254780244

254780244

30S ribosomal protein S5

GeneID in NCBI database:8209225Locus tag:CLIBASIA_00645
Protein GI in NCBI database:254780244Protein Accession:YP_003064657.1
Gene range:-(134556, 135155)Protein Length:199aa
Gene description:30S ribosomal protein S5
COG prediction:[J] Ribosomal protein S5
KEGG prediction:rpsE; 30S ribosomal protein S5; K02988 small subunit ribosomal protein S5
SEED prediction:SSU ribosomal protein S5p (S2e)
Pathway involved in KEGG:Ribosome [PATH:las03010]
Subsystem involved in SEED:Ribosome SSU bacterial;
Ribosomal protein S5p acylation
sequencesequence profile

Prediction of Local Sequence Properties

SourceSummaryResult
scaler
NCBI Databasesequence
PSIPREDsecondary structure
SSPROsecondary structure
DISEMBLcoil and loop
DISEMBLflexible loop
SEGlow complexity
DISOPREDdisordered
DISEMBLmissing residues
DISPROdisordered
TMHMMnone TM-Helix
TOPPRED1 TM-Helix
HMMTOPnone TM-Helix
MEMSATnone TM-Helix
MEMSAT_SVMnone TM-Helix
PHOBIUSnone TM-Helix
SignalP_HMMno
SignalP_NNno
COILScoiled coil
70% MSAconservation map
90% MSAconservation map
  
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------20
MAQKERSQRDNWQNREERDNSIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKRNMISVSLLDGRTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIGSSNPHNVIRATFEVLRSQSHPRDVANRRGIKHSLLQARRVVSSKSSSYSRDSKNKGGN
cccHHHHHHHHHcccccccccHHEEEEEEEEEEEEccccEEEEEEEEEEEEccccEEEEEEcccccHHHHHHHHHHHHHHcccEEEcccccEEEEEEEEEEccEEEEEEEccccccEEcccHHHHHHHHcccccHHHEEcccccHHHHHHHHHHHHHccccHHHHHHHccccHHHHHHHHHHccHHHHHHHHHHHHccc
cccccccHHHHccccccccHHHHHHHEEHHHHHHHHccccEEEEEEEEEEccccccEccccccccHcHHHHHHHHHHHHHccEEEEcccccEEcccccccccccEEEEEcccccccEEcccHHHHHHHHHcHHHHHHHHcccccHHHHHHHHHHHHHHcccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHccccc
maqkersqrdnwqnreerdnSIVDRIVAINRVstalpggrrfAFSVLVVVGdtkskvgfahstaREVPEAVRKATEAAKRNMISVSlldgrtlhhdgvgrhgagKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAksigssnphnvIRATFEVLrsqshprdvanrRGIKHSLLQARRVVSSksssysrdsknkggn
maqkersqrdnwqnreerdnsivdrIVAINRvstalpggrrFAFSVLVVVGDTKskvgfahstarevpeaVRKATEAAKRNMISVSLLDGRTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAksigssnphnVIRATFEvlrsqshprdvanrrgikhsllqarrvvssksssysrdsknkggn
MAQKERSQRDNWQNREERDNSIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKRNMISVSLLDGRTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIGSSNPHNVIRATFEVLRSQSHPRDVANRRGIKHSLLQArrvvssksssysrdskNKGGN
*************************IVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKRNMISVSLLDGRTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIGSSNPHNVIRATFEVLRSQSH********G*****************************
***************EERDNSIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKRNMISVSLLDGRTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIGSSNPHNVIRATFEVLRSQSHPRDVANRRGIKHSLLQA*********************
****************ERDNSIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKRNMISVSLLDGRTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIGSSNPHNVIRATFEVLRSQSHPRDVANRRGIKHSLLQARRVVSSKSS************
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MAQKERSQRDNWQNREERDNSIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKRNMISVSLLDGRTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIGSSNPHNVIRATFEVLRSQSHPRDVANRRGIKHSLLQARRVVSSKSSSYSRDSKNKGGN
MAQKERSQRDNWQNREERDNSIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKRNMISVSLLDGRTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIGSSNPHNVIRATFEVLRSQSHPRDVANRRGIKHSLLQARRVVSSKSSSYSRDSKNKGGN
MAQKERSQRDNWQNREERDNSIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKRNMISVSLLDGRTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIGSSNPHNVIRATFEVLRSQSHPRDVANRRGIKHSLLQARRVVSSKSSSYSRDSKNKGGN

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
Target199 30S ribosomal protein S5 [Candidatus Liberibacter asiat
315122801196 30S ribosomal protein S5 [Candidatus Liberibacter solan 1 2e-93
222148383189 30S ribosomal protein S5 [Agrobacterium vitis S4] Lengt 1 9e-68
116251557189 30S ribosomal protein S5 [Rhizobium leguminosarum bv. v 1 3e-67
159184984189 30S ribosomal protein S5 [Agrobacterium tumefaciens str 1 4e-67
86357322189 30S ribosomal protein S5 [Rhizobium etli CFN 42] Length 1 7e-67
325293319189 30S ribosomal protein S5 [Agrobacterium sp. H13-3] Leng 1 9e-67
227821773189 30S ribosomal protein S5 [Sinorhizobium fredii NGR234] 1 2e-66
15965126189 30S ribosomal protein S5 [Sinorhizobium meliloti 1021] 1 7e-65
49474387182 30S ribosomal protein S5 [Bartonella quintana str. Toul 1 2e-63
240850818182 30S ribosomal protein S5 [Bartonella grahamii as4aup] L 1 3e-63
>gi|315122801|ref|YP_004063290.1| 30S ribosomal protein S5 [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 196 Back     alignment and organism information
 Score =  345 bits (885), Expect = 2e-93,   Method: Compositional matrix adjust.
 Identities = 165/180 (91%), Positives = 177/180 (98%)

Query: 1   MAQKERSQRDNWQNREERDNSIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFA 60
           MAQKERSQRDNWQNREERDNSI+DRIV+INRVSTALPGGRRFAFSVLVVVGDTKSK GFA
Sbjct: 1   MAQKERSQRDNWQNREERDNSIIDRIVSINRVSTALPGGRRFAFSVLVVVGDTKSKAGFA 60

Query: 61  HSTAREVPEAVRKATEAAKRNMISVSLLDGRTLHHDGVGRHGAGKVIMRSAMAGTGVIAG 120
           HSTAREVPEAVRKATEAAKRNM+S+SLLDGRTLHHDG+GRHGAGKV++RSAM GTGVIAG
Sbjct: 61  HSTAREVPEAVRKATEAAKRNMVSISLLDGRTLHHDGLGRHGAGKVLIRSAMPGTGVIAG 120

Query: 121 GAIRAVCEVLGMHDVVAKSIGSSNPHNVIRATFEVLRSQSHPRDVANRRGIKHSLLQARR 180
           GAIRAVCEVLG+HD+VAKSIGSSNPHNV+RATF+ LRSQSHPRD+ANRRGIKHSLLQARR
Sbjct: 121 GAIRAVCEVLGVHDIVAKSIGSSNPHNVVRATFKALRSQSHPRDIANRRGIKHSLLQARR 180



Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|222148383|ref|YP_002549340.1| 30S ribosomal protein S5 [Agrobacterium vitis S4] Length = 189 Back     alignment and organism information
>gi|116251557|ref|YP_767395.1| 30S ribosomal protein S5 [Rhizobium leguminosarum bv. viciae 3841] Length = 189 Back     alignment and organism information
>gi|159184984|ref|NP_354907.2| 30S ribosomal protein S5 [Agrobacterium tumefaciens str. C58] Length = 189 Back     alignment and organism information
>gi|86357322|ref|YP_469214.1| 30S ribosomal protein S5 [Rhizobium etli CFN 42] Length = 189 Back     alignment and organism information
>gi|325293319|ref|YP_004279183.1| 30S ribosomal protein S5 [Agrobacterium sp. H13-3] Length = 189 Back     alignment and organism information
>gi|227821773|ref|YP_002825743.1| 30S ribosomal protein S5 [Sinorhizobium fredii NGR234] Length = 189 Back     alignment and organism information
>gi|15965126|ref|NP_385479.1| 30S ribosomal protein S5 [Sinorhizobium meliloti 1021] Length = 189 Back     alignment and organism information
>gi|49474387|ref|YP_032429.1| 30S ribosomal protein S5 [Bartonella quintana str. Toulouse] Length = 182 Back     alignment and organism information
>gi|240850818|ref|YP_002972218.1| 30S ribosomal protein S5 [Bartonella grahamii as4aup] Length = 182 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
Target199 30S ribosomal protein S5 [Candidatus Liberibacter asiat
PRK00550168 PRK00550, rpsE, 30S ribosomal protein S5; Validated 1e-61
TIGR01021154 TIGR01021, rpsE_bact, ribosomal protein S5, bacterial/o 6e-47
KOG2646396 KOG2646, KOG2646, KOG2646, Ribosomal protein S5 [Transl 1e-14
PRK04044211 PRK04044, rps5p, 30S ribosomal protein S5P; Reviewed 2e-13
TIGR01020212 TIGR01020, rpsE_arch, ribosomal protein S5(archaeal typ 8e-12
KOG0877213 KOG0877, KOG0877, KOG0877, 40S ribosomal protein S2/30S 4e-11
PTZ00070257 PTZ00070, PTZ00070, 40S ribosomal protein S2; Provision 7e-09
COG0098181 COG0098, RpsE, Ribosomal protein S5 [Translation, ribos 1e-49
CHL00138143 CHL00138, rps5, ribosomal protein S5; Validated 2e-25
pfam0371974 pfam03719, Ribosomal_S5_C, Ribosomal protein S5, C-term 4e-25
pfam0033367 pfam00333, Ribosomal_S5, Ribosomal protein S5, N-termin 1e-13
>gnl|CDD|179061 PRK00550, rpsE, 30S ribosomal protein S5; Validated Back     alignment and domain information
>gnl|CDD|130093 TIGR01021, rpsE_bact, ribosomal protein S5, bacterial/organelle type Back     alignment and domain information
>gnl|CDD|37857 KOG2646, KOG2646, KOG2646, Ribosomal protein S5 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|179727 PRK04044, rps5p, 30S ribosomal protein S5P; Reviewed Back     alignment and domain information
>gnl|CDD|162160 TIGR01020, rpsE_arch, ribosomal protein S5(archaeal type)/S2(eukaryote cytosolic type) Back     alignment and domain information
>gnl|CDD|36095 KOG0877, KOG0877, KOG0877, 40S ribosomal protein S2/30S ribosomal protein S5 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|185425 PTZ00070, PTZ00070, 40S ribosomal protein S2; Provisional Back     alignment and domain information
>gnl|CDD|30447 COG0098, RpsE, Ribosomal protein S5 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|177060 CHL00138, rps5, ribosomal protein S5; Validated Back     alignment and domain information
>gnl|CDD|146383 pfam03719, Ribosomal_S5_C, Ribosomal protein S5, C-terminal domain Back     alignment and domain information
>gnl|CDD|144065 pfam00333, Ribosomal_S5, Ribosomal protein S5, N-terminal domain 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 199 30S ribosomal protein S5 [Candidatus Liberibacter asiat
TIGR01021157 rpsE_bact ribosomal protein S5; InterPro: IPR005712 Rib 100.0
COG0098181 RpsE Ribosomal protein S5 [Translation, ribosomal struc 100.0
PRK00550156 rpsE 30S ribosomal protein S5; Validated 100.0
PRK04044211 rps5p 30S ribosomal protein S5P; Reviewed 100.0
TIGR01020220 rpsE_arch ribosomal protein S5; InterPro: IPR005711 Rib 100.0
PTZ00070261 40S ribosomal protein S2; Provisional 100.0
KOG2646396 consensus 100.0
KOG0877213 consensus 99.97
CHL00138139 rps5 ribosomal protein S5; Validated 100.0
pfam0371974 Ribosomal_S5_C Ribosomal protein S5, C-terminal domain. 99.93
pfam0033367 Ribosomal_S5 Ribosomal protein S5, N-terminal domain. 99.9
>TIGR01021 rpsE_bact ribosomal protein S5; InterPro: IPR005712 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>COG0098 RpsE Ribosomal protein S5 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK00550 rpsE 30S ribosomal protein S5; Validated Back     alignment and domain information
>PRK04044 rps5p 30S ribosomal protein S5P; Reviewed Back     alignment and domain information
>TIGR01020 rpsE_arch ribosomal protein S5; InterPro: IPR005711 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>PTZ00070 40S ribosomal protein S2; Provisional Back     alignment and domain information
>KOG2646 consensus Back     alignment and domain information
>KOG0877 consensus Back     alignment and domain information
>CHL00138 rps5 ribosomal protein S5; Validated Back     alignment and domain information
>pfam03719 Ribosomal_S5_C Ribosomal protein S5, C-terminal domain Back     alignment and domain information
>pfam00333 Ribosomal_S5 Ribosomal protein S5, N-terminal domain 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
Target199 30S ribosomal protein S5 [Candidatus Liberibacter asiat
1p6g_E166 Real Space Refined Coordinates Of The 30s Subunit F 6e-42
1vs5_E167 Crystal Structure Of The Bacterial Ribosome From Es 7e-42
3bbn_E308 Homology Model For The Spinach Chloroplast 30s Subu 2e-40
3e1a_S159 Structure Of The 30s Subunit And The Trnas Of E. Co 3e-39
3fih_E150 Ternary Complex-Bound E.Coli 70s Ribosome. This Ent 5e-39
1qd7_D145 Partial Model For 30s Ribosomal Subunit Length = 14 6e-39
1eg0_B148 Fitting Of Components With Known Structure Into An 9e-39
1pkp_A150 The Structure Of Ribosomal Protein S5 Reveals Sites 2e-38
2gy9_E148 Structure Of The 30s Subunit Of A Pre-Translocation 6e-38
1i94_E161 Crystal Structures Of The Small Ribosomal Subunit W 2e-34
3ohc_E160 Structure Of The Thermus Thermophilus Ribosome Comp 2e-34
1fka_E162 Structure Of Functionally Activated Small Ribosomal 3e-34
3fic_E151 T. Thermophilus 70s Ribosome In Complex With Mrna, 4e-34
1pns_E150 Crystal Structure Of A Streptomycin Dependent Ribos 4e-34
2zkq_e179 Structure Of A Mammalian Ribosomal 40s Subunit With 7e-28
3iz6_E274 Localization Of The Small Subunit Ribosomal Protein 3e-27
3izb_E254 Localization Of The Small Subunit Ribosomal Protein 3e-24
2xzm_E296 Crystal Structure Of The Eukaryotic 40s Ribosomal S 4e-24
3jyv_E162 Structure Of The 40s Rrna And Proteins And PE TRNA 6e-23
1s1h_E149 Structure Of The Ribosomal 80s-Eef2-Sordarin Comple 1e-21
>gi|33357882|pdb|1P6G|E Chain E, 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 = 166 Back     alignment and structure 
 Score =  174 bits (441), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 76/164 (46%), Positives = 111/164 (67%), Gaps = 1/164 (0%)

Query: 16  EERDNSIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKAT 75
           E++   + ++++A+NRVS  + GGR F+F+ L VVGD   +VGF +  AREVP A++KA 
Sbjct: 4   EKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAIQKAM 63

Query: 76  EAAKRNMISVSLLDGRTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDV 135
           E A+RNMI+V+L +  TL H   G H   +V M+ A  GTG+IAGGA+RAV EV G+H+V
Sbjct: 64  EKARRNMINVAL-NNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGVHNV 122

Query: 136 VAKSIGSSNPHNVIRATFEVLRSQSHPRDVANRRGIKHSLLQAR 179
           +AK+ GS+NP NV+RAT + L + + P  VA +RG     +  +
Sbjct: 123 LAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKSVEEILGK 166
gi|116666552|pdb|1VS5|E Chain E, 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 = 167 Back     alignment and structure
gi|188036206|pdb|3BBN|E Chain E, Homology Model For The Spinach Chloroplast 30s Subunit Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome. Length = 308 Back     alignment and structure
>gi|256032367|pdb|3E1A|S Chain S, Structure Of The 30s Subunit And The Trnas Of E. Coli Ribosome In Pre-Accommodation State Length = 159 Back     alignment and structure
>gi|224510726|pdb|3FIH|E Chain E, Ternary Complex-Bound E.Coli 70s Ribosome. This Entry Consists Of The 30s Subunit, Trnas And The Ternary Complex. Length = 150 Back     alignment and structure
>gi|6137688|pdb|1QD7|D Chain D, Partial Model For 30s Ribosomal Subunit Length = 145 Back     alignment and structure
>gi|157833512|pdb|1PKP|A Chain A, The Structure Of Ribosomal Protein S5 Reveals Sites Of Interaction With 16s Rrna Length = 150 Back     alignment and structure
>gi|116667414|pdb|2GY9|E Chain E, 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 = 148 Back     alignment and structure
>gi|14278534|pdb|1I94|E Chain E, Crystal Structures Of The Small Ribosomal Subunit With Tetracycline, Edeine And If3 Length = 161 Back     alignment and structure
>gi|309320341|pdb|3OHC|E Chain E, Structure Of The Thermus Thermophilus Ribosome Complexed With Erythromycin. This File Contains The 30s Subunit Of One 70s Ribosome. The Entire Crystal Structure Contains Two 70s Ribosomes. Length = 160 Back     alignment and structure
gi|10120568|pdb|1FKA|E Chain E, Structure Of Functionally Activated Small Ribosomal Subunit At 3.3 A Resolution Length = 162 Back     alignment and structure
>gi|224510687|pdb|3FIC|E Chain E, T. Thermophilus 70s Ribosome In Complex With Mrna, Trnas And Ef-Tu.Gdp.Kirromycin Ternary Complex, Fitted To A 6.4 A Cryo-Em Map. This File Contains The 30s Subunit And The Ligands Length = 151 Back     alignment and structure
>gi|34811533|pdb|1PNS|E Chain E, Crystal Structure Of A Streptomycin Dependent Ribosome From E. Coli, 30s Subunit Of 70s Ribosome. This File, 1pns, Contains The 30s Subunit, Two Trnas, And One Mrna Molecule. The 50s Ribosomal Subunit Is In File 1pnu. Length = 150 Back     alignment and structure
>gi|187609259|pdb|2ZKQ|EE Chain e, 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 = 179 Back     alignment and structure
gi|313103632|pdb|3IZ6|E Chain E, Localization Of The Small Subunit Ribosomal Proteins Into A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s Ribosome Length = 274 Back     alignment and structure
gi|313103668|pdb|3IZB|E Chain E, Localization Of The Small Subunit Ribosomal Proteins Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae Translating 80s Ribosome Length = 254 Back     alignment and structure
gi|319443360|pdb|2XZM|E Chain E, 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 = 296 Back     alignment and structure
>gi|281500811|pdb|3JYV|E Chain E, 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 = 162 Back     alignment and structure
>gi|49258825|pdb|1S1H|E Chain E, 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 = 149 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

IdentityAlignment graphLength Definition E-value
Target199 30S ribosomal protein S5 [Candidatus Liberibacter asiat
3bbn_E308 Ribosomal protein S5; small ribosomal subunit, spinach 4e-44
3ofo_E150 30S ribosomal protein S5; protein biosynthesis, ribosom 7e-38
3i1m_E167 30S ribosomal protein S5; ribosome structure, protein-R 7e-37
1pkp_A150 Ribosomal protein S5; 2.80A {Geobacillus stearothermoph 6e-35
3jyv_E162 40S ribosomal protein S2; eukaryotic ribosome, RACK1 pr 1e-33
2vqe_E162 30S ribosomal protein S5; tRNA-binding, rRNA-binding, m 4e-33
2zkq_e179 40S ribosomal protein S2E; protein-RNA complex, 40S rib 1e-29
>3bbn_E Ribosomal protein S5; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Length = 308 Back     alignment and structure
 Score =  172 bits (437), Expect = 4e-44
 Identities = 62/170 (36%), Positives = 96/170 (56%)

Query: 3   QKERSQRDNWQNREERDNSIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHS 62
            K+ +   +   +E+  +   + +V + RV+  + GG+   F  +VVVGD K +VG    
Sbjct: 133 IKKATGFGSKSKKEKIRDGFEENVVQVRRVTKVVKGGKHMRFRAIVVVGDKKGQVGVGVG 192

Query: 63  TAREVPEAVRKATEAAKRNMISVSLLDGRTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGA 122
            A+EV  AV+KA   A+RN+I+V +    T  H     +GA +V++R A  GTGVIAGGA
Sbjct: 193 KAKEVVSAVQKAAVDARRNIITVPMTKYLTFPHRNEADYGAARVMLRPAAPGTGVIAGGA 252

Query: 123 IRAVCEVLGMHDVVAKSIGSSNPHNVIRATFEVLRSQSHPRDVANRRGIK 172
           +R V E+ G+ + + K +GS+N  N  RAT   +++     DVA  RGI 
Sbjct: 253 VRTVLEMAGVENALGKQLGSNNALNNARATIVAVQTMRQFSDVARDRGIP 302
>3ofo_E 30S ribosomal protein S5; protein biosynthesis, ribosomes, RNA, tRNA, transfer, eryThr ketolide, macrolide, antibiotic, EXIT, peptidyl; 3.10A {Escherichia coli} PDB: 3fih_E* 3iy8_E 2wwl_E 3ofp_E 2qal_E* 1p6g_E 1p87_E 2aw7_E 2avy_E 2i2u_E 2i2p_E* 2qan_E* 2qb9_E* 2qbb_E* 2qbd_E 2qbf_E 2qbh_E* 2qbj_E* 2qou_E* 2qow_E* ... Length = 150 Back     alignment and structure
>3i1m_E 30S ribosomal protein S5; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_E* 1vs5_E 3i1o_E 3i1q_E 3i1s_E 3i1z_E 3i21_E 2qal_E* 1p6g_E 1p87_E 2aw7_E 2avy_E 2i2u_E 2i2p_E* 2qan_E* 2qb9_E* 2qbb_E* 2qbd_E 2qbf_E 2qbh_E* ... Length = 167 Back     alignment and structure
>1pkp_A Ribosomal protein S5; 2.80A {Geobacillus stearothermophilus} SCOP: d.14.1.1 d.50.1.2 PDB: 1eg0_B 1dv4_E* 1qd7_D Length = 150 Back     alignment and structure
>3jyv_E 40S ribosomal protein S2; eukaryotic ribosome, RACK1 protein, flexible fitting; HET: 2MG H2U M2G OMC OMG YYG PSU 5MC 7MG 5MU 1MA; 8.90A {Thermomyces lanuginosus} PDB: 1s1h_E Length = 162 Back     alignment and structure
>2vqe_E 30S ribosomal protein S5; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: i.1.1.3 PDB: 1fka_E 1gix_H* 1hnw_E* 1hnx_E* 1hnz_E* 1hr0_E 1ibk_E* 1ibl_E* 1ibm_E 1jgo_H* 1jgp_H* 1jgq_H* 1ml5_H* 1xmo_E* 1xmq_E* 1xnq_E* 1xnr_E* 1yl4_H 2b64_E* 2b9m_E* ... Length = 162 Back     alignment and structure
>2zkq_e 40S ribosomal protein S2E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Length = 179 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

Original result of HHsearch against PDB70 database

IdentityAlignment graphLength Definition Probability
Target199 30S ribosomal protein S5 [Candidatus Liberibacter asiat
3bbn_E308 Ribosomal protein S5; small ribosomal subunit, spinach 100.0
2vqe_E162 30S ribosomal protein S5; tRNA-binding, rRNA-binding, m 100.0
3i1m_E167 30S ribosomal protein S5; ribosome structure, protein-R 100.0
1pkp_A150 Ribosomal protein S5; 2.80A {Geobacillus stearothermoph 100.0
3ofo_E150 30S ribosomal protein S5; protein biosynthesis, ribosom 100.0
2zkq_e179 40S ribosomal protein S2E; protein-RNA complex, 40S rib 100.0
3jyv_E162 40S ribosomal protein S2; eukaryotic ribosome, RACK1 pr 100.0
>3bbn_E Ribosomal protein S5; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Back     alignment and structure
Probab=100.00  E-value=0  Score=400.89  Aligned_cols=167  Identities=37%  Similarity=0.575  Sum_probs=160.8

Q ss_pred             HHHHHCCCCCCCEEEEEEECCCCEECCCCEEEEEEEEEEECCCCCCEEEEECCCCCHHHHHHHHHHHHHHCEEEEECCCC
Q ss_conf             12210000116021000022444012787384679999980899838997047442478999999999630125220166
Q gi|254780244|r   11 NWQNREERDNSIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKRNMISVSLLDG   90 (199)
Q Consensus        11 ~~~~~~~~~~~l~ekvi~v~RV~k~tkgGr~~sf~alvvvGn~~G~vG~G~GKa~ev~~Ai~KA~~~Akknli~V~~~~~   90 (199)
                      ...+++...++|+|+||+|+||+|||+|||++||+|||+|||+||+||||+|||.|+++||+||+++|++||++|+++++
T Consensus       141 ~~~r~~~~~~ef~EkVV~I~RV~KvTKGGR~~sFrALVVVGNgnG~VG~G~GKA~EV~~AIrKA~~~AKkNLi~V~~~~~  220 (308)
T 3bbn_E          141 SKSKKEKIRDGFEENVVQVRRVTKVVKGGKHMRFRAIVVVGDKKGQVGVGVGKAKEVVSAVQKAAVDARRNIITVPMTKY  220 (308)
T ss_dssp             ----------CCEEEEEEEECCEEEETTEEEECCEEEEEEECSSSEEEEEEEECSSHHHHHHHHHHTTTTSCEECCCCSS
T ss_pred             CCCCCCCCCCCCCEEEEEEEEEEEEECCCCCEEEEEEEEEECCCCCEEEEEEECCCHHHHHHHHHHHHHHCEEEEECCCC
T ss_conf             64324454567001777585112240588715789999995799968678771566899999999999714898857679


Q ss_pred             CCCCEECCCCCCCEEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCCEEECCCCCHHHHHHHHHHHHHCCCCHHHHHHHCC
Q ss_conf             87620011033767999963675448503048999999809441004546898888999999999950699899998619
Q gi|254780244|r   91 RTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIGSSNPHNVIRATFEVLRSQSHPRDVANRRG  170 (199)
Q Consensus        91 ~TI~h~v~gk~g~~kV~l~Pap~G~Gi~a~~~vr~il~laGI~dv~aK~~GS~N~~NvvkAt~~AL~~~~t~~~iA~~RG  170 (199)
                      |||||++.+|||+++|+|+|||+|+||+||+.++.||+++||+||++|++||+|++|+++|||+||.+++|+++||+.||
T Consensus       221 ~TIPh~V~gK~gstkV~LkPAP~GTGIiAg~~vR~ILelAGIkDv~tKs~GS~N~lNvvKATf~AL~~lrS~eeIA~~RG  300 (308)
T 3bbn_E          221 LTFPHRNEADYGAARVMLRPAAPGTGVIAGGAVRTVLEMAGVENALGKQLGSNNALNNARATIVAVQTMRQFSDVARDRG  300 (308)
T ss_dssp             SBCSSCEEEEETTEEEEEEECCTTCCEECCTTTHHHHTTTTCCBEEEEEEECCCTTTTTTHHHHHHHTCCCHHHHHTTSC
T ss_pred             CCCCEEEEEEECCEEEEEECCCCCCCEECCCHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHC
T ss_conf             86785777787425999835998989743809999999679472777767788788899999999983699999999849


Q ss_pred             CCHHHHH
Q ss_conf             9798944
Q gi|254780244|r  171 IKHSLLQ  177 (199)
Q Consensus       171 ~~i~~~~  177 (199)
                      ++++|+.
T Consensus       301 k~i~EL~  307 (308)
T 3bbn_E          301 IPMEELW  307 (308)
T ss_dssp             CCSCCCC
T ss_pred             CCHHHHC
T ss_conf             9678863
>2vqe_E 30S ribosomal protein S5; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: i.1.1.3 PDB: 1fka_E 1gix_H* 1hnw_E* 1hnx_E* 1hnz_E* 1hr0_E 1ibk_E* 1ibl_E* 1ibm_E 1jgo_H* 1jgp_H* 1jgq_H* 1ml5_H* 1xmo_E* 1xmq_E* 1xnq_E* 1xnr_E* 1yl4_H 2b64_E* 2b9m_E* ... Back     alignment and structure
>3i1m_E 30S ribosomal protein S5; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_E* 1vs5_E 3i1o_E 3i1q_E 3i1s_E 3i1z_E 3i21_E 3kc4_E 2qal_E* 1p6g_E 1p87_E 2aw7_E 2avy_E 2i2u_E 2i2p_E* 2qan_E* 2qb9_E* 2qbb_E* 2qbd_E 2qbf_E ... Back     alignment and structure
>1pkp_A Ribosomal protein S5; 2.80A {Geobacillus stearothermophilus} SCOP: d.14.1.1 d.50.1.2 PDB: 1eg0_B 1dv4_E* 1qd7_D Back     alignment and structure
>3ofo_E 30S ribosomal protein S5; protein biosynthesis, ribosomes, RNA, tRNA, transfer, eryThr ketolide, macrolide, antibiotic, EXIT, peptidyl; 3.10A {Escherichia coli} PDB: 3fih_E* 3iy8_E 2wwl_E 3ofp_E 2qal_E* 1p6g_E 1p87_E 2aw7_E 2avy_E 2i2u_E 2i2p_E* 2qan_E* 2qb9_E* 2qbb_E* 2qbd_E 2qbf_E 2qbh_E* 2qbj_E* 2qou_E* 2qow_E* ... Back     alignment and structure
>2zkq_e 40S ribosomal protein S2E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Back     alignment and structure
>3jyv_E 40S ribosomal protein S2; eukaryotic ribosome, RACK1 protein, flexible fitting; HET: 2MG H2U M2G OMC OMG YYG PSU 5MC 7MG 5MU 1MA; 8.90A {Thermomyces lanuginosus} PDB: 1s1h_E Back     alignment and structure

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

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

Original result of RPS-BLAST against SCOP70(version1.75) database

IdentityAlignment graphLength Definition E-value
Target 199 30S ribosomal protein S5 [Candidatus Liberibacter asiat
d2qale181 d.14.1.1 (E:78-158) Ribosomal protein S5, C-terminal do 5e-24
d2uube181 d.14.1.1 (E:74-154) Ribosomal protein S5, C-terminal do 1e-21
d1pkpa171 d.14.1.1 (A:78-148) Ribosomal protein S5, C-terminal do 4e-21
d2uube269 d.50.1.2 (E:5-73) Ribosomal S5 protein, N-terminal doma 2e-17
d1pkpa274 d.50.1.2 (A:4-77) Ribosomal S5 protein, N-terminal doma 2e-16
d2qale269 d.50.1.2 (E:9-77) Ribosomal S5 protein, N-terminal doma 3e-16
>d2qale1 d.14.1.1 (E:78-158) Ribosomal protein S5, C-terminal domain {Escherichia coli [TaxId: 562]} Length = 81 Back     information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Translational machinery components
domain: Ribosomal protein S5, C-terminal domain
species: Escherichia coli [TaxId: 562]

 Score =  104 bits (262), Expect = 5e-24
 Identities = 41/79 (51%), Positives = 55/79 (69%)

Query: 92  TLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIGSSNPHNVIRA 151
           TL H   G H   +V M+ A  GTG+IAGGA+RAV EV G+H+V+AK+ GS+NP NV+RA
Sbjct: 2   TLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGVHNVLAKAYGSTNPINVVRA 61

Query: 152 TFEVLRSQSHPRDVANRRG 170
           T + L + + P  VA +RG
Sbjct: 62  TIDGLENMNSPEMVAAKRG 80
>d2uube1 d.14.1.1 (E:74-154) Ribosomal protein S5, C-terminal domain {Thermus thermophilus [TaxId: 274]} Length = 81 Back     information, alignment and structure
>d1pkpa1 d.14.1.1 (A:78-148) Ribosomal protein S5, C-terminal domain {Bacillus stearothermophilus [TaxId: 1422]} Length = 71 Back     information, alignment and structure
>d2uube2 d.50.1.2 (E:5-73) Ribosomal S5 protein, N-terminal domain {Thermus thermophilus [TaxId: 274]} Length = 69 Back     information, alignment and structure
>d1pkpa2 d.50.1.2 (A:4-77) Ribosomal S5 protein, N-terminal domain {Bacillus stearothermophilus [TaxId: 1422]} Length = 74 Back     information, alignment and structure
>d2qale2 d.50.1.2 (E:9-77) Ribosomal S5 protein, N-terminal domain {Escherichia coli [TaxId: 562]} Length = 69 Back     information, alignment and structure

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

Original result of HHsearch against SCOP70(version1.75) database

IdentityAlignment graphLength Definition Probability
Target199 30S ribosomal protein S5 [Candidatus Liberibacter asiat
d2qale181 Ribosomal protein S5, C-terminal domain {Escherichia co 99.96
d2uube181 Ribosomal protein S5, C-terminal domain {Thermus thermo 99.96
d1pkpa171 Ribosomal protein S5, C-terminal domain {Bacillus stear 99.93
d2uube269 Ribosomal S5 protein, N-terminal domain {Thermus thermo 99.9
d1pkpa274 Ribosomal S5 protein, N-terminal domain {Bacillus stear 99.89
d2qale269 Ribosomal S5 protein, N-terminal domain {Escherichia co 99.89
>d2qale1 d.14.1.1 (E:78-158) Ribosomal protein S5, C-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: Translational machinery components
domain: Ribosomal protein S5, C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=99.96  E-value=1.7e-30  Score=203.53  Aligned_cols=80  Identities=51%  Similarity=0.773  Sum_probs=79.4

Q ss_pred             CCCEECCCCCCCEEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCCEEECCCCCHHHHHHHHHHHHHCCCCHHHHHHHCCC
Q ss_conf             76200110337679999636754485030489999998094410045468988889999999999506998999986199
Q gi|254780244|r   92 TLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIGSSNPHNVIRATFEVLRSQSHPRDVANRRGI  171 (199)
Q Consensus        92 TI~h~v~gk~g~~kV~l~Pap~G~Gi~a~~~vr~il~laGI~dv~aK~~GS~N~~NvvkAt~~AL~~~~t~~~iA~~RG~  171 (199)
                      ||||++++||++++|+|+|||+|+||+||+.+|.|||++||+|+++|++||+||+|+++|||+||++++||+|+|+.||+
T Consensus         2 TIph~v~gk~gs~kV~l~PAp~GtGliag~~vr~ilelaGI~Dv~~K~~GS~n~~N~vkAt~~aL~~~~t~~~iA~~RGk   81 (81)
T d2qale1           2 TLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGVHNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGK   81 (81)
T ss_dssp             BCSSCBCCEETTEEEEBCBCCTTSCEECCHHHHHHHHHHTCCSEECEEEECCCHHHHHHHHHHHHTTCCCHHHHHHHTTC
T ss_pred             CCCEEEEEEECCEEEEEEECCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHCC
T ss_conf             61278899989699999978999841347799999998296626767589997899999999999818999999998286
>d2uube1 d.14.1.1 (E:74-154) Ribosomal protein S5, C-terminal domain {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1pkpa1 d.14.1.1 (A:78-148) Ribosomal protein S5, C-terminal domain {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure
>d2uube2 d.50.1.2 (E:5-73) Ribosomal S5 protein, N-terminal domain {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1pkpa2 d.50.1.2 (A:4-77) Ribosomal S5 protein, N-terminal domain {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure
>d2qale2 d.50.1.2 (E:9-77) Ribosomal S5 protein, N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

Original result of RPS-BLAST against MMDB70 database

IdentityAlignment graphLength Definition E-value
Target 199 30S ribosomal protein S5 [Candidatus Liberibacter
3i1m_E_167 (E:) 30S ribosomal protein S5; ribosome structure, 8e-34
2vqe_E_1-143143 (E:1-143) 30S ribosomal protein S5; tRNA-binding, 6e-30
2zkq_e_82-17998 (e:82-179) 40S ribosomal protein S2E; protein-RNA 1e-19
3jyv_E_75-16288 (E:75-162) 40S ribosomal protein S2; eukaryotic ri 2e-18
3bbn_E_221-28969 (E:221-289) Ribosomal protein S5; small ribosomal 2e-18
1pkp_A_79-15072 (A:79-150) Ribosomal protein S5; 2.80A {Geobacillu 2e-18
1pkp_A_1-7878 (A:1-78) Ribosomal protein S5; 2.80A {Geobacillus 6e-16
3bbn_E_1-220220 (E:1-220) Ribosomal protein S5; small ribosomal su 7e-14
3jyv_E_1-7474 (E:1-74) 40S ribosomal protein S2; eukaryotic ribo 2e-12
2zkq_e_1-8181 (e:1-81) 40S ribosomal protein S2E; protein-RNA co 3e-11
>3i1m_E (E:) 30S ribosomal protein S5; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_E* 1vs5_E 3i1o_E 3i1q_E 3i1s_E 3i1z_E 3i21_E 2qal_E* 1p6g_E 1p87_E 2aw7_E 2avy_E 2i2u_E 2i2p_E* 2qan_E* 2qb9_E* 2qbb_E* 2qbd_E 2qbf_E 2qbh_E* ...Length = 167 Back     alignment and structure
 Score =  137 bits (347), Expect = 8e-34
 Identities = 76/159 (47%), Positives = 109/159 (68%), Gaps = 1/159 (0%)

Query: 14  NREERDNSIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRK 73
           + E++   + ++++A+NRVS  + GGR F+F+ L VVGD   +VGF +  AREVP A++K
Sbjct: 3   HIEKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAIQK 62

Query: 74  ATEAAKRNMISVSLLDGRTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMH 133
           A E A+RNMI+V  L+  TL H   G H   +V M+ A  GTG+IAGGA+RAV EV G+H
Sbjct: 63  AMEKARRNMINV-ALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGVH 121

Query: 134 DVVAKSIGSSNPHNVIRATFEVLRSQSHPRDVANRRGIK 172
           +V+AK+ GS+NP NV+RAT + L + + P  VA +RG  
Sbjct: 122 NVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKS 160
>2vqe_E (E:1-143) 30S ribosomal protein S5; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus}Length = 143 Back     alignment and structure
>2zkq_e (e:82-179) 40S ribosomal protein S2E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris}Length = 98 Back     alignment and structure
>3jyv_E (E:75-162) 40S ribosomal protein S2; eukaryotic ribosome, RACK1 protein, flexible fitting; HET: 2MG H2U M2G OMC OMG YYG PSU 5MC 7MG 5MU 1MA; 8.90A {Thermomyces lanuginosus} PDB: 1s1h_ELength = 88 Back     alignment and structure
>3bbn_E (E:221-289) Ribosomal protein S5; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}Length = 69 Back     alignment and structure
>1pkp_A (A:79-150) Ribosomal protein S5; 2.80A {Geobacillus stearothermophilus}Length = 72 Back     alignment and structure
>1pkp_A (A:1-78) Ribosomal protein S5; 2.80A {Geobacillus stearothermophilus}Length = 78 Back     alignment and structure
>3bbn_E (E:1-220) Ribosomal protein S5; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}Length = 220 Back     alignment and structure
>3jyv_E (E:1-74) 40S ribosomal protein S2; eukaryotic ribosome, RACK1 protein, flexible fitting; HET: 2MG H2U M2G OMC OMG YYG PSU 5MC 7MG 5MU 1MA; 8.90A {Thermomyces lanuginosus} PDB: 1s1h_ELength = 74 Back     alignment and structure
>2zkq_e (e:1-81) 40S ribosomal protein S2E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris}Length = 81 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

Original result of HHsearch against MMDB70 database

IdentityAlignment graphLength Definition Probability
Target199 30S ribosomal protein S5 [Candidatus Liberibacter asiat
3i1m_E_167 30S ribosomal protein S5; ribosome structure, prot 100.0
2vqe_E_1-143143 30S ribosomal protein S5; tRNA-binding, rRNA-bindi 100.0
2zkq_e_82-17998 40S ribosomal protein S2E; protein-RNA complex, 40 99.96
3jyv_E_75-16288 40S ribosomal protein S2; eukaryotic ribosome, RAC 99.93
1pkp_A_79-15072 Ribosomal protein S5; 2.80A {Geobacillus stearothe 99.92
3bbn_E_221-28969 Ribosomal protein S5; small ribosomal subunit, spi 99.9
3bbn_E_1-220220 Ribosomal protein S5; small ribosomal subunit, spi 99.91
3jyv_E_1-7474 40S ribosomal protein S2; eukaryotic ribosome, RAC 99.9
1pkp_A_1-7878 Ribosomal protein S5; 2.80A {Geobacillus stearothe 99.9
2zkq_e_1-8181 40S ribosomal protein S2E; protein-RNA complex, 40 99.89
>3i1m_E (E:) 30S ribosomal protein S5; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_E* 1vs5_E 3i1o_E 3i1q_E 3i1s_E 3i1z_E 3i21_E 2qal_E* 1p6g_E 1p87_E 2aw7_E 2avy_E 2i2u_E 2i2p_E* 2qan_E* 2qb9_E* 2qbb_E* 2qbd_E 2qbf_E 2qbh_E* ... Back     alignment and structure
Probab=100.00  E-value=0  Score=374.43  Aligned_cols=164  Identities=46%  Similarity=0.735  Sum_probs=159.5

Q ss_pred             HHCCCCCCCEEEEEEECCCCEECCCCEEEEEEEEEEECCCCCCEEEEECCCCCHHHHHHHHHHHHHHCEEEEECCCCCCC
Q ss_conf             10000116021000022444012787384679999980899838997047442478999999999630125220166876
Q gi|254780244|r   14 NREERDNSIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKRNMISVSLLDGRTL   93 (199)
Q Consensus        14 ~~~~~~~~l~ekvi~v~RV~k~tkgGr~~sf~alvvvGn~~G~vG~G~GKa~ev~~Ai~KA~~~Akknli~V~~~~~~TI   93 (199)
                      +.|...++|+|+||+|+||+|||++||++||+|||+|||+||++|||.|||.|+++|++||..+|++||++||+.+ +||
T Consensus         3 ~~d~~~~~l~~~vl~i~rV~k~T~~Gr~~~f~alvvvGn~nG~vG~G~gka~ev~~Ai~kA~~~A~~nl~~V~~~~-~Ti   81 (167)
T 3i1m_E            3 HIEKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAIQKAMEKARRNMINVALNN-GTL   81 (167)
T ss_dssp             -------CCCEEEEEEEEEECCBTTBCCEEEEEEEEEECSSSCEEEECCEESSHHHHHHHHHHHHHSSEECCCCBT-TBC
T ss_pred             CCCCCCCCCCEEEEEEEEEEEEECCCCCEEEEEEEEEECCCCCEEEEEECCCCHHHHHHHHHHHHHHHHEEEECCC-CCC
T ss_conf             5013455600178988524457058862168999999679987875111176589999999999985412551335-623


Q ss_pred             CEECCCCCCCEEEEEEECCCCCCCCCCHHHHHHHHHHCCCCCCEEECCCCCHHHHHHHHHHHHHCCCCHHHHHHHCCCCH
Q ss_conf             20011033767999963675448503048999999809441004546898888999999999950699899998619979
Q gi|254780244|r   94 HHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIGSSNPHNVIRATFEVLRSQSHPRDVANRRGIKH  173 (199)
Q Consensus        94 ~h~v~gk~g~~kV~l~Pap~G~Gi~a~~~vr~il~laGI~dv~aK~~GS~N~~NvvkAt~~AL~~~~t~~~iA~~RG~~i  173 (199)
                      ||+++++|++++|+|+|||+|+||+||+.+++||+++||+|+++|++||+||+|+++|||+||++++||+++|+.||+++
T Consensus        82 ~~~v~gk~~~~~v~l~pap~G~Gl~~~~~i~~il~laGI~dv~~K~~Gs~n~~n~vkA~~~aL~~~~t~~~ia~~rg~~~  161 (167)
T 3i1m_E           82 QHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGVHNVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKSV  161 (167)
T ss_dssp             SSCEEEEETTEEEEEECCCCSSSCBCCSSSSSHHHHHTCCSCEEEEEECCCHHHHHHHTHHHHHSCCCSTTTTTTTTC--
T ss_pred             CCCCCEEECCCEEEEEECCCCCCEEECHHHHHHHHHHCCCHHHHHCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHCCCH
T ss_conf             24464355362379972479865078747777888816010212115789788999999999983899999999809969


Q ss_pred             HHHHH
Q ss_conf             89445
Q gi|254780244|r  174 SLLQA  178 (199)
Q Consensus       174 ~~~~~  178 (199)
                      +|+..
T Consensus       162 ~e~~~  166 (167)
T 3i1m_E          162 EEILG  166 (167)
T ss_dssp             -----
T ss_pred             HHHCC
T ss_conf             99617
>2vqe_E (E:1-143) 30S ribosomal protein S5; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} Back     alignment and structure
>2zkq_e (e:82-179) 40S ribosomal protein S2E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Back     alignment and structure
>3jyv_E (E:75-162) 40S ribosomal protein S2; eukaryotic ribosome, RACK1 protein, flexible fitting; HET: 2MG H2U M2G OMC OMG YYG PSU 5MC 7MG 5MU 1MA; 8.90A {Thermomyces lanuginosus} PDB: 1s1h_E Back     alignment and structure
>1pkp_A (A:79-150) Ribosomal protein S5; 2.80A {Geobacillus stearothermophilus} Back     alignment and structure
>3bbn_E (E:221-289) Ribosomal protein S5; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Back     alignment and structure
>3bbn_E (E:1-220) Ribosomal protein S5; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Back     alignment and structure
>3jyv_E (E:1-74) 40S ribosomal protein S2; eukaryotic ribosome, RACK1 protein, flexible fitting; HET: 2MG H2U M2G OMC OMG YYG PSU 5MC 7MG 5MU 1MA; 8.90A {Thermomyces lanuginosus} PDB: 1s1h_E Back     alignment and structure
>1pkp_A (A:1-78) Ribosomal protein S5; 2.80A {Geobacillus stearothermophilus} Back     alignment and structure
>2zkq_e (e:1-81) 40S ribosomal protein S2E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Back     alignment and structure