254780329

254780329

30S ribosomal protein S6

GeneID in NCBI database:8209314Locus tag:CLIBASIA_01070
Protein GI in NCBI database:254780329Protein Accession:YP_003064742.1
Gene range:+(224635, 225042)Protein Length:135aa
Gene description:30S ribosomal protein S6
COG prediction:[J] Ribosomal protein S6
KEGG prediction:rpsF; 30S ribosomal protein S6; K02990 small subunit ribosomal protein S6
SEED prediction:SSU ribosomal protein S6p
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
HMMTOP1 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-------130-----
MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYVFMNIASPPAAIHEMKRKMRIDENVLRSLTLLVDSHEQSPTLTIQRHDRDDRNDRFPRDRNVDRKQHVSEEKPLS
ccccEEEEEEcccccHHHHHHHHHHHHHHHHHcccEEEEEHHcccccccEEcccccEEEEEEEEEEccHHHHHHHHHHHcccHHHHHHEEEEEccccccccHHHHHHHHHHHHcccccccccHHHHHHHHHcccc
cccEEEEEEEcccccHHHHHHHHHHHHHHHHccccEEEEEcccccHHcEEHHHHHcccEEEEEcccccHHHHHHHHHHHcccHHHHHHHEEEcHcccccccHHHHcccHHHcccccccccccccccccccccccc
MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYVFMNIASPPAAIHEMKRKMRIDENVLRSLTLLVDsheqsptltiqrhdrddrndrfprdrnvdrkqhvseekpls
MKLYEHVFLLRQDISSQQIKDTIGQYQSLIqenggevrlvnelGMRTIAYRIRKNRKAYYVFMNIASPPAAIHEMKRKMRIDENVLRSLTLlvdsheqsptltiqrhdrddrndrfprdrnvdrkqhvseekpls
MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYVFMNIASPPAAIHEMKRKMRIDENVLRSLTLLVDSHEQSPTLTIQrhdrddrndrfprdrnvdrKQHVSEEKPLS
MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYVFMNIASPPAAIHEMKRKMRIDENVLRSLTLLVDSH***************************************
MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYVFMNIASPPAAIHEMKRKMRIDENVLRSLTLLVDSHEQSPTLTIQRHDRDDRNDRFPRDRNV*************
*KLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYVFMNIASPPAAIHEMKRKMRIDENVLRSLTLLVDSH***************************************
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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ooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
oooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYVFMNIASPPAAIHEMKRKMRIDENVLRSLTLLVDSHEQSPTLTIQRHDRDDRNDRFPRDRNVDRKQHVSEEKPLS
MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYVFMNIASPPAAIHEMKRKMRIDENVLRSLTLLVDSHEQSPTLTIQRHDRDDRNDRFPRDRNVDRKQHVSEEKPLS
MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYVFMNIASPPAAIHEMKRKMRIDENVLRSLTLLVDSHEQSPTLTIQRHDRDDRNDRFPRDRNVDRKQHVSEEKPLS

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

No hits with e-value below 0.05

Close Homologs Detected BLAST or PSI-BLAST in the First 2 Iterations

IdentityAlignment graphLength Definition Round E-value
Target135 30S ribosomal protein S6 [Candidatus Liberibacter asiat
315122246135 30S ribosomal protein S6 [Candidatus Liberibacter solan 1 1e-58
86357078152 30S ribosomal protein S6 [Rhizobium etli CFN 42] Length 1 2e-32
190891122152 30S ribosomal protein S6 [Rhizobium etli CIAT 652] Leng 1 2e-31
150395965145 30S ribosomal protein S6 [Sinorhizobium medicae WSM419] 1 1e-30
209548657155 30S ribosomal protein S6 [Rhizobium leguminosarum bv. t 1 8e-30
116251321155 30S ribosomal protein S6 [Rhizobium leguminosarum bv. v 1 8e-30
170740808134 30S ribosomal protein S6 [Methylobacterium sp. 4-46] Le 1 2e-28
222085436150 ribosomal protein S6 [Agrobacterium radiobacter K84] Le 1 3e-28
158425932150 30S ribosomal protein S6 [Azorhizobium caulinodans ORS 1 3e-28
260466963163 ribosomal protein S6 [Mesorhizobium opportunistum WSM20 1 4e-28
>gi|315122246|ref|YP_004062735.1| 30S ribosomal protein S6 [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 135 Back     alignment and organism information
 Score =  228 bits (582), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 109/135 (80%), Positives = 122/135 (90%)

Query: 1   MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYY 60
           M LYEHVFLLRQDI SQ+IKDTI QYQSLI+ENGGEVRLVNE GMRTIAYRI K+RKAYY
Sbjct: 1   MNLYEHVFLLRQDIPSQKIKDTIEQYQSLIKENGGEVRLVNEWGMRTIAYRINKHRKAYY 60

Query: 61  VFMNIASPPAAIHEMKRKMRIDENVLRSLTLLVDSHEQSPTLTIQRHDRDDRNDRFPRDR 120
           V MNIASPPA+IHE++R+MRIDENVLR LT+ VDSHE SP+LT+QR+DRDD+NDRFP+DR
Sbjct: 61  VLMNIASPPASIHELERRMRIDENVLRYLTISVDSHEDSPSLTMQRYDRDDKNDRFPKDR 120

Query: 121 NVDRKQHVSEEKPLS 135
           N DRK HV EEK LS
Sbjct: 121 NADRKSHVDEEKVLS 135


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|86357078|ref|YP_468970.1| 30S ribosomal protein S6 [Rhizobium etli CFN 42] Length = 152 Back     alignment and organism information
>gi|190891122|ref|YP_001977664.1| 30S ribosomal protein S6 [Rhizobium etli CIAT 652] Length = 152 Back     alignment and organism information
>gi|150395965|ref|YP_001326432.1| 30S ribosomal protein S6 [Sinorhizobium medicae WSM419] Length = 145 Back     alignment and organism information
>gi|209548657|ref|YP_002280574.1| 30S ribosomal protein S6 [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 155 Back     alignment and organism information
>gi|116251321|ref|YP_767159.1| 30S ribosomal protein S6 [Rhizobium leguminosarum bv. viciae 3841] Length = 155 Back     alignment and organism information
>gi|170740808|ref|YP_001769463.1| 30S ribosomal protein S6 [Methylobacterium sp. 4-46] Length = 134 Back     alignment and organism information
>gi|222085436|ref|YP_002543966.1| ribosomal protein S6 [Agrobacterium radiobacter K84] Length = 150 Back     alignment and organism information
>gi|158425932|ref|YP_001527224.1| 30S ribosomal protein S6 [Azorhizobium caulinodans ORS 571] Length = 150 Back     alignment and organism information
>gi|260466963|ref|ZP_05813145.1| ribosomal protein S6 [Mesorhizobium opportunistum WSM2075] Length = 163 Back     alignment and organism information

Conserved Domains in CDD Database
Detected by RPS-BLAST and HHsearch

Conserved Domains in CDD Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target135 30S ribosomal protein S6 [Candidatus Liberibacter asiat
PRK00453108 PRK00453, rpsF, 30S ribosomal protein S6; Reviewed 8e-29
COG0360112 COG0360, RpsF, Ribosomal protein S6 [Translation, ribos 1e-22
TIGR0016693 TIGR00166, S6, ribosomal protein S6 8e-16
CHL0012397 CHL00123, rps6, ribosomal protein S6; Validated 6e-10
KOG4708141 KOG4708, KOG4708, KOG4708, Mitochondrial ribosomal prot 3e-05
pfam0125092 pfam01250, Ribosomal_S6, Ribosomal protein S6 5e-26
PRK14074257 PRK14074, rpsF, 30S ribosomal protein S6; Provisional 6e-04
>gnl|CDD|179034 PRK00453, rpsF, 30S ribosomal protein S6; Reviewed Back     alignment and domain information
>gnl|CDD|30709 COG0360, RpsF, Ribosomal protein S6 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|129270 TIGR00166, S6, ribosomal protein S6 Back     alignment and domain information
>gnl|CDD|177046 CHL00123, rps6, ribosomal protein S6; Validated Back     alignment and domain information
>gnl|CDD|39906 KOG4708, KOG4708, KOG4708, Mitochondrial ribosomal protein MRP17 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|144734 pfam01250, Ribosomal_S6, Ribosomal protein S6 Back     alignment and domain information
>gnl|CDD|172564 PRK14074, rpsF, 30S ribosomal protein S6; Provisional Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 135 30S ribosomal protein S6 [Candidatus Liberibacter asiat
COG0360112 RpsF Ribosomal protein S6 [Translation, ribosomal struc 99.97
CHL0012397 rps6 ribosomal protein S6; Validated 99.97
PRK0045395 rpsF 30S ribosomal protein S6; Reviewed 99.97
pfam0125092 Ribosomal_S6 Ribosomal protein S6. 99.96
TIGR00166102 S6 ribosomal protein S6; InterPro: IPR000529 Ribosomes 99.59
KOG4708141 consensus 99.55
>COG0360 RpsF Ribosomal protein S6 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>CHL00123 rps6 ribosomal protein S6; Validated Back     alignment and domain information
>PRK00453 rpsF 30S ribosomal protein S6; Reviewed Back     alignment and domain information
>pfam01250 Ribosomal_S6 Ribosomal protein S6 Back     alignment and domain information
>TIGR00166 S6 ribosomal protein S6; InterPro: IPR000529 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>KOG4708 consensus Back     alignment and domain information

Homologous Structures in PDB Database
Detected by PSI-BLAST, RPS-BLAST and HHsearch

Homologous Structures Detected by PSI-BLAST against Nonredundant Database

IdentityAlignment graphLength Definition E-value
Target135 30S ribosomal protein S6 [Candidatus Liberibacter asiat
1p6g_F135 Real Space Refined Coordinates Of The 30s Subunit F 2e-28
3fih_F100 Ternary Complex-Bound E.Coli 70s Ribosome. This Ent 1e-25
2j5a_A110 Folding Of S6 Structures With Divergent Amino-Acid 3e-16
1vmb_A140 Crystal Structure Of 30s Ribosomal Protein S6 (Tm06 2e-13
2gy9_F95 Structure Of The 30s Subunit Of A Pre-Translocation 1e-24
3r3t_A99 Crystal Structure Of 30s Ribosomal Protein S From B 6e-18
1fka_F101 Structure Of Functionally Activated Small Ribosomal 7e-14
1g1x_A98 Structure Of Ribosomal Proteins S15, S6, S18, And 1 9e-14
1qd7_E97 Partial Model For 30s Ribosomal Subunit Length = 97 1e-13
1cqm_A101 Protein Aggregation And Alzheimer's Disease: Crysta 2e-13
2bvz_A101 Mutant Of The Ribosomal Protein S6 Length = 101 2e-13
1lou_A101 Ribosomal Protein S6 Length = 101 3e-13
2bxj_A101 Double Mutant Of The Ribosomal Protein S6 Length = 1e-12
1qjh_A101 Protein Aggregation And Alzheimer's Disease. Crysta 2e-12
3bbn_F168 Homology Model For The Spinach Chloroplast 30s Subu 8e-11
2kjw_A96 Solution Structure And Backbone Dynamics Of The Per 4e-04
gi|33357883|pdb|1P6G|F Chain F, 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 = 135 Back     alignment and structure
 Score =  128 bits (323), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 37/130 (28%), Positives = 67/130 (51%), Gaps = 2/130 (1%)

Query: 1   MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYY 60
           M+ YE VF++  D  S+Q+   I +Y + I    G++  + + G R +AY I K  KA+Y
Sbjct: 1   MRHYEIVFMVHPD-QSEQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHY 59

Query: 61  VFMNIASPPAAIHEMKRKMRIDENVLRSLTLLVDSHEQSPTLTIQ-RHDRDDRNDRFPRD 119
           V MN+ +P   I E++   R ++ V+RS+ +         +  ++ + +R +R D F  +
Sbjct: 60  VLMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASPMVKAKDERRERRDDFANE 119

Query: 120 RNVDRKQHVS 129
              D +   S
Sbjct: 120 TADDAEAGDS 129


>gi|224510727|pdb|3FIH|F Chain F, Ternary Complex-Bound E.Coli 70s Ribosome. This Entry Consists Of The 30s Subunit, Trnas And The Ternary Complex. Length = 100 Back     alignment and structure
>gi|118138636|pdb|2J5A|A Chain A, Folding Of S6 Structures With Divergent Amino-Acid Composition: Pathway Flexibility Within Partly Overlapping Foldons Length = 110 Back     alignment and structure
>gi|55670467|pdb|1VMB|A Chain A, Crystal Structure Of 30s Ribosomal Protein S6 (Tm0603) From Thermotoga Maritima At 1.70 A Resolution Length = 140 Back     alignment and structure
>gi|116667415|pdb|2GY9|F Chain F, 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 = 95 Back     alignment and structure
>gi|327200752|pdb|3R3T|A Chain A, Crystal Structure Of 30s Ribosomal Protein S From Bacillus Anthracis Length = 99 Back     alignment and structure
gi|10120569|pdb|1FKA|F Chain F, Structure Of Functionally Activated Small Ribosomal Subunit At 3.3 A Resolution Length = 101 Back     alignment and structure
>gi|11514242|pdb|1G1X|A Chain A, Structure Of Ribosomal Proteins S15, S6, S18, And 16s Ribosomal Rna Length = 98 Back     alignment and structure
>gi|6137689|pdb|1QD7|E Chain E, Partial Model For 30s Ribosomal Subunit Length = 97 Back     alignment and structure
>gi|10835884|pdb|1CQM|A Chain A, Protein Aggregation And Alzheimer's Disease: Crystallographic Analysis Of The Phenomenon. Engineered Version Of The Ribosomal Protein S6 Used As A Stable Scaffold To Study Oligomerization. Length = 101 Back     alignment and structure
>gi|82408146|pdb|2BVZ|A Chain A, Mutant Of The Ribosomal Protein S6 Length = 101 Back     alignment and structure
>gi|6730019|pdb|1LOU|A Chain A, Ribosomal Protein S6 Length = 101 Back     alignment and structure
>gi|82408150|pdb|2BXJ|A Chain A, Double Mutant Of The Ribosomal Protein S6 Length = 101 Back     alignment and structure
>gi|9256914|pdb|1QJH|A Chain A, Protein Aggregation And Alzheimer's Disease. Crystallographic Analysis Of The Phenomenon. Engineered Version Of The Ribosomal Protein S6 Used As A Stable Scaffold To Study Oligomerization Length = 101 Back     alignment and structure
gi|188036207|pdb|3BBN|F Chain F, Homology Model For The Spinach Chloroplast 30s Subunit Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome. Length = 168 Back     alignment and structure
>gi|281500592|pdb|2KJW|A Chain A, Solution Structure And Backbone Dynamics Of The Permutant P54-55 Length = 96 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target135 30S ribosomal protein S6 [Candidatus Liberibacter asiat
1cqm_A101 Ribosomal protein S6; alzheimer disease, oligomerizatio 1e-25
3ofo_F100 30S ribosomal protein S6; protein biosynthesis, ribosom 8e-25
3i1m_F135 30S ribosomal protein S6; ribosome structure, protein-R 2e-22
3bbn_F168 Ribosomal protein S6; small ribosomal subunit, spinach 4e-22
1vmb_A140 30S ribosomal protein S6; TM0603, structural genomics, 7e-21
2j5a_A110 30S ribosomal protein S6; ribonucleoprotein, RNA-bindin 6e-20
2kjw_A96 TS9, 30S ribosomal protein S6; S6 permutant, solution s 9e-10
>1cqm_A Ribosomal protein S6; alzheimer disease, oligomerization; 1.65A {Thermus thermophilus} SCOP: d.58.14.1 PDB: 1cqn_A 1qjh_A 1ris_A 1fka_F 1gix_I* 1hnw_F* 1hnx_F* 1hnz_F* 1hr0_F 1i94_F* 1i95_F* 1i96_F* 1i97_F* 1ibk_F* 1ibl_F* 1ibm_F 1j5e_F 1jgo_I* 1jgp_I* 1jgq_I* ... Length = 101 Back     alignment and structure
 Score =  110 bits (276), Expect = 1e-25
 Identities = 24/100 (24%), Positives = 49/100 (49%)

Query: 1   MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYY 60
           M+ YE   +L  ++   Q+       Q  ++  G  V  V  LG+R +AY I K+ + Y+
Sbjct: 1   MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVAILGLRRLAYPIAKDPQGYF 60

Query: 61  VFMNIASPPAAIHEMKRKMRIDENVLRSLTLLVDSHEQSP 100
           ++  +  P   ++++ R++RI +NV R + +       + 
Sbjct: 61  LWYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPFLAN 100


>3ofo_F 30S ribosomal protein S6; protein biosynthesis, ribosomes, RNA, tRNA, transfer, eryThr ketolide, macrolide, antibiotic, EXIT, peptidyl; 3.10A {Escherichia coli} PDB: 3fih_F* 3iy8_F 2wwl_F 3ofp_F 2gy9_F 2gyb_F Length = 100 Back     alignment and structure
>3i1m_F 30S ribosomal protein S6; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1p6g_F 1p87_F* 1vs7_F* 2avy_F 2aw7_F 1vs5_F 2i2u_F 2i2p_F* 2qan_F* 2qb9_F* 2qbb_F* 2qbd_F 2qbf_F 2qbh_F* 2qbj_F* 2qou_F* 2qow_F* 2qoy_F* 2qp0_F* 2vho_F ... Length = 135 Back     alignment and structure
>3bbn_F Ribosomal protein S6; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Length = 168 Back     alignment and structure
>1vmb_A 30S ribosomal protein S6; TM0603, structural genomics, JCSG, protein structure initiative, PSI, joint center for structural genomics; 1.70A {Thermotoga maritima} SCOP: d.58.14.1 Length = 140 Back     alignment and structure
>2j5a_A 30S ribosomal protein S6; ribonucleoprotein, RNA-binding, rRNA-binding, protein folding; 2.3A {Aquifex aeolicus} SCOP: d.58.14.1 Length = 110 Back     alignment and structure
>2kjw_A TS9, 30S ribosomal protein S6; S6 permutant, solution structure, backbone dynamics, folding, ribonucleoprotein, RNA-binding, rRNA-binding; NMR {Thermus thermophilus} Length = 96 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target135 30S ribosomal protein S6 [Candidatus Liberibacter asiat
3i1m_F135 30S ribosomal protein S6; ribosome structure, protein-R 99.97
1cqm_A101 Ribosomal protein S6; alzheimer disease, oligomerizatio 99.97
1vmb_A140 30S ribosomal protein S6; TM0603, structural genomics, 99.97
2j5a_A110 30S ribosomal protein S6; ribonucleoprotein, RNA-bindin 99.96
3ofo_F100 30S ribosomal protein S6; protein biosynthesis, ribosom 99.96
3bbn_F168 Ribosomal protein S6; small ribosomal subunit, spinach 99.95
2kjw_A96 TS9, 30S ribosomal protein S6; S6 permutant, solution s 99.59
>3i1m_F 30S ribosomal protein S6; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1p6g_F 1p87_F* 1vs7_F* 2avy_F 2aw7_F 1vs5_F 2i2u_F 2i2p_F* 2qan_F* 2qb9_F* 2qbb_F* 2qbd_F 2qbf_F 2qbh_F* 2qbj_F* 2qou_F* 2qow_F* 2qoy_F* 2qp0_F* 2vho_F ... Back     alignment and structure
Probab=99.97  E-value=7.8e-33  Score=211.75  Aligned_cols=109  Identities=29%  Similarity=0.544  Sum_probs=102.9

Q ss_pred             CCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEECCCCCEEEEEEEEEECCHHHHHHHHHHHC
Q ss_conf             98705999987899999999999999999985697899970368653530322241899999998089779999999808
Q gi|254780329|r    1 MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYVFMNIASPPAAIHEMKRKMR   80 (135)
Q Consensus         1 M~~YE~~~i~~p~~~~~~~~~~~~~~~~~i~~~gg~i~~~e~wG~r~LAY~I~k~~~G~Y~~~~f~~~~~~i~el~~~lk   80 (135)
                      ||+||+|||++|++++ ++..+++++.++|+++||+|.++++||+|+|||+|+|+++|+|++|+|.++|+.|++|++.|+
T Consensus         1 Mr~YE~~~Il~p~~~e-~~~~~~~~~~~~i~~~gg~i~~~~~wG~r~LAY~I~K~~~G~Y~~~~f~~~~~~i~el~~~lk   79 (135)
T 3i1m_F            1 MRHYEIVFMVHPDQSE-QVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHYVLMNVEAPQEVIDELETTFR   79 (135)
T ss_dssp             CCEECBEEEECSTTTT-SHHHHHHHHHHHHHHTTCEECCCEEEEEECCSSCTTSSSCEEEEECCEECCTTHHHHHHHHHH
T ss_pred             CCCCEEEEEECCCCHH-HHHHHHHHHHHHHHHCCCEEEEEECCCCCCHHCCCCCCCEEEEEEEEEEECHHHHHHHHHHHC
T ss_conf             9863399996888078-999999999999986898899975023421001135789899999999849999999999965


Q ss_pred             CCCHHEEEEEEEECCCCCCCCHHHHHHHHH
Q ss_conf             980210011244113455643576532121
Q gi|254780329|r   81 IDENVLRSLTLLVDSHEQSPTLTIQRHDRD  110 (135)
Q Consensus        81 ~~~~VLR~l~vk~~~~~~~~~~~~~~~~~~  110 (135)
                      ++++|||||+||+++....++++.+.....
T Consensus        80 ~~~~VLR~l~vk~~e~~~~~~~~~~~~~e~  109 (135)
T 3i1m_F           80 FNDAVIRSMVMRTKHAVTEASPMVKAKDER  109 (135)
T ss_dssp             HCSSEESCCBCCCSSCCCSCC---------
T ss_pred             CCCCEEEEEEEEECCCCCCCCHHHHHHHHH
T ss_conf             660400678998425666757544200110



>1cqm_A Ribosomal protein S6; alzheimer disease, oligomerization; 1.65A {Thermus thermophilus} SCOP: d.58.14.1 PDB: 1cqn_A 1qjh_A 1ris_A 1fka_F 1gix_I* 1hnw_F* 1hnx_F* 1hnz_F* 1hr0_F 1i94_F* 1i95_F* 1i96_F* 1i97_F* 1ibk_F* 1ibl_F* 1ibm_F 1j5e_F 1jgo_I* 1jgp_I* 1jgq_I* ... Back     alignment and structure
>1vmb_A 30S ribosomal protein S6; TM0603, structural genomics, JCSG, protein structure initiative, PSI, joint center for structural genomics; 1.70A {Thermotoga maritima} SCOP: d.58.14.1 Back     alignment and structure
>2j5a_A 30S ribosomal protein S6; ribonucleoprotein, RNA-binding, rRNA-binding, protein folding; 2.3A {Aquifex aeolicus} SCOP: d.58.14.1 Back     alignment and structure
>3ofo_F 30S ribosomal protein S6; protein biosynthesis, ribosomes, RNA, tRNA, transfer, eryThr ketolide, macrolide, antibiotic, EXIT, peptidyl; 3.10A {Escherichia coli} PDB: 3fih_F* 3iy8_F 2wwl_F 3ofp_F 2gy9_F 2gyb_F Back     alignment and structure
>3bbn_F Ribosomal protein S6; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Back     alignment and structure
>2kjw_A TS9, 30S ribosomal protein S6; S6 permutant, solution structure, backbone dynamics, folding, ribonucleoprotein, RNA-binding, rRNA-binding; NMR {Thermus thermophilus} Back     alignment and structure

Homologous Domains in SCOP and MMDB Database
Detected by RPS-BLAST and HHsearch

Homologous Domains in SCOP70 (Version1.75) Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 135 30S ribosomal protein S6 [Candidatus Liberibacter asiat
d2qalf1100 d.58.14.1 (F:1-100) Ribosomal protein S6 {Escherichia c 5e-24
d1loua_97 d.58.14.1 (A:) Ribosomal protein S6 {Thermus thermophil 1e-23
d1vmba_107 d.58.14.1 (A:) Ribosomal protein S6 {Thermotoga maritim 2e-22
d2j5aa1106 d.58.14.1 (A:3-108) Ribosomal protein S6 {Aquifex aeoli 3e-21
>d2qalf1 d.58.14.1 (F:1-100) Ribosomal protein S6 {Escherichia coli [TaxId: 562]} Length = 100 Back     information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: Ribosomal protein S6
family: Ribosomal protein S6
domain: Ribosomal protein S6
species: Escherichia coli [TaxId: 562]
 Score =  103 bits (259), Expect = 5e-24
 Identities = 31/100 (31%), Positives = 53/100 (53%), Gaps = 1/100 (1%)

Query: 1   MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYY 60
           M+ YE VF++  D S +Q+   I +Y + I    G++  + + G R +AY I K  KA+Y
Sbjct: 1   MRHYEIVFMVHPDQS-EQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHY 59

Query: 61  VFMNIASPPAAIHEMKRKMRIDENVLRSLTLLVDSHEQSP 100
           V MN+ +P   I E++   R ++ V+RS+ +         
Sbjct: 60  VLMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEA 99


>d1loua_ d.58.14.1 (A:) Ribosomal protein S6 {Thermus thermophilus [TaxId: 274]} Length = 97 Back     information, alignment and structure
>d1vmba_ d.58.14.1 (A:) Ribosomal protein S6 {Thermotoga maritima [TaxId: 2336]} Length = 107 Back     information, alignment and structure
>d2j5aa1 d.58.14.1 (A:3-108) Ribosomal protein S6 {Aquifex aeolicus [TaxId: 63363]} Length = 106 Back     information, alignment and structure

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

IdentityAlignment graphLength Definition Probability
Target135 30S ribosomal protein S6 [Candidatus Liberibacter asiat
d1loua_97 Ribosomal protein S6 {Thermus thermophilus [TaxId: 274] 99.97
d2j5aa1106 Ribosomal protein S6 {Aquifex aeolicus [TaxId: 63363]} 99.96
d2qalf1100 Ribosomal protein S6 {Escherichia coli [TaxId: 562]} 99.96
d1vmba_107 Ribosomal protein S6 {Thermotoga maritima [TaxId: 2336] 99.96
>d1loua_ d.58.14.1 (A:) Ribosomal protein S6 {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: Ribosomal protein S6
family: Ribosomal protein S6
domain: Ribosomal protein S6
species: Thermus thermophilus [TaxId: 274]
Probab=99.97  E-value=6.3e-31  Score=199.18  Aligned_cols=96  Identities=26%  Similarity=0.505  Sum_probs=94.6

Q ss_pred             CCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEECCCCCEEEEEEEEEECCHHHHHHHHHHHC
Q ss_conf             98705999987899999999999999999985697899970368653530322241899999998089779999999808
Q gi|254780329|r    1 MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYVFMNIASPPAAIHEMKRKMR   80 (135)
Q Consensus         1 M~~YE~~~i~~p~~~~~~~~~~~~~~~~~i~~~gg~i~~~e~wG~r~LAY~I~k~~~G~Y~~~~f~~~~~~i~el~~~lk   80 (135)
                      ||+||+++|++|++++++++++++++.++|+++||+|.++++||+|+|||||+|+++|+|++++|+++|+.+++|++.|+
T Consensus         1 M~~YE~~~i~~p~l~~~~~~~~~~~~~~~i~~~gg~i~~~e~~G~r~LAY~I~k~~~G~Y~~~~f~~~~~~i~el~~~l~   80 (97)
T d1loua_           1 MRRYEVNIVLNPNLDQSQLALEKEIIQRAAENYGARVEKVEELGLRRLAYPIAKDPQGYFLWYQVEMPEDRVNDLARELR   80 (97)
T ss_dssp             CEEEEEEEEECTTCCHHHHHHHHHHHHHHHHHTTCEEEEEEEEEEEEEEEEETTEEEEEEEEEEEEECGGGHHHHHHHHH
T ss_pred             CCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEEECCCCCCCCCEEEEEEEEEEECHHHHHHHHHHHC
T ss_conf             98613999989999989999999999999986898899985007782420246466369999999968999999999866


Q ss_pred             CCCHHEEEEEEEECCC
Q ss_conf             9802100112441134
Q gi|254780329|r   81 IDENVLRSLTLLVDSH   96 (135)
Q Consensus        81 ~~~~VLR~l~vk~~~~   96 (135)
                      +|++|||||+||++++
T Consensus        81 l~~~VlR~l~vk~~e~   96 (97)
T d1loua_          81 IRDNVRRVMVVKSQEP   96 (97)
T ss_dssp             TSTTEEEEEEEECSSC
T ss_pred             CCCCEEEEEEEEECCC
T ss_conf             7747278999971689



>d2j5aa1 d.58.14.1 (A:3-108) Ribosomal protein S6 {Aquifex aeolicus [TaxId: 63363]} Back     information, alignment and structure
>d2qalf1 d.58.14.1 (F:1-100) Ribosomal protein S6 {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1vmba_ d.58.14.1 (A:) Ribosomal protein S6 {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 135 30S ribosomal protein S6 [Candidatus Liberibacter
1cqm_A_101 (A:) Ribosomal protein S6; alzheimer disease, olig 2e-25
2j5a_A_110 (A:) 30S ribosomal protein S6; ribonucleoprotein, 2e-24
3bbn_F_168 (F:) Ribosomal protein S6; small ribosomal subunit 5e-23
1vmb_A_140 (A:) 30S ribosomal protein S6; TM0603, structural 2e-22
3i1m_F_135 (F:) 30S ribosomal protein S6; ribosome structure, 3e-25
2kjw_A_96 (A:) TS9, 30S ribosomal protein S6; S6 permutant, 6e-11
>1cqm_A (A:) Ribosomal protein S6; alzheimer disease, oligomerization; 1.65A {Thermus thermophilus}Length = 101 Back     alignment and structure
 Score =  109 bits (273), Expect = 2e-25
 Identities = 24/100 (24%), Positives = 49/100 (49%)

Query: 1   MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYY 60
           M+ YE   +L  ++   Q+       Q  ++  G  V  V  LG+R +AY I K+ + Y+
Sbjct: 1   MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVAILGLRRLAYPIAKDPQGYF 60

Query: 61  VFMNIASPPAAIHEMKRKMRIDENVLRSLTLLVDSHEQSP 100
           ++  +  P   ++++ R++RI +NV R + +       + 
Sbjct: 61  LWYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPFLAN 100


>2j5a_A (A:) 30S ribosomal protein S6; ribonucleoprotein, RNA-binding, rRNA-binding, protein folding; 2.3A {Aquifex aeolicus}Length = 110 Back     alignment and structure
>3bbn_F (F:) Ribosomal protein S6; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}Length = 168 Back     alignment and structure
>1vmb_A (A:) 30S ribosomal protein S6; TM0603, structural genomics, JCSG, protein structure initiative, PSI, joint center for structural genomics; 1.70A {Thermotoga maritima}Length = 140 Back     alignment and structure
>3i1m_F (F:) 30S ribosomal protein S6; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1p6g_F 1p87_F* 1vs7_F* 2avy_F 2aw7_F 1vs5_F 2i2u_F 2i2p_F* 2qan_F* 2qb9_F* 2qbb_F* 2qbd_F 2qbf_F 2qbh_F* 2qbj_F* 2qou_F* 2qow_F* 2qoy_F* 2qp0_F* 2vho_F ...Length = 135 Back     alignment and structure
>2kjw_A (A:) TS9, 30S ribosomal protein S6; S6 permutant, solution structure, backbone dynamics, folding, ribonucleoprotein, RNA-binding, rRNA-binding; NMR {Thermus thermophilus}Length = 96 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target135 30S ribosomal protein S6 [Candidatus Liberibacter asiat
1cqm_A_101 Ribosomal protein S6; alzheimer disease, oligomeri 99.96
3i1m_F_135 30S ribosomal protein S6; ribosome structure, prot 99.96
2j5a_A_110 30S ribosomal protein S6; ribonucleoprotein, RNA-b 99.96
1vmb_A_140 30S ribosomal protein S6; TM0603, structural genom 99.96
3bbn_F_168 Ribosomal protein S6; small ribosomal subunit, spi 99.94
2kjw_A_96 TS9, 30S ribosomal protein S6; S6 permutant, solut 99.65
>1cqm_A (A:) Ribosomal protein S6; alzheimer disease, oligomerization; 1.65A {Thermus thermophilus} Back     alignment and structure
Probab=99.96  E-value=1e-29  Score=194.39  Aligned_cols=101  Identities=24%  Similarity=0.451  Sum_probs=97.7

Q ss_pred             CCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCEECCCCCEEEEEEEEEECCHHHHHHHHHHHC
Q ss_conf             98705999987899999999999999999985697899970368653530322241899999998089779999999808
Q gi|254780329|r    1 MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYVFMNIASPPAAIHEMKRKMR   80 (135)
Q Consensus         1 M~~YE~~~i~~p~~~~~~~~~~~~~~~~~i~~~gg~i~~~e~wG~r~LAY~I~k~~~G~Y~~~~f~~~~~~i~el~~~lk   80 (135)
                      ||+||++||++|++++++++++++++.+.|.++||.|.++++||+|+|||||+|+++|+|++++|+++|+.+++|++.|+
T Consensus         1 M~~YE~~~i~~~~~~~~~~~~~~~~~~~~i~~~gg~i~~~e~~G~r~LaY~Ikk~~~G~Y~~~~f~~~~~~i~el~~~lr   80 (101)
T 1cqm_A            1 MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVAILGLRRLAYPIAKDPQGYFLWYQVEMPEDRVNDLARELR   80 (101)
T ss_dssp             CEEEEEEEEECTTCCHHHHHHHHHHHHHHHHHTTCEEEEEEEEEEEEEEEEETTEEEEEEEEEEEEECHHHHHHHHHHHH
T ss_pred             CCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEEEECCCCCEECCCCCEEEEEEEEEEECHHHHHHHHHHHC
T ss_conf             98614999988999999999999999999987898999998761510660747876899999999959999999999867


Q ss_pred             CCCHHEEEEEEEECCCCCCCC
Q ss_conf             980210011244113455643
Q gi|254780329|r   81 IDENVLRSLTLLVDSHEQSPT  101 (135)
Q Consensus        81 ~~~~VLR~l~vk~~~~~~~~~  101 (135)
                      +|++|||||++|+++....++
T Consensus        81 ~~~~VlR~l~vk~~~~~~~~s  101 (101)
T 1cqm_A           81 IRDNVRRVMVVKSQEPFLANA  101 (101)
T ss_dssp             TSTTEEEEEEEECSSCCC---
T ss_pred             CCCCEEEEEEEECCCCCCCCC
T ss_conf             898848999997277668999



>3i1m_F (F:) 30S ribosomal protein S6; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1p6g_F 1p87_F* 1vs7_F* 2avy_F 2aw7_F 1vs5_F 2i2u_F 2i2p_F* 2qan_F* 2qb9_F* 2qbb_F* 2qbd_F 2qbf_F 2qbh_F* 2qbj_F* 2qou_F* 2qow_F* 2qoy_F* 2qp0_F* 2vho_F ... Back     alignment and structure
>2j5a_A (A:) 30S ribosomal protein S6; ribonucleoprotein, RNA-binding, rRNA-binding, protein folding; 2.3A {Aquifex aeolicus} Back     alignment and structure
>1vmb_A (A:) 30S ribosomal protein S6; TM0603, structural genomics, JCSG, protein structure initiative, PSI, joint center for structural genomics; 1.70A {Thermotoga maritima} Back     alignment and structure
>3bbn_F (F:) Ribosomal protein S6; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Back     alignment and structure
>2kjw_A (A:) TS9, 30S ribosomal protein S6; S6 permutant, solution structure, backbone dynamics, folding, ribonucleoprotein, RNA-binding, rRNA-binding; NMR {Thermus thermophilus} Back     alignment and structure