254780383

254780383

endonuclease III

GeneID in NCBI database:8209368Locus tag:CLIBASIA_01340
Protein GI in NCBI database:254780383Protein Accession:YP_003064796.1
Gene range:+(279613, 280296)Protein Length:227aa
Gene description:endonuclease III
COG prediction:[L] Predicted EndoIII-related endonuclease
KEGG prediction:endonuclease III; K10773 endonuclease III [EC:4.2.99.18]
SEED prediction:Endonuclease III (EC 4.2.99.18)
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
TOPPRED2 TM-Helix
HMMTOP2 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-------
MVSSKKSDSYQGNSPLGCLYTPKELEEIFYLFSLKWPSPKGELYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMAFGIPTIGVDTHIFRISNRIGLAPGKTPNKVEQSLLRIIPPKHQYNAHYWLVLHGRYVCKARKPQCQSCIISNLCKRIKQ
cccccccccccccccHHHcccHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHccccHHHHHHHHHHHHHHcccHHHHHHccHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHcccccHHHHHHHHcccccHHHHHHHHHHHcccccEEccHHHHHHHHHHcccccccHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHcc
ccccccccccccccccHHcccHHHHHHHHHHHHHHccccccccccccHHHHHHHHHHcccccHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHccccccccHHHHHHcccccHHHHHHHHHHHHccccccccHHHHHHHHHHcccccccHHHHHHHHHHHccHHHcccHHHHHHHHHHHccccccccHHHcccHHHcccccc
mvsskksdsyqgnsplgclytpkeLEEIFYLFslkwpspkgelyyvNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINefdnkipqtlegltrlpgigrkgANVILSMAfgiptigvdthifrisnriglapgktpnkVEQSLlriippkhqynaHYWLVLHGRyvckarkpqcqscIISNLCKRIKQ
mvsskksdsyqgnsplGCLYTPKELEEIFYLFSLKWPSPKGELYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMAFGIPTIGVDTHIFRISNRiglapgktpNKVEQSLLRIIPPKHQYNAHYWLVLHGRYVCKARkpqcqsciisnlckrikq
MVSSKKSDSYQGNSPLGCLYTPKELEEIFYLFSLKWPSPKGELYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMAFGIPTIGVDTHIFRISNRIGLAPGKTPNKVEQSLLRIIPPKHQYNAHYWLVLHGRYVCKARKPQCQSCIISNLCKRIKQ
************************LEEIFYLFSLKWPSPKGELYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMAFGIPTIGVDTHIFRISNRIGLAPGKTPNKVEQSLLRIIPPKHQYNAHYWLVLHGRYVCKARKPQCQSCIISNLCKRIK*
************NSPLGCLYTPKELEEIFYLFSLKWPSPKGELYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMAFGIPTIGVDTHIFRISNRIGLAPGKTPNKVEQSLLRIIPPKHQYNAHYWLVLHGRYVCKARKPQCQSCIISNLCKRIKQ
***************LGCLYTPKELEEIFYLFSLKWPSPKGELYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMAFGIPTIGVDTHIFRISNRIGLAPGKTPNKVEQSLLRIIPPKHQYNAHYWLVLHGRYVCKARKPQCQSCIISNLCKRI**
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxHHHHHHHHHHHHHHHHHHHHxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxHHHHHHHHHHHHHHHHHHHHxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
ooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MVSSKKSDSYQGNSPLGCLYTPKELEEIFYLFSLKWPSPKGELYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMAFGIPTIGVDTHIFRISNRIGLAPGKTPNKVEQSLLRIIPPKHQYNAHYWLVLHGRYVCKARKPQCQSCIISNLCKRIKQ
MVSSKKSDSYQGNSPLGCLYTPKELEEIFYLFSLKWPSPKGELYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMAFGIPTIGVDTHIFRISNRIGLAPGKTPNKVEQSLLRIIPPKHQYNAHYWLVLHGRYVCKARKPQCQSCIISNLCKRIKQ
MVSSKKSDSYQGNSPLGCLYTPKELEEIFYLFSLKWPSPKGELYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMAFGIPTIGVDTHIFRISNRIGLAPGKTPNKVEQSLLRIIPPKHQYNAHYWLVLHGRYVCKARKPQCQSCIISNLCKRIKQ

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

IdentityAlignment graphLength Definition E-value
Target227 endonuclease III [Candidatus Liberibacter asiaticus str
254780479 356 A/G-specific adenine glycosylase [Candidatus Liber 1e-08
>gi|254780479|ref|YP_003064892.1| A/G-specific adenine glycosylase [Candidatus Liberibacter asiaticus str. psy62] Length = 356 Back     alignment
 Score = 51.2 bits (121), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 34/125 (27%), Positives = 61/125 (48%), Gaps = 3/125 (2%)

Query: 101 YRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMAFGIPTIGVDTHI 160
           Y  ++ N+   + I++ +++   P  +E L +LPGIG   A+ I+++AF    + VDT+I
Sbjct: 91  YYTRARNLKKCADIIVKKYEGNFPHKVEILKKLPGIGDYTASAIVAIAFNHFAVVVDTNI 150

Query: 161 FRISNRIG--LAPGKTPNKVEQSLLRIIPPKHQYNAHYWLVLH-GRYVCKARKPQCQSCI 217
            RI +R    + P    +K  ++  R I    +       ++  G  +C + KP C  C 
Sbjct: 151 ERIISRYFDIIKPAPLYHKTIKNYARKITSTSRPGDFVQAMMDLGALICTSNKPLCPLCP 210

Query: 218 ISNLC 222
           I   C
Sbjct: 211 IQKNC 215

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

IdentityAlignment graphLength Definition Round E-value
Target227 endonuclease III [Candidatus Liberibacter asiaticus str
315122204177 endonuclease III [Candidatus Liberibacter solanacearum 1 1e-87
222087212259 endonuclease III [Agrobacterium radiobacter K84] Length 1 4e-79
327194662260 endonuclease III protein [Rhizobium etli CNPAF512] Leng 1 2e-77
190893518268 endonuclease III protein [Rhizobium etli CIAT 652] Leng 1 3e-77
227823996317 putative endonuclease III protein [Sinorhizobium fredii 1 2e-76
15963921263 endonuclease III protein [Sinorhizobium meliloti 1021] 1 2e-76
222149822254 endonuclease III [Agrobacterium vitis S4] Length = 254 1 2e-76
86359261271 endonuclease III protein [Rhizobium etli CFN 42] Length 1 3e-76
332717121260 endonuclease III [Agrobacterium sp. H13-3] Length = 260 1 6e-76
241206427260 endonuclease III [Rhizobium leguminosarum bv. trifolii 1 9e-76
>gi|315122204|ref|YP_004062693.1| endonuclease III [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 177 Back     alignment and organism information
 Score =  327 bits (837), Expect = 1e-87,   Method: Compositional matrix adjust.
 Identities = 153/177 (86%), Positives = 170/177 (96%)

Query: 51  LIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIIS 110
           + +AVLLSAQSTDVNVNKATK LF+IADTPQKMLAIGEK LQN+I+TIGIYR+K++NIIS
Sbjct: 1   MAIAVLLSAQSTDVNVNKATKSLFDIADTPQKMLAIGEKNLQNHIKTIGIYRRKAKNIIS 60

Query: 111 LSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMAFGIPTIGVDTHIFRISNRIGLA 170
           LSH LINEFD++IP+TLE LTRL GIGRKGANVILSMAFGIPTIGVDTHIFRI+NRIGLA
Sbjct: 61  LSHTLINEFDSEIPKTLEELTRLSGIGRKGANVILSMAFGIPTIGVDTHIFRIANRIGLA 120

Query: 171 PGKTPNKVEQSLLRIIPPKHQYNAHYWLVLHGRYVCKARKPQCQSCIISNLCKRIKQ 227
           PGKTPN+VEQSLLRIIP KHQYNAHYWLVLHGRYVCKARKPQCQSC+ISN+CKR++Q
Sbjct: 121 PGKTPNQVEQSLLRIIPQKHQYNAHYWLVLHGRYVCKARKPQCQSCVISNICKRVQQ 177


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|222087212|ref|YP_002545747.1| endonuclease III [Agrobacterium radiobacter K84] Length = 259 Back     alignment and organism information
>gi|327194662|gb|EGE61511.1| endonuclease III protein [Rhizobium etli CNPAF512] Length = 260 Back     alignment and organism information
>gi|190893518|ref|YP_001980060.1| endonuclease III protein [Rhizobium etli CIAT 652] Length = 268 Back     alignment and organism information
>gi|227823996|ref|YP_002827969.1| putative endonuclease III protein [Sinorhizobium fredii NGR234] Length = 317 Back     alignment and organism information
>gi|15963921|ref|NP_384274.1| endonuclease III protein [Sinorhizobium meliloti 1021] Length = 263 Back     alignment and organism information
>gi|222149822|ref|YP_002550779.1| endonuclease III [Agrobacterium vitis S4] Length = 254 Back     alignment and organism information
>gi|86359261|ref|YP_471153.1| endonuclease III protein [Rhizobium etli CFN 42] Length = 271 Back     alignment and organism information
>gi|332717121|ref|YP_004444587.1| endonuclease III [Agrobacterium sp. H13-3] Length = 260 Back     alignment and organism information
>gi|241206427|ref|YP_002977523.1| endonuclease III [Rhizobium leguminosarum bv. trifolii WSM1325] Length = 260 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
Target227 endonuclease III [Candidatus Liberibacter asiaticus str
TIGR01083191 TIGR01083, nth, endonuclease III 6e-72
PRK10702211 PRK10702, PRK10702, endonuclease III; Provisional 2e-60
cd00056158 cd00056, ENDO3c, endonuclease III; includes endonucleas 1e-33
pfam00730144 pfam00730, HhH-GPD, HhH-GPD superfamily base excision D 1e-29
KOG1921286 KOG1921, KOG1921, KOG1921, Endonuclease III [Replicatio 1e-27
COG2231215 COG2231, COG2231, Uncharacterized protein related to En 6e-14
COG0177211 COG0177, Nth, Predicted EndoIII-related endonuclease [D 4e-74
smart00478149 smart00478, ENDO3c, endonuclease III 2e-40
COG1194 342 COG1194, MutY, A/G-specific DNA glycosylase [DNA replic 1e-15
COG0122285 COG0122, AlkA, 3-methyladenine DNA glycosylase/8-oxogua 4e-07
TIGR01084275 TIGR01084, mutY, A/G-specific adenine glycosylase 2e-10
KOG2457 555 KOG2457, KOG2457, KOG2457, A/G-specific adenine DNA gly 5e-09
PRK13910 289 PRK13910, PRK13910, DNA glycosylase MutY; Provisional 1e-07
PRK10880 350 PRK10880, PRK10880, adenine DNA glycosylase; Provisiona 5e-06
PRK13913218 PRK13913, PRK13913, 3-methyladenine DNA glycosylase; Pr 2e-04
TIGR00588310 TIGR00588, ogg, 8-oxoguanine DNA-glycosylase (ogg) 0.001
KOG2875323 KOG2875, KOG2875, KOG2875, 8-oxoguanine DNA glycosylase 0.001
pfam0063330 pfam00633, HHH, Helix-hairpin-helix motif 0.002
>gnl|CDD|130155 TIGR01083, nth, endonuclease III Back     alignment and domain information
>gnl|CDD|182661 PRK10702, PRK10702, endonuclease III; Provisional Back     alignment and domain information
>gnl|CDD|28938 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
>gnl|CDD|144361 pfam00730, HhH-GPD, HhH-GPD superfamily base excision DNA repair protein Back     alignment and domain information
>gnl|CDD|37132 KOG1921, KOG1921, KOG1921, Endonuclease III [Replication, recombination and repair] Back     alignment and domain information
>gnl|CDD|32412 COG2231, COG2231, Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|30526 COG0177, Nth, Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|128754 smart00478, ENDO3c, endonuclease III Back     alignment and domain information
>gnl|CDD|31387 COG1194, MutY, A/G-specific DNA glycosylase [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|30471 COG0122, AlkA, 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|130156 TIGR01084, mutY, A/G-specific adenine glycosylase Back     alignment and domain information
>gnl|CDD|37668 KOG2457, KOG2457, KOG2457, A/G-specific adenine DNA glycosylase [Replication, recombination and repair] Back     alignment and domain information
>gnl|CDD|172427 PRK13910, PRK13910, DNA glycosylase MutY; Provisional Back     alignment and domain information
>gnl|CDD|182805 PRK10880, PRK10880, adenine DNA glycosylase; Provisional Back     alignment and domain information
>gnl|CDD|184390 PRK13913, PRK13913, 3-methyladenine DNA glycosylase; Provisional Back     alignment and domain information
>gnl|CDD|129676 TIGR00588, ogg, 8-oxoguanine DNA-glycosylase (ogg) Back     alignment and domain information
>gnl|CDD|38086 KOG2875, KOG2875, KOG2875, 8-oxoguanine DNA glycosylase [Replication, recombination and repair] Back     alignment and domain information
>gnl|CDD|109681 pfam00633, HHH, Helix-hairpin-helix motif Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 227 endonuclease III [Candidatus Liberibacter asiaticus str
TIGR01083192 nth endonuclease III; InterPro: IPR005759 The spectrum 100.0
COG0177211 Nth Predicted EndoIII-related endonuclease [DNA replica 100.0
PRK10702211 endonuclease III; Provisional 100.0
PRK10880 350 adenine DNA glycosylase; Provisional 100.0
TIGR01084297 mutY A/G-specific adenine glycosylase; InterPro: IPR005 100.0
KOG1921286 consensus 100.0
COG1194 342 MutY A/G-specific DNA glycosylase [DNA replication, rec 100.0
COG2231215 Uncharacterized protein related to Endonuclease III [DN 100.0
PRK13913218 3-methyladenine DNA glycosylase; Provisional 100.0
KOG2457 555 consensus 100.0
PRK10308283 3-methyl-adenine DNA glycosylase II; Provisional 99.42
KOG1918254 consensus 99.2
smart00483 334 POLXc DNA polymerase X family. includes vertebrate poly 93.17
PRK13910 290 DNA glycosylase MutY; Provisional 100.0
smart00478149 ENDO3c endonuclease III. includes endonuclease III (DNA 100.0
cd00056158 ENDO3c endonuclease III; includes endonuclease III (DNA 100.0
pfam00730144 HhH-GPD HhH-GPD superfamily base excision DNA repair pr 99.96
TIGR00588379 ogg 8-oxoguanine DNA-glycosylase (ogg); InterPro: IPR00 99.76
COG0122285 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA g 99.67
KOG2875323 consensus 99.63
PRK01229208 N-glycosylase/DNA lyase; Provisional 99.0
COG1059210 Thermostable 8-oxoguanine DNA glycosylase [DNA replicat 98.65
TIGR03252177 uncharacterized HhH-GPD family protein. This model desc 98.03
TIGR00084217 ruvA Holliday junction DNA helicase RuvA; InterPro: IPR 94.52
PRK07956668 ligA NAD-dependent DNA ligase LigA; Validated 94.01
pfam0063330 HHH Helix-hairpin-helix motif. The helix-hairpin-helix 97.34
TIGR00575706 dnlj DNA ligase, NAD-dependent; InterPro: IPR001679 DNA 94.96
PRK08097563 ligB NAD-dependent DNA ligase LigB; Reviewed 93.49
TIGR00615205 recR recombination protein RecR; InterPro: IPR000093 Th 92.61
pfam05559319 DUF763 Protein of unknown function (DUF763). This famil 91.05
KOG2841254 consensus 90.98
PRK00076197 recR recombination protein RecR; Reviewed 90.81
PRK13844200 recombination protein RecR; Provisional 90.81
COG0353198 RecR Recombinational DNA repair protein (RecF pathway) 90.44
PRK08609 570 hypothetical protein; Provisional 90.29
smart0052526 FES FES domain. iron-sulpphur binding domain in DNA-(ap 96.54
pfam1057626 EndIII_4Fe-2S Iron-sulfur binding domain of endonucleas 94.1
pfam09674230 DUF2400 Protein of unknown function (DUF2400). Members 95.25
TIGR02757269 TIGR02757 conserved hypothetical protein TIGR02757; Int 94.53
PRK10353189 3-methyl-adenine DNA glycosylase I; Provisional 94.21
PRK00024224 radC DNA repair protein RadC; Reviewed 92.31
COG2818188 Tag 3-methyladenine DNA glycosylase [DNA replication, r 91.17
TIGR0042670 TIGR00426 competence protein ComEA helix-hairpin-helix 93.55
PRK00116198 ruvA Holliday junction DNA helicase RuvA; Reviewed 91.79
PRK00024224 radC DNA repair protein RadC; Reviewed 91.56
TIGR01259124 comE comEA protein; InterPro: IPR004787 The comE locus 90.52
>TIGR01083 nth endonuclease III; InterPro: IPR005759 The spectrum of DNA damage caused by reactive oxygen species includes a wide variety of modifications of purine and pyrimidine bases Back     alignment and domain information
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK10702 endonuclease III; Provisional Back     alignment and domain information
>PRK10880 adenine DNA glycosylase; Provisional Back     alignment and domain information
>TIGR01084 mutY A/G-specific adenine glycosylase; InterPro: IPR005760 The DNA repair enzyme MutY plays an important role in the prevention of DNA mutations resulting from the presence of the oxidatively damaged lesion 7,8-dihydro-8-oxo-2'-deoxyguanosine (8-OxoG) Back     alignment and domain information
>KOG1921 consensus Back     alignment and domain information
>COG1194 MutY A/G-specific DNA glycosylase [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
>KOG2457 consensus Back     alignment and domain information
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional Back     alignment and domain information
>KOG1918 consensus Back     alignment and domain information
>smart00483 POLXc DNA polymerase X family Back     alignment and domain information
>PRK13910 DNA glycosylase MutY; Provisional Back     alignment and domain information
>smart00478 ENDO3c endonuclease III 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
>TIGR00588 ogg 8-oxoguanine DNA-glycosylase (ogg); InterPro: IPR004577 All proteins in this family for which functions are known are 8-oxo-guanaine DNA glycosylases that function in base excision repair Back     alignment and domain information
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair] Back     alignment and domain information
>KOG2875 consensus Back     alignment and domain information
>PRK01229 N-glycosylase/DNA lyase; Provisional Back     alignment and domain information
>COG1059 Thermostable 8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair] Back     alignment and domain information
>TIGR03252 uncharacterized HhH-GPD family protein Back     alignment and domain information
>TIGR00084 ruvA Holliday junction DNA helicase RuvA; InterPro: IPR000085 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction Back     alignment and domain information
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated Back     alignment and domain information
>pfam00633 HHH Helix-hairpin-helix motif 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
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed Back     alignment and domain information
>TIGR00615 recR recombination protein RecR; InterPro: IPR000093 The bacterial protein recR seems to play a role in a recombinational process of DNA repair Back     alignment and domain information
>pfam05559 DUF763 Protein of unknown function (DUF763) Back     alignment and domain information
>KOG2841 consensus Back     alignment and domain information
>PRK00076 recR recombination protein RecR; Reviewed Back     alignment and domain information
>PRK13844 recombination protein RecR; Provisional Back     alignment and domain information
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK08609 hypothetical protein; Provisional Back     alignment and domain information
>smart00525 FES FES domain Back     alignment and domain information
>pfam10576 EndIII_4Fe-2S Iron-sulfur binding domain of endonuclease III Back     alignment and domain information
>pfam09674 DUF2400 Protein of unknown function (DUF2400) Back     alignment and domain information
>TIGR02757 TIGR02757 conserved hypothetical protein TIGR02757; InterPro: IPR014127 Members of this uncharacterised protein family are found sporadically, so far only among spirochetes, epsilon and delta proteobacteria, and Bacteroides Back     alignment and domain information
>PRK10353 3-methyl-adenine DNA glycosylase I; Provisional Back     alignment and domain information
>PRK00024 radC DNA repair protein RadC; Reviewed Back     alignment and domain information
>COG2818 Tag 3-methyladenine DNA glycosylase [DNA replication, recombination, and repair] Back     alignment and domain information
>TIGR00426 TIGR00426 competence protein ComEA helix-hairpin-helix repeat region; InterPro: IPR004509 This domain is found in competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae Back     alignment and domain information
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed Back     alignment and domain information
>PRK00024 radC DNA repair protein RadC; Reviewed 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

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
Target227 endonuclease III [Candidatus Liberibacter asiaticus str
2abk_A211 Refinement Of The Native Structure Of Endonuclease 3e-35
1orn_A226 Structure Of A Trapped Endonuclease Iii-Dna Covalen 9e-31
1p59_A226 Structure Of A Non-Covalent Endonuclease Iii-Dna Co 1e-30
3fsp_A 369 Muty Adenine Glycosylase Bound To A Transition Stat 7e-25
1rrs_A 369 Muty Adenine Glycosylase In Complex With Dna Contai 9e-25
3g0q_A 352 Crystal Structure Of Muty Bound To Its Inhibitor Dn 1e-24
1rrq_A 369 Muty Adenine Glycosylase In Complex With Dna Contai 1e-24
3n5n_X287 Crystal Structure Analysis Of The Catalytic Domain 2e-22
1wef_A225 Catalytic Domain Of Muty From Escherichia Coli K20a 8e-20
1kg6_A225 Crystal Structure Of The K142r Mutant Of E.Coli Mut 2e-19
1muy_A225 Catalytic Domain Of Muty From Escherichia Coli Leng 2e-19
1kg5_A225 Crystal Structure Of The K142q Mutant Of E.Coli Mut 2e-19
1mud_A225 Catalytic Domain Of Muty From Escherichia Coli, D13 3e-19
1kg4_A225 Crystal Structure Of The K142a Mutant Of E. Coli Mu 3e-19
1kg7_A225 Crystal Structure Of The E161a Mutant Of E.Coli Mut 1e-18
1kqj_A225 Crystal Structure Of A Mutant Of Muty Catalytic Dom 7e-18
1kea_A221 Structure Of A Thermostable Thymine-Dna Glycosylase 5e-16
gi|157834527|pdb|2ABK|A Chain A, Refinement Of The Native Structure Of Endonuclease Iii To A Resolution Of 1.85 Angstrom Length = 211 Back     alignment and structure
 Score =  152 bits (384), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 99/208 (47%), Positives = 141/208 (67%)

Query: 20  YTPKELEEIFYLFSLKWPSPKGELYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADT 79
               +  EI        P P  EL + + F L++AVLLSAQ+TDV+VNKAT  L+ +A+T
Sbjct: 1   MNKAKRLEILTRLRENNPHPTTELNFSSPFELLIAVLLSAQATDVSVNKATAKLYPVANT 60

Query: 80  PQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRK 139
           P  ML +G + ++ YI+TIG+Y  K+ENII    IL+ + + ++P+    L  LPG+GRK
Sbjct: 61  PAAMLELGVEGVKTYIKTIGLYNSKAENIIKTCRILLEQHNGEVPEDRAALEALPGVGRK 120

Query: 140 GANVILSMAFGIPTIGVDTHIFRISNRIGLAPGKTPNKVEQSLLRIIPPKHQYNAHYWLV 199
            ANV+L+ AFG PTI VDTHIFR+ NR   APGK   +VE+ LL+++P + + + H+WL+
Sbjct: 121 TANVVLNTAFGWPTIAVDTHIFRVCNRTQFAPGKNVEQVEEKLLKVVPAEFKVDCHHWLI 180

Query: 200 LHGRYVCKARKPQCQSCIISNLCKRIKQ 227
           LHGRY C ARKP+C SCII +LC+  ++
Sbjct: 181 LHGRYTCIARKPRCGSCIIEDLCEYKEK 208


>gi|34811453|pdb|1ORN|A Chain A, Structure Of A Trapped Endonuclease Iii-Dna Covalent Intermediate: Estranged-Guanine Complex Length = 226 Back     alignment and structure
>gi|34811270|pdb|1P59|A Chain A, Structure Of A Non-Covalent Endonuclease Iii-Dna Complex Length = 226 Back     alignment and structure
>gi|284055514|pdb|3FSP|A Chain A, Muty Adenine Glycosylase Bound To A Transition State Analog (1n) Paired With Dg In Duplexed Dna Length = 369 Back     alignment and structure
>gi|46015547|pdb|1RRS|A Chain A, Muty Adenine Glycosylase In Complex With Dna Containing An Abasic Site Length = 369 Back     alignment and structure
>gi|268612274|pdb|3G0Q|A Chain A, Crystal Structure Of Muty Bound To Its Inhibitor Dna Length = 352 Back     alignment and structure
>gi|46015544|pdb|1RRQ|A Chain A, Muty Adenine Glycosylase In Complex With Dna Containing An A:oxog Pair Length = 369 Back     alignment and structure
>gi|311772157|pdb|3N5N|X Chain X, Crystal Structure Analysis Of The Catalytic Domain And Interdomain Connector Of Human Muty Homologue Length = 287 Back     alignment and structure
>gi|55670670|pdb|1WEF|A Chain A, Catalytic Domain Of Muty From Escherichia Coli K20a Mutant Length = 225 Back     alignment and structure
>gi|27065214|pdb|1KG6|A Chain A, Crystal Structure Of The K142r Mutant Of E.Coli Muty (Core Fragment) Length = 225 Back     alignment and structure
>gi|5822134|pdb|1MUY|A Chain A, Catalytic Domain Of Muty From Escherichia Coli Length = 225 Back     alignment and structure
>gi|27065210|pdb|1KG5|A Chain A, Crystal Structure Of The K142q Mutant Of E.Coli Muty (Core Fragment) Length = 225 Back     alignment and structure
>gi|6137464|pdb|1MUD|A Chain A, Catalytic Domain Of Muty From Escherichia Coli, D138n Mutant Complexed To Adenine Length = 225 Back     alignment and structure
>gi|27065209|pdb|1KG4|A Chain A, Crystal Structure Of The K142a Mutant Of E. Coli Muty (Core Fragment) Length = 225 Back     alignment and structure
>gi|27065216|pdb|1KG7|A Chain A, Crystal Structure Of The E161a Mutant Of E.Coli Muty (Core Fragment) Length = 225 Back     alignment and structure
>gi|20664167|pdb|1KQJ|A Chain A, Crystal Structure Of A Mutant Of Muty Catalytic Domain Length = 225 Back     alignment and structure
gi|18655713|pdb|1KEA|A Chain A, Structure Of A Thermostable Thymine-Dna Glycosylase Length = 221 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target227 endonuclease III [Candidatus Liberibacter asiaticus str
1orn_A226 Endonuclease III; DNA repair, DNA glycosylase, [4Fe-4S] 1e-46
1kea_A221 Possible G-T mismatches repair enzyme; DNA repair, DNA 1e-41
1kg2_A225 A/G-specific adenine glycosylase; DNA repair, hydrolase 4e-38
3fsp_A 369 A/G-specific adenine glycosylase; protein-DNA complex, 4e-37
1pu6_A218 3-methyladenine DNA glycosylase; helix-hairpin-helix, b 6e-35
2abk_A211 Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {E 4e-32
3n5n_X287 A/G-specific adenine DNA glycosylase; alpha-helices, he 7e-32
1m3q_A317 8-oxoguanine DNA glycosylase; DNA repair, END product, 3e-14
3i0w_A290 8-oxoguanine-DNA-glycosylase; OGG, cacogg, DNA, 8-OXOG, 4e-13
2jhn_A295 ALKA, 3-methyladenine DNA-glycosylase; DNA repair, N1-m 3e-10
3fhf_A214 Mjogg, N-glycosylase/DNA lyase, DNA-; helix-hairpin-hel 9e-26
3fhg_A207 Mjogg, N-glycosylase/DNA lyase, DNA-; helix-hairpin-hel 4e-20
1ngn_A155 Methyl-CPG binding protein MBD4; mismacth repair in met 9e-20
>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* Length = 226 Back     alignment and structure
 Score =  181 bits (460), Expect = 1e-46
 Identities = 84/204 (41%), Positives = 133/204 (65%), Gaps = 1/204 (0%)

Query: 21  TPKELEEIFYLFSLKWPSPKGELYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTP 80
           T +++       +  +P    EL + N F L++AV+LSAQ TD  VNK TK LFE   TP
Sbjct: 6   TKQQIRYCLDEMAKMFPDAHCELVHRNPFELLIAVVLSAQCTDALVNKVTKRLFEKYRTP 65

Query: 81  QKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKG 140
              +A+  ++L+  IR+IG+YR K+ NI  L  +LI++++ ++P+  + L +LPG+GRK 
Sbjct: 66  HDYIAVPLEELEQDIRSIGLYRNKARNIQKLCAMLIDKYNGEVPRDRDELMKLPGVGRKT 125

Query: 141 ANVILSMAFGIPTIGVDTHIFRISNRIGLAPG-KTPNKVEQSLLRIIPPKHQYNAHYWLV 199
           ANV++S+AFG+P I VDTH+ R+S R+G      +  +VE++L++IIP +     H+ ++
Sbjct: 126 ANVVVSVAFGVPAIAVDTHVERVSKRLGFCRWDDSVLEVEKTLMKIIPKEEWSITHHRMI 185

Query: 200 LHGRYVCKARKPQCQSCIISNLCK 223
             GRY CKA+ PQC SC + +LC+
Sbjct: 186 FFGRYHCKAQSPQCPSCPLLHLCR 209


>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 Length = 221 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 Length = 225 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* Length = 369 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* Length = 218 Back     alignment and structure
>2abk_A Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {Escherichia coli} SCOP: a.96.1.1 Length = 211 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} Length = 287 Back     alignment and structure
>1m3q_A 8-oxoguanine DNA glycosylase; DNA repair, END product, HOGG, 8-aminoguanine, RE-ligation, hydrolase/DNA complex; HET: DRZ ANG; 1.90A {Homo sapiens} SCOP: a.96.1.3 d.129.1.2 PDB: 1m3h_A* 1n39_A* 1lwy_A* 1hu0_A* 1lwv_A* 1lww_A* 1fn7_A* 1n3a_A* 1n3c_A* 1ebm_A* 1ko9_A 2noe_A* 2noh_A* 2nol_A* 1yqk_A 2noz_A* 2nof_A* 1yqr_A* 1yql_A* 1yqm_A* ... Length = 317 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 Length = 290 Back     alignment and structure
>2jhn_A ALKA, 3-methyladenine DNA-glycosylase; DNA repair, N1-methyladenine, N3-methylcytosine, hyperthermophiles, hydrolase; HET: MBO MES; 1.8A {Archaeoglobus fulgidus} PDB: 2jhj_A Length = 295 Back     alignment and structure
>3fhf_A Mjogg, N-glycosylase/DNA lyase, DNA-; helix-hairpin-helix, 8-oxoguanine, 8-OXOG, DNA damage, DNA repair, glycosidase, hydrolase; 2.00A {Methanocaldococcus jannaschii} Length = 214 Back     alignment and structure
>3fhg_A Mjogg, N-glycosylase/DNA lyase, DNA-; helix-hairpin-helix, 8-oxoguanine, 8-OXOG, ssogg, DNA damage, DNA repair, glycosidase, hydrolase; 1.90A {Sulfolobus solfataricus} Length = 207 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 Length = 155 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target227 endonuclease III [Candidatus Liberibacter asiaticus str
1orn_A226 Endonuclease III; DNA repair, DNA glycosylase, [4Fe-4S] 100.0
2abk_A211 Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {E 100.0
1kea_A221 Possible G-T mismatches repair enzyme; DNA repair, DNA 100.0
3fsp_A 369 A/G-specific adenine glycosylase; protein-DNA complex, 100.0
1kg2_A225 A/G-specific adenine glycosylase; DNA repair, hydrolase 100.0
3n5n_X287 A/G-specific adenine DNA glycosylase; alpha-helices, he 100.0
1pu6_A218 3-methyladenine DNA glycosylase; helix-hairpin-helix, b 100.0
3fhf_A214 Mjogg, N-glycosylase/DNA lyase, DNA-; helix-hairpin-hel 100.0
3i0w_A290 8-oxoguanine-DNA-glycosylase; OGG, cacogg, DNA, 8-OXOG, 99.87
2jhn_A295 ALKA, 3-methyladenine DNA-glycosylase; DNA repair, N1-m 99.86
2ihm_A 360 POL MU, DNA polymerase MU; helix-turn-helix, transferas 94.95
2fmp_A 335 DNA polymerase beta; nucleotidyl transferase, transfera 91.32
2bcq_A 335 DNA polymerase lambda; misalignment, extrahelical, muta 90.02
1ngn_A155 Methyl-CPG binding protein MBD4; mismacth repair in met 99.97
3fhg_A207 Mjogg, N-glycosylase/DNA lyase, DNA-; helix-hairpin-hel 99.94
1m3q_A317 8-oxoguanine DNA glycosylase; DNA repair, END product, 99.85
2h56_A233 DNA-3-methyladenine glycosidase; 10174367, EC 3.2.2.-, 99.77
1mpg_A282 ALKA, 3-methyladenine DNA glycosylase II; DNA repair, b 99.72
3bz1_U104 Photosystem II 12 kDa extrinsic protein; electron trans 93.35
1cuk_A203 RUVA protein; DNA repair, SOS response, DNA-binding, DN 92.15
1ixr_A191 Holliday junction DNA helicase RUVA; heterooligomeric c 91.76
2ztd_A212 Holliday junction ATP-dependent DNA helicase RUVA; reco 91.46
1dgs_A667 DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 91.06
2ofk_A183 3-methyladenine DNA glycosylase I, constitutive; DNA re 93.1
2a1j_B91 DNA excision repair protein ERCC-1; XPF, xeroderma pigm 91.7
2csb_A519 Topoisomerase V, TOP61; topoisomerase IB, helix-turn-he 91.14
1z00_A89 DNA excision repair protein ERCC-1; helix-hairpin-helix 91.1
1vdd_A 228 Recombination protein RECR; helix-hairpin-helix, zinc f 90.19
2ihm_A 360 POL MU, DNA polymerase MU; helix-turn-helix, transferas 90.1
2fmp_A 335 DNA polymerase beta; nucleotidyl transferase, transfera 90.13
>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
Probab=100.00  E-value=0  Score=436.89  Aligned_cols=210  Identities=40%  Similarity=0.717  Sum_probs=204.7

Q ss_pred             HCCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHH
Q ss_conf             23998999999999999767999877778689999999996333203567998998731762000101268999999997
Q gi|254780383|r   18 CLYTPKELEEIFYLFSLKWPSPKGELYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIRT   97 (227)
Q Consensus        18 ~~~~~~~~~~I~~~L~~~yp~~~~~l~~~~p~~~LVa~iLs~qT~d~~v~~~~~~L~~~ypt~e~l~~a~~~el~~~ir~   97 (227)
                      -|.+++++.+|+++|.++||+++.+|+|+|||++||++||||||+|++|++++++|+++||||++++.++.+|++++|++
T Consensus         3 ~m~~~~~~~~i~~~L~~~y~~~~~~l~~rdP~~vLVs~iLsqqT~~~~v~~~~~~l~~~~p~~~~la~a~~~el~~~i~~   82 (226)
T 1orn_A            3 HMLTKQQIRYCLDEMAKMFPDAHCELVHRNPFELLIAVVLSAQCTDALVNKVTKRLFEKYRTPHDYIAVPLEELEQDIRS   82 (226)
T ss_dssp             -CCCHHHHHHHHHHHHHHCTTCCCCSCCSSHHHHHHHHHHHTTSCHHHHHHHHHHHHHHCCSHHHHHSSCHHHHHHHTGG
T ss_pred             CCCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCHHHHHCCCHHHHHHHHHH
T ss_conf             77889999999999998779999999989979999999998408599999999999871399999863899899898874


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHC-CCCHH
Q ss_conf             30037999999752355444200100001456777643235888899998754210001210467877656540-78889
Q gi|254780383|r   98 IGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMAFGIPTIGVDTHIFRISNRIGLAP-GKTPN  176 (227)
Q Consensus        98 ~G~~~~KAk~I~~~a~~i~~~~~g~vP~~~~~L~~LpGVG~ktA~~il~~~~~~p~~~VDthv~Rv~~Rlgl~~-~~~~~  176 (227)
                      +|||++||++|+++++.|+++|+|.+|.++++|++|||||+|||++||+|+||+|+|+|||||+||++|+|+++ ++++.
T Consensus        83 ~g~y~~ka~~i~~~a~~i~~~~~g~vP~~~~~L~~LpGVG~kTA~~il~~a~~~p~~~VDtnv~RV~~Rlg~~~~~~~~~  162 (226)
T 1orn_A           83 IGLYRNKARNIQKLCAMLIDKYNGEVPRDRDELMKLPGVGRKTANVVVSVAFGVPAIAVDTHVERVSKRLGFCRWDDSVL  162 (226)
T ss_dssp             GSSHHHHHHHHHHHHHHHHHHSTTSCCSCHHHHTTSTTCCHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHTSSCTTCCHH
T ss_pred             HCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCCCCCCHH
T ss_conf             22199999999999999999929979878999974877536799999999816886778855568998828666554036


Q ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHCHHHCC
Q ss_conf             999999621884226789999999966516489989472840331768519
Q gi|254780383|r  177 KVEQSLLRIIPPKHQYNAHYWLVLHGRYVCKARKPQCQSCIISNLCKRIKQ  227 (227)
Q Consensus       177 ~~~~~l~~~~p~~~~~~~~~~li~~G~~iC~~~~P~C~~C~l~~~C~~~k~  227 (227)
                      +++..+++++|.+.|.+||++||+||+.||++++|+|+.|||++.|++|++
T Consensus       163 ~~~~~l~~~~p~~~~~~~~~~l~~~G~~iC~~~~P~C~~CPl~~~C~~~~~  213 (226)
T 1orn_A          163 EVEKTLMKIIPKEEWSITHHRMIFFGRYHCKAQSPQCPSCPLLHLCREGKK  213 (226)
T ss_dssp             HHHHHHHHHSCGGGHHHHHHHHHHHHHHTSCSSCCCGGGCTTGGGCHHHHH
T ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHCHHHHC
T ss_conf             789999983865330599999999999884589999998988221678771



>2abk_A Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {Escherichia coli} SCOP: a.96.1.1 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
>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
>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
>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
>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
>3fhf_A Mjogg, N-glycosylase/DNA lyase, DNA-; helix-hairpin-helix, 8-oxoguanine, 8-OXOG, DNA damage, DNA repair, glycosidase, hydrolase; 2.00A {Methanocaldococcus jannaschii} PDB: 3knt_A* 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
>2jhn_A ALKA, 3-methyladenine DNA-glycosylase; DNA repair, N1-methyladenine, N3-methylcytosine, hyperthermophiles, hydrolase; HET: MBO MES; 1.8A {Archaeoglobus fulgidus} PDB: 2jhj_A Back     alignment and structure
>2ihm_A POL MU, DNA polymerase MU; helix-turn-helix, transferase/DNA complex; HET: DNA D3T; 2.40A {Mus musculus} Back     alignment and structure
>2fmp_A DNA polymerase beta; nucleotidyl transferase, transferase/DNA complex; HET: DNA DOC DCT; 1.65A {Homo sapiens} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1bpx_A* 1bpz_A* 1mq2_A* 1mq3_A* 1bpy_A* 1tva_A* 1zjm_A* 1zjn_A* 1zqa_A* 1zqb_A* 1zqc_A* 1zqd_A* 1zqe_A* 1zqf_A* 1zqg_A* 1zqh_A* 1zqi_A* 1zqj_A* 1zqk_A* 1zql_A* ... Back     alignment and structure
>2bcq_A DNA polymerase lambda; misalignment, extrahelical, mutagenesis, mutation, deletion, streisinger, slippage, transferase, lyase/DNA complex; HET: DNA; 1.65A {Homo sapiens} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1xsl_A* 2bcr_A* 2bcs_A* 2bcu_A* 2bcv_A* 2gws_A* 3c5g_A* 3c5f_A* 2pfn_A* 1xsp_A* 1xsn_A* 2pfo_A* 2pfp_A* 2pfq_A* 3hw8_A* 3hwt_A* 1rzt_A* 3hx0_A* 3mdc_A* 3mda_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
>3fhg_A Mjogg, N-glycosylase/DNA lyase, DNA-; helix-hairpin-helix, 8-oxoguanine, 8-OXOG, ssogg, DNA damage, DNA repair, glycosidase, hydrolase; 1.90A {Sulfolobus solfataricus} Back     alignment and structure
>1m3q_A 8-oxoguanine DNA glycosylase; DNA repair, END product, HOGG, 8-aminoguanine, RE-ligation, hydrolase/DNA complex; HET: DRZ ANG; 1.90A {Homo sapiens} SCOP: a.96.1.3 d.129.1.2 PDB: 1m3h_A* 1n39_A* 1lwy_A* 1hu0_A* 1lwv_A* 1lww_A* 1fn7_A* 1n3a_A* 1n3c_A* 1ebm_A* 1ko9_A 2noe_A* 2noh_A* 2nol_A* 3ktu_A* 1yqk_A 2noz_A* 2nof_A* 1yqr_A* 1yql_A* ... Back     alignment and structure
>2h56_A DNA-3-methyladenine glycosidase; 10174367, EC 3.2.2.-, structural genomics, PSI-2, protein structure initiative; 2.55A {Bacillus halodurans} Back     alignment and structure
>1mpg_A ALKA, 3-methyladenine DNA glycosylase II; DNA repair, base excision, methylation, hydrolase; 1.80A {Escherichia coli} SCOP: a.96.1.3 d.129.1.2 PDB: 1diz_A 1pvs_A* 3cvs_A* 3cvt_A* 3cw7_A* 3cwa_A* 3cws_A* 3cwt_A* 3cwu_A* 3d4v_A* Back     alignment and structure
>3bz1_U Photosystem II 12 kDa extrinsic protein; electron transport photosystem, membrane complex, transmembrane alpha-helix; HET: CLA PHO HEM PL9 BCR DGD LHG SQD LMG LMT; 2.90A {Thermosynechococcus elongatus} PDB: 2axt_U* 3bz2_U* 3kzi_U* 3a0b_U* 3a0h_U* Back     alignment and structure
>1cuk_A RUVA protein; DNA repair, SOS response, DNA-binding, DNA recombination, helicase; 1.90A {Escherichia coli} SCOP: a.5.1.1 a.60.2.1 b.40.4.2 PDB: 1hjp_A 1bdx_A* 1c7y_A 1d8l_A Back     alignment and structure
>1ixr_A Holliday junction DNA helicase RUVA; heterooligomeric complex, octameric RUVA, AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ANP; 3.30A {Thermus thermophilus} SCOP: a.60.2.1 b.40.4.2 Back     alignment and structure
>2ztd_A 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
>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
>2ofk_A 3-methyladenine DNA glycosylase I, constitutive; DNA repair, base excision, helix-hairpin-helix, hydrolase; HET: PGE; 1.50A {Salmonella typhi} PDB: 2ofi_A* 1lmz_A 1nku_A 1p7m_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
>2csb_A Topoisomerase V, TOP61; topoisomerase IB, helix-turn-helix, helix- hairpin-helix, HHH motif, three helix bundle; 2.30A {Methanopyrus kandleri} SCOP: a.60.2.4 a.60.2.4 a.60.2.4 a.60.2.4 a.267.1.1 PDB: 2csd_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
>1vdd_A Recombination protein RECR; helix-hairpin-helix, zinc finger, toprim, walker B ATP binding motif; 2.50A {Deinococcus radiodurans} SCOP: e.49.1.1 PDB: 2v1c_A Back     alignment and structure
>2ihm_A POL MU, DNA polymerase MU; helix-turn-helix, transferase/DNA complex; HET: DNA D3T; 2.40A {Mus musculus} Back     alignment and structure
>2fmp_A DNA polymerase beta; nucleotidyl transferase, transferase/DNA complex; HET: DNA DOC DCT; 1.65A {Homo sapiens} SCOP: a.60.6.1 a.60.12.1 d.218.1.2 PDB: 1bpx_A* 1bpz_A* 1mq2_A* 1mq3_A* 1bpy_A* 1tva_A* 1zjm_A* 1zjn_A* 1zqa_A* 1zqb_A* 1zqc_A* 1zqd_A* 1zqe_A* 1zqf_A* 1zqg_A* 1zqh_A* 1zqi_A* 1zqj_A* 1zqk_A* 1zql_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 227 endonuclease III [Candidatus Liberibacter asiaticus str
d2abka_211 a.96.1.1 (A:) Endonuclease III {Escherichia coli [TaxId 1e-31
d1orna_214 a.96.1.1 (A:) Endonuclease III {Escherichia coli [TaxId 1e-31
d1pu6a_217 a.96.1.5 (A:) 3-Methyladenine DNA glycosylase III (MagI 5e-25
d1rrqa1221 a.96.1.2 (A:9-229) Catalytic domain of MutY {Bacillus s 4e-24
d1keaa_217 a.96.1.2 (A:) Thymine-DNA glycosylase {Archaeon Methano 1e-23
d1kg2a_224 a.96.1.2 (A:) Catalytic domain of MutY {Escherichia col 3e-22
d2noha1190 a.96.1.3 (A:136-325) 8-oxoguanine glycosylase {Human (H 2e-15
d1ngna_144 a.96.1.2 (A:) Mismatch-specific thymine glycosylase dom 5e-15
>d2abka_ a.96.1.1 (A:) Endonuclease III {Escherichia coli [TaxId: 562]} Length = 211 Back     information, alignment and structure

class: All alpha proteins
fold: DNA-glycosylase
superfamily: DNA-glycosylase
family: Endonuclease III
domain: Endonuclease III
species: Escherichia coli [TaxId: 562]
 Score =  130 bits (327), Expect = 1e-31
 Identities = 99/203 (48%), Positives = 139/203 (68%)

Query: 21  TPKELEEIFYLFSLKWPSPKGELYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTP 80
              +  EI        P P  EL + + F L++AVLLSAQ+TDV+VNKAT  L+ +A+TP
Sbjct: 2   NKAKRLEILTRLRENNPHPTTELNFSSPFELLIAVLLSAQATDVSVNKATAKLYPVANTP 61

Query: 81  QKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKG 140
             ML +G + ++ YI+TIG+Y  K+ENII    IL+ + + ++P+    L  LPG+GRK 
Sbjct: 62  AAMLELGVEGVKTYIKTIGLYNSKAENIIKTCRILLEQHNGEVPEDRAALEALPGVGRKT 121

Query: 141 ANVILSMAFGIPTIGVDTHIFRISNRIGLAPGKTPNKVEQSLLRIIPPKHQYNAHYWLVL 200
           ANV+L+ AFG PTI VDTHIFR+ NR   APGK   +VE+ LL+++P + + + H+WL+L
Sbjct: 122 ANVVLNTAFGWPTIAVDTHIFRVCNRTQFAPGKNVEQVEEKLLKVVPAEFKVDCHHWLIL 181

Query: 201 HGRYVCKARKPQCQSCIISNLCK 223
           HGRY C ARKP+C SCII +LC+
Sbjct: 182 HGRYTCIARKPRCGSCIIEDLCE 204


>d1orna_ a.96.1.1 (A:) Endonuclease III {Escherichia coli [TaxId: 562]} Length = 214 Back     information, alignment and structure
>d1pu6a_ a.96.1.5 (A:) 3-Methyladenine DNA glycosylase III (MagIII) {Helicobacter pylori [TaxId: 210]} Length = 217 Back     information, alignment and structure
>d1rrqa1 a.96.1.2 (A:9-229) Catalytic domain of MutY {Bacillus stearothermophilus [TaxId: 1422]} Length = 221 Back     information, alignment and structure
>d1keaa_ a.96.1.2 (A:) Thymine-DNA glycosylase {Archaeon Methanobacterium thermoformicicum [TaxId: 145262]} Length = 217 Back     information, alignment and structure
>d1kg2a_ a.96.1.2 (A:) Catalytic domain of MutY {Escherichia coli [TaxId: 562]} Length = 224 Back     information, alignment and structure
>d2noha1 a.96.1.3 (A:136-325) 8-oxoguanine glycosylase {Human (Homo sapiens) [TaxId: 9606]} Length = 190 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]} Length = 144 Back     information, alignment and structure

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

IdentityAlignment graphLength Definition Probability
Target227 endonuclease III [Candidatus Liberibacter asiaticus str
d2abka_211 Endonuclease III {Escherichia coli [TaxId: 562]} 100.0
d1orna_214 Endonuclease III {Escherichia coli [TaxId: 562]} 100.0
d1keaa_217 Thymine-DNA glycosylase {Archaeon Methanobacterium ther 100.0
d1rrqa1221 Catalytic domain of MutY {Bacillus stearothermophilus [ 100.0
d1kg2a_224 Catalytic domain of MutY {Escherichia coli [TaxId: 562] 100.0
d1pu6a_217 3-Methyladenine DNA glycosylase III (MagIII) {Helicobac 100.0
d1ngna_144 Mismatch-specific thymine glycosylase domain of the met 99.96
d2noha1190 8-oxoguanine glycosylase {Human (Homo sapiens) [TaxId: 99.91
d1mpga1183 3-Methyladenine DNA glycosylase II (gene alkA or aidA) 99.81
d2fmpa182 DNA polymerase beta, N-terminal (8 kD)-domain {Human (H 93.94
d2bcqa176 DNA polymerase lambda {Human (Homo sapiens) [TaxId: 960 93.52
d1jmsa195 Terminal deoxynucleotidyl transferase {Mouse (Mus muscu 92.34
d1cuka278 DNA helicase RuvA subunit, middle domain {Escherichia c 92.49
d1dgsa1181 NAD+-dependent DNA ligase, domain 3 {Thermus filiformis 91.83
d1ixra173 DNA helicase RuvA subunit, middle domain {Thermus therm 91.4
d1bvsa271 DNA helicase RuvA subunit, middle domain {Mycobacterium 90.56
d2i1qa160 DNA repair protein Rad51, N-terminal domain {Archaeon M 90.74
d1nkua_187 3-Methyladenine DNA glycosylase I (Tag) {Escherichia co 90.42
>d2abka_ a.96.1.1 (A:) Endonuclease III {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
class: All alpha proteins
fold: DNA-glycosylase
superfamily: DNA-glycosylase
family: Endonuclease III
domain: Endonuclease III
species: Escherichia coli [TaxId: 562]
Probab=100.00  E-value=0  Score=435.60  Aligned_cols=207  Identities=48%  Similarity=0.867  Sum_probs=202.5

Q ss_pred             CHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHH
Q ss_conf             98999999999999767999877778689999999996333203567998998731762000101268999999997300
Q gi|254780383|r   21 TPKELEEIFYLFSLKWPSPKGELYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIRTIGI  100 (227)
Q Consensus        21 ~~~~~~~I~~~L~~~yp~~~~~l~~~~p~~~LVa~iLs~qT~d~~v~~~~~~L~~~ypt~e~l~~a~~~el~~~ir~~G~  100 (227)
                      .+++..+|+.+|.+.||+++.||+++|||++||++||||||+|++|++++++|+++||||+++++++.++|+++|+|+||
T Consensus         2 ~~~~~~~i~~~l~~~~~~~~~~l~~~~p~~vli~~iLsqqT~~~~v~~~~~~l~~~~~t~~~la~a~~~~l~~~i~~~G~   81 (211)
T d2abka_           2 NKAKRLEILTRLRENNPHPTTELNFSSPFELLIAVLLSAQATDVSVNKATAKLYPVANTPAAMLELGVEGVKTYIKTIGL   81 (211)
T ss_dssp             CHHHHHHHHHHHHHHCSSCCCSSCCSSHHHHHHHHHHTTTSCHHHHHHHHHHHTTTCCSHHHHHHHHHHHHHHHHTTSTT
T ss_pred             CHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             88999999999999789999977789879999999995626399999999988874147278876557676777777544


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCHHHHHH
Q ss_conf             37999999752355444200100001456777643235888899998754210001210467877656540788899999
Q gi|254780383|r  101 YRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMAFGIPTIGVDTHIFRISNRIGLAPGKTPNKVEQ  180 (227)
Q Consensus       101 ~~~KAk~I~~~a~~i~~~~~g~vP~~~~~L~~LpGVG~ktA~~il~~~~~~p~~~VDthv~Rv~~Rlgl~~~~~~~~~~~  180 (227)
                      |++||++|+++++.|+++|||.+|.++++|++|||||+|||++||+|+||+|+|+||+||+||++|+|+.+++++.+++.
T Consensus        82 y~~Ka~~l~~~a~~i~~~~~g~~p~~~~~L~~LpGVG~~TA~~Il~~a~~~p~~~vD~nv~Rv~~R~g~~~~~~~~~~~~  161 (211)
T d2abka_          82 YNSKAENIIKTCRILLEQHNGEVPEDRAALEALPGVGRKTANVVLNTAFGWPTIAVDTHIFRVCNRTQFAPGKNVEQVEE  161 (211)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTTSCCSCHHHHHHSTTCCHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCSSCCSSHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCCCCHHHHHHH
T ss_conf             11578899999888998714860477999999986051789999999856803225679999999706675420467888


Q ss_pred             HHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHCHHHCC
Q ss_conf             99621884226789999999966516489989472840331768519
Q gi|254780383|r  181 SLLRIIPPKHQYNAHYWLVLHGRYVCKARKPQCQSCIISNLCKRIKQ  227 (227)
Q Consensus       181 ~l~~~~p~~~~~~~~~~li~~G~~iC~~~~P~C~~C~l~~~C~~~k~  227 (227)
                      .+.+++|.+.|.++|++||+||+.||++++|+|+.|||++.|+||+|
T Consensus       162 ~~~~~~p~~~~~~~~~~l~~~G~~vC~~~~P~C~~Cpl~~~C~~~~k  208 (211)
T d2abka_         162 KLLKVVPAEFKVDCHHWLILHGRYTCIARKPRCGSCIIEDLCEYKEK  208 (211)
T ss_dssp             HHHHHSCGGGTTTHHHHHHHHHHHTSCSSSCCGGGCTTGGGCCCTTC
T ss_pred             HHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             88604860348999999999855552599989999979055898676



>d1orna_ a.96.1.1 (A:) Endonuclease III {Escherichia coli [TaxId: 562]} 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
>d1pu6a_ a.96.1.5 (A:) 3-Methyladenine DNA glycosylase III (MagIII) {Helicobacter pylori [TaxId: 210]} 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
>d2noha1 a.96.1.3 (A:136-325) 8-oxoguanine glycosylase {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1mpga1 a.96.1.3 (A:100-282) 3-Methyladenine DNA glycosylase II (gene alkA or aidA) {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2fmpa1 a.60.6.1 (A:10-91) DNA polymerase beta, N-terminal (8 kD)-domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d2bcqa1 a.60.6.1 (A:252-327) DNA polymerase lambda {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1jmsa1 a.60.6.1 (A:148-242) Terminal deoxynucleotidyl transferase {Mouse (Mus musculus) [TaxId: 10090]} 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
>d1dgsa1 a.60.2.2 (A:401-581) NAD+-dependent DNA ligase, domain 3 {Thermus filiformis [TaxId: 276]} Back     information, alignment and structure
>d1ixra1 a.60.2.1 (A:63-135) DNA helicase RuvA subunit, middle domain {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1bvsa2 a.60.2.1 (A:64-134) DNA helicase RuvA subunit, middle domain {Mycobacterium leprae [TaxId: 1769]} 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
>d1nkua_ a.96.1.4 (A:) 3-Methyladenine DNA glycosylase I (Tag) {Escherichia coli [TaxId: 562]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 227 endonuclease III [Candidatus Liberibacter asiaticu
1kg2_A_1-23_110-225139 (A:1-23,A:110-225) A/G-specific adenine glycosylas 2e-26
2h56_A_1-49_127-233156 (A:1-49,A:127-233) DNA-3-methyladenine glycosidase 5e-23
2abk_A_23-133111 (A:23-133) Endonuclease III; DNA-repair, DNA glyco 2e-25
1orn_A_28-137110 (A:28-137) Endonuclease III; DNA repair, DNA glyco 4e-25
1kea_A_29-139111 (A:29-139) Possible G-T mismatches repair enzyme; 4e-23
3fsp_A_34-143110 (A:34-143) A/G-specific adenine glycosylase; prote 8e-22
1ngn_A_1-129129 (A:1-129) Methyl-CPG binding protein MBD4; mismact 9e-21
1pu6_A_23-145123 (A:23-145) 3-methyladenine DNA glycosylase; helix- 2e-20
1kg2_A_24-10986 (A:24-109) A/G-specific adenine glycosylase; DNA r 1e-18
1m3q_A_123-255133 (A:123-255) 8-oxoguanine DNA glycosylase; DNA repa 4e-18
1mpg_A_105-231127 (A:105-231) ALKA, 3-methyladenine DNA glycosylase 5e-18
3fhf_A_38-150113 (A:38-150) Mjogg, N-glycosylase/DNA lyase, DNA-; h 1e-16
2h56_A_50-12677 (A:50-126) DNA-3-methyladenine glycosidase; 101743 1e-14
2abk_A_1-22_134-211100 (A:1-22,A:134-211) Endonuclease III; DNA-repair, D 7e-22
1kea_A_1-28_140-221110 (A:1-28,A:140-221) Possible G-T mismatches repair 3e-21
1orn_A_1-27_138-226116 (A:1-27,A:138-226) Endonuclease III; DNA repair, D 3e-21
3fsp_A_1-33_144-218108 (A:1-33,A:144-218) A/G-specific adenine glycosylas 5e-21
>1kg2_A (A:1-23,A:110-225) A/G-specific adenine glycosylase; DNA repair, hydrolase; 1.20A {Escherichia coli}Length = 139 Back     alignment and structure
 Score =  113 bits (284), Expect = 2e-26
 Identities = 29/118 (24%), Positives = 51/118 (43%), Gaps = 5/118 (4%)

Query: 111 LSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMAFGIPTIGVDTHIFRISNRIGLA 170
            S  +++ +D    +TL  +  LPG+GR  A  ILS++ G     +D ++ R+  R    
Sbjct: 6   FSAQVLDWYDKYGRKTLPEVAALPGVGRSTAGAILSLSLGKHFPILDGNVKRVLARCYAV 65

Query: 171 PGKT-----PNKVEQSLLRIIPPKHQYNAHYWLVLHGRYVCKARKPQCQSCIISNLCK 223
            G        NK+     ++ P       +  ++  G  +C   KP+C  C + N C 
Sbjct: 66  SGWPGKKEVENKLWSLSEQVTPAVGVERFNQAMMDLGAMICTRSKPKCSLCPLQNGCI 123


>2h56_A (A:1-49,A:127-233) DNA-3-methyladenine glycosidase; 10174367, EC 3.2.2.-, structural genomics, PSI-2, protein structure initiative; 2.55A {Bacillus halodurans}Length = 156 Back     alignment and structure
>2abk_A (A:23-133) Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {Escherichia coli}Length = 111 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}Length = 110 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}Length = 111 Back     alignment and structure
>3fsp_A (A:34-143) 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*Length = 110 Back     alignment and structure
>1ngn_A (A:1-129) Methyl-CPG binding protein MBD4; mismacth repair in methylated DNA, DNA binding protein; 2.10A {Mus musculus}Length = 129 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}Length = 123 Back     alignment and structure
>1kg2_A (A:24-109) A/G-specific adenine glycosylase; DNA repair, hydrolase; 1.20A {Escherichia coli}Length = 86 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}Length = 133 Back     alignment and structure
>1mpg_A (A:105-231) ALKA, 3-methyladenine DNA glycosylase II; DNA repair, base excision, methylation, hydrolase; 1.80A {Escherichia coli}Length = 127 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}Length = 113 Back     alignment and structure
>2h56_A (A:50-126) DNA-3-methyladenine glycosidase; 10174367, EC 3.2.2.-, structural genomics, PSI-2, protein structure initiative; 2.55A {Bacillus halodurans}Length = 77 Back     alignment and structure
>2abk_A (A:1-22,A:134-211) Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {Escherichia coli}Length = 100 Back     alignment and structure
>1kea_A (A:1-28,A:140-221) Possible G-T mismatches repair enzyme; DNA repair, DNA glycosylase, DNA mismatch, methylation, base twisting, hydrolase; 2.00A {Methanothermobacterthermautotrophicus}Length = 110 Back     alignment and structure
>1orn_A (A:1-27,A:138-226) Endonuclease III; DNA repair, DNA glycosylase, [4Fe-4S] cluster, iron-sulfur cluster, hydrolase/DNA complex; HET: PED; 1.70A {Geobacillus stearothermophilus}Length = 116 Back     alignment and structure
>3fsp_A (A:1-33,A:144-218) 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*Length = 108 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target227 endonuclease III [Candidatus Liberibacter asiaticus str
1kg2_A_1-23_110-225139 A/G-specific adenine glycosylase; DNA repair, hydr 99.95
2h56_A_1-49_127-233156 DNA-3-methyladenine glycosidase; 10174367, EC 3.2. 99.78
1kea_A_1-28_140-221110 Possible G-T mismatches repair enzyme; DNA repair, 99.76
1ixr_A_191 Holliday junction DNA helicase RUVA; heterooligome 91.99
2abk_A_23-133111 Endonuclease III; DNA-repair, DNA glycosylase; 1.8 99.92
1orn_A_28-137110 Endonuclease III; DNA repair, DNA glycosylase, [4F 99.92
1kea_A_29-139111 Possible G-T mismatches repair enzyme; DNA repair, 99.91
3fsp_A_34-143110 A/G-specific adenine glycosylase; protein-DNA comp 99.89
1pu6_A_23-145123 3-methyladenine DNA glycosylase; helix-hairpin-hel 99.89
1ngn_A_1-129129 Methyl-CPG binding protein MBD4; mismacth repair i 99.89
1kg2_A_24-10986 A/G-specific adenine glycosylase; DNA repair, hydr 99.86
1m3q_A_123-255133 8-oxoguanine DNA glycosylase; DNA repair, END prod 99.85
1mpg_A_105-231127 ALKA, 3-methyladenine DNA glycosylase II; DNA repa 99.84
3fhf_A_38-150113 Mjogg, N-glycosylase/DNA lyase, DNA-; helix-hairpi 99.76
1orn_A_1-27_138-226116 Endonuclease III; DNA repair, DNA glycosylase, [4F 99.81
2abk_A_1-22_134-211100 Endonuclease III; DNA-repair, DNA glycosylase; 1.8 99.8
3fsp_A_1-33_144-218108 A/G-specific adenine glycosylase; protein-DNA comp 99.69
1pu6_A_1-22_146-21895 3-methyladenine DNA glycosylase; helix-hairpin-hel 98.3
3i0w_A_81-110_237-29084 8-oxoguanine-DNA-glycosylase; OGG, cacogg, DNA, 8- 96.15
2jhn_A_235-29561 ALKA, 3-methyladenine DNA-glycosylase; DNA repair, 90.35
2h56_A_50-12677 DNA-3-methyladenine glycosidase; 10174367, EC 3.2. 99.59
3fhg_A_29-10173 Mjogg, N-glycosylase/DNA lyase, DNA-; helix-hairpi 96.73
3i0w_A_111-127_196-23658 8-oxoguanine-DNA-glycosylase; OGG, cacogg, DNA, 8- 97.62
2jhn_A_112-130_199-23455 ALKA, 3-methyladenine DNA-glycosylase; DNA repair, 96.0
2fmp_A_1-119119 DNA polymerase beta; nucleotidyl transferase, tran 92.74
2ztd_A_80-15475 Holliday junction ATP-dependent DNA helicase RUVA; 92.31
2w9m_A_1-118118 Polymerase X; SAXS, DNA repair, DNA polymerase, DN 92.29
1vdd_A_1-6666 Recombination protein RECR; helix-hairpin-helix, z 91.92
1jms_A_1-154154 Terminal deoxynucleotidyltransferase; polymerase; 91.85
2ihm_A_1-129129 POL MU, DNA polymerase MU; helix-turn-helix, trans 91.4
1m3q_A_96-122_256-31789 8-oxoguanine DNA glycosylase; DNA repair, END prod 91.12
2jhn_A_1-66_131-198134 ALKA, 3-methyladenine DNA-glycosylase; DNA repair, 96.41
3i0w_A_128-19568 8-oxoguanine-DNA-glycosylase; OGG, cacogg, DNA, 8- 94.55
1ixr_A_191 Holliday junction DNA helicase RUVA; heterooligome 93.15
2bcq_A_1-128128 DNA polymerase lambda; misalignment, extrahelical, 93.09
1cuk_A_66-14479 RUVA protein; DNA repair, SOS response, DNA-bindin 92.83
2kp7_A_87 Crossover junction endonuclease MUS81; helix-hairp 91.32
3c1y_A_304-37774 DNA integrity scanning protein DISA; DNA damage, D 91.19
>1kg2_A (A:1-23,A:110-225) A/G-specific adenine glycosylase; DNA repair, hydrolase; 1.20A {Escherichia coli} Back     alignment and structure
Probab=99.95  E-value=5.3e-28  Score=208.81  Aligned_cols=108  Identities=25%  Similarity=0.403  Sum_probs=96.1

Q ss_pred             HHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCH-----HHHHHHHHHCCCHHHH
Q ss_conf             42001000014567776432358888999987542100012104678776565407888-----9999999621884226
Q gi|254780383|r  117 NEFDNKIPQTLEGLTRLPGIGRKGANVILSMAFGIPTIGVDTHIFRISNRIGLAPGKTP-----NKVEQSLLRIIPPKHQ  191 (227)
Q Consensus       117 ~~~~g~vP~~~~~L~~LpGVG~ktA~~il~~~~~~p~~~VDthv~Rv~~Rlgl~~~~~~-----~~~~~~l~~~~p~~~~  191 (227)
                      ++||.   .+.-+|++|||||+|||++||+|+||+++|+|||||+||++|+|+++.+..     ...+..+...++...+
T Consensus        15 ~~~~~---~~~~eL~~LpGIG~ktAd~Illfa~~~~~~pVDthv~RVl~Rlg~~~~~~~~~~~~~~~~~~~~~~~~~~~~   91 (139)
T 1kg2_A           15 DKYGR---KTLPEVAALPGVGRSTAGAILSLSLGKHFPILDGNVKRVLARCYAVSGWPGKKEVENKLWSLSEQVTPAVGV   91 (139)
T ss_dssp             HHHCC---CCSGHHHTSTTCCHHHHHHHHHHHHCCSCCCCCHHHHHHHHHHHTCCSCTTSHHHHHHHHHHHHHHCCSTTH
T ss_pred             HHCCC---CCCCHHHCCCCCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCCCC
T ss_conf             98199---879998628987278999999984498607679986775333025678996268999999987523861100


Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCCCCHHHCHHHCC
Q ss_conf             789999999966516489989472840331768519
Q gi|254780383|r  192 YNAHYWLVLHGRYVCKARKPQCQSCIISNLCKRIKQ  227 (227)
Q Consensus       192 ~~~~~~li~~G~~iC~~~~P~C~~C~l~~~C~~~k~  227 (227)
                      .++|++||+||+.+|++++|+|+.|||++.|+++++
T Consensus        92 ~~~h~~L~~~Gr~vC~~r~P~C~~CpL~~~C~~~~~  127 (139)
T 1kg2_A           92 ERFNQAMMDLGAMICTRSKPKCSLCPLQNGCIAAAN  127 (139)
T ss_dssp             HHHHHHHHHHHHHTSCSSSCCGGGCTTTTTCHHHHH
T ss_pred             CHHHHHHHHHHHHHCCCCCCCCCCCCCHHHCHHHHC
T ss_conf             177799999978881499999998978333988776



>2h56_A (A:1-49,A:127-233) DNA-3-methyladenine glycosidase; 10174367, EC 3.2.2.-, structural genomics, PSI-2, protein structure initiative; 2.55A {Bacillus halodurans} Back     alignment and structure
>1kea_A (A:1-28,A:140-221) Possible G-T mismatches repair enzyme; DNA repair, DNA glycosylase, DNA mismatch, methylation, base twisting, hydrolase; 2.00A {Methanothermobacterthermautotrophicus} 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
>2abk_A (A:23-133) Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {Escherichia coli} 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
>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
>3fsp_A (A:34-143) 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
>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
>1ngn_A (A:1-129) Methyl-CPG binding protein MBD4; mismacth repair in methylated DNA, DNA binding protein; 2.10A {Mus musculus} 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
>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
>1mpg_A (A:105-231) ALKA, 3-methyladenine DNA glycosylase II; DNA repair, base excision, methylation, hydrolase; 1.80A {Escherichia coli} 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
>1orn_A (A:1-27,A:138-226) 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
>2abk_A (A:1-22,A:134-211) Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {Escherichia coli} Back     alignment and structure
>3fsp_A (A:1-33,A:144-218) 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
>1pu6_A (A:1-22,A:146-218) 3-methyladenine DNA glycosylase; helix-hairpin-helix, base excision repair, hydrolase; HET: KCX; 1.64A {Helicobacter pylori} Back     alignment and structure
>3i0w_A (A:81-110,A:237-290) 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
>2jhn_A (A:235-295) ALKA, 3-methyladenine DNA-glycosylase; DNA repair, N1-methyladenine, N3-methylcytosine, hyperthermophiles, hydrolase; HET: MBO MES; 1.8A {Archaeoglobus fulgidus} PDB: 2jhj_A Back     alignment and structure
>2h56_A (A:50-126) DNA-3-methyladenine glycosidase; 10174367, EC 3.2.2.-, structural genomics, PSI-2, protein structure initiative; 2.55A {Bacillus halodurans} Back     alignment and structure
>3fhg_A (A:29-101) Mjogg, N-glycosylase/DNA lyase, DNA-; helix-hairpin-helix, 8-oxoguanine, 8-OXOG, ssogg, DNA damage, DNA repair, glycosidase, hydrolase; 1.90A {Sulfolobus solfataricus} Back     alignment and structure
>3i0w_A (A:111-127,A:196-236) 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
>2jhn_A (A:112-130,A:199-234) ALKA, 3-methyladenine DNA-glycosylase; DNA repair, N1-methyladenine, N3-methylcytosine, hyperthermophiles, hydrolase; HET: MBO MES; 1.8A {Archaeoglobus fulgidus} PDB: 2jhj_A Back     alignment and structure
>2fmp_A (A:1-119) DNA polymerase beta; nucleotidyl transferase, transferase/DNA complex; HET: DNA DOC DCT; 1.65A {Homo sapiens} Back     alignment and structure