254780247
30S ribosomal protein S8
GeneID in NCBI database: | 8209228 | Locus tag: | CLIBASIA_00660 |
Protein GI in NCBI database: | 254780247 | Protein 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 | ||
sequence | sequence profile |
Prediction of Local Sequence Properties
Source | Summary | Result |
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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
Identity | Alignment graph | Length | Definition | Round | E-value |
Target | 129 | 30S ribosomal protein S8 [Candidatus Liberibacter asiat | |||
315122804 | 129 | 30S ribosomal protein S8 [Candidatus Liberibacter solan | 1 | 9e-54 | |
222148380 | 132 | 30S ribosomal protein S8 [Agrobacterium vitis S4] Lengt | 1 | 9e-42 | |
150396221 | 132 | 30S ribosomal protein S8 [Sinorhizobium medicae WSM419] | 1 | 7e-41 | |
15965123 | 132 | 30S ribosomal protein S8 [Sinorhizobium meliloti 1021] | 1 | 1e-40 | |
227821770 | 132 | 30S ribosomal protein S8 [Sinorhizobium fredii NGR234] | 1 | 2e-40 | |
116251554 | 132 | 30S ribosomal protein S8 [Rhizobium leguminosarum bv. v | 1 | 4e-40 | |
86357319 | 132 | 30S ribosomal protein S8 [Rhizobium etli CFN 42] Length | 1 | 4e-40 | |
222085689 | 132 | 30S ribosomal protein S8 [Agrobacterium radiobacter K84 | 1 | 1e-39 | |
15889229 | 132 | 30S ribosomal protein S8 [Agrobacterium tumefaciens str | 1 | 3e-39 | |
325293322 | 132 | 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 |
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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 |
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>gi|150396221|ref|YP_001326688.1| 30S ribosomal protein S8 [Sinorhizobium medicae WSM419] Length = 132 | Back alignment and organism information |
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>gi|15965123|ref|NP_385476.1| 30S ribosomal protein S8 [Sinorhizobium meliloti 1021] Length = 132 | Back alignment and organism information |
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>gi|227821770|ref|YP_002825740.1| 30S ribosomal protein S8 [Sinorhizobium fredii NGR234] Length = 132 | Back alignment and organism information |
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>gi|116251554|ref|YP_767392.1| 30S ribosomal protein S8 [Rhizobium leguminosarum bv. viciae 3841] Length = 132 | Back alignment and organism information |
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>gi|86357319|ref|YP_469211.1| 30S ribosomal protein S8 [Rhizobium etli CFN 42] Length = 132 | Back alignment and organism information |
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>gi|222085689|ref|YP_002544219.1| 30S ribosomal protein S8 [Agrobacterium radiobacter K84] Length = 132 | Back alignment and organism information |
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>gi|15889229|ref|NP_354910.1| 30S ribosomal protein S8 [Agrobacterium tumefaciens str. C58] Length = 132 | Back alignment and organism information |
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>gi|325293322|ref|YP_004279186.1| 30S ribosomal protein S8 [Agrobacterium sp. H13-3] Length = 132 | Back alignment and organism information |
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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
Identity | Alignment graph | Length | Definition | E-value |
Target | 129 | 30S ribosomal protein S8 [Candidatus Liberibacter asiat | ||
PRK00136 | 130 | PRK00136, rpsH, 30S ribosomal protein S8; Validated | 1e-49 | |
COG0096 | 132 | COG0096, RpsH, Ribosomal protein S8 [Translation, ribos | 1e-37 | |
CHL00042 | 132 | CHL00042, rps8, ribosomal protein S8 | 3e-32 | |
PRK04034 | 130 | PRK04034, rps8p, 30S ribosomal protein S8P; Reviewed | 5e-17 | |
KOG1754 | 130 | KOG1754, KOG1754, KOG1754, 40S ribosomal protein S15/S2 | 4e-11 | |
PLN00146 | 130 | PLN00146, PLN00146, 40S ribosomal protein S15a; Provisi | 5e-08 | |
PTZ00158 | 130 | PTZ00158, PTZ00158, 40S ribosomal protein S15A; Provisi | 7e-08 | |
pfam00410 | 129 | pfam00410, Ribosomal_S8, Ribosomal protein S8 | 4e-44 |
>gnl|CDD|178892 PRK00136, rpsH, 30S ribosomal protein S8; Validated | Back alignment and domain information |
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>gnl|CDD|30445 COG0096, RpsH, Ribosomal protein S8 [Translation, ribosomal structure and biogenesis] | Back alignment and domain information |
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>gnl|CDD|176983 CHL00042, rps8, ribosomal protein S8 | Back alignment and domain information |
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>gnl|CDD|179721 PRK04034, rps8p, 30S ribosomal protein S8P; Reviewed | Back alignment and domain information |
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>gnl|CDD|36965 KOG1754, KOG1754, KOG1754, 40S ribosomal protein S15/S22 [Translation, ribosomal structure and biogenesis] | Back alignment and domain information |
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>gnl|CDD|177750 PLN00146, PLN00146, 40S ribosomal protein S15a; Provisional | Back alignment and domain information |
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>gnl|CDD|185487 PTZ00158, PTZ00158, 40S ribosomal protein S15A; Provisional | Back alignment and domain information |
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>gnl|CDD|144123 pfam00410, Ribosomal_S8, Ribosomal protein S8 | Back alignment and domain information |
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Conserved Domains in CDD Database Detected by HHsearch
Original result of HHsearch against CDD database
Identity | Alignment graph | Length | Definition | Probability |
Target | 129 | 30S ribosomal protein S8 [Candidatus Liberibacter asiat | ||
CHL00042 | 132 | rps8 ribosomal protein S8 | 100.0 | |
PRK00136 | 131 | rpsH 30S ribosomal protein S8; Validated | 100.0 | |
pfam00410 | 129 | Ribosomal_S8 Ribosomal protein S8. | 100.0 | |
COG0096 | 132 | RpsH Ribosomal protein S8 [Translation, ribosomal struc | 100.0 | |
PTZ00158 | 130 | 40S ribosomal protein S15A; Provisional | 100.0 | |
PRK04034 | 130 | rps8p 30S ribosomal protein S8P; Reviewed | 100.0 | |
KOG1754 | 130 | consensus | 99.97 |
>CHL00042 rps8 ribosomal protein S8 | Back alignment and domain information |
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>PRK00136 rpsH 30S ribosomal protein S8; Validated | Back alignment and domain information |
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>pfam00410 Ribosomal_S8 Ribosomal protein S8 | Back alignment and domain information |
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>COG0096 RpsH Ribosomal protein S8 [Translation, ribosomal structure and biogenesis] | Back alignment and domain information |
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>PTZ00158 40S ribosomal protein S15A; Provisional | Back alignment and domain information |
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>PRK04034 rps8p 30S ribosomal protein S8P; Reviewed | Back alignment and domain information |
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>KOG1754 consensus | Back alignment and domain information |
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Homologous Structures in PDB Database
Detected by PSI-BLAST, RPS-BLAST and HHsearch
Homologous Structures Detected by PSI-BLAST against Nonredundant Database
Identity | Alignment graph | Length | Definition | E-value |
Target | 129 | 30S ribosomal protein S8 [Candidatus Liberibacter asiat | ||
1p6g_H | 129 | Real Space Refined Coordinates Of The 30s Subunit F | 1e-36 | |
1vs5_H | 130 | Crystal Structure Of The Bacterial Ribosome From Es | 1e-36 | |
2gy9_H | 127 | Structure Of The 30s Subunit Of A Pre-Translocation | 2e-36 | |
1sei_A | 130 | Structure Of 30s Ribosomal Protein S8 Length = 130 | 5e-35 | |
1an7_A | 136 | Ribosomal Protein S8 From Thermus Thermophilus Leng | 3e-34 | |
1fka_H | 138 | Fitting Of Components With Known Structure Into An | 4e-34 | |
1i94_H | 138 | Crystal Structures Of The Small Ribosomal Subunit W | 1e-33 | |
3bbn_H | 134 | Homology Model For The Spinach Chloroplast 30s Subu | 2e-28 | |
2zkq_h | 130 | Structure Of A Mammalian Ribosomal 40s Subunit With | 2e-23 | |
1i6u_A | 130 | Rna-Protein Interactions: The Crystal Structure Of | 1e-22 | |
3iz6_H | 130 | Localization Of The Small Subunit Ribosomal Protein | 4e-21 | |
1s1h_H | 129 | Structure Of The Ribosomal 80s-Eef2-Sordarin Comple | 6e-21 | |
3izb_H | 130 | Localization Of The Small Subunit Ribosomal Protein | 7e-21 | |
3jyv_H | 125 | Structure Of The 40s Rrna And Proteins And PE TRNA | 8e-21 | |
2xzm_H | 130 | 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
Identity | Alignment graph | Length | Definition | E-value |
Target | 129 | 30S ribosomal protein S8 [Candidatus Liberibacter asiat | ||
1i6u_A | 130 | 30S ribosomal protein S8P; protein-RNA interactions, ri | 4e-34 | |
2vqe_H | 138 | 30S ribosomal protein S8, 30S ribosomal protein S6; tRN | 1e-33 | |
1s03_H | 129 | 30S ribosomal protein S8; protein-RNA complex, SPC oper | 7e-33 | |
3bbn_H | 134 | Ribosomal protein S8; small ribosomal subunit, spinach | 5e-32 | |
1sei_A | 130 | Ribosomal protein S8; prokaryotic, rRNA-binding; 1.90A | 2e-31 | |
2zkq_h | 130 | 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 |
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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 |
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>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 |
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>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 |
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>1sei_A Ribosomal protein S8; prokaryotic, rRNA-binding; 1.90A {Geobacillus stearothermophilus} SCOP: d.140.1.1 Length = 130 | Back alignment and structure |
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>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 |
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Homologous Structures in PDB70 Database Detected by HHsearch
Original result of HHsearch against PDB70 database
Identity | Alignment graph | Length | Definition | Probability |
Target | 129 | 30S ribosomal protein S8 [Candidatus Liberibacter asiat | ||
1sei_A | 130 | Ribosomal protein S8; prokaryotic, rRNA-binding; 1.90A | 100.0 | |
3bbn_H | 134 | Ribosomal protein S8; small ribosomal subunit, spinach | 100.0 | |
1s03_H | 129 | 30S ribosomal protein S8; protein-RNA complex, SPC oper | 100.0 | |
2vqe_H | 138 | 30S ribosomal protein S8, 30S ribosomal protein S6; tRN | 100.0 | |
1i6u_A | 130 | 30S ribosomal protein S8P; protein-RNA interactions, ri | 100.0 | |
2zkq_h | 130 | 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 |
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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 |
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>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 |
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>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 |
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>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 |
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>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 |
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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
Identity | Alignment graph | Length | Definition | E-value |
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 | |
d2gy9h1 | 126 | 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 |
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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 |
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>d2gy9h1 d.140.1.1 (H:3-128) Ribosomal protein S8 {Escherichia coli [TaxId: 562]} Length = 126 | Back information, alignment and structure |
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>d1i6ua_ d.140.1.1 (A:) Ribosomal protein S8 {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 129 | Back information, alignment and structure |
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Homologous Domains in SCOP70 (Version 1.75) Database Detected by HHsearch
Original result of HHsearch against SCOP70(version1.75) database
Identity | Alignment graph | Length | Definition | Probability |
Target | 129 | 30S ribosomal protein S8 [Candidatus Liberibacter asiat | ||
d1seia_ | 130 | Ribosomal protein S8 {Bacillus stearothermophilus [TaxI | 100.0 | |
d2gy9h1 | 126 | 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 |
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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 |
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>d1i6ua_ d.140.1.1 (A:) Ribosomal protein S8 {Archaeon Methanococcus jannaschii [TaxId: 2190]} | Back information, alignment and structure |
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>d1an7a_ d.140.1.1 (A:) Ribosomal protein S8 {Thermus thermophilus [TaxId: 274]} | Back information, alignment and structure |
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Homologous Domains in MMDB70 Database Detected by RPS-BLAST
Original result of RPS-BLAST against MMDB70 database
Identity | Alignment graph | Length | Definition | E-value |
Target | 129 | 30S ribosomal protein S8 [Candidatus Liberibacter | ||
1sei_A_69-130 | 62 | (A:69-130) Ribosomal protein S8; prokaryotic, rRNA | 3e-19 | |
3bbn_H_77-134 | 58 | (H:77-134) Ribosomal protein S8; small ribosomal s | 3e-18 | |
2vqe_H_81-138 | 58 | (H:81-138) 30S ribosomal protein S8, 30S ribosomal | 1e-17 | |
1s03_H_72-129 | 58 | (H:72-129) 30S ribosomal protein S8; protein-RNA c | 5e-17 | |
2zkq_h_69-130 | 62 | (h:69-130) 40S ribosomal protein S15AE; protein-RN | 3e-15 | |
1i6u_A_69-130 | 62 | (A:69-130) 30S ribosomal protein S8P; protein-RNA | 2e-14 | |
1s03_H_1-71 | 71 | (H:1-71) 30S ribosomal protein S8; protein-RNA com | 4e-19 | |
1sei_A_1-68 | 68 | (A:1-68) Ribosomal protein S8; prokaryotic, rRNA-b | 3e-16 | |
3bbn_H_1-63 | 63 | (H:1-63) Ribosomal protein S8; small ribosomal sub | 2e-15 | |
2vqe_H_1-63 | 63 | (H:1-63) 30S ribosomal protein S8, 30S ribosomal p | 2e-15 | |
2zkq_h_1-68 | 68 | (h:1-68) 40S ribosomal protein S15AE; protein-RNA | 1e-14 | |
1i6u_A_1-68 | 68 | (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 |
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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 |
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>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 |
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>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 |
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>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 |
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>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 |
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>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 |
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>1sei_A (A:1-68) Ribosomal protein S8; prokaryotic, rRNA-binding; 1.90A {Geobacillus stearothermophilus}Length = 68 | Back alignment and structure |
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>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 |
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>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 |
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>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 |
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>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 |
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Homologous Domains in MMDB70 Database Detected by HHsearch
Original result of HHsearch against MMDB70 database
Identity | Alignment graph | Length | Definition | Probability |
Target | 129 | 30S ribosomal protein S8 [Candidatus Liberibacter asiat | ||
1sei_A_69-130 | 62 | Ribosomal protein S8; prokaryotic, rRNA-binding; 1 | 99.9 | |
2vqe_H_81-138 | 58 | 30S ribosomal protein S8, 30S ribosomal protein S6 | 99.87 | |
3bbn_H_77-134 | 58 | Ribosomal protein S8; small ribosomal subunit, spi | 99.86 | |
2zkq_h_69-130 | 62 | 40S ribosomal protein S15AE; protein-RNA complex, | 99.86 | |
1s03_H_72-129 | 58 | 30S ribosomal protein S8; protein-RNA complex, SPC | 99.84 | |
1i6u_A_69-130 | 62 | 30S ribosomal protein S8P; protein-RNA interaction | 99.84 | |
1s03_H_1-71 | 71 | 30S ribosomal protein S8; protein-RNA complex, SPC | 99.87 | |
1sei_A_1-68 | 68 | Ribosomal protein S8; prokaryotic, rRNA-binding; 1 | 99.82 | |
1i6u_A_1-68 | 68 | 30S ribosomal protein S8P; protein-RNA interaction | 99.81 | |
2zkq_h_1-68 | 68 | 40S ribosomal protein S15AE; protein-RNA complex, | 99.8 | |
3bbn_H_1-63 | 63 | Ribosomal protein S8; small ribosomal subunit, spi | 99.77 | |
2vqe_H_1-63 | 63 | 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 |
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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 |
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>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 |
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>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 |
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>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 |
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>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 |
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>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 |
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>1sei_A (A:1-68) Ribosomal protein S8; prokaryotic, rRNA-binding; 1.90A {Geobacillus stearothermophilus} | Back alignment and structure |
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>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 |
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>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 |
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>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 |
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>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 |
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