254780239

254780239

30S ribosomal protein S13

GeneID in NCBI database:8209220Locus tag:CLIBASIA_00620
Protein GI in NCBI database:254780239Protein Accession:YP_003064652.1
Gene range:-(131308, 131676)Protein Length:122aa
Gene description:30S ribosomal protein S13
COG prediction:[J] Ribosomal protein S13
KEGG prediction:rpsM; 30S ribosomal protein S13; K02952 small subunit ribosomal protein S13
SEED prediction:SSU ribosomal protein S13p (S18e)
Pathway involved in KEGG:Ribosome [PATH:las03010]
Subsystem involved in SEED:Ribosome SSU bacterial
sequencesequence profile

Prediction of Local Sequence Properties

SourceSummaryResult
scaler
NCBI Databasesequence
PSIPREDsecondary structure
SSPROsecondary structure
DISEMBLcoil and loop
DISEMBLflexible loop
SEGlow complexity
DISOPREDdisordered
DISEMBLmissing residues
DISPROdisordered
TMHMMnone TM-Helix
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--
MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQDYQVEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVRGQRTHTNARTRKKFGKGGVARKR
ccEEEccccccccEEEEEEEEEEEccHHHHHHHHHHccccHHHEHHHccHHHHHHHHHHHHcccEEcHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccc
ccEEccccccccccEEEEEEEEcccccHHHHHHHHHHcccHHHHHHcccHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHcccccccHccccccccccccccccccccccccHccccc
mariagvnipRAKRVVRALCYIHgigfkssqdicnklaipperrvhQLVESEVIQIRQAIEQDYQVEGDLRRTVAMNIKRLMDLGcyrglrhrrglpvrgqrthtnartrkkfgkggvarkr
mariagvniprakrVVRALCYIHGigfkssqdICNKLAIPPERRVHQLVESEVIQIRQAIeqdyqvegdlRRTVAMNIKRLMDLGcyrglrhrrglpvrgqrthtnartrkkfgkggvarkr
MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQDYQVEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVRGQRTHTNARTRKKFGKGGVARKR
MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQDYQVEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVRGQRTHTNARTRKK**********
MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQDYQVEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVRGQRTHTNART*************
*ARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQDYQVEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVRG**********************
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
iiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQDYQVEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVRGQRTHTNARTRKKFGKGGVARKR
MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQDYQVEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVRGQRTHTNARTRKKFGKGGVARKR
MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQDYQVEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVRGQRTHTNARTRKKFGKGGVARKR

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

Original result of BLAST against C. L. asiaticus genome

No hits with e-value below 0.05

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

Original result of PSI-BLAST first 2 iterations

IdentityAlignment graphLength Definition Round E-value
Target122 30S ribosomal protein S13 [Candidatus Liberibacter asia
315122796123 30S ribosomal protein S13 [Candidatus Liberibacter sola 1 8e-52
241204187122 30S ribosomal protein S13 [Rhizobium leguminosarum bv. 1 7e-46
190891377122 30S ribosomal protein S13 [Rhizobium etli CIAT 652] Len 1 1e-45
209548957122 30S ribosomal protein S13 [Rhizobium leguminosarum bv. 1 1e-45
116251562122 30S ribosomal protein S13 [Rhizobium leguminosarum bv. 1 2e-45
159184981122 30S ribosomal protein S13 [Agrobacterium tumefaciens st 1 3e-45
150396229122 30S ribosomal protein S13 [Sinorhizobium medicae WSM419 1 3e-45
86357327122 30S ribosomal protein S13 [Rhizobium etli CFN 42] Lengt 1 4e-45
15965131122 30S ribosomal protein S13 [Sinorhizobium meliloti 1021] 1 4e-45
325293314122 30S ribosomal protein S13 [Agrobacterium sp. H13-3] Len 1 1e-44
>gi|315122796|ref|YP_004063285.1| 30S ribosomal protein S13 [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 123 Back     alignment and organism information
 Score =  206 bits (524), Expect = 8e-52,   Method: Compositional matrix adjust.
 Identities = 101/117 (86%), Positives = 104/117 (88%)

Query: 1   MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI 60
           MARIAGVNIP  KRVVRALCYIHGIGFKSSQDICNKL I PERRVH LVESE+I+IRQAI
Sbjct: 1   MARIAGVNIPSTKRVVRALCYIHGIGFKSSQDICNKLGISPERRVHHLVESEIIKIRQAI 60

Query: 61  EQDYQVEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVRGQRTHTNARTRKKFGKGG 117
           EQ YQVEGDLRR   MNIKRLMDLGCYRGLRHRR LPVRGQRT TNA TRK+ GKGG
Sbjct: 61  EQTYQVEGDLRRMTVMNIKRLMDLGCYRGLRHRRNLPVRGQRTRTNACTRKRSGKGG 117



Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|241204187|ref|YP_002975283.1| 30S ribosomal protein S13 [Rhizobium leguminosarum bv. trifolii WSM1325] Length = 122 Back     alignment and organism information
>gi|190891377|ref|YP_001977919.1| 30S ribosomal protein S13 [Rhizobium etli CIAT 652] Length = 122 Back     alignment and organism information
>gi|209548957|ref|YP_002280874.1| 30S ribosomal protein S13 [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 122 Back     alignment and organism information
>gi|116251562|ref|YP_767400.1| 30S ribosomal protein S13 [Rhizobium leguminosarum bv. viciae 3841] Length = 122 Back     alignment and organism information
>gi|159184981|ref|NP_354901.2| 30S ribosomal protein S13 [Agrobacterium tumefaciens str. C58] Length = 122 Back     alignment and organism information
>gi|150396229|ref|YP_001326696.1| 30S ribosomal protein S13 [Sinorhizobium medicae WSM419] Length = 122 Back     alignment and organism information
>gi|86357327|ref|YP_469219.1| 30S ribosomal protein S13 [Rhizobium etli CFN 42] Length = 122 Back     alignment and organism information
>gi|15965131|ref|NP_385484.1| 30S ribosomal protein S13 [Sinorhizobium meliloti 1021] Length = 122 Back     alignment and organism information
>gi|325293314|ref|YP_004279178.1| 30S ribosomal protein S13 [Agrobacterium sp. H13-3] Length = 122 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

Original result of RPS-BLAST against CDD database part I

Original result of RPS-BLASTagainst CDD database part II

IdentityAlignment graphLength Definition E-value
Target122 30S ribosomal protein S13 [Candidatus Liberibacter asia
PRK05179122 PRK05179, rpsM, 30S ribosomal protein S13; Validated 7e-52
TIGR03631113 TIGR03631, bact_S13, 30S ribosomal protein S13 4e-46
CHL00137122 CHL00137, rps13, ribosomal protein S13; Validated 7e-36
pfam00416106 pfam00416, Ribosomal_S13, Ribosomal protein S13/S18 8e-29
PRK04053149 PRK04053, rps13p, 30S ribosomal protein S13P; Reviewed 9e-16
TIGR03629144 TIGR03629, arch_S13P, archaeal ribosomal protein S13P 2e-15
KOG3311152 KOG3311, KOG3311, KOG3311, Ribosomal protein S18 [Trans 1e-11
PTZ00134154 PTZ00134, PTZ00134, 40S ribosomal protein S18; Provisio 2e-06
COG0099121 COG0099, RpsM, Ribosomal protein S13 [Translation, ribo 4e-38
>gnl|CDD|179955 PRK05179, rpsM, 30S ribosomal protein S13; Validated Back     alignment and domain information
>gnl|CDD|163364 TIGR03631, bact_S13, 30S ribosomal protein S13 Back     alignment and domain information
>gnl|CDD|177059 CHL00137, rps13, ribosomal protein S13; Validated Back     alignment and domain information
>gnl|CDD|144128 pfam00416, Ribosomal_S13, Ribosomal protein S13/S18 Back     alignment and domain information
>gnl|CDD|179731 PRK04053, rps13p, 30S ribosomal protein S13P; Reviewed Back     alignment and domain information
>gnl|CDD|132668 TIGR03629, arch_S13P, archaeal ribosomal protein S13P Back     alignment and domain information
>gnl|CDD|38521 KOG3311, KOG3311, KOG3311, Ribosomal protein S18 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|185469 PTZ00134, PTZ00134, 40S ribosomal protein S18; Provisional Back     alignment and domain information
>gnl|CDD|30448 COG0099, RpsM, Ribosomal protein S13 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

Original result of HHsearch against CDD database

IdentityAlignment graphLength Definition Probability
Target 122 30S ribosomal protein S13 [Candidatus Liberibacter asia
CHL00137122 rps13 ribosomal protein S13; Validated 100.0
PRK05179122 rpsM 30S ribosomal protein S13; Validated 100.0
COG0099121 RpsM Ribosomal protein S13 [Translation, ribosomal stru 100.0
PRK04053149 rps13p 30S ribosomal protein S13P; Reviewed 100.0
PTZ00134154 40S ribosomal protein S18; Provisional 100.0
TIGR03629144 arch_S13P archaeal ribosomal protein S13P. This model d 100.0
TIGR03631113 bact_S13 30S ribosomal protein S13. This model describe 100.0
pfam00416106 Ribosomal_S13 Ribosomal protein S13/S18. This family in 100.0
KOG3311152 consensus 99.96
PRK13945283 formamidopyrimidine-DNA glycosylase; Provisional 96.8
pfam0683193 H2TH Formamidopyrimidine-DNA glycosylase H2TH domain. F 96.42
PRK01103273 formamidopyrimidine-DNA glycosylase; Validated 96.37
PRK10445263 endonuclease VIII; Provisional 96.13
TIGR00577292 fpg formamidopyrimidine-DNA glycosylase; InterPro: IPR0 95.35
PRK04184 533 DNA topoisomerase VI subunit B; Validated 94.91
COG0266273 Nei Formamidopyrimidine-DNA glycosylase [DNA replicatio 94.13
pfam05833 447 FbpA Fibronectin-binding protein A N-terminus (FbpA). T 93.04
>CHL00137 rps13 ribosomal protein S13; Validated Back     alignment and domain information
>PRK05179 rpsM 30S ribosomal protein S13; Validated Back     alignment and domain information
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed Back     alignment and domain information
>PTZ00134 40S ribosomal protein S18; Provisional Back     alignment and domain information
>TIGR03629 arch_S13P archaeal ribosomal protein S13P Back     alignment and domain information
>TIGR03631 bact_S13 30S ribosomal protein S13 Back     alignment and domain information
>pfam00416 Ribosomal_S13 Ribosomal protein S13/S18 Back     alignment and domain information
>KOG3311 consensus Back     alignment and domain information
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional Back     alignment and domain information
>pfam06831 H2TH Formamidopyrimidine-DNA glycosylase H2TH domain Back     alignment and domain information
>PRK01103 formamidopyrimidine-DNA glycosylase; Validated Back     alignment and domain information
>PRK10445 endonuclease VIII; Provisional Back     alignment and domain information
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase; InterPro: IPR000191 Formamidopyrimidine-DNA glycosylase (3 Back     alignment and domain information
>PRK04184 DNA topoisomerase VI subunit B; Validated Back     alignment and domain information
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair] Back     alignment and domain information
>pfam05833 FbpA Fibronectin-binding protein A N-terminus (FbpA) 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

Original result of PSI-BLAST

IdentityAlignment graphLength Definition E-value
Target122 30S ribosomal protein S13 [Candidatus Liberibacter asia
1fjg_M126 Structure Of The Thermus Thermophilus 30s Ribosomal 5e-36
1i94_M125 Crystal Structures Of The Small Ribosomal Subunit W 5e-35
3mr8_M117 Recognition Of The Amber Stop Codon By Release Fact 1e-33
3pyn_M116 Crystal Structure Of A Complex Containing Domain 3 3e-33
1vs5_M118 Crystal Structure Of The Bacterial Ribosome From Es 1e-32
2gy9_M115 Structure Of The 30s Subunit Of A Pre-Translocation 4e-32
3ofo_M114 Crystal Structure Of The E. Coli Ribosome Bound To 5e-32
1p6g_M117 Real Space Refined Coordinates Of The 30s Subunit F 1e-31
3fih_M113 Ternary Complex-Bound E.Coli 70s Ribosome. This Ent 1e-31
3bbn_M145 Homology Model For The Spinach Chloroplast 30s Subu 2e-23
2xzm_M155 Crystal Structure Of The Eukaryotic 40s Ribosomal S 3e-21
3iz6_M152 Localization Of The Small Subunit Ribosomal Protein 7e-21
2zkq_m152 Structure Of A Mammalian Ribosomal 40s Subunit With 2e-20
3izb_M146 Localization Of The Small Subunit Ribosomal Protein 6e-20
1s1h_M132 Structure Of The Ribosomal 80s-Eef2-Sordarin Comple 5e-19
3jyv_M130 Structure Of The 40s Rrna And Proteins And PE TRNA 9e-19
gi|10835597|pdb|1FJG|M Chain M, Structure Of The Thermus Thermophilus 30s Ribosomal Subunit In Complex With The Antibiotics Streptomycin, Spectinomycin, And Paromomycin Length = 126 Back     alignment and structure 
 Score =  154 bits (389), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 72/122 (59%), Positives = 89/122 (72%)

Query: 1   MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI 60
           MARIAGV IPR KRV  AL YI+GIG   +++   K  I P  RV  L E+EV+++R+ +
Sbjct: 1   MARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYV 60

Query: 61  EQDYQVEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVRGQRTHTNARTRKKFGKGGVAR 120
           E  +++EG+LR  VA NIKRLMD+GCYRGLRHRRGLPVRGQRT TNARTRK   K    +
Sbjct: 61  ENTWKLEGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKTVAGK 120

Query: 121 KR 122
           K+
Sbjct: 121 KK 122
>gi|14278542|pdb|1I94|M Chain M, Crystal Structures Of The Small Ribosomal Subunit With Tetracycline, Edeine And If3 Length = 125 Back     alignment and structure
>gi|300508617|pdb|3MR8|M Chain M, Recognition Of The Amber Stop Codon By Release Factor Rf1. This Entry 3mr8 Contains 30s Ribosomal Subunit. The 50s Ribosomal Subunit Can Be Found In Pdb Entry 3ms1. Molecule B In The Same Asymmetric Unit Is Deposited As 3mrz (50s) And 3ms0 (30s). Length = 117 Back     alignment and structure
>gi|322812562|pdb|3PYN|M Chain M, Crystal Structure Of A Complex Containing Domain 3 From The Psiv Igr Ires Rna Bound To The 70s Ribosome. This File Contains The 30s Subunit Of The First 70s Ribosome. Length = 116 Back     alignment and structure
gi|116666560|pdb|1VS5|M Chain M, Crystal Structure Of The Bacterial Ribosome From Escherichia Coli In Complex With The Antibiotic Kasugamyin At 3.5a Resolution. This File Contains The 30s Subunit Of One 70s Ribosome. The Entire Crystal Structure Contains Two 70s Ribosomes And Is Described In Remark 400. Length = 118 Back     alignment and structure
>gi|116667422|pdb|2GY9|M Chain M, Structure Of The 30s Subunit Of A Pre-Translocational E. Coli Ribosome Obtained By Fitting Atomic Models For Rna And Protein Components Into Cryo-Em Map Emd-1056 Length = 115 Back     alignment and structure
>gi|308387977|pdb|3OFO|M Chain M, Crystal Structure Of The E. Coli Ribosome Bound To Erythromycin. This File Contains The 30s Subunit Of The First 70s Ribosome. Length = 114 Back     alignment and structure
>gi|33357890|pdb|1P6G|M Chain M, Real Space Refined Coordinates Of The 30s Subunit Fitted Into The Low Resolution Cryo-Em Map Of The Ef-G.Gtp State Of E. Coli 70s Ribosome Length = 117 Back     alignment and structure
>gi|224510714|pdb|3FIH|M Chain M, Ternary Complex-Bound E.Coli 70s Ribosome. This Entry Consists Of The 30s Subunit, Trnas And The Ternary Complex. Length = 113 Back     alignment and structure
gi|188036214|pdb|3BBN|M Chain M, Homology Model For The Spinach Chloroplast 30s Subunit Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome Length = 145 Back     alignment and structure
gi|319443368|pdb|2XZM|M Chain M, Crystal Structure Of The Eukaryotic 40s Ribosomal Subunit In Complex With Initiation Factor 1. This File Contains The 40s Subunit And Initiation Factor For Molecule 1 Length = 155 Back     alignment and structure
>gi|313103638|pdb|3IZ6|M Chain M, Localization Of The Small Subunit Ribosomal Proteins Into A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s Ribosome Length = 152 Back     alignment and structure
gi|187609266|pdb|2ZKQ|MM Chain m, Structure Of A Mammalian Ribosomal 40s Subunit Within An 80s Complex Obtained By Docking Homology Models Of The Rna And Proteins Into An 8.7 A Cryo-Em Map Length = 152 Back     alignment and structure
gi|313103676|pdb|3IZB|M Chain M, Localization Of The Small Subunit Ribosomal Proteins Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae Translating 80s Ribosome Length = 146 Back     alignment and structure
>gi|49258832|pdb|1S1H|M Chain M, Structure Of The Ribosomal 80s-Eef2-Sordarin Complex From Yeast Obtained By Docking Atomic Models For Rna And Protein Components Into A 11.7 A Cryo-Em Map. This File, 1s1h, Contains 40s Subunit. The 60s Ribosomal Subunit Is In File 1s1i Length = 132 Back     alignment and structure
>gi|281500818|pdb|3JYV|M Chain M, Structure Of The 40s Rrna And Proteins And PE TRNA FOR EUKARYOTIC Ribosome Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome At 8.9a Resolution Length = 130 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

IdentityAlignment graphLength Definition E-value
Target122 30S ribosomal protein S13 [Candidatus Liberibacter asia
3ofp_M113 30S ribosomal protein S13; protein biosynthesis, riboso 1e-36
2vqe_M126 30S ribosomal protein S13, 30S ribosomal protein S6; tR 2e-34
3i1m_M118 30S ribosomal protein S13; ribosome structure, protein- 8e-33
2zkq_m152 40S ribosomal protein S18E; protein-RNA complex, 40S ri 2e-30
3bbn_M145 Ribosomal protein S13; small ribosomal subunit, spinach 6e-28
>3ofp_M 30S ribosomal protein S13; protein biosynthesis, ribosomes, RNA, tRNA, transfer, eryThr ketolide, macrolide, antibiotic, EXIT, peptidyl; 3.10A {Escherichia coli} PDB: 3fih_M* 2wwl_M 2qal_M* 1p6g_M 1p87_M 2aw7_M 2avy_M 2i2u_M 2i2p_M* 2qan_M* 2qb9_M* 2qbb_M* 2qbd_M 2qbf_M 2qbh_M* 2qbj_M* 2qou_M* 2qow_M* 2qoy_M* 2qp0_M* ... Length = 113 Back     alignment and structure
 Score =  146 bits (370), Expect = 1e-36
 Identities = 62/111 (55%), Positives = 79/111 (71%), Gaps = 1/111 (0%)

Query: 2   ARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIE 61
           ARIAG+NIP  K  V AL  I+G+G   S+ I     I  + ++ +L E ++  +R  + 
Sbjct: 1   ARIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEVA 60

Query: 62  QDYQVEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVRGQRTHTNARTRKK 112
           + + VEGDLRR ++M+IKRLMDLGCYRGLRHRRGLPVRGQRT TNARTRK 
Sbjct: 61  K-FVVEGDLRREISMSIKRLMDLGCYRGLRHRRGLPVRGQRTKTNARTRKG 110
>2vqe_M 30S ribosomal protein S13, 30S ribosomal protein S6; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: a.156.1.1 PDB: 1gix_P* 1hnw_M* 1hnx_M* 1hnz_M* 1hr0_M 1ibk_M* 1ibl_M* 1ibm_M 1j5e_M 1jgo_P* 1jgp_P* 1jgq_P* 1mj1_P* 1ml5_P* 1n32_M* 1n33_M* 1n34_M 1n36_M 1xmo_M* 1xmq_M* ... Length = 126 Back     alignment and structure
>3i1m_M 30S ribosomal protein S13; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_M* 3e1a_F 3e1c_F 1vs5_M 3i1o_M 3i1q_M 3i1s_M 3i1z_M 3i21_M 2qal_M* 1p6g_M 1p87_M 2aw7_M 2avy_M 2i2u_M 2i2p_M* 2qan_M* 2qb9_M* 2qbb_M* 2qbd_M ... Length = 118 Back     alignment and structure
>2zkq_m 40S ribosomal protein S18E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} PDB: 1s1h_M Length = 152 Back     alignment and structure
>3bbn_M Ribosomal protein S13; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Oryza sativa} Length = 145 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

Original result of HHsearch against PDB70 database

IdentityAlignment graphLength Definition Probability
Target122 30S ribosomal protein S13 [Candidatus Liberibacter asia
2vqe_M126 30S ribosomal protein S13, 30S ribosomal protein S6; tR 100.0
2zkq_m152 40S ribosomal protein S18E; protein-RNA complex, 40S ri 100.0
3ofp_M113 30S ribosomal protein S13; protein biosynthesis, riboso 100.0
3bbn_M145 Ribosomal protein S13; small ribosomal subunit, spinach 100.0
1ee8_A266 MUTM (FPG) protein; beta sandwich, zinc finger, helix t 96.51
3gpu_A256 DNA glycosylase; DNA glycosylase, DNA repair, damage se 96.47
1tdz_A272 Formamidopyrimidine-DNA glycosylase; DNA repair, FPG, M 96.45
3a46_A289 Formamidopyrimidine-DNA glycosylase; helix two turns he 96.44
1k3x_A262 Endonuclease VIII; hydrolase/DNA; HET: BRU PED; 1.25A { 96.32
1k82_A268 Formamidopyrimidine-DNA glycosylase; protein-DNA comple 96.27
>2vqe_M 30S ribosomal protein S13, 30S ribosomal protein S6; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: a.156.1.1 PDB: 1gix_P* 1hnw_M* 1hnx_M* 1hnz_M* 1hr0_M 1ibk_M* 1ibl_M* 1ibm_M 1j5e_M 1jgo_P* 1jgp_P* 1jgq_P* 1mj1_P* 1ml5_P* 1n32_M* 1n33_M* 1n34_M 1n36_M 1xmo_M* 1xmq_M* ... Back     alignment and structure
Probab=100.00  E-value=0  Score=311.47  Aligned_cols=122  Identities=59%  Similarity=0.919  Sum_probs=117.9

Q ss_pred             CCEEECCCCCCCCEEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHH
Q ss_conf             94551675899857666431200717689999999808882120022798999999986124564333788999999999
Q gi|254780239|r    1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQDYQVEGDLRRTVAMNIKR   80 (122)
Q Consensus         1 mvrI~g~~i~~~K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~~~~i~~~L~~~~~~~i~r   80 (122)
                      |+||+|+|||++|+|.+|||+|||||+++|.+||+.+||||++++++||++|+++|+++|+++|.+|+||++.+.+||+|
T Consensus         1 M~RI~g~~i~~~K~v~~aLt~I~GIG~~~A~~Ic~~lGId~~~kvg~Lt~~qi~~l~~~i~~~~~i~~~L~~~~~~~i~r   80 (126)
T 2vqe_M            1 MARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVENTWKLEGELRAEVAANIKR   80 (126)
T ss_dssp             -CCCSTTCCCCSSBHHHHHTTSSSCCSHHHHHHTTTTTCCTTSBGGGCCHHHHHHHHHHHHTTSCCHHHHHHHHHHHHHH
T ss_pred             CCEECCCCCCCCCEEEEEECCEECCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHH
T ss_conf             97265744899978787620434838999999999859796630163999999999999831451147899999998999


Q ss_pred             HHHCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             973031001233179878770778776577776655423469
Q gi|254780239|r   81 LMDLGCYRGLRHRRGLPVRGQRTHTNARTRKKFGKGGVARKR  122 (122)
Q Consensus        81 l~~i~syrG~RH~~gLpvRGQRT~tn~rt~k~~~~~~~~kkk  122 (122)
                      |++|+||||+||.+|||||||||||||||+|+..+++.++||
T Consensus        81 l~~i~syrG~RH~~gLpvRGQrT~tn~rt~kg~~~~~~~kk~  122 (126)
T 2vqe_M           81 LMDIGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKTVAGKKK  122 (126)
T ss_dssp             HHHTTCHHHHHHHTTCCSSSCCCSSCCHHHHCSCCCCCCCCS
T ss_pred             HHHHCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             887431212334069987777787775567888553555667
>2zkq_m 40S ribosomal protein S18E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} PDB: 1s1h_M 3jyv_M* Back     alignment and structure
>3ofp_M 30S ribosomal protein S13; protein biosynthesis, ribosomes, RNA, tRNA, transfer, eryThr ketolide, macrolide, antibiotic, EXIT, peptidyl; 3.10A {Escherichia coli} PDB: 3fih_M* 2wwl_M 2qal_M* 1p6g_M 1p87_M 2aw7_M 2avy_M 2i2u_M 2i2p_M* 2qan_M* 2qb9_M* 2qbb_M* 2qbd_M 2qbf_M 2qbh_M* 2qbj_M* 2qou_M* 2qow_M* 2qoy_M* 2qp0_M* ... Back     alignment and structure
>3bbn_M Ribosomal protein S13; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Oryza sativa} Back     alignment and structure
>1ee8_A MUTM (FPG) protein; beta sandwich, zinc finger, helix two-turns helix, riken structural genomics/proteomics initiative, RSGI; 1.90A {Thermus thermophilus HB8} SCOP: a.156.1.2 b.113.1.1 g.39.1.8 Back     alignment and structure
>3gpu_A DNA glycosylase; DNA glycosylase, DNA repair, damage search, base extrusion; HET: DNA 8OG; 1.62A {Geobacillus stearothermophilus} PDB: 3gpx_A* 3gq3_A* 3go8_A* 2f5n_A 2f5o_A 2f5p_A 3gp1_A* 3gq4_A* 3gpy_A* 3gq5_A* 3gpp_A* 2f5q_A* 2f5s_A* 1l1z_A* 1l1t_A* 1l2b_A* 1l2c_A* 1l2d_A* 1r2z_A* 1r2y_A* ... Back     alignment and structure
>1tdz_A Formamidopyrimidine-DNA glycosylase; DNA repair, FPG, MUTM, FAPY G, hydrolase/DNA complex; HET: FOX; 1.80A {Lactococcus lactis} SCOP: a.156.1.2 b.113.1.1 g.39.1.8 PDB: 1pji_A* 1pm5_A* 1xc8_A* 3c58_A* 1nnj_A 1kfv_A 1pjj_A* Back     alignment and structure
>3a46_A Formamidopyrimidine-DNA glycosylase; helix two turns helix, zinc-LESS finger, hydrolase, THF, glycosidase, lyase, multifunctional enzyme; HET: DNA 3DR; 2.20A {Acanthamoeba polyphaga mimivirus} PDB: 3a45_A* 3a42_A Back     alignment and structure
>1k3x_A Endonuclease VIII; hydrolase/DNA; HET: BRU PED; 1.25A {Escherichia coli} SCOP: a.156.1.2 b.113.1.1 g.39.1.8 PDB: 1k3w_A* 1q39_A 2ea0_A* 2oq4_A* 1q3c_A 2opf_A* 1q3b_A* Back     alignment and structure
>1k82_A Formamidopyrimidine-DNA glycosylase; protein-DNA complex, DNA repair, beta sandwich, zinc finger, helix two-turns helix, hydrolase/DNA complex; HET: PED; 2.10A {Escherichia coli} SCOP: a.156.1.2 b.113.1.1 g.39.1.8 Back     alignment and structure

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

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

Original result of RPS-BLAST against SCOP70(version1.75) database

IdentityAlignment graphLength Definition E-value
Target 122 30S ribosomal protein S13 [Candidatus Liberibacter asia
d2uubm1125 a.156.1.1 (M:2-126) Ribosomal protein S13 {Thermus ther 2e-33
d2gy9m1114 a.156.1.1 (M:1-114) Ribosomal protein S13 {Escherichia 5e-33
>d2uubm1 a.156.1.1 (M:2-126) Ribosomal protein S13 {Thermus thermophilus [TaxId: 274]} Length = 125 Back     information, alignment and structure

class: All alpha proteins
fold: S13-like H2TH domain
superfamily: S13-like H2TH domain
family: Ribosomal protein S13
domain: Ribosomal protein S13
species: Thermus thermophilus [TaxId: 274]

 Score =  134 bits (339), Expect = 2e-33
 Identities = 71/121 (58%), Positives = 88/121 (72%)

Query: 2   ARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIE 61
           ARIAGV IPR KRV  AL YI+GIG   +++   K  I P  RV  L E+EV+++R+ +E
Sbjct: 1   ARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVE 60

Query: 62  QDYQVEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVRGQRTHTNARTRKKFGKGGVARK 121
             +++EG+LR  VA NIKRLMD+GCYRGLRHRRGLPVRGQRT TNARTRK   K    +K
Sbjct: 61  NTWKLEGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKTVAGKK 120

Query: 122 R 122
           +
Sbjct: 121 K 121
>d2gy9m1 a.156.1.1 (M:1-114) Ribosomal protein S13 {Escherichia coli [TaxId: 562]} Length = 114 Back     information, alignment and structure

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

Original result of HHsearch against SCOP70(version1.75) database

IdentityAlignment graphLength Definition Probability
Target122 30S ribosomal protein S13 [Candidatus Liberibacter asia
d2uubm1125 Ribosomal protein S13 {Thermus thermophilus [TaxId: 274 100.0
d2gy9m1114 Ribosomal protein S13 {Escherichia coli [TaxId: 562]} 100.0
d2hkja178 Topoisomerase VI-B subunit middle domain {Archaeon Sulf 97.14
d1k82a188 DNA repair protein MutM (Fpg) {Escherichia coli [TaxId: 96.7
d1r2za194 DNA repair protein MutM (Fpg) {Bacillus stearothermophi 96.68
d1tdza188 DNA repair protein MutM (Fpg) {Lactococcus lactis [TaxI 96.64
d1ee8a189 DNA repair protein MutM (Fpg) {Thermus thermophilus [Ta 96.61
d1k3xa189 Endonuclease VIII {Escherichia coli [TaxId: 562]} 96.57
d1tdha1115 Endonuclease VIII-like 1 (NEIL1) {Human (Homo sapiens) 90.69
>d2uubm1 a.156.1.1 (M:2-126) Ribosomal protein S13 {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
class: All alpha proteins
fold: S13-like H2TH domain
superfamily: S13-like H2TH domain
family: Ribosomal protein S13
domain: Ribosomal protein S13
species: Thermus thermophilus [TaxId: 274]

Probab=100.00  E-value=0  Score=304.10  Aligned_cols=121  Identities=59%  Similarity=0.915  Sum_probs=115.9

Q ss_pred             CEEECCCCCCCCEEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             45516758998576664312007176899999998088821200227989999999861245643337889999999999
Q gi|254780239|r    2 ARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQDYQVEGDLRRTVAMNIKRL   81 (122)
Q Consensus         2 vrI~g~~i~~~K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~~~~i~~~L~~~~~~~i~rl   81 (122)
                      +||+|+|||++|+|.+|||+|||||+++|.+||+.+||||++++++||++|+++|+++|+++|.+|+||++.+.+||+||
T Consensus         1 aRI~g~di~~~K~v~~ALt~I~GIG~~~A~~Ic~~lgId~~~k~~~Lt~~qi~~I~~~i~~~~~i~~~L~~~~~~dIkrl   80 (125)
T d2uubm1           1 ARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVENTWKLEGELRAEVAANIKRL   80 (125)
T ss_dssp             CCCSTTCCCCSSBHHHHHTTSTTCCHHHHHHHHHTTTCCTTSBGGGCCHHHHHHHHHHHHHHSCCTTHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCEEEEEEEEEECCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             92268669999788876320558189999999998299833333525699999999998411164778999999989999


Q ss_pred             HHCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             73031001233179878770778776577776655423469
Q gi|254780239|r   82 MDLGCYRGLRHRRGLPVRGQRTHTNARTRKKFGKGGVARKR  122 (122)
Q Consensus        82 ~~i~syrG~RH~~gLpvRGQRT~tn~rt~k~~~~~~~~kkk  122 (122)
                      ++|+||||+||.+|||||||||||||||+|+..+++.++||
T Consensus        81 ~~i~~yRG~RH~~gLpvRGQRT~tN~rt~kg~~~~v~~kk~  121 (125)
T d2uubm1          81 MDIGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKTVAGKKK  121 (125)
T ss_dssp             HHTTCHHHHHHHHTCCSSSCCCSSCCHHHHCSCCCCCCCSS
T ss_pred             HHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             87610333432279987777787775466888542555667
>d2gy9m1 a.156.1.1 (M:1-114) Ribosomal protein S13 {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2hkja1 a.156.1.3 (A:229-306) Topoisomerase VI-B subunit middle domain {Archaeon Sulfolobus shibatae [TaxId: 2286]} Back     information, alignment and structure
>d1k82a1 a.156.1.2 (A:129-216) DNA repair protein MutM (Fpg) {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1r2za1 a.156.1.2 (A:135-228) DNA repair protein MutM (Fpg) {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure
>d1tdza1 a.156.1.2 (A:132-219) DNA repair protein MutM (Fpg) {Lactococcus lactis [TaxId: 1358]} Back     information, alignment and structure
>d1ee8a1 a.156.1.2 (A:122-210) DNA repair protein MutM (Fpg) {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1k3xa1 a.156.1.2 (A:125-213) Endonuclease VIII {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1tdha1 a.156.1.2 (A:132-246) Endonuclease VIII-like 1 (NEIL1) {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

Original result of RPS-BLAST against MMDB70 database

IdentityAlignment graphLength Definition E-value
Target 122 30S ribosomal protein S13 [Candidatus Liberibacter
3bbn_M_145 (M:) Ribosomal protein S13; small ribosomal subuni 1e-27
2zkq_m_1-8888 (m:1-88) 40S ribosomal protein S18E; protein-RNA c 4e-19
2vqe_M_1-6464 (M:1-64) 30S ribosomal protein S13, 30S ribosomal 2e-17
3i1m_M_1-6363 (M:1-63) 30S ribosomal protein S13; ribosome struc 3e-16
2zbk_B_229-31082 (B:229-310) Type 2 DNA topoisomerase 6 subunit B; 3e-15
>3bbn_M (M:) Ribosomal protein S13; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Oryza sativa}Length = 145 Back     alignment and structure
 Score =  116 bits (292), Expect = 1e-27
 Identities = 48/111 (43%), Positives = 60/111 (54%), Gaps = 12/111 (10%)

Query: 1   MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI 60
             RI GV IP  KRV  +L YIHGIG   S+ I   L     +    L E EVI +R+  
Sbjct: 46  CIRIGGVEIPNHKRVEYSLQYIHGIGRSRSRQILLDLNFDN-KVTKDLSEEEVIILRK-- 102

Query: 61  EQDYQVEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVRGQRTHTNARTRK 111
                     +R   + I+RL ++ CYRG+RH+ GLPVRGQRT  N RT K
Sbjct: 103 ---------EKRFNRVAIERLKEIRCYRGIRHKLGLPVRGQRTKNNCRTLK 144
>2zkq_m (m:1-88) 40S ribosomal protein S18E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} PDB: 1s1h_MLength = 88 Back     alignment and structure
>2vqe_M (M:1-64) 30S ribosomal protein S13, 30S ribosomal protein S6; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus}Length = 64 Back     alignment and structure
>3i1m_M (M:1-63) 30S ribosomal protein S13; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_M* 3e1a_F 3e1c_F 1vs5_M 3i1o_M 3i1q_M 3i1s_M 3i1z_M 3i21_M 2qal_M* 1p6g_M 1p87_M 2aw7_M 2avy_M 2i2u_M 2i2p_M* 2qan_M* 2qb9_M* 2qbb_M* 2qbd_M ...Length = 63 Back     alignment and structure
>2zbk_B (B:229-310) Type 2 DNA topoisomerase 6 subunit B; DNA binding protein, decatenation, ATPase, drug design, DNA-binding, magnesium, metal-binding; HET: RDC; 3.56A {Sulfolobus shibatae}Length = 82 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

Original result of HHsearch against MMDB70 database

IdentityAlignment graphLength Definition Probability
Target122 30S ribosomal protein S13 [Candidatus Liberibacter asia
3bbn_M_145 Ribosomal protein S13; small ribosomal subunit, sp 100.0
2zkq_m_1-8888 40S ribosomal protein S18E; protein-RNA complex, 4 99.81
2vqe_M_1-6464 30S ribosomal protein S13, 30S ribosomal protein S 99.78
3i1m_M_1-6363 30S ribosomal protein S13; ribosome structure, pro 99.74
2zbk_B_229-31082 Type 2 DNA topoisomerase 6 subunit B; DNA binding 99.52
1mu5_A_230-31182 Type II DNA topoisomerase VI subunit B; GHKL ATPas 97.03
1k82_A_129-22597 Formamidopyrimidine-DNA glycosylase; protein-DNA c 96.79
1tdz_A_137-272136 Formamidopyrimidine-DNA glycosylase; DNA repair, F 96.57
3a46_A_144-289146 Formamidopyrimidine-DNA glycosylase; helix two tur 96.33
3gpu_A_133-256124 DNA glycosylase; DNA glycosylase, DNA repair, dama 96.32
1ee8_A_121-21999 MUTM (FPG) protein; beta sandwich, zinc finger, he 96.24
1k3x_A_125-262138 Endonuclease VIII; hydrolase/DNA; HET: BRU PED; 1. 96.19
1tdh_A_156-364209 NEI endonuclease VIII-like 1; helix two turns heli 94.99
2i0z_A_302-36867 NAD(FAD)-utilizing dehydrogenases; structural geno 91.75
>3bbn_M (M:) Ribosomal protein S13; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Oryza sativa} Back     alignment and structure
Probab=100.00  E-value=6.2e-37  Score=250.33  Aligned_cols=100  Identities=48%  Similarity=0.735  Sum_probs=93.6

Q ss_pred             CCEEECCCCCCCCEEEEEEEEEECCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHH
Q ss_conf             94551675899857666431200717689999999808882120022798999999986124564333788999999999
Q gi|254780239|r    1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQDYQVEGDLRRTVAMNIKR   80 (122)
Q Consensus         1 mvrI~g~~i~~~K~i~~aLt~I~GIG~~~A~~Ic~~lgId~~~kv~~Lt~~qi~~l~~~I~~~~~i~~~L~~~~~~~i~r   80 (122)
                      ||||+|+|||++|+|.+|||+|||||+++|.+||+++||||+. +++|+++|+..|.+..           +.+++||+|
T Consensus        46 mvrI~gt~i~~~K~i~~ALt~IyGIG~~~A~~Ic~~lGi~~~k-~~~Lt~~qi~~l~~L~-----------r~v~~dI~R  113 (145)
T 3bbn_M           46 CIRIGGVEIPNHKRVEYSLQYIHGIGRSRSRQILLDLNFDNKV-TKDLSEEEVIILRKEK-----------RFNRVAIER  113 (145)
T ss_dssp             -CCCSSSCCCCSSBTTTGGGGSTTCCSSTTTGGGTTTTCCSCB-TTSCCSSTTHHHHSSC-----------CCCSTTTHH
T ss_pred             EEEEECCCCCCCCEEEEEEEEEECCCHHHHHHHHHHCCCCHHH-HHHCCHHHHHHHHHHH-----------HHHHHHHHH
T ss_conf             8999586379997889986537550899999999986985454-6543588999989999-----------988999999


Q ss_pred             HHHCCCCCCHHHHCCCCCCCCCCCCCCCCCCC
Q ss_conf             97303100123317987877077877657777
Q gi|254780239|r   81 LMDLGCYRGLRHRRGLPVRGQRTHTNARTRKK  112 (122)
Q Consensus        81 l~~i~syrG~RH~~gLpvRGQRT~tn~rt~k~  112 (122)
                      |++|+||||+||.+|||||||||||||||+|+
T Consensus       114 l~~I~sYRG~RH~~GLPVRGQRTrTNart~kg  145 (145)
T 3bbn_M          114 LKEIRCYRGIRHKLGLPVRGQRTKNNCRTLKG  145 (145)
T ss_dssp             HHCCCCSCCTTTTTTCCSSSCCTTTCCCSSCC
T ss_pred             HHHHCCEEEHHHCCCCCCCCCCCCCCCCCCCC
T ss_conf             87523101013306998787778777546788
>2zkq_m (m:1-88) 40S ribosomal protein S18E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} PDB: 1s1h_M Back     alignment and structure
>2vqe_M (M:1-64) 30S ribosomal protein S13, 30S ribosomal protein S6; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} Back     alignment and structure
>3i1m_M (M:1-63) 30S ribosomal protein S13; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_M* 3e1a_F 3e1c_F 1vs5_M 3i1o_M 3i1q_M 3i1s_M 3i1z_M 3i21_M 2qal_M* 1p6g_M 1p87_M 2aw7_M 2avy_M 2i2u_M 2i2p_M* 2qan_M* 2qb9_M* 2qbb_M* 2qbd_M ... Back     alignment and structure
>2zbk_B (B:229-310) Type 2 DNA topoisomerase 6 subunit B; DNA binding protein, decatenation, ATPase, drug design, DNA-binding, magnesium, metal-binding; HET: RDC; 3.56A {Sulfolobus shibatae} Back     alignment and structure
>1mu5_A (A:230-311) Type II DNA topoisomerase VI subunit B; GHKL ATPase, helix two-turns helix; 2.00A {Sulfolobus shibatae} Back     alignment and structure
>1k82_A (A:129-225) Formamidopyrimidine-DNA glycosylase; protein-DNA complex, DNA repair, beta sandwich, zinc finger, helix two-turns helix, hydrolase/DNA complex; HET: PED; 2.10A {Escherichia coli} Back     alignment and structure
>1tdz_A (A:137-272) Formamidopyrimidine-DNA glycosylase; DNA repair, FPG, MUTM, FAPY G, hydrolase/DNA complex; HET: FOX; 1.80A {Lactococcus lactis} Back     alignment and structure
>3a46_A (A:144-289) Formamidopyrimidine-DNA glycosylase; helix two turns helix, zinc-LESS finger, hydrolase, THF, glycosidase, lyase, multifunctional enzyme; HET: DNA 3DR; 2.20A {Acanthamoeba polyphaga mimivirus} PDB: 3a45_A* 3a42_A Back     alignment and structure
>3gpu_A (A:133-256) DNA glycosylase; DNA glycosylase, DNA repair, damage search, base extrusion; HET: DNA 8OG; 1.62A {Geobacillus stearothermophilus} PDB: 3gpx_A* 3gq3_A* 2f5n_A 2f5o_A 2f5p_A 3gp1_A* 3gq4_A* 3gpy_A* 3gq5_A* 3gpp_A* 2f5q_A* 2f5s_A* 1l1z_A* 1l1t_A* 1l2b_A* 1l2c_A* 1l2d_A* 1r2z_A* 1r2y_A* 3jr5_A* ... Back     alignment and structure
>1ee8_A (A:121-219) MUTM (FPG) protein; beta sandwich, zinc finger, helix two-turns helix, riken structural genomics/proteomics initiative, RSGI; 1.90A {Thermus thermophilus HB8} Back     alignment and structure
>1k3x_A (A:125-262) Endonuclease VIII; hydrolase/DNA; HET: BRU PED; 1.25A {Escherichia coli} Back     alignment and structure
>1tdh_A (A:156-364) NEI endonuclease VIII-like 1; helix two turns helix, zinc-LESS finger, hydrolase; 2.10A {Homo sapiens} Back     alignment and structure
>2i0z_A (A:302-368) NAD(FAD)-utilizing dehydrogenases; structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; HET: FAD; 1.84A {Bacillus cereus} Back     alignment and structure