENRDHPvKFPAKEKFYQDLQSYLEQNLSPQSQVIIMGDMNISPTD 158
Cdd:TIGR00633  81 GFGGEPHDEEGRVITAEF----DGFTVVNVYVPNGGSRDLE-RLEYKLQFWDALFQYLEKELDAGKPVVICGDMNVAHTE 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299  159 LDIGIGDNNqkrwlkTGKCSFLPEERDWMDRLKNWGLVDTFRRLNPECNDQFSWFDYRSKGFDDNRGLRIDLLLASKPLV 238
Cdd:TIGR00633 156 IDLGNPKEN------KGNAGFTPEEREWFDELLEAGFVDTFRHFNPDTGDAYTWWDYRSGARDRNRGWRIDYFLVSEPLA 229

                         250       260
                  ....*....|....*....|....*....
gi 738887299  239 ERCIATGIDYKIREmekpSDHAPVWAEFE 267
Cdd:TIGR00633 230 ERVVDSYIDSEIRG----SDHCPIVLELD 254
ExoIII_AP-endo cd09073
Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ...
 2-266 8.11e-106

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: 306.91  E-value: 8.11e-106
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299   2 KFISFNINGLRARPH-QLAAIVELHQPDVIGLQETKVHDEMFPLEEVSKLGYHVFYYGQ--KAHYGVALLTRQAPIAVRR 78
Cdd:cd09073    1 KIISWNVNGLRARLKkGVLKWLKEEKPDILCLQETKADEDKLPEELQHVEGYHSYWSPArkKGYSGVATLSKEEPLDVSY 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299  79 GFPGDDEDSQRRIIMADLETphglLTVINGYFPQGENRdhPVKFPAKEKFYQDLQSYLEQNLSPQSQVIIMGDMNISPTD 158
Cdd:cd09073   81 GIGGEEFDSEGRVITAEFDD----FYLINVYFPNGGRG--LERLDYKLRFYEAFLEFLEKLRKRGKPVVICGDFNVAHEE 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299 159 LDIGIGDNNQKRWlktgkcSFLPEERDWMDRLKNWGLVDTFRRLNPEcNDQFSWFDYRSKGFDDNRGLRIDLLLASKPLV 238
Cdd:cd09073  155 IDLARPKKNEKNA------GFTPEERAWFDKLLSLGYVDTFRHFHPE-PGAYTWWSYRGNARERNVGWRIDYFLVSEELA 227

                        250       260
                 ....*....|....*....|....*...
gi 738887299 239 ERCIATGIDYKIremeKPSDHAPVWAEF 266
Cdd:cd09073  228 EKVKDSGILSKV----KGSDHAPVTLEL 251
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This ...
 1-266 6.60e-60

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: 190.46  E-value: 6.60e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299   1 MKFISFNINGLRAR-PHQLAAIVELHQPDVIGLQETKVHDEMFPLEEVSKL-GYHVFY-YGQKAHY-GVALLTRQAPIAV 76
Cdd:cd09087    1 LKIISWNVNGLRALlKKGLLDYVKKEDPDILCLQETKLQEGDVPKELKELLkGYHQYWnAAEKKGYsGTAILSKKKPLSV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299  77 RRGFPGDDEDSQRRIIMADLETphglLTVINGYFP---QGENRdhpvkFPAKEKFYQDLQSYLeQNLSPQSQVIIMGDMN 153
Cdd:cd09087   81 TYGIGIEEHDQEGRVITAEFEN----FYLVNTYVPnsgRGLER-----LDRRKEWDVDFRAYL-KKLDSKKPVIWCGDLN 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299 154 ISPTDLDIGIGDNNQKrwlktgKCSFLPEERDWMDRLKNWGLVDTFRRLNPECNDQFSWFDYRSKGFDDNRGLRIDLLLA 233
Cdd:cd09087  151 VAHEEIDLANPKTNKK------SAGFTPEERESFTELLEAGFVDTFRHLHPDKEGAYTFWSYRGNARAKNVGWRLDYFLV 224

                        250       260       270
                 ....*....|....*....|....*....|...
gi 738887299 234 SKPLVERciatGIDYKIREMEKPSDHAPVWAEF 266
Cdd:cd09087  225 SERLKDR----VVDSFIRSDIMGSDHCPIGLEL 253
Nape_like_AP-endo cd10281
Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) ...
 1-266 2.48e-58

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: 186.28  E-value: 2.48e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299   1 MKFISFNINGLRArphqlAA------IVELHQPDVIGLQETKVHDEMFPLEEVSKLGYHVFY-YGQKAHY-GVALLTRQA 72
Cdd:cd10281    1 MRVISVNVNGIRA-----AAkkgfleWLAAQDADVVCLQEVRAQEEQLDDDFFEPEGYNAYFfDAEKKGYaGVAIYSRTQ 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299  73 PIAVRRGFPGDDEDSQRRIIMADLETphglLTVINGYFPQGENRDhpVKFPAKEKFYQDLQSYLEQNLSPQSQVIIMGDM 152
Cdd:cd10281   76 PKAVIYGLGFEEFDDEGRYIEADFDN----VSVASLYVPSGSSGD--ERQEAKMAFLDAFLEHLKELRRKRREFIVCGDF 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299 153 NISPTDLDIGIGDNNQKrwlKTGkcsFLPEERDWMDRL-KNWGLVDTFRRLNPEcNDQFSWFDYRSKGFDDNRGLRIDLL 231
Cdd:cd10281  150 NIAHTEIDIKNWKANQK---NSG---FLPEERAWLDQVfGELGYVDAFRELNPD-EGQYTWWSNRGQARANNVGWRIDYQ 222

                        250       260       270
                 ....*....|....*....|....*....|....*
gi 738887299 232 LASKPLVERCIATGIDykiREmEKPSDHAPVWAEF 266
Cdd:cd10281  223 IATPGLASKVVSAWIY---RE-ERFSDHAPLIVDY 253
Mth212-like_AP-endo cd09085
Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic ...
 1-265 2.78e-56

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: 180.94  E-value: 2.78e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299   1 MKFISFNINGLRA-RPHQLAAIVELHQPDVIGLQETKVHDEMFPLEEVSKLGYHVFY-YGQKAHY-GVALLTRQAPIAVR 77
Cdd:cd09085    1 MKIISWNVNGLRAvHKKGFLDWFKEEKPDILCLQETKAQPEQLPEDLRNIEGYHSYFnSAERKGYsGVALYSKIEPDSVR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299  78 RGFPGDDEDSQRRIIMADLETphglLTVINGYFPQGENRDHPVKFpaKEKFYQDLQSYLEQNLSPQSQVIIMGDMNISPT 157
Cdd:cd09085   81 EGLGVEEFDNEGRILIADFDD----FTLFNIYFPNGQMSEERLDY--KLEFYDAFLEYLNELRDSGKNVIICGDFNTAHK 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299 158 DLDIGIGDNNQKrwlKTGkcsFLPEERDWMDRLKNWGLVDTFRRLNPEcNDQFSWFDYRSKGFDDNRGLRIDLLLASKPL 237
Cdd:cd09085  155 EIDLARPKENEK---VSG---FLPEERAWMDKFIENGYVDTFRMFNKE-PGQYTWWSYRTRARERNVGWRIDYFFVNEEF 227

                        250       260
                 ....*....|....*....|....*...
gi 738887299 238 VERCIATGIDYKIREmekpSDHAPVWAE 265
Cdd:cd09085  228 KPKVKDAGILPDVMG----SDHCPVSLE 251
Ape2-like_AP-endo cd09088
Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This ...
 2-266 3.46e-32

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: 120.11  E-value: 3.46e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299   2 KFISFNINGLRARPHQ--------LAAIVELHQPDVIGLQETKVHDEMFPLEEVSKLGYHVFY---YGQKAHYGVALLTR 70
Cdd:cd09088    1 RIVTWNVNGIRTRLQYqpwnkensLKSFLDSLDADIICLQETKLTRDELDEPSAIVEGYDSFFsfsRGRKGYSGVATYCR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299  71 ---QAPIAVRRGFPG---------------------DDEDSQRRIIMADLE-------TPHGLLTVINGYFP----QGEN 115
Cdd:cd09088   81 dsaATPVAAEEGLTGvlsspnqknelsenddigcygEMLEFTDSKELLELDsegrcvlTDHGTFVLINVYCPradpEKEE 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299 116 RDhpvKFpaKEKFYQDLQSYLEQNLSPQSQVIIMGDMNISPTDLD------------IGIGDNNQKRWLKtgkcSFL--P 181
Cdd:cd09088  161 RL---EF--KLDFYRLLEERVEALLKAGRRVILVGDVNVSHRPIDhcdpddsedfggESFEDNPSRQWLD----QLLgdS 231

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299 182 EERDWMDRLKnwgLVDTFRRLNPECNDQFSWFDYRSKGFDDNRGLRIDLLLASKPLVERCIATGIDYKIREmekpSDHAP 261
Cdd:cd09088  232 GEGGGSPGGL---LIDSFRYFHPTRKGAYTCWNTLTGARPTNYGTRIDYILADRGLLPWVKAADILPEVEG----SDHCP 304


                 ....*
gi 738887299 262 VWAEF 266
Cdd:cd09088  305 VYADL 309
L1-EN cd09076
Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; ...
 3-266 1.44e-30

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: 113.99  E-value: 1.44e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299   3 FISFNINGLR--ARPHQLAAIVELHQPDVIGLQETKvHDEMFPLEEVSKLGYHVFYYGQKAHY-GVALLTRQAPIAVRRG 79
Cdd:cd09076    1 IGTLNVRGLRspGKRAQLLEELKRKKLDILGLQETH-WTGEGELKKKREGGTILYSGSDSGKSrGVAILLSKTAANKLLE 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299  80 FPGDDEDsqrRIIMADLETPHGLLTVINGYFPqgeNRDHPvkfPAKEKFYQDLQSYLeQNLSPQSQVIIMGDMN--ISPT 157
Cdd:cd09076   80 YTKVVSG---RIIMVRFKIKGKRLTIINVYAP---TARDE---EEKEEFYDQLQDVL-DKVPRHDTLIIGGDFNavLGPK 149

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299 158 DLDI-GIGDNNQKrwlktgkcsflpEERDWMDRLKNWGLVDTFRRLNPECNdQFSWfdyRSKGFDDNRglRIDLLLASKP 236
Cdd:cd09076  150 DDGRkGLDKRNEN------------GERALSALIEEHDLVDVWRENNPKTR-EYTW---RSPDHGSRS--RIDRILVSKR 211

                        250       260       270
                 ....*....|....*....|....*....|
gi 738887299 237 LVERCIATGIDYKIremekPSDHAPVWAEF 266
Cdd:cd09076  212 LRVKVKKTKITPGA-----GSDHRLVTLKL 236
EEP cd08372
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 4-265 1.63e-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: 98.32  E-value: 1.63e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299   4 ISFNINGLRA--RPHQLAAIVELHQPDVIGLQETKVHDEMFPLEEVSKLGYHvFYYGQKAHY-----GVALLTR---QAP 73
Cdd:cd08372    2 ASYNVNGLNAatRASGIARWVRELDPDIVCLQEVKDSQYSAVALNQLLPEGY-HQYQSGPSRkegyeGVAILSKtpkFKI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299  74 IAVRRGFPGDDEDSQRRIIMADLETPHGLLTVINGYFPQGENRDHpVKFPAKEKFYQDLQSYLEQNLSPqsqVIIMGDMN 153
Cdd:cd08372   81 VEKHQYKFGEGDSGERRAVVVKFDVHDKELCVVNAHLQAGGTRAD-VRDAQLKEVLEFLKRLRQPNSAP---VVICGDFN 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299 154 ISPTDLDigigdnnqkrwlktgkcsfLPEERDWMDRLKNWGLVDTFRrlnpECNDQFSWfdyrsKGFDDNRGLRIDLLLA 233
Cdd:cd08372  157 VRPSEVD-------------------SENPSSMLRLFVALNLVDSFE----TLPHAYTF-----DTYMHNVKSRLDYIFV 208

                        250       260       270
                 ....*....|....*....|....*....|..
gi 738887299 234 SKPLVERCIATGIDYKIREMEKPSDHAPVWAE 265
Cdd:cd08372  209 SKSLLPSVKSSKILSDAARARIPSDHYPIEVT 240
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 1-266 5.35e-24

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 97.07  E-value: 5.35e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299   1 MKFISFNINGLRA-RPHQLAAIVELHQPDVIGLQETKVHDEMFPLEEVsklGYHVFYYG--QKAHYGVALLTRQAPIAVR 77
Cdd:PRK13911   1 MKLISWNVNGLRAcMTKGFMDFFNSVDADVFCIQESKMQQEQNTFEFK---GYFDFWNCaiKKGYSGVVTFTKKEPLSVS 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299  78 RGFPGDDEDSQRRIIMADLETphglLTVINGYFPQGENRDHPVKFpaKEKFYQDLQSYLEQnLSPQSQVIIMGDMNISPT 157
Cdd:PRK13911  78 YGINIEEHDKEGRVITCEFES----FYLVNVYTPNSQQALSRLSY--RMSWEVEFKKFLKA-LELKKPVIVCGDLNVAHN 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299 158 DLDIGIGDNNQKrwlktgKCSFLPEERDWMDRLKNWGLVDTFRRLNPECNDQFSWFDYRSKGFDDNRGLRIDLLLASKPL 237
Cdd:PRK13911 151 EIDLENPKTNRK------NAGFSDEERGKFSELLNAGFIDTFRYFYPNKEKAYTWWSYMQQARDKNIGWRIDYFLCSNPL 224

                        250       260
                 ....*....|....*....|....*....
gi 738887299 238 VERCiatgIDYKIREMEKPSDHAPVWAEF 266
Cdd:PRK13911 225 KTRL----KDALIYKDILGSDHCPVGLEL 249
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 4-154 9.39e-20

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: 84.20  E-value: 9.39e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299    4 ISFNINGLRARP-------HQLAAIVELHQPDVIGLQETKVHDEMFPLEEVSKLGYHVFYY---GQKAHYGVALLTRQAP 73
Cdd:pfam03372   1 LTWNVNGGNADAagddrklDALAALIRAYDPDVVALQETDDDDASRLLLALLAYGGFLSYGgpgGGGGGGGVAILSRYPL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299   74 IAVRRGFPGDDEDSQRRIIMADLETPHGLLTVINGyfpqgeNRDHPVKFPAKEKFYQDLQSYLEQNLSPQSQVIIMGDMN 153
Cdd:pfam03372  81 SSVILVDLGEFGDPALRGAIAPFAGVLVVPLVLTL------APHASPRLARDEQRADLLLLLLALLAPRSEPVILAGDFN 154


                  .
gi 738887299  154 I 154
Cdd:pfam03372 155 A 155
YafD COG3021
Uncharacterized conserved protein YafD, endonuclease/exonuclease/phosphatase (EEP) superfamily ...
 1-266 2.85e-15

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


Pssm-ID: 442257 [Multi-domain]  Cd Length: 310  Bit Score: 73.88  E-value: 2.85e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299   1 MKFISFNINGLRARPHQLAAIVELHQPDVIGLQET--KVHDEMFPLEEVskLGYHVFyYGQKAHYGVALLTRqAPIAVRR 78
Cdd:COG3021   95 LRVLTANVLFGNADAEALAALVREEDPDVLVLQETtpAWEEALAALEAD--YPYRVL-CPLDNAYGMALLSR-LPLTEAE 170

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299  79 GFPGDDEDsqRRIIMADLETPHGLLTVINGyfpqgenrdHPVKfPAKEKFYQD-----LQSYLEQNLSPqsqVIIMGDMN 153
Cdd:COG3021  171 VVYLVGDD--IPSIRATVELPGGPVRLVAV---------HPAP-PVGGSAERDaelaaLAKAVAALDGP---VIVAGDFN 235

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299 154 ISPTDLDIgigdnnqKRWLKTGKCsflpeerdwMDRLKNWGLVDTFRRLNPecndqfswfdyrskgfddNRGLRIDLLLA 233
Cdd:COG3021  236 ATPWSPTL-------RRLLRASGL---------RDARAGRGLGPTWPANLP------------------FLRLPIDHVLV 281

                        250       260       270
                 ....*....|....*....|....*....|....
gi 738887299 234 SKPLVERciatgidyKIREMEKP-SDHAPVWAEF 266
Cdd:COG3021  282 SRGLTVV--------DVRVLPVIgSDHRPLLAEL 307
ElsH COG3568
Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function ...
 1-160 2.83e-11

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


Pssm-ID: 442789 [Multi-domain]  Cd Length: 167  Bit Score: 60.31  E-value: 2.83e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299   1 MKFISFNI-NGL----RARPHQLAAIVELHQPDVIGLQEtkvhdemfpleevsklgyhvfyygqkahygVALLTRQAPIA 75
Cdd:COG3568    8 LRVMTYNIrYGLgtdgRADLERIARVIRALDPDVVALQE------------------------------NAILSRYPIVS 57

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299  76 VRRGFPGDDEDSQRRIIMADLETPHGLLTVIN---GYFPQGENRDHpvkfpakekfYQDLQSYLEQnLSPQSQVIIMGDM 152
Cdd:COG3568   58 SGTFDLPDPGGEPRGALWADVDVPGKPLRVVNthlDLRSAAARRRQ----------ARALAELLAE-LPAGAPVILAGDF 126


                 ....*...
gi 738887299 153 NisptDLD 160
Cdd:COG3568  127 N----DID 130
TDP2 cd09080
Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related ...
 1-266 5.58e-11

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: 61.21  E-value: 5.58e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299   1 MKFISFNINGLRARPHQ-----LAAIVELHQPDVIGLQE-TKVHDEMFPLEEVSKLGYHVFYYGQKAH---YGVALLTRQ 71
Cdd:cd09080    1 LKVLTWNVDFLDDVNLAermraILKLLEELDPDVIFLQEvTPPFLAYLLSQPWVRKNYYFSEGPPSPAvdpYGVLILSKK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299  72 APIAVRRGFPgdDEDSQRRIIMADLETPHGL-LTVINGYFpqgenrDHPVKFPAK-----EKFYQDLQSYLEQNlspqsQ 145
Cdd:cd09080   81 SLVVRRVPFT--STRMGRNLLAAEINLGSGEpLRLATTHL------ESLKSHSSErtaqlEEIAKKLKKPPGAA-----N 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299 146 VIIMGDMNISPTDLDIGIGDNnqkrwlktgkcsflpeerdwmdrlknwGLVDTFRRLNPECNDQFSWfDYRSKGF----D 221
Cdd:cd09080  148 VILGGDFNLRDKEDDTGGLPN---------------------------GFVDAWEELGPPGEPGYTW-DTQKNPMlrkgE 199

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 738887299 222 DNRGLRIDLLLAsKPLVERCIATGI--DYKIREMEK---PSDHAPVWAEF 266
Cdd:cd09080  200 AGPRKRFDRVLL-RGSDLKPKSIELigTEPIPGDEEglfPSDHFGLLAEL 248
EEP-2 cd09084
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This ...
 5-266 1.74e-09

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: 56.54  E-value: 1.74e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299   5 SFNINGLRARPHQLAAIVELHQPDVIGLQETkVHDEMFPLEEVSKL-----GYHVFYYGQKAHYGVALLTRQaPIAVRRG 79
Cdd:cd09084    8 SFNRYKWKDDPDKILDFIKKQDPDILCLQEY-YGSEGDKDDDLRLLlkgypYYYVVYKSDSGGTGLAIFSKY-PILNSGS 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299  80 FPGDDEDSQRriIMADLETPHGLLTVINGYFPQGENRDHPVKFPAKEKFYQDLQSYLEQNLSP-----QSQ--------- 145
Cdd:cd09084   86 IDFPNTNNNA--IFADIRVGGDTIRVYNVHLESFRITPSDKELYKEEKKAKELSRNLLRKLAEafkrrAAQadllaadia 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299 146 -----VIIMGDMN---ISPTdldigigdnnqkrwlktgkcsflpeerdwMDRLKNwGLVDTFRrlnpECNDQFSWfDYRS 217
Cdd:cd09084  164 aspypVIVCGDFNdtpASYV-----------------------------YRTLKK-GLTDAFV----EAGSGFGY-TFNG 208

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 738887299 218 KGFddnrGLRIDLLLASKPL-VERCIATGIDYkiremekpSDHAPVWAEF 266
Cdd:cd09084  209 LFF----PLRIDYILTSKGFkVLRYRVDPGKY--------SDHYPIVATL 246
RgfB-like cd09079
Streptococcus agalactiae RgfB, part of a putative two component signal transduction system, ...
 18-153 1.32e-07

Streptococcus agalactiae RgfB, part of a putative two component signal transduction system, and related proteins; This family includes Streptococcus agalactiae RgfB (for regulator of fibrinogen binding) and related proteins. The function of RgfB is unknown. It is part of a putative two component signal transduction system designated rgfBDAC (the rgf locus was identified in a screen for mutants of Streptococcus agalactiae with altered binding to fibrinogen). RgfA,-C,and -D do not belong to this superfamily: rgfA encodes a putative response regulator, and rgfC, a putative histidine kinase. All four genes are co-transcribed, and may be involved in regulating expression of bacterial cell surface components. 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: 197313 [Multi-domain]  Cd Length: 259  Bit Score: 51.50  E-value: 1.32e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299  18 LAAIVELHQPDVIGLQE-----------TKVHDEMFPLEEVSKLGYH-VFYYG---------QKAHYGVALLTRQaPIAV 76
Cdd:cd09079   21 LAKIIAEEDYDVIALQEvnqsidapvsqVPIKEDNFALLLYEKLRELgATYYWtwilshigyDKYDEGLAILSKR-PIAE 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299  77 RRGF---PGDDEDS--QRRIIMADLETPHGLLTVINGYF--PQGENrdhpvkfpakEKFYQDLQ---SYLEQNLSPqsqV 146
Cdd:cd09079  100 VEDFyvsKSQDYTDykSRKILGATIEINGQPIDVYSCHLgwWYDEE----------EPFAYEWSkleKALAEAGRP---V 166


                 ....*..
gi 738887299 147 IIMGDMN 153
Cdd:cd09079  167 LLMGDFN 173
EEP-1 cd09083
Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of ...
 146-266 1.54e-03

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


Pssm-ID: 197317 [Multi-domain]  Cd Length: 252  Bit Score: 39.12  E-value: 1.54e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299 146 VIIMGDMNISPTDldigigdnnqkrwlktgkcsflpeerDWMDRLKNWGLVDTFRRLN-PECNDQFSWFDYRskgfDDNR 224
Cdd:cd09083  163 VILTGDFNAEPDS--------------------------EPYKTLTSGGLKDARDTAAtTDGGPEGTFHGFK----GPPG 212

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 738887299 225 GLRIDLLLASKPLVerCIATGIDYKIREMEKPSDHAPVWAEF 266
Cdd:cd09083  213 GSRIDYIFVSPGVK--VLSYEILTDRYDGRYPSDHFPVVADL 252
Exo_endo_phos_3 pfam19580
Endonuclease/Exonuclease/phosphatase family; This domain appears to be related to pfam03372.
 27-158 2.63e-03

Endonuclease/Exonuclease/phosphatase family; This domain appears to be related to pfam03372.


Pssm-ID: 437412 [Multi-domain]  Cd Length: 311  Bit Score: 38.65  E-value: 2.63e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 738887299   27 PDVIGLQET---KVHDEMFPLEEVSKLGYHVFYYGQKAHYG--VALLTRQAPIAV------RRGFPGDDEDSQRRIIMAD 95
Cdd:pfam19580  57 PEIIGLCEVenkKVVEDLVKTGALKKYNYKIVHYDSPDRRGidVALIYRPDYFKVtssksyRLVDPVDPGFITRDQLLVT 136

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 738887299   96 LETPHGLLTVINGYFPQ---GENRDHPVKFPAKEKFYQDLQSYLEQNlsPQSQVIIMGDMNISPTD 158
Cdd:pfam19580 137 GKLDGEEMHFIVNHWPSrggGEKKSRPKRMVAAELTRSIADSLLAAN--PNAKIVIMGDLNDEPNN 200
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH