254780625

254780625

formamidopyrimidine-DNA glycosylase

GeneID in NCBI database:8209625Locus tag:CLIBASIA_02560
Protein GI in NCBI database:254780625Protein Accession:YP_003065038.1
Gene range:-(645888, 646757)Protein Length:289aa
Gene description:formamidopyrimidine-DNA glycosylase
COG prediction:[L] Formamidopyrimidine-DNA glycosylase
KEGG prediction:fpg; formamidopyrimidine-DNA glycosylase (EC:3.2.2.23); K10563 formamidopyrimidine-DNA glycosylase [EC:3.2.2.23 4.2.99.18]
SEED prediction:Formamidopyrimidine-DNA glycosylase (EC 3.2.2.23)
Pathway involved in KEGG:Base excision repair [PATH:las03410]
Subsystem involved in SEED:DNA Repair Base Excision
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
HMMTOPnone 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-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------29
MPELPEVEIIRRNLMMVMKNMTVTDICLHRKNLRFDFPHHFSAATRGKKIIDVSRRAKYLLIELEGNLSIIVHLGMSGSFIIEHTSCAKPIKNPQHNHVTISLTNNTNTKKYRVIYNDPRRFGFMDLVETSLKYQYPPLRTLGPEPADNSFNAIYLTHQFHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDAGGSSLRDYVHIDGSIGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQK
cccccHHHHHHHHHHHHHcccEEEEEEEEcccccccccHHHHHHHcccEEEEEEEEEEEEEEEEccccEEEEEccccEEEEEEcccccccccccccEEEEEEEccccccccEEEEEEcccccEEEEEEEcccccccHHHHHHccccccccccHHHHHHHHccccccHHHHHHcccEEEEEHHHHHHHHHHHHcccccccHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccHHHEEEccccccccccccccEEEEEEEccccEEEcccccc
ccccccHHHccccccccccccEEEEEEEEccccccccHHHHHHHHccEEEEEEEEEccEEEEEEcccEEEEEEcccccEEEccccccccccccccccEEEEEEccccEEEEEEEEEEccccccEEEEEEHHHHcccccccccccccccccccHHHHHHHHcccccEHHHHHHcccccccccHHHHHHHHHHHccccccEHHHccHHHccHHHHHHHHHHHHHHHHHHHHHcccccHHHccccccccccHHHHEEEEcccccccccccccEEEEEEEcccccEEcccccc
MPELPEVEIIRRNLMMVMKNMTVTDIclhrknlrfdfphhfsaatrgkkIIDVSRRAKYLLIELEGNLSIIVHLGMSGSFIiehtscakpiknpqhnhvtisltnntntkkyrviyndprrfgfmDLVETslkyqypplrtlgpepadnsfnAIYLTHQFHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKlspirktrsliqnngtpKDILYKLIQEIQKVLIDAIDaggsslrdyvhidgsigyFQNAFSvygktgepclsncGQMIRRIVQAGRSTFYCTYCQK
mpelpeveIIRRNLMMVMKNMTVTDICLHRKNLRFDFPhhfsaatrgkkiidVSRRAKYLLIELEGNLSIIVHLGMSGSFIIEHTSCAKPIKNPQHNHvtisltnntntkkyRVIYNDPRRFGFMDLVETSLKYQYPPLRTLGPEPADNSFNAIYLTHQFHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSpirktrsliqnngtpkDILYKLIQEIQKVLIDAIDAGGSSLRDYVHIDGSIGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQK
MPELPEVEIIRRNLMMVMKNMTVTDICLHRKNLRFDFPHHFSAATRGKKIIDVSRRAKYLLIELEGNLSIIVHLGMSGSFIIEHTSCAKPIKNPQHNHVTISLTNNTNTKKYRVIYNDPRRFGFMDLVETSLKYQYPPLRTLGPEPADNSFNAIYLTHQFHkknsnlknallnqkIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDAGGSSLRDYVHIDGSIGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQK
MPELPEVEIIRRNLMMVMKNMTVTDICLHRKNLRFDFPHHFSAATRGKKIIDVSRRAKYLLIELEGNLSIIVHLGMSGSFIIEHTSCAKPIKNPQHNHVTISLTNNTNTKKYRVIYNDPRRFGFMDLVETSLKYQYPPLRTLGPEPADNSFNAIYLTHQFHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDAGGSSLRDYVHIDGSIGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQK
MPELPEVEIIRRNLMMVMKNMTVTDICLHRKNLRFDFPHHFSAATRGKKIIDVSRRAKYLLIELEGNLSIIVHLGMSGSFIIEHTSCAKPIKNPQHNHVTISLTNNTNTKKYRVIYNDPRRFGFMDLVETSLKYQYPPLRTLGPEPADNSFNAIYLTHQFHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDAGGSSLRDYVHIDGSIGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQK
***LPEVEIIRRNLMMVMKNMTVTDICLHRKNLRFDFPHHFSAATRGKKIIDVSRRAKYLLIELEGNLSIIVHLGMSGSFIIEHTSCAKPIKNPQHNHVTISLTNNTNTKKYRVIYNDPRRFGFMDLVETSLKYQYPPLRTLGPEPADNSFNAIYLTHQFHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDAGGSSLRDYVHIDGSIGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQ*
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xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxHHHHHHHHHHHHHHHHHHHHxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
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MPELPEVEIIRRNLMMVMKNMTVTDICLHRKNLRFDFPHHFSAATRGKKIIDVSRRAKYLLIELEGNLSIIVHLGMSGSFIIEHTSCAKPIKNPQHNHVTISLTNNTNTKKYRVIYNDPRRFGFMDLVETSLKYQYPPLRTLGPEPADNSFNAIYLTHQFHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDAGGSSLRDYVHIDGSIGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQK
MPELPEVEIIRRNLMMVMKNMTVTDICLHRKNLRFDFPHHFSAATRGKKIIDVSRRAKYLLIELEGNLSIIVHLGMSGSFIIEHTSCAKPIKNPQHNHVTISLTNNTNTKKYRVIYNDPRRFGFMDLVETSLKYQYPPLRTLGPEPADNSFNAIYLTHQFHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDAGGSSLRDYVHIDGSIGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQK
MPELPEVEIIRRNLMMVMKNMTVTDICLHRKNLRFDFPHHFSAATRGKKIIDVSRRAKYLLIELEGNLSIIVHLGMSGSFIIEHTSCAKPIKNPQHNHVTISLTNNTNTKKYRVIYNDPRRFGFMDLVETSLKYQYPPLRTLGPEPADNSFNAIYLTHQFHKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDAGGSSLRDYVHIDGSIGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQK

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
Target289 formamidopyrimidine-DNA glycosylase [Candidatus Liberib
315121826295 formamidopyrimidine-DNA glycosylase [Candidatus Liberib 1 1e-129
159184256298 formamidopyrimidine-DNA glycosylase [Agrobacterium tume 1 8e-82
325291755311 Formamidopyrimidine-DNA glycosylase [Agrobacterium sp. 1 2e-81
190890023296 formamidopyrimidine-DNA glycosylase [Rhizobium etli CIA 1 7e-80
209551935301 formamidopyrimidine-DNA glycosylase [Rhizobium legumino 1 2e-79
15964118301 formamidopyrimidine-DNA glycosylase [Sinorhizobium meli 1 4e-79
116250141296 formamidopyrimidine-DNA glycosylase [Rhizobium legumino 1 4e-79
227824215296 formamidopyrimidine-DNA glycosylase [Sinorhizobium fred 1 7e-79
241207318296 formamidopyrimidine-DNA glycosylase [Rhizobium legumino 1 3e-78
150398756306 formamidopyrimidine-DNA glycosylase [Sinorhizobium medi 1 6e-77
>gi|315121826|ref|YP_004062315.1| formamidopyrimidine-DNA glycosylase [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 295 Back     alignment and organism information
 Score =  464 bits (1194), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 220/292 (75%), Positives = 254/292 (86%), Gaps = 3/292 (1%)

Query: 1   MPELPEVEIIRRNLMMVMKNMTVTDICLHRKNLRFDFPHHFSAATRGKKIIDVSRRAKYL 60
           MPELPEVEIIRRNL+ VMKNM +TDI LHRKNLRFDFP +F+   RGKKI +V RRAKYL
Sbjct: 4   MPELPEVEIIRRNLIPVMKNMILTDIWLHRKNLRFDFPPNFALNVRGKKITNVVRRAKYL 63

Query: 61  LIELEGNLSIIVHLGMSGSFIIEHTSCA---KPIKNPQHNHVTISLTNNTNTKKYRVIYN 117
           LIELE NLSII HLGMSGSFIIE TS     K IK+P+HNHVTISL+N   T+KYRVIYN
Sbjct: 64  LIELEDNLSIIAHLGMSGSFIIEDTSSTNSQKKIKDPRHNHVTISLSNEDKTQKYRVIYN 123

Query: 118 DPRRFGFMDLVETSLKYQYPPLRTLGPEPADNSFNAIYLTHQFHKKNSNLKNALLNQKIV 177
           DPRRFGFMDLV+TSL+ QYP L  +GPEP D++FNA YLTHQF+K+NSNLKNALLNQ+IV
Sbjct: 124 DPRRFGFMDLVKTSLRDQYPSLIKIGPEPTDSAFNATYLTHQFYKRNSNLKNALLNQRIV 183

Query: 178 AGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDAGGSSLR 237
           AG+GNIYVCEALWRA++SP+R  +SL+Q+N TP + + +LIQEIQKV+ DAI+AGGSSLR
Sbjct: 184 AGLGNIYVCEALWRARISPVRTAKSLVQDNKTPNEKISRLIQEIQKVITDAINAGGSSLR 243

Query: 238 DYVHIDGSIGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQK 289
           DYVH DGSIG FQN+F+VYGKTG+ C SNCGQMIRRIVQ+GRSTFYCTYCQ+
Sbjct: 244 DYVHTDGSIGSFQNSFAVYGKTGKSCPSNCGQMIRRIVQSGRSTFYCTYCQE 295


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|159184256|ref|NP_353352.2| formamidopyrimidine-DNA glycosylase [Agrobacterium tumefaciens str. C58] Length = 298 Back     alignment and organism information
>gi|325291755|ref|YP_004277619.1| Formamidopyrimidine-DNA glycosylase [Agrobacterium sp. H13-3] Length = 311 Back     alignment and organism information
>gi|190890023|ref|YP_001976565.1| formamidopyrimidine-DNA glycosylase [Rhizobium etli CIAT 652] Length = 296 Back     alignment and organism information
>gi|209551935|ref|YP_002283852.1| formamidopyrimidine-DNA glycosylase [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 301 Back     alignment and organism information
>gi|15964118|ref|NP_384471.1| formamidopyrimidine-DNA glycosylase [Sinorhizobium meliloti 1021] Length = 301 Back     alignment and organism information
>gi|116250141|ref|YP_765979.1| formamidopyrimidine-DNA glycosylase [Rhizobium leguminosarum bv. viciae 3841] Length = 296 Back     alignment and organism information
>gi|227824215|ref|YP_002828188.1| formamidopyrimidine-DNA glycosylase [Sinorhizobium fredii NGR234] Length = 296 Back     alignment and organism information
>gi|241207318|ref|YP_002978414.1| formamidopyrimidine-DNA glycosylase [Rhizobium leguminosarum bv. trifolii WSM1325] Length = 296 Back     alignment and organism information
>gi|150398756|ref|YP_001329223.1| formamidopyrimidine-DNA glycosylase [Sinorhizobium medicae WSM419] Length = 306 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
Target289 formamidopyrimidine-DNA glycosylase [Candidatus Liberib
PRK01103274 PRK01103, PRK01103, formamidopyrimidine/5-formyluracil/ 1e-105
TIGR00577272 TIGR00577, fpg, formamidopyrimidine-DNA glycosylase (fp 3e-72
PRK14811269 PRK14811, PRK14811, formamidopyrimidine-DNA glycosylase 2e-54
PRK14810272 PRK14810, PRK14810, formamidopyrimidine-DNA glycosylase 3e-48
PRK13945282 PRK13945, PRK13945, formamidopyrimidine-DNA glycosylase 1e-47
PRK10445263 PRK10445, PRK10445, endonuclease VIII; Provisional 2e-13
COG0266273 COG0266, Nei, Formamidopyrimidine-DNA glycosylase [DNA 1e-82
cd08966120 cd08966, EcFpg-like_N, N-terminal domain of Escherichia 8e-36
pfam01149117 pfam01149, Fapy_DNA_glyco, Formamidopyrimidine-DNA glyc 2e-28
cd08773117 cd08773, FpgNei_N, N-terminal domain of Fpg (formamidop 6e-19
cd08972137 cd08972, PF_Nei_N, N-terminal domain of the plant and f 1e-12
cd08976117 cd08976, BaFpgNei_N_4, Uncharacterized bacterial subgro 2e-10
pfam0683193 pfam06831, H2TH, Formamidopyrimidine-DNA glycosylase H2 1e-18
cd08973122 cd08973, BaFpgNei_N_1, Uncharacterized bacterial subgro 2e-11
cd08971114 cd08971, AcNei2_N, N-terminal domain of the actinomycet 2e-05
pfam0682730 pfam06827, zf-FPG_IleRS, Zinc finger found in FPG and I 4e-04
>gnl|CDD|179222 PRK01103, PRK01103, formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated Back     alignment and domain information
>gnl|CDD|161937 TIGR00577, fpg, formamidopyrimidine-DNA glycosylase (fpg) Back     alignment and domain information
>gnl|CDD|184831 PRK14811, PRK14811, formamidopyrimidine-DNA glycosylase; Provisional Back     alignment and domain information
>gnl|CDD|173271 PRK14810, PRK14810, formamidopyrimidine-DNA glycosylase; Provisional Back     alignment and domain information
>gnl|CDD|184410 PRK13945, PRK13945, formamidopyrimidine-DNA glycosylase; Provisional Back     alignment and domain information
>gnl|CDD|182467 PRK10445, PRK10445, endonuclease VIII; Provisional Back     alignment and domain information
>gnl|CDD|30615 COG0266, Nei, Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|176800 cd08966, EcFpg-like_N, N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases Back     alignment and domain information
>gnl|CDD|144661 pfam01149, Fapy_DNA_glyco, Formamidopyrimidine-DNA glycosylase N-terminal domain Back     alignment and domain information
>gnl|CDD|176798 cd08773, FpgNei_N, N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases Back     alignment and domain information
>gnl|CDD|176806 cd08972, PF_Nei_N, N-terminal domain of the plant and fungal Nei and related proteins Back     alignment and domain information
>gnl|CDD|176810 cd08976, BaFpgNei_N_4, Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases Back     alignment and domain information
>gnl|CDD|115485 pfam06831, H2TH, Formamidopyrimidine-DNA glycosylase H2TH domain Back     alignment and domain information
>gnl|CDD|176807 cd08973, BaFpgNei_N_1, Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases Back     alignment and domain information
>gnl|CDD|176805 cd08971, AcNei2_N, N-terminal domain of the actinomycetal Nei2 and related DNA glycosylases Back     alignment and domain information
>gnl|CDD|148438 pfam06827, zf-FPG_IleRS, Zinc finger found in FPG and IleRS Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 289 formamidopyrimidine-DNA glycosylase [Candidatus Liberib
TIGR00577292 fpg formamidopyrimidine-DNA glycosylase; InterPro: IPR0 100.0
PRK01103273 formamidopyrimidine-DNA glycosylase; Validated 100.0
COG0266273 Nei Formamidopyrimidine-DNA glycosylase [DNA replicatio 100.0
PRK13945283 formamidopyrimidine-DNA glycosylase; Provisional 100.0
PRK10445263 endonuclease VIII; Provisional 100.0
pfam0683193 H2TH Formamidopyrimidine-DNA glycosylase H2TH domain. F 99.97
pfam05833 447 FbpA Fibronectin-binding protein A N-terminus (FbpA). T 98.01
COG1293 564 Predicted RNA-binding protein homologous to eukaryotic 97.46
PRK04184 533 DNA topoisomerase VI subunit B; Validated 96.99
PTZ00134154 40S ribosomal protein S18; Provisional 96.69
pfam00416106 Ribosomal_S13 Ribosomal protein S13/S18. This family in 96.08
PRK04053149 rps13p 30S ribosomal protein S13P; Reviewed 95.85
COG0099121 RpsM Ribosomal protein S13 [Translation, ribosomal stru 95.52
PRK05179122 rpsM 30S ribosomal protein S13; Validated 95.5
TIGR03629144 arch_S13P archaeal ribosomal protein S13P. This model d 95.35
TIGR03631113 bact_S13 30S ribosomal protein S13. This model describe 95.1
CHL00137122 rps13 ribosomal protein S13; Validated 94.79
pfam01149117 Fapy_DNA_glyco Formamidopyrimidine-DNA glycosylase N-te 99.95
pfam0682730 zf-FPG_IleRS Zinc finger found in FPG and IleRS. This z 97.68
PRK12495 221 hypothetical protein; Provisional 93.11
pfam0667741 Auto_anti-p27 Sjogren's syndrome/scleroderma autoantige 91.4
COG1645131 Uncharacterized Zn-finger containing protein [General f 90.44
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase; InterPro: IPR000191 Formamidopyrimidine-DNA glycosylase (3 Back     alignment and domain information
>PRK01103 formamidopyrimidine-DNA glycosylase; Validated Back     alignment and domain information
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional Back     alignment and domain information
>PRK10445 endonuclease VIII; Provisional Back     alignment and domain information
>pfam06831 H2TH Formamidopyrimidine-DNA glycosylase H2TH domain Back     alignment and domain information
>pfam05833 FbpA Fibronectin-binding protein A N-terminus (FbpA) Back     alignment and domain information
>COG1293 Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription] Back     alignment and domain information
>PRK04184 DNA topoisomerase VI subunit B; Validated Back     alignment and domain information
>PTZ00134 40S ribosomal protein S18; Provisional Back     alignment and domain information
>pfam00416 Ribosomal_S13 Ribosomal protein S13/S18 Back     alignment and domain information
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed Back     alignment and domain information
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK05179 rpsM 30S ribosomal protein S13; Validated Back     alignment and domain information
>TIGR03629 arch_S13P archaeal ribosomal protein S13P Back     alignment and domain information
>TIGR03631 bact_S13 30S ribosomal protein S13 Back     alignment and domain information
>CHL00137 rps13 ribosomal protein S13; Validated Back     alignment and domain information
>pfam01149 Fapy_DNA_glyco Formamidopyrimidine-DNA glycosylase N-terminal domain Back     alignment and domain information
>pfam06827 zf-FPG_IleRS Zinc finger found in FPG and IleRS Back     alignment and domain information
>PRK12495 hypothetical protein; Provisional Back     alignment and domain information
>pfam06677 Auto_anti-p27 Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27) Back     alignment and domain information
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only] 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

IdentityAlignment graphLength Definition E-value
Target289 formamidopyrimidine-DNA glycosylase [Candidatus Liberib
1l1t_A274 Mutm (Fpg) Bound To Abasic-Site Containing Dna Leng 6e-53
2f5n_A274 Mutm Crosslinked To Undamaged Dna Sampling A:t Base 5e-52
1k82_A268 Crystal Structure Of E.Coli Formamidopyrimidine-Dna 7e-52
1r2y_A274 Mutm (Fpg) Bound To 8-Oxoguanine (Oxog) Containing 8e-51
3gp1_A273 Mutm Encountering An Intrahelical 8-Oxoguanine (Oxo 8e-51
3gpp_A273 Mutm Encountering An Intrahelical 8-Oxoguanine (Oxo 1e-50
1tdz_A272 Crystal Structure Complex Between The Lactococcus L 3e-50
2f5q_A274 Catalytically Inactive (E3q) Mutm Crosslinked To Ox 6e-50
1pji_A271 Crystal Structure Of Wild Type Lactococcus Lactis F 8e-49
3gpy_A273 Sequence-Matched Mutm Lesion Recognition Complex 3 1e-48
3jr4_A273 Mutm Interrogating An Extrahelical G Length = 273 1e-48
1nnj_A271 Crystal Structure Complex Between The Lactococcus L 1e-47
1kfv_A271 Crystal Structure Of Lactococcus Lactis Formamido- 5e-47
1ee8_A266 Crystal Structure Of Mutm (Fpg) Protein From Thermu 7e-43
3gpx_A257 Sequence-Matched Mutm Interrogation Complex 4 (Ic4) 9e-43
3go8_A257 Mutm Encountering An Intrahelical 8-Oxoguanine (Oxo 3e-42
3gpu_A256 Mutm Encountering An Intrahelical 8-Oxoguanine (Oxo 5e-42
1k3w_A262 Crystal Structure Of A Trapped Reaction Intermediat 4e-30
1q3b_A262 Crystal Structure Of The Dna Repair Enzyme Endonucl 5e-28
2oq4_A262 Crystal Structure Of The Dna Repair Enzyme Endonucl 5e-28
1q3c_A262 Crystal Structure Of The Dna Repair Enzyme Endonucl 5e-28
3a45_A289 Crystal Structure Of Mvnei1_2 Length = 289 3e-16
3a42_A295 Crystal Structure Of Mvnei1 Length = 295 3e-16
>gi|21730608|pdb|1L1T|A Chain A, Mutm (Fpg) Bound To Abasic-Site Containing Dna Length = 274 Back     alignment and structure
 Score =  212 bits (538), Expect = 6e-53,   Method: Composition-based stats.
 Identities = 100/291 (34%), Positives = 146/291 (50%), Gaps = 19/291 (6%)

Query: 1   MPELPEVEIIRRNLMMVMKNMTVTDICLHRKNLRFD--FPHHFSAATRGKKIIDVSRRAK 58
           MPELPEVE IRR L+ ++   T+ D+ +   N+         F+A   G+ +  + RR K
Sbjct: 1   MPELPEVETIRRTLLPLIVGKTIEDVRIFWPNIIRHPRDSEAFAARMIGQTVRGLERRGK 60

Query: 59  YLLIELEGNLSIIVHLGMSGSFIIEHTSCAKPIKNPQHNHVTISLTNNTNTKKYRVIYND 118
           +L   L    ++I HL M G + +             H HV    T+ +      + Y D
Sbjct: 61  FLKF-LLDRDALISHLRMEGRYAVASALEPLEP----HTHVVFCFTDGS-----ELRYRD 110

Query: 119 PRRFGFMDLVETSLKYQYPPLRTLGPEPADNSFNAIYLTHQFHKKNSNLKNALLNQKIVA 178
            R+FG M +       + PPL  LGPEP   +F+   L  +  K   ++K  LL+Q +VA
Sbjct: 111 VRKFGTMHVYAKEEADRRPPLAELGPEPLSPAFSPAVLAERAVKTKRSVKALLLDQTVVA 170

Query: 179 GIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDAGGSSLRD 238
           G GNIYV E+L+RA + P R   SL          + +L +E+   + +A+  GGS++R 
Sbjct: 171 GFGNIYVDESLFRAGILPGRPAASLSSKE------IERLHEEMVATIGEAVMKGGSTVRT 224

Query: 239 YVHIDGSIGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQK 289
           YV+  G  G FQ+   VYG+ G PC   CG  I + V AGR T YC  CQ+
Sbjct: 225 YVNTQGEAGTFQHHLYVYGRQGNPC-KRCGTPIEKTVVAGRGTHYCPRCQR 274


>gi|93279440|pdb|2F5N|A Chain A, Mutm Crosslinked To Undamaged Dna Sampling A:t Base Pair Ic1 Length = 274 Back     alignment and structure
>gi|21730426|pdb|1K82|A Chain A, Crystal Structure Of E.Coli Formamidopyrimidine-Dna Glycosylase (Fpg) Covalently Trapped With Dna Length = 268 Back     alignment and structure
>gi|38492995|pdb|1R2Y|A Chain A, Mutm (Fpg) Bound To 8-Oxoguanine (Oxog) Containing Dna Length = 274 Back     alignment and structure
>gi|266618586|pdb|3GP1|A Chain A, Mutm Encountering An Intrahelical 8-Oxoguanine (Oxog) Lesion In Ec3-V222p Complex Length = 273 Back     alignment and structure
>gi|266618589|pdb|3GPP|A Chain A, Mutm Encountering An Intrahelical 8-Oxoguanine (Oxog) Lesion In Ec3-T224p Complex Length = 273 Back     alignment and structure
gi|55669903|pdb|1TDZ|A Chain A, Crystal Structure Complex Between The Lactococcus Lactis Fpg (Mutm) And A Fapy-Dg Containing Dna Length = 272 Back     alignment and structure
>gi|93279449|pdb|2F5Q|A Chain A, Catalytically Inactive (E3q) Mutm Crosslinked To Oxog:c Containing Dna Cc2 Length = 274 Back     alignment and structure
>gi|51247145|pdb|1PJI|A Chain A, Crystal Structure Of Wild Type Lactococcus Lactis Fpg Complexed To A 1,3 Propanediol Containing Dna Length = 271 Back     alignment and structure
>gi|266618598|pdb|3GPY|A Chain A, Sequence-Matched Mutm Lesion Recognition Complex 3 (Lrc3) Length = 273 Back     alignment and structure
>gi|262368041|pdb|3JR4|A Chain A, Mutm Interrogating An Extrahelical G Length = 273 Back     alignment and structure
>gi|28948974|pdb|1NNJ|A Chain A, Crystal Structure Complex Between The Lactococcus Lactis Fpg And An Abasic Site Containing Dna Length = 271 Back     alignment and structure
>gi|21730465|pdb|1KFV|A Chain A, Crystal Structure Of Lactococcus Lactis Formamido- Pyrimidine Dna Glycosylase (Alias Fpg Or Mutm) Non Covalently Bound To An Ap Site Containing Dna. Length = 271 Back     alignment and structure
>gi|13096238|pdb|1EE8|A Chain A, Crystal Structure Of Mutm (Fpg) Protein From Thermus Thermophilus Hb8 Length = 266 Back     alignment and structure
>gi|266618595|pdb|3GPX|A Chain A, Sequence-Matched Mutm Interrogation Complex 4 (Ic4) Length = 257 Back     alignment and structure
>gi|281307047|pdb|3GO8|A Chain A, Mutm Encountering An Intrahelical 8-Oxoguanine (Oxog) Lesion In Ec3-Loop Deletion Complex Length = 257 Back     alignment and structure
>gi|266618592|pdb|3GPU|A Chain A, Mutm Encountering An Intrahelical 8-Oxoguanine (Oxog) Lesion In Ec4-Loop Deletion Complex Length = 256 Back     alignment and structure
>gi|24987423|pdb|1K3W|A Chain A, Crystal Structure Of A Trapped Reaction Intermediate Of The Dna Repair Enzyme Endonuclease Viii With Dna Length = 262 Back     alignment and structure
>gi|51247248|pdb|1Q3B|A Chain A, Crystal Structure Of The Dna Repair Enzyme Endonuclease- Viii (Nei) From E. Coli: The R252a Mutant At 2.05 Resolution. Length = 262 Back     alignment and structure
>gi|168988643|pdb|2OQ4|A Chain A, Crystal Structure Of The Dna Repair Enzyme Endonuclease- Viii (Nei) From E. Coli (E2q) In Complex With Ap-Site Containing Dna Substrate Length = 262 Back     alignment and structure
>gi|51247249|pdb|1Q3C|A Chain A, Crystal Structure Of The Dna Repair Enzyme Endonuclease- Viii (Nei) From E. Coli: The E2a Mutant At 2.3 Resolution Length = 262 Back     alignment and structure
>gi|254574788|pdb|3A45|A Chain A, Crystal Structure Of Mvnei1_2 Length = 289 Back     alignment and structure
>gi|254574787|pdb|3A42|A Chain A, Crystal Structure Of Mvnei1 Length = 295 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target289 formamidopyrimidine-DNA glycosylase [Candidatus Liberib
1ee8_A266 MUTM (FPG) protein; beta sandwich, zinc finger, helix t 2e-73
1k82_A268 Formamidopyrimidine-DNA glycosylase; protein-DNA comple 1e-61
1tdh_A364 NEI endonuclease VIII-like 1; helix two turns helix, zi 5e-50
1k3x_A262 Endonuclease VIII; hydrolase/DNA; HET: BRU PED; 1.25A { 5e-49
3a46_A289 Formamidopyrimidine-DNA glycosylase; helix two turns he 3e-46
1tdz_A272 Formamidopyrimidine-DNA glycosylase; DNA repair, FPG, M 5e-41
3gpu_A256 DNA glycosylase; DNA glycosylase, DNA repair, damage se 7e-33
>1ee8_A MUTM (FPG) protein; beta sandwich, zinc finger, helix two-turns helix, riken structural genomics/proteomics initiative, RSGI; 1.90A {Thermus thermophilus HB8} SCOP: a.156.1.2 b.113.1.1 g.39.1.8 Length = 266 Back     alignment and structure
 Score =  270 bits (692), Expect = 2e-73
 Identities = 104/290 (35%), Positives = 150/290 (51%), Gaps = 29/290 (10%)

Query: 2   PELPEVEIIRRNLMMVMKNMTVTDICLHRKNLRFDFPHHFSAATRGKKIIDVSRRAKYLL 61
           PELPEVE  RR L  ++   T+  +       R    +  +A   G++I++V RR K+LL
Sbjct: 1   PELPEVETTRRRLRPLVLGQTLRQV-----VHRDPARYRNTALAEGRRILEVDRRGKFLL 55

Query: 62  IELEGNLSIIVHLGMSGSFIIEHTSCAKPIKNPQHNHVTISLTNNTNTKKYRVIYNDPRR 121
             LEG + ++ HLGM+G F +E            H    + L   T      + ++DPRR
Sbjct: 56  FALEGGVELVAHLGMTGGFRLE---------PTPHTRAALVLEGRT------LYFHDPRR 100

Query: 122 FGFMDLVETSLKYQYPPLRTLGPEPADNSFNAIYLTHQFHKKNSNLKNALLNQKIVAGIG 181
           FG +  V      + P L  LGPEP   +F          +    LK  LL+Q++ AG+G
Sbjct: 101 FGRLFGVRRGDYREIPLLLRLGPEPLSEAFAFPGFFRGLKESARPLKALLLDQRLAAGVG 160

Query: 182 NIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDAGGSSLRD--Y 239
           NIY  EAL+RA+LSP R  RSL       ++   +L + +++VL +A++ GGS+L D  Y
Sbjct: 161 NIYADEALFRARLSPFRPARSL------TEEEARRLYRALREVLAEAVELGGSTLSDQSY 214

Query: 240 VHIDGSIGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQK 289
              DG  G FQ   +VYG+ G PC   CG+ + R V AGR T +C  CQ 
Sbjct: 215 RQPDGLPGGFQTRHAVYGREGLPCP-ACGRPVERRVVAGRGTHFCPTCQG 263


>1k82_A Formamidopyrimidine-DNA glycosylase; protein-DNA complex, DNA repair, beta sandwich, zinc finger, helix two-turns helix, hydrolase/DNA complex; HET: PED; 2.10A {Escherichia coli} SCOP: a.156.1.2 b.113.1.1 g.39.1.8 Length = 268 Back     alignment and structure
>1tdh_A NEI endonuclease VIII-like 1; helix two turns helix, zinc-LESS finger, hydrolase; 2.10A {Homo sapiens} SCOP: a.156.1.2 b.113.1.1 g.39.1.8 Length = 364 Back     alignment and structure
>1k3x_A Endonuclease VIII; hydrolase/DNA; HET: BRU PED; 1.25A {Escherichia coli} SCOP: a.156.1.2 b.113.1.1 g.39.1.8 PDB: 1k3w_A* 1q39_A 2ea0_A* 2oq4_A* 1q3c_A 2opf_A* 1q3b_A* Length = 262 Back     alignment and structure
>3a46_A Formamidopyrimidine-DNA glycosylase; helix two turns helix, zinc-LESS finger, hydrolase, THF, glycosidase, lyase, multifunctional enzyme; HET: DNA 3DR; 2.20A {Acanthamoeba polyphaga mimivirus} PDB: 3a45_A* 3a42_A Length = 289 Back     alignment and structure
>1tdz_A Formamidopyrimidine-DNA glycosylase; DNA repair, FPG, MUTM, FAPY G, hydrolase/DNA complex; HET: FOX; 1.80A {Lactococcus lactis} SCOP: a.156.1.2 b.113.1.1 g.39.1.8 PDB: 1pji_A* 1pm5_A* 1xc8_A* 3c58_A* 1nnj_A 1kfv_A 1pjj_A* Length = 272 Back     alignment and structure
>3gpu_A DNA glycosylase; DNA glycosylase, DNA repair, damage search, base extrusion; HET: DNA 8OG; 1.62A {Geobacillus stearothermophilus} PDB: 3gpx_A* 3gq3_A* 2f5n_A 2f5o_A 2f5p_A 3gp1_A* 3gq4_A* 3gpy_A* 3gq5_A* 3gpp_A* 2f5q_A* 2f5s_A* 1l1z_A* 1l1t_A* 1l2b_A* 1l2c_A* 1l2d_A* 1r2z_A* 1r2y_A* 3jr5_A* ... Length = 256 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target289 formamidopyrimidine-DNA glycosylase [Candidatus Liberib
1tdz_A272 Formamidopyrimidine-DNA glycosylase; DNA repair, FPG, M 100.0
1k82_A268 Formamidopyrimidine-DNA glycosylase; protein-DNA comple 100.0
1ee8_A266 MUTM (FPG) protein; beta sandwich, zinc finger, helix t 100.0
3gpu_A256 DNA glycosylase; DNA glycosylase, DNA repair, damage se 100.0
1k3x_A262 Endonuclease VIII; hydrolase/DNA; HET: BRU PED; 1.25A { 100.0
3a46_A289 Formamidopyrimidine-DNA glycosylase; helix two turns he 100.0
1tdh_A364 NEI endonuclease VIII-like 1; helix two turns helix, zi 100.0
3doa_A288 Fibrinogen binding protein; structural genomics, MCSG., 96.3
2zkq_m152 40S ribosomal protein S18E; protein-RNA complex, 40S ri 95.57
2vqe_M126 30S ribosomal protein S13, 30S ribosomal protein S6; tR 95.4
3ofp_M113 30S ribosomal protein S13; protein biosynthesis, riboso 93.22
1mu5_A 471 Type II DNA topoisomerase VI subunit B; GHKL ATPase, he 96.16
>1tdz_A Formamidopyrimidine-DNA glycosylase; DNA repair, FPG, MUTM, FAPY G, hydrolase/DNA complex; HET: FOX; 1.80A {Lactococcus lactis} SCOP: a.156.1.2 b.113.1.1 g.39.1.8 PDB: 1pji_A* 1pm5_A* 1xc8_A* 3c58_A* 1nnj_A 1kfv_A 1pjj_A* Back     alignment and structure
Probab=100.00  E-value=0  Score=546.54  Aligned_cols=271  Identities=38%  Similarity=0.669  Sum_probs=254.9

Q ss_pred             CCCCCHHHHHHHHHHHHHCCCEEEEEEECCCCCCCCCCHHHHHHHCCCEEEEEEECCEEEEEEECCCCCCCCCCCCCCEE
Q ss_conf             96764367889889998679778899964833265787789997289889999605308999503553100152553279
Q gi|254780625|r    1 MPELPEVEIIRRNLMMVMKNMTVTDICLHRKNLRFDFPHHFSAATRGKKIIDVSRRAKYLLIELEGNLSIIVHLGMSGSF   80 (289)
Q Consensus         1 MPElPEVe~~~~~l~~~l~g~~I~~V~~~~~~~~~~~~~~~~~~L~G~~I~~v~r~GK~l~l~l~~~~~L~~HlgM~G~~   80 (289)
                      ||||||||++++.|++.++|++|++|++.++++++..++++.+.|.|++|++|.|+||||+|+|+++.+|++||||+|+|
T Consensus         1 MPElPEVe~~~~~L~~~l~g~~I~~v~~~~~~~~~~~~~~~~~~L~G~~i~~v~r~GK~l~~~~~~~~~l~~HlgMtG~~   80 (272)
T 1tdz_A            1 MPELPEVETVRRELEKRIVGQKIISIEATYPRMVLTGFEQLKKELTGKTIQGISRRGKYLIFEIGDDFRLISHLRMEGKY   80 (272)
T ss_dssp             --CHHHHHHHHHHHHHHHTTCBCCEEEESCGGGBTTCHHHHHHHHTTCBEEEEEEETTEEEEEETTTEEEEEECTTTCEE
T ss_pred             CCCHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCCCCHHHHHHHCCCCEEEEEEEEEEEEEEEECCCCEEEEEECCCCEE
T ss_conf             98479999999999997389999999989864347872889977599899999820489999854894699863114446


Q ss_pred             EEECCCCCCCCCCCCCCEEEEEEECCCCCEEEEEEEECCCCCCCEECCCCCCHHHCCCCCCCCCCCCCCCCHHHHHHHHH
Q ss_conf             98147854224587663389997068876048999815876641001455301005323565553322111067888742
Q gi|254780625|r   81 IIEHTSCAKPIKNPQHNHVTISLTNNTNTKKYRVIYNDPRRFGFMDLVETSLKYQYPPLRTLGPEPADNSFNAIYLTHQF  160 (289)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~D~R~fG~~~~~~~~~~~~~~~l~~lGpD~l~~~~~~~~~~~~l  160 (289)
                      ++.+..    ...++|.++.+.++++      .++|.|+|+||.+.+....+...++.++++||||+++.++.+.|.+.+
T Consensus        81 ~~~~~~----~~~~~~~~~~~~~~~~------~~~~~D~r~fg~~~~~~~~~~~~~~~~~~lgpd~l~~~~~~~~~~~~~  150 (272)
T 1tdz_A           81 RLATLD----APREKHDHLTMKFADG------QLIYADVRKFGTWELISTDQVLPYFLKKKIGPEPTYEDFDEKLFREKL  150 (272)
T ss_dssp             EEECTT----CCCCTTEEEEEECSSC------EEEEECTTSCCEEEEEEGGGHHHHHHHHTCCCCSSTTTCCHHHHHHHH
T ss_pred             EEECCC----CCCCCCCEEEEECCCC------EEEEEECCCCEEEEEECCCCCCCCHHHHCCCCCCCCCCCCHHHHHHHH
T ss_conf             750366----8887652699960398------499996232306777514101232133148987554435199999866


Q ss_pred             HCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf             01454210011126543564136899999987178778312222001015899999999878876765421887553111
Q gi|254780625|r  161 HKKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDAGGSSLRDYV  240 (289)
Q Consensus       161 ~~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~~~i~~vl~~a~~~gG~~~~~~~  240 (289)
                      ..++++||++||||++||||||||+|||||+|||||++++++|+++|      +.+|+++++.+|..|++.||+++++| 
T Consensus       151 ~~~~~~Ik~~LlDQ~~iaGIGNiy~~EiLf~a~I~P~~~~~~L~~~e------~~~L~~~~~~vl~~a~~~~~~~~~~~-  223 (272)
T 1tdz_A          151 RKSTKKIKPYLLEQTLVAGLGNIYVDEVLWLAKIHPEKETNQLIESS------IHLLHDSIIEILQKAIKLGGSSIRTY-  223 (272)
T ss_dssp             HHCCSBHHHHHHTSSSSSCCCHHHHHHHHHHTTCCTTCBGGGCCHHH------HHHHHHHHHHHHHHHHHTTCCCC----
T ss_pred             HHCCCCCCEEEECCCEECCCCHHHHHHHHHHHCCCCCCCHHHCCHHH------HHHHHHHHHHHHHHHHHCCCCCCCCC-
T ss_conf             42033200267507635444473798998872798676752407999------99999999999999998199823245-


Q ss_pred             CCCCCCCCCHHHEEEECCCCCCCCCCCCCEEEEEEECCCCEEECCCCCC
Q ss_conf             6778778741331665738771078778878999987812063877679
Q gi|254780625|r  241 HIDGSIGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQK  289 (289)
Q Consensus       241 ~~~g~~g~~~~~~~vy~r~g~~C~~~CG~~I~~~~~~gR~ty~Cp~CQk  289 (289)
                      ...++.|.++.+|+||+|+|+|| |+||++|++++++||+|||||.|||
T Consensus       224 ~~~~~~g~~~~~~~Vy~r~g~~C-p~Cg~~I~~~~~~gR~t~~Cp~CQk  271 (272)
T 1tdz_A          224 SALGSTGKMQNELQVYGKTGEKC-SRCGAEIQKIKVAGRGTHFCPVCQQ  271 (272)
T ss_dssp             --CCCCCCGGGGCSSTTCTTSBC-TTTCCBCEEEEETTEEEEECTTTSC
T ss_pred             CCCCCCCCCCCEEEEECCCCCCC-CCCCCEEEEEEECCCCEEECCCCCC
T ss_conf             77898787764048838898979-9999989999999981099927789



>1k82_A Formamidopyrimidine-DNA glycosylase; protein-DNA complex, DNA repair, beta sandwich, zinc finger, helix two-turns helix, hydrolase/DNA complex; HET: PED; 2.10A {Escherichia coli} SCOP: a.156.1.2 b.113.1.1 g.39.1.8 Back     alignment and structure
>1ee8_A MUTM (FPG) protein; beta sandwich, zinc finger, helix two-turns helix, riken structural genomics/proteomics initiative, RSGI; 1.90A {Thermus thermophilus HB8} SCOP: a.156.1.2 b.113.1.1 g.39.1.8 Back     alignment and structure
>3gpu_A DNA glycosylase; DNA glycosylase, DNA repair, damage search, base extrusion; HET: DNA 8OG; 1.62A {Geobacillus stearothermophilus} PDB: 3gpx_A* 3gq3_A* 3go8_A* 2f5n_A 2f5o_A 2f5p_A 3gp1_A* 3gq4_A* 3gpy_A* 3gq5_A* 3gpp_A* 2f5q_A* 2f5s_A* 1l1z_A* 1l1t_A* 1l2b_A* 1l2c_A* 1l2d_A* 1r2z_A* 1r2y_A* ... Back     alignment and structure
>1k3x_A Endonuclease VIII; hydrolase/DNA; HET: BRU PED; 1.25A {Escherichia coli} SCOP: a.156.1.2 b.113.1.1 g.39.1.8 PDB: 1k3w_A* 1q39_A 2ea0_A* 2oq4_A* 1q3c_A 2opf_A* 1q3b_A* Back     alignment and structure
>3a46_A Formamidopyrimidine-DNA glycosylase; helix two turns helix, zinc-LESS finger, hydrolase, THF, glycosidase, lyase, multifunctional enzyme; HET: DNA 3DR; 2.20A {Acanthamoeba polyphaga mimivirus} PDB: 3a45_A* 3a42_A Back     alignment and structure
>1tdh_A NEI endonuclease VIII-like 1; helix two turns helix, zinc-LESS finger, hydrolase; 2.10A {Homo sapiens} SCOP: a.156.1.2 b.113.1.1 g.39.1.8 Back     alignment and structure
>3doa_A Fibrinogen binding protein; structural genomics, MCSG., PSI-2, protein structure initiative, midwest center for structural genomics; 2.81A {Staphylococcus aureus subsp} Back     alignment and structure
>2zkq_m 40S ribosomal protein S18E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} PDB: 1s1h_M 3jyv_M* Back     alignment and structure
>2vqe_M 30S ribosomal protein S13, 30S ribosomal protein S6; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: a.156.1.1 PDB: 1gix_P* 1hnw_M* 1hnx_M* 1hnz_M* 1hr0_M 1ibk_M* 1ibl_M* 1ibm_M 1j5e_M 1jgo_P* 1jgp_P* 1jgq_P* 1mj1_P* 1ml5_P* 1n32_M* 1n33_M* 1n34_M 1n36_M 1xmo_M* 1xmq_M* ... Back     alignment and structure
>3ofp_M 30S ribosomal protein S13; protein biosynthesis, ribosomes, RNA, tRNA, transfer, eryThr ketolide, macrolide, antibiotic, EXIT, peptidyl; 3.10A {Escherichia coli} PDB: 3fih_M* 2wwl_M 2qal_M* 1p6g_M 1p87_M 2aw7_M 2avy_M 2i2u_M 2i2p_M* 2qan_M* 2qb9_M* 2qbb_M* 2qbd_M 2qbf_M 2qbh_M* 2qbj_M* 2qou_M* 2qow_M* 2qoy_M* 2qp0_M* ... Back     alignment and structure
>1mu5_A Type II DNA topoisomerase VI subunit B; GHKL ATPase, helix two-turns helix; 2.00A {Sulfolobus shibatae} SCOP: a.156.1.3 d.14.1.3 d.122.1.2 PDB: 1mx0_A* 1z5b_A* 1z5a_A* 1z59_A* 1z5c_A* 2hkj_A* 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

IdentityAlignment graphLength Definition E-value
Target 289 formamidopyrimidine-DNA glycosylase [Candidatus Liberib
d1tdha2130 b.113.1.1 (A:2-131) Endonuclease VIII-like 1 (NEIL1) {H 2e-23
d1tdza2130 b.113.1.1 (A:2-131) DNA repair protein MutM (Fpg) {Lact 1e-21
d1k82a2128 b.113.1.1 (A:1-128) DNA repair protein MutM (Fpg) {Esch 2e-20
d1r2za2133 b.113.1.1 (A:2-134) DNA repair protein MutM (Fpg) {Baci 4e-20
d1ee8a2121 b.113.1.1 (A:1-121) DNA repair protein MutM (Fpg) {Ther 8e-19
d1k3xa2124 b.113.1.1 (A:1-124) Endonuclease VIII {Escherichia coli 1e-18
d1r2za194 a.156.1.2 (A:135-228) DNA repair protein MutM (Fpg) {Ba 8e-20
d1tdza188 a.156.1.2 (A:132-219) DNA repair protein MutM (Fpg) {La 6e-19
d1ee8a189 a.156.1.2 (A:122-210) DNA repair protein MutM (Fpg) {Th 2e-18
d1k82a188 a.156.1.2 (A:129-216) DNA repair protein MutM (Fpg) {Es 4e-18
d1tdha1115 a.156.1.2 (A:132-246) Endonuclease VIII-like 1 (NEIL1) 3e-17
d1k3xa189 a.156.1.2 (A:125-213) Endonuclease VIII {Escherichia co 3e-17
d2hkja178 a.156.1.3 (A:229-306) Topoisomerase VI-B subunit middle 7e-09
d1ee8a356 g.39.1.8 (A:211-266) DNA repair protein MutM (Fpg) {The 2e-16
d1r2za346 g.39.1.8 (A:229-274) DNA repair protein MutM (Fpg) {Bac 3e-15
d1k82a344 g.39.1.8 (A:225-268) DNA repair protein MutM (Fpg) {Esc 6e-15
d1tdza347 g.39.1.8 (A:225-271) DNA repair protein MutM (Fpg) {Lac 9e-15
d1k3xa340 g.39.1.8 (A:223-262) Endonuclease VIII {Escherichia col 6e-11
>d1tdha2 b.113.1.1 (A:2-131) Endonuclease VIII-like 1 (NEIL1) {Human (Homo sapiens) [TaxId: 9606]} Length = 130 Back     information, alignment and structure

class: All beta proteins
fold: N-terminal domain of MutM-like DNA repair proteins
superfamily: N-terminal domain of MutM-like DNA repair proteins
family: N-terminal domain of MutM-like DNA repair proteins
domain: Endonuclease VIII-like 1 (NEIL1)
species: Human (Homo sapiens) [TaxId: 9606]
 Score =  103 bits (257), Expect = 2e-23
 Identities = 29/138 (21%), Positives = 45/138 (32%), Gaps = 20/138 (14%)

Query: 2   PELPEVEIIRRNLMMVMKNMTVTDICLHRKNLRFDFPHHFSAATRGKKIIDVSRRAKYLL 61
           PE PE+ +  + +    + +            R       S        I  S R K L 
Sbjct: 1   PEGPELHLASQFVNEACRALVFGGCVEKSSVSRNPEVPFES----SAYRISASARGKELR 56

Query: 62  IELEG---------NLSIIVHLGMSGSFIIEHTSCAKPIKNPQHNHVTISLTNNTNTKKY 112
           + L            L+++   GMSGSF +           P+H H+           + 
Sbjct: 57  LILSPLPGAQPQQEPLALVFRFGMSGSFQLVPREEL-----PRHAHLRFYTAP--PGPRL 109

Query: 113 RVIYNDPRRFGFMDLVET 130
            + + D RRFG  DL   
Sbjct: 110 ALCFVDIRRFGRWDLGGK 127


>d1tdza2 b.113.1.1 (A:2-131) DNA repair protein MutM (Fpg) {Lactococcus lactis [TaxId: 1358]} Length = 130 Back     information, alignment and structure
>d1k82a2 b.113.1.1 (A:1-128) DNA repair protein MutM (Fpg) {Escherichia coli [TaxId: 562]} Length = 128 Back     information, alignment and structure
>d1r2za2 b.113.1.1 (A:2-134) DNA repair protein MutM (Fpg) {Bacillus stearothermophilus [TaxId: 1422]} Length = 133 Back     information, alignment and structure
>d1ee8a2 b.113.1.1 (A:1-121) DNA repair protein MutM (Fpg) {Thermus thermophilus [TaxId: 274]} Length = 121 Back     information, alignment and structure
>d1k3xa2 b.113.1.1 (A:1-124) Endonuclease VIII {Escherichia coli [TaxId: 562]} Length = 124 Back     information, alignment and structure
>d1r2za1 a.156.1.2 (A:135-228) DNA repair protein MutM (Fpg) {Bacillus stearothermophilus [TaxId: 1422]} Length = 94 Back     information, alignment and structure
>d1tdza1 a.156.1.2 (A:132-219) DNA repair protein MutM (Fpg) {Lactococcus lactis [TaxId: 1358]} Length = 88 Back     information, alignment and structure
>d1ee8a1 a.156.1.2 (A:122-210) DNA repair protein MutM (Fpg) {Thermus thermophilus [TaxId: 274]} Length = 89 Back     information, alignment and structure
>d1k82a1 a.156.1.2 (A:129-216) DNA repair protein MutM (Fpg) {Escherichia coli [TaxId: 562]} Length = 88 Back     information, alignment and structure
>d1tdha1 a.156.1.2 (A:132-246) Endonuclease VIII-like 1 (NEIL1) {Human (Homo sapiens) [TaxId: 9606]} Length = 115 Back     information, alignment and structure
>d1k3xa1 a.156.1.2 (A:125-213) Endonuclease VIII {Escherichia coli [TaxId: 562]} Length = 89 Back     information, alignment and structure
>d2hkja1 a.156.1.3 (A:229-306) Topoisomerase VI-B subunit middle domain {Archaeon Sulfolobus shibatae [TaxId: 2286]} Length = 78 Back     information, alignment and structure
>d1ee8a3 g.39.1.8 (A:211-266) DNA repair protein MutM (Fpg) {Thermus thermophilus [TaxId: 274]} Length = 56 Back     information, alignment and structure
>d1r2za3 g.39.1.8 (A:229-274) DNA repair protein MutM (Fpg) {Bacillus stearothermophilus [TaxId: 1422]} Length = 46 Back     information, alignment and structure
>d1k82a3 g.39.1.8 (A:225-268) DNA repair protein MutM (Fpg) {Escherichia coli [TaxId: 562]} Length = 44 Back     information, alignment and structure
>d1tdza3 g.39.1.8 (A:225-271) DNA repair protein MutM (Fpg) {Lactococcus lactis [TaxId: 1358]} Length = 47 Back     information, alignment and structure
>d1k3xa3 g.39.1.8 (A:223-262) Endonuclease VIII {Escherichia coli [TaxId: 562]} Length = 40 Back     information, alignment and structure

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

IdentityAlignment graphLength Definition Probability
Target289 formamidopyrimidine-DNA glycosylase [Candidatus Liberib
d1r2za2133 DNA repair protein MutM (Fpg) {Bacillus stearothermophi 99.97
d1tdza2130 DNA repair protein MutM (Fpg) {Lactococcus lactis [TaxI 99.96
d1k82a2128 DNA repair protein MutM (Fpg) {Escherichia coli [TaxId: 99.96
d1ee8a2121 DNA repair protein MutM (Fpg) {Thermus thermophilus [Ta 99.95
d1k3xa2124 Endonuclease VIII {Escherichia coli [TaxId: 562]} 99.91
d1tdha2130 Endonuclease VIII-like 1 (NEIL1) {Human (Homo sapiens) 99.9
d1r2za194 DNA repair protein MutM (Fpg) {Bacillus stearothermophi 99.96
d1k82a188 DNA repair protein MutM (Fpg) {Escherichia coli [TaxId: 99.95
d1tdza188 DNA repair protein MutM (Fpg) {Lactococcus lactis [TaxI 99.95
d1ee8a189 DNA repair protein MutM (Fpg) {Thermus thermophilus [Ta 99.95
d1k3xa189 Endonuclease VIII {Escherichia coli [TaxId: 562]} 99.94
d1tdha1115 Endonuclease VIII-like 1 (NEIL1) {Human (Homo sapiens) 99.84
d2hkja178 Topoisomerase VI-B subunit middle domain {Archaeon Sulf 99.68
d2gy9m1114 Ribosomal protein S13 {Escherichia coli [TaxId: 562]} 95.78
d2uubm1125 Ribosomal protein S13 {Thermus thermophilus [TaxId: 274 95.65
d1ee8a356 DNA repair protein MutM (Fpg) {Thermus thermophilus [Ta 99.57
d1r2za346 DNA repair protein MutM (Fpg) {Bacillus stearothermophi 99.5
d1tdza347 DNA repair protein MutM (Fpg) {Lactococcus lactis [TaxI 99.48
d1k82a344 DNA repair protein MutM (Fpg) {Escherichia coli [TaxId: 99.46
d1k3xa340 Endonuclease VIII {Escherichia coli [TaxId: 562]} 99.18
>d1r2za2 b.113.1.1 (A:2-134) DNA repair protein MutM (Fpg) {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure
class: All beta proteins
fold: N-terminal domain of MutM-like DNA repair proteins
superfamily: N-terminal domain of MutM-like DNA repair proteins
family: N-terminal domain of MutM-like DNA repair proteins
domain: DNA repair protein MutM (Fpg)
species: Bacillus stearothermophilus [TaxId: 1422]
Probab=99.97  E-value=2.2e-30  Score=212.34  Aligned_cols=131  Identities=31%  Similarity=0.547  Sum_probs=115.1

Q ss_pred             CCCCHHHHHHHHHHHHHCCCEEEEEEECCCCC-CCC-CCHHHHHHHCCCEEEEEEECCEEEEEEECCCCCCCCCCCCCCE
Q ss_conf             67643678898899986797788999648332-657-8778999728988999960530899950355310015255327
Q gi|254780625|r    2 PELPEVEIIRRNLMMVMKNMTVTDICLHRKNL-RFD-FPHHFSAATRGKKIIDVSRRAKYLLIELEGNLSIIVHLGMSGS   79 (289)
Q Consensus         2 PElPEVe~~~~~l~~~l~g~~I~~V~~~~~~~-~~~-~~~~~~~~L~G~~I~~v~r~GK~l~l~l~~~~~L~~HlgM~G~   79 (289)
                      |||||||++++.|++.+.|++|++|++.+++. +.+ .++.|.+.|.|++|.+|.|+||||+++||++ +|++||||||+
T Consensus         1 PELPEVe~~~~~L~~~~~g~~I~~v~v~~~~~~~~~~~~~~~~~~l~g~~I~~v~RrGK~l~~~l~~~-~l~~HLgMtG~   79 (133)
T d1r2za2           1 PQLPEVETIRRTLLPLIVGKTIEDVRIFWPNIIRHPRDSEAFAARMIGQTVRGLERRGKFLKFLLDRD-ALISHLRMEGR   79 (133)
T ss_dssp             CCHHHHHHHHHHHHHHHTTCBEEEEEESCGGGEEESSSHHHHHHHHTTCBCCEEEEETTEEEEECSSE-EEEEECTTTCE
T ss_pred             CCCCCHHHHHHHHHHHHCCCEEEEEEEECCCHHCCCCCHHHHHHHHCCCCEEEEEEEEEEEEEECCCE-EEEEECCCCCE
T ss_conf             98702999999999985898999999807722137789899998734871444786579999904660-68975034725


Q ss_pred             EEEECCCCCCCCCCCCCCEEEEEEECCCCCEEEEEEEECCCCCCCEECCCCCCHHHCCCCCCC
Q ss_conf             998147854224587663389997068876048999815876641001455301005323565
Q gi|254780625|r   80 FIIEHTSCAKPIKNPQHNHVTISLTNNTNTKKYRVIYNDPRRFGFMDLVETSLKYQYPPLRTL  142 (289)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~D~R~fG~~~~~~~~~~~~~~~l~~l  142 (289)
                      |.+.+...    ..++|+|+.|.|+|+.     .++|.|+|+||++++++..+...+|+|++|
T Consensus        80 ~~~~~~~~----~~~kh~~~~~~~~~g~-----~l~f~D~RrFG~i~l~~~~~~~~~~~l~~L  133 (133)
T d1r2za2          80 YAVASALE----PLEPHTHVVFCFTDGS-----ELRYRDVRKFGTMHVYAKEEADRRPPLAEL  133 (133)
T ss_dssp             EEEEETTS----CCCTTEEEEEEETTSE-----EEEEECTTCCCEEEEEEHHHHTTSTTTTTC
T ss_pred             EEEEECCC----CCCCCEEEEEEECCCC-----EEEEECCCCCEEEEEEECCCCCCCCCCCCC
T ss_conf             88873278----7766559999947999-----999985898239999708640129310029



>d1tdza2 b.113.1.1 (A:2-131) DNA repair protein MutM (Fpg) {Lactococcus lactis [TaxId: 1358]} Back     information, alignment and structure
>d1k82a2 b.113.1.1 (A:1-128) DNA repair protein MutM (Fpg) {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1ee8a2 b.113.1.1 (A:1-121) DNA repair protein MutM (Fpg) {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1k3xa2 b.113.1.1 (A:1-124) Endonuclease VIII {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1tdha2 b.113.1.1 (A:2-131) Endonuclease VIII-like 1 (NEIL1) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1r2za1 a.156.1.2 (A:135-228) DNA repair protein MutM (Fpg) {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure
>d1k82a1 a.156.1.2 (A:129-216) DNA repair protein MutM (Fpg) {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1tdza1 a.156.1.2 (A:132-219) DNA repair protein MutM (Fpg) {Lactococcus lactis [TaxId: 1358]} Back     information, alignment and structure
>d1ee8a1 a.156.1.2 (A:122-210) DNA repair protein MutM (Fpg) {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1k3xa1 a.156.1.2 (A:125-213) Endonuclease VIII {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1tdha1 a.156.1.2 (A:132-246) Endonuclease VIII-like 1 (NEIL1) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2hkja1 a.156.1.3 (A:229-306) Topoisomerase VI-B subunit middle domain {Archaeon Sulfolobus shibatae [TaxId: 2286]} Back     information, alignment and structure
>d2gy9m1 a.156.1.1 (M:1-114) Ribosomal protein S13 {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2uubm1 a.156.1.1 (M:2-126) Ribosomal protein S13 {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1ee8a3 g.39.1.8 (A:211-266) DNA repair protein MutM (Fpg) {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1r2za3 g.39.1.8 (A:229-274) DNA repair protein MutM (Fpg) {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure
>d1tdza3 g.39.1.8 (A:225-271) DNA repair protein MutM (Fpg) {Lactococcus lactis [TaxId: 1358]} Back     information, alignment and structure
>d1k82a3 g.39.1.8 (A:225-268) DNA repair protein MutM (Fpg) {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1k3xa3 g.39.1.8 (A:223-262) Endonuclease VIII {Escherichia coli [TaxId: 562]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 289 formamidopyrimidine-DNA glycosylase [Candidatus Li
1k3x_A_125-262138 (A:125-262) Endonuclease VIII; hydrolase/DNA; HET: 4e-35
1tdz_A_137-272136 (A:137-272) Formamidopyrimidine-DNA glycosylase; D 5e-35
3a46_A_144-289146 (A:144-289) Formamidopyrimidine-DNA glycosylase; h 1e-33
3gpu_A_133-256124 (A:133-256) DNA glycosylase; DNA glycosylase, DNA 1e-32
1tdh_A_156-364209 (A:156-364) NEI endonuclease VIII-like 1; helix tw 1e-27
1tdz_A_1-136136 (A:1-136) Formamidopyrimidine-DNA glycosylase; DNA 3e-32
3a46_A_1-143143 (A:1-143) Formamidopyrimidine-DNA glycosylase; hel 4e-30
1ee8_A_1-120120 (A:1-120) MUTM (FPG) protein; beta sandwich, zinc 7e-28
1tdh_A_1-133133 (A:1-133) NEI endonuclease VIII-like 1; helix two 7e-27
3gpu_A_1-132132 (A:1-132) DNA glycosylase; DNA glycosylase, DNA re 9e-27
1k82_A_1-128128 (A:1-128) Formamidopyrimidine-DNA glycosylase; pro 5e-25
1k3x_A_1-124124 (A:1-124) Endonuclease VIII; hydrolase/DNA; HET: B 1e-23
1k82_A_129-22597 (A:129-225) Formamidopyrimidine-DNA glycosylase; p 9e-27
1ee8_A_121-21999 (A:121-219) MUTM (FPG) protein; beta sandwich, zin 3e-25
1mu5_A_230-31182 (A:230-311) Type II DNA topoisomerase VI subunit B 6e-16
1k82_A_226-26843 (A:226-268) Formamidopyrimidine-DNA glycosylase; p 9e-15
1ee8_A_220-26647 (A:220-266) MUTM (FPG) protein; beta sandwich, zin 2e-14
>1k3x_A (A:125-262) Endonuclease VIII; hydrolase/DNA; HET: BRU PED; 1.25A {Escherichia coli}Length = 138 Back     alignment and structure
 Score =  142 bits (360), Expect = 4e-35
 Identities = 34/151 (22%), Positives = 58/151 (38%), Gaps = 16/151 (10%)

Query: 142 LGPEPADNSFNAIYLTHQFHK---KNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIR 198
           +GP+  D +     +  +      +N      LL+Q  +AG+GN    E LW+  L+   
Sbjct: 1   VGPDVLDPNLTPEVVKERLLSPRFRNRQFAGLLLDQAFLAGLGNYLRVEILWQVGLTGNH 60

Query: 199 KTRSLIQNNGTPKDILYKLIQEIQKVLIDAIDAGGSSLRDYVHIDGSIGYFQNAFSVYGK 258
           K + L          L  L   + ++   +    G    +  H     G       V+ +
Sbjct: 61  KAKDL------NAAQLDALAHALLEIPRFSYATRGQVDENKHH-----GALFRFK-VFHR 108

Query: 259 TGEPCLSNCGQMIRRIVQAGRSTFYCTYCQK 289
            GEPC   CG +I +   + R  ++C  CQ 
Sbjct: 109 DGEPCE-RCGSIIEKTTLSSRPFYWCPGCQH 138


>1tdz_A (A:137-272) Formamidopyrimidine-DNA glycosylase; DNA repair, FPG, MUTM, FAPY G, hydrolase/DNA complex; HET: FOX; 1.80A {Lactococcus lactis}Length = 136 Back     alignment and structure
>3a46_A (A:144-289) Formamidopyrimidine-DNA glycosylase; helix two turns helix, zinc-LESS finger, hydrolase, THF, glycosidase, lyase, multifunctional enzyme; HET: DNA 3DR; 2.20A {Acanthamoeba polyphaga mimivirus} PDB: 3a45_A* 3a42_ALength = 146 Back     alignment and structure
>3gpu_A (A:133-256) DNA glycosylase; DNA glycosylase, DNA repair, damage search, base extrusion; HET: DNA 8OG; 1.62A {Geobacillus stearothermophilus} PDB: 3gpx_A* 3gq3_A* 2f5n_A 2f5o_A 2f5p_A 3gp1_A* 3gq4_A* 3gpy_A* 3gq5_A* 3gpp_A* 2f5q_A* 2f5s_A* 1l1z_A* 1l1t_A* 1l2b_A* 1l2c_A* 1l2d_A* 1r2z_A* 1r2y_A* 3jr5_A* ...Length = 124 Back     alignment and structure
>1tdh_A (A:156-364) NEI endonuclease VIII-like 1; helix two turns helix, zinc-LESS finger, hydrolase; 2.10A {Homo sapiens}Length = 209 Back     alignment and structure
>1tdz_A (A:1-136) Formamidopyrimidine-DNA glycosylase; DNA repair, FPG, MUTM, FAPY G, hydrolase/DNA complex; HET: FOX; 1.80A {Lactococcus lactis}Length = 136 Back     alignment and structure
>3a46_A (A:1-143) Formamidopyrimidine-DNA glycosylase; helix two turns helix, zinc-LESS finger, hydrolase, THF, glycosidase, lyase, multifunctional enzyme; HET: DNA 3DR; 2.20A {Acanthamoeba polyphaga mimivirus} PDB: 3a45_A* 3a42_ALength = 143 Back     alignment and structure
>1ee8_A (A:1-120) MUTM (FPG) protein; beta sandwich, zinc finger, helix two-turns helix, riken structural genomics/proteomics initiative, RSGI; 1.90A {Thermus thermophilus HB8}Length = 120 Back     alignment and structure
>1tdh_A (A:1-133) NEI endonuclease VIII-like 1; helix two turns helix, zinc-LESS finger, hydrolase; 2.10A {Homo sapiens}Length = 133 Back     alignment and structure
>3gpu_A (A:1-132) DNA glycosylase; DNA glycosylase, DNA repair, damage search, base extrusion; HET: DNA 8OG; 1.62A {Geobacillus stearothermophilus} PDB: 3gpx_A* 3gq3_A* 2f5n_A 2f5o_A 2f5p_A 3gp1_A* 3gq4_A* 3gpy_A* 3gq5_A* 3gpp_A* 2f5q_A* 2f5s_A* 1l1z_A* 1l1t_A* 1l2b_A* 1l2c_A* 1l2d_A* 1r2z_A* 1r2y_A* 3jr5_A* ...Length = 132 Back     alignment and structure
>1k82_A (A:1-128) Formamidopyrimidine-DNA glycosylase; protein-DNA complex, DNA repair, beta sandwich, zinc finger, helix two-turns helix, hydrolase/DNA complex; HET: PED; 2.10A {Escherichia coli}Length = 128 Back     alignment and structure
>1k3x_A (A:1-124) Endonuclease VIII; hydrolase/DNA; HET: BRU PED; 1.25A {Escherichia coli}Length = 124 Back     alignment and structure
>1k82_A (A:129-225) Formamidopyrimidine-DNA glycosylase; protein-DNA complex, DNA repair, beta sandwich, zinc finger, helix two-turns helix, hydrolase/DNA complex; HET: PED; 2.10A {Escherichia coli}Length = 97 Back     alignment and structure
>1ee8_A (A:121-219) MUTM (FPG) protein; beta sandwich, zinc finger, helix two-turns helix, riken structural genomics/proteomics initiative, RSGI; 1.90A {Thermus thermophilus HB8}Length = 99 Back     alignment and structure
>1mu5_A (A:230-311) Type II DNA topoisomerase VI subunit B; GHKL ATPase, helix two-turns helix; 2.00A {Sulfolobus shibatae}Length = 82 Back     alignment and structure
>1k82_A (A:226-268) Formamidopyrimidine-DNA glycosylase; protein-DNA complex, DNA repair, beta sandwich, zinc finger, helix two-turns helix, hydrolase/DNA complex; HET: PED; 2.10A {Escherichia coli}Length = 43 Back     alignment and structure
>1ee8_A (A:220-266) MUTM (FPG) protein; beta sandwich, zinc finger, helix two-turns helix, riken structural genomics/proteomics initiative, RSGI; 1.90A {Thermus thermophilus HB8}Length = 47 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target289 formamidopyrimidine-DNA glycosylase [Candidatus Liberib
1k3x_A_125-262138 Endonuclease VIII; hydrolase/DNA; HET: BRU PED; 1. 100.0
1tdz_A_137-272136 Formamidopyrimidine-DNA glycosylase; DNA repair, F 100.0
3gpu_A_133-256124 DNA glycosylase; DNA glycosylase, DNA repair, dama 100.0
3a46_A_144-289146 Formamidopyrimidine-DNA glycosylase; helix two tur 100.0
1tdh_A_156-364209 NEI endonuclease VIII-like 1; helix two turns heli 100.0
1tdz_A_1-136136 Formamidopyrimidine-DNA glycosylase; DNA repair, F 100.0
3a46_A_1-143143 Formamidopyrimidine-DNA glycosylase; helix two tur 99.98
3gpu_A_1-132132 DNA glycosylase; DNA glycosylase, DNA repair, dama 99.95
1tdh_A_1-133133 NEI endonuclease VIII-like 1; helix two turns heli 99.95
1k82_A_1-128128 Formamidopyrimidine-DNA glycosylase; protein-DNA c 99.95
1k3x_A_1-124124 Endonuclease VIII; hydrolase/DNA; HET: BRU PED; 1. 99.94
1ee8_A_1-120120 MUTM (FPG) protein; beta sandwich, zinc finger, he 99.94
1ee8_A_121-21999 MUTM (FPG) protein; beta sandwich, zinc finger, he 99.96
1k82_A_129-22597 Formamidopyrimidine-DNA glycosylase; protein-DNA c 99.96
1mu5_A_230-31182 Type II DNA topoisomerase VI subunit B; GHKL ATPas 99.84
2zbk_B_229-31082 Type 2 DNA topoisomerase 6 subunit B; DNA binding 98.23
2zkq_m_1-8888 40S ribosomal protein S18E; protein-RNA complex, 4 96.4
2vqe_M_1-6464 30S ribosomal protein S13, 30S ribosomal protein S 96.34
3i1m_M_1-6363 30S ribosomal protein S13; ribosome structure, pro 95.97
1k82_A_226-26843 Formamidopyrimidine-DNA glycosylase; protein-DNA c 99.48
1ee8_A_220-26647 MUTM (FPG) protein; beta sandwich, zinc finger, he 99.45
3doa_A_166-23570 Fibrinogen binding protein; structural genomics, M 95.54
>1k3x_A (A:125-262) Endonuclease VIII; hydrolase/DNA; HET: BRU PED; 1.25A {Escherichia coli} Back     alignment and structure
Probab=100.00  E-value=0  Score=319.83  Aligned_cols=135  Identities=25%  Similarity=0.491  Sum_probs=125.7

Q ss_pred             CCCCCCCCCCHHHHHHHHHH---CCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             55533221110678887420---145421001112654356413689999998717877831222200101589999999
Q gi|254780625|r  142 LGPEPADNSFNAIYLTHQFH---KKNSNLKNALLNQKIVAGIGNIYVCEALWRAKLSPIRKTRSLIQNNGTPKDILYKLI  218 (289)
Q Consensus       142 lGpD~l~~~~~~~~~~~~l~---~~~~~Ik~~LlDQ~~iaGIGN~y~~EiLf~a~I~P~~~~~~Ls~~e~~~~~~~~~L~  218 (289)
                      ||||||+++|+.+.|.+.+.   +++++||++||||++||||||||+|||||+|||||++++++||++|      +.+|+
T Consensus         1 LGpDpl~~~~~~~~~~~~l~~~r~~~~~ik~~LlDQ~~iaGiGNiy~dEiLf~a~ihP~~~~~~Ls~~~------~~~L~   74 (138)
T 1k3x_A            1 VGPDVLDPNLTPEVVKERLLSPRFRNRQFAGLLLDQAFLAGLGNYLRVEILWQVGLTGNHKAKDLNAAQ------LDALA   74 (138)
T ss_dssp             CCCBTTCTTCCHHHHHHHHHSTTTTTSCHHHHTTCTTTSBTCCHHHHHHHHHHHTCCSSCCGGGSCHHH------HHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCCCCEEHEHHHHH------HHHHH
T ss_conf             699879857768999998765310026899998427743465689999999860048766101002778------99999


Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHEEEECCCCCCCCCCCCCEEEEEEECCCCEEECCCCCC
Q ss_conf             98788767654218875531116778778741331665738771078778878999987812063877679
Q gi|254780625|r  219 QEIQKVLIDAIDAGGSSLRDYVHIDGSIGYFQNAFSVYGKTGEPCLSNCGQMIRRIVQAGRSTFYCTYCQK  289 (289)
Q Consensus       219 ~~i~~vl~~a~~~gG~~~~~~~~~~g~~g~~~~~~~vy~r~g~~C~~~CG~~I~~~~~~gR~ty~Cp~CQk  289 (289)
                      .+++++|..|++.||++..++.+      +++.+++||+|+|+|| |+||++|++++++||+|||||+|||
T Consensus        75 ~~i~~vl~~ai~~gg~~~~~~~~------~~~~~~~v~~r~g~~C-~~Cg~~I~~~~~~gR~t~~CP~CQk  138 (138)
T 1k3x_A           75 HALLEIPRFSYATRGQVDENKHH------GALFRFKVFHRDGEPC-ERCGSIIEKTTLSSRPFYWCPGCQH  138 (138)
T ss_dssp             HHHHHHHHHHHHHCC---------------CCCCCSSTTCTTSBC-TTTCCBCEEEEETTEEEEECTTTCC
T ss_pred             HHHHHHHHHHHHCCCEECCCCCC------CCEEEEEEECCCCCCC-CCCCCEEEEEEECCCCCEECCCCCC
T ss_conf             99999998785528664777888------8446889815487969-9999899999989890389914269



>1tdz_A (A:137-272) Formamidopyrimidine-DNA glycosylase; DNA repair, FPG, MUTM, FAPY G, hydrolase/DNA complex; HET: FOX; 1.80A {Lactococcus lactis} Back     alignment and structure
>3gpu_A (A:133-256) DNA glycosylase; DNA glycosylase, DNA repair, damage search, base extrusion; HET: DNA 8OG; 1.62A {Geobacillus stearothermophilus} PDB: 3gpx_A* 3gq3_A* 2f5n_A 2f5o_A 2f5p_A 3gp1_A* 3gq4_A* 3gpy_A* 3gq5_A* 3gpp_A* 2f5q_A* 2f5s_A* 1l1z_A* 1l1t_A* 1l2b_A* 1l2c_A* 1l2d_A* 1r2z_A* 1r2y_A* 3jr5_A* ... Back     alignment and structure
>3a46_A (A:144-289) Formamidopyrimidine-DNA glycosylase; helix two turns helix, zinc-LESS finger, hydrolase, THF, glycosidase, lyase, multifunctional enzyme; HET: DNA 3DR; 2.20A {Acanthamoeba polyphaga mimivirus} PDB: 3a45_A* 3a42_A Back     alignment and structure
>1tdh_A (A:156-364) NEI endonuclease VIII-like 1; helix two turns helix, zinc-LESS finger, hydrolase; 2.10A {Homo sapiens} Back     alignment and structure
>1tdz_A (A:1-136) Formamidopyrimidine-DNA glycosylase; DNA repair, FPG, MUTM, FAPY G, hydrolase/DNA complex; HET: FOX; 1.80A {Lactococcus lactis} Back     alignment and structure
>3a46_A (A:1-143) Formamidopyrimidine-DNA glycosylase; helix two turns helix, zinc-LESS finger, hydrolase, THF, glycosidase, lyase, multifunctional enzyme; HET: DNA 3DR; 2.20A {Acanthamoeba polyphaga mimivirus} PDB: 3a45_A* 3a42_A Back     alignment and structure
>3gpu_A (A:1-132) DNA glycosylase; DNA glycosylase, DNA repair, damage search, base extrusion; HET: DNA 8OG; 1.62A {Geobacillus stearothermophilus} PDB: 3gpx_A* 3gq3_A* 2f5n_A 2f5o_A 2f5p_A 3gp1_A* 3gq4_A* 3gpy_A* 3gq5_A* 3gpp_A* 2f5q_A* 2f5s_A* 1l1z_A* 1l1t_A* 1l2b_A* 1l2c_A* 1l2d_A* 1r2z_A* 1r2y_A* 3jr5_A* ... Back     alignment and structure
>1tdh_A (A:1-133) NEI endonuclease VIII-like 1; helix two turns helix, zinc-LESS finger, hydrolase; 2.10A {Homo sapiens} Back     alignment and structure
>1k82_A (A:1-128) Formamidopyrimidine-DNA glycosylase; protein-DNA complex, DNA repair, beta sandwich, zinc finger, helix two-turns helix, hydrolase/DNA complex; HET: PED; 2.10A {Escherichia coli} Back     alignment and structure
>1k3x_A (A:1-124) Endonuclease VIII; hydrolase/DNA; HET: BRU PED; 1.25A {Escherichia coli} Back     alignment and structure
>1ee8_A (A:1-120) MUTM (FPG) protein; beta sandwich, zinc finger, helix two-turns helix, riken structural genomics/proteomics initiative, RSGI; 1.90A {Thermus thermophilus HB8} Back     alignment and structure
>1ee8_A (A:121-219) MUTM (FPG) protein; beta sandwich, zinc finger, helix two-turns helix, riken structural genomics/proteomics initiative, RSGI; 1.90A {Thermus thermophilus HB8} Back     alignment and structure
>1k82_A (A:129-225) Formamidopyrimidine-DNA glycosylase; protein-DNA complex, DNA repair, beta sandwich, zinc finger, helix two-turns helix, hydrolase/DNA complex; HET: PED; 2.10A {Escherichia coli} Back     alignment and structure
>1mu5_A (A:230-311) Type II DNA topoisomerase VI subunit B; GHKL ATPase, helix two-turns helix; 2.00A {Sulfolobus shibatae} Back     alignment and structure
>2zbk_B (B:229-310) Type 2 DNA topoisomerase 6 subunit B; DNA binding protein, decatenation, ATPase, drug design, DNA-binding, magnesium, metal-binding; HET: RDC; 3.56A {Sulfolobus shibatae} Back     alignment and structure
>2zkq_m (m:1-88) 40S ribosomal protein S18E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} PDB: 1s1h_M Back     alignment and structure
>2vqe_M (M:1-64) 30S ribosomal protein S13, 30S ribosomal protein S6; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} Back     alignment and structure
>3i1m_M (M:1-63) 30S ribosomal protein S13; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_M* 3e1a_F 3e1c_F 1vs5_M 3i1o_M 3i1q_M 3i1s_M 3i1z_M 3i21_M 2qal_M* 1p6g_M 1p87_M 2aw7_M 2avy_M 2i2u_M 2i2p_M* 2qan_M* 2qb9_M* 2qbb_M* 2qbd_M ... Back     alignment and structure
>1k82_A (A:226-268) Formamidopyrimidine-DNA glycosylase; protein-DNA complex, DNA repair, beta sandwich, zinc finger, helix two-turns helix, hydrolase/DNA complex; HET: PED; 2.10A {Escherichia coli} Back     alignment and structure
>1ee8_A (A:220-266) MUTM (FPG) protein; beta sandwich, zinc finger, helix two-turns helix, riken structural genomics/proteomics initiative, RSGI; 1.90A {Thermus thermophilus HB8} Back     alignment and structure
>3doa_A (A:166-235) Fibrinogen binding protein; structural genomics, MCSG., PSI-2, protein structure initiative, midwest center for structural genomics; 2.81A {Staphylococcus aureus subsp} Back     alignment and structure