254780136

254780136

ribonucleotide-diphosphate reductase subunit beta

GeneID in NCBI database:8209111Locus tag:CLIBASIA_00075
Protein GI in NCBI database:254780136Protein Accession:YP_003064549.1
Gene range:+(11173, 11550)Protein Length:125aa
Gene description:ribonucleotide-diphosphate reductase subunit beta
COG prediction:[F] Ribonucleotide reductase, beta subunit
KEGG prediction:ribonucleotide-diphosphate reductase subunit beta (EC:1.17.4.1)
SEED prediction:Ribonucleotide reductase of class Ia (aerobic), beta subunit (EC 1.17.4.1)
Pathway involved in KEGG:not defined
Subsystem involved in SEED:Ribonucleotide reduction
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-----
MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGAELKWD
ccHHHHHHHHHHHHHHHHHHHcHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHccccccccccccccccHHHHHccccc
ccccccccHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHccccccccccccccccHHHcccccccccHHHHHHHHEcccccccc
mrdeslhlnfgidvinqikienphlwtKEFQQKSRTMLHEATLLEIAYAHetmpkgfvglnapsCEQYMQFIANrrchqigleplfkytenpfpwmsEVIDLKKEKNFFETRVTEYQQGAELKWD
mrdeslhlnfgidvinqikienphLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEyqqgaelkwd
MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGAELKWD
MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGA*L***
MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGAELKWD
****SLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGAE****
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGAELKWD
MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGAELKWD
MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGLNAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGAELKWD

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

IdentityAlignment graphLength Definition E-value
Target125 ribonucleotide-diphosphate reductase subunit beta [Cand
254780964352 ribonucleotide-diphosphate reductase subunit beta 3e-74
254780845352 ribonucleotide-diphosphate reductase subunit beta 3e-74
254781006125 ribonucleotide-diphosphate reductase subunit beta 2e-73
>gi|254780964|ref|YP_003065377.1| ribonucleotide-diphosphate reductase subunit beta [Candidatus Liberibacter asiaticus str. psy62] Length = 352 Back     alignment
 Score =  268 bits (684), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 125/125 (100%), Positives = 125/125 (100%)

Query: 1   MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL 60
           MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL
Sbjct: 228 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL 287

Query: 61  NAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGA 120
           NAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGA
Sbjct: 288 NAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGA 347

Query: 121 ELKWD 125
           ELKWD
Sbjct: 348 ELKWD 352

>gi|254780845|ref|YP_003065258.1| ribonucleotide-diphosphate reductase subunit beta [Candidatus Liberibacter asiaticus str. psy62] Length = 352 Back     alignment
 Score =  268 bits (684), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 125/125 (100%), Positives = 125/125 (100%)

Query: 1   MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL 60
           MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL
Sbjct: 228 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL 287

Query: 61  NAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGA 120
           NAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGA
Sbjct: 288 NAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGA 347

Query: 121 ELKWD 125
           ELKWD
Sbjct: 348 ELKWD 352

>gi|254781006|ref|YP_003065419.1| ribonucleotide-diphosphate reductase subunit beta [Candidatus Liberibacter asiaticus str. psy62] Length = 125 Back     alignment
 Score =  265 bits (677), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 125/125 (100%), Positives = 125/125 (100%)

Query: 1   MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL 60
           MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL
Sbjct: 1   MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL 60

Query: 61  NAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGA 120
           NAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGA
Sbjct: 61  NAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGA 120

Query: 121 ELKWD 125
           ELKWD
Sbjct: 121 ELKWD 125

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

IdentityAlignment graphLength Definition Round E-value
Target125 ribonucleotide-diphosphate reductase subunit beta [Cand
254780845352 ribonucleotide-diphosphate reductase subunit beta [Cand 1 2e-70
315122301372 ribonucleotide-diphosphate reductase subunit beta [Cand 1 1e-52
209885874377 ribonucleoside-diphosphate reductase, beta subunit [Oli 1 1e-51
256377255358 ribonucleoside-diphosphate reductase [Actinosynnema mir 1 1e-50
134097869360 ribonucleotide-diphosphate reductase subunit beta [Sacc 1 2e-50
226227154371 ribonucleoside-diphosphate reductase beta subunit [Gemm 1 2e-50
110635036369 ribonucleotide-diphosphate reductase subunit beta [Meso 1 5e-50
72163401354 ribonucleotide-diphosphate reductase subunit beta [Ther 1 8e-50
92119123416 ribonucleotide-diphosphate reductase subunit beta [Nitr 1 8e-50
85714830389 ribonucleotide reductase [Nitrobacter sp. Nb-311A] Leng 1 1e-49
>gi|254780845|ref|YP_003065258.1| ribonucleotide-diphosphate reductase subunit beta [Candidatus Liberibacter asiaticus str. psy62] Length = 352 Back     alignment and organism information
 Score =  268 bits (684), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 125/125 (100%), Positives = 125/125 (100%)

Query: 1   MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL 60
           MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL
Sbjct: 228 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL 287

Query: 61  NAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGA 120
           NAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGA
Sbjct: 288 NAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGA 347

Query: 121 ELKWD 125
           ELKWD
Sbjct: 348 ELKWD 352


Species: Candidatus Liberibacter asiaticus
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|315122301|ref|YP_004062790.1| ribonucleotide-diphosphate reductase subunit beta [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 372 Back     alignment and organism information
>gi|209885874|ref|YP_002289731.1| ribonucleoside-diphosphate reductase, beta subunit [Oligotropha carboxidovorans OM5] Length = 377 Back     alignment and organism information
>gi|256377255|ref|YP_003100915.1| ribonucleoside-diphosphate reductase [Actinosynnema mirum DSM 43827] Length = 358 Back     alignment and organism information
>gi|134097869|ref|YP_001103530.1| ribonucleotide-diphosphate reductase subunit beta [Saccharopolyspora erythraea NRRL 2338] Length = 360 Back     alignment and organism information
>gi|226227154|ref|YP_002761260.1| ribonucleoside-diphosphate reductase beta subunit [Gemmatimonas aurantiaca T-27] Length = 371 Back     alignment and organism information
>gi|110635036|ref|YP_675244.1| ribonucleotide-diphosphate reductase subunit beta [Mesorhizobium sp. BNC1] Length = 369 Back     alignment and organism information
>gi|72163401|ref|YP_291058.1| ribonucleotide-diphosphate reductase subunit beta [Thermobifida fusca YX] Length = 354 Back     alignment and organism information
>gi|92119123|ref|YP_578852.1| ribonucleotide-diphosphate reductase subunit beta [Nitrobacter hamburgensis X14] Length = 416 Back     alignment and organism information
>gi|85714830|ref|ZP_01045816.1| ribonucleotide reductase [Nitrobacter sp. Nb-311A] Length = 389 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
Target125 ribonucleotide-diphosphate reductase subunit beta [Cand
PRK07209369 PRK07209, PRK07209, ribonucleotide-diphosphate reductas 3e-66
cd01049288 cd01049, RNRR2, Ribonucleotide Reductase, R2/beta subun 8e-25
PRK09614324 PRK09614, nrdF, ribonucleotide-diphosphate reductase su 2e-19
PLN02492324 PLN02492, PLN02492, ribonucleoside-diphosphate reductas 6e-15
PTZ00211330 PTZ00211, PTZ00211, ribonucleoside-diphosphate reductas 8e-15
KOG1567344 KOG1567, KOG1567, KOG1567, Ribonucleotide reductase, be 3e-14
PRK12759410 PRK12759, PRK12759, bifunctional gluaredoxin/ribonucleo 5e-14
PRK09101376 PRK09101, nrdB, ribonucleotide-diphosphate reductase su 2e-08
pfam00268281 pfam00268, Ribonuc_red_sm, Ribonucleotide reductase, sm 8e-08
COG0208348 COG0208, NrdF, Ribonucleotide reductase, beta subunit [ 1e-31
>gnl|CDD|180886 PRK07209, PRK07209, ribonucleotide-diphosphate reductase subunit beta; Validated Back     alignment and domain information
>gnl|CDD|153108 cd01049, RNRR2, Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain Back     alignment and domain information
>gnl|CDD|181991 PRK09614, nrdF, ribonucleotide-diphosphate reductase subunit beta; Reviewed Back     alignment and domain information
>gnl|CDD|178110 PLN02492, PLN02492, ribonucleoside-diphosphate reductase Back     alignment and domain information
>gnl|CDD|173476 PTZ00211, PTZ00211, ribonucleoside-diphosphate reductase small subunit; Provisional Back     alignment and domain information
>gnl|CDD|36780 KOG1567, KOG1567, KOG1567, Ribonucleotide reductase, beta subunit [Nucleotide transport and metabolism] Back     alignment and domain information
>gnl|CDD|139206 PRK12759, PRK12759, bifunctional gluaredoxin/ribonucleoside-diphosphate reductase subunit beta; Provisional Back     alignment and domain information
>gnl|CDD|181647 PRK09101, nrdB, ribonucleotide-diphosphate reductase subunit beta; Reviewed Back     alignment and domain information
>gnl|CDD|144013 pfam00268, Ribonuc_red_sm, Ribonucleotide reductase, small chain Back     alignment and domain information
>gnl|CDD|30557 COG0208, NrdF, Ribonucleotide reductase, beta subunit [Nucleotide transport and metabolism] Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 125 ribonucleotide-diphosphate reductase subunit beta [Cand
PRK07209391 ribonucleotide-diphosphate reductase subunit beta; Vali 100.0
PRK12759410 bifunctional gluaredoxin/ribonucleoside-diphosphate red 100.0
PRK09101376 nrdB ribonucleotide-diphosphate reductase subunit beta; 100.0
PTZ00211330 ribonucleotide reductase small subunit; Provisional 100.0
COG0208348 NrdF Ribonucleotide reductase, beta subunit [Nucleotide 100.0
PRK09614325 nrdF ribonucleotide-diphosphate reductase subunit beta; 100.0
PRK13966324 nrdF2 ribonucleotide-diphosphate reductase subunit beta 99.97
PRK13965337 ribonucleotide-diphosphate reductase subunit beta; Prov 99.96
KOG1567344 consensus 99.96
PRK13967322 nrdF1 ribonucleotide-diphosphate reductase subunit beta 99.95
cd01049288 RNRR2 Ribonucleotide Reductase, R2/beta subunit, ferrit 99.94
pfam00268281 Ribonuc_red_sm Ribonucleotide reductase, small chain. 99.88
cd07911280 RNRR2_Rv0233_like Ribonucleotide Reductase R2-like prot 99.5
PRK08326318 ribonucleotide-diphosphate reductase subunit beta; Vali 98.96
pfam11266219 DUF3066 Protein of unknown function (DUF3066). This fam 92.45
cd07911280 RNRR2_Rv0233_like Ribonucleotide Reductase R2-like prot 94.88
TIGR01647 835 ATPase-IIIA_H plasma-membrane proton-efflux P-type ATPa 90.54
>PRK07209 ribonucleotide-diphosphate reductase subunit beta; Validated Back     alignment and domain information
>PRK12759 bifunctional gluaredoxin/ribonucleoside-diphosphate reductase subunit beta; Provisional Back     alignment and domain information
>PRK09101 nrdB ribonucleotide-diphosphate reductase subunit beta; Reviewed Back     alignment and domain information
>PTZ00211 ribonucleotide reductase small subunit; Provisional Back     alignment and domain information
>COG0208 NrdF Ribonucleotide reductase, beta subunit [Nucleotide transport and metabolism] Back     alignment and domain information
>PRK09614 nrdF ribonucleotide-diphosphate reductase subunit beta; Reviewed Back     alignment and domain information
>PRK13966 nrdF2 ribonucleotide-diphosphate reductase subunit beta; Provisional Back     alignment and domain information
>PRK13965 ribonucleotide-diphosphate reductase subunit beta; Provisional Back     alignment and domain information
>KOG1567 consensus Back     alignment and domain information
>PRK13967 nrdF1 ribonucleotide-diphosphate reductase subunit beta; Provisional Back     alignment and domain information
>cd01049 RNRR2 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain Back     alignment and domain information
>pfam00268 Ribonuc_red_sm Ribonucleotide reductase, small chain Back     alignment and domain information
>cd07911 RNRR2_Rv0233_like Ribonucleotide Reductase R2-like protein, ferritin-like diiron-binding domain Back     alignment and domain information
>PRK08326 ribonucleotide-diphosphate reductase subunit beta; Validated Back     alignment and domain information
>pfam11266 DUF3066 Protein of unknown function (DUF3066) Back     alignment and domain information
>cd07911 RNRR2_Rv0233_like Ribonucleotide Reductase R2-like protein, ferritin-like diiron-binding domain Back     alignment and domain information
>TIGR01647 ATPase-IIIA_H plasma-membrane proton-efflux P-type ATPase; InterPro: IPR006534 These sequences represent the plasma membrane proton efflux P-type ATPase found in plants, fungi, protozoa, slime molds and archaea 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
Target125 ribonucleotide-diphosphate reductase subunit beta [Cand
2ani_A346 Crystal Structure Of The F127y Mutant Of Ribonucleo 4e-32
1syy_A346 Crystal Structure Of The R2 Subunit Of Ribonucleoti 5e-32
1h0n_A390 Cobalt Substitution Of Mouse R2 Ribonucleotide Redu 2e-26
2uw2_A332 Crystal Structure Of Human Ribonucleotide Reductase 2e-25
3hf1_A351 Crystal Structure Of Human P53r2 Length = 351 3e-25
1jk0_A419 Ribonucleotide Reductase Y2y4 Heterodimer Length = 1e-24
1smq_A399 Structure Of The Ribonucleotide Reductase Rnr2 Homo 2e-24
2p1i_A349 Plasmodium Yoelii Ribonucleotide Reductase Subunit 4e-24
2rcc_A346 Crystal Structure Of Putative Class I Ribonucleotid 1e-18
2vux_A326 Human Ribonucleotide Reductase, Subunit M2 B Length 4e-18
1jk0_B345 Ribonucleotide Reductase Y2y4 Heterodimer Length = 2e-15
2o1z_A311 Plasmodium Vivax Ribonucleotide Reductase Subunit R 4e-14
1rnr_A375 Autocatalytic Generation Of Dopa In The Engineered 6e-14
1mrr_A375 Substitution Of Manganese For Iron In Ribonucleotid 7e-14
1pj0_A375 Ribonucleotide Reductase R2-D84eW48F MUTANT SOAKED 8e-14
1piy_A375 Ribonucleotide Reductase R2 Soaked With Ferrous Ion 8e-14
1pim_A375 Dithionite Reduced E. Coli Ribonucleotide Reductase 8e-14
1rsr_A375 Azide Complex Of The Diferrous F208a Mutant R2 Subu 2e-13
2xof_A375 Ribonucleotide Reductase Y122no2y Modified R2 Subun 3e-13
1xik_A375 Ribonucleoside-Diphosphate Reductase 1 Beta Chain L 3e-13
1yfd_A375 Crystal Structure Of The Y122h Mutant Of Ribonucleo 3e-13
1biq_A375 Ribonucleoside-Diphosphate Reductase 1 Beta Chain M 1e-11
1pm2_A339 Crystal Structure Of Manganese Substituted R2-D84e 1e-11
1biq_B375 Ribonucleoside-Diphosphate Reductase 1 Beta Chain M 1e-11
1pfr_A340 Ribonucleoside-Diphosphate Reductase 1 Beta Chain L 4e-11
1av8_A340 Ribonucleotide Reductase R2 Subunit From E. Coli Le 4e-11
2av8_A340 Y122f Mutant Of Ribonucleotide Reductase From Esche 5e-11
2alx_A340 Ribonucleotide Reductase R2 From Escherichia Coli I 5e-11
1kgn_A329 R2f From Corynebacterium Ammoniagenes In Its Oxidis 5e-04
3n37_A319 Ribonucleotide Reductase Dimanganese(Ii)-Nrdf From 0.002
>gi|112489977|pdb|2ANI|A Chain A, Crystal Structure Of The F127y Mutant Of Ribonucleotide Reductase R2 From Chlamydia Trachomatis Length = 346 Back     alignment and structure
 Score =  140 bits (354), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 71/124 (57%), Positives = 91/124 (73%), Gaps = 1/124 (0%)

Query: 1   MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL 60
           +RDE++HLNFGID+IN IK ENP +WT E QQ+   ++  A  LEI YA + +P+G +GL
Sbjct: 224 LRDETIHLNFGIDLINGIKEENPEIWTPELQQEIVELIKRAVDLEIEYAQDCLPRGILGL 283

Query: 61  NAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGA 120
            A     Y+Q IA+RR  +IGL+P++ +T+NPFPWMSE IDL KEKNFFETRV EYQ  A
Sbjct: 284 RASMFIDYVQHIADRRLERIGLKPIY-HTKNPFPWMSETIDLNKEKNFFETRVIEYQHAA 342

Query: 121 ELKW 124
            L W
Sbjct: 343 SLTW 346


gi|51247460|pdb|1SYY|A Chain A, Crystal Structure Of The R2 Subunit Of Ribonucleotide Reductase From Chlamydia Trachomatis Length = 346 Back     alignment and structure
gi|22218698|pdb|1H0N|A Chain A, Cobalt Substitution Of Mouse R2 Ribonucleotide Reductase To Model The Reactive Diferrous State Length = 390 Back     alignment and structure
>gi|145580571|pdb|2UW2|A Chain A, Crystal Structure Of Human Ribonucleotide Reductase Subunit R2 Length = 332 Back     alignment and structure
gi|261278726|pdb|3HF1|A Chain A, Crystal Structure Of Human P53r2 Length = 351 Back     alignment and structure
>gi|15826569|pdb|1JK0|A Chain A, Ribonucleotide Reductase Y2y4 Heterodimer Length = 419 Back     alignment and structure
gi|52695523|pdb|1SMQ|A Chain A, Structure Of The Ribonucleotide Reductase Rnr2 Homodimer From Saccharomyces Cerevisiae Length = 399 Back     alignment and structure
gi|145580416|pdb|2P1I|A Chain A, Plasmodium Yoelii Ribonucleotide Reductase Subunit R2 (Py03671) Length = 349 Back     alignment and structure
>gi|158430770|pdb|2RCC|A Chain A, Crystal Structure Of Putative Class I Ribonucleotide Reductase (Np_241368.1) From Bacillus Halodurans At 1.90 A Resolution Length = 346 Back     alignment and structure
>gi|194319980|pdb|2VUX|A Chain A, Human Ribonucleotide Reductase, Subunit M2 B Length = 326 Back     alignment and structure
gi|15826570|pdb|1JK0|B Chain B, Ribonucleotide Reductase Y2y4 Heterodimer Length = 345 Back     alignment and structure
>gi|122921307|pdb|2O1Z|A Chain A, Plasmodium Vivax Ribonucleotide Reductase Subunit R2 (Pv086155) Length = 311 Back     alignment and structure
>gi|157879968|pdb|1RNR|A Chain A, Autocatalytic Generation Of Dopa In The Engineered Protein R2 F208y From Escherichia Coli Ribonucleotide Reductase And Crystal Structure Of The Dopa-208 Protein Length = 375 Back     alignment and structure
>gi|494379|pdb|1MRR|A Chain A, Substitution Of Manganese For Iron In Ribonucleotide Reductase From Escherichia Coli. Spectroscopic And Crystallographic Characterization Length = 375 Back     alignment and structure
>gi|42543287|pdb|1PJ0|A Chain A, Ribonucleotide Reductase R2-D84eW48F MUTANT SOAKED WITH Ferrous Ions At Neutral Ph Length = 375 Back     alignment and structure
>gi|42543283|pdb|1PIY|A Chain A, Ribonucleotide Reductase R2 Soaked With Ferrous Ion At Neutral Ph Length = 375 Back     alignment and structure
>gi|33358114|pdb|1PIM|A Chain A, Dithionite Reduced E. Coli Ribonucleotide Reductase R2 Subunit, D84e Mutant Length = 375 Back     alignment and structure
>gi|40889712|pdb|1RSR|A Chain A, Azide Complex Of The Diferrous F208a Mutant R2 Subunit Of Ribonucleotide Reductase Length = 375 Back     alignment and structure
>gi|304445703|pdb|2XOF|A Chain A, Ribonucleotide Reductase Y122no2y Modified R2 Subunit Of E. Coli Length = 375 Back     alignment and structure
>gi|1942079|pdb|1XIK|A Chain A, Ribonucleoside-Diphosphate Reductase 1 Beta Chain Length = 375 Back     alignment and structure
>gi|61680624|pdb|1YFD|A Chain A, Crystal Structure Of The Y122h Mutant Of Ribonucleotide Reductase R2 Protein From E. Coli Length = 375 Back     alignment and structure
>gi|4389291|pdb|1BIQ|A Chain A, Ribonucleoside-Diphosphate Reductase 1 Beta Chain Mutant E238a Length = 375 Back     alignment and structure
>gi|42543295|pdb|1PM2|A Chain A, Crystal Structure Of Manganese Substituted R2-D84e (D84e Mutant Of The R2 Subunit Of E. Coli Ribonucleotide Reductase) Length = 339 Back     alignment and structure
>gi|4389292|pdb|1BIQ|B Chain B, Ribonucleoside-Diphosphate Reductase 1 Beta Chain Mutant E238a Length = 375 Back     alignment and structure
>gi|1941986|pdb|1PFR|A Chain A, Ribonucleoside-Diphosphate Reductase 1 Beta Chain Length = 340 Back     alignment and structure
>gi|3891582|pdb|1AV8|A Chain A, Ribonucleotide Reductase R2 Subunit From E. Coli Length = 340 Back     alignment and structure
>gi|3891570|pdb|2AV8|A Chain A, Y122f Mutant Of Ribonucleotide Reductase From Escherichia Coli Length = 340 Back     alignment and structure
>gi|83754022|pdb|2ALX|A Chain A, Ribonucleotide Reductase R2 From Escherichia Coli In Space Group P6(1)22 Length = 340 Back     alignment and structure
>gi|18158911|pdb|1KGN|A Chain A, R2f From Corynebacterium Ammoniagenes In Its Oxidised, Fe Containing, Form Length = 329 Back     alignment and structure
gi|303325061|pdb|3N37|A Chain A, Ribonucleotide Reductase Dimanganese(Ii)-Nrdf From Escherichia Coli Length = 319 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target125 ribonucleotide-diphosphate reductase subunit beta [Cand
1syy_A346 Ribonucleoside-diphosphate reductase beta chain; DIIRON 9e-31
1h0o_A390 Ribonucleoside-diphosphate reductase; oxidoreductase, r 3e-26
3dhz_A329 Ribonucleotide reductase subunit R2F; metal free, hydro 4e-26
1jk0_A419 RNR Y2, ribonucleoside-diphosphate reductase small chai 4e-25
1mxr_A375 Ribonucleotide reductase R2; radical protein, DI iron, 2e-24
3n37_A319 Ribonucleoside-diphosphate reductase 2 subunit BE; ribo 2e-24
1jk0_B345 RNR Y4, ribonucleoside-diphosphate reductase small chai 1e-23
1r2f_A319 Protein (ribonucleotide reductase R2); nucleotide metab 6e-23
2p1i_A349 Ribonucleotide reductase, small chain; F222 twinning, p 8e-20
2rcc_A346 Ribonucleoside-diphosphate reductase subunit beta; NP_2 1e-19
3mjo_A296 Ribonucleotide reductase subunit R2F; Mn ribonucleotide 2e-15
2o1z_A311 Ribonucleotide reductase subunit R2; small subunit ribo 3e-15
3ee4_A323 Probable ribonucleoside-diphosphate reductase; manganes 2e-13
>1syy_A Ribonucleoside-diphosphate reductase beta chain; DIIRON, oxygen activation, iron coupled radical, immune evasion, replication; 1.70A {Chlamydia trachomatis} SCOP: a.25.1.2 PDB: 2ani_A Length = 346 Back     alignment and structure
 Score =  127 bits (319), Expect = 9e-31
 Identities = 71/124 (57%), Positives = 90/124 (72%), Gaps = 1/124 (0%)

Query: 1   MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL 60
           +RDE++HLNFGID+IN IK ENP +WT E QQ+   ++  A  LEI YA + +P+G +GL
Sbjct: 224 LRDETIHLNFGIDLINGIKEENPEIWTPELQQEIVELIKRAVDLEIEYAQDCLPRGILGL 283

Query: 61  NAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGA 120
            A     Y+Q IA+RR  +IGL+P++  T+NPFPWMSE IDL KEKNFFETRV EYQ  A
Sbjct: 284 RASMFIDYVQHIADRRLERIGLKPIYH-TKNPFPWMSETIDLNKEKNFFETRVIEYQHAA 342

Query: 121 ELKW 124
            L W
Sbjct: 343 SLTW 346


>1h0o_A Ribonucleoside-diphosphate reductase; oxidoreductase, ribonucleotide reductase, dinuclear metal-cluster; 2.2A {Mus musculus} SCOP: a.25.1.2 PDB: 1h0n_A 1w68_A 1w69_A 1xsm_A 2uw2_A 3hf1_A 2vux_A Length = 390 Back     alignment and structure
>3dhz_A Ribonucleotide reductase subunit R2F; metal free, hydrogen bond, metal binding protein; 1.63A {Corynebacterium ammoniagenes} SCOP: a.25.1.2 PDB: 1kgo_A 1kgp_A 1oqu_A 1kgn_A 1uzr_A* Length = 329 Back     alignment and structure
>1jk0_A RNR Y2, ribonucleoside-diphosphate reductase small chain 1; ribonucleotide reductase, oxidoreductase; 2.80A {Saccharomyces cerevisiae} SCOP: a.25.1.2 PDB: 1smq_A Length = 419 Back     alignment and structure
>1mxr_A Ribonucleotide reductase R2; radical protein, DI iron, oxidoreductase; 1.42A {Escherichia coli} SCOP: a.25.1.2 PDB: 1jpr_A 1jqc_A 1xik_A 1yfd_A 1piy_A 1r65_A 1biq_B* 1rsv_A 1piz_A 1piu_A 1pim_A 1rsr_A 1biq_A* 1rib_A 1mrr_A 1rnr_A* 1pj0_A 1pj1_A 1av8_A 1pfr_A ... Length = 375 Back     alignment and structure
>3n37_A Ribonucleoside-diphosphate reductase 2 subunit BE; ribonucleotide reductase, four-helix bundle, dimanganese CLU oxidoreductase; 1.65A {Escherichia coli} PDB: 3n38_A 3n39_B* 3n3a_B* 3n3b_B* 1r2f_A 2bq1_I* 2r2f_A Length = 319 Back     alignment and structure
>1jk0_B RNR Y4, ribonucleoside-diphosphate reductase small chain 2; ribonucleotide reductase, oxidoreductase; 2.80A {Saccharomyces cerevisiae} SCOP: a.25.1.2 PDB: 1sms_A Length = 345 Back     alignment and structure
>1r2f_A Protein (ribonucleotide reductase R2); nucleotide metabolism, oxidoreductase; 2.10A {Salmonella typhimurium} SCOP: a.25.1.2 PDB: 2bq1_I* 2r2f_A Length = 319 Back     alignment and structure
>2p1i_A Ribonucleotide reductase, small chain; F222 twinning, plasmodb PY03671, structural genomics consortium, SGC, oxidoreductase; 2.70A {Plasmodium yoelii yoelii str} Length = 349 Back     alignment and structure
>2rcc_A Ribonucleoside-diphosphate reductase subunit beta; NP_241368.1, putative class I ribonucleotide reductase, ribonucleotide reductase; HET: MSE PGE PG4; 1.90A {Bacillus halodurans c-125} Length = 346 Back     alignment and structure
>3mjo_A Ribonucleotide reductase subunit R2F; Mn ribonucleotide reductase, RNR, radical enzyme, split SIGN metallocofactor; 1.36A {Corynebacterium ammoniagenes} PDB: 1uzr_A* Length = 296 Back     alignment and structure
>2o1z_A Ribonucleotide reductase subunit R2; small subunit ribonucleotide reductase, oxidoreductase, DNA replication, iron, DIIRON, radical, R2 subunit; 2.40A {Plasmodium vivax} Length = 311 Back     alignment and structure
>3ee4_A Probable ribonucleoside-diphosphate reductase; manganese, iron, DIIRON, carboxylate, oxidase, ligand, cavity, monooxygenase; HET: MYR; 1.90A {Mycobacterium tuberculosis} Length = 323 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target125 ribonucleotide-diphosphate reductase subunit beta [Cand
1syy_A346 Ribonucleoside-diphosphate reductase beta chain; DIIRON 100.0
2rcc_A346 Ribonucleoside-diphosphate reductase subunit beta; NP_2 100.0
1mxr_A375 Ribonucleotide reductase R2; radical protein, DI iron, 100.0
1h0o_A390 Ribonucleoside-diphosphate reductase; oxidoreductase, r 99.98
3n37_A319 Ribonucleoside-diphosphate reductase 2 subunit BE; ribo 99.98
1jk0_A419 RNR Y2, ribonucleoside-diphosphate reductase small chai 99.97
2p1i_A349 Ribonucleotide reductase, small chain; F222 twinning, p 99.97
3dhz_A329 Ribonucleotide reductase subunit R2F; metal free, hydro 99.97
1jk0_B345 RNR Y4, ribonucleoside-diphosphate reductase small chai 99.96
3mjo_A296 Ribonucleotide reductase subunit R2F; Mn ribonucleotide 99.89
3ee4_A323 Probable ribonucleoside-diphosphate reductase; manganes 99.62
2o1z_A311 Ribonucleotide reductase subunit R2; small subunit ribo 99.9
2oc5_A244 Hypothetical protein; NP_895059.1, structural genomics, 92.88
>1syy_A Ribonucleoside-diphosphate reductase beta chain; DIIRON, oxygen activation, iron coupled radical, immune evasion, replication; 1.70A {Chlamydia trachomatis} SCOP: a.25.1.2 PDB: 2ani_A Back     alignment and structure
Probab=100.00  E-value=9.7e-38  Score=248.94  Aligned_cols=123  Identities=57%  Similarity=1.023  Sum_probs=119.7

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHC
Q ss_conf             94037899999999999996770003112299999999999999999857630876018899999999999999999985
Q gi|254780136|r    1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGLNAPSCEQYMQFIANRRCHQI   80 (125)
Q Consensus         1 ~RDE~lH~~~~~~l~~~l~~e~pe~~~~~~~~~i~~~~~eave~E~~~~~~~~~~~~~Gl~~~~~~~Yiky~an~rL~~l   80 (125)
                      +|||++|+.+++.+++++++|+|++++++++++|++|+.+||++|.+|++++|+.|++|||++++++||+|+||+||.+|
T Consensus       224 ~RDE~~H~~~~~~l~~~l~~e~~~~~~~~~~~~i~~l~~~ave~E~~~~~~~~~~~~~Gl~~~~~~~Yv~y~an~rL~~l  303 (346)
T 1syy_A          224 LRDETIHLNFGIDLINGIKEENPEIWTPELQQEIVELIKRAVDLEIEYAQDCLPRGILGLRASMFIDYVQHIADRRLERI  303 (346)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHCGGGCCHHHHHHHHHHHHHHHHHHHHHHHHHCSSCBTTBCHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHC
T ss_conf             14578899999999999985197875689999999999999999999999856588789999999999999999999977


Q ss_pred             CCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCHHHHHHHCCCCC
Q ss_conf             97878898788868999983466573213100333343065778
Q gi|254780136|r   81 GLEPLFKYTENPFPWMSEVIDLKKEKNFFETRVTEYQQGAELKW  124 (125)
Q Consensus        81 Gl~~~f~~~~nPl~W~~~~~~~~~~~nFFE~r~t~Y~k~~~~~~  124 (125)
                      |++|+|+. +||+|||++.+++++++||||+|||+|+|||+++|
T Consensus       304 G~~~~f~~-~nP~~w~~~~~~~~~~~nFFe~r~~~Y~k~~~~~~  346 (346)
T 1syy_A          304 GLKPIYHT-KNPFPWMSETIDLNKEKNFFETRVIEYQHAASLTW  346 (346)
T ss_dssp             TCCCSSCC-CCSCTTC----------------------------
T ss_pred             CCCCCCCC-CCCHHHHHHHHCCCCCCCCCCCCHHCCCCCCCCCC
T ss_conf             99998999-99637899863867776878897210454577889



>2rcc_A Ribonucleoside-diphosphate reductase subunit beta; NP_241368.1, putative class I ribonucleotide reductase, ribonucleotide reductase; HET: MSE PGE PG4; 1.90A {Bacillus halodurans c-125} Back     alignment and structure
>1mxr_A Ribonucleotide reductase R2; radical protein, DI iron, oxidoreductase; 1.42A {Escherichia coli} SCOP: a.25.1.2 PDB: 1jpr_A 1jqc_A 1xik_A 1yfd_A 1piy_A 1r65_A 1biq_B* 1rsv_A 1piz_A 1piu_A 1pim_A 1rsr_A 1biq_A* 1rib_A 1mrr_A 1rnr_A* 1pj0_A 1pj1_A 1av8_A 1pfr_A ... Back     alignment and structure
>1h0o_A Ribonucleoside-diphosphate reductase; oxidoreductase, ribonucleotide reductase, dinuclear metal-cluster; 2.2A {Mus musculus} SCOP: a.25.1.2 PDB: 1h0n_A 1w68_A 1w69_A 1xsm_A 2uw2_A 3hf1_A 2vux_A Back     alignment and structure
>3n37_A Ribonucleoside-diphosphate reductase 2 subunit BE; ribonucleotide reductase, four-helix bundle, dimanganese CLU oxidoreductase; 1.65A {Escherichia coli} PDB: 3n38_A 3n39_B* 3n3a_B* 3n3b_B* 1r2f_A 2bq1_I* 2r2f_A Back     alignment and structure
>1jk0_A RNR Y2, ribonucleoside-diphosphate reductase small chain 1; ribonucleotide reductase, oxidoreductase; 2.80A {Saccharomyces cerevisiae} SCOP: a.25.1.2 PDB: 1smq_A Back     alignment and structure
>2p1i_A Ribonucleotide reductase, small chain; F222 twinning, plasmodb PY03671, structural genomics consortium, SGC, oxidoreductase; 2.70A {Plasmodium yoelii yoelii str} Back     alignment and structure
>3dhz_A Ribonucleotide reductase subunit R2F; metal free, hydrogen bond, metal binding protein; 1.63A {Corynebacterium ammoniagenes} SCOP: a.25.1.2 PDB: 1kgo_A 1kgp_A 1oqu_A 1kgn_A 1uzr_A* Back     alignment and structure
>1jk0_B RNR Y4, ribonucleoside-diphosphate reductase small chain 2; ribonucleotide reductase, oxidoreductase; 2.80A {Saccharomyces cerevisiae} SCOP: a.25.1.2 PDB: 1sms_A Back     alignment and structure
>3mjo_A Ribonucleotide reductase subunit R2F; Mn ribonucleotide reductase, RNR, radical enzyme, split SIGN metallocofactor; 1.36A {Corynebacterium ammoniagenes} PDB: 1uzr_A* Back     alignment and structure
>3ee4_A Probable ribonucleoside-diphosphate reductase; manganese, iron, DIIRON, carboxylate, oxidase, ligand, cavity, monooxygenase; HET: MYR; 1.90A {Mycobacterium tuberculosis} Back     alignment and structure
>2o1z_A Ribonucleotide reductase subunit R2; small subunit ribonucleotide reductase, oxidoreductase, DNA replication, iron, DIIRON, radical, R2 subunit; 2.40A {Plasmodium vivax} Back     alignment and structure
>2oc5_A Hypothetical protein; NP_895059.1, structural genomics, joint center for structural genomics, JCSG, protein structure initiative; HET: UNL; 1.68A {Prochlorococcus marinus str} SCOP: a.25.1.6 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 125 ribonucleotide-diphosphate reductase subunit beta [Cand
d1syya_317 a.25.1.2 (A:) Ribonucleotide reductase R2 {Chlamydia tr 2e-21
d1mxra_339 a.25.1.2 (A:) Ribonucleotide reductase R2 {Escherichia 2e-17
d1jk0a_334 a.25.1.2 (A:) Ribonucleotide reductase R2 {Baker's yeas 5e-16
d1w68a_281 a.25.1.2 (A:) Ribonucleotide reductase R2 {Mouse (Mus m 4e-13
d3dhza1284 a.25.1.2 (A:14-297) Ribonucleotide reductase R2 {Coryne 4e-11
d1jk0b_285 a.25.1.2 (B:) Ribonucleotide reductase R2 {Baker's yeas 4e-11
d1r2fa_283 a.25.1.2 (A:) Ribonucleotide reductase R2 {Salmonella t 4e-10
>d1syya_ a.25.1.2 (A:) Ribonucleotide reductase R2 {Chlamydia trachomatis [TaxId: 813]} Length = 317 Back     information, alignment and structure

class: All alpha proteins
fold: Ferritin-like
superfamily: Ferritin-like
family: Ribonucleotide reductase-like
domain: Ribonucleotide reductase R2
species: Chlamydia trachomatis [TaxId: 813]
 Score = 94.8 bits (235), Expect = 2e-21
 Identities = 50/96 (52%), Positives = 69/96 (71%), Gaps = 1/96 (1%)

Query: 1   MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL 60
           +RDE++HLNFGID+IN IK ENP +WT E QQ+   ++  A  LEI YA + +P+G +GL
Sbjct: 223 LRDETIHLNFGIDLINGIKEENPEIWTPELQQEIVELIKRAVDLEIEYAQDCLPRGILGL 282

Query: 61  NAPSCEQYMQFIANRRCHQIGLEPLFKYTENPFPWM 96
            A     Y+Q IA+RR  +IGL+P++  T+NPFPWM
Sbjct: 283 RASMFIDYVQHIADRRLERIGLKPIYH-TKNPFPWM 317


>d1mxra_ a.25.1.2 (A:) Ribonucleotide reductase R2 {Escherichia coli [TaxId: 562]} Length = 339 Back     information, alignment and structure
>d1jk0a_ a.25.1.2 (A:) Ribonucleotide reductase R2 {Baker's yeast (Saccharomyces cerevisiae), Y2 [TaxId: 4932]} Length = 334 Back     information, alignment and structure
>d1w68a_ a.25.1.2 (A:) Ribonucleotide reductase R2 {Mouse (Mus musculus) [TaxId: 10090]} Length = 281 Back     information, alignment and structure
>d3dhza1 a.25.1.2 (A:14-297) Ribonucleotide reductase R2 {Corynebacterium ammoniagenes [TaxId: 1697]} Length = 284 Back     information, alignment and structure
>d1jk0b_ a.25.1.2 (B:) Ribonucleotide reductase R2 {Baker's yeast (Saccharomyces cerevisiae), Y4 [TaxId: 4932]} Length = 285 Back     information, alignment and structure
>d1r2fa_ a.25.1.2 (A:) Ribonucleotide reductase R2 {Salmonella typhimurium [TaxId: 90371]} Length = 283 Back     information, alignment and structure

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

IdentityAlignment graphLength Definition Probability
Target125 ribonucleotide-diphosphate reductase subunit beta [Cand
d1syya_317 Ribonucleotide reductase R2 {Chlamydia trachomatis [Tax 99.95
d1mxra_339 Ribonucleotide reductase R2 {Escherichia coli [TaxId: 5 99.94
d1jk0a_334 Ribonucleotide reductase R2 {Baker's yeast (Saccharomyc 99.91
d3dhza1284 Ribonucleotide reductase R2 {Corynebacterium ammoniagen 99.87
d1r2fa_283 Ribonucleotide reductase R2 {Salmonella typhimurium [Ta 99.84
d1w68a_281 Ribonucleotide reductase R2 {Mouse (Mus musculus) [TaxI 99.83
d1jk0b_285 Ribonucleotide reductase R2 {Baker's yeast (Saccharomyc 99.79
d2oc5a1222 Hypothetical protein PMT1231 {Prochlorococcus marinus [ 93.32
>d1syya_ a.25.1.2 (A:) Ribonucleotide reductase R2 {Chlamydia trachomatis [TaxId: 813]} Back     information, alignment and structure
class: All alpha proteins
fold: Ferritin-like
superfamily: Ferritin-like
family: Ribonucleotide reductase-like
domain: Ribonucleotide reductase R2
species: Chlamydia trachomatis [TaxId: 813]
Probab=99.95  E-value=1.5e-27  Score=185.58  Aligned_cols=95  Identities=52%  Similarity=0.983  Sum_probs=92.4

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHC
Q ss_conf             94037899999999999996770003112299999999999999999857630876018899999999999999999985
Q gi|254780136|r    1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGLNAPSCEQYMQFIANRRCHQI   80 (125)
Q Consensus         1 ~RDE~lH~~~~~~l~~~l~~e~pe~~~~~~~~~i~~~~~eave~E~~~~~~~~~~~~~Gl~~~~~~~Yiky~an~rL~~l   80 (125)
                      .|||++|+.|++.|++.+++|+|+++++++.++|++|+++||++|++|++++|+.|++|||++++++||+|+||+||.+|
T Consensus       223 ~RDE~lH~~f~~~l~~~l~~e~~e~~~~~~~~~i~el~~eav~~E~~~~~~~~~~~~~Gl~~~~l~~Yv~y~an~~L~~L  302 (317)
T d1syya_         223 LRDETIHLNFGIDLINGIKEENPEIWTPELQQEIVELIKRAVDLEIEYAQDCLPRGILGLRASMFIDYVQHIADRRLERI  302 (317)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHCGGGCCHHHHHHHHHHHHHHHHHHHHHHHHHCSSCBTTBCHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHC
T ss_conf             81188786699999999855059998633599999999999999999999983798789999999999999999999977


Q ss_pred             CCCCCCCCCCCCHHHH
Q ss_conf             9787889878886899
Q gi|254780136|r   81 GLEPLFKYTENPFPWM   96 (125)
Q Consensus        81 Gl~~~f~~~~nPl~W~   96 (125)
                      |++|+|++ +||+|||
T Consensus       303 G~~~~f~~-~NP~~wm  317 (317)
T d1syya_         303 GLKPIYHT-KNPFPWM  317 (317)
T ss_dssp             TCCCSSCC-CCSCTTC
T ss_pred             CCCCCCCC-CCCCCCC
T ss_conf             99999989-9998979



>d1mxra_ a.25.1.2 (A:) Ribonucleotide reductase R2 {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1jk0a_ a.25.1.2 (A:) Ribonucleotide reductase R2 {Baker's yeast (Saccharomyces cerevisiae), Y2 [TaxId: 4932]} Back     information, alignment and structure
>d3dhza1 a.25.1.2 (A:14-297) Ribonucleotide reductase R2 {Corynebacterium ammoniagenes [TaxId: 1697]} Back     information, alignment and structure
>d1r2fa_ a.25.1.2 (A:) Ribonucleotide reductase R2 {Salmonella typhimurium [TaxId: 90371]} Back     information, alignment and structure
>d1w68a_ a.25.1.2 (A:) Ribonucleotide reductase R2 {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1jk0b_ a.25.1.2 (B:) Ribonucleotide reductase R2 {Baker's yeast (Saccharomyces cerevisiae), Y4 [TaxId: 4932]} Back     information, alignment and structure
>d2oc5a1 a.25.1.6 (A:20-241) Hypothetical protein PMT1231 {Prochlorococcus marinus [TaxId: 1219]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 125 ribonucleotide-diphosphate reductase subunit beta
2rcc_A_150-346197 (A:150-346) Ribonucleoside-diphosphate reductase s 3e-28
1r2f_A_129-319191 (A:129-319) Protein (ribonucleotide reductase R2); 5e-27
1syy_A_346 (A:) Ribonucleoside-diphosphate reductase beta cha 4e-26
3dhz_A_139-329191 (A:139-329) Ribonucleotide reductase subunit R2F; 5e-26
1jk0_B_147-345199 (B:147-345) RNR Y4, ribonucleoside-diphosphate red 4e-24
1jk0_A_1-103_228-419295 (A:1-103,A:228-419) RNR Y2, ribonucleoside-diphosp 7e-24
1h0o_A_219-390172 (A:219-390) Ribonucleoside-diphosphate reductase; 5e-23
1mxr_A_375 (A:) Ribonucleotide reductase R2; radical protein, 1e-22
2p1i_A_162-349188 (A:162-349) Ribonucleotide reductase, small chain; 2e-22
2o1z_A_161-311151 (A:161-311) Ribonucleotide reductase subunit R2; s 1e-18
3ee4_A_323 (A:) Probable ribonucleoside-diphosphate reductase 3e-17
3chh_A_336 (A:) P-aminobenzoate N-oxygenase; DI-iron oxygenas 8e-11
>2rcc_A (A:150-346) Ribonucleoside-diphosphate reductase subunit beta; NP_241368.1, putative class I ribonucleotide reductase, ribonucleotide reductase; HET: MSE PGE PG4; 1.90A {Bacillus halodurans c-125}Length = 197 Back     alignment and structure
 Score =  118 bits (296), Expect = 3e-28
 Identities = 38/128 (29%), Positives = 63/128 (49%), Gaps = 3/128 (2%)

Query: 1   MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGL 60
            RDE LH+    ++  ++ +E P L T+E +   +T L +A  LE  +    +     G+
Sbjct: 68  NRDEQLHVYLFTNIFKELLVEFPELNTEETKTFVKTTLXKAADLEKDWFRYIIGDKIPGI 127

Query: 61  NAPSCEQYMQFIANRRCHQIGLEPLFK-YTENPFPWMSEVIDLKKEK-NFFETRVTEYQQ 118
           N    E Y+ FIAN+R  Q+G E  +     NP  W+    D+   K +FFE +  +Y +
Sbjct: 128 NPEDXETYISFIANKRAVQLGXEKPYPEIKHNPXKWIRAYEDVNSGKSDFFEQKSRQYAK 187

Query: 119 G-AELKWD 125
             A+  +D
Sbjct: 188 VSADNGFD 195


>1r2f_A (A:129-319) Protein (ribonucleotide reductase R2); nucleotide metabolism, oxidoreductase; 2.10A {Salmonella typhimurium}Length = 191 Back     alignment and structure
>1syy_A (A:) Ribonucleoside-diphosphate reductase beta chain; DIIRON, oxygen activation, iron coupled radical, immune evasion, replication; 1.70A {Chlamydia trachomatis}Length = 346 Back     alignment and structure
>3dhz_A (A:139-329) Ribonucleotide reductase subunit R2F; metal free, hydrogen bond, metal binding protein; 1.63A {Corynebacterium ammoniagenes}Length = 191 Back     alignment and structure
>1jk0_B (B:147-345) RNR Y4, ribonucleoside-diphosphate reductase small chain 2; ribonucleotide reductase, oxidoreductase; 2.80A {Saccharomyces cerevisiae}Length = 199 Back     alignment and structure
>1jk0_A (A:1-103,A:228-419) RNR Y2, ribonucleoside-diphosphate reductase small chain 1; ribonucleotide reductase, oxidoreductase; 2.80A {Saccharomyces cerevisiae}Length = 295 Back     alignment and structure
>1h0o_A (A:219-390) Ribonucleoside-diphosphate reductase; oxidoreductase, ribonucleotide reductase, dinuclear metal-cluster; 2.2A {Mus musculus}Length = 172 Back     alignment and structure
>1mxr_A (A:) Ribonucleotide reductase R2; radical protein, DI iron, oxidoreductase; 1.42A {Escherichia coli}Length = 375 Back     alignment and structure
>2p1i_A (A:162-349) Ribonucleotide reductase, small chain; F222 twinning, plasmodb PY03671, structural genomics consortium, SGC, oxidoreductase; 2.70A {Plasmodium yoelii yoelii str}Length = 188 Back     alignment and structure
>2o1z_A (A:161-311) Ribonucleotide reductase subunit R2; small subunit ribonucleotide reductase, oxidoreductase, DNA replication, iron, DIIRON, radical, R2 subunit; 2.40A {Plasmodium vivax}Length = 151 Back     alignment and structure
>3ee4_A (A:) Probable ribonucleoside-diphosphate reductase; manganese, iron, DIIRON, carboxylate, oxidase, ligand, cavity, monooxygenase; HET: MYR; 1.90A {Mycobacterium tuberculosis}Length = 323 Back     alignment and structure
>3chh_A (A:) P-aminobenzoate N-oxygenase; DI-iron oxygenase, oxidoreductase; 2.00A {Streptomyces thioluteus} PDB: 3chi_A 3cht_A* 3chu_A 2jcd_ALength = 336 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target125 ribonucleotide-diphosphate reductase subunit beta [Cand
2rcc_A_150-346197 Ribonucleoside-diphosphate reductase subunit beta; 100.0
1syy_A_346 Ribonucleoside-diphosphate reductase beta chain; D 100.0
1r2f_A_129-319191 Protein (ribonucleotide reductase R2); nucleotide 99.97
3dhz_A_139-329191 Ribonucleotide reductase subunit R2F; metal free, 99.97
1jk0_A_1-103_228-419295 RNR Y2, ribonucleoside-diphosphate reductase small 99.97
2p1i_A_162-349188 Ribonucleotide reductase, small chain; F222 twinni 99.97
1h0o_A_219-390172 Ribonucleoside-diphosphate reductase; oxidoreducta 99.97
1jk0_B_147-345199 RNR Y4, ribonucleoside-diphosphate reductase small 99.97
1mxr_A_375 Ribonucleotide reductase R2; radical protein, DI i 99.97
3ee4_A_323 Probable ribonucleoside-diphosphate reductase; man 99.92
3chh_A_336 P-aminobenzoate N-oxygenase; DI-iron oxygenase, ox 98.76
2o1z_A_161-311151 Ribonucleotide reductase subunit R2; small subunit 99.9
2oc5_A_244 Hypothetical protein; NP_895059.1, structural geno 92.99
>2rcc_A (A:150-346) Ribonucleoside-diphosphate reductase subunit beta; NP_241368.1, putative class I ribonucleotide reductase, ribonucleotide reductase; HET: MSE PGE PG4; 1.90A {Bacillus halodurans c-125} Back     alignment and structure
Probab=100.00  E-value=2.7e-35  Score=235.04  Aligned_cols=125  Identities=29%  Similarity=0.491  Sum_probs=117.9

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHC
Q ss_conf             94037899999999999996770003112299999999999999999857630876018899999999999999999985
Q gi|254780136|r    1 MRDESLHLNFGIDVINQIKIENPHLWTKEFQQKSRTMLHEATLLEIAYAHETMPKGFVGLNAPSCEQYMQFIANRRCHQI   80 (125)
Q Consensus         1 ~RDE~lH~~~~~~l~~~l~~e~pe~~~~~~~~~i~~~~~eave~E~~~~~~~~~~~~~Gl~~~~~~~Yiky~an~rL~~l   80 (125)
                      .|||++|+.+++.+|+++++|+|+.++++++++|++|+++||++|++|++++++.+++|++++.+++||+|+||+||++|
T Consensus        68 ~RDE~~H~~~~~~l~~~l~~e~~~~~~~~~~~~i~~l~~eave~E~~~~~~~~~~~~~g~~~~~~~~yiky~an~~L~~l  147 (197)
T 2rcc_A           68 NRDEQLHVYLFTNIFKELLVEFPELNTEETKTFVKTTLXKAADLEKDWFRYIIGDKIPGINPEDXETYISFIANKRAVQL  147 (197)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHCGGGCSHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSTTCCHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHC
T ss_conf             74488999889999998754066321001489999999999999999999970676579889999999999999999977


Q ss_pred             CCCCCCCC-CCCCHHHHHHHHCCC-CCCCCCCCCHHHHHHHCCC-CCC
Q ss_conf             97878898-788868999983466-5732131003333430657-789
Q gi|254780136|r   81 GLEPLFKY-TENPFPWMSEVIDLK-KEKNFFETRVTEYQQGAEL-KWD  125 (125)
Q Consensus        81 Gl~~~f~~-~~nPl~W~~~~~~~~-~~~nFFE~r~t~Y~k~~~~-~~D  125 (125)
                      |++|+|++ .+||+|||..+++.. +++||||+|+|+|++|+.. +||
T Consensus       148 G~~~~f~~~~~np~~w~~~~~~~~~~~~nFFe~~~~~Y~~~~~~~~~d  195 (197)
T 2rcc_A          148 GXEKPYPEIKHNPXKWIRAYEDVNSGKSDFFEQKSRQYAKVSADNGFD  195 (197)
T ss_dssp             TCCCSCTTCCSCSCTTC-------------------------------
T ss_pred             CCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCHHHHHHCCCCCCCC
T ss_conf             999899987799588999865347653588888768751066778866



>1syy_A (A:) Ribonucleoside-diphosphate reductase beta chain; DIIRON, oxygen activation, iron coupled radical, immune evasion, replication; 1.70A {Chlamydia trachomatis} Back     alignment and structure
>1r2f_A (A:129-319) Protein (ribonucleotide reductase R2); nucleotide metabolism, oxidoreductase; 2.10A {Salmonella typhimurium} Back     alignment and structure
>3dhz_A (A:139-329) Ribonucleotide reductase subunit R2F; metal free, hydrogen bond, metal binding protein; 1.63A {Corynebacterium ammoniagenes} Back     alignment and structure
>1jk0_A (A:1-103,A:228-419) RNR Y2, ribonucleoside-diphosphate reductase small chain 1; ribonucleotide reductase, oxidoreductase; 2.80A {Saccharomyces cerevisiae} Back     alignment and structure
>2p1i_A (A:162-349) Ribonucleotide reductase, small chain; F222 twinning, plasmodb PY03671, structural genomics consortium, SGC, oxidoreductase; 2.70A {Plasmodium yoelii yoelii str} Back     alignment and structure
>1h0o_A (A:219-390) Ribonucleoside-diphosphate reductase; oxidoreductase, ribonucleotide reductase, dinuclear metal-cluster; 2.2A {Mus musculus} Back     alignment and structure
>1jk0_B (B:147-345) RNR Y4, ribonucleoside-diphosphate reductase small chain 2; ribonucleotide reductase, oxidoreductase; 2.80A {Saccharomyces cerevisiae} Back     alignment and structure
>1mxr_A (A:) Ribonucleotide reductase R2; radical protein, DI iron, oxidoreductase; 1.42A {Escherichia coli} Back     alignment and structure
>3ee4_A (A:) Probable ribonucleoside-diphosphate reductase; manganese, iron, DIIRON, carboxylate, oxidase, ligand, cavity, monooxygenase; HET: MYR; 1.90A {Mycobacterium tuberculosis} Back     alignment and structure
>3chh_A (A:) P-aminobenzoate N-oxygenase; DI-iron oxygenase, oxidoreductase; 2.00A {Streptomyces thioluteus} PDB: 3chi_A 3cht_A* 3chu_A 2jcd_A Back     alignment and structure
>2o1z_A (A:161-311) Ribonucleotide reductase subunit R2; small subunit ribonucleotide reductase, oxidoreductase, DNA replication, iron, DIIRON, radical, R2 subunit; 2.40A {Plasmodium vivax} Back     alignment and structure
>2oc5_A (A:) Hypothetical protein; NP_895059.1, structural genomics, joint center for structural genomics, JCSG, protein structure initiative; HET: UNL; 1.68A {Prochlorococcus marinus str} Back     alignment and structure