NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|15227354|ref|NP_181677|]
View 

apurinic endonuclease-redox protein [Arabidopsis thaliana]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This ...
 277-534 1.20e-147

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: 423.89  E-value: 1.20e-147
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 277 KVMTWNVNGLRGLLKFEsfsALQLAQRENFDILCLQETKLQVKDVEEIKKTLIDGYdHSFWSCSvSKLGYSGTAIISRIK 356
Cdd:cd09087   2 KIISWNVNGLRALLKKG---LLDYVKKEDPDILCLQETKLQEGDVPKELKELLKGY-HQYWNAA-EKKGYSGTAILSKKK 76

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 357 PLSVRYGTGLSGHDTEGRIVTAEFDSFYLINTYVPNSGDGLKRLSYRiEEWDRTLSNHIKELEKSKPVVLTGDLNCAHEE 436
Cdd:cd09087  77 PLSVTYGIGIEEHDQEGRVITAEFENFYLVNTYVPNSGRGLERLDRR-KEWDVDFRAYLKKLDSKKPVIWCGDLNVAHEE 155

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 437 IDIFNPAGNKRSAGFTIEERQSFGAnLLDKGFVDTFRKQHPGVVG-YTYWGYRHGGRKTNKGWRLDYFLVSQSIAANVHD 515
Cdd:cd09087 156 IDLANPKTNKKSAGFTPEERESFTE-LLEAGFVDTFRHLHPDKEGaYTFWSYRGNARAKNVGWRLDYFLVSERLKDRVVD 234

                       250
                ....*....|....*....
gi 15227354 516 SYILPDINGSDHCPIGLIL 534
Cdd:cd09087 235 SFIRSDIMGSDHCPIGLEL 253
SAP smart00513
Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation;
97-131 3.85e-07

Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation;


:

Pssm-ID: 128789 [Multi-domain]  Cd Length: 35  Bit Score: 46.33  E-value: 3.85e-07
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 15227354     97 IEAMTVQELRSTLRKLGVPVKGRKQELISTLRLHM 131
Cdd:smart00513   1 LAKLKVSELKDELKKRGLSTSGTKAELVDRLLEAL 35
 
Name Accession Description Interval E-value
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This ...
 277-534 1.20e-147

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: 423.89  E-value: 1.20e-147
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 277 KVMTWNVNGLRGLLKFEsfsALQLAQRENFDILCLQETKLQVKDVEEIKKTLIDGYdHSFWSCSvSKLGYSGTAIISRIK 356
Cdd:cd09087   2 KIISWNVNGLRALLKKG---LLDYVKKEDPDILCLQETKLQEGDVPKELKELLKGY-HQYWNAA-EKKGYSGTAILSKKK 76

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 357 PLSVRYGTGLSGHDTEGRIVTAEFDSFYLINTYVPNSGDGLKRLSYRiEEWDRTLSNHIKELEKSKPVVLTGDLNCAHEE 436
Cdd:cd09087  77 PLSVTYGIGIEEHDQEGRVITAEFENFYLVNTYVPNSGRGLERLDRR-KEWDVDFRAYLKKLDSKKPVIWCGDLNVAHEE 155

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 437 IDIFNPAGNKRSAGFTIEERQSFGAnLLDKGFVDTFRKQHPGVVG-YTYWGYRHGGRKTNKGWRLDYFLVSQSIAANVHD 515
Cdd:cd09087 156 IDLANPKTNKKSAGFTPEERESFTE-LLEAGFVDTFRHLHPDKEGaYTFWSYRGNARAKNVGWRLDYFLVSERLKDRVVD 234

                       250
                ....*....|....*....
gi 15227354 516 SYILPDINGSDHCPIGLIL 534
Cdd:cd09087 235 SFIRSDIMGSDHCPIGLEL 253
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 276-535 3.18e-133

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: 387.02  E-value: 3.18e-133
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354   276 VKVMTWNVNGLRGLLKFESfsaLQLAQRENFDILCLQETKLQVkDVEEIKKTLIDGYDHSFWSCsvsKLGYSGTAIISRI 355
Cdd:TIGR00633   1 MKIISWNVNGLRARLHKLF---LDWLKEEQPDVLCLQETKVAD-EQFPAELFEELGYHVFFHGA---KKGYSGVAILSKV 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354   356 KPLSVRYGTGLSGHDTEGRIVTAEFDSFYLINTYVPNSG-DGLKRLSYRIEEWDRTLSNHIKELEKSKPVVLTGDLNCAH 434
Cdd:TIGR00633  74 EPLDVRYGFGGEPHDEEGRVITAEFDGFTVVNVYVPNGGsRDLERLEYKLQFWDALFQYLEKELDAGKPVVICGDMNVAH 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354   435 EEIDIFNPAGNKRSAGFTIEERQSFGaNLLDKGFVDTFRKQHPGVVG-YTYWGYRHGGRKTNKGWRLDYFLVSQSIAANV 513
Cdd:TIGR00633 154 TEIDLGNPKENKGNAGFTPEEREWFD-ELLEAGFVDTFRHFNPDTGDaYTWWDYRSGARDRNRGWRIDYFLVSEPLAERV 232

                         250       260
                  ....*....|....*....|..
gi 15227354   514 HDSYILPDINGSDHCPIGLILK 535
Cdd:TIGR00633 233 VDSYIDSEIRGSDHCPIVLELD 254
XthA COG0708
Exonuclease III [Replication, recombination and repair];
277-535 1.89e-94

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 288.13  E-value: 1.89e-94
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 277 KVMTWNVNGLRGLL-KFesfsaLQLAQRENFDILCLQETKLQVKDV--EEIKKtliDGYdHSFWScsvSKLGYSGTAIIS 353
Cdd:COG0708   2 KIASWNVNGIRARLpKL-----LDWLAEEDPDVLCLQETKAQDEQFplEAFEA---AGY-HVYFH---GQKGYNGVAILS 69

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 354 RIKPLSVRYGTGLSGHDTEGRIVTAEFDSFYLINTYVPNSGD-GLKRLSYRIeEWDRTLSNHIKELEKS-KPVVLTGDLN 431
Cdd:COG0708  70 RLPPEDVRRGLGGDEFDAEGRYIEADFGGVRVVSLYVPNGGSvGSEKFDYKL-RFLDALRAYLAELLAPgRPLILCGDFN 148

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 432 CAHEEIDIFNPAGNKRSAGFTIEERQSFGAnLLDKGFVDTFRKQHPGVVG-YTYWGYRHGGRKTNKGWRLDYFLVSQSIA 510
Cdd:COG0708 149 IAPTEIDVKNPKANLKNAGFLPEERAWFDR-LLELGLVDAFRALHPDVEGqYTWWSYRAGAFARNRGWRIDYILASPALA 227

                       250       260
                ....*....|....*....|....*....
gi 15227354 511 ANVHDSYILP----DINGSDHCPIGLILK 535
Cdd:COG0708 228 DRLKDAGIDReprgDERPSDHAPVVVELD 256
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 276-534 6.99e-73

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 232.28  E-value: 6.99e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354  276 VKVMTWNVNGLRGLLkfeSFSALQLAQRENFDILCLQETKLQvkdvEEIKKTLIDGYdHSFWSCSVSKlGYSGTAIISRI 355
Cdd:PRK13911   1 MKLISWNVNGLRACM---TKGFMDFFNSVDADVFCIQESKMQ----QEQNTFEFKGY-FDFWNCAIKK-GYSGVVTFTKK 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354  356 KPLSVRYGTGLSGHDTEGRIVTAEFDSFYLINTYVPNSGDGLKRLSYRIeEWDRTLSNHIKELEKSKPVVLTGDLNCAHE 435
Cdd:PRK13911  72 EPLSVSYGINIEEHDKEGRVITCEFESFYLVNVYTPNSQQALSRLSYRM-SWEVEFKKFLKALELKKPVIVCGDLNVAHN 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354  436 EIDIFNPAGNKRSAGFTIEERQSFgANLLDKGFVDTFRKQHPGV-VGYTYWGYRHGGRKTNKGWRLDYFLVSQSIAANVH 514
Cdd:PRK13911 151 EIDLENPKTNRKNAGFSDEERGKF-SELLNAGFIDTFRYFYPNKeKAYTWWSYMQQARDKNIGWRIDYFLCSNPLKTRLK 229

                        250       260
                 ....*....|....*....|
gi 15227354  515 DSYILPDINGSDHCPIGLIL 534
Cdd:PRK13911 230 DALIYKDILGSDHCPVGLEL 249
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 279-431 1.66e-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: 89.21  E-value: 1.66e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354   279 MTWNVNGLRGLLKFESFSALQLAQ---RENFDILCLQETKLQvkDVEEIKKTLIDGYDHSFWSCSVSKLGYSGTAIISRI 355
Cdd:pfam03372   1 LTWNVNGGNADAAGDDRKLDALAAlirAYDPDVVALQETDDD--DASRLLLALLAYGGFLSYGGPGGGGGGGGVAILSRY 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15227354   356 KPLSVRYGTGLSGHDTEGRIVTAEFDSFYLINTYVPNSGDGLKRLSYRIEEWDRTLSNHIKELEKSKPVVLTGDLN 431
Cdd:pfam03372  79 PLSSVILVDLGEFGDPALRGAIAPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALLAPRSEPVILAGDFN 154
SAP smart00513
Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation;
97-131 3.85e-07

Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation;


Pssm-ID: 128789 [Multi-domain]  Cd Length: 35  Bit Score: 46.33  E-value: 3.85e-07
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 15227354     97 IEAMTVQELRSTLRKLGVPVKGRKQELISTLRLHM 131
Cdd:smart00513   1 LAKLKVSELKDELKKRGLSTSGTKAELVDRLLEAL 35
SAP pfam02037
SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding ...
 97-130 5.43e-07

SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding domain found in diverse nuclear and cytoplasmic proteins.


Pssm-ID: 460424 [Multi-domain]  Cd Length: 35  Bit Score: 45.85  E-value: 5.43e-07
                          10        20        30
                  ....*....|....*....|....*....|....
gi 15227354    97 IEAMTVQELRSTLRKLGVPVKGRKQELISTLRLH 130
Cdd:pfam02037   1 LSKLTVAELKEELRKRGLPTSGKKAELIERLQEY 34
 
Name Accession Description Interval E-value
Ape1-like_AP-endo cd09087
Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases; This ...
 277-534 1.20e-147

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: 423.89  E-value: 1.20e-147
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 277 KVMTWNVNGLRGLLKFEsfsALQLAQRENFDILCLQETKLQVKDVEEIKKTLIDGYdHSFWSCSvSKLGYSGTAIISRIK 356
Cdd:cd09087   2 KIISWNVNGLRALLKKG---LLDYVKKEDPDILCLQETKLQEGDVPKELKELLKGY-HQYWNAA-EKKGYSGTAILSKKK 76

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 357 PLSVRYGTGLSGHDTEGRIVTAEFDSFYLINTYVPNSGDGLKRLSYRiEEWDRTLSNHIKELEKSKPVVLTGDLNCAHEE 436
Cdd:cd09087  77 PLSVTYGIGIEEHDQEGRVITAEFENFYLVNTYVPNSGRGLERLDRR-KEWDVDFRAYLKKLDSKKPVIWCGDLNVAHEE 155

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 437 IDIFNPAGNKRSAGFTIEERQSFGAnLLDKGFVDTFRKQHPGVVG-YTYWGYRHGGRKTNKGWRLDYFLVSQSIAANVHD 515
Cdd:cd09087 156 IDLANPKTNKKSAGFTPEERESFTE-LLEAGFVDTFRHLHPDKEGaYTFWSYRGNARAKNVGWRLDYFLVSERLKDRVVD 234

                       250
                ....*....|....*....
gi 15227354 516 SYILPDINGSDHCPIGLIL 534
Cdd:cd09087 235 SFIRSDIMGSDHCPIGLEL 253
xth TIGR00633
exodeoxyribonuclease III (xth); All proteins in this family for which functions are known are ...
 276-535 3.18e-133

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: 387.02  E-value: 3.18e-133
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354   276 VKVMTWNVNGLRGLLKFESfsaLQLAQRENFDILCLQETKLQVkDVEEIKKTLIDGYDHSFWSCsvsKLGYSGTAIISRI 355
Cdd:TIGR00633   1 MKIISWNVNGLRARLHKLF---LDWLKEEQPDVLCLQETKVAD-EQFPAELFEELGYHVFFHGA---KKGYSGVAILSKV 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354   356 KPLSVRYGTGLSGHDTEGRIVTAEFDSFYLINTYVPNSG-DGLKRLSYRIEEWDRTLSNHIKELEKSKPVVLTGDLNCAH 434
Cdd:TIGR00633  74 EPLDVRYGFGGEPHDEEGRVITAEFDGFTVVNVYVPNGGsRDLERLEYKLQFWDALFQYLEKELDAGKPVVICGDMNVAH 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354   435 EEIDIFNPAGNKRSAGFTIEERQSFGaNLLDKGFVDTFRKQHPGVVG-YTYWGYRHGGRKTNKGWRLDYFLVSQSIAANV 513
Cdd:TIGR00633 154 TEIDLGNPKENKGNAGFTPEEREWFD-ELLEAGFVDTFRHFNPDTGDaYTWWDYRSGARDRNRGWRIDYFLVSEPLAERV 232

                         250       260
                  ....*....|....*....|..
gi 15227354   514 HDSYILPDINGSDHCPIGLILK 535
Cdd:TIGR00633 233 VDSYIDSEIRGSDHCPIVLELD 254
ExoIII_AP-endo cd09073
Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases; The ...
 277-534 4.84e-102

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: 307.29  E-value: 4.84e-102
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 277 KVMTWNVNGLRGLLKFEsfsALQLAQRENFDILCLQETKLQVKDVEEiKKTLIDGYdHSFWSCSvSKLGYSGTAIISRIK 356
Cdd:cd09073   1 KIISWNVNGLRARLKKG---VLKWLKEEKPDILCLQETKADEDKLPE-ELQHVEGY-HSYWSPA-RKKGYSGVATLSKEE 74

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 357 PLSVRYGTGLSGHDTEGRIVTAEFDSFYLINTYVPNSGDGLKRLSYRIEeWDRTLSNHIKEL-EKSKPVVLTGDLNCAHE 435
Cdd:cd09073  75 PLDVSYGIGGEEFDSEGRVITAEFDDFYLINVYFPNGGRGLERLDYKLR-FYEAFLEFLEKLrKRGKPVVICGDFNVAHE 153

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 436 EIDIFNPAGNKRSAGFTIEERQSFGaNLLDKGFVDTFRKQHPGVVGYTYWGYRHGGRKTNKGWRLDYFLVSQSIAANVHD 515
Cdd:cd09073 154 EIDLARPKKNEKNAGFTPEERAWFD-KLLSLGYVDTFRHFHPEPGAYTWWSYRGNARERNVGWRIDYFLVSEELAEKVKD 232

                       250
                ....*....|....*....
gi 15227354 516 SYILPDINGSDHCPIGLIL 534
Cdd:cd09073 233 SGILSKVKGSDHAPVTLEL 251
XthA COG0708
Exonuclease III [Replication, recombination and repair];
277-535 1.89e-94

Exonuclease III [Replication, recombination and repair];


Pssm-ID: 440472 [Multi-domain]  Cd Length: 256  Bit Score: 288.13  E-value: 1.89e-94
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 277 KVMTWNVNGLRGLL-KFesfsaLQLAQRENFDILCLQETKLQVKDV--EEIKKtliDGYdHSFWScsvSKLGYSGTAIIS 353
Cdd:COG0708   2 KIASWNVNGIRARLpKL-----LDWLAEEDPDVLCLQETKAQDEQFplEAFEA---AGY-HVYFH---GQKGYNGVAILS 69

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 354 RIKPLSVRYGTGLSGHDTEGRIVTAEFDSFYLINTYVPNSGD-GLKRLSYRIeEWDRTLSNHIKELEKS-KPVVLTGDLN 431
Cdd:COG0708  70 RLPPEDVRRGLGGDEFDAEGRYIEADFGGVRVVSLYVPNGGSvGSEKFDYKL-RFLDALRAYLAELLAPgRPLILCGDFN 148

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 432 CAHEEIDIFNPAGNKRSAGFTIEERQSFGAnLLDKGFVDTFRKQHPGVVG-YTYWGYRHGGRKTNKGWRLDYFLVSQSIA 510
Cdd:COG0708 149 IAPTEIDVKNPKANLKNAGFLPEERAWFDR-LLELGLVDAFRALHPDVEGqYTWWSYRAGAFARNRGWRIDYILASPALA 227

                       250       260
                ....*....|....*....|....*....
gi 15227354 511 ANVHDSYILP----DINGSDHCPIGLILK 535
Cdd:COG0708 228 DRLKDAGIDReprgDERPSDHAPVVVELD 256
Mth212-like_AP-endo cd09085
Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic ...
 276-534 1.61e-91

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: 280.32  E-value: 1.61e-91
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 276 VKVMTWNVNGLRGLLKFEsfsALQLAQRENFDILCLQETKLQVKDVEEiKKTLIDGYdHSFWScSVSKLGYSGTAIISRI 355
Cdd:cd09085   1 MKIISWNVNGLRAVHKKG---FLDWFKEEKPDILCLQETKAQPEQLPE-DLRNIEGY-HSYFN-SAERKGYSGVALYSKI 74

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 356 KPLSVRYGTGLSGHDTEGRIVTAEFDSFYLINTYVPNSGDGLKRLSYRIEEWDRTLSNHIKELEKSKPVVLTGDLNCAHE 435
Cdd:cd09085  75 EPDSVREGLGVEEFDNEGRILIADFDDFTLFNIYFPNGQMSEERLDYKLEFYDAFLEYLNELRDSGKNVIICGDFNTAHK 154

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 436 EIDIFNPAGNKRSAGFTIEERQSFGaNLLDKGFVDTFRKQHPGVVGYTYWGYRHGGRKTNKGWRLDYFLVSQSIAANVHD 515
Cdd:cd09085 155 EIDLARPKENEKVSGFLPEERAWMD-KFIENGYVDTFRMFNKEPGQYTWWSYRTRARERNVGWRIDYFFVNEEFKPKVKD 233

                       250
                ....*....|....*....
gi 15227354 516 SYILPDINGSDHCPIGLIL 534
Cdd:cd09085 234 AGILPDVMGSDHCPVSLEL 252
exoDNase_III TIGR00195
exodeoxyribonuclease III; The model brings in reverse transcriptases at scores below 50, model ...
 277-534 2.25e-85

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: 264.63  E-value: 2.25e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354   277 KVMTWNVNGLRGLLKfesfSALQLAQRENFDILCLQETKLQVKDVEEiKKTLIDGYdHSFWSCSVsklGYSGTAIISRIK 356
Cdd:TIGR00195   2 KIISWNVNGLRARPH----KGLAWLKENQPDVLCLQETKVQDEQFPL-EPFHKEGY-HVFFSGQK---GYSGVAIFSKEE 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354   357 PLSVRYGTGLSGHDTEGRIVTAEFDSFYLINTYVPN-SGDGLKRLSYRiEEWDRTLSNHIKELE-KSKPVVLTGDLNCAH 434
Cdd:TIGR00195  73 PISVRRGFGVEEEDAEGRIIMAEFDSFLVINGYFPNgSRDDSEKLPYK-LQWLEALQNYLEKLVdKDKPVLICGDMNIAP 151

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354   435 EEIDIFNPAGNKRSAGFTIEERQSFgANLLDKGFVDTFRKQHPGVVGYTYWGYRHGGRKTNKGWRLDYFLVSQSIAANVH 514
Cdd:TIGR00195 152 TEIDLHIPDENRNHTGFLPEEREWL-DRLLEAGLVDTFRKFNPDEGAYSWWDYRTKARDRNRGWRIDYFLVSEPLKERCV 230

                         250       260
                  ....*....|....*....|....
gi 15227354   515 DSYILPDING----SDHCPIGLIL 534
Cdd:TIGR00195 231 DCGIDYDIRGsekpSDHCPVVLEF 254
PRK13911 PRK13911
exodeoxyribonuclease III; Provisional
 276-534 6.99e-73

exodeoxyribonuclease III; Provisional


Pssm-ID: 139971 [Multi-domain]  Cd Length: 250  Bit Score: 232.28  E-value: 6.99e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354  276 VKVMTWNVNGLRGLLkfeSFSALQLAQRENFDILCLQETKLQvkdvEEIKKTLIDGYdHSFWSCSVSKlGYSGTAIISRI 355
Cdd:PRK13911   1 MKLISWNVNGLRACM---TKGFMDFFNSVDADVFCIQESKMQ----QEQNTFEFKGY-FDFWNCAIKK-GYSGVVTFTKK 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354  356 KPLSVRYGTGLSGHDTEGRIVTAEFDSFYLINTYVPNSGDGLKRLSYRIeEWDRTLSNHIKELEKSKPVVLTGDLNCAHE 435
Cdd:PRK13911  72 EPLSVSYGINIEEHDKEGRVITCEFESFYLVNVYTPNSQQALSRLSYRM-SWEVEFKKFLKALELKKPVIVCGDLNVAHN 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354  436 EIDIFNPAGNKRSAGFTIEERQSFgANLLDKGFVDTFRKQHPGV-VGYTYWGYRHGGRKTNKGWRLDYFLVSQSIAANVH 514
Cdd:PRK13911 151 EIDLENPKTNRKNAGFSDEERGKF-SELLNAGFIDTFRYFYPNKeKAYTWWSYMQQARDKNIGWRIDYFLCSNPLKTRLK 229

                        250       260
                 ....*....|....*....|
gi 15227354  515 DSYILPDINGSDHCPIGLIL 534
Cdd:PRK13911 230 DALIYKDILGSDHCPVGLEL 249
ExoIII-like_AP-endo cd09086
Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of ...
 277-530 1.92e-67

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


Pssm-ID: 197320 [Multi-domain]  Cd Length: 254  Bit Score: 218.15  E-value: 1.92e-67
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 277 KVMTWNVNGLR---GLLkfesfsaLQLAQRENFDILCLQETKLQ-----VKDVEEIkktlidGYdHSFWSCSvsKlGYSG 348
Cdd:cd09086   2 KIATWNVNSIRarlEQV-------LDWLKEEDPDVLCLQETKVEddqfpADAFEAL------GY-HVAVHGQ--K-AYNG 64

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 349 TAIISRIKPLSVRYGTGLSGHDTEGRIVTAEFDSFYLINTYVPNSGD-GLKRLSYRIEeWDRTLSNHI-KELEKSKPVVL 426
Cdd:cd09086  65 VAILSRLPLEDVRTGFPGDPDDDQARLIAARVGGVRVINLYVPNGGDiGSPKFAYKLD-WLDRLIRYLqKLLKPDDPLVL 143

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 427 TGDLNCAHEEIDIFNPAGNKRSAGFTIEERQSFgANLLDKGFVDTFRKQHPGVVGYTYWGYRHGGRKTNKGWRLDYFLVS 506
Cdd:cd09086 144 VGDFNIAPEDIDVWDPKQLLGKVLFTPEEREAL-RALLDLGFVDAFRALHPDEKLFTWWDYRAGAFERNRGLRIDHILAS 222

                       250       260
                ....*....|....*....|....*...
gi 15227354 507 QSIAANVHDSYILPDING----SDHCPI 530
Cdd:cd09086 223 PALADRLKDVGIDREPRGwekpSDHAPV 250
Nape_like_AP-endo cd10281
Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) ...
 277-530 9.04e-67

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: 216.32  E-value: 9.04e-67
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 277 KVMTWNVNGLRGLLKfESFsaLQLAQRENFDILCLQETKLQVKDVEEIKKtLIDGYDHSFWSCSvsKLGYSGTAIISRIK 356
Cdd:cd10281   2 RVISVNVNGIRAAAK-KGF--LEWLAAQDADVVCLQEVRAQEEQLDDDFF-EPEGYNAYFFDAE--KKGYAGVAIYSRTQ 75

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 357 PLSVRYGTGLSGHDTEGRIVTAEFDSFYLINTYVPNSGDGLKRLSYRIEEWDRTLSnHIKELEKSKP-VVLTGDLNCAHE 435
Cdd:cd10281  76 PKAVIYGLGFEEFDDEGRYIEADFDNVSVASLYVPSGSSGDERQEAKMAFLDAFLE-HLKELRRKRReFIVCGDFNIAHT 154

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 436 EIDIFNPAGNKRSAGFTIEERQSFGANLLDKGFVDTFRKQHPGVVGYTYWGYRHGGRKTNKGWRLDYFLVSQSIAANVHD 515
Cdd:cd10281 155 EIDIKNWKANQKNSGFLPEERAWLDQVFGELGYVDAFRELNPDEGQYTWWSNRGQARANNVGWRIDYQIATPGLASKVVS 234

                       250
                ....*....|....*
gi 15227354 516 SYILPDINGSDHCPI 530
Cdd:cd10281 235 AWIYREERFSDHAPL 249
Ape2-like_AP-endo cd09088
Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; This ...
 277-534 9.09e-50

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: 173.66  E-value: 9.09e-50
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 277 KVMTWNVNGLRGLL------KFESFSALqLAQRENfDILCLQETKLQVKDVEEiKKTLIDGYDhSFWSCSVSKLGYSGTA 350
Cdd:cd09088   1 RIVTWNVNGIRTRLqyqpwnKENSLKSF-LDSLDA-DIICLQETKLTRDELDE-PSAIVEGYD-SFFSFSRGRKGYSGVA 76

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 351 IISRIKPLSVRYGT-GLSGH----------------------------------DTEGRIVTAEFDSFYLINTYVP-NSG 394
Cdd:cd09088  77 TYCRDSAATPVAAEeGLTGVlsspnqknelsenddigcygemleftdskellelDSEGRCVLTDHGTFVLINVYCPrADP 156

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 395 DGLKRLSYRIEeWDRTLSNHIKELEKS-KPVVLTGDLNCAHEEIDIFNPAGNKRSAGFTIEE---RQSFGANLLDKG--- 467
Cdd:cd09088 157 EKEERLEFKLD-FYRLLEERVEALLKAgRRVILVGDVNVSHRPIDHCDPDDSEDFGGESFEDnpsRQWLDQLLGDSGegg 235

                       250       260       270       280       290       300       310
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15227354 468 ------FVDTFRKQHPGVVG-YTYWGYRHGGRKTNKGWRLDYFLVSQSIAANVHDSYILPDINGSDHCPIGLIL 534
Cdd:cd09088 236 gspgglLIDSFRYFHPTRKGaYTCWNTLTGARPTNYGTRIDYILADRGLLPWVKAADILPEVEGSDHCPVYADL 309
EEP cd08372
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; This large superfamily includes ...
 278-534 1.29e-37

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: 138.77  E-value: 1.29e-37
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 278 VMTWNVNGLRGLLKFESFsaLQLAQRENFDILCLQETKL-QVKDVeeIKKTLIDGYDHSFWSCSVSKLGYSGTAIISR-- 354
Cdd:cd08372   1 VASYNVNGLNAATRASGI--ARWVRELDPDIVCLQEVKDsQYSAV--ALNQLLPEGYHQYQSGPSRKEGYEGVAILSKtp 76

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 355 -IKPLSVRYGTGLSGHDTEGRIVTAEFDS----FYLINTYVPNSGdglKRLSYRIEeWDRTLSNHIKELEK--SKPVVLT 427
Cdd:cd08372  77 kFKIVEKHQYKFGEGDSGERRAVVVKFDVhdkeLCVVNAHLQAGG---TRADVRDA-QLKEVLEFLKRLRQpnSAPVVIC 152

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 428 GDLNCAHEEIDIfnpagnkrsagftiEERQSFGANLLDKGFVDTFRKQHpgvVGYTYWGYRHggrktNKGWRLDYFLVSQ 507
Cdd:cd08372 153 GDFNVRPSEVDS--------------ENPSSMLRLFVALNLVDSFETLP---HAYTFDTYMH-----NVKSRLDYIFVSK 210

                       250       260       270
                ....*....|....*....|....*....|.
gi 15227354 508 SIAANVHDSYILPD----INGSDHCPIGLIL 534
Cdd:cd08372 211 SLLPSVKSSKILSDaaraRIPSDHYPIEVTL 241
PRK11756 PRK11756
exonuclease III; Provisional
 277-536 1.85e-29

exonuclease III; Provisional


Pssm-ID: 236970 [Multi-domain]  Cd Length: 268  Bit Score: 116.92  E-value: 1.85e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354  277 KVMTWNVNGLRGLLKfesfsalQLA---QRENFDILCLQETKLQ-----VKDVEEIkktlidGYdHSFWScsvSKLGYSG 348
Cdd:PRK11756   2 KFVSFNINGLRARPH-------QLEaiiEKHQPDVIGLQETKVHdemfpLEEVEAL------GY-HVFYH---GQKGHYG 64

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354  349 TAIISRIKPLSVRYGTGLSGHDTEGRIVTAEFDS----FYLINTYVPN--SGDGLKRLSYRiEEWDRTLSNHI-KELEKS 421
Cdd:PRK11756  65 VALLSKQTPIAVRKGFPTDDEEAQRRIIMATIPTpngnLTVINGYFPQgeSRDHPTKFPAK-RQFYQDLQNYLeTELSPD 143

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354  422 KPVVLTGDLNCAHEEIDIFNPAGN-KR--SAG---FTIEERQSFgANLLDKGFVDTFRKQHPGVVG-YTYWGYRHGGRKT 494
Cdd:PRK11756 144 NPLLIMGDMNISPTDLDIGIGEENrKRwlRTGkcsFLPEEREWL-DRLMDWGLVDTFRQLNPDVNDrFSWFDYRSKGFDD 222

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*.
gi 15227354  495 NKGWRLDYFLVSQSIAANVHDSYILPDING----SDHCPIGLILKL 536
Cdd:PRK11756 223 NRGLRIDLILATQPLAERCVETGIDYDIRGmekpSDHAPIWATFKL 268
L1-EN cd09076
Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains; ...
 280-530 2.23e-29

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: 115.91  E-value: 2.23e-29
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 280 TWNVNGLRGLLKFESfsALQLAQRENFDILCLQETKLqvKDVEEIKKTLIDGYdhSFWSCSVSKLGySGTAII----SRI 355
Cdd:cd09076   3 TLNVRGLRSPGKRAQ--LLEELKRKKLDILGLQETHW--TGEGELKKKREGGT--ILYSGSDSGKS-RGVAILlsktAAN 75

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 356 KPLSVRygtglsgHDTEGRIVTAEFD----SFYLINTYVPNSGDGLKRlsyriEEWDRTLSNHIKELEKSKPVVLTGDLN 431
Cdd:cd09076  76 KLLEYT-------KVVSGRIIMVRFKikgkRLTIINVYAPTARDEEEK-----EEFYDQLQDVLDKVPRHDTLIIGGDFN 143

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 432 CaheeidifnPAGNKRSAGFTIEER-----QSFGANLLDKGFVDTFRKQHPGVVGYTywgYRHGGRKTNKgwRLDYFLVS 506
Cdd:cd09076 144 A---------VLGPKDDGRKGLDKRnengeRALSALIEEHDLVDVWRENNPKTREYT---WRSPDHGSRS--RIDRILVS 209

                       250       260
                ....*....|....*....|....
gi 15227354 507 QSIAANVHDSYILPDInGSDHCPI 530
Cdd:cd09076 210 KRLRVKVKKTKITPGA-GSDHRLV 232
Exo_endo_phos pfam03372
Endonuclease/Exonuclease/phosphatase family; This large family of proteins includes magnesium ...
 279-431 1.66e-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: 89.21  E-value: 1.66e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354   279 MTWNVNGLRGLLKFESFSALQLAQ---RENFDILCLQETKLQvkDVEEIKKTLIDGYDHSFWSCSVSKLGYSGTAIISRI 355
Cdd:pfam03372   1 LTWNVNGGNADAAGDDRKLDALAAlirAYDPDVVALQETDDD--DASRLLLALLAYGGFLSYGGPGGGGGGGGVAILSRY 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15227354   356 KPLSVRYGTGLSGHDTEGRIVTAEFDSFYLINTYVPNSGDGLKRLSYRIEEWDRTLSNHIKELEKSKPVVLTGDLN 431
Cdd:pfam03372  79 PLSSVILVDLGEFGDPALRGAIAPFAGVLVVPLVLTLAPHASPRLARDEQRADLLLLLLALLAPRSEPVILAGDFN 154
EEP-2 cd09084
Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2; This ...
 278-530 1.61e-14

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: 73.48  E-value: 1.61e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 278 VMTWNVNGLRGLLKFESF-SALQLAQRENFDILCLQETKLQVKDVEEIKKTLIDGYDHSFWSCSvSKLGYSGTAIISRIK 356
Cdd:cd09084   1 VMSYNVRSFNRYKWKDDPdKILDFIKKQDPDILCLQEYYGSEGDKDDDLRLLLKGYPYYYVVYK-SDSGGTGLAIFSKYP 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 357 PLSVRygtGLSGHDTEGRIVTAEF----DSFYLINTYVP------------NSGDGLKRLSYRIEE------WDR----- 409
Cdd:cd09084  80 ILNSG---SIDFPNTNNNAIFADIrvggDTIRVYNVHLEsfritpsdkelyKEEKKAKELSRNLLRklaeafKRRaaqad 156

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 410 TLSNHIKelEKSKPVVLTGDLNcaheeidifNPAGnkrsagftieerqSFGANLLDKGFVDTFRKQHPGvVGYTYWGYRH 489
Cdd:cd09084 157 LLAADIA--ASPYPVIVCGDFN---------DTPA-------------SYVYRTLKKGLTDAFVEAGSG-FGYTFNGLFF 211

                       250       260       270       280
                ....*....|....*....|....*....|....*....|.
gi 15227354 490 ggrktnkGWRLDYFLVSQSIaaNVHdSYILPDINGSDHCPI 530
Cdd:cd09084 212 -------PLRIDYILTSKGF--KVL-RYRVDPGKYSDHYPI 242
YafD COG3021
Uncharacterized conserved protein YafD, endonuclease/exonuclease/phosphatase (EEP) superfamily ...
 265-530 1.59e-12

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


Pssm-ID: 442257 [Multi-domain]  Cd Length: 310  Bit Score: 68.48  E-value: 1.59e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 265 RPPPLPEGTKCVKVMTWNVNGLRGllkfESFSALQLAQRENFDILCLQE-TKLQVKDVEEIKktliDGYDHSFwscSVSK 343
Cdd:COG3021  84 APKSAPAGGPDLRVLTANVLFGNA----DAEALAALVREEDPDVLVLQEtTPAWEEALAALE----ADYPYRV---LCPL 152

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 344 LGYSGTAIISR--IKPLSVRYGTGlsghdTEGRIVTAEFD------SFYLINTYVPnsgdglkrlSYRIEEWDRTLSNHI 415
Cdd:COG3021 153 DNAYGMALLSRlpLTEAEVVYLVG-----DDIPSIRATVElpggpvRLVAVHPAPP---------VGGSAERDAELAALA 218

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 416 KELEKSK-PVVLTGDLNCAHeeidifnpagnkRSAGFtieerQSFGAN--LLD----KGFVDTFRKQHPGVvgytywgyr 488
Cdd:COG3021 219 KAVAALDgPVIVAGDFNATP------------WSPTL-----RRLLRAsgLRDaragRGLGPTWPANLPFL--------- 272

                       250       260       270       280
                ....*....|....*....|....*....|....*....|..
gi 15227354 489 hggrktnkGWRLDYFLVSQSIAanVHDSYILPDInGSDHCPI 530
Cdd:COG3021 273 --------RLPIDHVLVSRGLT--VVDVRVLPVI-GSDHRPL 303
EEP-1 cd09083
Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1; This family of ...
 277-530 4.07e-12

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: 66.47  E-value: 4.07e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 277 KVMTWNVnglrgllKFESFS------------ALQLAQRENFDILCLQETKL-QVKDVEEikktLIDGYDHsfwscsvsk 343
Cdd:cd09083   1 RVMTFNI-------RYDNPSdgenswenrkdlVAELIKFYDPDIIGTQEALPhQLADLEE----LLPEYDW--------- 60

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 344 LGYS---------GTAII---SRIKPLSvrygtglSGH-------DTEG---------RIVT-AEF------DSFYLINT 388
Cdd:cd09083  61 IGVGrddgkekgeFSAIFyrkDRFELLD-------SGTfwlsetpDVVGskgwdaalpRICTwARFkdkktgKEFYVFNT 133

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 389 YVPNSGDGLKRLSYRIeewdrtLSNHIKELEKSKPVVLTGDLNCAHEeidifnpagnkrSAGFTIeerqsfganLLDKGF 468
Cdd:cd09083 134 HLDHVGEEAREESAKL------ILERIKEIAGDLPVILTGDFNAEPD------------SEPYKT---------LTSGGL 186

                       250       260       270       280       290       300
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15227354 469 VDTFR--KQHPGVVGYTYwgyrHGGRKTNKGWRLDYFLVSQSIaaNVHDSYILPD-ING---SDHCPI 530
Cdd:cd09083 187 KDARDtaATTDGGPEGTF----HGFKGPPGGSRIDYIFVSPGV--KVLSYEILTDrYDGrypSDHFPV 248
ElsH COG3568
Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function ...
 276-440 7.81e-11

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


Pssm-ID: 442789 [Multi-domain]  Cd Length: 167  Bit Score: 60.69  E-value: 7.81e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 276 VKVMTWNV---NGLRGLLKFESFsaLQLAQRENFDILCLQETklqvkdveeikktlidgydhsfwscsvsklgysgtAII 352
Cdd:COG3568   8 LRVMTYNIrygLGTDGRADLERI--ARVIRALDPDVVALQEN-----------------------------------AIL 50

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 353 SRIKPLSVRYGTgLSGHDTEGRIVT-AEFD----SFYLINTYVpnsgdGLKRLSYRIEEWDRtLSNHIKELEKSKPVVLT 427
Cdd:COG3568  51 SRYPIVSSGTFD-LPDPGGEPRGALwADVDvpgkPLRVVNTHL-----DLRSAAARRRQARA-LAELLAELPAGAPVILA 123

                       170
                ....*....|....
gi 15227354 428 GDLNCaheeID-IF 440
Cdd:COG3568 124 GDFND----IDyIL 133
SAP smart00513
Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation;
97-131 3.85e-07

Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation;


Pssm-ID: 128789 [Multi-domain]  Cd Length: 35  Bit Score: 46.33  E-value: 3.85e-07
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 15227354     97 IEAMTVQELRSTLRKLGVPVKGRKQELISTLRLHM 131
Cdd:smart00513   1 LAKLKVSELKDELKKRGLSTSGTKAELVDRLLEAL 35
R1-I-EN cd09077
Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat ...
 276-530 4.47e-07

Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons; This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.


Pssm-ID: 197311 [Multi-domain]  Cd Length: 205  Bit Score: 50.75  E-value: 4.47e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 276 VKVMTWNVNGLRGllkfESFSALQLAQRENFDILCLQETklqvkdveeikktlidgYDHSFWSCSVSKLGYSGTAII--S 353
Cdd:cd09077   1 LRILQINLNRCKA----AQDLLLQTAREEGADIALIQEP-----------------YLVPVNNPNWVTDESGRAAIVvsD 59

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 354 RIKPLSVRYGTGLSGhdtegrIVTAEFDSFYLINTYVPNSGDGLKrlsyrIEEWDRTLSNHIKELekSKPVVLTGDLNCA 433
Cdd:cd09077  60 RLPRKPIQRLSLGLG------IVAARVGGITVVSCYAPPSESLEE-----FEEYLENLVRIVRGL--SRPVIIGGDFNAW 126

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 434 HEEIdiFNPAGNKRsaGFTIEER-QSFGANLLDKGFVDTFRkqhpgvvgytywgyrHGGRKTNkgwrLDYFLVSQSIAAN 512
Cdd:cd09077 127 SPAW--GSKRTDRR--GRLLEDWiANLGLVLLNDGNSPTFV---------------RPRGTSI----IDVTFCSPSLARR 183

                       250
                ....*....|....*...
gi 15227354 513 VHDSYILPDINGSDHCPI 530
Cdd:cd09077 184 ISNWRVLEDETLSDHRYI 201
SAP pfam02037
SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding ...
 97-130 5.43e-07

SAP domain; The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding domain found in diverse nuclear and cytoplasmic proteins.


Pssm-ID: 460424 [Multi-domain]  Cd Length: 35  Bit Score: 45.85  E-value: 5.43e-07
                          10        20        30
                  ....*....|....*....|....*....|....
gi 15227354    97 IEAMTVQELRSTLRKLGVPVKGRKQELISTLRLH 130
Cdd:pfam02037   1 LSKLTVAELKEELRKRGLPTSGKKAELIERLQEY 34
TDP2 cd09080
Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related ...
 277-505 6.58e-05

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: 44.64  E-value: 6.58e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 277 KVMTWNVNGLRGLLKFESFSA-LQLAQRENFDILCLQETklqvkdVEEIKKTLIDgyDHSFWS---CSVSK----LGYSG 348
Cdd:cd09080   2 KVLTWNVDFLDDVNLAERMRAiLKLLEELDPDVIFLQEV------TPPFLAYLLS--QPWVRKnyyFSEGPpspaVDPYG 73

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 349 TAIISRIKPLSVRYGTGLSGHDTEGRIVTAEFDS---FYLINT----YVPNSgdglkrlSYRIEEwDRTLSNHIKELEKS 421
Cdd:cd09080  74 VLILSKKSLVVRRVPFTSTRMGRNLLAAEINLGSgepLRLATThlesLKSHS-------SERTAQ-LEEIAKKLKKPPGA 145

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 422 KPVVLTGDLNCAHEEIDIFnpagnkrsagftieerqsfganLLDKGFVDTFRKQHP-GVVGYTyWGYR----HGGRKTNK 496
Cdd:cd09080 146 ANVILGGDFNLRDKEDDTG----------------------GLPNGFVDAWEELGPpGEPGYT-WDTQknpmLRKGEAGP 202


                ....*....
gi 15227354 497 GWRLDYFLV 505
Cdd:cd09080 203 RKRFDRVLL 211
MnuA_DNase1-like cd10283
Mycoplasma pulmonis MnuA nuclease-like; This subfamily includes Mycoplasma pulmonis MnuA, a ...
 276-530 9.81e-04

Mycoplasma pulmonis MnuA nuclease-like; This subfamily includes Mycoplasma pulmonis MnuA, a membrane-associated nuclease related to Deoxyribonuclease 1 (DNase1 or DNase I, EC 3.1.21.1). The in vivo role of MnuA is as yet undetermined. This subfamily belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds.


Pssm-ID: 197338 [Multi-domain]  Cd Length: 266  Bit Score: 41.23  E-value: 9.81e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 276 VKVMTWNVNGLRGLLKFESFSAL-QLAQRENFDILCLQEtklqVKDVEEIKKTLID-----GYDHSFWSCSVSK--LGYS 347
Cdd:cd10283   1 LRIASWNILNFGNSKGKEKNPAIaEIISAFDLDLIALQE----VMDNGGGLDALAKlvnelNKPGGTWKYIVSDktGGSS 76

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 348 G----TAII--SRIKPLSVRYGTGLSGHDTEG---------RIVTAEFDsFYLINT-----YVPNSGDGLKRL--SYRIE 405
Cdd:cd10283  77 GdkerYAFLykSSKVRKVGKAVLEKDSNTDGFarppyaakfKSGGTGFD-FTLVNVhlksgGSSKSGQGAKRVaeAQALA 155

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 406 EWdrtlSNHIKELEKSKPVVLTGDLNC--AHEEIDIFnpagnkRSAGFTieerqsfgaNLLDKgfvdtfrkqhPGVVGYT 483
Cdd:cd10283 156 EY----LKELADEDPDDDVILLGDFNIpaDEDAFKAL------TKAGFK---------SLLPD----------STNLSTS 206

                       250       260       270       280       290       300
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15227354 484 YWGYRHggrktnkgwRLDYFLVSQSIAANVHDSYILPDING------------------SDHCPI 530
Cdd:cd10283 207 FKGYAN---------SYDNIFVSGNLKEKFSNSGVFDFNILvdeageedldyskwrkqiSDHDPV 262
RgfB-like cd09079
Streptococcus agalactiae RgfB, part of a putative two component signal transduction system, ...
 278-527 2.13e-03

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: 39.94  E-value: 2.13e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 278 VMTWNVNGLR---GLLKFESFSALqlAQRENFDILCLQETKlQVKD-----------------VEEIKKTLIDGYdhsfW 337
Cdd:cd09079   1 LLTLNTHSWLeenQKEKLERLAKI--IAEEDYDVIALQEVN-QSIDapvsqvpikednfalllYEKLRELGATYY----W 73

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 338 SCSVSKLGYS----GTAIISRiKPLsvrygtglsghdtegrivtAEFDSFYLINTYVPNSGDGLKRLSYRIEEWDRTL-- 411
Cdd:cd09079  74 TWILSHIGYDkydeGLAILSK-RPI-------------------AEVEDFYVSKSQDYTDYKSRKILGATIEINGQPIdv 133

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15227354 412 ---------------SNHIKELEK-----SKPVVLTGDLNC-AHEE------------IDIFNPAGNKRSaGFTIEERqs 458
Cdd:cd09079 134 yschlgwwydeeepfAYEWSKLEKalaeaGRPVLLMGDFNNpAGSRgegydlisslglQDTYDLAEEKDG-GVTVEKA-- 210

                       250       260       270       280       290       300       310
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15227354 459 fganlldkgfVDTFRKQHPGVvgytywgyrhggrktnkgwRLDYFLVSQSIAANVHdSYILPDING---SDH 527
Cdd:cd09079 211 ----------IDGWRGNKEAK-------------------RIDYIFVNRKVKVKSS-RVIFNGKNPpivSDH 252
 
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