peg_817

peg_817

GeneID in NCBI database:Locus tag:
Protein GI in NCBI database:not defined in NCBI databaseProtein Accession:
Gene range:-(875116, 875562)Protein Length:148aa
Gene description:
COG prediction:none
KEGG prediction:not defined in KEGG
SEED prediction:DNA repair protein RadC
Pathway involved in KEGG:not defined
Subsystem involved in SEED:DNA repair, bacterial
sequencesequence profile

Prediction of Local Sequence Properties

SourceSummaryResult
scaler
NCBI Databasesequence
PSIPREDsecondary structure
SSPROsecondary structure
DISEMBLcoil and loop
DISEMBLflexible loop
SEGlow complexity
DISOPREDdisordered
DISEMBLmissing residues
DISPROdisordered
TMHMMnone TM-Helix
TOPPRED1 TM-Helix
HMMTOP1 TM-Helix
MEMSATnone TM-Helix
MEMSAT_SVMnone TM-Helix
PHOBIUSnone TM-Helix
SignalP_HMMno
SignalP_NNno
COILScoiled coil
70% MSAconservation map
90% MSAconservation map
  
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------15
LEDFRMSKAPSKDSHLDYIGHHNRLRDRFLQKGENALAYYEILELILFRLIPRKDTKSIAKALLKRFATLGGVFGAPLHLLQEINRIGKRVALELKLVSVASQRILKANWSIKKFLTPGQPCLISVERHYPMKNANNFAYCFSINIIF
ccccccccccccccccccccHHHHHHHHHHHcccccccHHHHHHHHHHHccccccHHHHHHHHHHHHccHHHHHcccHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHccccccEEEEEEEccccc
cccEEEccccccccccccccHHHHHHHHHHHccccHccHHHHHHHHHHHccccccHHHHHHHHHHHHccHHHHHcccHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHcccccccEEEEEEEEEEc
ledfrmskapskdshldyighHNRLRDRFLQKGENALAYYEILELILFRLIPRKDTKSIAKALLKRFATlggvfgaplhLLQEINRIGKRVALELKLVSVASQRILKANWSIkkfltpgqpclisverhypmknannfayCFSINIIF
ledfrmskapskdshldyighHNRLRDRFLQKGENALAYYEILELILFRLIPRKDTKSIAKALLKRFATLGGVFGAPLHLLQEINRIGKRVALELKLVSVASQRILKanwsikkfltpgQPCLISVERHYPMKNANNFAYCFSINIIF
LEDFRMSKAPSKDSHLDYIGHHNRLRDRFLQKGENALAYYEILELILFRLIPRKDTKSIAKALLKRFATLGGVFGAPLHLLQEINRIGKRVALELKLVSVASQRILKANWSIKKFLTPGQPCLISVERHYPMKNANNFAYCFSINIIF
***********************RLRDRFLQKGENALAYYEILELILFRLIPRKDTKSIAKALLKRFATLGGVFGAPLHLLQEINRIGKRVALELKLVSVASQRIL**********TPGQPCLISVERHYPMKNANNFAYCFSINIIF
*************SHLDYIGHHNRLRDRFLQKGENALAYYEILELILFRLIPRKDTKSIAKALLKRFATLGGVFGAPLHLLQEINRIGKRVALELKLVSVASQRILKANWSIKKFLTPGQPCLISVERHYPMKNANNFAYCFSINIIF
*EDFRMSKAPSKDSHLDYIGHHNRLRDRFLQKGENALAYYEILELILFRLIPRKDTKSIAKALLKRFATLGGVFGAPLHLLQEINRIGKRVALELKLVSVASQRILKANWSIKKFLTPGQPCLISVERHYPMKNANNFAYCFSINIIF
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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LEDFRMSKAPSKDSHLDYIGHHNRLRDRFLQKGENALAYYEILELILFRLIPRKDTKSIAKALLKRFATLGGVFGAPLHLLQEINRIGKRVALELKLVSVASQRILKANWSIKKFLTPGQPCLISVERHYPMKNANNFAYCFSINIIF
LEDFRMSKAPSKDSHLDYIGHHNRLRDRFLQKGENALAYYEILELILFRLIPRKDTKSIAKALLKRFATLGGVFGAPLHLLQEINRIGKRVALELKLVSVASQRILKANWSIKKFLTPGQPCLISVERHYPMKNANNFAYCFSINIIF
LEDFRMSKAPSKDSHLDYIGHHNRLRDRFLQKGENALAYYEILELILFRLIPRKDTKSIAKALLKRFATLGGVFGAPLHLLQEINRIGKRVALELKLVSVASQRILKANWSIKKFLTPGQPCLISVERHYPMKNANNFAYCFSINIIF

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

No hits with e-value below 0.05

Close Homologs Detected BLAST or PSI-BLAST in the First 2 Iterations

IdentityAlignment graphLength Definition Round E-value
Target148
315122683237 DNA repair protein RadC [Candidatus Liberibacter solana 1 7e-39
15965481262 DNA repair protein RadC [Sinorhizobium meliloti 1021] L 1 5e-30
227821958263 DNA repair protein RadC [Sinorhizobium fredii NGR234] L 1 1e-27
150396672260 DNA repair protein RadC [Sinorhizobium medicae WSM419] 1 1e-27
218458578261 DNA repair protein RadC [Rhizobium etli Kim 5] Length = 1 6e-27
222148674278 DNA repair protein RadC [Agrobacterium vitis S4] Length 1 8e-27
218510678274 DNA repair protein RadC [Rhizobium etli Brasil 5] Lengt 1 9e-27
209549111275 DNA repair protein RadC [Rhizobium leguminosarum bv. tr 1 9e-27
327192095274 DNA repair protein RadC [Rhizobium etli CNPAF512] Lengt 1 9e-27
218672510274 DNA repair protein RadC [Rhizobium etli GR56] Length = 1 9e-27
>gi|315122683|ref|YP_004063172.1| DNA repair protein RadC [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 237 Back     alignment and organism information
 Score =  163 bits (413), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 85/113 (75%), Positives = 94/113 (83%)

Query: 4   FRMSKAPSKDSHLDYIGHHNRLRDRFLQKGENALAYYEILELILFRLIPRKDTKSIAKAL 63
           F MSK  +KD  +D IGH NRLRDRFLQ G++ALA YEILELILF+LIPR+DTKSIAKAL
Sbjct: 4   FLMSKRSAKDFDIDCIGHRNRLRDRFLQGGDSALADYEILELILFKLIPRRDTKSIAKAL 63

Query: 64  LKRFATLGGVFGAPLHLLQEINRIGKRVALELKLVSVASQRILKANWSIKKFL 116
           LKRF TLGGVFGAPLHLLQEI  IGK  ALELKL+SVASQRILK+    +K L
Sbjct: 64  LKRFITLGGVFGAPLHLLQEIEGIGKTAALELKLISVASQRILKSKLINQKIL 116


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|15965481|ref|NP_385834.1| DNA repair protein RadC [Sinorhizobium meliloti 1021] Length = 262 Back     alignment and organism information
>gi|227821958|ref|YP_002825929.1| DNA repair protein RadC [Sinorhizobium fredii NGR234] Length = 263 Back     alignment and organism information
>gi|150396672|ref|YP_001327139.1| DNA repair protein RadC [Sinorhizobium medicae WSM419] Length = 260 Back     alignment and organism information
>gi|218458578|ref|ZP_03498669.1| DNA repair protein RadC [Rhizobium etli Kim 5] Length = 261 Back     alignment and organism information
>gi|222148674|ref|YP_002549631.1| DNA repair protein RadC [Agrobacterium vitis S4] Length = 278 Back     alignment and organism information
>gi|218510678|ref|ZP_03508556.1| DNA repair protein RadC [Rhizobium etli Brasil 5] Length = 274 Back     alignment and organism information
>gi|209549111|ref|YP_002281028.1| DNA repair protein RadC [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 275 Back     alignment and organism information
>gi|327192095|gb|EGE59073.1| DNA repair protein RadC [Rhizobium etli CNPAF512] Length = 274 Back     alignment and organism information
>gi|218672510|ref|ZP_03522179.1| DNA repair protein RadC [Rhizobium etli GR56] Length = 274 Back     alignment and organism information

Conserved Domains in CDD Database
Detected by RPS-BLAST and HHsearch

Conserved Domains in CDD Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target148
PRK00024224 PRK00024, PRK00024, hypothetical protein; Reviewed 1e-15
TIGR00608218 TIGR00608, radc, DNA repair protein radc 9e-08
COG2003224 COG2003, RadC, DNA repair proteins [DNA replication, re 6e-16
>gnl|CDD|178801 PRK00024, PRK00024, hypothetical protein; Reviewed Back     alignment and domain information
>gnl|CDD|161955 TIGR00608, radc, DNA repair protein radc Back     alignment and domain information
>gnl|CDD|32186 COG2003, RadC, DNA repair proteins [DNA replication, recombination, and repair] Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 148
PRK00024224 radC DNA repair protein RadC; Reviewed 100.0
COG2003224 RadC DNA repair proteins [DNA replication, recombinatio 100.0
TIGR00608223 radc DNA repair protein RadC; InterPro: IPR001405 RadC 100.0
cd00056158 ENDO3c endonuclease III; includes endonuclease III (DNA 96.21
pfam00730144 HhH-GPD HhH-GPD superfamily base excision DNA repair pr 95.06
smart00478149 ENDO3c endonuclease III. includes endonuclease III (DNA 94.42
COG0177211 Nth Predicted EndoIII-related endonuclease [DNA replica 91.63
COG2231215 Uncharacterized protein related to Endonuclease III [DN 91.33
PRK13913218 3-methyladenine DNA glycosylase; Provisional 90.59
PRK13482352 DNA integrity scanning protein DisA; Provisional 98.01
PRK13766764 Hef nuclease; Provisional 97.95
COG1948254 MUS81 ERCC4-type nuclease [DNA replication, recombinati 97.45
PRK07956668 ligA NAD-dependent DNA ligase LigA; Validated 96.03
TIGR00575706 dnlj DNA ligase, NAD-dependent; InterPro: IPR001679 DNA 95.9
COG0272667 Lig NAD-dependent DNA ligase (contains BRCT domain type 95.38
PRK10702211 endonuclease III; Provisional 95.38
PRK10702211 endonuclease III; Provisional 94.74
PRK01172674 ski2-like helicase; Provisional 94.31
COG0177211 Nth Predicted EndoIII-related endonuclease [DNA replica 94.27
PRK10880 350 adenine DNA glycosylase; Provisional 92.9
PRK00254717 ski2-like helicase; Provisional 92.29
cd00056158 ENDO3c endonuclease III; includes endonuclease III (DNA 91.91
PTZ00035 350 Rad51; Provisional 91.56
smart00478149 ENDO3c endonuclease III. includes endonuclease III (DNA 90.72
KOG2841254 consensus 97.74
PRK00558609 uvrC excinuclease ABC subunit C; Validated 96.91
COG1623349 Predicted nucleic-acid-binding protein (contains the HH 96.68
COG0322581 UvrC Nuclease subunit of the excinuclease complex [DNA 96.02
TIGR01259124 comE comEA protein; InterPro: IPR004787 The comE locus 94.22
pfam0063330 HHH Helix-hairpin-helix motif. The helix-hairpin-helix 94.14
PRK0775895 hypothetical protein; Provisional 92.29
PRK08097563 ligB NAD-dependent DNA ligase LigB; Reviewed 92.19
COG5241224 RAD10 Nucleotide excision repair endonuclease NEF1, RAD 90.51
>PRK00024 radC DNA repair protein RadC; Reviewed Back     alignment and domain information
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair] Back     alignment and domain information
>TIGR00608 radc DNA repair protein RadC; InterPro: IPR001405 RadC is a DNA repair protein found in many bacteria Back     alignment and domain information
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases Back     alignment and domain information
>pfam00730 HhH-GPD HhH-GPD superfamily base excision DNA repair protein Back     alignment and domain information
>smart00478 ENDO3c endonuclease III Back     alignment and domain information
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair] Back     alignment and domain information
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK13913 3-methyladenine DNA glycosylase; Provisional Back     alignment and domain information
>PRK13482 DNA integrity scanning protein DisA; Provisional Back     alignment and domain information
>PRK13766 Hef nuclease; Provisional Back     alignment and domain information
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated Back     alignment and domain information
>TIGR00575 dnlj DNA ligase, NAD-dependent; InterPro: IPR001679 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalyzing the formation of an internucleotide ester bond between phosphate and deoxyribose Back     alignment and domain information
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK10702 endonuclease III; Provisional Back     alignment and domain information
>PRK10702 endonuclease III; Provisional Back     alignment and domain information
>PRK01172 ski2-like helicase; Provisional Back     alignment and domain information
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK10880 adenine DNA glycosylase; Provisional Back     alignment and domain information
>PRK00254 ski2-like helicase; Provisional Back     alignment and domain information
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases Back     alignment and domain information
>PTZ00035 Rad51; Provisional Back     alignment and domain information
>smart00478 ENDO3c endonuclease III Back     alignment and domain information
>KOG2841 consensus Back     alignment and domain information
>PRK00558 uvrC excinuclease ABC subunit C; Validated Back     alignment and domain information
>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only] Back     alignment and domain information
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair] Back     alignment and domain information
>TIGR01259 comE comEA protein; InterPro: IPR004787 The comE locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA Back     alignment and domain information
>pfam00633 HHH Helix-hairpin-helix motif Back     alignment and domain information
>PRK07758 hypothetical protein; Provisional Back     alignment and domain information
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed Back     alignment and domain information
>COG5241 RAD10 Nucleotide excision repair endonuclease NEF1, RAD10 subunit [DNA replication, recombination, and repair] Back     alignment and domain information

Homologous Structures in PDB Database
Detected by PSI-BLAST, RPS-BLAST and HHsearch

Homologous Structures Detected by PSI-BLAST against Nonredundant Database

No homologous structure with e-value below 0.005

Homologous Structures in PDB70 Database Detected by RPS-BLAST

No hit with e-value below 0.005

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target148
3c1y_A377 DNA integrity scanning protein DISA; DNA damage, DNA re 97.96
1x2i_A75 HEF helicase/nuclease; alpha helix, helix-hairpin-helix 97.88
2bgw_A219 XPF endonuclease; hydrolase, structure specific endonuc 97.85
1z00_A89 DNA excision repair protein ERCC-1; helix-hairpin-helix 97.62
1z00_B84 DNA repair endonuclease XPF; helix-hairpin-helix, hydro 96.5
3c65_A226 Uvrabc system protein C; UVRC, endonuclease, nucleotide 96.03
1dgs_A667 DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 95.95
1kea_A221 Possible G-T mismatches repair enzyme; DNA repair, DNA 95.65
1pu6_A218 3-methyladenine DNA glycosylase; helix-hairpin-helix, b 95.62
1ngn_A155 Methyl-CPG binding protein MBD4; mismacth repair in met 95.56
2owo_A671 DNA ligase; protein/DNA complex, ligase/DNA complex; HE 95.45
1orn_A226 Endonuclease III; DNA repair, DNA glycosylase, [4Fe-4S] 94.75
1kg2_A225 A/G-specific adenine glycosylase; DNA repair, hydrolase 94.7
1kea_A221 Possible G-T mismatches repair enzyme; DNA repair, DNA 94.25
2abk_A211 Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {E 93.83
1kg2_A225 A/G-specific adenine glycosylase; DNA repair, hydrolase 93.64
3fsp_A 369 A/G-specific adenine glycosylase; protein-DNA complex, 93.57
3n5n_X 287 A/G-specific adenine DNA glycosylase; alpha-helices, he 93.57
3fsp_A 369 A/G-specific adenine glycosylase; protein-DNA complex, 93.07
1orn_A226 Endonuclease III; DNA repair, DNA glycosylase, [4Fe-4S] 92.97
2abk_A211 Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {E 92.96
3i0w_A290 8-oxoguanine-DNA-glycosylase; OGG, cacogg, DNA, 8-OXOG, 91.57
2a1j_B91 DNA excision repair protein ERCC-1; XPF, xeroderma pigm 97.52
1kft_A78 UVRC, excinuclease ABC subunit C; helix-hairpin-helix, 97.36
2a1j_A63 DNA repair endonuclease XPF; XPF, xeroderma pigmentosum 96.71
2nrt_A220 Uvrabc system protein C; UVRC, endonuclease, RNAse H, h 95.33
2zj8_A720 DNA helicase, putative SKI2-type helicase; RECA fold, A 94.92
1vq8_Y 241 50S ribosomal protein L32E; ribosome 50S, protein-prote 91.07
>3c1y_A DNA integrity scanning protein DISA; DNA damage, DNA repair, DNA-binding, DNA binding protein; HET: DNA 2BA; 2.10A {Thermotoga maritima} PDB: 3c1z_A* 3c21_A* 3c23_A* Back     alignment and structure
Probab=97.96  E-value=2.5e-05  Score=53.86  Aligned_cols=82  Identities=13%  Similarity=0.104  Sum_probs=63.0

Q ss_pred             HHHHHHHCCHHHCCHHHHHHHHHHCCCCCC-CH--------------------HHHHHHHHHHCCCHHHHHCCCHHHHHH
Q ss_conf             999998239221898999999973379989-88--------------------999999997379978985099789973
Q 537021.9.peg.8   25 LRDRFLQKGENALAYYEILELILFRLIPRK-DT--------------------KSIAKALLKRFATLGGVFGAPLHLLQE   83 (148)
Q Consensus        25 ~RErll~~G~~~LsD~ELLallL~~g~~~~-~~--------------------~~lA~~lL~~fGsL~~ll~as~~eL~~   83 (148)
                      ..+.+-.--.+.+.|.+-++-+|++...+. ++                    ..++.+|.++||+|..+++||.+||..
T Consensus       272 a~~~L~~L~~~elldl~~ia~~LGy~~~g~~~llD~~v~pRGyRiLskiprlp~~vienLV~~FgsLq~Ll~AS~EeL~e  351 (377)
T 3c1y_A          272 AQNILQDFITRREPSPISISRVLGYDVQQAAQLDDVLVSARGYRLLKTVARIPLSIGYNVVRMFKTLDQISKASVEDLKK  351 (377)
T ss_dssp             HHHHHHHHHTTSCCCHHHHHHHTTCCCSCGGGGGGCBCCCCSHHHHHHTSCCCHHHHHHHHHHHCSHHHHTTCCHHHHTT
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHH
T ss_conf             99999862222446768999982999878666444565741788872389997889999999846899998589988964


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             78988999999754999999999987
Q 537021.9.peg.8   84 INRIGKRVALELKLVSVASQRILKAN  109 (148)
Q Consensus        84 i~GIG~aka~~l~a~~El~rR~~~~~  109 (148)
                      |+|||+..|.+|+   |--+|+....
T Consensus       352 VeGIGe~RAr~Ir---eGL~Rl~e~~  374 (377)
T 3c1y_A          352 VEGIGEKRARAIS---ESISSLKHRK  374 (377)
T ss_dssp             STTCCHHHHHHHH---HHHHHHHHHH
T ss_pred             CCCCCHHHHHHHH---HHHHHHHHCC
T ss_conf             5885899999999---9999987430



>1x2i_A HEF helicase/nuclease; alpha helix, helix-hairpin-helix DNA binding domain, homodimer, hydrolase; 1.45A {Pyrococcus furiosus} SCOP: a.60.2.5 Back     alignment and structure
>2bgw_A XPF endonuclease; hydrolase, structure specific endonuclease, nucleotide excision repair; 2.8A {Aeropyrum pernix} SCOP: a.60.2.5 c.52.1.20 PDB: 2bhn_A Back     alignment and structure
>1z00_A DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 Back     alignment and structure
>1z00_B DNA repair endonuclease XPF; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 PDB: 2aq0_A* Back     alignment and structure
>3c65_A Uvrabc system protein C; UVRC, endonuclease, nucleotide excision repair, DNA repair, RNAse H, cytoplasm, DNA damage, DNA excision; 1.90A {Bacillus stearothermophilus} Back     alignment and structure
>1dgs_A DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 2.90A {Thermus filiformis} SCOP: a.60.2.2 b.40.4.6 d.142.2.2 PDB: 1v9p_A* Back     alignment and structure
>1kea_A Possible G-T mismatches repair enzyme; DNA repair, DNA glycosylase, DNA mismatch, methylation, base twisting, hydrolase; 2.00A {Methanothermobacterthermautotrophicus} SCOP: a.96.1.2 Back     alignment and structure
>1pu6_A 3-methyladenine DNA glycosylase; helix-hairpin-helix, base excision repair, hydrolase; HET: KCX; 1.64A {Helicobacter pylori} SCOP: a.96.1.5 PDB: 1pu7_A* 1pu8_A* Back     alignment and structure
>1ngn_A Methyl-CPG binding protein MBD4; mismacth repair in methylated DNA, DNA binding protein; 2.10A {Mus musculus} SCOP: a.96.1.2 PDB: 3iho_A Back     alignment and structure
>2owo_A DNA ligase; protein/DNA complex, ligase/DNA complex; HET: DNA OMC AMP; 2.30A {Escherichia coli K12} Back     alignment and structure
>1orn_A Endonuclease III; DNA repair, DNA glycosylase, [4Fe-4S] cluster, iron-sulfur cluster, hydrolase/DNA complex; HET: PED; 1.70A {Geobacillus stearothermophilus} SCOP: a.96.1.1 PDB: 1orp_A* 1p59_A* Back     alignment and structure
>1kg2_A A/G-specific adenine glycosylase; DNA repair, hydrolase; 1.20A {Escherichia coli} SCOP: a.96.1.2 PDB: 1kg3_A 1muy_A 1kg6_A 1kg5_A 1mun_A 1mud_A 1kg4_A 1weg_A 1wei_A* 1wef_A* 1kg7_A 1kqj_A Back     alignment and structure
>1kea_A Possible G-T mismatches repair enzyme; DNA repair, DNA glycosylase, DNA mismatch, methylation, base twisting, hydrolase; 2.00A {Methanothermobacterthermautotrophicus} SCOP: a.96.1.2 Back     alignment and structure
>2abk_A Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {Escherichia coli} SCOP: a.96.1.1 Back     alignment and structure
>1kg2_A A/G-specific adenine glycosylase; DNA repair, hydrolase; 1.20A {Escherichia coli} SCOP: a.96.1.2 PDB: 1kg3_A 1muy_A 1kg6_A 1kg5_A 1mun_A 1mud_A 1kg4_A 1weg_A 1wei_A* 1wef_A* 1kg7_A 1kqj_A Back     alignment and structure
>3fsp_A A/G-specific adenine glycosylase; protein-DNA complex, DNA glycosylase, transition state analog, DNA repair; HET: NRI; 2.20A {Geobacillus stearothermophilus} PDB: 3fsq_A* 1rrs_A* 1vrl_A* 1rrq_A* 3g0q_A* Back     alignment and structure
>3n5n_X A/G-specific adenine DNA glycosylase; alpha-helices, helix-hairpin-helix motif, iron-sulfur cluste hydrolase; 2.30A {Homo sapiens} Back     alignment and structure
>3fsp_A A/G-specific adenine glycosylase; protein-DNA complex, DNA glycosylase, transition state analog, DNA repair; HET: NRI; 2.20A {Geobacillus stearothermophilus} PDB: 3fsq_A* 1rrs_A* 1vrl_A* 1rrq_A* 3g0q_A* Back     alignment and structure
>1orn_A Endonuclease III; DNA repair, DNA glycosylase, [4Fe-4S] cluster, iron-sulfur cluster, hydrolase/DNA complex; HET: PED; 1.70A {Geobacillus stearothermophilus} SCOP: a.96.1.1 PDB: 1orp_A* 1p59_A* Back     alignment and structure
>2abk_A Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {Escherichia coli} SCOP: a.96.1.1 Back     alignment and structure
>3i0w_A 8-oxoguanine-DNA-glycosylase; OGG, cacogg, DNA, 8-OXOG, 8OXOG, glycosylase, cytosine, hydrolase,lyase/DNA complex; HET: 8OG; 1.73A {Clostridium acetobutylicum} PDB: 3i0x_A* 3f10_A* 3f0z_A Back     alignment and structure
>2a1j_B DNA excision repair protein ERCC-1; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5 Back     alignment and structure
>1kft_A UVRC, excinuclease ABC subunit C; helix-hairpin-helix, HHH domain, DNA-binding domain, DNA binding protein; NMR {Escherichia coli} SCOP: a.60.2.3 Back     alignment and structure
>2a1j_A DNA repair endonuclease XPF; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} SCOP: a.60.2.5 PDB: 2kn7_A* Back     alignment and structure
>2nrt_A Uvrabc system protein C; UVRC, endonuclease, RNAse H, helix hairpin helix, NER, hydrolase; 1.50A {Thermotoga maritima} PDB: 2nrv_A 2nrw_A 2nrx_A 2nrz_A Back     alignment and structure
>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A* Back     alignment and structure
>1vq8_Y 50S ribosomal protein L32E; ribosome 50S, protein-protein complex, RNA-RNA complex, protein-RNA complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: c.9.2.1 PDB: 1vq4_Y* 1vq5_Y* 1vq6_Y* 1vq7_Y* 1s72_Y* 1vq9_Y* 1vqk_Y* 1vql_Y* 1vqm_Y* 1vqn_Y* 1vqo_Y* 1vqp_Y* 1yhq_Y* 1yi2_Y* 1yij_Y* 1yit_Y* 1yj9_Y* 1yjn_Y* 1yjw_Y* 2otj_Y* ... Back     alignment and structure

Homologous Domains in SCOP and MMDB Database
Detected by RPS-BLAST and HHsearch

Homologous Domains in SCOP70 (Version1.75) Database Detected by RPS-BLAST

No hit with e-value below 0.005

Homologous Domains in SCOP70 (Version 1.75) Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target148
d2bgwa170 DNA repair endonuclease XPF {Aeropyrum pernix [TaxId: 5 98.26
d1x2ia168 ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus 97.89
d1kfta_56 Excinuclease UvrC C-terminal domain {Escherichia coli [ 97.62
d2a1jb178 DNA excision repair protein ERCC-1 {Human (Homo sapiens 97.55
d1dgsa1181 NAD+-dependent DNA ligase, domain 3 {Thermus filiformis 97.2
d2a1ja162 DNA repair endonuclease XPF {Human (Homo sapiens) [TaxI 96.94
d2i1qa160 DNA repair protein Rad51, N-terminal domain {Archaeon M 96.89
d1pzna161 DNA repair protein Rad51, N-terminal domain {Archaeon P 96.38
d1keaa_217 Thymine-DNA glycosylase {Archaeon Methanobacterium ther 96.02
d1keaa_217 Thymine-DNA glycosylase {Archaeon Methanobacterium ther 95.83
d1rrqa1221 Catalytic domain of MutY {Bacillus stearothermophilus [ 95.25
d1kg2a_224 Catalytic domain of MutY {Escherichia coli [TaxId: 562] 95.06
d1ngna_144 Mismatch-specific thymine glycosylase domain of the met 95.0
d1kg2a_224 Catalytic domain of MutY {Escherichia coli [TaxId: 562] 94.18
d1rrqa1221 Catalytic domain of MutY {Bacillus stearothermophilus [ 93.96
d2noha1190 8-oxoguanine glycosylase {Human (Homo sapiens) [TaxId: 93.57
d1szpa164 DNA repair protein Rad51, N-terminal domain {Baker's ye 93.51
d1orna_214 Endonuclease III {Escherichia coli [TaxId: 562]} 92.64
d2abka_211 Endonuclease III {Escherichia coli [TaxId: 562]} 92.29
d1cuka278 DNA helicase RuvA subunit, middle domain {Escherichia c 91.15
d1pu6a_217 3-Methyladenine DNA glycosylase III (MagIII) {Helicobac 95.23
d1orna_214 Endonuclease III {Escherichia coli [TaxId: 562]} 94.75
d2abka_211 Endonuclease III {Escherichia coli [TaxId: 562]} 94.23
>d2bgwa1 a.60.2.5 (A:160-229) DNA repair endonuclease XPF {Aeropyrum pernix [TaxId: 56636]} Back     information, alignment and structure
class: All alpha proteins
fold: SAM domain-like
superfamily: RuvA domain 2-like
family: Hef domain-like
domain: DNA repair endonuclease XPF
species: Aeropyrum pernix [TaxId: 56636]
Probab=98.26  E-value=2e-06  Score=59.38  Aligned_cols=63  Identities=24%  Similarity=0.383  Sum_probs=56.9

Q ss_pred             HCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHCCCHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf             1898999999973379989889999999973799789850997899737898899999975499
Q 537021.9.peg.8   36 ALAYYEILELILFRLIPRKDTKSIAKALLKRFATLGGVFGAPLHLLQEINRIGKRVALELKLVS   99 (148)
Q Consensus        36 ~LsD~ELLallL~~g~~~~~~~~lA~~lL~~fGsL~~ll~as~~eL~~i~GIG~aka~~l~a~~   99 (148)
                      .++|.+.+.+.+-++.|+-.-. .|+.|+++|||+..+.+||+++|.+|+|||+.+|..|...+
T Consensus         3 ~~~~~~~~~~~~L~~IpgIG~~-~a~~L~~~F~s~~~l~~As~eeL~~v~GIG~~~A~~I~~~~   65 (70)
T d2bgwa1           3 RLSDVREWQLYILQSFPGIGRR-TAERILERFGSLERFFTASKAEISKVEGIGEKRAEEIKKIL   65 (70)
T ss_dssp             CCCHHHHHHHHHHHTSTTCCHH-HHHHHHHHHSSHHHHTTCCHHHHHHSTTCCHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHCCCCCCCHH-HHHHHHHHHCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHH
T ss_conf             8588999899998089995799-99999998298899988699999757998999999999998



>d1x2ia1 a.60.2.5 (A:2-69) ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d1kfta_ a.60.2.3 (A:) Excinuclease UvrC C-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2a1jb1 a.60.2.5 (B:219-296) DNA excision repair protein ERCC-1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1dgsa1 a.60.2.2 (A:401-581) NAD+-dependent DNA ligase, domain 3 {Thermus filiformis [TaxId: 276]} Back     information, alignment and structure
>d2a1ja1 a.60.2.5 (A:837-898) DNA repair endonuclease XPF {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2i1qa1 a.60.4.1 (A:5-64) DNA repair protein Rad51, N-terminal domain {Archaeon Methanococcus voltae [TaxId: 2188]} Back     information, alignment and structure
>d1pzna1 a.60.4.1 (A:35-95) DNA repair protein Rad51, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d1keaa_ a.96.1.2 (A:) Thymine-DNA glycosylase {Archaeon Methanobacterium thermoformicicum [TaxId: 145262]} Back     information, alignment and structure
>d1keaa_ a.96.1.2 (A:) Thymine-DNA glycosylase {Archaeon Methanobacterium thermoformicicum [TaxId: 145262]} Back     information, alignment and structure
>d1rrqa1 a.96.1.2 (A:9-229) Catalytic domain of MutY {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure
>d1kg2a_ a.96.1.2 (A:) Catalytic domain of MutY {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1ngna_ a.96.1.2 (A:) Mismatch-specific thymine glycosylase domain of the methyl-GpG binding protein mbd4 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1kg2a_ a.96.1.2 (A:) Catalytic domain of MutY {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1rrqa1 a.96.1.2 (A:9-229) Catalytic domain of MutY {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure
>d2noha1 a.96.1.3 (A:136-325) 8-oxoguanine glycosylase {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1szpa1 a.60.4.1 (A:81-144) DNA repair protein Rad51, N-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1orna_ a.96.1.1 (A:) Endonuclease III {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2abka_ a.96.1.1 (A:) Endonuclease III {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1cuka2 a.60.2.1 (A:65-142) DNA helicase RuvA subunit, middle domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1pu6a_ a.96.1.5 (A:) 3-Methyladenine DNA glycosylase III (MagIII) {Helicobacter pylori [TaxId: 210]} Back     information, alignment and structure
>d1orna_ a.96.1.1 (A:) Endonuclease III {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2abka_ a.96.1.1 (A:) Endonuclease III {Escherichia coli [TaxId: 562]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

No hit with e-value below 0.005

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target148
3c1y_A_304-37774 DNA integrity scanning protein DISA; DNA damage, D 97.7
1kft_A_78 UVRC, excinuclease ABC subunit C; helix-hairpin-he 97.62
1z00_A_89 DNA excision repair protein ERCC-1; helix-hairpin- 97.61
1pzn_A_1-9595 RAD51, DNA repair and recombination protein RAD51, 97.18
2nrt_A_157-22064 Uvrabc system protein C; UVRC, endonuclease, RNAse 96.71
3c65_A_226 Uvrabc system protein C; UVRC, endonuclease, nucle 96.31
2a1j_A_63 DNA repair endonuclease XPF; XPF, xeroderma pigmen 95.8
1z00_B_1-7171 DNA repair endonuclease XPF; helix-hairpin-helix, 95.58
1pu6_A_23-145123 3-methyladenine DNA glycosylase; helix-hairpin-hel 94.97
1m3q_A_123-255133 8-oxoguanine DNA glycosylase; DNA repair, END prod 94.26
1kg2_A_24-10986 A/G-specific adenine glycosylase; DNA repair, hydr 94.13
1wcn_A_70 Transcription elongation protein NUSA; RNA-binding 93.72
2ztd_A_80-15475 Holliday junction ATP-dependent DNA helicase RUVA; 92.31
1cuk_A_66-14479 RUVA protein; DNA repair, SOS response, DNA-bindin 91.91
1x2i_A_1-4949 HEF helicase/nuclease; alpha helix, helix-hairpin- 91.31
1kea_A_29-139111 Possible G-T mismatches repair enzyme; DNA repair, 91.2
3fhf_A_38-150113 Mjogg, N-glycosylase/DNA lyase, DNA-; helix-hairpi 91.04
2bgw_A_149-19749 XPF endonuclease; hydrolase, structure specific en 90.71
1orn_A_28-137110 Endonuclease III; DNA repair, DNA glycosylase, [4F 90.62
1szp_A_26-8156 DNA repair protein RAD51; homologous recombination 90.56
1ixr_A_191 Holliday junction DNA helicase RUVA; heterooligome 95.98
>3c1y_A (A:304-377) DNA integrity scanning protein DISA; DNA damage, DNA repair, DNA-binding, DNA binding protein; HET: DNA 2BA; 2.10A {Thermotoga maritima} PDB: 3c1z_A* 3c21_A* 3c23_A* Back     alignment and structure
Probab=97.70  E-value=7.2e-05  Score=51.84  Aligned_cols=50  Identities=22%  Similarity=0.297  Sum_probs=41.9

Q ss_pred             CCCCCHHHHHHHHHHHCCCHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf             998988999999997379978985099789973789889999997549999
Q 537021.9.peg.8   51 IPRKDTKSIAKALLKRFATLGGVFGAPLHLLQEINRIGKRVALELKLVSVA  101 (148)
Q Consensus        51 ~~~~~~~~lA~~lL~~fGsL~~ll~as~~eL~~i~GIG~aka~~l~a~~El  101 (148)
                      .|+.. ...|+.|+.+|||+..+.+||+++|.+++|||+.+|..|...+.-
T Consensus        17 I~giG-~~~a~~L~~~fgsl~~i~~as~~~L~~v~GiG~~~A~~i~~~~~~   66 (74)
T 3c1y_A           17 VARIP-LSIGYNVVRMFKTLDQISKASVEDLKKVEGIGEKRARAISESISS   66 (74)
T ss_dssp             TSCCC-HHHHHHHHHHHCSHHHHTTCCHHHHTTSTTCCHHHHHHHHHHHHH
T ss_pred             CCCCC-HHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHH
T ss_conf             99998-999999999853899998579988854478469999999999999



>1kft_A (A:) UVRC, excinuclease ABC subunit C; helix-hairpin-helix, HHH domain, DNA-binding domain, DNA binding protein; NMR {Escherichia coli} Back     alignment and structure
>1z00_A (A:) DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} Back     alignment and structure
>1pzn_A (A:1-95) RAD51, DNA repair and recombination protein RAD51, RADA; heptameric ring, heptamer, ring, oligomer, RAD51 polymerization motif; HET: DNA; 2.85A {Pyrococcus furiosus} Back     alignment and structure
>2nrt_A (A:157-220) Uvrabc system protein C; UVRC, endonuclease, RNAse H, helix hairpin helix, NER, hydrolase; 1.50A {Thermotoga maritima} PDB: 2nrv_A 2nrw_A 2nrx_A 2nrz_A Back     alignment and structure
>3c65_A (A:) Uvrabc system protein C; UVRC, endonuclease, nucleotide excision repair, DNA repair, RNAse H, cytoplasm, DNA damage, DNA excision; 1.90A {Bacillus stearothermophilus} Back     alignment and structure
>2a1j_A (A:) DNA repair endonuclease XPF; XPF, xeroderma pigmentosum, DNA repair, endonuclease, helix-hairpin-helix, DNA binding protein; HET: DNA; 2.70A {Homo sapiens} Back     alignment and structure
>1z00_B (B:1-71) DNA repair endonuclease XPF; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} Back     alignment and structure
>1pu6_A (A:23-145) 3-methyladenine DNA glycosylase; helix-hairpin-helix, base excision repair, hydrolase; HET: KCX; 1.64A {Helicobacter pylori} Back     alignment and structure
>1m3q_A (A:123-255) 8-oxoguanine DNA glycosylase; DNA repair, END product, HOGG, 8-aminoguanine, RE-ligation, hydrolase/DNA complex; HET: DRZ ANG; 1.90A {Homo sapiens} Back     alignment and structure
>1kg2_A (A:24-109) A/G-specific adenine glycosylase; DNA repair, hydrolase; 1.20A {Escherichia coli} Back     alignment and structure
>1wcn_A (A:) Transcription elongation protein NUSA; RNA-binding protein, escherichia coli NUSA, transcription regulation, regulation of RNA binding; NMR {Escherichia coli} PDB: 2jzb_B Back     alignment and structure
>2ztd_A (A:80-154) Holliday junction ATP-dependent DNA helicase RUVA; recombination, branch migration, DNA binding, oligomerization, acidic PIN; 2.40A {Mycobacterium tuberculosis} PDB: 2ztc_A 2zte_A 2h5x_A 1bvs_A Back     alignment and structure
>1cuk_A (A:66-144) RUVA protein; DNA repair, SOS response, DNA-binding, DNA recombination, helicase; 1.90A {Escherichia coli} Back     alignment and structure
>1x2i_A (A:1-49) HEF helicase/nuclease; alpha helix, helix-hairpin-helix DNA binding domain, homodimer, hydrolase; 1.45A {Pyrococcus furiosus} Back     alignment and structure
>1kea_A (A:29-139) Possible G-T mismatches repair enzyme; DNA repair, DNA glycosylase, DNA mismatch, methylation, base twisting, hydrolase; 2.00A {Methanothermobacterthermautotrophicus} Back     alignment and structure
>3fhf_A (A:38-150) Mjogg, N-glycosylase/DNA lyase, DNA-; helix-hairpin-helix, 8-oxoguanine, 8-OXOG, DNA damage, DNA repair, glycosidase, hydrolase; 2.00A {Methanocaldococcus jannaschii} Back     alignment and structure
>2bgw_A (A:149-197) XPF endonuclease; hydrolase, structure specific endonuclease, nucleotide excision repair; 2.8A {Aeropyrum pernix} Back     alignment and structure
>1orn_A (A:28-137) Endonuclease III; DNA repair, DNA glycosylase, [4Fe-4S] cluster, iron-sulfur cluster, hydrolase/DNA complex; HET: PED; 1.70A {Geobacillus stearothermophilus} Back     alignment and structure
>1szp_A (A:26-81) DNA repair protein RAD51; homologous recombination, asymmetry, RAD51 filament, DNA binding protein; HET: DNA; 3.25A {Saccharomyces cerevisiae} Back     alignment and structure
>1ixr_A (A:) Holliday junction DNA helicase RUVA; heterooligomeric complex, octameric RUVA, AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ANP; 3.30A {Thermus thermophilus} Back     alignment and structure