254780247

254780247

30S ribosomal protein S8

GeneID in NCBI database:8209228Locus tag:CLIBASIA_00660
Protein GI in NCBI database:254780247Protein Accession:YP_003064660.1
Gene range:-(136171, 136560)Protein Length:129aa
Gene description:30S ribosomal protein S8
COG prediction:[J] Ribosomal protein S8
KEGG prediction:rpsH; 30S ribosomal protein S8; K02994 small subunit ribosomal protein S8
SEED prediction:SSU ribosomal protein S8p (S15Ae)
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
TOPPRED1 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-------13
MSCLGDMLTRIRNANLRYKPSVVIPFSRLHARVLDVLKTEGYIGEYCEIDAGKGRIQLKVDLKYHNGASVIRKIDCVSKPGRRLYSSFKDIPQVCNGLGIMIVTTSKGVMAGHQARECKVGGEVLCSVF
ccHHHHHHHHHHHHHHccccEEEccccHHHHHHHHHHHHccccccEEEEEccccEEEEEEEEEEccccccccccEEccccccEEEccHHHHHHHHccccEEEEEcccccccHHHHHHcccccEEEEEEc
ccHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHcccEccEEEEcccccccEEEEEEcEccccEccccEEEccEccEccEEcHHHcccccccccEEEEEEccEEEEHHHHHHHcccEEEEEEEc
MSCLGDMLTRIRNanlrykpsvvipfsRLHARVLDVlktegyigeyceidagkgriQLKVdlkyhngasVIRKidcvskpgrrlyssfkdipQVCNGLGIMIVTtskgvmaghqareckvggevlcsvf
MSCLGDMLTRirnanlrykpsvvipfsrlHARVLDVLKTEGYIGEYCEIDAGKGRIQLKVDlkyhngasvirkidcvskpgRRLYSSFKDIPQVCNGLGIMIVTTSKGVMAGHQAreckvggevlcsvf
MSCLGDMLTRIRNANLRYKPSVVIPFSRLHARVLDVLKTEGYIGEYCEIDAGKGRIQLKVDLKYHNGASVIRKIDCVSKPGRRLYSSFKDIPQVCNGLGIMIVTTSKGVMAGHQARECKVGGEVLCSVF
MSCLGDMLTRIRNANLRYKPSVVIPFSRLHARVLDVLKTEGYIGEYCEIDAGKGRIQLKVDLKYHNGASVIRKIDCVSKPGRRLYSSFKDIPQVCNGLGIMIVTTSKGVMAGHQARECKVGGEVLCSVF
MSCLGDMLTRIRNANLRYKPSVVIPFSRLHARVLDVLKTEGYIGEYCEIDAGKGRIQLKVDLKYHNGASVIRKIDCVSKPGRRLYSSFKDIPQVCNGLGIMIVTTSKGVMAGHQARECKVGGEVLCSVF
MSCLGDMLTRIRNANLRYKPSVVIPFSRLHARVLDVLKTEGYIGEYCEIDAGKGRIQLKVDLKYHNGASVIRKIDCVSKPGRRLYSSFKDIPQVCNGLGIMIVTTSKGVMAGHQARECKVGGEVLCSVF
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MSCLGDMLTRIRNANLRYKPSVVIPFSRLHARVLDVLKTEGYIGEYCEIDAGKGRIQLKVDLKYHNGASVIRKIDCVSKPGRRLYSSFKDIPQVCNGLGIMIVTTSKGVMAGHQARECKVGGEVLCSVF
MSCLGDMLTRIRNANLRYKPSVVIPFSRLHARVLDVLKTEGYIGEYCEIDAGKGRIQLKVDLKYHNGASVIRKIDCVSKPGRRLYSSFKDIPQVCNGLGIMIVTTSKGVMAGHQARECKVGGEVLCSVF
MSCLGDMLTRIRNANLRYKPSVVIPFSRLHARVLDVLKTEGYIGEYCEIDAGKGRIQLKVDLKYHNGASVIRKIDCVSKPGRRLYSSFKDIPQVCNGLGIMIVTTSKGVMAGHQARECKVGGEVLCSVF

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
Target129 30S ribosomal protein S8 [Candidatus Liberibacter asiat
315122804129 30S ribosomal protein S8 [Candidatus Liberibacter solan 1 9e-54
222148380132 30S ribosomal protein S8 [Agrobacterium vitis S4] Lengt 1 9e-42
150396221132 30S ribosomal protein S8 [Sinorhizobium medicae WSM419] 1 7e-41
15965123132 30S ribosomal protein S8 [Sinorhizobium meliloti 1021] 1 1e-40
227821770132 30S ribosomal protein S8 [Sinorhizobium fredii NGR234] 1 2e-40
116251554132 30S ribosomal protein S8 [Rhizobium leguminosarum bv. v 1 4e-40
86357319132 30S ribosomal protein S8 [Rhizobium etli CFN 42] Length 1 4e-40
222085689132 30S ribosomal protein S8 [Agrobacterium radiobacter K84 1 1e-39
15889229132 30S ribosomal protein S8 [Agrobacterium tumefaciens str 1 3e-39
325293322132 30S ribosomal protein S8 [Agrobacterium sp. H13-3] Leng 1 4e-39
>gi|315122804|ref|YP_004063293.1| 30S ribosomal protein S8 [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 129 Back     alignment and organism information
 Score =  213 bits (541), Expect = 9e-54,   Method: Compositional matrix adjust.
 Identities = 104/129 (80%), Positives = 114/129 (88%)

Query: 1   MSCLGDMLTRIRNANLRYKPSVVIPFSRLHARVLDVLKTEGYIGEYCEIDAGKGRIQLKV 60
           MSCLGDMLTRIRNANLR KPSVVIPFSRLHA VLDVL+ EGYI  Y  +D GK RIQL+V
Sbjct: 1   MSCLGDMLTRIRNANLRRKPSVVIPFSRLHASVLDVLQEEGYIKTYRRVDVGKDRIQLEV 60

Query: 61  DLKYHNGASVIRKIDCVSKPGRRLYSSFKDIPQVCNGLGIMIVTTSKGVMAGHQARECKV 120
           DLKYH+G SVIR+I+CVSKPGRR Y+S K+IPQV NGLGIMIVTTSKGVMA H+ARE +V
Sbjct: 61  DLKYHDGVSVIREINCVSKPGRRFYASSKEIPQVYNGLGIMIVTTSKGVMADHRAREYRV 120

Query: 121 GGEVLCSVF 129
           GGEVLCSVF
Sbjct: 121 GGEVLCSVF 129



Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|222148380|ref|YP_002549337.1| 30S ribosomal protein S8 [Agrobacterium vitis S4] Length = 132 Back     alignment and organism information
>gi|150396221|ref|YP_001326688.1| 30S ribosomal protein S8 [Sinorhizobium medicae WSM419] Length = 132 Back     alignment and organism information
>gi|15965123|ref|NP_385476.1| 30S ribosomal protein S8 [Sinorhizobium meliloti 1021] Length = 132 Back     alignment and organism information
>gi|227821770|ref|YP_002825740.1| 30S ribosomal protein S8 [Sinorhizobium fredii NGR234] Length = 132 Back     alignment and organism information
>gi|116251554|ref|YP_767392.1| 30S ribosomal protein S8 [Rhizobium leguminosarum bv. viciae 3841] Length = 132 Back     alignment and organism information
>gi|86357319|ref|YP_469211.1| 30S ribosomal protein S8 [Rhizobium etli CFN 42] Length = 132 Back     alignment and organism information
>gi|222085689|ref|YP_002544219.1| 30S ribosomal protein S8 [Agrobacterium radiobacter K84] Length = 132 Back     alignment and organism information
>gi|15889229|ref|NP_354910.1| 30S ribosomal protein S8 [Agrobacterium tumefaciens str. C58] Length = 132 Back     alignment and organism information
>gi|325293322|ref|YP_004279186.1| 30S ribosomal protein S8 [Agrobacterium sp. H13-3] Length = 132 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
Target129 30S ribosomal protein S8 [Candidatus Liberibacter asiat
PRK00136130 PRK00136, rpsH, 30S ribosomal protein S8; Validated 1e-49
COG0096132 COG0096, RpsH, Ribosomal protein S8 [Translation, ribos 1e-37
CHL00042132 CHL00042, rps8, ribosomal protein S8 3e-32
PRK04034130 PRK04034, rps8p, 30S ribosomal protein S8P; Reviewed 5e-17
KOG1754130 KOG1754, KOG1754, KOG1754, 40S ribosomal protein S15/S2 4e-11
PLN00146130 PLN00146, PLN00146, 40S ribosomal protein S15a; Provisi 5e-08
PTZ00158130 PTZ00158, PTZ00158, 40S ribosomal protein S15A; Provisi 7e-08
pfam00410129 pfam00410, Ribosomal_S8, Ribosomal protein S8 4e-44
>gnl|CDD|178892 PRK00136, rpsH, 30S ribosomal protein S8; Validated Back     alignment and domain information
>gnl|CDD|30445 COG0096, RpsH, Ribosomal protein S8 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|176983 CHL00042, rps8, ribosomal protein S8 Back     alignment and domain information
>gnl|CDD|179721 PRK04034, rps8p, 30S ribosomal protein S8P; Reviewed Back     alignment and domain information
>gnl|CDD|36965 KOG1754, KOG1754, KOG1754, 40S ribosomal protein S15/S22 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|177750 PLN00146, PLN00146, 40S ribosomal protein S15a; Provisional Back     alignment and domain information
>gnl|CDD|185487 PTZ00158, PTZ00158, 40S ribosomal protein S15A; Provisional Back     alignment and domain information
>gnl|CDD|144123 pfam00410, Ribosomal_S8, Ribosomal protein S8 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 129 30S ribosomal protein S8 [Candidatus Liberibacter asiat
CHL00042132 rps8 ribosomal protein S8 100.0
PRK00136131 rpsH 30S ribosomal protein S8; Validated 100.0
pfam00410129 Ribosomal_S8 Ribosomal protein S8. 100.0
COG0096132 RpsH Ribosomal protein S8 [Translation, ribosomal struc 100.0
PTZ00158130 40S ribosomal protein S15A; Provisional 100.0
PRK04034130 rps8p 30S ribosomal protein S8P; Reviewed 100.0
KOG1754130 consensus 99.97
>CHL00042 rps8 ribosomal protein S8 Back     alignment and domain information
>PRK00136 rpsH 30S ribosomal protein S8; Validated Back     alignment and domain information
>pfam00410 Ribosomal_S8 Ribosomal protein S8 Back     alignment and domain information
>COG0096 RpsH Ribosomal protein S8 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PTZ00158 40S ribosomal protein S15A; Provisional Back     alignment and domain information
>PRK04034 rps8p 30S ribosomal protein S8P; Reviewed Back     alignment and domain information
>KOG1754 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

Original result of PSI-BLAST

IdentityAlignment graphLength Definition E-value
Target129 30S ribosomal protein S8 [Candidatus Liberibacter asiat
1p6g_H129 Real Space Refined Coordinates Of The 30s Subunit F 1e-36
1vs5_H130 Crystal Structure Of The Bacterial Ribosome From Es 1e-36
2gy9_H127 Structure Of The 30s Subunit Of A Pre-Translocation 2e-36
1sei_A130 Structure Of 30s Ribosomal Protein S8 Length = 130 5e-35
1an7_A136 Ribosomal Protein S8 From Thermus Thermophilus Leng 3e-34
1fka_H138 Fitting Of Components With Known Structure Into An 4e-34
1i94_H138 Crystal Structures Of The Small Ribosomal Subunit W 1e-33
3bbn_H134 Homology Model For The Spinach Chloroplast 30s Subu 2e-28
2zkq_h130 Structure Of A Mammalian Ribosomal 40s Subunit With 2e-23
1i6u_A130 Rna-Protein Interactions: The Crystal Structure Of 1e-22
3iz6_H130 Localization Of The Small Subunit Ribosomal Protein 4e-21
1s1h_H129 Structure Of The Ribosomal 80s-Eef2-Sordarin Comple 6e-21
3izb_H130 Localization Of The Small Subunit Ribosomal Protein 7e-21
3jyv_H125 Structure Of The 40s Rrna And Proteins And PE TRNA 8e-21
2xzm_H130 Crystal Structure Of The Eukaryotic 40s Ribosomal S 1e-15
>gi|33357885|pdb|1P6G|H Chain H, 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 = 129 Back     alignment and structure 
 Score =  156 bits (395), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 53/127 (41%), Positives = 79/127 (62%), Gaps = 2/127 (1%)

Query: 2   SCLGDMLTRIRNANLRYKPSVVIPFSRLHARVLDVLKTEGYIGEYCEIDAGKGRIQLKVD 61
             + DMLTRIRN     K +V +P S+L   + +VLK EG+I ++     G  + +L++ 
Sbjct: 4   DPIADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKV--EGDTKPELELT 61

Query: 62  LKYHNGASVIRKIDCVSKPGRRLYSSFKDIPQVCNGLGIMIVTTSKGVMAGHQARECKVG 121
           LKY  G +V+  I  VS+PG R+Y    ++P+V  GLGI +V+TSKGVM    AR+  +G
Sbjct: 62  LKYFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAGLG 121

Query: 122 GEVLCSV 128
           GE++C V
Sbjct: 122 GEIICYV 128
gi|116666555|pdb|1VS5|H Chain H, 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 = 130 Back     alignment and structure
>gi|116667417|pdb|2GY9|H Chain H, 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 = 127 Back     alignment and structure
>gi|1942032|pdb|1SEI|A Chain A, Structure Of 30s Ribosomal Protein S8 Length = 130 Back     alignment and structure
>gi|3318726|pdb|1AN7|A Chain A, Ribosomal Protein S8 From Thermus Thermophilus Length = 136 Back     alignment and structure
>gi|10120571|pdb|1FKA|H Chain H, Structure Of Functionally Activated Small Ribosomal Subunit At 3.3 A Resolution Length = 138 Back     alignment and structure
>gi|14278537|pdb|1I94|H Chain H, Crystal Structures Of The Small Ribosomal Subunit With Tetracycline, Edeine And If3 Length = 138 Back     alignment and structure
gi|188036209|pdb|3BBN|H Chain H, Homology Model For The Spinach Chloroplast 30s Subunit Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome. Length = 134 Back     alignment and structure
gi|187609261|pdb|2ZKQ|HH Chain h, 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 = 130 Back     alignment and structure
>gi|15825871|pdb|1I6U|A Chain A, Rna-Protein Interactions: The Crystal Structure Of Ribosomal Protein S8RRNA COMPLEX FROM METHANOCOCCUS Jannaschii Length = 130 Back     alignment and structure
gi|313103654|pdb|3IZ6|H Chain H, Localization Of The Small Subunit Ribosomal Proteins Into A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s Ribosome Length = 130 Back     alignment and structure
>gi|49258827|pdb|1S1H|H Chain H, 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 = 129 Back     alignment and structure
gi|313103671|pdb|3IZB|H Chain H, Localization Of The Small Subunit Ribosomal Proteins Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae Translating 80s Ribosome Length = 130 Back     alignment and structure
>gi|281500813|pdb|3JYV|H Chain H, 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 = 125 Back     alignment and structure
gi|319443363|pdb|2XZM|H Chain H, 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 = 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
Target129 30S ribosomal protein S8 [Candidatus Liberibacter asiat
1i6u_A130 30S ribosomal protein S8P; protein-RNA interactions, ri 4e-34
2vqe_H138 30S ribosomal protein S8, 30S ribosomal protein S6; tRN 1e-33
1s03_H129 30S ribosomal protein S8; protein-RNA complex, SPC oper 7e-33
3bbn_H134 Ribosomal protein S8; small ribosomal subunit, spinach 5e-32
1sei_A130 Ribosomal protein S8; prokaryotic, rRNA-binding; 1.90A 2e-31
2zkq_h130 40S ribosomal protein S15AE; protein-RNA complex, 40S r 5e-25
>1i6u_A 30S ribosomal protein S8P; protein-RNA interactions, ribosome, RNA, X-RAY crystallography; 2.60A {Methanocaldococcus jannaschii} SCOP: d.140.1.1 Length = 130 Back     alignment and structure
 Score =  138 bits (349), Expect = 4e-34
 Identities = 40/127 (31%), Positives = 61/127 (48%), Gaps = 4/127 (3%)

Query: 4   LGDMLTRIRNANLRYKPSVVI-PFSRLHARVLDVLKTEGYIGEYCEIDAGKGRIQLKVDL 62
           L + L  I N     K  V I P S+L  RVL V++  GYIGE+  I+ G+  I     +
Sbjct: 7   LANALNHISNCERVGKKVVYIKPASKLIGRVLKVMQDNGYIGEFEFIEDGRAGIFKVELI 66

Query: 63  KYHNGASVIRKIDCVSKPGRRLYSSFKDIPQVCNGLGIMIVTTSKGVMAGHQARECKVGG 122
              N    I+    V K G   +             GI+IV+T++GVM+  +A++  +GG
Sbjct: 67  GKINKCGAIKPRFPVKKFGYEKFEKRYLPA---RDFGILIVSTTQGVMSHEEAKKRGLGG 123

Query: 123 EVLCSVF 129
            +L  V+
Sbjct: 124 RLLAYVY 130
>2vqe_H 30S ribosomal protein S8, 30S ribosomal protein S6; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: d.140.1.1 PDB: 1eg0_E* 1fka_H 1gix_K* 1hnw_H* 1hnx_H* 1hnz_H* 1hr0_H 1ibk_H* 1ibl_H* 1ibm_H 1j5e_H 1jgo_K* 1jgp_K* 1jgq_K* 1ml5_K* 1n32_H* 1n33_H* 1n34_H 1n36_H 1pns_H ... Length = 138 Back     alignment and structure
>1s03_H 30S ribosomal protein S8; protein-RNA complex, SPC operon, transcription/RNA complex; 2.70A {Escherichia coli} SCOP: d.140.1.1 PDB: 1p6g_H 1p87_H 2avy_H 2aw7_H 2i2p_H 2i2u_H 2qal_H* 2qan_H* 2qb9_H* 2qbb_H* 2qbd_H 2qbf_H 2qbh_H* 2qbj_H* 2qou_H* 2qow_H* 2qoy_H* 2qp0_H* 2vho_H 2vhp_H ... Length = 129 Back     alignment and structure
>3bbn_H Ribosomal protein S8; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Length = 134 Back     alignment and structure
>1sei_A Ribosomal protein S8; prokaryotic, rRNA-binding; 1.90A {Geobacillus stearothermophilus} SCOP: d.140.1.1 Length = 130 Back     alignment and structure
>2zkq_h 40S ribosomal protein S15AE; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} PDB: 1s1h_H Length = 130 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

Original result of HHsearch against PDB70 database

IdentityAlignment graphLength Definition Probability
Target129 30S ribosomal protein S8 [Candidatus Liberibacter asiat
1sei_A130 Ribosomal protein S8; prokaryotic, rRNA-binding; 1.90A 100.0
3bbn_H134 Ribosomal protein S8; small ribosomal subunit, spinach 100.0
1s03_H129 30S ribosomal protein S8; protein-RNA complex, SPC oper 100.0
2vqe_H138 30S ribosomal protein S8, 30S ribosomal protein S6; tRN 100.0
1i6u_A130 30S ribosomal protein S8P; protein-RNA interactions, ri 100.0
2zkq_h130 40S ribosomal protein S15AE; protein-RNA complex, 40S r 100.0
>1sei_A Ribosomal protein S8; prokaryotic, rRNA-binding; 1.90A {Geobacillus stearothermophilus} SCOP: d.140.1.1 Back     alignment and structure
Probab=100.00  E-value=0  Score=288.46  Aligned_cols=128  Identities=38%  Similarity=0.656  Sum_probs=123.3

Q ss_pred             CCHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHCCCEEEEEEEECCCCEEEEEEECCCCCCCCEECCCEEEECC
Q ss_conf             97789999752548857997899517578999999776312100179983487204788721676543000141676461
Q gi|254780247|r    1 MSCLGDMLTRIRNANLRYKPSVVIPFSRLHARVLDVLKTEGYIGEYCEIDAGKGRIQLKVDLKYHNGASVIRKIDCVSKP   80 (129)
Q Consensus         1 mD~iad~lt~IrNA~~~~k~~v~ip~Skl~~~il~iL~~eGyI~~~~~~~~~~~~~~i~v~Lky~~~~~vi~~i~~iSkP   80 (129)
                      .|||||||++||||++++|.+|.+|+||++.++|++|++||||++|++.++++.+ .++|.|+|.+++|+|+++++||||
T Consensus         3 ~D~iaD~Lt~IrNA~~a~k~~V~iP~Skl~~~il~vL~~eGyI~~f~~~~~~~~~-~i~v~Lky~~~~~~i~~~~~vSkp   81 (130)
T 1sei_A            3 TDPIADMLTAIRNANMVRHEKLEVPASKIKREIAEILKREGFIRDYEYIEDNKQG-ILRIFLKYGPNERVITGLKRISKP   81 (130)
T ss_dssp             SHHHHHHHHHHHHHHHTTCSEEEEECCHHHHHHHHHHHHTTSEEEEEEEESSSCE-EEEEEECBSSSSBSCCCEEECCBT
T ss_pred             CCHHHHHHHHHHHHHHCCCCEEEECCCHHHHHHHHHHHHCCCCCEEEEEECCCCC-EEEEEECCCCCCCCCCCCEECCCC
T ss_conf             6349999998787987699889961758999999999871832014786046775-599991145776432332551235


Q ss_pred             CCCEECCHHHCCCHHCCCCEEEEECCCCEECHHHHHHCCCCCEEEEEEC
Q ss_conf             2120328111711104971899818866003799996499958999989
Q gi|254780247|r   81 GRRLYSSFKDIPQVCNGLGIMIVTTSKGVMAGHQARECKVGGEVLCSVF  129 (129)
Q Consensus        81 ~~r~y~~~~~l~~~~~g~G~~IiSTskGimt~~eA~~~~iGGeil~~v~  129 (129)
                      |+|+|.+++++|++.+|+|++|+|||+|+|||+||+++++|||+||||-
T Consensus        82 g~r~y~~~~~l~~~~~g~G~~IlSTskGimt~~eA~~~~iGGell~~V~  130 (130)
T 1sei_A           82 GLRVYVKAHEVPRVLNGLGIAILSTSQGVLTDKEARQKGTGGEIIAYVI  130 (130)
T ss_dssp             TBCCEECGGGCCCCCTTSCEEEEEETTEEEEHHHHHHHTCCEEEEEEEC
T ss_pred             CCEEECCHHHHHHHHHHCEEEEEECCCCCCCHHHHHHCCCCCEEEEEEC
T ss_conf             6203636435244553340999978997223899998299968999989
>3bbn_H Ribosomal protein S8; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Back     alignment and structure
>1s03_H 30S ribosomal protein S8; protein-RNA complex, SPC operon, transcription/RNA complex; 2.70A {Escherichia coli} SCOP: d.140.1.1 PDB: 1p6g_H 1p87_H 2avy_H 2aw7_H 2i2p_H 2i2u_H 2qal_H* 2qan_H* 2qb9_H* 2qbb_H* 2qbd_H 2qbf_H 2qbh_H* 2qbj_H* 2qou_H* 2qow_H* 2qoy_H* 2qp0_H* 2vho_H 2vhp_H ... Back     alignment and structure
>2vqe_H 30S ribosomal protein S8, 30S ribosomal protein S6; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: d.140.1.1 PDB: 1eg0_E* 1fka_H 1gix_K* 1hnw_H* 1hnx_H* 1hnz_H* 1hr0_H 1ibk_H* 1ibl_H* 1ibm_H 1j5e_H 1jgo_K* 1jgp_K* 1jgq_K* 1ml5_K* 1n32_H* 1n33_H* 1n34_H 1n36_H 1pns_H ... Back     alignment and structure
>1i6u_A 30S ribosomal protein S8P; protein-RNA interactions, ribosome, RNA, X-RAY crystallography; 2.60A {Methanocaldococcus jannaschii} SCOP: d.140.1.1 Back     alignment and structure
>2zkq_h 40S ribosomal protein S15AE; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} PDB: 1s1h_H 3jyv_H* 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 129 30S ribosomal protein S8 [Candidatus Liberibacter asiat
d1an7a_136 d.140.1.1 (A:) Ribosomal protein S8 {Thermus thermophil 3e-34
d1seia_130 d.140.1.1 (A:) Ribosomal protein S8 {Bacillus stearothe 2e-33
d2gy9h1126 d.140.1.1 (H:3-128) Ribosomal protein S8 {Escherichia c 3e-32
d1i6ua_129 d.140.1.1 (A:) Ribosomal protein S8 {Archaeon Methanoco 8e-29
>d1an7a_ d.140.1.1 (A:) Ribosomal protein S8 {Thermus thermophilus [TaxId: 274]} Length = 136 Back     information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S8
superfamily: Ribosomal protein S8
family: Ribosomal protein S8
domain: Ribosomal protein S8
species: Thermus thermophilus [TaxId: 274]

 Score =  137 bits (346), Expect = 3e-34
 Identities = 54/133 (40%), Positives = 72/133 (54%), Gaps = 7/133 (5%)

Query: 4   LGDMLTRIRNANLRYKPSVVIPFSRLHARVLDVLKTEGYIGEYCEIDAGKGRIQLKVD-- 61
           + DMLTRIRNA   YK S  +P SR    +L +L  EG+I  Y  +D             
Sbjct: 4   IADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLRVYLKY 63

Query: 62  -----LKYHNGASVIRKIDCVSKPGRRLYSSFKDIPQVCNGLGIMIVTTSKGVMAGHQAR 116
                        VI  I  +SKPGRR+Y   K+IP+V  GLGI I++TSKGV+   +AR
Sbjct: 64  GPRRQGPDPRPEQVIHHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLTDREAR 123

Query: 117 ECKVGGEVLCSVF 129
           +  VGGE++C V+
Sbjct: 124 KLGVGGELICEVW 136
>d1seia_ d.140.1.1 (A:) Ribosomal protein S8 {Bacillus stearothermophilus [TaxId: 1422]} Length = 130 Back     information, alignment and structure
>d2gy9h1 d.140.1.1 (H:3-128) Ribosomal protein S8 {Escherichia coli [TaxId: 562]} Length = 126 Back     information, alignment and structure
>d1i6ua_ d.140.1.1 (A:) Ribosomal protein S8 {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 129 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
Target129 30S ribosomal protein S8 [Candidatus Liberibacter asiat
d1seia_130 Ribosomal protein S8 {Bacillus stearothermophilus [TaxI 100.0
d2gy9h1126 Ribosomal protein S8 {Escherichia coli [TaxId: 562]} 100.0
d1i6ua_129 Ribosomal protein S8 {Archaeon Methanococcus jannaschii 100.0
d1an7a_136 Ribosomal protein S8 {Thermus thermophilus [TaxId: 274] 100.0
>d1seia_ d.140.1.1 (A:) Ribosomal protein S8 {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S8
superfamily: Ribosomal protein S8
family: Ribosomal protein S8
domain: Ribosomal protein S8
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=100.00  E-value=0  Score=293.05  Aligned_cols=127  Identities=39%  Similarity=0.663  Sum_probs=123.7

Q ss_pred             CHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHCCCEEEEEEEECCCCEEEEEEECCCCCCCCEECCCEEEECCC
Q ss_conf             77899997525488579978995175789999997763121001799834872047887216765430001416764612
Q gi|254780247|r    2 SCLGDMLTRIRNANLRYKPSVVIPFSRLHARVLDVLKTEGYIGEYCEIDAGKGRIQLKVDLKYHNGASVIRKIDCVSKPG   81 (129)
Q Consensus         2 D~iad~lt~IrNA~~~~k~~v~ip~Skl~~~il~iL~~eGyI~~~~~~~~~~~~~~i~v~Lky~~~~~vi~~i~~iSkP~   81 (129)
                      ||||||||+||||++++|.+|.+|+||++.++|++|++||||++|++.++++.+ .++|.|+|.+++|+|+++++||+||
T Consensus         4 D~iaD~lt~IrNA~~a~k~~V~ip~Skl~~~il~vL~~eGyI~~f~~~~~~~~~-~i~v~Lk~~~~~~~i~~~~~vSkpg   82 (130)
T d1seia_           4 DPIADMLTAIRNANMVRHEKLEVPASKIKREIAEILKREGFIRDYEYIEDNKQG-ILRIFLKYGPNERVITGLKRISKPG   82 (130)
T ss_dssp             HHHHHHHHHHHHHHHTTCSEEEEECCHHHHHHHHHHHHTTSEEEEEEEESSSCE-EEEEEECBSSSSBSCCCEEECCBTT
T ss_pred             CHHHHHHHHHHHHHHCCCCEEEECCCHHHHHHHHHHHHHCCCCEEEEEECCCCC-EEEEEECCCCCCCCCCCCEECCCCC
T ss_conf             359999998787988699889952748999999999870610003785046774-5999912467763103426503477


Q ss_pred             CCEECCHHHCCCHHCCCCEEEEECCCCEECHHHHHHCCCCCEEEEEEC
Q ss_conf             120328111711104971899818866003799996499958999989
Q gi|254780247|r   82 RRLYSSFKDIPQVCNGLGIMIVTTSKGVMAGHQARECKVGGEVLCSVF  129 (129)
Q Consensus        82 ~r~y~~~~~l~~~~~g~G~~IiSTskGimt~~eA~~~~iGGeil~~v~  129 (129)
                      +|+|.+++++|++.+|+|++|+|||+|||||+||+++++|||+|||||
T Consensus        83 ~r~y~~~~~l~~~~~g~G~~IvSTskGimt~~eA~~~~iGGell~~Vf  130 (130)
T d1seia_          83 LRVYVKAHEVPRVLNGLGIAILSTSQGVLTDKEARQKGTGGEIIAYVI  130 (130)
T ss_dssp             BCCEECGGGCCCCCTTSCEEEEEETTEEEEHHHHHHHTCCEEEEEEEC
T ss_pred             EEEECCHHHHHHHHHHCEEEEEECCCCEEEHHHHHHHCCCCEEEEEEC
T ss_conf             478835334034552341999988997040999998099967999989
>d2gy9h1 d.140.1.1 (H:3-128) Ribosomal protein S8 {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1i6ua_ d.140.1.1 (A:) Ribosomal protein S8 {Archaeon Methanococcus jannaschii [TaxId: 2190]} Back     information, alignment and structure
>d1an7a_ d.140.1.1 (A:) Ribosomal protein S8 {Thermus thermophilus [TaxId: 274]} 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 129 30S ribosomal protein S8 [Candidatus Liberibacter
1sei_A_69-13062 (A:69-130) Ribosomal protein S8; prokaryotic, rRNA 3e-19
3bbn_H_77-13458 (H:77-134) Ribosomal protein S8; small ribosomal s 3e-18
2vqe_H_81-13858 (H:81-138) 30S ribosomal protein S8, 30S ribosomal 1e-17
1s03_H_72-12958 (H:72-129) 30S ribosomal protein S8; protein-RNA c 5e-17
2zkq_h_69-13062 (h:69-130) 40S ribosomal protein S15AE; protein-RN 3e-15
1i6u_A_69-13062 (A:69-130) 30S ribosomal protein S8P; protein-RNA 2e-14
1s03_H_1-7171 (H:1-71) 30S ribosomal protein S8; protein-RNA com 4e-19
1sei_A_1-6868 (A:1-68) Ribosomal protein S8; prokaryotic, rRNA-b 3e-16
3bbn_H_1-6363 (H:1-63) Ribosomal protein S8; small ribosomal sub 2e-15
2vqe_H_1-6363 (H:1-63) 30S ribosomal protein S8, 30S ribosomal p 2e-15
2zkq_h_1-6868 (h:1-68) 40S ribosomal protein S15AE; protein-RNA 1e-14
1i6u_A_1-6868 (A:1-68) 30S ribosomal protein S8P; protein-RNA in 2e-14
>1sei_A (A:69-130) Ribosomal protein S8; prokaryotic, rRNA-binding; 1.90A {Geobacillus stearothermophilus}Length = 62 Back     alignment and structure
 Score = 88.4 bits (220), Expect = 3e-19
 Identities = 26/61 (42%), Positives = 40/61 (65%)

Query: 69  SVIRKIDCVSKPGRRLYSSFKDIPQVCNGLGIMIVTTSKGVMAGHQARECKVGGEVLCSV 128
            VI  +  +SKPG R+Y    ++P+V NGLGI I++TS+GV+   +AR+   GGE++  V
Sbjct: 2   RVITGLKRISKPGLRVYVKAHEVPRVLNGLGIAILSTSQGVLTDKEARQKGTGGEIIAYV 61

Query: 129 F 129
            
Sbjct: 62  I 62
>3bbn_H (H:77-134) Ribosomal protein S8; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}Length = 58 Back     alignment and structure
>2vqe_H (H:81-138) 30S ribosomal protein S8, 30S ribosomal protein S6; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus}Length = 58 Back     alignment and structure
>1s03_H (H:72-129) 30S ribosomal protein S8; protein-RNA complex, SPC operon, transcription/RNA complex; 2.70A {Escherichia coli}Length = 58 Back     alignment and structure
>2zkq_h (h:69-130) 40S ribosomal protein S15AE; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} PDB: 1s1h_HLength = 62 Back     alignment and structure
>1i6u_A (A:69-130) 30S ribosomal protein S8P; protein-RNA interactions, ribosome, RNA, X-RAY crystallography; 2.60A {Methanocaldococcus jannaschii}Length = 62 Back     alignment and structure
>1s03_H (H:1-71) 30S ribosomal protein S8; protein-RNA complex, SPC operon, transcription/RNA complex; 2.70A {Escherichia coli}Length = 71 Back     alignment and structure
>1sei_A (A:1-68) Ribosomal protein S8; prokaryotic, rRNA-binding; 1.90A {Geobacillus stearothermophilus}Length = 68 Back     alignment and structure
>3bbn_H (H:1-63) Ribosomal protein S8; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}Length = 63 Back     alignment and structure
>2vqe_H (H:1-63) 30S ribosomal protein S8, 30S ribosomal protein S6; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus}Length = 63 Back     alignment and structure
>2zkq_h (h:1-68) 40S ribosomal protein S15AE; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} PDB: 1s1h_HLength = 68 Back     alignment and structure
>1i6u_A (A:1-68) 30S ribosomal protein S8P; protein-RNA interactions, ribosome, RNA, X-RAY crystallography; 2.60A {Methanocaldococcus jannaschii}Length = 68 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

Original result of HHsearch against MMDB70 database

IdentityAlignment graphLength Definition Probability
Target129 30S ribosomal protein S8 [Candidatus Liberibacter asiat
1sei_A_69-13062 Ribosomal protein S8; prokaryotic, rRNA-binding; 1 99.9
2vqe_H_81-13858 30S ribosomal protein S8, 30S ribosomal protein S6 99.87
3bbn_H_77-13458 Ribosomal protein S8; small ribosomal subunit, spi 99.86
2zkq_h_69-13062 40S ribosomal protein S15AE; protein-RNA complex, 99.86
1s03_H_72-12958 30S ribosomal protein S8; protein-RNA complex, SPC 99.84
1i6u_A_69-13062 30S ribosomal protein S8P; protein-RNA interaction 99.84
1s03_H_1-7171 30S ribosomal protein S8; protein-RNA complex, SPC 99.87
1sei_A_1-6868 Ribosomal protein S8; prokaryotic, rRNA-binding; 1 99.82
1i6u_A_1-6868 30S ribosomal protein S8P; protein-RNA interaction 99.81
2zkq_h_1-6868 40S ribosomal protein S15AE; protein-RNA complex, 99.8
3bbn_H_1-6363 Ribosomal protein S8; small ribosomal subunit, spi 99.77
2vqe_H_1-6363 30S ribosomal protein S8, 30S ribosomal protein S6 99.75
>1sei_A (A:69-130) Ribosomal protein S8; prokaryotic, rRNA-binding; 1.90A {Geobacillus stearothermophilus} Back     alignment and structure
Probab=99.90  E-value=3.5e-24  Score=156.12  Aligned_cols=62  Identities=42%  Similarity=0.754  Sum_probs=61.2

Q ss_pred             CCEECCCEEEECCCCCEECCHHHCCCHHCCCCEEEEECCCCEECHHHHHHCCCCCEEEEEEC
Q ss_conf             30001416764612120328111711104971899818866003799996499958999989
Q gi|254780247|r   68 ASVIRKIDCVSKPGRRLYSSFKDIPQVCNGLGIMIVTTSKGVMAGHQARECKVGGEVLCSVF  129 (129)
Q Consensus        68 ~~vi~~i~~iSkP~~r~y~~~~~l~~~~~g~G~~IiSTskGimt~~eA~~~~iGGeil~~v~  129 (129)
                      +|+|+++++||||++|+|.++++++++++|+|++|+|||+|||||+||+++++|||+||+||
T Consensus         1 k~vI~~~~~iSkP~~Rvy~~~~~l~~~~~g~g~~iisTskGim~~~eA~~~~iGGevL~~v~   62 (62)
T 1sei_A            1 ERVITGLKRISKPGLRVYVKAHEVPRVLNGLGIAILSTSQGVLTDKEARQKGTGGEIIAYVI   62 (62)
T ss_dssp             SBSCCCEEECCBTTBCCEECGGGCCCCCTTSCEEEEEETTEEEEHHHHHHHTCCEEEEEEEC
T ss_pred             CCCCCCCEECCCCCCEEECCHHHHHHHHHHCEEEEEECCCCCCCHHHHHHCCCCCEEEEEEC
T ss_conf             64323325512356203636435244553340999978997223899998299968999989
>2vqe_H (H:81-138) 30S ribosomal protein S8, 30S ribosomal protein S6; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} Back     alignment and structure
>3bbn_H (H:77-134) Ribosomal protein S8; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Back     alignment and structure
>2zkq_h (h:69-130) 40S ribosomal protein S15AE; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} PDB: 1s1h_H Back     alignment and structure
>1s03_H (H:72-129) 30S ribosomal protein S8; protein-RNA complex, SPC operon, transcription/RNA complex; 2.70A {Escherichia coli} Back     alignment and structure
>1i6u_A (A:69-130) 30S ribosomal protein S8P; protein-RNA interactions, ribosome, RNA, X-RAY crystallography; 2.60A {Methanocaldococcus jannaschii} Back     alignment and structure
>1s03_H (H:1-71) 30S ribosomal protein S8; protein-RNA complex, SPC operon, transcription/RNA complex; 2.70A {Escherichia coli} Back     alignment and structure
>1sei_A (A:1-68) Ribosomal protein S8; prokaryotic, rRNA-binding; 1.90A {Geobacillus stearothermophilus} Back     alignment and structure
>1i6u_A (A:1-68) 30S ribosomal protein S8P; protein-RNA interactions, ribosome, RNA, X-RAY crystallography; 2.60A {Methanocaldococcus jannaschii} Back     alignment and structure
>2zkq_h (h:1-68) 40S ribosomal protein S15AE; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} PDB: 1s1h_H Back     alignment and structure
>3bbn_H (H:1-63) Ribosomal protein S8; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Back     alignment and structure
>2vqe_H (H:1-63) 30S ribosomal protein S8, 30S ribosomal protein S6; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} Back     alignment and structure