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Conserved domains on  [gi|659121238|ref|XP_008460559|]
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methyl-CpG-binding domain protein 4-like protein [Cucumis melo]

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];
366-449 3.32e-13

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: 68.20  E-value: 3.32e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 659121238 366 DPWRVLVICMLLNRTSGRQAKEVIPKLFSLCPNPKATLEVSREQIEDIIRPLGLYRKRSRTMHRLSEMYLKESWSHV--- 442
Cdd:COG0177   19 DPFELLVATILSAQTTDERVNKATPRLFARYPTPEALAAADLEELEELIRPIGLYRNKAKNIIALARILVEKYGGEVpet 98

                         90
                 ....*....|.
gi 659121238 443 ----TQLPGVG 449
Cdd:COG0177   99 reelESLPGVG 109
 
Name Accession Description Interval E-value
Nth COG0177
Endonuclease III [Replication, recombination and repair];
366-449 3.32e-13

Endonuclease III [Replication, recombination and repair];


Pssm-ID: 439947 [Multi-domain]  Cd Length: 198  Bit Score: 68.20  E-value: 3.32e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 659121238 366 DPWRVLVICMLLNRTSGRQAKEVIPKLFSLCPNPKATLEVSREQIEDIIRPLGLYRKRSRTMHRLSEMYLKESWSHV--- 442
Cdd:COG0177   19 DPFELLVATILSAQTTDERVNKATPRLFARYPTPEALAAADLEELEELIRPIGLYRNKAKNIIALARILVEKYGGEVpet 98

                         90
                 ....*....|.
gi 659121238 443 ----TQLPGVG 449
Cdd:COG0177   99 reelESLPGVG 109
ENDO3c cd00056
endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), ...
 368-460 2.35e-11

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: 61.87  E-value: 2.35e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 659121238 368 WRVLVICMLLNRTSGRQAKEVIPKLFSLC-PNPKATLEVSREQIEDIIRPLGlYRKRSRTMHRLSEM----YLKESWSH- 441
Cdd:cd00056    1 FEVLVSEILSQQTTDKAVNKAYERLFERYgPTPEALAAADEEELRELIRSLG-YRRKAKYLKELARAivegFGGLVLDDp 79

                         90       100
                 ....*....|....*....|....
gi 659121238 442 -----VTQLPGVGKYGADAHAIFC 460
Cdd:cd00056   80 dareeLLALPGVGRKTANVVLLFA 103
ENDO3c smart00478
endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), ...
 376-460 5.94e-11

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


Pssm-ID: 214684 [Multi-domain]  Cd Length: 149  Bit Score: 60.36  E-value: 5.94e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 659121238   376 LLNRTSGRQAKEVIPKLFSLCPNPKATLEVSREQIEDIIRPLGLYRKRSRTMHRLSEMYLKESWSHV-------TQLPGV 448
Cdd:smart00478   1 LSQQTTDERVNKATERLFEKFPTPEDLAAADEEELEELIRGLGFYRRKARYLIELARILVEEYGGEVpddreelLKLPGV 80

                           90
                   ....*....|..
gi 659121238   449 GKYGADAHAIFC 460
Cdd:smart00478  81 GRKTANAVLSFA 92
HhH-GPD pfam00730
HhH-GPD superfamily base excision DNA repair protein; This family contains a diverse range of ...
 374-463 1.45e-10

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: 59.22  E-value: 1.45e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 659121238  374 CMLLNRTSGRQAKEVIPKLFSLC-PNPKATLEVSREQIEDIIRPLGLYRKRSRTMHRLSEMYLKESWSHV--------TQ 444
Cdd:pfam00730   3 AILSQQTSDKAVNKITERLFEKFfPTPEDLADADEEELRELIRGLGFYRRKAKYLKELARILVEGYGGEVpldeeeleAL 82

                          90
                  ....*....|....*....
gi 659121238  445 LPGVGKYGADAHAIFCTGY 463
Cdd:pfam00730  83 LKGVGRWTAEAVLIFALGR 101
PRK10702 PRK10702
endonuclease III; Provisional
 367-454 5.32e-03

endonuclease III; Provisional


Pssm-ID: 182661 [Multi-domain]  Cd Length: 211  Bit Score: 38.46  E-value: 5.32e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 659121238 367 PWRVLVICMLLNRTSGRQAKEVIPKLFSLCPNPKATLEVSREQIEDIIRPLGLYRKRSRTMHRLSEMYLKESWSHVTQ-- 444
Cdd:PRK10702  29 PFELLIAVLLSAQATDVSVNKATAKLYPVANTPAAMLELGVEGVKTYIKTIGLYNSKAENVIKTCRILLEQHNGEVPEdr 108

                         90
                 ....*....|....*
gi 659121238 445 -----LPGVGKYGAD 454
Cdd:PRK10702 109 aaleaLPGVGRKTAN 123
 
Name Accession Description Interval E-value
Nth COG0177
Endonuclease III [Replication, recombination and repair];
366-449 3.32e-13

Endonuclease III [Replication, recombination and repair];


Pssm-ID: 439947 [Multi-domain]  Cd Length: 198  Bit Score: 68.20  E-value: 3.32e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 659121238 366 DPWRVLVICMLLNRTSGRQAKEVIPKLFSLCPNPKATLEVSREQIEDIIRPLGLYRKRSRTMHRLSEMYLKESWSHV--- 442
Cdd:COG0177   19 DPFELLVATILSAQTTDERVNKATPRLFARYPTPEALAAADLEELEELIRPIGLYRNKAKNIIALARILVEKYGGEVpet 98

                         90
                 ....*....|.
gi 659121238 443 ----TQLPGVG 449
Cdd:COG0177   99 reelESLPGVG 109
ENDO3c cd00056
endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), ...
 368-460 2.35e-11

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: 61.87  E-value: 2.35e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 659121238 368 WRVLVICMLLNRTSGRQAKEVIPKLFSLC-PNPKATLEVSREQIEDIIRPLGlYRKRSRTMHRLSEM----YLKESWSH- 441
Cdd:cd00056    1 FEVLVSEILSQQTTDKAVNKAYERLFERYgPTPEALAAADEEELRELIRSLG-YRRKAKYLKELARAivegFGGLVLDDp 79

                         90       100
                 ....*....|....*....|....
gi 659121238 442 -----VTQLPGVGKYGADAHAIFC 460
Cdd:cd00056   80 dareeLLALPGVGRKTANVVLLFA 103
ENDO3c smart00478
endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), ...
 376-460 5.94e-11

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


Pssm-ID: 214684 [Multi-domain]  Cd Length: 149  Bit Score: 60.36  E-value: 5.94e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 659121238   376 LLNRTSGRQAKEVIPKLFSLCPNPKATLEVSREQIEDIIRPLGLYRKRSRTMHRLSEMYLKESWSHV-------TQLPGV 448
Cdd:smart00478   1 LSQQTTDERVNKATERLFEKFPTPEDLAAADEEELEELIRGLGFYRRKARYLIELARILVEEYGGEVpddreelLKLPGV 80

                           90
                   ....*....|..
gi 659121238   449 GKYGADAHAIFC 460
Cdd:smart00478  81 GRKTANAVLSFA 92
HhH-GPD pfam00730
HhH-GPD superfamily base excision DNA repair protein; This family contains a diverse range of ...
 374-463 1.45e-10

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: 59.22  E-value: 1.45e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 659121238  374 CMLLNRTSGRQAKEVIPKLFSLC-PNPKATLEVSREQIEDIIRPLGLYRKRSRTMHRLSEMYLKESWSHV--------TQ 444
Cdd:pfam00730   3 AILSQQTSDKAVNKITERLFEKFfPTPEDLADADEEELRELIRGLGFYRRKAKYLKELARILVEGYGGEVpldeeeleAL 82

                          90
                  ....*....|....*....
gi 659121238  445 LPGVGKYGADAHAIFCTGY 463
Cdd:pfam00730  83 LKGVGRWTAEAVLIFALGR 101
PRK10702 PRK10702
endonuclease III; Provisional
 367-454 5.32e-03

endonuclease III; Provisional


Pssm-ID: 182661 [Multi-domain]  Cd Length: 211  Bit Score: 38.46  E-value: 5.32e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 659121238 367 PWRVLVICMLLNRTSGRQAKEVIPKLFSLCPNPKATLEVSREQIEDIIRPLGLYRKRSRTMHRLSEMYLKESWSHVTQ-- 444
Cdd:PRK10702  29 PFELLIAVLLSAQATDVSVNKATAKLYPVANTPAAMLELGVEGVKTYIKTIGLYNSKAENVIKTCRILLEQHNGEVPEdr 108

                         90
                 ....*....|....*
gi 659121238 445 -----LPGVGKYGAD 454
Cdd:PRK10702 109 aaleaLPGVGRKTAN 123
 
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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