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Conserved domains on  [gi|85813718|emb|CAJ55826|]
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putative methyl-CpG binding protein [Homo sapiens]

Protein Classification

endonuclease III domain-containing protein( domain architecture ID 1903256)

endonuclease III domain-containing protein such as endonuclease III, a DNA repair enzyme that has both DNA N-glycosylase and AP-lyase activities

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Nth super family cl43050
Endonuclease III [Replication, recombination and repair];
135-202 1.62e-07

Endonuclease III [Replication, recombination and repair];


The actual alignment was detected with superfamily member COG0177:

Pssm-ID: 439947 [Multi-domain]  Cd Length: 198  Bit Score: 50.48  E-value: 1.62e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 85813718 135 FHDPWKLLIATIFLNRTSGKMAIPVLWKFLEKYPSAEVARTADWRDVSELLKPLGLYDLRAKTIVKFS 202
Cdd:COG0177  17 YRDPFELLVATILSAQTTDERVNKATPRLFARYPTPEALAAADLEELEELIRPIGLYRNKAKNIIALA 84
 
Name Accession Description Interval E-value
Nth COG0177
Endonuclease III [Replication, recombination and repair];
135-202 1.62e-07

Endonuclease III [Replication, recombination and repair];


Pssm-ID: 439947 [Multi-domain]  Cd Length: 198  Bit Score: 50.48  E-value: 1.62e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 85813718 135 FHDPWKLLIATIFLNRTSGKMAIPVLWKFLEKYPSAEVARTADWRDVSELLKPLGLYDLRAKTIVKFS 202
Cdd:COG0177  17 YRDPFELLVATILSAQTTDERVNKATPRLFARYPTPEALAAADLEELEELIRPIGLYRNKAKNIIALA 84
ENDO3c cd00056
endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), ...
 139-222 3.60e-04

endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases


Pssm-ID: 238013 [Multi-domain]  Cd Length: 158  Bit Score: 39.92  E-value: 3.60e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85813718 139 WKLLIATIFLNRTSGKMAIPVLWKFLEKY-PSAEVARTADWRDVSELLKPLGlYDLRAKTIVKFS----DEYLTKQWKYP 213
Cdd:cd00056   1 FEVLVSEILSQQTTDKAVNKAYERLFERYgPTPEALAAADEEELRELIRSLG-YRRKAKYLKELAraivEGFGGLVLDDP 79

                        90
                ....*....|....*
gi 85813718 214 ------IELHGIGKY 222
Cdd:cd00056  80 dareelLALPGVGRK 94
HhH-GPD pfam00730
HhH-GPD superfamily base excision DNA repair protein; This family contains a diverse range of ...
 143-256 3.28e-03

HhH-GPD superfamily base excision DNA repair protein; This family contains a diverse range of structurally related DNA repair proteins. The superfamily is called the HhH-GPD family after its hallmark Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate. This includes endonuclease III, EC:4.2.99.18 and MutY an A/G-specific adenine glycosylase, both have a C terminal 4Fe-4S cluster. The family also includes 8-oxoguanine DNA glycosylases. The methyl-CPG binding protein MBD4 also contains a related domain that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II EC:3.2.2.21 and other members of the AlkA family.


Pssm-ID: 425841 [Multi-domain]  Cd Length: 141  Bit Score: 36.88  E-value: 3.28e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85813718   143 IATIFLNRTSGKMAIPVLWKFLEK-YPSAEVARTADWRDVSELLKPLGLYDLRAKTIVKFS----DEYLTKQWKYPIELH 217
Cdd:pfam00730   1 VSAILSQQTSDKAVNKITERLFEKfFPTPEDLADADEEELRELIRGLGFYRRKAKYLKELArilvEGYGGEVPLDEEELE 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 85813718   218 ----GIGKYGNDSYRIFCVNEWKQVHPED---HKLNKYHDWLWENH 256
Cdd:pfam00730  81 allkGVGRWTAEAVLIFALGRPDPLPVVDthvRRVLKRLGLIKEKP 126
 
Name Accession Description Interval E-value
Nth COG0177
Endonuclease III [Replication, recombination and repair];
135-202 1.62e-07

Endonuclease III [Replication, recombination and repair];


Pssm-ID: 439947 [Multi-domain]  Cd Length: 198  Bit Score: 50.48  E-value: 1.62e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 85813718 135 FHDPWKLLIATIFLNRTSGKMAIPVLWKFLEKYPSAEVARTADWRDVSELLKPLGLYDLRAKTIVKFS 202
Cdd:COG0177  17 YRDPFELLVATILSAQTTDERVNKATPRLFARYPTPEALAAADLEELEELIRPIGLYRNKAKNIIALA 84
ENDO3c cd00056
endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), ...
 139-222 3.60e-04

endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases


Pssm-ID: 238013 [Multi-domain]  Cd Length: 158  Bit Score: 39.92  E-value: 3.60e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85813718 139 WKLLIATIFLNRTSGKMAIPVLWKFLEKY-PSAEVARTADWRDVSELLKPLGlYDLRAKTIVKFS----DEYLTKQWKYP 213
Cdd:cd00056   1 FEVLVSEILSQQTTDKAVNKAYERLFERYgPTPEALAAADEEELRELIRSLG-YRRKAKYLKELAraivEGFGGLVLDDP 79

                        90
                ....*....|....*
gi 85813718 214 ------IELHGIGKY 222
Cdd:cd00056  80 dareelLALPGVGRK 94
HhH-GPD pfam00730
HhH-GPD superfamily base excision DNA repair protein; This family contains a diverse range of ...
 143-256 3.28e-03

HhH-GPD superfamily base excision DNA repair protein; This family contains a diverse range of structurally related DNA repair proteins. The superfamily is called the HhH-GPD family after its hallmark Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate. This includes endonuclease III, EC:4.2.99.18 and MutY an A/G-specific adenine glycosylase, both have a C terminal 4Fe-4S cluster. The family also includes 8-oxoguanine DNA glycosylases. The methyl-CPG binding protein MBD4 also contains a related domain that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II EC:3.2.2.21 and other members of the AlkA family.


Pssm-ID: 425841 [Multi-domain]  Cd Length: 141  Bit Score: 36.88  E-value: 3.28e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85813718   143 IATIFLNRTSGKMAIPVLWKFLEK-YPSAEVARTADWRDVSELLKPLGLYDLRAKTIVKFS----DEYLTKQWKYPIELH 217
Cdd:pfam00730   1 VSAILSQQTSDKAVNKITERLFEKfFPTPEDLADADEEELRELIRGLGFYRRKAKYLKELArilvEGYGGEVPLDEEELE 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 85813718   218 ----GIGKYGNDSYRIFCVNEWKQVHPED---HKLNKYHDWLWENH 256
Cdd:pfam00730  81 allkGVGRWTAEAVLIFALGRPDPLPVVDthvRRVLKRLGLIKEKP 126
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

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