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Conserved domains on  [gi|488219626|ref|WP_002290834|]
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MULTISPECIES: GIY-YIG nuclease family protein [Enterococcus]

Protein Classification

excinuclease ABC subunit UvrC( domain architecture ID 1002393)

excinuclease ABC subunit UvrC is part of the UvrABC repair system that catalyzes the recognition and processing of DNA lesions

CATH:  3.30.420.340
Gene Ontology:  GO:0009381|GO:0003677|GO:0006289|GO:0009380
PubMed:  16464004|2144612
SCOP:  4007100

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
UvrC super family cl33836
Excinuclease UvrABC, nuclease subunit [Replication, recombination and repair];
2-222 1.44e-44

Excinuclease UvrABC, nuclease subunit [Replication, recombination and repair];


The actual alignment was detected with superfamily member COG0322:

Pssm-ID: 440091 [Multi-domain]  Cd Length: 603  Bit Score: 160.29  E-value: 1.44e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488219626   2 LKEKIKNLPMLPGVYLMKNQEGMVIYVGKAKRLKNRVSSYFhQNKQHSKKVLRMIHHITDFDFVVVDTELDALLLECQLI 81
Cdd:COG0322    6 LKEKLKTLPTSPGVYLMKDANGEVIYVGKAKNLKNRVSSYF-QKSDLSPKTRRMVSEIADIEYIVTDTETEALLLENNLI 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488219626  82 QHYRPFYNRQMNYFSNYNYVHISNKGF---VLT---DTPTARTYGPFrlykkmPS------ILRIMEETYQM----PWLS 145
Cdd:COG0322   85 KKHKPRYNILLKDDKSYPYIKITNEEFpriFVTrgvKKDGGRYFGPY------PSagavreTLDLLQKLFPLrtcsDSLF 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488219626 146 EIS----LL----------ALRVQLPDLQEMTfeqkkKEIQGLFQGRNKKLLTYLKKRQQHFIYQLNFEKAGMLQKDIEL 211
Cdd:COG0322  159 KNRsrpcLLyqigrcsapcVGLISEEEYREDV-----EQARRFLEGKTKELIKELEEKMEEAAEELEFERAARLRDQIRA 233

                        250
                 ....*....|.
gi 488219626 212 vtyfIRRIQEQ 222
Cdd:COG0322  234 ----LEKVQEK 240
 
Name Accession Description Interval E-value
UvrC COG0322
Excinuclease UvrABC, nuclease subunit [Replication, recombination and repair];
2-222 1.44e-44

Excinuclease UvrABC, nuclease subunit [Replication, recombination and repair];


Pssm-ID: 440091 [Multi-domain]  Cd Length: 603  Bit Score: 160.29  E-value: 1.44e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488219626   2 LKEKIKNLPMLPGVYLMKNQEGMVIYVGKAKRLKNRVSSYFhQNKQHSKKVLRMIHHITDFDFVVVDTELDALLLECQLI 81
Cdd:COG0322    6 LKEKLKTLPTSPGVYLMKDANGEVIYVGKAKNLKNRVSSYF-QKSDLSPKTRRMVSEIADIEYIVTDTETEALLLENNLI 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488219626  82 QHYRPFYNRQMNYFSNYNYVHISNKGF---VLT---DTPTARTYGPFrlykkmPS------ILRIMEETYQM----PWLS 145
Cdd:COG0322   85 KKHKPRYNILLKDDKSYPYIKITNEEFpriFVTrgvKKDGGRYFGPY------PSagavreTLDLLQKLFPLrtcsDSLF 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488219626 146 EIS----LL----------ALRVQLPDLQEMTfeqkkKEIQGLFQGRNKKLLTYLKKRQQHFIYQLNFEKAGMLQKDIEL 211
Cdd:COG0322  159 KNRsrpcLLyqigrcsapcVGLISEEEYREDV-----EQARRFLEGKTKELIKELEEKMEEAAEELEFERAARLRDQIRA 233

                        250
                 ....*....|.
gi 488219626 212 vtyfIRRIQEQ 222
Cdd:COG0322  234 ----LEKVQEK 240
uvrC PRK00558
excinuclease ABC subunit UvrC;
1-89 9.44e-39

excinuclease ABC subunit UvrC;


Pssm-ID: 234792 [Multi-domain]  Cd Length: 598  Bit Score: 144.11  E-value: 9.44e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488219626   1 MLKEKIKNLPMLPGVYLMKNQEGMVIYVGKAKRLKNRVSSYFhQNKQHSKKVLRMIHHITDFDFVVVDTELDALLLECQL 80
Cdd:PRK00558   3 FLKEKLKTLPDSPGVYRMKDANGTVIYVGKAKNLKNRVRSYF-RKSHDSPKTRAMVSEIADIEYIVTRSETEALLLENNL 81


                 ....*....
gi 488219626  81 IQHYRPFYN 89
Cdd:PRK00558  82 IKKYKPRYN 90
GIY-YIG_UvrC_Cho cd10434
Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar ...
 9-90 8.87e-35

Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; UvrC is essential for nucleotide excision repair (NER). The N-terminal catalytic GIY-YIG domain of UvrC (also known as Uri domain) is responsible for the 3' incision reaction and the C-terminal half of UvrC, consisting of an UvrB-binding domain (UvrBb), EndoV-like nuclease domain and a helix-hairpin-helix (HhH) DNA-binding domain, contains the residues involved in 5' incision. The N- and C-terminal regions are joined by a common Cys-rich domain containing four conserved Cys residues. Besides UvrC, protein Cho (UvrC homolog) serves as a second endonuclease in E. coli NER. Cho contains GIY-YIG motif followed by a Cys-rich region and shares sequence homology with the N-terminal half of UvrC. It is capable of incising the DNA at the 3' side of a lesion in the presence of the UvrA and UvrB proteins during NER. The C-terminal half of Cho is a unique uncharacterized domain, which is distinct from that of UvrC. Moreover, unlike UvrC, Cho does not require the UvrC-binding domain of UvrB for the 3' incision reaction, which might cause the shift in incision position and the difference in incision efficiencies between Cho and UvrC on different damaged substrates. Due to this, the range of NER in E. coli can be broadened by combining action of Cho and UvrC. This family also includes many uncharacterized epsilon proofreading subunits of DNA polymerase III, which have an additional N-terminal ExoIII domain and a 3'-5' exonuclease domain homolog, fused to an UvrC-like region or a Cho-like region. The UvrC-like region includes a GIY-YIG motif, followed by a Cys-rich region, and an UvrB-binding domain (UvrBb), but lacks the EndoV-like nuclease domain and the helix-hairpin-helix (HhH) DNA-binding domain. The Cho-like region consists of a GIY-YIG motif, followed by the Cys-rich region, and the unique uncharacterized domain presenting in the C-terminal half of Cho. Some family members may not carry the Cys-rich region. This family also includes a specific Cho-like protein from G. violaceus, which possesses only UvrBb domain at the C-terminus, but lacks the additional N-terminal ExoIII domain. The oother two remote homologs of UvrC, Bacillus-I and -II, are included in this family as well. Both of them contain a GIY-YIG domain, but no Cys-rich region. Moreover, the whole C-terminal region of Bacillus-I is replaces by an unknown domain, and Bacillus-II possesses another unknown N-terminal extension.


Pssm-ID: 198381 [Multi-domain]  Cd Length: 81  Bit Score: 121.44  E-value: 8.87e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488219626   9 LPMLPGVYLMKNQEGMVIYVGKAKRLKNRVSSYFhQNKQHSKKVLRMIHHITDFDFVVVDTELDALLLECQLIQHYRPFY 88
Cdd:cd10434    1 LPDSPGVYLFKDADGEVLYVGKAKNLRKRVSSYF-TGERHSPKTRRLVEEIRDIEYIVTDSELEALLLEANLIKKYKPRY 79


                 ..
gi 488219626  89 NR 90
Cdd:cd10434   80 NI 81
uvrC TIGR00194
excinuclease ABC, C subunit; This family consists of the DNA repair enzyme UvrC, an ABC ...
 2-212 2.90e-32

excinuclease ABC, C subunit; This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 272953 [Multi-domain]  Cd Length: 574  Bit Score: 125.94  E-value: 2.90e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488219626    2 LKEKIKNLPMLPGVYLMKNQEGMVIYVGKAKRLKNRVSSYFhqNKQHSKKVLRMIHHITDFDFVVVDTELDALLLECQLI 81
Cdd:TIGR00194   1 LKEKLKNLPDKPGCYLMKDRNGQVLYVGKAKNLKKRVSSYF--RENNSAKTQALVKQIADIEYILTKNENEALILEANLI 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488219626   82 QHYRPFYNRQMNYFSNYNYVHISNKGF---VLTDT---PTARTYGPFRLYKKMPSILRIMEETYQM----PWLSEISLLA 151
Cdd:TIGR00194  79 KQYQPRYNVLLKDDKGYPYIYITHEKYprlLITRKlkqDKGKYFGPFTNAFALRETLDLLLKLFPLrkcaKHNRNRPCLY 158

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 488219626  152 LRVQL---PDLQEMTFEQKKKEIQG---LFQGRNKKLLTYLKKRQQHFIYQLNFEKAGMLQKDIELV 212
Cdd:TIGR00194 159 YQIGRclgPCVKEITEEEYQQIVEKielFFNGRPQEVIKELEQKMEKASENLEFEEAARIRDQIAAV 225
GIYc smart00465
GIY-YIG type nucleases (URI domain);
13-93 8.97e-13

GIY-YIG type nucleases (URI domain);


Pssm-ID: 214677 [Multi-domain]  Cd Length: 84  Bit Score: 62.82  E-value: 8.97e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488219626    13 PGVYLMKNQEGMVIYVGKAKRLKNRVSSYFHQNKQHSKKVLRMIHHITDFDFVVVDTE-LDALLLECQLIQHYRPFYNRQ 91
Cdd:smart00465   2 PGVYYITNKKNGKLYVGKAKNLRNRLKRHFSGSRKGRLLIDALLKYGGNFEFIILESFdESALELEKYLIKEYKPKYNLL 81


                   ..
gi 488219626    92 MN 93
Cdd:smart00465  82 LK 83
GIY-YIG pfam01541
GIY-YIG catalytic domain; This domain called GIY-YIG is found in the amino terminal region of ...
 13-89 2.05e-05

GIY-YIG catalytic domain; This domain called GIY-YIG is found in the amino terminal region of excinuclease abc subunit c (uvrC), bacteriophage T4 endonucleases segA, segB, segC, segD and segE; it is also found in putative endonucleases encoded by group I introns of fungi and phage. The structure of I-TevI a GIY-YIG endonuclease, reveals a novel alpha/beta-fold with a central three-stranded antiparallel beta-sheet flanked by three helices. The most conserved and putative catalytic residues are located on a shallow, concave surface and include a metal coordination site.


Pssm-ID: 426314 [Multi-domain]  Cd Length: 78  Bit Score: 41.94  E-value: 2.05e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488219626   13 PGVYLMKNQEGMVIYVGKAKRLKNRVSSYFhQNKQHSKKVLRMIHHITDFDFVVVDTELDALLLECQLIQHYRPF-YN 89
Cdd:pfam01541   2 GGIYIIRNKDNKLLYVGSTKNLERRLNQHN-AGKGAKYTRGKGVEPFKLIYLEEFPTKSEALELEKYLIKLYRPNkYN 78
 
Name Accession Description Interval E-value
UvrC COG0322
Excinuclease UvrABC, nuclease subunit [Replication, recombination and repair];
2-222 1.44e-44

Excinuclease UvrABC, nuclease subunit [Replication, recombination and repair];


Pssm-ID: 440091 [Multi-domain]  Cd Length: 603  Bit Score: 160.29  E-value: 1.44e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488219626   2 LKEKIKNLPMLPGVYLMKNQEGMVIYVGKAKRLKNRVSSYFhQNKQHSKKVLRMIHHITDFDFVVVDTELDALLLECQLI 81
Cdd:COG0322    6 LKEKLKTLPTSPGVYLMKDANGEVIYVGKAKNLKNRVSSYF-QKSDLSPKTRRMVSEIADIEYIVTDTETEALLLENNLI 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488219626  82 QHYRPFYNRQMNYFSNYNYVHISNKGF---VLT---DTPTARTYGPFrlykkmPS------ILRIMEETYQM----PWLS 145
Cdd:COG0322   85 KKHKPRYNILLKDDKSYPYIKITNEEFpriFVTrgvKKDGGRYFGPY------PSagavreTLDLLQKLFPLrtcsDSLF 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488219626 146 EIS----LL----------ALRVQLPDLQEMTfeqkkKEIQGLFQGRNKKLLTYLKKRQQHFIYQLNFEKAGMLQKDIEL 211
Cdd:COG0322  159 KNRsrpcLLyqigrcsapcVGLISEEEYREDV-----EQARRFLEGKTKELIKELEEKMEEAAEELEFERAARLRDQIRA 233

                        250
                 ....*....|.
gi 488219626 212 vtyfIRRIQEQ 222
Cdd:COG0322  234 ----LEKVQEK 240
uvrC PRK00558
excinuclease ABC subunit UvrC;
1-89 9.44e-39

excinuclease ABC subunit UvrC;


Pssm-ID: 234792 [Multi-domain]  Cd Length: 598  Bit Score: 144.11  E-value: 9.44e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488219626   1 MLKEKIKNLPMLPGVYLMKNQEGMVIYVGKAKRLKNRVSSYFhQNKQHSKKVLRMIHHITDFDFVVVDTELDALLLECQL 80
Cdd:PRK00558   3 FLKEKLKTLPDSPGVYRMKDANGTVIYVGKAKNLKNRVRSYF-RKSHDSPKTRAMVSEIADIEYIVTRSETEALLLENNL 81


                 ....*....
gi 488219626  81 IQHYRPFYN 89
Cdd:PRK00558  82 IKKYKPRYN 90
GIY-YIG_UvrC_Cho cd10434
Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar ...
 9-90 8.87e-35

Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; UvrC is essential for nucleotide excision repair (NER). The N-terminal catalytic GIY-YIG domain of UvrC (also known as Uri domain) is responsible for the 3' incision reaction and the C-terminal half of UvrC, consisting of an UvrB-binding domain (UvrBb), EndoV-like nuclease domain and a helix-hairpin-helix (HhH) DNA-binding domain, contains the residues involved in 5' incision. The N- and C-terminal regions are joined by a common Cys-rich domain containing four conserved Cys residues. Besides UvrC, protein Cho (UvrC homolog) serves as a second endonuclease in E. coli NER. Cho contains GIY-YIG motif followed by a Cys-rich region and shares sequence homology with the N-terminal half of UvrC. It is capable of incising the DNA at the 3' side of a lesion in the presence of the UvrA and UvrB proteins during NER. The C-terminal half of Cho is a unique uncharacterized domain, which is distinct from that of UvrC. Moreover, unlike UvrC, Cho does not require the UvrC-binding domain of UvrB for the 3' incision reaction, which might cause the shift in incision position and the difference in incision efficiencies between Cho and UvrC on different damaged substrates. Due to this, the range of NER in E. coli can be broadened by combining action of Cho and UvrC. This family also includes many uncharacterized epsilon proofreading subunits of DNA polymerase III, which have an additional N-terminal ExoIII domain and a 3'-5' exonuclease domain homolog, fused to an UvrC-like region or a Cho-like region. The UvrC-like region includes a GIY-YIG motif, followed by a Cys-rich region, and an UvrB-binding domain (UvrBb), but lacks the EndoV-like nuclease domain and the helix-hairpin-helix (HhH) DNA-binding domain. The Cho-like region consists of a GIY-YIG motif, followed by the Cys-rich region, and the unique uncharacterized domain presenting in the C-terminal half of Cho. Some family members may not carry the Cys-rich region. This family also includes a specific Cho-like protein from G. violaceus, which possesses only UvrBb domain at the C-terminus, but lacks the additional N-terminal ExoIII domain. The oother two remote homologs of UvrC, Bacillus-I and -II, are included in this family as well. Both of them contain a GIY-YIG domain, but no Cys-rich region. Moreover, the whole C-terminal region of Bacillus-I is replaces by an unknown domain, and Bacillus-II possesses another unknown N-terminal extension.


Pssm-ID: 198381 [Multi-domain]  Cd Length: 81  Bit Score: 121.44  E-value: 8.87e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488219626   9 LPMLPGVYLMKNQEGMVIYVGKAKRLKNRVSSYFhQNKQHSKKVLRMIHHITDFDFVVVDTELDALLLECQLIQHYRPFY 88
Cdd:cd10434    1 LPDSPGVYLFKDADGEVLYVGKAKNLRKRVSSYF-TGERHSPKTRRLVEEIRDIEYIVTDSELEALLLEANLIKKYKPRY 79


                 ..
gi 488219626  89 NR 90
Cdd:cd10434   80 NI 81
uvrC TIGR00194
excinuclease ABC, C subunit; This family consists of the DNA repair enzyme UvrC, an ABC ...
 2-212 2.90e-32

excinuclease ABC, C subunit; This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 272953 [Multi-domain]  Cd Length: 574  Bit Score: 125.94  E-value: 2.90e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488219626    2 LKEKIKNLPMLPGVYLMKNQEGMVIYVGKAKRLKNRVSSYFhqNKQHSKKVLRMIHHITDFDFVVVDTELDALLLECQLI 81
Cdd:TIGR00194   1 LKEKLKNLPDKPGCYLMKDRNGQVLYVGKAKNLKKRVSSYF--RENNSAKTQALVKQIADIEYILTKNENEALILEANLI 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488219626   82 QHYRPFYNRQMNYFSNYNYVHISNKGF---VLTDT---PTARTYGPFRLYKKMPSILRIMEETYQM----PWLSEISLLA 151
Cdd:TIGR00194  79 KQYQPRYNVLLKDDKGYPYIYITHEKYprlLITRKlkqDKGKYFGPFTNAFALRETLDLLLKLFPLrkcaKHNRNRPCLY 158

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 488219626  152 LRVQL---PDLQEMTFEQKKKEIQG---LFQGRNKKLLTYLKKRQQHFIYQLNFEKAGMLQKDIELV 212
Cdd:TIGR00194 159 YQIGRclgPCVKEITEEEYQQIVEKielFFNGRPQEVIKELEQKMEKASENLEFEEAARIRDQIAAV 225
uvrC PRK14669
excinuclease ABC subunit C; Provisional
 2-104 3.85e-23

excinuclease ABC subunit C; Provisional


Pssm-ID: 237784 [Multi-domain]  Cd Length: 624  Bit Score: 99.60  E-value: 3.85e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488219626   2 LKEKIKNLPMLPGVYLMKNQEGMVIYVGKAKRLKNRVSSYFHQNKQHSKKVLRMIHHITDFDFVVVDTELDALLLECQLI 81
Cdd:PRK14669   3 LRDKIRTLPTSPGVYLYKNAGGEVIYVGKAKNLRSRVRSYFSEDKLGNIKTGSLIREAVDIDYILVDNEKEALALENNLI 82

                         90       100
                 ....*....|....*....|...
gi 488219626  82 QHYRPFYNRQMNYFSNYNYVHIS 104
Cdd:PRK14669  83 KQYKPRFNILLRDDKTYPYVKLT 105
uvrC PRK14666
excinuclease ABC subunit C; Provisional
 1-218 1.13e-22

excinuclease ABC subunit C; Provisional


Pssm-ID: 237782 [Multi-domain]  Cd Length: 694  Bit Score: 98.42  E-value: 1.13e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488219626   1 MLKEKIKNLPMLPGVYLMKNQEGMVIYVGKAKRLKNRVSSYFHQNKQHSKKVLRMIHHITDFDFVVVDTELDALLLECQL 80
Cdd:PRK14666   1 MQKPDLSTIPLTPGVYLYKDEAGRIIYVGKARHLRRRVASYFRDVSALTPKTVAMLRHAVTIDTLSTTTEKEALLLEASL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488219626  81 IQHYRPFYNRQMNYFSNYNYVHISNKG----FVLTDTPT---ARTYGPFRLYKKMPSILRIMEETYQMPWLSEISlLALR 153
Cdd:PRK14666  81 IKKHRPRYNIVLRDDKQYVLFRLGAKHpyprLEIVRKARrdgARYFGPFTSASAARETWKTIHRAFPLRRCSDRA-FGNR 159

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488219626 154 V---------QLP-----DLQEMTFEQKKKEIQGLFQGRNKKLLTYLKKRQQHFIYQLNFEKAGMLQKDIELVTYFIRR 218
Cdd:PRK14666 160 VraclyhfmgQCLgpcvnDVPRETYAALVRKVEMLLSGRSGELVDALRTEMEAASEALEFERAAVLRDQIRAVERTVER 238
PRK07883 PRK07883
DEDD exonuclease domain-containing protein;
8-123 2.34e-21

DEDD exonuclease domain-containing protein;


Pssm-ID: 236123 [Multi-domain]  Cd Length: 557  Bit Score: 94.21  E-value: 2.34e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488219626   8 NLPMLPGVYLMKNQEGMVIYVGKAKRLKNRVSSYFHQNKQHSkKVLRMIHHITDFDFVVVDTELDALLLECQLIQHYRPF 87
Cdd:PRK07883 213 GLPHAPGVYLFRGPSGEVLYVGTAVNLRRRVRSYFTAAETRG-RMREMVALAERVDHVECAHALEAEVRELRLIAAHKPP 291

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 488219626  88 YNRQMNYFSNYNYVhisnkgfVLTDTP-------------TARTYGPFR 123
Cdd:PRK07883 292 YNRRSKFPERRWWV-------RLTDEAfprlsvvraveddGAAYLGPFR 333
uvrC PRK14668
excinuclease ABC subunit C; Provisional
 2-139 4.77e-19

excinuclease ABC subunit C; Provisional


Pssm-ID: 184785 [Multi-domain]  Cd Length: 577  Bit Score: 87.51  E-value: 4.77e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488219626   2 LKEKIKNLPMLPGVYLMKnQEGMVIYVGKAKRLKNRVSSYfhqNKQHSKKVLRMIHHITDFDFVVVDTELDALLLECQLI 81
Cdd:PRK14668   6 VRERAAELPREPGVYQFV-AGGTVLYVGKAVDLRDRVRSY---ADPRSERIRRMVERADDIDFAVTDTETQALLLEANLI 81

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488219626  82 QHYRPFYNRQMNYFSNYNYVHISNKGFV---LTDTP--TARTYGPFRLYKKMPSILRIMEETY 139
Cdd:PRK14668  82 KRHQPRYNVRLKDDKSYPLVQLTDHPVPrieVTRDPdeGATVFGPYTDKGRVETVVKALRETY 144
uvrC PRK14672
excinuclease ABC subunit C; Provisional
 10-212 1.12e-15

excinuclease ABC subunit C; Provisional


Pssm-ID: 173135 [Multi-domain]  Cd Length: 691  Bit Score: 77.47  E-value: 1.12e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488219626  10 PMLPGVYLMKNQEGMVIYVGKAKRLKNRVSSYFHQnkQHSKKVLRMIHHITDFDFVVVDTELDALLLECQLIQHYRPFYN 89
Cdd:PRK14672  19 PSTSGVYLWKDVHGVVIYVGKAKSLRTRLTSYFRC--RHDPKTRVLMSRAAALEYLQTQHEYEALLLENTLIKKHTPRYN 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488219626  90 RQMNYFSNYNYVHISNKGFVLTDTPT------ARTYGPFRLYKKMPSILRIMEETYQMPWLSEIS-----LLALRVQLPD 158
Cdd:PRK14672  97 ICLKDGKTYPLLKLTCEPFPRIFRTRqfcqdgARYFGPFPDVQILDSFLKLILRTYKIRTCTTLRkrknpCLYYHLKRCD 176

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 488219626 159 ------LQEMTFEQKKKEIQGLFQGRNKKLLTYLKKRQQHFIYQLNFEKAGMLQKDIELV 212
Cdd:PRK14672 177 apccgwVSPRTYQKDIHEITLLLEGNIDATVARLEKRMKRAVRQEAFEAAARIRDDIQAI 236
uvrC PRK14667
excinuclease ABC subunit C; Provisional
 2-209 9.86e-14

excinuclease ABC subunit C; Provisional


Pssm-ID: 237783 [Multi-domain]  Cd Length: 567  Bit Score: 71.69  E-value: 9.86e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488219626   2 LKEKIKNLPMLPGVYLMKNQeGMVIYVGKAKRLKNRVSSYFHQNKQhSKKVLRMIHHITDFDFVVVDTELDALLLECQLI 81
Cdd:PRK14667   6 ALELIEKAPEEPGVYLFKKK-KRYIYIGKAKNIKNRLLQHYKQSET-DPKERAIFSESSSLEWIITRNEYEALVLEIDLI 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488219626  82 QHYRPFYNRQMNYFSNYNYVHISNKGFvltdtPTART----------YGPFRLYKKMPSILRIMEETYQ------MPWLS 145
Cdd:PRK14667  84 QQYKPKYNVLLKSGSGYPMLLITDDEY-----PTVKIvrgtgekgeyFGPFLPARKARKVKKLIHKLFKlrtcdpMPKRK 158

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488219626 146 EISL---LAL----RVQLPDLQEmtFEQKKKEIQGLFQGRNKKLLTYLKKRQQHFIYQLNFEKAGMLQKDI 209
Cdd:PRK14667 159 EPCMdyhLGLcsgpCCGKISKED--YELSVKSAKAFLSGNVKEVLPELYDKIEEYSQKLMFEKAAVIRDQI 227
GIYc smart00465
GIY-YIG type nucleases (URI domain);
13-93 8.97e-13

GIY-YIG type nucleases (URI domain);


Pssm-ID: 214677 [Multi-domain]  Cd Length: 84  Bit Score: 62.82  E-value: 8.97e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488219626    13 PGVYLMKNQEGMVIYVGKAKRLKNRVSSYFHQNKQHSKKVLRMIHHITDFDFVVVDTE-LDALLLECQLIQHYRPFYNRQ 91
Cdd:smart00465   2 PGVYYITNKKNGKLYVGKAKNLRNRLKRHFSGSRKGRLLIDALLKYGGNFEFIILESFdESALELEKYLIKEYKPKYNLL 81


                   ..
gi 488219626    92 MN 93
Cdd:smart00465  82 LK 83
uvrC PRK14670
excinuclease ABC subunit C; Provisional
 18-207 1.31e-12

excinuclease ABC subunit C; Provisional


Pssm-ID: 173133 [Multi-domain]  Cd Length: 574  Bit Score: 68.40  E-value: 1.31e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488219626  18 MKNQEGMVIYVGKAKRLKNRVSSYFHQNKQHSKKVLrmIHHITDFDFVVVDTELDALLLECQLIQHYRPFYNRQMNYFSN 97
Cdd:PRK14670   1 MYSENNKILYIGKAKNLRSRVKNYFLEKISHKTKIL--MKNVKNIEVITTNSEYEALLLECNLIKTHKPDYNIKLKDDKG 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488219626  98 YNYVHISNKGF--------VLTDtpTARTYGPFRLYKKMPSILRIMEETYQM---------PWLSEISLLALRVQLPDLQ 160
Cdd:PRK14670  79 YPMIRITCEKYprifktrkIIND--GSEYFGPYVNVKKLDLVLDLINKTFKTrkckkksknPCLYFHMGQCLGVCYREDL 156

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 488219626 161 EMTFEQKKKEIQGLFQGRNKKLLTYLKKRQQHFIYQLNFEKAGMLQK 207
Cdd:PRK14670 157 EKEYQKEVDKIKHILNGNISKLLSQIEIKMKEAIQKEDFEAAIKLKE 203
PRK10545 PRK10545
excinuclease Cho;
2-92 5.08e-10

excinuclease Cho;


Pssm-ID: 182535  Cd Length: 286  Bit Score: 59.30  E-value: 5.08e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488219626   2 LKEKIKNLPMLPGVYLMKNQ-EGMVIYVGKAKRLKNRVSSYFHQNKQHSkkVLRMIHHITdfdFVVVDTELDALLLECQL 80
Cdd:PRK10545  24 LRPFLEDLPKLPGVYLFHGEsDTMPLYIGKSVNIRSRVLSHLRTPDEAA--MLRQSRRIS---WICTAGEIGALLLEARL 98

                         90
                 ....*....|..
gi 488219626  81 IQHYRPFYNRQM 92
Cdd:PRK10545  99 IKEQQPLFNKRL 110
GIY-YIG_SF cd00719
GIY-YIG nuclease domain superfamily; The GIY-YIG nuclease domain superfamily includes a large ...
 14-84 2.00e-07

GIY-YIG nuclease domain superfamily; The GIY-YIG nuclease domain superfamily includes a large and diverse group of proteins involved in many cellular processes, such as class I homing GIY-YIG family endonucleases, prokaryotic nucleotide excision repair proteins UvrC and Cho, type II restriction enzymes, the endonuclease/reverse transcriptase of eukaryotic retrotransposable elements, and a family of eukaryotic enzymes that repair stalled replication forks. All of these members contain a conserved GIY-YIG nuclease domain that may serve as a scaffold for the coordination of a divalent metal ion required for catalysis of the phosphodiester bond cleavage. By combining with different specificity, targeting, or other domains, the GIY-YIG nucleases may perform different functions.


Pssm-ID: 198380 [Multi-domain]  Cd Length: 69  Bit Score: 47.36  E-value: 2.00e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488219626  14 GVYLMKNQEGMVIYVGKAKRLKNRVSSYFHQNKQHSKKVLRmihhITDFDFVVVD--TELDALLLECQLIQHY 84
Cdd:cd00719    1 GVYVLYDEDNGLIYVGQTKNLRNRIKEHLRKQRSDWTKGLK----PFEILYLEVApeAESELLDLEAALIKKL 69
GIY-YIG pfam01541
GIY-YIG catalytic domain; This domain called GIY-YIG is found in the amino terminal region of ...
 13-89 2.05e-05

GIY-YIG catalytic domain; This domain called GIY-YIG is found in the amino terminal region of excinuclease abc subunit c (uvrC), bacteriophage T4 endonucleases segA, segB, segC, segD and segE; it is also found in putative endonucleases encoded by group I introns of fungi and phage. The structure of I-TevI a GIY-YIG endonuclease, reveals a novel alpha/beta-fold with a central three-stranded antiparallel beta-sheet flanked by three helices. The most conserved and putative catalytic residues are located on a shallow, concave surface and include a metal coordination site.


Pssm-ID: 426314 [Multi-domain]  Cd Length: 78  Bit Score: 41.94  E-value: 2.05e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488219626   13 PGVYLMKNQEGMVIYVGKAKRLKNRVSSYFhQNKQHSKKVLRMIHHITDFDFVVVDTELDALLLECQLIQHYRPF-YN 89
Cdd:pfam01541   2 GGIYIIRNKDNKLLYVGSTKNLERRLNQHN-AGKGAKYTRGKGVEPFKLIYLEEFPTKSEALELEKYLIKLYRPNkYN 78
GIY-YIG_bI1_like cd10445
Catalytic GIY-YIG domain of putative intron-encoded endonuclease bI1 and similar proteins; The ...
 13-89 4.04e-04

Catalytic GIY-YIG domain of putative intron-encoded endonuclease bI1 and similar proteins; The prototype of this family is a putative intron-encoded mitochondrial DNA endonuclease bI1 found in mitochondrion Ustilago maydis. This protein may arise from proteolytic cleavage of an in-frame translation of COB exon 1 plus intron 1, containing the bI1 open reading frame. It contains an N-terminal truncated non-functional cytochrome b region and a C-terminal intron-encoded endonuclease bI1 region. The bI1 region shows high sequence similarity to endonucleases of group I introns of fungi and phage and might be involved in intron homing. Many uncharacterized bI1 homologs existing in fungi and chlorophyta in this family do not contain the cytochrome b region, but have a standalone bI1-like region, which contains a GIY-YIG domain and a minor-groove binding alpha-helix nuclease-associated modular domain (NUMOD). This family also includes a Yarrowia lipolytica mobile group-II intron COX1-i1, also called intron alpha, encoding protein with reverse transcriptase activity. The group-II intron COX1-i1 may be involv ed both in the generation of the circular multimeric DNA molecules (senDNA alpha) which amplify during the senescence syndrome and in the generation of the site-specific deletion which accumulates in the premature-death syndrome.


Pssm-ID: 198392 [Multi-domain]  Cd Length: 88  Bit Score: 38.75  E-value: 4.04e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488219626  13 PGVYLMKNQEGMVIYVGKAKRLKNRVSSYF-HQNKQHSKKVLRMIHH--ITDFDFVVV-----DTELDALLLECQLIQHY 84
Cdd:cd10445    1 SGIYIWINKINGKIYVGSSINLYKRLRSYLnPSYLKKNSPILRALLKygLSNFTLTILeyyngENKEELLELEQYYIDLL 80


                 ....*
gi 488219626  85 RPFYN 89
Cdd:cd10445   81 KPEYN 85
GIY-YIG_RE_Eco29kI_like cd10435
Catalytic GIY-YIG domain of type II restriction endonucleases R.Eco29kI, R.Cfr42I, and similar ...
 26-99 7.79e-04

Catalytic GIY-YIG domain of type II restriction endonucleases R.Eco29kI, R.Cfr42I, and similar proteins; This family corresponds to the catalytic GIY-YIG domain of a group of GGCGCC-specific type II restriction endonucleases R.Eco29kI, R.Cfr42I, and similar proteins. R.Eco29kI is encoded on plasmid pECO29 in the E. coli strain 29K. This enzyme recognizes the palindromic 5'-CCGC/GG-3' target and cuts between Cyt4 and Gua5 on each strand of the restriction site to generate 3'-staggered ends. R.Eco29kI forms a domain-swapped homodimeric catalytically active complex during DNA binding and cleavage. Each subunit contains one GIY-YIG catalytic motif. Restriction endonucleases R.Cfr42I is an isoschizomer of R.Eco29kI. Unlike R.Eco29kI, R.Cfr42I is functional as a homotetramer, binding and cleaving two cognate DNA molecules in a cooperative manner. Members in this family are single-domain proteins sharing sequence similarities with the catalytic domain of GIY-YIG endonucleases, such as homing endonuclease I-TevI. However, they utilize loop insertions and terminal extensions instead of the separate DNA-binding domain to interact with the target site 5'-CCGC/GG-3'. A divalent metal-ion cofactor is required for their catalysis, but not for substrate binding. This family also includes a hypothetical protein from Deinococcus radiodurans that corresponds to MraI, a type II restriction enzyme similar to GIY-YIG family of homing endonucleases. MraI is shown to be an isoschizomer of Eco29kI, Cfr42I recognizing the palindromic nucleotide sequence 5'-CCGC reduced GG-3'. The enzyme shows an absolute requirement of Mg2+, but is active in the absence of added 2-mercaptoethanol. MraI represents the first restriction enzyme from a bacterium whose DNA lacks modified methylated bases.


Pssm-ID: 198382  Cd Length: 117  Bit Score: 38.54  E-value: 7.79e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488219626  26 IYVGKAKRLKNRVsSYFHQNKQHSKKVLRMIHH-----------ITDFDFVVVDTELDAL-LLECQLIQHYRPFYNRQMN 93
Cdd:cd10435   31 IYVGKAVPAGARQ-GEGKKAEQGSALYKRLSEHrksiaatsnldVADFYCRVLVVAPGWIpLAESVLISLFRPAWNSHVD 109


                 ....*.
gi 488219626  94 YFSNYN 99
Cdd:cd10435  110 GFGNHG 115
RE_Eco29kI pfam09517
Eco29kI restriction endonuclease; This family includes the Eco29kI (recognizes and cleaves ...
 19-97 9.62e-04

Eco29kI restriction endonuclease; This family includes the Eco29kI (recognizes and cleaves CCGC^GG ) restriction endonuclease.


Pssm-ID: 370543  Cd Length: 161  Bit Score: 39.23  E-value: 9.62e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488219626   19 KNQEGMVIYVGKA----KRlKNRVSSY-------FHQNKQHSKKV-----LRmihhITDFD--FVVVDTELDAlLLECQL 80
Cdd:pfam09517  27 RGSFHAPIYVGKAvpkgWR-KGGGSDSavqgtelFNRLREHARSIaqaenLD----LADFRcrFLVVEDDWIP-LGEAAL 100

                          90
                  ....*....|....*..
gi 488219626   81 IQHYRPFYNRQMNYFSN 97
Cdd:pfam09517 101 IRKYQPLWNTVVDGFGN 117
 
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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