254780762

254780762

recombination protein RecR

GeneID in NCBI database:8209768Locus tag:CLIBASIA_03255
Protein GI in NCBI database:254780762Protein Accession:YP_003065175.1
Gene range:+(501676, 502281)Protein Length:201aa
Gene description:recombination protein RecR
COG prediction:[L] Recombinational DNA repair protein (RecF pathway)
KEGG prediction:recR; recombination protein RecR; K06187 recombination protein RecR
SEED prediction:Recombination protein RecR
Pathway involved in KEGG:Homologous recombination [PATH:las03440]
Subsystem involved in SEED:DNA-replication;
DNA repair, bacterial RecFOR pathway;
DNA processing cluster
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
TOPPREDnone 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-
MQKKITGKEIENLIKILARIPGFGPRSARRATLHLVKKKEQLLGPLAEAMANIYNKVCLCSICGNVDTTDPCAICIDQQRDASVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPEDIGIQSLIERIEVKKIRELIFAISATIEGQTTAHYIMDKLKGIDVKITRLAYGIPMGSELDYLDDGTIFEAIRSRTVL
ccccccHHHHHHHHHHHHHcccccHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccEEEEccHHHHHHHHHHccccccEEEEcccccccccccHHHccHHHHHHHHHccccEEEEEEccccccHHHHHHHHHHHHHHcccEEEEEccccccccHHHHHHHHHHHHHHHccccc
cccccccHHHHHHHHHHHcccccccHHHHHHHHHHHcccccHHHHHHHHHHHHHHHccccHHcccccccccccccccccccccEEEEEEcHHHHHHHHHccccccEEEEEcccEcccccccHHHccHHHHHHHHHcccccEEEEEccccccHHHHHHHHHHHHHHcccEEEEEccccccccccccccHHHHHHHHHccccc
MQKKITGKEIENLIKILAripgfgprsARRATLHLVKKKEQLLGPLAEAMANIYNKVCLCsicgnvdttdpcaicidqqrdaSVIIVVEDVADLWALERSKAVNALYHVLggslspldrigpedigIQSLIERIEVKKIRELIFAISATIEGQTTAHYIMDKLKGIDVKITRLAygipmgseldylddgtiFEAIRSRTVL
MQKKITGKEIENLIKIlaripgfgprSARRATLHLVKKKEQLLGPLAEAMANIYNKVCLCSICGNVDTTDPCAICIDQQRDASVIIVVEDVADLWALERSKAVNALYHVLGgslspldrigpeDIGIQSLIERIEVKKIRELIFAISATIEGQTTAHYIMDKLKGIDVKITRLAYGIPMgseldylddgtiFEAIRSRTVL
MQKKITGKEIENLIKILARIPGFGPRSARRATLHLVKKKEQLLGPLAEAMANIYNKVCLCSICGNVDTTDPCAICIDQQRDASVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPEDIGIQSLIERIEVKKIRELIFAISATIEGQTTAHYIMDKLKGIDVKITRLAYGIPMGSELDYLDDGTIFEAIRSRTVL
*****TG**IENLIKILARIPGFGPRSARRATLHLVKKKEQLLGPLAEAMANIYNKVCLCSICGNVDTTDPCAICIDQQRDASVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPEDIGIQSLIERIEVKKIRELIFAISATIEGQTTAHYIMDKLKGIDVKITRLAYGIPMGSELDYLDDGTIFEAIRSRT**
MQKKITGKEIENLIKILARIPGFGPRSARRATLHLVKKKEQLLGPLAEAMANIYNKVCLCSICGNVDTTDPCAICIDQQRDASVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPEDIGIQSLIERIEVKKIRELIFAISATIEGQTTAHYIMDKLKGIDVKITRLAYGIPMGSELDYLDDGTIFEAIRSRTVL
***KITGKEIENLIKILARIPGFGPRSARRATLHLVKKKEQLLGPLAEAMANIYNKVCLCSICGNVDTTDPCAICIDQQRDASVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPEDIGIQSLIERIEVKKIRELIFAISATIEGQTTAHYIMDKLKGIDVKITRLAYGIPMGSELDYLDDGTIFEAIRS****
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MQKKITGKEIENLIKILARIPGFGPRSARRATLHLVKKKEQLLGPLAEAMANIYNKVCLCSICGNVDTTDPCAICIDQQRDASVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPEDIGIQSLIERIEVKKIRELIFAISATIEGQTTAHYIMDKLKGIDVKITRLAYGIPMGSELDYLDDGTIFEAIRSRTVL
MQKKITGKEIENLIKILARIPGFGPRSARRATLHLVKKKEQLLGPLAEAMANIYNKVCLCSICGNVDTTDPCAICIDQQRDASVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPEDIGIQSLIERIEVKKIRELIFAISATIEGQTTAHYIMDKLKGIDVKITRLAYGIPMGSELDYLDDGTIFEAIRSRTVL
MQKKITGKEIENLIKILARIPGFGPRSARRATLHLVKKKEQLLGPLAEAMANIYNKVCLCSICGNVDTTDPCAICIDQQRDASVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPEDIGIQSLIERIEVKKIRELIFAISATIEGQTTAHYIMDKLKGIDVKITRLAYGIPMGSELDYLDDGTIFEAIRSRTVL

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
Target201 recombination protein RecR [Candidatus Liberibacter asi
315121977201 recombination protein RecR [Candidatus Liberibacter sol 1 5e-99
218514436201 recombination protein RecR [Rhizobium etli 8C-3] Length 1 2e-79
15963986201 recombination protein RecR [Sinorhizobium meliloti 1021 1 2e-79
190889792201 DNA recombination protein [Rhizobium etli CIAT 652] Len 1 3e-79
86355783201 recombination protein RecR [Rhizobium etli CFN 42] Leng 1 3e-79
218679359201 recombination protein RecR [Rhizobium etli CIAT 894] Le 1 8e-79
227824063201 recombination protein RecR [Sinorhizobium fredii NGR234 1 8e-79
209551645201 recombination protein RecR [Rhizobium leguminosarum bv. 1 1e-78
116249898201 recombination protein RecR [Rhizobium leguminosarum bv. 1 1e-78
241207075201 recombination protein RecR [Rhizobium leguminosarum bv. 1 2e-78
>gi|315121977|ref|YP_004062466.1| recombination protein RecR [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 201 Back     alignment and organism information
 Score =  363 bits (933), Expect = 5e-99,   Method: Compositional matrix adjust.
 Identities = 174/201 (86%), Positives = 192/201 (95%)

Query: 1   MQKKITGKEIENLIKILARIPGFGPRSARRATLHLVKKKEQLLGPLAEAMANIYNKVCLC 60
           M+KKITG EIENLIK+LARIPGFGPRSARRATLHLVKKKEQLLGPLA+ MA+IY KVCLC
Sbjct: 1   MKKKITGIEIENLIKMLARIPGFGPRSARRATLHLVKKKEQLLGPLADTMADIYKKVCLC 60

Query: 61  SICGNVDTTDPCAICIDQQRDASVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRI 120
           SICGN+DT DPC ICID+QRD+SVI+V+EDVADLWALER+ AVNALYHVLGG+LSPLD I
Sbjct: 61  SICGNIDTIDPCIICIDEQRDSSVIVVIEDVADLWALERAGAVNALYHVLGGTLSPLDSI 120

Query: 121 GPEDIGIQSLIERIEVKKIRELIFAISATIEGQTTAHYIMDKLKGIDVKITRLAYGIPMG 180
           GPEDIGIQSLIERI+VKKIRELI AISATIEGQTTAHYIMDKLK +++KITRLAYGIP+G
Sbjct: 121 GPEDIGIQSLIERIKVKKIRELILAISATIEGQTTAHYIMDKLKNMNIKITRLAYGIPIG 180

Query: 181 SELDYLDDGTIFEAIRSRTVL 201
           SELDYLD+GT+FEAIRSRTVL
Sbjct: 181 SELDYLDEGTLFEAIRSRTVL 201


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|218514436|ref|ZP_03511276.1| recombination protein RecR [Rhizobium etli 8C-3] Length = 201 Back     alignment and organism information
>gi|15963986|ref|NP_384339.1| recombination protein RecR [Sinorhizobium meliloti 1021] Length = 201 Back     alignment and organism information
>gi|190889792|ref|YP_001976334.1| DNA recombination protein [Rhizobium etli CIAT 652] Length = 201 Back     alignment and organism information
>gi|86355783|ref|YP_467675.1| recombination protein RecR [Rhizobium etli CFN 42] Length = 201 Back     alignment and organism information
>gi|218679359|ref|ZP_03527256.1| recombination protein RecR [Rhizobium etli CIAT 894] Length = 201 Back     alignment and organism information
>gi|227824063|ref|YP_002828036.1| recombination protein RecR [Sinorhizobium fredii NGR234] Length = 201 Back     alignment and organism information
>gi|209551645|ref|YP_002283562.1| recombination protein RecR [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 201 Back     alignment and organism information
>gi|116249898|ref|YP_765736.1| recombination protein RecR [Rhizobium leguminosarum bv. viciae 3841] Length = 201 Back     alignment and organism information
>gi|241207075|ref|YP_002978171.1| recombination protein RecR [Rhizobium leguminosarum bv. trifolii WSM1325] Length = 201 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
Target201 recombination protein RecR [Candidatus Liberibacter asi
PRK00076196 PRK00076, recR, recombination protein RecR; Reviewed 4e-78
TIGR00615195 TIGR00615, recR, recombination protein RecR 3e-52
PRK13844200 PRK13844, PRK13844, recombination protein RecR; Provisi 4e-33
COG0353198 COG0353, RecR, Recombinational DNA repair protein (RecF 2e-65
cd01025112 cd01025, TOPRIM_recR, TOPRIM_recR: topoisomerase-primas 4e-39
pfam0175189 pfam01751, Toprim, Toprim domain 5e-05
cd0018883 cd00188, TOPRIM, Topoisomerase-primase domain 5e-04
smart0049376 smart00493, TOPRIM, topoisomerases, DnaG-type primases, 0.001
pfam0213241 pfam02132, RecR, RecR protein 1e-07
>gnl|CDD|178844 PRK00076, recR, recombination protein RecR; Reviewed Back     alignment and domain information
>gnl|CDD|161960 TIGR00615, recR, recombination protein RecR Back     alignment and domain information
>gnl|CDD|139904 PRK13844, PRK13844, recombination protein RecR; Provisional Back     alignment and domain information
>gnl|CDD|30702 COG0353, RecR, Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair] Back     alignment and domain information
>gnl|CDD|173775 cd01025, TOPRIM_recR, TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in Escherichia coli RecR Back     alignment and domain information
>gnl|CDD|145089 pfam01751, Toprim, Toprim domain Back     alignment and domain information
>gnl|CDD|173773 cd00188, TOPRIM, Topoisomerase-primase domain Back     alignment and domain information
>gnl|CDD|128769 smart00493, TOPRIM, topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins Back     alignment and domain information
>gnl|CDD|145340 pfam02132, RecR, RecR protein Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 201 recombination protein RecR [Candidatus Liberibacter asi
PRK13844200 recombination protein RecR; Provisional 100.0
TIGR00615205 recR recombination protein RecR; InterPro: IPR000093 Th 100.0
PRK00076197 recR recombination protein RecR; Reviewed 100.0
COG0353198 RecR Recombinational DNA repair protein (RecF pathway) 100.0
cd01025112 TOPRIM_recR TOPRIM_recR: topoisomerase-primase (TOPRIM) 100.0
pfam0175189 Toprim Toprim domain. This is a conserved region from D 99.66
LOAD_Toprim98 consensus 98.73
cd0018883 TOPRIM Topoisomerase-primase domain. This is a nucleoti 97.16
PRK05823 691 consensus 96.98
PRK09138 887 DNA topoisomerase I; Validated 96.97
PRK07561 878 DNA topoisomerase I; Validated 96.86
PRK05582 692 DNA topoisomerase I; Validated 96.75
PRK08938 692 DNA topoisomerase I; Validated 96.71
PRK08413 733 consensus 96.5
COG0550 570 TopA Topoisomerase IA [DNA replication, recombination, 96.46
PRK07941 933 DNA topoisomerase I; Validated 96.41
PRK08780 783 DNA topoisomerase III; Provisional 96.14
PRK06319 864 DNA topoisomerase I/SWI domain fusion protein; Validate 95.98
PRK09137 761 DNA topoisomerase I; Validated 95.97
PRK06599 776 DNA topoisomerase I; Validated 95.95
COG1658127 Small primase-like proteins (Toprim domain) [DNA replic 95.77
TIGR01051 688 topA_bact DNA topoisomerase I; InterPro: IPR005733 DNA 93.97
PRK04017132 hypothetical protein; Provisional 92.09
cd0336479 TOPRIM_DnaG_primases TOPRIM_DnaG_primases: The topoisom 90.89
smart0049376 TOPRIM topoisomerases, DnaG-type primases, OLD family n 99.3
cd0102781 TOPRIM_RNase_M5_like TOPRIM_ RNase M5_like: The topoiso 91.2
pfam0213241 RecR RecR protein. 98.66
PRK09401 1176 reverse gyrase; Reviewed 97.88
TIGR01054 1843 rgy reverse gyrase; InterPro: IPR005736 DNA topoisomera 95.66
cd03361170 TOPRIM_TopoIA_RevGyr TopoIA_RevGyr : The topoisomerase- 97.22
COG1110 1187 Reverse gyrase [DNA replication, recombination, and rep 96.84
PRK09001 869 DNA topoisomerase I; Validated 96.84
cd03363123 TOPRIM_TopoIA_TopoI TOPRIM_TopoIA_TopoI: The topoisomer 96.79
PRK08620 726 DNA topoisomerase III; Provisional 96.71
cd01028142 TOPRIM_TopoIA TOPRIM_TopoIA: topoisomerase-primase (TOP 96.6
PRK07141 622 DNA topoisomerase I; Validated 96.33
PRK05776 675 DNA topoisomerase III; Provisional 94.93
PRK07726 716 DNA topoisomerase III; Provisional 94.89
PRK07219 769 DNA topoisomerase I; Validated 94.73
TIGR01056 755 topB DNA topoisomerase III; InterPro: IPR005738 DNA top 94.24
PRK08174 670 DNA topoisomerase III; Validated 93.59
PRK08173 857 DNA topoisomerase III; Validated 93.27
PRK07220 740 DNA topoisomerase I; Validated 92.66
cd03362151 TOPRIM_TopoIA_TopoIII TOPRIM_TopoIA_TopoIII: The topois 91.63
PRK09031 649 DNA topoisomerase III; Provisional 90.08
PRK13901196 ruvA Holliday junction DNA helicase motor protein; Prov 96.74
COG0632201 RuvA Holliday junction resolvasome, DNA-binding subunit 96.63
PRK00116198 ruvA Holliday junction DNA helicase RuvA; Reviewed 96.56
TIGR00084217 ruvA Holliday junction DNA helicase RuvA; InterPro: IPR 96.12
cd00056158 ENDO3c endonuclease III; includes endonuclease III (DNA 93.32
pfam0063330 HHH Helix-hairpin-helix motif. The helix-hairpin-helix 93.13
TIGR01083192 nth endonuclease III; InterPro: IPR005759 The spectrum 93.01
COG0122285 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA g 91.84
PRK10702211 endonuclease III; Provisional 91.31
COG0177211 Nth Predicted EndoIII-related endonuclease [DNA replica 91.13
smart00478149 ENDO3c endonuclease III. includes endonuclease III (DNA 90.47
PRK0835161 DNA-directed RNA polymerase subunit E''; Validated 92.16
PRK0639364 rpoE DNA-directed RNA polymerase subunit E''; Validated 90.72
COG2816279 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, 92.16
>PRK13844 recombination protein RecR; Provisional 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
>PRK00076 recR recombination protein RecR; Reviewed Back     alignment and domain information
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair] Back     alignment and domain information
>cd01025 TOPRIM_recR TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in Escherichia coli RecR Back     alignment and domain information
>pfam01751 Toprim Toprim domain Back     alignment and domain information
>LOAD_Toprim consensus Back     alignment and domain information
>cd00188 TOPRIM Topoisomerase-primase domain Back     alignment and domain information
>PRK05823 consensus Back     alignment and domain information
>PRK09138 DNA topoisomerase I; Validated Back     alignment and domain information
>PRK07561 DNA topoisomerase I; Validated Back     alignment and domain information
>PRK05582 DNA topoisomerase I; Validated Back     alignment and domain information
>PRK08938 DNA topoisomerase I; Validated Back     alignment and domain information
>PRK08413 consensus Back     alignment and domain information
>COG0550 TopA Topoisomerase IA [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK07941 DNA topoisomerase I; Validated Back     alignment and domain information
>PRK08780 DNA topoisomerase III; Provisional Back     alignment and domain information
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated Back     alignment and domain information
>PRK09137 DNA topoisomerase I; Validated Back     alignment and domain information
>PRK06599 DNA topoisomerase I; Validated Back     alignment and domain information
>COG1658 Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair] Back     alignment and domain information
>TIGR01051 topA_bact DNA topoisomerase I; InterPro: IPR005733 DNA topoisomerases regulate the number of topological links between two DNA strands (i Back     alignment and domain information
>PRK04017 hypothetical protein; Provisional Back     alignment and domain information
>cd03364 TOPRIM_DnaG_primases TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG Back     alignment and domain information
>smart00493 TOPRIM topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins Back     alignment and domain information
>cd01027 TOPRIM_RNase_M5_like TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in Ribonuclease M5: (RNase M5) and other small primase-like proteins from bacteria and archaea Back     alignment and domain information
>pfam02132 RecR RecR protein Back     alignment and domain information
>PRK09401 reverse gyrase; Reviewed Back     alignment and domain information
>TIGR01054 rgy reverse gyrase; InterPro: IPR005736 DNA topoisomerases regulate the number of topological links between two DNA strands (i Back     alignment and domain information
>cd03361 TOPRIM_TopoIA_RevGyr TopoIA_RevGyr : The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to the ATP-dependent reverse gyrase found in archaea and thermophilic bacteria Back     alignment and domain information
>COG1110 Reverse gyrase [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK09001 DNA topoisomerase I; Validated Back     alignment and domain information
>cd03363 TOPRIM_TopoIA_TopoI TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I Back     alignment and domain information
>PRK08620 DNA topoisomerase III; Provisional Back     alignment and domain information
>cd01028 TOPRIM_TopoIA TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IA family of DNA topoisomerases (TopoIA) Back     alignment and domain information
>PRK07141 DNA topoisomerase I; Validated Back     alignment and domain information
>PRK05776 DNA topoisomerase III; Provisional Back     alignment and domain information
>PRK07726 DNA topoisomerase III; Provisional Back     alignment and domain information
>PRK07219 DNA topoisomerase I; Validated Back     alignment and domain information
>TIGR01056 topB DNA topoisomerase III; InterPro: IPR005738 DNA topoisomerases regulate the number of topological links between two DNA strands (i Back     alignment and domain information
>PRK08174 DNA topoisomerase III; Validated Back     alignment and domain information
>PRK08173 DNA topoisomerase III; Validated Back     alignment and domain information
>PRK07220 DNA topoisomerase I; Validated Back     alignment and domain information
>cd03362 TOPRIM_TopoIA_TopoIII TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III Back     alignment and domain information
>PRK09031 DNA topoisomerase III; Provisional Back     alignment and domain information
>PRK13901 ruvA Holliday junction DNA helicase motor protein; Provisional Back     alignment and domain information
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed 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
>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
>pfam00633 HHH Helix-hairpin-helix motif Back     alignment and domain information
>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
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair] Back     alignment and domain information
>PRK10702 endonuclease III; Provisional Back     alignment and domain information
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair] Back     alignment and domain information
>smart00478 ENDO3c endonuclease III Back     alignment and domain information
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated Back     alignment and domain information
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated Back     alignment and domain information
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair] Back     alignment and domain information

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

Homologous Structures Detected by PSI-BLAST against Nonredundant Database

IdentityAlignment graphLength Definition E-value
Target201 recombination protein RecR [Candidatus Liberibacter asi
1vdd_A228 Crystal Structure Of Recombinational Repair Protein 3e-61
2v1c_A220 Crystal Structure And Mutational Study Of Recor Pro 3e-61
>gi|49259537|pdb|1VDD|A Chain A, Crystal Structure Of Recombinational Repair Protein Recr Length = 228 Back     alignment and structure
 Score =  238 bits (608), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 72/195 (36%), Positives = 113/195 (57%), Gaps = 2/195 (1%)

Query: 6   TGKEIENLIKILARIPGFGPRSARRATLHLVKKKEQLLGPLAEAMANIYNKVCLCSICGN 65
               + +LI+ L+R+PG GP+SA+R   HL ++  + +  LA A+      + +C IC N
Sbjct: 3   YPPSLVSLIRELSRLPGIGPKSAQRLAFHLFEQPREDIERLASALLEAKRDLHVCPICFN 62

Query: 66  VDTTDPCAICIDQQRDASVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPEDI 125
           +   + C +C D  RD   I VVE+  D+ ALERS     LYHVL G LSP++ +GP+ +
Sbjct: 63  ITDAEKCDVCADPSRDQRTICVVEEPGDVIALERSGEYRGLYHVLHGVLSPMNGVGPDKL 122

Query: 126 GIQSLIERIEVKKIRELIFAISATIEGQTTAHYIMDKLKGIDVKITRLAYGIPMGSELDY 185
            I+ L+ R+   +  E+I A   T+EG  TA Y+   L+ +   I+R+AYG+P+G  L+Y
Sbjct: 123 HIKPLLPRV--GQGMEVILATGTTVEGDATALYLQRLLEPLGAAISRIAYGVPVGGSLEY 180

Query: 186 LDDGTIFEAIRSRTV 200
            D+ T+  A+  R  
Sbjct: 181 TDEVTLGRALTGRQT 195


gi|151568115|pdb|2V1C|A Chain A, Crystal Structure And Mutational Study Of Recor Provide Insight Into Its Role In Dna Repair Length = 220 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target201 recombination protein RecR [Candidatus Liberibacter asi
1vdd_A228 Recombination protein RECR; helix-hairpin-helix, zinc f 2e-58
>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 Length = 228 Back     alignment and structure
 Score =  220 bits (561), Expect = 2e-58
 Identities = 71/194 (36%), Positives = 110/194 (56%), Gaps = 2/194 (1%)

Query: 8   KEIENLIKILARIPGFGPRSARRATLHLVKKKEQLLGPLAEAMANIYNKVCLCSICGNVD 67
             + +LI+ L+R+PG GP+SA+R   HL ++  + +  LA A+      + +C IC N+ 
Sbjct: 5   PSLVSLIRELSRLPGIGPKSAQRLAFHLFEQPREDIERLASALLEAKRDLHVCPICFNIT 64

Query: 68  TTDPCAICIDQQRDASVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPEDIGI 127
             + C +C D  RD   I VVE+  D+ ALERS     LYHVL G LSP++ +GP+ + I
Sbjct: 65  DAEKCDVCADPSRDQRTICVVEEPGDVIALERSGEYRGLYHVLHGVLSPMNGVGPDKLHI 124

Query: 128 QSLIERIEVKKIRELIFAISATIEGQTTAHYIMDKLKGIDVKITRLAYGIPMGSELDYLD 187
                   V +  E+I A   T+EG  TA Y+   L+ +   I+R+AYG+P+G  L+Y D
Sbjct: 125 --KPLLPRVGQGMEVILATGTTVEGDATALYLQRLLEPLGAAISRIAYGVPVGGSLEYTD 182

Query: 188 DGTIFEAIRSRTVL 201
           + T+  A+  R  +
Sbjct: 183 EVTLGRALTGRQTV 196


Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target201 recombination protein RecR [Candidatus Liberibacter asi
1vdd_A228 Recombination protein RECR; helix-hairpin-helix, zinc f 100.0
1cuk_A203 RUVA protein; DNA repair, SOS response, DNA-binding, DN 96.76
2ztd_A212 Holliday junction ATP-dependent DNA helicase RUVA; reco 96.69
1ixr_A191 Holliday junction DNA helicase RUVA; heterooligomeric c 96.62
3fhg_A207 Mjogg, N-glycosylase/DNA lyase, DNA-; helix-hairpin-hel 93.08
3i0w_A290 8-oxoguanine-DNA-glycosylase; OGG, cacogg, DNA, 8-OXOG, 92.13
1mpg_A282 ALKA, 3-methyladenine DNA glycosylase II; DNA repair, b 91.83
1m3q_A317 8-oxoguanine DNA glycosylase; DNA repair, END product, 91.71
2abk_A211 Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {E 91.55
1z00_B84 DNA repair endonuclease XPF; helix-hairpin-helix, hydro 91.45
3fhf_A214 Mjogg, N-glycosylase/DNA lyase, DNA-; helix-hairpin-hel 91.3
1z00_A89 DNA excision repair protein ERCC-1; helix-hairpin-helix 91.11
2jhn_A295 ALKA, 3-methyladenine DNA-glycosylase; DNA repair, N1-m 90.92
1orn_A226 Endonuclease III; DNA repair, DNA glycosylase, [4Fe-4S] 90.82
2h56_A233 DNA-3-methyladenine glycosidase; 10174367, EC 3.2.2.-, 90.61
1pu6_A218 3-methyladenine DNA glycosylase; helix-hairpin-helix, b 90.41
1kea_A221 Possible G-T mismatches repair enzyme; DNA repair, DNA 90.16
1kg2_A225 A/G-specific adenine glycosylase; DNA repair, hydrolase 90.12
1mw9_X 592 DNA topoisomerase I; decatenase enzyme, toprim domain; 96.39
2gai_A 633 DNA topoisomerase I; zinc ribbon; HET: DNA; 1.70A {Ther 92.69
1i7d_A 659 DNA topoisomerase III; decatenating enzyme, protein-DNA 90.03
2fcj_A119 Small toprim domain protein; structural genomics, PSI, 93.77
1t6t_1118 Putative protein; structural genomics, PSI, protein str 91.11
1lko_A191 Rubrerythrin all-iron(II) form; reduced form, DIIRON, f 93.56
1nnq_A171 Rubrerythrin; structural genomics, PSI, protein structu 93.15
1yuz_A202 Nigerythrin; rubrythrin, rubredoxin, hemerythrin, elect 90.5
>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
Probab=100.00  E-value=0  Score=529.17  Aligned_cols=194  Identities=37%  Similarity=0.685  Sum_probs=190.2

Q ss_pred             CCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCEE
Q ss_conf             86679999999975689995379999999971998999999999999998518288999733456541003555567369
Q gi|254780762|r    6 TGKEIENLIKILARIPGFGPRSARRATLHLVKKKEQLLGPLAEAMANIYNKVCLCSICGNVDTTDPCAICIDQQRDASVI   85 (201)
Q Consensus         6 ~~~~l~~LI~~l~kLPGIG~KsA~R~a~~Ll~~~~~~~~~l~~~l~~~~~~i~~C~~C~~l~~~~~C~iC~d~~Rd~~~l   85 (201)
                      +|++|++||++|++|||||||||+|||||||+++++.+++|+++|.+++++|++|+.||+++++++|+||+|++||+++|
T Consensus         3 ~p~~ie~LI~~l~kLPGIG~KsA~RlA~~LL~~~~~~~~~La~~i~~~k~~i~~C~~C~~lse~~~C~IC~D~~Rd~~~i   82 (228)
T 1vdd_A            3 YPPSLVSLIRELSRLPGIGPKSAQRLAFHLFEQPREDIERLASALLEAKRDLHVCPICFNITDAEKCDVCADPSRDQRTI   82 (228)
T ss_dssp             CCHHHHHHHHHHHTSTTCCHHHHHHHHHHHSSSCHHHHHHHHHHHHHHHHHCEECSSSCCEESSSSCHHHHCSSSCTTEE
T ss_pred             CCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCEE
T ss_conf             95999999999966899988999999999981999999999999999998188386788716777766435777765458


Q ss_pred             EEEECHHHHHHHHHHCCEEEEEEEHHHHCCCCCCCCHHHCCHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             99835889999975174013421012100200026811128899999851578554999946997868999999998201
Q gi|254780762|r   86 IVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPEDIGIQSLIERIEVKKIRELIFAISATIEGQTTAHYIMDKLKG  165 (201)
Q Consensus        86 CVVE~~~Di~~IE~t~~y~G~YhVLgG~ispl~g~~p~~l~i~~L~~ri~~~~i~EVIlA~~~t~EGe~Ta~yi~~~lk~  165 (201)
                      ||||++.|+++||+||.|+|+||||||+|||++|++|++|++++|++|+++  ++|||||||||+|||+||+||++.|++
T Consensus        83 CVVE~~~Dl~aIE~tg~y~G~YhVLgG~iSpldgigp~~l~i~~L~~Ri~~--~~EVIlA~~~t~EGe~Ta~yi~~~Lk~  160 (228)
T 1vdd_A           83 CVVEEPGDVIALERSGEYRGLYHVLHGVLSPMNGVGPDKLHIKPLLPRVGQ--GMEVILATGTTVEGDATALYLQRLLEP  160 (228)
T ss_dssp             EEESSHHHHHHTTTTSSCCSEEEECSSCCBGGGTBCTTTSTTGGGGGGCCT--TCEEEECCCSSHHHHHHHHHHHHHHTT
T ss_pred             EEECCHHHHHHHHHCCCCCEEEEECCCCCCCCCCCCCCCCCHHHHHHHHCC--CCEEEEEECCCCCHHHHHHHHHHHHHH
T ss_conf             997789999999860811269986687637234899410036999998635--867999817985518999999998544


Q ss_pred             CCCEEEEEECCCCCCCCHHHHHHHHHHHHHHCCCCC
Q ss_conf             798088741467488206663479999998306479
Q gi|254780762|r  166 IDVKITRLAYGIPMGSELDYLDDGTIFEAIRSRTVL  201 (201)
Q Consensus       166 ~~ikitrla~GiP~G~~ley~D~~TL~~Al~~R~~l  201 (201)
                      +++||||||+|||+||+|||+|+.||++||++|++|
T Consensus       161 ~~ikiTRLA~GlP~G~~LeY~D~~TL~~Al~~R~~i  196 (228)
T 1vdd_A          161 LGAAISRIAYGVPVGGSLEYTDEVTLGRALTGRQTV  196 (228)
T ss_dssp             SSCEEEECCBCBCTTCCGGGSCHHHHHHHHHTCEEE
T ss_pred             CCCEEEEECCCCCCCCCHHHCCHHHHHHHHHCCCCC
T ss_conf             497087610068778420016899999999808325



>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
>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
>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
>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
>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
>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
>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
>2abk_A Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {Escherichia coli} SCOP: a.96.1.1 Back     alignment and structure
>1z00_B DNA repair endonuclease XPF; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} SCOP: a.60.2.5 PDB: 2aq0_A* Back     alignment and structure
>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
>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
>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
>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
>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
>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
>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
>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
>1mw9_X DNA topoisomerase I; decatenase enzyme, toprim domain; HET: DNA; 1.67A {Escherichia coli} SCOP: e.10.1.1 PDB: 1mw8_X* 1cy1_A* 1cy0_A* 1cy2_A* 1cy4_A* 1cy6_A* 1cy7_A* 1cy8_A* 1ecl_A 1cy9_A* 1cyy_A* Back     alignment and structure
>2gai_A DNA topoisomerase I; zinc ribbon; HET: DNA; 1.70A {Thermotoga maritima MSB8} PDB: 2gaj_A* Back     alignment and structure
>1i7d_A DNA topoisomerase III; decatenating enzyme, protein-DNA complex, single-stranded DNA, isomerase/DNA complex; HET: DNA; 2.05A {Escherichia coli} SCOP: e.10.1.1 PDB: 2o5c_A* 2o54_A* 2o59_A* 2o19_A* 2o5e_A* 1d6m_A* Back     alignment and structure
>2fcj_A Small toprim domain protein; structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: MES; 1.30A {Geobacillus stearothermophilus} SCOP: c.136.1.1 PDB: 2i5r_A* Back     alignment and structure
>1t6t_1 Putative protein; structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG, unknown function; 1.80A {Aquifex aeolicus VF5} SCOP: c.136.1.1 Back     alignment and structure
>1lko_A Rubrerythrin all-iron(II) form; reduced form, DIIRON, four-helix bundle, rubredoxin-like, electron transport; 1.63A {Desulfovibrio vulgaris} SCOP: a.25.1.1 g.41.5.1 PDB: 1dvb_A 1jyb_A 1b71_A 1lkm_A 1lkp_A 1qyb_A 1s2z_A 1s30_A 1ryt_A Back     alignment and structure
>1nnq_A Rubrerythrin; structural genomics, PSI, protein structure initiative, southeast collaboratory for structural genomics, secsg; 2.35A {Pyrococcus furiosus} SCOP: a.25.1.1 g.41.5.1 PDB: 2hr5_A Back     alignment and structure
>1yuz_A Nigerythrin; rubrythrin, rubredoxin, hemerythrin, electron transfer, DIIRON center, oxidoreductase; 1.40A {Desulfovibrio vulgaris subsp} SCOP: a.25.1.1 g.41.5.1 PDB: 1yv1_A 1yux_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 201 recombination protein RecR [Candidatus Liberibacter asi
d1vdda_199 e.49.1.1 (A:) Recombination protein RecR {Deinococcus r 2e-55
>d1vdda_ e.49.1.1 (A:) Recombination protein RecR {Deinococcus radiodurans [TaxId: 1299]} Length = 199 Back     information, alignment and structure

class: Multi-domain proteins (alpha and beta)
fold: Recombination protein RecR
superfamily: Recombination protein RecR
family: Recombination protein RecR
domain: Recombination protein RecR
species: Deinococcus radiodurans [TaxId: 1299]
 Score =  208 bits (532), Expect = 2e-55
 Identities = 71/194 (36%), Positives = 110/194 (56%), Gaps = 2/194 (1%)

Query: 8   KEIENLIKILARIPGFGPRSARRATLHLVKKKEQLLGPLAEAMANIYNKVCLCSICGNVD 67
             + +LI+ L+R+PG GP+SA+R   HL ++  + +  LA A+      + +C IC N+ 
Sbjct: 5   PSLVSLIRELSRLPGIGPKSAQRLAFHLFEQPREDIERLASALLEAKRDLHVCPICFNIT 64

Query: 68  TTDPCAICIDQQRDASVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPEDIGI 127
             + C +C D  RD   I VVE+  D+ ALERS     LYHVL G LSP++ +GP+ + I
Sbjct: 65  DAEKCDVCADPSRDQRTICVVEEPGDVIALERSGEYRGLYHVLHGVLSPMNGVGPDKLHI 124

Query: 128 QSLIERIEVKKIRELIFAISATIEGQTTAHYIMDKLKGIDVKITRLAYGIPMGSELDYLD 187
                   V +  E+I A   T+EG  TA Y+   L+ +   I+R+AYG+P+G  L+Y D
Sbjct: 125 --KPLLPRVGQGMEVILATGTTVEGDATALYLQRLLEPLGAAISRIAYGVPVGGSLEYTD 182

Query: 188 DGTIFEAIRSRTVL 201
           + T+  A+  R  +
Sbjct: 183 EVTLGRALTGRQTV 196


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

IdentityAlignment graphLength Definition Probability
Target201 recombination protein RecR [Candidatus Liberibacter asi
d1vdda_199 Recombination protein RecR {Deinococcus radiodurans [Ta 100.0
d1bvsa271 DNA helicase RuvA subunit, middle domain {Mycobacterium 96.49
d1cuka278 DNA helicase RuvA subunit, middle domain {Escherichia c 96.36
d1ixra173 DNA helicase RuvA subunit, middle domain {Thermus therm 96.34
d2noha1190 8-oxoguanine glycosylase {Human (Homo sapiens) [TaxId: 93.38
d1pu6a_217 3-Methyladenine DNA glycosylase III (MagIII) {Helicobac 92.15
d1orna_214 Endonuclease III {Escherichia coli [TaxId: 562]} 91.89
d1mpga1183 3-Methyladenine DNA glycosylase II (gene alkA or aidA) 91.75
d2abka_211 Endonuclease III {Escherichia coli [TaxId: 562]} 91.64
d2a1jb178 DNA excision repair protein ERCC-1 {Human (Homo sapiens 91.45
d1keaa_217 Thymine-DNA glycosylase {Archaeon Methanobacterium ther 91.3
d1kg2a_224 Catalytic domain of MutY {Escherichia coli [TaxId: 562] 91.23
d1mw9x_ 591 DNA topoisomerase I, 67K N-terminal domain {Escherichia 96.32
d1gkub3 556 Topoisomerase "domain" of reverse gyrase {Archaeon Arch 95.67
d1i7da_ 620 DNA topoisomerase III {Escherichia coli [TaxId: 562]} 94.74
d1t6t1_108 Hypothetical protein aq_2086 {Aquifex aeolicus [TaxId: 93.89
d2fcja1114 Hypothetical protein RBSTP2199 {Bacillus stearothermoph 93.22
>d1vdda_ e.49.1.1 (A:) Recombination protein RecR {Deinococcus radiodurans [TaxId: 1299]} Back     information, alignment and structure
class: Multi-domain proteins (alpha and beta)
fold: Recombination protein RecR
superfamily: Recombination protein RecR
family: Recombination protein RecR
domain: Recombination protein RecR
species: Deinococcus radiodurans [TaxId: 1299]
Probab=100.00  E-value=0  Score=528.96  Aligned_cols=194  Identities=37%  Similarity=0.685  Sum_probs=190.2

Q ss_pred             CCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCEE
Q ss_conf             86679999999975689995379999999971998999999999999998518288999733456541003555567369
Q gi|254780762|r    6 TGKEIENLIKILARIPGFGPRSARRATLHLVKKKEQLLGPLAEAMANIYNKVCLCSICGNVDTTDPCAICIDQQRDASVI   85 (201)
Q Consensus         6 ~~~~l~~LI~~l~kLPGIG~KsA~R~a~~Ll~~~~~~~~~l~~~l~~~~~~i~~C~~C~~l~~~~~C~iC~d~~Rd~~~l   85 (201)
                      +|++|++||++|++|||||||||+|||||||+++++++++|+++|.+++++|++|+.||+++++++|+||+|++||+++|
T Consensus         3 ~p~~i~~LI~~l~kLPGIG~KsA~Rla~~LL~~~~~~~~~l~~~l~~~~~~I~~C~~C~~l~e~~~C~iC~d~~Rd~~~i   82 (199)
T d1vdda_           3 YPPSLVSLIRELSRLPGIGPKSAQRLAFHLFEQPREDIERLASALLEAKRDLHVCPICFNITDAEKCDVCADPSRDQRTI   82 (199)
T ss_dssp             CCHHHHHHHHHHHTSTTCCHHHHHHHHHHHSSSCHHHHHHHHHHHHHHHHHCEECSSSCCEESSSSCHHHHCSSSCTTEE
T ss_pred             CCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCEE
T ss_conf             96899999999987899889999999999983998899999999999998609898877042677744114767776469


Q ss_pred             EEEECHHHHHHHHHHCCEEEEEEEHHHHCCCCCCCCHHHCCHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             99835889999975174013421012100200026811128899999851578554999946997868999999998201
Q gi|254780762|r   86 IVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPEDIGIQSLIERIEVKKIRELIFAISATIEGQTTAHYIMDKLKG  165 (201)
Q Consensus        86 CVVE~~~Di~~IE~t~~y~G~YhVLgG~ispl~g~~p~~l~i~~L~~ri~~~~i~EVIlA~~~t~EGe~Ta~yi~~~lk~  165 (201)
                      ||||++.|+|+||+||.|+|+||||||+|||++|++|++|++++|++|+++  ++|||||||||+|||+||+||++.|++
T Consensus        83 CVVE~~~Dl~~iE~t~~y~G~YhVL~G~ispl~gi~p~~l~i~~L~~r~~~--~~EiIlA~~~t~EGe~Ta~yi~~~l~~  160 (199)
T d1vdda_          83 CVVEEPGDVIALERSGEYRGLYHVLHGVLSPMNGVGPDKLHIKPLLPRVGQ--GMEVILATGTTVEGDATALYLQRLLEP  160 (199)
T ss_dssp             EEESSHHHHHHTTTTSSCCSEEEECSSCCBGGGTBCTTTSTTGGGGGGCCT--TCEEEECCCSSHHHHHHHHHHHHHHTT
T ss_pred             EEEECHHHHHHHHHCCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHCCC--CCEEEEEECCCCCHHHHHHHHHHHHHH
T ss_conf             999668998999852310001554157558444877410112677775057--767999826986508999999998523


Q ss_pred             CCCEEEEEECCCCCCCCHHHHHHHHHHHHHHCCCCC
Q ss_conf             798088741467488206663479999998306479
Q gi|254780762|r  166 IDVKITRLAYGIPMGSELDYLDDGTIFEAIRSRTVL  201 (201)
Q Consensus       166 ~~ikitrla~GiP~G~~ley~D~~TL~~Al~~R~~l  201 (201)
                      .++||||||+|||+||+|||+|+.||++||++|++|
T Consensus       161 ~~ikitrlA~GiP~G~~ley~D~~TL~~Al~~R~~i  196 (199)
T d1vdda_         161 LGAAISRIAYGVPVGGSLEYTDEVTLGRALTGRQTV  196 (199)
T ss_dssp             SSCEEEECCBCBCTTCCGGGSCHHHHHHHHHTCEEE
T ss_pred             CCCEEEEECCCCCCCCCHHHCCHHHHHHHHHCCCCC
T ss_conf             496287602268778310006899999999727247



>d1bvsa2 a.60.2.1 (A:64-134) DNA helicase RuvA subunit, middle domain {Mycobacterium leprae [TaxId: 1769]} 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
>d1ixra1 a.60.2.1 (A:63-135) DNA helicase RuvA subunit, middle domain {Thermus thermophilus [TaxId: 274]} 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
>d1pu6a_ a.96.1.5 (A:) 3-Methyladenine DNA glycosylase III (MagIII) {Helicobacter pylori [TaxId: 210]} Back     information, alignment and structure
>d1orna_ a.96.1.1 (A:) Endonuclease III {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>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
>d2abka_ a.96.1.1 (A:) Endonuclease III {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2a1jb1 a.60.2.5 (B:219-296) DNA excision repair protein ERCC-1 {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1keaa_ a.96.1.2 (A:) Thymine-DNA glycosylase {Archaeon Methanobacterium thermoformicicum [TaxId: 145262]} Back     information, alignment and structure
>d1kg2a_ a.96.1.2 (A:) Catalytic domain of MutY {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1mw9x_ e.10.1.1 (X:) DNA topoisomerase I, 67K N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1gkub3 e.10.1.1 (B:499-1054) Topoisomerase "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} Back     information, alignment and structure
>d1i7da_ e.10.1.1 (A:) DNA topoisomerase III {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1t6t1_ c.136.1.1 (1:) Hypothetical protein aq_2086 {Aquifex aeolicus [TaxId: 63363]} Back     information, alignment and structure
>d2fcja1 c.136.1.1 (A:1-114) Hypothetical protein RBSTP2199 {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 201 recombination protein RecR [Candidatus Liberibacte
1vdd_A_67-175109 (A:67-175) Recombination protein RECR; helix-hairp 2e-39
1vdd_A_1-6666 (A:1-66) Recombination protein RECR; helix-hairpin 1e-14
>1vdd_A (A:67-175) Recombination protein RECR; helix-hairpin-helix, zinc finger, toprim, walker B ATP binding motif; 2.50A {Deinococcus radiodurans}Length = 109 Back     alignment and structure
 Score =  156 bits (396), Expect = 2e-39
 Identities = 47/111 (42%), Positives = 68/111 (61%), Gaps = 2/111 (1%)

Query: 70  DPCAICIDQQRDASVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPEDIGIQS 129
           + C +C D  RD   I VVE+  D+ ALERS     LYHVL G LSP++ +GP+ + I+ 
Sbjct: 1   EKCDVCADPSRDQRTICVVEEPGDVIALERSGEYRGLYHVLHGVLSPMNGVGPDKLHIKP 60

Query: 130 LIERIEVKKIRELIFAISATIEGQTTAHYIMDKLKGIDVKITRLAYGIPMG 180
           L+ R  V +  E+I A   T+EG  TA Y+   L+ +   I+R+AYG+P+G
Sbjct: 61  LLPR--VGQGMEVILATGTTVEGDATALYLQRLLEPLGAAISRIAYGVPVG 109


>1vdd_A (A:1-66) Recombination protein RECR; helix-hairpin-helix, zinc finger, toprim, walker B ATP binding motif; 2.50A {Deinococcus radiodurans}Length = 66 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target201 recombination protein RecR [Candidatus Liberibacter asi
1vdd_A_67-175109 Recombination protein RECR; helix-hairpin-helix, z 100.0
1mw9_X_1-32_89-156100 DNA topoisomerase I; decatenase enzyme, toprim dom 96.67
1nui_A_138-255118 DNA primase/helicase; zinc-biding domain, toprim f 94.13
2gai_A_1-35_63-127100 DNA topoisomerase I; zinc ribbon; HET: DNA; 1.70A 93.3
1i7d_A_1-152152 DNA topoisomerase III; decatenating enzyme, protei 92.97
2au3_A_225-349125 DNA primase; zinc ribbon, toprim, RNA polymerase, 92.41
2fcj_A_119 Small toprim domain protein; structural genomics, 91.81
1t6t_1_118 Putative protein; structural genomics, PSI, protei 91.46
1dd9_A_146-285140 DNA primase, DNAG; toprim, 3-helix bundle, DNA-bin 90.15
1vdd_A_1-6666 Recombination protein RECR; helix-hairpin-helix, z 99.76
2w9m_A_1-118118 Polymerase X; SAXS, DNA repair, DNA polymerase, DN 92.96
2nrt_A_157-22064 Uvrabc system protein C; UVRC, endonuclease, RNAse 91.66
1z00_B_1-7171 DNA repair endonuclease XPF; helix-hairpin-helix, 90.36
1z00_A_89 DNA excision repair protein ERCC-1; helix-hairpin- 90.16
1nnq_A_67-171105 Rubrerythrin; structural genomics, PSI, protein st 90.05
1cuk_A_66-14479 RUVA protein; DNA repair, SOS response, DNA-bindin 96.48
2ztd_A_80-15475 Holliday junction ATP-dependent DNA helicase RUVA; 96.34
1ixr_A_191 Holliday junction DNA helicase RUVA; heterooligome 96.06
3i0w_A_111-127_196-23658 8-oxoguanine-DNA-glycosylase; OGG, cacogg, DNA, 8- 94.56
2h56_A_1-49_127-233156 DNA-3-methyladenine glycosidase; 10174367, EC 3.2. 94.25
3fsp_A_34-143110 A/G-specific adenine glycosylase; protein-DNA comp 93.94
3fhf_A_38-150113 Mjogg, N-glycosylase/DNA lyase, DNA-; helix-hairpi 93.88
2abk_A_23-133111 Endonuclease III; DNA-repair, DNA glycosylase; 1.8 92.21
1kea_A_29-139111 Possible G-T mismatches repair enzyme; DNA repair, 92.15
1orn_A_28-137110 Endonuclease III; DNA repair, DNA glycosylase, [4F 92.12
2jhn_A_112-130_199-23455 ALKA, 3-methyladenine DNA-glycosylase; DNA repair, 91.46
1kg2_A_1-23_110-225139 A/G-specific adenine glycosylase; DNA repair, hydr 91.01
1gku_B_1-29_235-251_501-675221 Reverse gyrase, TOP-RG; topoisomerase, DNA superco 95.33
>1vdd_A (A:67-175) Recombination protein RECR; helix-hairpin-helix, zinc finger, toprim, walker B ATP binding motif; 2.50A {Deinococcus radiodurans} Back     alignment and structure
Probab=100.00  E-value=3.3e-43  Score=311.48  Aligned_cols=109  Identities=42%  Similarity=0.782  Sum_probs=107.1

Q ss_pred             CCCCCCCCCCCCCCEEEEEECHHHHHHHHHHCCEEEEEEEHHHHCCCCCCCCHHHCCHHHHHHHHCCCCCCEEEEEECCC
Q ss_conf             65410035555673699983588999997517401342101210020002681112889999985157855499994699
Q gi|254780762|r   70 DPCAICIDQQRDASVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPEDIGIQSLIERIEVKKIRELIFAISAT  149 (201)
Q Consensus        70 ~~C~iC~d~~Rd~~~lCVVE~~~Di~~IE~t~~y~G~YhVLgG~ispl~g~~p~~l~i~~L~~ri~~~~i~EVIlA~~~t  149 (201)
                      ++|+||+|++||+++|||||++.|+|+||+||.|+|+||||||+|||++|++|++|++++|++|+  .+++|||||||||
T Consensus         1 d~C~IC~d~~Rd~~~lcVVE~~~Di~~iE~s~~y~G~YhVL~g~isp~~gi~p~~l~~~~L~~r~--~~i~EvIlA~s~t   78 (109)
T 1vdd_A            1 EKCDVCADPSRDQRTICVVEEPGDVIALERSGEYRGLYHVLHGVLSPMNGVGPDKLHIKPLLPRV--GQGMEVILATGTT   78 (109)
T ss_dssp             SSCHHHHCSSSCTTEEEEESSHHHHHHTTTTSSCCSEEEECSSCCBGGGTBCTTTSTTGGGGGGC--CTTCEEEECCCSS
T ss_pred             CCCCCCCCCCCCCCEEEEEECHHHHHHHHHCCHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHH--CCCCEEEEEECCC
T ss_conf             77431037777752699995689989998512222104230574473448885201125667762--4776799982698


Q ss_pred             CCHHHHHHHHHHHHCCCCCEEEEEECCCCCC
Q ss_conf             7868999999998201798088741467488
Q gi|254780762|r  150 IEGQTTAHYIMDKLKGIDVKITRLAYGIPMG  180 (201)
Q Consensus       150 ~EGe~Ta~yi~~~lk~~~ikitrla~GiP~G  180 (201)
                      +|||+||+||+++||++++||||||+|||+|
T Consensus        79 ~EGe~Ta~yi~~~lk~~~ikvtrlA~GiP~G  109 (109)
T 1vdd_A           79 VEGDATALYLQRLLEPLGAAISRIAYGVPVG  109 (109)
T ss_dssp             HHHHHHHHHHHHHHTTSSCEEEECCBCBCTT
T ss_pred             CCCHHHHHHHHHHHHHCCCEEEEECCCCCCC
T ss_conf             6508999999998423496187602268778



>1mw9_X (X:1-32,X:89-156) DNA topoisomerase I; decatenase enzyme, toprim domain; HET: DNA; 1.67A {Escherichia coli} Back     alignment and structure
>1nui_A (A:138-255) DNA primase/helicase; zinc-biding domain, toprim fold, DNA replication, DNA- directed RNA polymerase, primosome, late protein; HET: DNA; 2.90A {Enterobacteria phage T7} Back     alignment and structure
>2gai_A (A:1-35,A:63-127) DNA topoisomerase I; zinc ribbon; HET: DNA; 1.70A {Thermotoga maritima MSB8} PDB: 2gaj_A* Back     alignment and structure
>1i7d_A (A:1-152) DNA topoisomerase III; decatenating enzyme, protein-DNA complex, single-stranded DNA, isomerase/DNA complex; HET: DNA; 2.05A {Escherichia coli} Back     alignment and structure
>2au3_A (A:225-349) DNA primase; zinc ribbon, toprim, RNA polymerase, DNA replication, transferase; HET: DNA; 2.00A {Aquifex aeolicus} Back     alignment and structure
>2fcj_A (A:) Small toprim domain protein; structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: MES; 1.30A {Geobacillus stearothermophilus} Back     alignment and structure
>1t6t_1 (1:) Putative protein; structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG, unknown function; 1.80A {Aquifex aeolicus VF5} Back     alignment and structure
>1dd9_A (A:146-285) DNA primase, DNAG; toprim, 3-helix bundle, DNA-binding protein, RNA polymerase, replication protein; HET: DNA; 1.60A {Escherichia coli} Back     alignment and structure
>1vdd_A (A:1-66) Recombination protein RECR; helix-hairpin-helix, zinc finger, toprim, walker B ATP binding motif; 2.50A {Deinococcus radiodurans} Back     alignment and structure
>2w9m_A (A:1-118) Polymerase X; SAXS, DNA repair, DNA polymerase, DNA replication; 2.46A {Deinococcus radiodurans} Back     alignment and structure
>2nrt_A (A:157-220) Uvrabc system protein C; UVRC, endonuclease, RNAse H, helix hairpin helix, NER, hydrolase; 1.50A {Thermotoga maritima} PDB: 2nrv_A 2nrw_A 2nrx_A 2nrz_A Back     alignment and structure
>1z00_B (B:1-71) DNA repair endonuclease XPF; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} Back     alignment and structure
>1z00_A (A:) DNA excision repair protein ERCC-1; helix-hairpin-helix, hydrolase; HET: DNA; NMR {Homo sapiens} Back     alignment and structure
>1nnq_A (A:67-171) Rubrerythrin; structural genomics, PSI, protein structure initiative, southeast collaboratory for structural genomics, secsg; 2.35A {Pyrococcus furiosus} Back     alignment and structure
>1cuk_A (A:66-144) RUVA protein; DNA repair, SOS response, DNA-binding, DNA recombination, helicase; 1.90A {Escherichia coli} Back     alignment and structure
>2ztd_A (A:80-154) Holliday junction ATP-dependent DNA helicase RUVA; recombination, branch migration, DNA binding, oligomerization, acidic PIN; 2.40A {Mycobacterium tuberculosis} PDB: 2ztc_A 2zte_A 2h5x_A 1bvs_A Back     alignment and structure
>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
>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
>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
>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
>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
>2abk_A (A:23-133) Endonuclease III; DNA-repair, DNA glycosylase; 1.85A {Escherichia coli} 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
>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
>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
>1kg2_A (A:1-23,A:110-225) A/G-specific adenine glycosylase; DNA repair, hydrolase; 1.20A {Escherichia coli} Back     alignment and structure
>1gku_B (B:1-29,B:235-251,B:501-675) Reverse gyrase, TOP-RG; topoisomerase, DNA supercoiling, archaea, helicase; 2.7A {Archaeoglobus fulgidus} Back     alignment and structure