254780266

254780266

30S ribosomal protein S12

GeneID in NCBI database:8209247Locus tag:CLIBASIA_00755
Protein GI in NCBI database:254780266Protein Accession:YP_003064679.1
Gene range:-(147423, 147797)Protein Length:124aa
Gene description:30S ribosomal protein S12
COG prediction:[J] Ribosomal protein S12
KEGG prediction:rpsL; 30S ribosomal protein S12; K02950 small subunit ribosomal protein S12
SEED prediction:SSU ribosomal protein S12p (S23e)
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_NNyes
COILScoiled coil
70% MSAconservation map
90% MSAconservation map
  
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120----
MPTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYGAERPK
cccHHHHHHcccccccccccccccccccccccEEEEEEEEEcccccccccEEEEEEEEccccEEEEEEcccccccccccEEEEEccccccccccEEEEEEccccccccccHHHHHHHccccccc
ccHHHHHHccccccccHHHccccHHHHcccccccEEEEEEccccccccHHHHHEEEEcccccEEEEEcccccccccHcEEEEEEccccccccccEEEEEEccccccccccHHHccHHccccccc
mptvnqlirkprkgsfrACAKVTalrgnpqkrgvclrvytvtpkkpnsALRKVIKARLTSGVEViayvpgeghnlqeHSVVMLCggrvkdlpgvkyRVIRGVLdaqgvknrkqarsrygaerpk
mptvnqlirkprkgsfracakvtalrgnpqkrgvclrvytvtpkkpnsalrKVIKARLTSGVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIrgvldaqgvknrkqarsrygaerpk
MPTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYGAERPK
MPTVNQLI*******************NPQKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRGVLDAQG*****************
MPTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRGVLDAQGV****************
MPTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRGVLDAQGVK***************
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SSSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
MPTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYGAERPK
MPTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYGAERPK
MPTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYGAERPK

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
Target124 30S ribosomal protein S12 [Candidatus Liberibacter asia
315122824124 30S ribosomal protein S12 [Candidatus Liberibacter sola 1 1e-54
225627708154 ribosomal protein S12 [Brucella ceti str. Cudo] Length 1 8e-48
190891350123 30S ribosomal protein S12 [Rhizobium etli CIAT 652] Len 1 1e-47
17982691134 ssu ribosomal protein s12p [Brucella melitensis bv. 1 s 1 2e-47
222148361202 30S ribosomal protein S12 [Agrobacterium vitis S4] Leng 1 2e-47
150396202123 30S ribosomal protein S12 [Sinorhizobium medicae WSM419 1 2e-47
23502115123 30S ribosomal protein S12 [Brucella suis 1330] Length = 1 2e-47
298291433123 ribosomal protein S12 [Starkeya novella DSM 506] Length 1 2e-47
256159975123 30S ribosomal protein S12 [Brucella ceti M490/95/1] Len 1 3e-47
86357300123 30S ribosomal protein S12 [Rhizobium etli CFN 42] Lengt 1 3e-47
>gi|315122824|ref|YP_004063313.1| 30S ribosomal protein S12 [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 124 Back     alignment and organism information
 Score =  215 bits (548), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 105/124 (84%), Positives = 112/124 (90%)

Query: 1   MPTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTS 60
           MPTVNQLIRKPRK + R CAKVTALRG+PQKRGVCLRVYT TPKKPNSALRKV K RLT+
Sbjct: 1   MPTVNQLIRKPRKSAIRTCAKVTALRGSPQKRGVCLRVYTSTPKKPNSALRKVTKVRLTN 60

Query: 61  GVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYGA 120
           G EVI Y+PG GHNLQEHSVVMLCGGRVKDLPGVKYRV+RGVLD  GVK+RKQ+RSRYGA
Sbjct: 61  GAEVIGYIPGVGHNLQEHSVVMLCGGRVKDLPGVKYRVVRGVLDTAGVKDRKQSRSRYGA 120

Query: 121 ERPK 124
            RPK
Sbjct: 121 GRPK 124


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|225627708|ref|ZP_03785745.1| ribosomal protein S12 [Brucella ceti str. Cudo] Length = 154 Back     alignment and organism information
>gi|190891350|ref|YP_001977892.1| 30S ribosomal protein S12 [Rhizobium etli CIAT 652] Length = 123 Back     alignment and organism information
>gi|17982691|gb|AAL51933.1| ssu ribosomal protein s12p [Brucella melitensis bv. 1 str. 16M] Length = 134 Back     alignment and organism information
>gi|222148361|ref|YP_002549318.1| 30S ribosomal protein S12 [Agrobacterium vitis S4] Length = 202 Back     alignment and organism information
>gi|150396202|ref|YP_001326669.1| 30S ribosomal protein S12 [Sinorhizobium medicae WSM419] Length = 123 Back     alignment and organism information
>gi|23502115|ref|NP_698242.1| 30S ribosomal protein S12 [Brucella suis 1330] Length = 123 Back     alignment and organism information
>gi|298291433|ref|YP_003693372.1| ribosomal protein S12 [Starkeya novella DSM 506] Length = 123 Back     alignment and organism information
>gi|256159975|ref|ZP_05457690.1| 30S ribosomal protein S12 [Brucella ceti M490/95/1] Length = 123 Back     alignment and organism information
>gi|86357300|ref|YP_469192.1| 30S ribosomal protein S12 [Rhizobium etli CFN 42] Length = 123 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
Target124 30S ribosomal protein S12 [Candidatus Liberibacter asia
PRK05163124 PRK05163, rpsL, 30S ribosomal protein S12; Validated 9e-56
TIGR00981124 TIGR00981, rpsL_bact, ribosomal protein S12, bacterial/ 2e-47
COG0048129 COG0048, RpsL, Ribosomal protein S12 [Translation, ribo 2e-40
pfam00164112 pfam00164, Ribosomal_S12, Ribosomal protein S12 3e-40
cd03368108 cd03368, Ribosomal_S12, S12-like family, 30S ribosomal 3e-39
KOG1750139 KOG1750, KOG1750, KOG1750, Mitochondrial/chloroplast ri 3e-33
PTZ00115290 PTZ00115, PTZ00115, 40S ribosomal protein S12; Provisio 6e-30
cd0031995 cd00319, Ribosomal_S12_like, Ribosomal protein S12-like 1e-13
cd03367115 cd03367, Ribosomal_S23, S12-like family, 40S ribosomal 6e-09
PRK04211145 PRK04211, rps12P, 30S ribosomal protein S12P; Reviewed 7e-09
TIGR00982139 TIGR00982, S23_S12_E_A, ribosomal protein S23 (S12) 1e-08
PTZ00067143 PTZ00067, PTZ00067, 40S ribosomal S23; Provisional 2e-05
KOG1749143 KOG1749, KOG1749, KOG1749, 40S ribosomal protein S23 [T 3e-05
CHL00051123 CHL00051, rps12, ribosomal protein S12 1e-48
>gnl|CDD|179949 PRK05163, rpsL, 30S ribosomal protein S12; Validated Back     alignment and domain information
>gnl|CDD|130054 TIGR00981, rpsL_bact, ribosomal protein S12, bacterial/organelle Back     alignment and domain information
>gnl|CDD|30397 COG0048, RpsL, Ribosomal protein S12 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|143932 pfam00164, Ribosomal_S12, Ribosomal protein S12 Back     alignment and domain information
>gnl|CDD|48341 cd03368, Ribosomal_S12, S12-like family, 30S ribosomal protein S12 subfamily; S12 is located at the interface of the large and small ribosomal subunits of prokaryotes, chloroplasts and mitochondria, where it plays an important role in both tRNA and ribosomal subunit interactions Back     alignment and domain information
>gnl|CDD|36961 KOG1750, KOG1750, KOG1750, Mitochondrial/chloroplast ribosomal protein S12 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|185456 PTZ00115, PTZ00115, 40S ribosomal protein S12; Provisional Back     alignment and domain information
>gnl|CDD|48339 cd00319, Ribosomal_S12_like, Ribosomal protein S12-like family; composed of prokaryotic 30S ribosomal protein S12, eukaryotic 40S ribosomal protein S23 and similar proteins Back     alignment and domain information
>gnl|CDD|48340 cd03367, Ribosomal_S23, S12-like family, 40S ribosomal protein S23 subfamily; S23 is located at the interface of the large and small ribosomal subunits of eukaryotes, adjacent to the decoding center Back     alignment and domain information
>gnl|CDD|179789 PRK04211, rps12P, 30S ribosomal protein S12P; Reviewed Back     alignment and domain information
>gnl|CDD|130055 TIGR00982, S23_S12_E_A, ribosomal protein S23 (S12) Back     alignment and domain information
>gnl|CDD|185422 PTZ00067, PTZ00067, 40S ribosomal S23; Provisional Back     alignment and domain information
>gnl|CDD|36960 KOG1749, KOG1749, KOG1749, 40S ribosomal protein S23 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|176992 CHL00051, rps12, ribosomal protein S12 Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 124 30S ribosomal protein S12 [Candidatus Liberibacter asia
CHL00051123 rps12 ribosomal protein S12 100.0
PRK05163124 rpsL 30S ribosomal protein S12; Validated 100.0
TIGR00981124 rpsL_bact ribosomal protein S12; InterPro: IPR005679 Ri 100.0
COG0048129 RpsL Ribosomal protein S12 [Translation, ribosomal stru 100.0
PTZ00115288 40S ribosomal protein S12; Provisional 100.0
pfam00164112 Ribosomal_S12 Ribosomal protein S12. 100.0
cd03368108 Ribosomal_S12 S12-like family, 30S ribosomal protein S1 100.0
cd0031995 Ribosomal_S12_like Ribosomal protein S12-like family; c 100.0
KOG1750139 consensus 100.0
cd03367115 Ribosomal_S23 S12-like family, 40S ribosomal protein S2 100.0
PTZ00067143 40S ribosomal S23; Provisional 100.0
PRK04211146 rps12P 30S ribosomal protein S12P; Reviewed 100.0
TIGR00982139 S23_S12_E_A ribosomal protein S23 (S12); InterPro: IPR0 99.91
KOG1749143 consensus 99.91
>CHL00051 rps12 ribosomal protein S12 Back     alignment and domain information
>PRK05163 rpsL 30S ribosomal protein S12; Validated Back     alignment and domain information
>TIGR00981 rpsL_bact ribosomal protein S12; InterPro: IPR005679 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>COG0048 RpsL Ribosomal protein S12 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PTZ00115 40S ribosomal protein S12; Provisional Back     alignment and domain information
>pfam00164 Ribosomal_S12 Ribosomal protein S12 Back     alignment and domain information
>cd03368 Ribosomal_S12 S12-like family, 30S ribosomal protein S12 subfamily; S12 is located at the interface of the large and small ribosomal subunits of prokaryotes, chloroplasts and mitochondria, where it plays an important role in both tRNA and ribosomal subunit interactions Back     alignment and domain information
>cd00319 Ribosomal_S12_like Ribosomal protein S12-like family; composed of prokaryotic 30S ribosomal protein S12, eukaryotic 40S ribosomal protein S23 and similar proteins Back     alignment and domain information
>KOG1750 consensus Back     alignment and domain information
>cd03367 Ribosomal_S23 S12-like family, 40S ribosomal protein S23 subfamily; S23 is located at the interface of the large and small ribosomal subunits of eukaryotes, adjacent to the decoding center Back     alignment and domain information
>PTZ00067 40S ribosomal S23; Provisional Back     alignment and domain information
>PRK04211 rps12P 30S ribosomal protein S12P; Reviewed Back     alignment and domain information
>TIGR00982 S23_S12_E_A ribosomal protein S23 (S12); InterPro: IPR005680 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>KOG1749 consensus 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
Target124 30S ribosomal protein S12 [Candidatus Liberibacter asia
1vs5_L124 Crystal Structure Of The Bacterial Ribosome From Es 3e-47
3bbn_L123 Homology Model For The Spinach Chloroplast 30s Subu 1e-46
3fic_L125 T. Thermophilus 70s Ribosome In Complex With Mrna, 1e-46
1pn7_O124 Coordinates Of S12, L11 Proteins And P-Trna, From T 2e-46
1p6g_L123 Real Space Refined Coordinates Of The 30s Subunit F 5e-46
2f4v_L132 30s Ribosome + Designer Antibiotic Length = 132 1e-45
3d5a_L134 Structural Basis For Translation Termination On The 5e-45
1fjg_L135 Structure Of The Thermus Thermophilus 30s Ribosomal 5e-45
1i94_L131 Crystal Structures Of The Small Ribosomal Subunit W 2e-44
2gy9_L101 Structure Of The 30s Subunit Of A Pre-Translocation 2e-40
1zn1_L97 Coordinates Of Rrf Fitted Into Cryo-Em Map Of The 7 1e-37
2zkq_l143 Structure Of A Mammalian Ribosomal 40s Subunit With 5e-16
1s1h_L118 Structure Of The Ribosomal 80s-Eef2-Sordarin Comple 4e-15
3iz6_L142 Localization Of The Small Subunit Ribosomal Protein 7e-15
3izb_L145 Localization Of The Small Subunit Ribosomal Protein 3e-14
2xzm_L142 Crystal Structure Of The Eukaryotic 40s Ribosomal S 5e-13
gi|116666559|pdb|1VS5|L Chain L, 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 = 124 Back     alignment and structure
 Score =  191 bits (486), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 84/124 (67%), Positives = 98/124 (79%), Gaps = 1/124 (0%)

Query: 1   MPTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTS 60
           M TVNQL+RKPR     A + V AL   PQKRGVC RVYT TPKKPNSALRKV + RLT+
Sbjct: 1   MATVNQLVRKPRARKV-AKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTN 59

Query: 61  GVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYGA 120
           G EV +Y+ GEGHNLQEHSV+++ GGRVKDLPGV+Y  +RG LD  GVK+RKQARS+YG 
Sbjct: 60  GFEVTSYIGGEGHNLQEHSVILIRGGRVKDLPGVRYHTVRGALDCSGVKDRKQARSKYGV 119

Query: 121 ERPK 124
           +RPK
Sbjct: 120 KRPK 123


gi|188036213|pdb|3BBN|L Chain L, Homology Model For The Spinach Chloroplast 30s Subunit Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome. Length = 123 Back     alignment and structure
>gi|224510691|pdb|3FIC|L Chain L, T. Thermophilus 70s Ribosome In Complex With Mrna, Trnas And Ef-Tu.Gdp.Kirromycin Ternary Complex, Fitted To A 6.4 A Cryo-Em Map. This File Contains The 30s Subunit And The Ligands Length = 125 Back     alignment and structure
>gi|34811523|pdb|1PN7|O Chain O, Coordinates Of S12, L11 Proteins And P-Trna, From The 70s X- Ray Structure Aligned To The 70s Cryo-Em Map Of E.Coli Ribosome Length = 124 Back     alignment and structure
>gi|33357889|pdb|1P6G|L Chain L, 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 = 123 Back     alignment and structure
gi|110591334|pdb|2F4V|L Chain L, 30s Ribosome + Designer Antibiotic Length = 132 Back     alignment and structure
gi|209156507|pdb|3D5A|L Chain L, Structural Basis For Translation Termination On The 70s Ribosome. This File Contains The 30s Subunit, Release Factor 1 (Rf1), Two Trna, And Mrna Molecules Of One 70s Ribosome. The Entire Crystal Structure Contains Two 70s Ribosomes As Described In Remark 400. Length = 134 Back     alignment and structure
gi|10835596|pdb|1FJG|L Chain L, Structure Of The Thermus Thermophilus 30s Ribosomal Subunit In Complex With The Antibiotics Streptomycin, Spectinomycin, And Paromomycin Length = 135 Back     alignment and structure
>gi|14278541|pdb|1I94|L Chain L, Crystal Structures Of The Small Ribosomal Subunit With Tetracycline, Edeine And If3 Length = 131 Back     alignment and structure
>gi|116667421|pdb|2GY9|L Chain L, 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 = 101 Back     alignment and structure
>gi|71042417|pdb|1ZN1|L Chain L, Coordinates Of Rrf Fitted Into Cryo-Em Map Of The 70s Post- Termination Complex Length = 97 Back     alignment and structure
gi|187609265|pdb|2ZKQ|LL Chain l, 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 = 143 Back     alignment and structure
>gi|49258831|pdb|1S1H|L Chain L, 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 = 118 Back     alignment and structure
gi|313103637|pdb|3IZ6|L Chain L, Localization Of The Small Subunit Ribosomal Proteins Into A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s Ribosome Length = 142 Back     alignment and structure
gi|313103675|pdb|3IZB|L Chain L, Localization Of The Small Subunit Ribosomal Proteins Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae Translating 80s Ribosome Length = 145 Back     alignment and structure
gi|319443367|pdb|2XZM|L Chain L, 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 = 142 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target124 30S ribosomal protein S12 [Candidatus Liberibacter asia
2vqe_L135 30S ribosomal protein S12, 30S ribosomal protein S6; tR 1e-42
2zkq_l143 40S ribosomal protein S23E; protein-RNA complex, 40S ri 2e-21
>2vqe_L 30S ribosomal protein S12, 30S ribosomal protein S6; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: i.1.1.1 PDB: 1gix_O* 1hnw_L* 1hnx_L* 1hnz_L* 1hr0_L 1ibk_L* 1ibl_L* 1ibm_L 1j5e_L 1jgo_O* 1jgp_O* 1jgq_O* 1mj1_O* 1ml5_O* 1mvr_O 1n32_L* 1n33_L* 1n34_L 1n36_L 1xmo_L* ... Length = 135 Back     alignment and structure
 Score =  166 bits (421), Expect = 1e-42
 Identities = 84/124 (67%), Positives = 103/124 (83%), Gaps = 1/124 (0%)

Query: 1   MPTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTS 60
           +PT+NQL+RK R+   R  +KV AL+G P +RGVC  V TVTPKKPNSALRKV K RLTS
Sbjct: 4   LPTINQLVRKGRE-KVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTS 62

Query: 61  GVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYGA 120
           G EV AY+PGEGHNLQEHSVV++ GGRVKDLPGV+Y ++RGV DA GVK+RK++RS+YG 
Sbjct: 63  GYEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKYGT 122

Query: 121 ERPK 124
           ++PK
Sbjct: 123 KKPK 126


>2zkq_l 40S ribosomal protein S23E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} PDB: 1s1h_L Length = 143 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target124 30S ribosomal protein S12 [Candidatus Liberibacter asia
2vqe_L135 30S ribosomal protein S12, 30S ribosomal protein S6; tR 100.0
2zkq_l143 40S ribosomal protein S23E; protein-RNA complex, 40S ri 100.0
>2vqe_L 30S ribosomal protein S12, 30S ribosomal protein S6; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: i.1.1.1 PDB: 1gix_O* 1hnw_L* 1hnx_L* 1hnz_L* 1hr0_L 1ibk_L* 1ibl_L* 1ibm_L 1j5e_L 1jgo_O* 1jgp_O* 1jgq_O* 1mj1_O* 1ml5_O* 1mvr_O 1n32_L* 1n33_L* 1n34_L 1n36_L 1xmo_L* ... Back     alignment and structure
Probab=100.00  E-value=0  Score=414.85  Aligned_cols=123  Identities=67%  Similarity=1.086  Sum_probs=119.5

Q ss_pred             CCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCEEEEEEECCCCEEEEEECCCCCCCCCCCE
Q ss_conf             95502354268737864666677000686212478756751845674424328899966996999980788875464678
Q gi|254780266|r    1 MPTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGHNLQEHSV   80 (124)
Q Consensus         1 MpTinQlir~~Rkk~~~~~~K~~~L~~~PqkkGVclkv~~~~PKKPNSA~RKvarV~Lsng~~v~ayIPGeGhnlqehs~   80 (124)
                      |||||||++++|++.. .+.++++|++|||++|||++|++++|||||||+||||+|+||||++||||||||||||||||+
T Consensus         4 M~T~nQl~r~~R~~~~-~k~k~~aL~~~PqkkGvc~kv~~~tPKKPNSA~RKvarVrLsng~~vtayIPGeGhnlqEHs~   82 (135)
T 2vqe_L            4 LPTINQLVRKGREKVR-KKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSGYEVTAYIPGEGHNLQEHSV   82 (135)
T ss_dssp             -CCHHHHHHTCCCCCC-CCCSCCCSSSCSEEEEEESCCCEECCCTTCCCCEECCEEEETTSCEEEEECCSSCCCCCTTCE
T ss_pred             CCCHHHHHCCCCCCCC-CCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCEEEEEEEEECCCCEEEEECCCCCCCCCCCCE
T ss_conf             4768897514888776-567785023797415588997774689965300137899936997999981899867554788


Q ss_pred             EEEECCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             99953783888875478980400144334200121125610789
Q gi|254780266|r   81 VMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYGAERPK  124 (124)
Q Consensus        81 VLvrGGrv~DlPGVry~ivRG~~D~~gv~~Rk~~RSkYG~kkpk  124 (124)
                      |||||||++|||||+||+|||+|||+||.+|+++|||||+|+||
T Consensus        83 VLvrGGrv~DLPGVry~vvRG~~D~~gV~~Rk~~RSkYG~Kkpk  126 (135)
T 2vqe_L           83 VLIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKYGTKKPK  126 (135)
T ss_dssp             EEEEECCCTTSTTCCEEECTTSTTSCCCTTCCSSGGGGTCCCCC
T ss_pred             EEEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             99928877889984079964112243346642145546646852



>2zkq_l 40S ribosomal protein S23E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} PDB: 3jyv_L* 1s1h_L* 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 124 30S ribosomal protein S12 [Candidatus Liberibacter asia
d2uubl1118 b.40.4.5 (L:5-122) Ribosomal protein S12 {Thermus therm 2e-42
>d2uubl1 b.40.4.5 (L:5-122) Ribosomal protein S12 {Thermus thermophilus [TaxId: 274]} Length = 118 Back     information, alignment and structure

class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Ribosomal protein S12
species: Thermus thermophilus [TaxId: 274]
 Score =  164 bits (417), Expect = 2e-42
 Identities = 82/118 (69%), Positives = 98/118 (83%), Gaps = 1/118 (0%)

Query: 2   PTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTSG 61
           PT+NQL+RK R+   R  +KV AL+G P +RGVC  V TVTPKKPNSALRKV K RLTSG
Sbjct: 1   PTINQLVRKGRE-KVRKKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSG 59

Query: 62  VEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYG 119
            EV AY+PGEGHNLQEHSVV++ GGRVKDLPGV+Y ++RGV DA GVK+RK++RS+YG
Sbjct: 60  YEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKYG 117


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

IdentityAlignment graphLength Definition Probability
Target124 30S ribosomal protein S12 [Candidatus Liberibacter asia
d2uubl1118 Ribosomal protein S12 {Thermus thermophilus [TaxId: 274 100.0
>d2uubl1 b.40.4.5 (L:5-122) Ribosomal protein S12 {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
class: All beta proteins
fold: OB-fold
superfamily: Nucleic acid-binding proteins
family: Cold shock DNA-binding domain-like
domain: Ribosomal protein S12
species: Thermus thermophilus [TaxId: 274]
Probab=100.00  E-value=0  Score=395.87  Aligned_cols=118  Identities=69%  Similarity=1.083  Sum_probs=114.6

Q ss_pred             CCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCEEEEEEECCCCEEEEEECCCCCCCCCCCEE
Q ss_conf             55023542687378646666770006862124787567518456744243288999669969999807888754646789
Q gi|254780266|r    2 PTVNQLIRKPRKGSFRACAKVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGHNLQEHSVV   81 (124)
Q Consensus         2 pTinQlir~~Rkk~~~~~~K~~~L~~~PqkkGVclkv~~~~PKKPNSA~RKvarV~Lsng~~v~ayIPGeGhnlqehs~V   81 (124)
                      ||||||+|++|+++. .+.++++|++|||++|||++++|++|||||||+||||+|+||||++||||||||||||||||+|
T Consensus         1 PTinQL~rk~R~kk~-~k~k~~aL~~~PqkkGvc~kv~~~~PKKPNSA~RKvarVrLsng~~v~AyIPG~GhnlqEHs~V   79 (118)
T d2uubl1           1 PTINQLVRKGREKVR-KKSKVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSGYEVTAYIPGEGHNLQEHSVV   79 (118)
T ss_dssp             CCHHHHHHHCCCCCC-CCCSCCCTTTCSCEEEEEEEEEEECCCTTCCSCEEEEEEEETTSCEEEEECCSSCCCCCTTCEE
T ss_pred             CCHHHHCCCCCCCCC-CCCCCCCCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCEEEEEECCCCCCCCCCCCEE
T ss_conf             987671036888776-6788852236976043888988822688861021389999629909999818997674557889


Q ss_pred             EEECCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCC
Q ss_conf             995378388887547898040014433420012112561
Q gi|254780266|r   82 MLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYGA  120 (124)
Q Consensus        82 LvrGGrv~DlPGVry~ivRG~~D~~gv~~Rk~~RSkYG~  120 (124)
                      ||||||++|||||+||+|||+|||++|.+|+++||||||
T Consensus        80 LvrGGrv~DlPGVry~vvrG~~D~~~v~~Rk~~RSkYGt  118 (118)
T d2uubl1          80 LIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKYGT  118 (118)
T ss_dssp             EECCCCCTTSTTCCEEBCTTSTTCCCCTTCCSSTTTTTC
T ss_pred             EEECCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCC
T ss_conf             994886666777478997231014333665326676789



Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 124 30S ribosomal protein S12 [Candidatus Liberibacter
2vqe_L_23-135113 (L:23-135) 30S ribosomal protein S12, 30S ribosoma 2e-35
2zkq_l_143 (l:) 40S ribosomal protein S23E; protein-RNA compl 1e-24
>2vqe_L (L:23-135) 30S ribosomal protein S12, 30S ribosomal protein S6; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus}Length = 113 Back     alignment and structure
 Score =  141 bits (358), Expect = 2e-35
 Identities = 75/104 (72%), Positives = 89/104 (85%)

Query: 21  KVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGHNLQEHSV 80
           KV AL+G P +RGVC  V TVTPKKPNSALRKV K RLTSG EV AY+PGEGHNLQEHSV
Sbjct: 1   KVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSGYEVTAYIPGEGHNLQEHSV 60

Query: 81  VMLCGGRVKDLPGVKYRVIRGVLDAQGVKNRKQARSRYGAERPK 124
           V++ GGRVKDLPGV+Y ++RGV DA GVK+RK++RS+YG ++PK
Sbjct: 61  VLIRGGRVKDLPGVRYHIVRGVYDAAGVKDRKKSRSKYGTKKPK 104


>2zkq_l (l:) 40S ribosomal protein S23E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} PDB: 1s1h_LLength = 143 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target124 30S ribosomal protein S12 [Candidatus Liberibacter asia
2vqe_L_23-135113 30S ribosomal protein S12, 30S ribosomal protein S 100.0
2zkq_l_143 40S ribosomal protein S23E; protein-RNA complex, 4 100.0
>2vqe_L (L:23-135) 30S ribosomal protein S12, 30S ribosomal protein S6; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} Back     alignment and structure
Probab=100.00  E-value=0  Score=356.93  Aligned_cols=104  Identities=72%  Similarity=1.174  Sum_probs=102.6

Q ss_pred             CCCCCCCCCCCCEEEEEEEECCCCCCCCCCCEEEEEEECCCCEEEEEECCCCCCCCCCCEEEEECCCCCCCCCCEEEEEE
Q ss_conf             67700068621247875675184567442432889996699699998078887546467899953783888875478980
Q gi|254780266|r   21 KVTALRGNPQKRGVCLRVYTVTPKKPNSALRKVIKARLTSGVEVIAYVPGEGHNLQEHSVVMLCGGRVKDLPGVKYRVIR  100 (124)
Q Consensus        21 K~~~L~~~PqkkGVclkv~~~~PKKPNSA~RKvarV~Lsng~~v~ayIPGeGhnlqehs~VLvrGGrv~DlPGVry~ivR  100 (124)
                      |+++|++|||++|||+++++++|||||||+||||+|+|+||++||||||||||||||||+|||||||++|||||+||+||
T Consensus         1 K~~~L~g~Pq~kGi~l~v~~~~pKKPNSA~RKvarVrL~ngk~v~AyIPG~ghnlqehs~VLVrGgrv~DlPGVrykiVr   80 (113)
T 2vqe_L            1 KVPALKGAPFRRGVCTVVRTVTPKKPNSALRKVAKVRLTSGYEVTAYIPGEGHNLQEHSVVLIRGGRVKDLPGVRYHIVR   80 (113)
T ss_dssp             SCCCSSSCSEEEEEESCCCEECCCTTCCCCEECCEEEETTSCEEEEECCSSCCCCCTTCEEEEEECCCTTSTTCCEEECT
T ss_pred             CCCCCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCEEEEEECCCCCCCCCCCEEEEECCCCCCCCCCEEEEEE
T ss_conf             88534799751079988878336776501312789996699599999578886555378899958756778875789984


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             400144334200121125610789
Q gi|254780266|r  101 GVLDAQGVKNRKQARSRYGAERPK  124 (124)
Q Consensus       101 G~~D~~gv~~Rk~~RSkYG~kkpk  124 (124)
                      |+|||++|.+|+++||+||+|+||
T Consensus        81 G~~d~~~v~~Rk~~rSkyG~k~~k  104 (113)
T 2vqe_L           81 GVYDAAGVKDRKKSRSKYGTKKPK  104 (113)
T ss_dssp             TSTTSCCCTTCCSSGGGGTCCCCC
T ss_pred             EECCCCCCCCCCCCCCCCCCCCCH
T ss_conf             501364446653245546645730



>2zkq_l (l:) 40S ribosomal protein S23E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} PDB: 1s1h_L Back     alignment and structure