254780437

254780437

30S ribosomal protein S21

GeneID in NCBI database:8209423Locus tag:CLIBASIA_01610
Protein GI in NCBI database:254780437Protein 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
sequencesequence profile

Prediction of Local Sequence Properties

SourceSummaryResult
scaler
NCBI Databasesequence
PSIPREDsecondary structure
SSPROsecondary structure
DISEMBLcoil and loop
DISEMBLflexible loop
SEGlow complexity
DISOPREDdisordered
DISEMBLmissing residues
DISPROdisordered
TMHMMnone TM-Helix
TOPPREDnone TM-Helix
HMMTOPnone TM-Helix
MEMSATnone TM-Helix
MEMSAT_SVMnone TM-Helix
PHOBIUSnone TM-Helix
SignalP_HMMno
SignalP_NNno
COILScoiled coil
70% MSAconservation map
90% MSAconservation map
  
--------10--------20--------30--------40--------50--------60--------70--------80--------90-----
MLVFNAFRGIFSEGREISAVYVLVRDNNVEQALRVLKKKMQGEGVLRELKMRGHYEKPSQKRVRLKSEAIRRSRKLMRKIAQREGAPVSRLRQHR
ccHHHHHHHHHccccEEEEEEEEEEcccHHHHHHHHHHHHHHccHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccc
cEEEEcccccccHHHHHHHHEEEEHcccHHHHHHHHHHHHHHcccHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccc
MLVFNAFRGIFSEGREISAVYVLVRDNNVEQALRVLKKKMqgegvlrelkmrghyekpsqkrVRLKSEAIRRSRKLMRKIAQregapvsrlrqhr
MLVFNAFrgifsegreiSAVYVLVRDNNVEQALRVlkkkmqgegvlrelkmrghyekpsqkrvrlkseairRSRKLMrkiaqregapvsrlrqhr
MLVFNAFRGIFSEGREISAVYVLVRDNNVEQALRVLKKKMQGEGVLRELKMRGHYEKPSQKRVRLKSEAIRRSRKLMRKIAQREGAPVSRLRQHR
MLVFNAFRGIFSEGREISAVYVLVRDNNVEQALRVLKKKMQGEGVLRELK*********************************************
MLVFNAFRGIFSEGREISAVYVLVRDNNVEQALRVLKKKMQGEGVLRELKMRGHY**********KSEAIRRSRKLMRKI***************
MLVFNAFRGIFSEGREISAVYVLVRDNNVEQALRVLKKKMQGEGVLRELKMRGHYEKPSQKRVRLKSEAIRRSRKLMRKIAQRE**P********
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MLVFNAFRGIFSEGREISAVYVLVRDNNVEQALRVLKKKMQGEGVLRELKMRGHYEKPSQKRVRLKSEAIRRSRKLMRKIAQREGAPVSRLRQHR
MLVFNAFRGIFSEGREISAVYVLVRDNNVEQALRVLKKKMQGEGVLRELKMRGHYEKPSQKRVRLKSEAIRRSRKLMRKIAQREGAPVSRLRQHR
MLVFNAFRGIFSEGREISAVYVLVRDNNVEQALRVLKKKMQGEGVLRELKMRGHYEKPSQKRVRLKSEAIRRSRKLMRKIAQREGAPVSRLRQHR

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
Target95 30S ribosomal protein S21 [Candidatus Liberibacter asia
31512211477 30S ribosomal protein S21 [Candidatus Liberibacter sola 1 8e-30
31940371977 30S ribosomal protein S21 [Bartonella rochalimae ATCC B 1 2e-20
31940672777 30S ribosomal protein S21 [Bartonella sp. 1-1C] Length 1 3e-20
31940518677 30S ribosomal protein S21 [Bartonella sp. AR 15-3] Leng 1 6e-20
12160228577 30S ribosomal protein S21 [Bartonella bacilliformis KC5 1 7e-20
31940812477 30S ribosomal protein S21 [Bartonella schoenbuchensis R 1 8e-20
25470016575 30S ribosomal protein S21 [Brucella suis bv. 5 str. 513 1 8e-20
4947380277 30S ribosomal protein S21 [Bartonella quintana str. Tou 1 9e-20
218680070124 30S ribosomal protein S21 [Rhizobium etli CIAT 894] Len 1 9e-20
254473213106 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
 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
>gi|319406727|emb|CBI80360.1| 30S ribosomal protein S21 [Bartonella sp. 1-1C] Length = 77 Back     alignment and organism information
>gi|319405186|emb|CBI78791.1| 30S ribosomal protein S21 [Bartonella sp. AR 15-3] Length = 77 Back     alignment and organism information
>gi|121602285|ref|YP_988624.1| 30S ribosomal protein S21 [Bartonella bacilliformis KC583] Length = 77 Back     alignment and organism information
>gi|319408124|emb|CBI81777.1| 30S ribosomal protein S21 [Bartonella schoenbuchensis R1] Length = 77 Back     alignment and organism information
>gi|254700165|ref|ZP_05161993.1| 30S ribosomal protein S21 [Brucella suis bv. 5 str. 513] Length = 75 Back     alignment and organism information
>gi|49473802|ref|YP_031844.1| 30S ribosomal protein S21 [Bartonella quintana str. Toulouse] Length = 77 Back     alignment and organism information
>gi|218680070|ref|ZP_03527967.1| 30S ribosomal protein S21 [Rhizobium etli CIAT 894] Length = 124 Back     alignment and organism information
>gi|254473213|ref|ZP_05086611.1| ribosomal protein S21 [Pseudovibrio sp. JE062] Length = 106 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
Target95 30S ribosomal protein S21 [Candidatus Liberibacter asia
PRK0027064 PRK00270, rpsU, 30S ribosomal protein S21; Reviewed 5e-08
TIGR0003058 TIGR00030, S21p, ribosomal protein S21 2e-05
COG082867 COG0828, RpsU, Ribosomal protein S21 [Translation, ribo 7e-05
pfam0116557 pfam01165, Ribosomal_S21, Ribosomal protein S21 3e-07
>gnl|CDD|178952 PRK00270, rpsU, 30S ribosomal protein S21; Reviewed Back     alignment and domain information
>gnl|CDD|129141 TIGR00030, S21p, ribosomal protein S21 Back     alignment and domain information
>gnl|CDD|31170 COG0828, RpsU, Ribosomal protein S21 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|144672 pfam01165, Ribosomal_S21, Ribosomal protein S21 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 95 30S ribosomal protein S21 [Candidatus Liberibacter asia
PRK1244162 30S ribosomal protein S21; Reviewed 99.78
TIGR0003058 S21p ribosomal protein S21; InterPro: IPR001911 Ribosom 99.73
PRK0027066 rpsU 30S ribosomal protein S21; Reviewed 99.7
COG082867 RpsU Ribosomal protein S21 [Translation, ribosomal stru 99.67
pfam0116557 Ribosomal_S21 Ribosomal protein S21. 99.55
>PRK12441 30S ribosomal protein S21; Reviewed Back     alignment and domain information
>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
>PRK00270 rpsU 30S ribosomal protein S21; Reviewed Back     alignment and domain information
>COG0828 RpsU Ribosomal protein S21 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>pfam01165 Ribosomal_S21 Ribosomal protein S21 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
Target95 30S ribosomal protein S21 [Candidatus Liberibacter asia
3bbn_U190 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

IdentityAlignment graphLength Definition E-value
Target95 30S ribosomal protein S21 [Candidatus Liberibacter asia
3bbn_U190 Ribosomal protein S21; small ribosomal subunit, spinach 1e-12
3i1m_U71 30S ribosomal protein S21; ribosome structure, protein- 1e-07
3ofo_U51 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
 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
>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

Homologous Structures in PDB70 Database Detected by HHsearch

Original result of HHsearch against PDB70 database

IdentityAlignment graphLength Definition Probability
Target95 30S ribosomal protein S21 [Candidatus Liberibacter asia
3bbn_U190 Ribosomal protein S21; small ribosomal subunit, spinach 99.58
3i1m_U71 30S ribosomal protein S21; ribosome structure, protein- 99.57
3ofo_U51 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
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
>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

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

IdentityAlignment graphLength 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
 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

Homologous Domains in MMDB70 Database Detected by HHsearch

Original result of HHsearch against MMDB70 database

IdentityAlignment graphLength Definition Probability
Target95 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
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