254780437
30S ribosomal protein S21
GeneID in NCBI database: | 8209423 | Locus tag: | CLIBASIA_01610 |
Protein GI in NCBI database: | 254780437 | Protein Accession: | YP_003064850.1 |
Gene range: | -(344500, 344787) | Protein Length: | 95aa |
Gene description: | 30S ribosomal protein S21 | ||
COG prediction: | [J] Ribosomal protein S21 | ||
KEGG prediction: | rpsU; 30S ribosomal protein S21; K02970 small subunit ribosomal protein S21 | ||
SEED prediction: | SSU ribosomal protein S21p | ||
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 | 95 | 30S ribosomal protein S21 [Candidatus Liberibacter asia | |||
315122114 | 77 | 30S ribosomal protein S21 [Candidatus Liberibacter sola | 1 | 8e-30 | |
319403719 | 77 | 30S ribosomal protein S21 [Bartonella rochalimae ATCC B | 1 | 2e-20 | |
319406727 | 77 | 30S ribosomal protein S21 [Bartonella sp. 1-1C] Length | 1 | 3e-20 | |
319405186 | 77 | 30S ribosomal protein S21 [Bartonella sp. AR 15-3] Leng | 1 | 6e-20 | |
121602285 | 77 | 30S ribosomal protein S21 [Bartonella bacilliformis KC5 | 1 | 7e-20 | |
319408124 | 77 | 30S ribosomal protein S21 [Bartonella schoenbuchensis R | 1 | 8e-20 | |
254700165 | 75 | 30S ribosomal protein S21 [Brucella suis bv. 5 str. 513 | 1 | 8e-20 | |
49473802 | 77 | 30S ribosomal protein S21 [Bartonella quintana str. Tou | 1 | 9e-20 | |
218680070 | 124 | 30S ribosomal protein S21 [Rhizobium etli CIAT 894] Len | 1 | 9e-20 | |
254473213 | 106 | ribosomal protein S21 [Pseudovibrio sp. JE062] Length = | 1 | 9e-20 |
>gi|315122114|ref|YP_004062603.1| 30S ribosomal protein S21 [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 77 | Back alignment and organism information |
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Score = 133 bits (335), Expect = 8e-30, Method: Compositional matrix adjust. Identities = 67/73 (91%), Positives = 71/73 (97%) Query: 20 VYVLVRDNNVEQALRVLKKKMQGEGVLRELKMRGHYEKPSQKRVRLKSEAIRRSRKLMRK 79 +YVLVRDNNVEQALRVLKKKMQGEGVLRELKMR HYEKPSQKRVRLKSEAIRRSRKL+RK Sbjct: 1 MYVLVRDNNVEQALRVLKKKMQGEGVLRELKMRDHYEKPSQKRVRLKSEAIRRSRKLIRK 60 Query: 80 IAQREGAPVSRLR 92 +AQREG+PVSR R Sbjct: 61 LAQREGSPVSRFR 73 |
Species: Candidatus Liberibacter solanacearum Genus: Candidatus Liberibacter Family: Rhizobiaceae Order: Rhizobiales Class: Alphaproteobacteria Phylum: Proteobacteria Superkingdom: Bacteria |
>gi|319403719|emb|CBI77304.1| 30S ribosomal protein S21 [Bartonella rochalimae ATCC BAA-1498] Length = 77 | Back alignment and organism information |
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>gi|319406727|emb|CBI80360.1| 30S ribosomal protein S21 [Bartonella sp. 1-1C] Length = 77 | Back alignment and organism information |
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>gi|319405186|emb|CBI78791.1| 30S ribosomal protein S21 [Bartonella sp. AR 15-3] Length = 77 | Back alignment and organism information |
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>gi|121602285|ref|YP_988624.1| 30S ribosomal protein S21 [Bartonella bacilliformis KC583] Length = 77 | Back alignment and organism information |
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>gi|319408124|emb|CBI81777.1| 30S ribosomal protein S21 [Bartonella schoenbuchensis R1] Length = 77 | Back alignment and organism information |
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>gi|254700165|ref|ZP_05161993.1| 30S ribosomal protein S21 [Brucella suis bv. 5 str. 513] Length = 75 | Back alignment and organism information |
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>gi|49473802|ref|YP_031844.1| 30S ribosomal protein S21 [Bartonella quintana str. Toulouse] Length = 77 | Back alignment and organism information |
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>gi|218680070|ref|ZP_03527967.1| 30S ribosomal protein S21 [Rhizobium etli CIAT 894] Length = 124 | Back alignment and organism information |
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>gi|254473213|ref|ZP_05086611.1| ribosomal protein S21 [Pseudovibrio sp. JE062] Length = 106 | 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 | 95 | 30S ribosomal protein S21 [Candidatus Liberibacter asia | ||
PRK00270 | 64 | PRK00270, rpsU, 30S ribosomal protein S21; Reviewed | 5e-08 | |
TIGR00030 | 58 | TIGR00030, S21p, ribosomal protein S21 | 2e-05 | |
COG0828 | 67 | COG0828, RpsU, Ribosomal protein S21 [Translation, ribo | 7e-05 | |
pfam01165 | 57 | pfam01165, Ribosomal_S21, Ribosomal protein S21 | 3e-07 |
>gnl|CDD|178952 PRK00270, rpsU, 30S ribosomal protein S21; Reviewed | Back alignment and domain information |
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>gnl|CDD|129141 TIGR00030, S21p, ribosomal protein S21 | Back alignment and domain information |
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>gnl|CDD|31170 COG0828, RpsU, Ribosomal protein S21 [Translation, ribosomal structure and biogenesis] | Back alignment and domain information |
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>gnl|CDD|144672 pfam01165, Ribosomal_S21, Ribosomal protein S21 | 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 | 95 | 30S ribosomal protein S21 [Candidatus Liberibacter asia | ||
PRK12441 | 62 | 30S ribosomal protein S21; Reviewed | 99.78 | |
TIGR00030 | 58 | S21p ribosomal protein S21; InterPro: IPR001911 Ribosom | 99.73 | |
PRK00270 | 66 | rpsU 30S ribosomal protein S21; Reviewed | 99.7 | |
COG0828 | 67 | RpsU Ribosomal protein S21 [Translation, ribosomal stru | 99.67 | |
pfam01165 | 57 | Ribosomal_S21 Ribosomal protein S21. | 99.55 |
>PRK12441 30S ribosomal protein S21; Reviewed | Back alignment and domain information |
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>TIGR00030 S21p ribosomal protein S21; InterPro: IPR001911 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms | Back alignment and domain information |
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>PRK00270 rpsU 30S ribosomal protein S21; Reviewed | Back alignment and domain information |
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>COG0828 RpsU Ribosomal protein S21 [Translation, ribosomal structure and biogenesis] | Back alignment and domain information |
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>pfam01165 Ribosomal_S21 Ribosomal protein S21 | 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 | 95 | 30S ribosomal protein S21 [Candidatus Liberibacter asia | ||
3bbn_U | 190 | Homology Model For The Spinach Chloroplast 30s Subu | 2e-07 |
>gi|188036222|pdb|3BBN|U Chain U, Homology Model For The Spinach Chloroplast 30s Subunit Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome. Length = 190 | Back alignment and structure |
Score = 59.1 bits (142), Expect = 2e-07, Method: Composition-based stats. Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 1/58 (1%) Query: 15 REISAVYVLVRDNNVE-QALRVLKKKMQGEGVLRELKMRGHYEKPSQKRVRLKSEAIR 71 R V V+V DN E + L ++++ GV++E K R +E R R EA + Sbjct: 92 RSAYNVQVVVDDNEPEERLLNRFRREVMRAGVIQECKRRRFFENTQDVRKRKTREAAK 149 |
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 | 95 | 30S ribosomal protein S21 [Candidatus Liberibacter asia | ||
3bbn_U | 190 | Ribosomal protein S21; small ribosomal subunit, spinach | 1e-12 | |
3i1m_U | 71 | 30S ribosomal protein S21; ribosome structure, protein- | 1e-07 | |
3ofo_U | 51 | 30S ribosomal protein S21; protein biosynthesis, riboso | 5e-06 |
>3bbn_U Ribosomal protein S21; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Cucumis sativus} Length = 190 | Back alignment and structure |
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Score = 66.9 bits (163), Expect = 1e-12 Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 1/61 (1%) Query: 20 VYVLVRDN-NVEQALRVLKKKMQGEGVLRELKMRGHYEKPSQKRVRLKSEAIRRSRKLMR 78 V V+V DN E+ L ++++ GV++E K R +E R R EA +R+R+ Sbjct: 97 VQVVVDDNEPEERLLNRFRREVMRAGVIQECKRRRFFENTQDVRKRKTREAAKRNRRRRP 156 Query: 79 K 79 + Sbjct: 157 Q 157 |
>3i1m_U 30S ribosomal protein S21; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_U* 2avy_U 2aw7_U 2vho_U 2vhp_U 3df1_U* 3df3_U* 3e1a_Q 3e1c_Q 1vs5_U 3i1o_U 3i1q_U 3i1s_U 3i1z_U 3i21_U 2qal_U* 2i2u_U 2i2p_U* 2qan_U* 2qb9_U* ... Length = 71 | Back alignment and structure |
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>3ofo_U 30S ribosomal protein S21; protein biosynthesis, ribosomes, RNA, tRNA, transfer, eryThr ketolide, macrolide, antibiotic, EXIT, peptidyl; 3.10A {Escherichia coli} PDB: 3fih_U* 2wwl_U 3ofp_U Length = 51 | 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 | 95 | 30S ribosomal protein S21 [Candidatus Liberibacter asia | ||
3bbn_U | 190 | Ribosomal protein S21; small ribosomal subunit, spinach | 99.58 | |
3i1m_U | 71 | 30S ribosomal protein S21; ribosome structure, protein- | 99.57 | |
3ofo_U | 51 | 30S ribosomal protein S21; protein biosynthesis, riboso | 99.28 |
>3bbn_U Ribosomal protein S21; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Cucumis sativus} | Back alignment and structure |
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Probab=99.58 E-value=4.1e-18 Score=120.97 Aligned_cols=64 Identities=30% Similarity=0.427 Sum_probs=59.2 Q ss_pred CCEEEEEEECCC-HHHHHHHHHHHHHHCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 310688872795-8999999999996434499987435126955899999999988899999999 Q gi|254780437|r 17 ISAVYVLVRDNN-VEQALRVLKKKMQGEGVLRELKMRGHYEKPSQKRVRLKSEAIRRSRKLMRKI 80 (95) Q Consensus 17 ~~~i~V~V~~nn-vE~AlR~lKrkv~~eGi~~elR~R~~YEKPsekRrRkk~ea~kR~~K~~rK~ 80 (95) .+++.|.|++|+ +|.|||+|||+|+++||++|+|+|+||||||++|++++++|.+|+++....- T Consensus 94 ~ynv~V~VkenEsiE~ALRRFKKkV~ksGIi~ElR~Rr~YEKPSekKRRKk~eA~rR~kKrr~~~ 158 (190) T 3bbn_U 94 AYNVQVVVDDNEPEERLLNRFRREVMRAGVIQECKRRRFFENTQDVRKRKTREAAKRNRRRRPQA 158 (190) T ss_dssp ---CCCCCCCCSSCCCCCCSSSTTTTTTHHHHSSSSCCCTTTTTTHHHHHHHHTTC--------- T ss_pred CEEEEEEECCCCCHHHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 70379985899999999999999999827599997540458858999999999999999986651 |
>3i1m_U 30S ribosomal protein S21; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_U* 2avy_U 2aw7_U 2vho_U 2vhp_U 3df1_U* 3df3_U* 3e1a_Q 3e1c_Q 1vs5_U 3i1o_U 3i1q_U 3i1s_U 3i1z_U 3i21_U 3kc4_U 2qal_U* 2i2u_U 2i2p_U* 2qan_U* ... | Back alignment and structure |
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>3ofo_U 30S ribosomal protein S21; protein biosynthesis, ribosomes, RNA, tRNA, transfer, eryThr ketolide, macrolide, antibiotic, EXIT, peptidyl; 3.10A {Escherichia coli} PDB: 3fih_U* 2wwl_U 3ofp_U | 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
No hit with e-value below 0.005
Homologous Domains in SCOP70 (Version 1.75) Database Detected by HHsearch
Original result of HHsearch against SCOP70(version1.75) database
No hit with probability above 90.00
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 | 95 | 30S ribosomal protein S21 [Candidatus Liberibacter | ||
3bbn_U_ | 190 | (U:) Ribosomal protein S21; small ribosomal subuni | 1e-14 | |
3i1m_U_ | 71 | (U:) 30S ribosomal protein S21; ribosome structure | 2e-07 |
>3bbn_U (U:) Ribosomal protein S21; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Cucumis sativus}Length = 190 | Back alignment and structure |
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Score = 72.8 bits (178), Expect = 1e-14 Identities = 16/92 (17%), Positives = 33/92 (35%) Query: 4 FNAFRGIFSEGREISAVYVLVRDNNVEQALRVLKKKMQGEGVLRELKMRGHYEKPSQKRV 63 A+ + V+ + E+ L ++++ GV++E K R +E R Sbjct: 82 SLAYANTMFFRSAYNVQVVVDDNEPEERLLNRFRREVMRAGVIQECKRRRFFENTQDVRK 141 Query: 64 RLKSEAIRRSRKLMRKIAQREGAPVSRLRQHR 95 R EA +R+R+ + + Sbjct: 142 RKTREAAKRNRRRRPQARFTPQNKQDVPATKQ 173 |
>3i1m_U (U:) 30S ribosomal protein S21; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_U* 2avy_U 2aw7_U 2vho_U 2vhp_U 3df1_U* 3df3_U* 3e1a_Q 3e1c_Q 1vs5_U 3i1o_U 3i1q_U 3i1s_U 3i1z_U 3i21_U 2qal_U* 2i2u_U 2i2p_U* 2qan_U* 2qb9_U* ...Length = 71 | 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 | 95 | 30S ribosomal protein S21 [Candidatus Liberibacter asia | ||
3i1m_U_ | 71 | 30S ribosomal protein S21; ribosome structure, pro | 99.5 | |
3bbn_U_ | 190 | Ribosomal protein S21; small ribosomal subunit, sp | 99.46 |
>3i1m_U (U:) 30S ribosomal protein S21; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_U* 2avy_U 2aw7_U 2vho_U 2vhp_U 3df1_U* 3df3_U* 3e1a_Q 3e1c_Q 1vs5_U 3i1o_U 3i1q_U 3i1s_U 3i1z_U 3i21_U 2qal_U* 2i2u_U 2i2p_U* 2qan_U* 2qb9_U* ... | Back alignment and structure |
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Probab=99.50 E-value=8.9e-17 Score=114.38 Aligned_cols=66 Identities=35% Similarity=0.559 Sum_probs=60.0 Q ss_pred EEEEEEECCC-HHHHHHHHHHHHHHCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 0688872795-89999999999964344999874351269558999999999888999999999850 Q gi|254780437|r 19 AVYVLVRDNN-VEQALRVLKKKMQGEGVLRELKMRGHYEKPSQKRVRLKSEAIRRSRKLMRKIAQRE 84 (95) Q Consensus 19 ~i~V~V~~nn-vE~AlR~lKrkv~~eGi~~elR~R~~YEKPsekRrRkk~ea~kR~~K~~rK~~~~~ 84 (95) +++|.|.+|+ +|.||+.||++|+++||++|+|.|+||||||++++++..+|.++..+..++..... T Consensus 1 M~~V~v~enE~~e~ALrRFKr~~~k~Gil~E~R~R~~yEkPs~~rkrk~~~a~kr~~k~~r~~~~~~ 67 (71) T 3i1m_U 1 MPVIKVRENEPFDVALRRFKRSCEKAGVLAEVRRREFYEKPTTERKRAKASAVKRHAKKLARENARR 67 (71) T ss_dssp ---CEEECCSSCCSCCCTTTTSSSTHHHHTTSSSCCCSSSHHHHHHHHHHTSCC------------- T ss_pred CCEEECCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 9843618999899999999999998466999987760258389999999999999999999974201 |
>3bbn_U (U:) Ribosomal protein S21; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Cucumis sativus} | Back alignment and structure |
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