254780255

254780255

30S ribosomal protein S3

GeneID in NCBI database:8209236Locus tag:CLIBASIA_00700
Protein GI in NCBI database:254780255Protein Accession:YP_003064668.1
Gene range:-(139204, 139887)Protein Length:227aa
Gene description:30S ribosomal protein S3
COG prediction:[J] Ribosomal protein S3
KEGG prediction:rpsC; 30S ribosomal protein S3; K02982 small subunit ribosomal protein S3
SEED prediction:SSU ribosomal protein S3p (S3e)
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-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------
MGQKINPILFRLGVNCTWNSRWFARGSEYGALLHEDLKIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKPEINATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEGRVPLQTLRAHIDYGTAVAETAYGSCGIKVYVSLRDEVSDSDSTIPAAEHRVVEKDS
cccccccccEEEEEcccccEEEcccHHHHHHHHHHHHHHHHHHHHHHHHccccEEEEEEcccEEEEEEEEcccEEEEccccHHHHHHHHHHHHcccccEEEEEEEEEcccccHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHcccccEEEEEEEEccHHHHHHHHHHcccccccccccHHHHHHEEEEEEcccEEEEEEEEEEccccccccccccccccccccccc
ccccccccccEEEEEccccccccccccHHHHHHHHHHHHHHHHHHHHHHccccEEEEEEcccccEEEEEcccccEEEEcccccHHHHHHHHHHHHcccEEEEEEEEcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccEEEEEEccccccHHHHHHHHHcccccccEEEEccccccccccccEEEEEEEEEEEEccEcccccHHHcccccccccccc
mgqkinpilfrlgvnctwnsrwfargseygaLLHEDLKIREYLQCHLKQAGVAKILIERTHKNCRIIVysarpgliigkkgTDIEKIRKKLSNmtnseihlsvnevpkpeiNATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGrlngaelsrtecylegrvplQTLRAHIDYGTAVAETAYGSCGIKVYVSLrdevsdsdstipaaehrvvekds
mgqkinpilfRLGVNCTWNSRWFARGSEYGALLHEDLKIREYLQCHLKQAGVAKILIERTHKNCRIIvysarpgliigkkgTDIEKIRKKLSNMTNSEIHLSVNEVPKPEINATLIAQSIAQQLERRVVFRRAMKRAVQsamrfgadgvkviASGRLNGAELSRTECYLEGRVPLQTLRAHIDYGTAVAETAYGSCGIKVYVSLRdevsdsdstipaaehrvvekds
MGQKINPILFRLGVNCTWNSRWFARGSEYGALLHEDLKIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKPEINATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEGRVPLQTLRAHIDYGTAVAETAYGSCGIKVYVSLRDEVSDSDSTIPAAEHRVVEKDS
*GQKINPILFRLGVNCTWNSRWFARGSEYGALLHEDLKIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKPEINATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEGRVPLQTLRAHIDYGTAVAETAYGSCGIKVYVSLRD*********************
MGQKINPILFRLGVNCTWNSRWFARGSEYGALLHEDLKIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKPEINATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEGRVPLQTLRAHIDYGTAVAETAYGSCGIKVYVSLRDEVSDSDSTIPAAEHRVVEKDS
***KINPILFRLGVNCTWNSRWFARGSEYGALLHEDLKIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKPEINATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEGRVPLQTLRAHIDYGTAVAETAYGSCGIKVYVSLRDEVSDS****************
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MGQKINPILFRLGVNCTWNSRWFARGSEYGALLHEDLKIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKPEINATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEGRVPLQTLRAHIDYGTAVAETAYGSCGIKVYVSLRDEVSDSDSTIPAAEHRVVEKDS
MGQKINPILFRLGVNCTWNSRWFARGSEYGALLHEDLKIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKPEINATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEGRVPLQTLRAHIDYGTAVAETAYGSCGIKVYVSLRDEVSDSDSTIPAAEHRVVEKDS
MGQKINPILFRLGVNCTWNSRWFARGSEYGALLHEDLKIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKPEINATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEGRVPLQTLRAHIDYGTAVAETAYGSCGIKVYVSLRDEVSDSDSTIPAAEHRVVEKDS

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
Target227 30S ribosomal protein S3 [Candidatus Liberibacter asiat
315122812225 30S ribosomal protein S3 [Candidatus Liberibacter solan 1 1e-103
15965115237 30S ribosomal protein S3 [Sinorhizobium meliloti 1021] 1 3e-86
227821762237 30S ribosomal protein S3 [Sinorhizobium fredii NGR234] 1 3e-86
150396213237 30S ribosomal protein S3 [Sinorhizobium medicae WSM419] 1 3e-86
209548941243 30S ribosomal protein S3 [Rhizobium leguminosarum bv. t 1 9e-86
86357311244 30S ribosomal protein S3 [Rhizobium etli CFN 42] Length 1 1e-85
15889236243 30S ribosomal protein S3 [Agrobacterium tumefaciens str 1 1e-85
116251546243 30S ribosomal protein S3 [Rhizobium leguminosarum bv. v 1 1e-85
325293330243 30S ribosomal protein S3 [Agrobacterium sp. H13-3] Leng 1 2e-85
222085681241 ribosomal protein S3 [Agrobacterium radiobacter K84] Le 1 3e-85
>gi|315122812|ref|YP_004063301.1| 30S ribosomal protein S3 [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 225 Back     alignment and organism information
 Score =  379 bits (973), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 185/227 (81%), Positives = 207/227 (91%), Gaps = 2/227 (0%)

Query: 1   MGQKINPILFRLGVNCTWNSRWFARGSEYGALLHEDLKIREYLQCHLKQAGVAKILIERT 60
           MGQKINPILFRLGVNCTW+SRWFARGSEYG LLHEDLKIR+YL+ +LKQAGVAKILIERT
Sbjct: 1   MGQKINPILFRLGVNCTWSSRWFARGSEYGTLLHEDLKIRKYLEGNLKQAGVAKILIERT 60

Query: 61  HKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKPEINATLIAQSI 120
           HK C I VYSARPGLIIGKKG+DI++IRK LS MT SEIHL+VNEV KPEINATLIAQSI
Sbjct: 61  HKKCFITVYSARPGLIIGKKGSDIDRIRKNLSKMTPSEIHLNVNEVSKPEINATLIAQSI 120

Query: 121 AQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEGRVPLQTLRA 180
           AQQLERRVVFRRAMKRAVQSAMRFGA+G+K+I SGRLNG ELSRTECYLEGRVPLQTLRA
Sbjct: 121 AQQLERRVVFRRAMKRAVQSAMRFGAEGIKIICSGRLNGLELSRTECYLEGRVPLQTLRA 180

Query: 181 HIDYGTAVAETAYGSCGIKVYVSLRDEVSDSDSTIPAAEHRVVEKDS 227
           +IDYG+A+A+TAYG CG+KVYVS+R EVSDSD+   ++  R +EK +
Sbjct: 181 NIDYGSAIAKTAYGICGVKVYVSIR-EVSDSDNA-TSSNRRPLEKSN 225


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|15965115|ref|NP_385468.1| 30S ribosomal protein S3 [Sinorhizobium meliloti 1021] Length = 237 Back     alignment and organism information
>gi|227821762|ref|YP_002825732.1| 30S ribosomal protein S3 [Sinorhizobium fredii NGR234] Length = 237 Back     alignment and organism information
>gi|150396213|ref|YP_001326680.1| 30S ribosomal protein S3 [Sinorhizobium medicae WSM419] Length = 237 Back     alignment and organism information
>gi|209548941|ref|YP_002280858.1| 30S ribosomal protein S3 [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 243 Back     alignment and organism information
>gi|86357311|ref|YP_469203.1| 30S ribosomal protein S3 [Rhizobium etli CFN 42] Length = 244 Back     alignment and organism information
>gi|15889236|ref|NP_354917.1| 30S ribosomal protein S3 [Agrobacterium tumefaciens str. C58] Length = 243 Back     alignment and organism information
>gi|116251546|ref|YP_767384.1| 30S ribosomal protein S3 [Rhizobium leguminosarum bv. viciae 3841] Length = 243 Back     alignment and organism information
>gi|325293330|ref|YP_004279194.1| 30S ribosomal protein S3 [Agrobacterium sp. H13-3] Length = 243 Back     alignment and organism information
>gi|222085681|ref|YP_002544211.1| ribosomal protein S3 [Agrobacterium radiobacter K84] Length = 241 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
Target227 30S ribosomal protein S3 [Candidatus Liberibacter asiat
PRK00310232 PRK00310, rpsC, 30S ribosomal protein S3; Reviewed 2e-99
TIGR01009211 TIGR01009, rpsC_bact, ribosomal protein S3, bacterial t 2e-81
CHL00048214 CHL00048, rps3, ribosomal protein S3 3e-62
COG0092233 COG0092, RpsC, Ribosomal protein S3 [Translation, ribos 6e-69
cd02412109 cd02412, 30S_S3_KH, K homology RNA-binding (KH) domain 1e-35
pfam0018985 pfam00189, Ribosomal_S3_C, Ribosomal protein S3, C-term 3e-28
PRK04191207 PRK04191, rps3p, 30S ribosomal protein S3P; Reviewed 2e-25
TIGR01008195 TIGR01008, rpsC_E_A, ribosomal protein S3, eukaryotic/a 6e-23
KOG3181244 KOG3181, KOG3181, KOG3181, 40S ribosomal protein S3 [Tr 1e-07
pfam0041762 pfam00417, Ribosomal_S3_N, Ribosomal protein S3, N-term 4e-18
pfam0765055 pfam07650, KH_2, KH domain 3e-11
cd0241185 cd02411, archeal_30S_S3_KH, K homology RNA-binding doma 8e-07
cd0240968 cd02409, KH-II, KH-II (K homology RNA-binding domain, t 8e-07
smart0032269 smart00322, KH, K homology RNA-binding domain 5e-04
PTZ00084220 PTZ00084, PTZ00084, 40S ribosomal protein S3; Provision 6e-07
>gnl|CDD|178972 PRK00310, rpsC, 30S ribosomal protein S3; Reviewed Back     alignment and domain information
>gnl|CDD|130082 TIGR01009, rpsC_bact, ribosomal protein S3, bacterial type Back     alignment and domain information
>gnl|CDD|176989 CHL00048, rps3, ribosomal protein S3 Back     alignment and domain information
>gnl|CDD|30441 COG0092, RpsC, Ribosomal protein S3 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|48410 cd02412, 30S_S3_KH, K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3 Back     alignment and domain information
>gnl|CDD|143952 pfam00189, Ribosomal_S3_C, Ribosomal protein S3, C-terminal domain Back     alignment and domain information
>gnl|CDD|179775 PRK04191, rps3p, 30S ribosomal protein S3P; Reviewed Back     alignment and domain information
>gnl|CDD|130081 TIGR01008, rpsC_E_A, ribosomal protein S3, eukaryotic/archaeal type Back     alignment and domain information
>gnl|CDD|38391 KOG3181, KOG3181, KOG3181, 40S ribosomal protein S3 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|109474 pfam00417, Ribosomal_S3_N, Ribosomal protein S3, N-terminal domain Back     alignment and domain information
>gnl|CDD|116265 pfam07650, KH_2, KH domain Back     alignment and domain information
>gnl|CDD|48409 cd02411, archeal_30S_S3_KH, K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein Back     alignment and domain information
>gnl|CDD|48407 cd02409, KH-II, KH-II (K homology RNA-binding domain, type II) Back     alignment and domain information
>gnl|CDD|128617 smart00322, KH, K homology RNA-binding domain Back     alignment and domain information
>gnl|CDD|185435 PTZ00084, PTZ00084, 40S ribosomal protein S3; Provisional Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 227 30S ribosomal protein S3 [Candidatus Liberibacter asiat
TIGR01009217 rpsC_bact ribosomal protein S3; InterPro: IPR005704 Rib 100.0
PRK00310233 rpsC 30S ribosomal protein S3; Reviewed 100.0
CHL00048218 rps3 ribosomal protein S3 100.0
COG0092233 RpsC Ribosomal protein S3 [Translation, ribosomal struc 100.0
PRK04191225 rps3p 30S ribosomal protein S3P; Reviewed 100.0
PTZ00084220 40S ribosomal protein S3; Provisional 100.0
TIGR01008204 rpsC_E_A ribosomal protein S3; InterPro: IPR005703 Ribo 100.0
KOG3181244 consensus 99.94
cd02412109 30S_S3_KH K homology RNA-binding (KH) domain of the pro 100.0
cd0241185 archeal_30S_S3_KH K homology RNA-binding domain (KH) of 99.79
pfam0018985 Ribosomal_S3_C Ribosomal protein S3, C-terminal domain. 99.98
pfam0041762 Ribosomal_S3_N Ribosomal protein S3, N-terminal domain. 99.93
cd0241381 40S_S3_KH K homology RNA-binding (KH) domain of the euk 99.02
cd0240968 KH-II KH-II (K homology RNA-binding domain, type II). K 98.34
cd0241477 jag_KH jag_K homology RNA-binding domain. The KH domain 95.89
smart0032269 KH K homology RNA-binding domain. 92.63
pfam0765055 KH_2 KH domain. 98.81
cd02410145 archeal_CPSF_KH The archaeal cleavage and polyadenylati 92.91
COG1847208 Jag Predicted RNA-binding protein [General function pre 95.98
>TIGR01009 rpsC_bact ribosomal protein S3; InterPro: IPR005704 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed Back     alignment and domain information
>CHL00048 rps3 ribosomal protein S3 Back     alignment and domain information
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed Back     alignment and domain information
>PTZ00084 40S ribosomal protein S3; Provisional Back     alignment and domain information
>TIGR01008 rpsC_E_A ribosomal protein S3; InterPro: IPR005703 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>KOG3181 consensus Back     alignment and domain information
>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3 Back     alignment and domain information
>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein Back     alignment and domain information
>pfam00189 Ribosomal_S3_C Ribosomal protein S3, C-terminal domain Back     alignment and domain information
>pfam00417 Ribosomal_S3_N Ribosomal protein S3, N-terminal domain Back     alignment and domain information
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3 Back     alignment and domain information
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II) Back     alignment and domain information
>cd02414 jag_KH jag_K homology RNA-binding domain Back     alignment and domain information
>smart00322 KH K homology RNA-binding domain Back     alignment and domain information
>pfam07650 KH_2 KH domain Back     alignment and domain information
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH) Back     alignment and domain information
>COG1847 Jag Predicted RNA-binding protein [General function prediction only] 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
Target227 30S ribosomal protein S3 [Candidatus Liberibacter asiat
1vs5_C233 Crystal Structure Of The Bacterial Ribosome From Es 1e-70
1p6g_C232 Real Space Refined Coordinates Of The 30s Subunit F 2e-69
2gy9_C206 Structure Of The 30s Subunit Of A Pre-Translocation 6e-68
1fjg_C239 Structure Of The Thermus Thermophilus 30s Ribosomal 5e-67
1i94_C238 Crystal Structures Of The Small Ribosomal Subunit W 9e-66
3fic_C207 T. Thermophilus 70s Ribosome In Complex With Mrna, 4e-65
1pns_C206 Crystal Structure Of A Streptomycin Dependent Ribos 7e-65
3bbn_C218 Homology Model For The Spinach Chloroplast 30s Subu 7e-58
3izb_B240 Localization Of The Small Subunit Ribosomal Protein 1e-19
1s1h_C192 Structure Of The Ribosomal 80s-Eef2-Sordarin Comple 6e-19
3jyv_C188 Structure Of The 40s Rrna And Proteins And PE TRNA 7e-19
3iz6_B227 Localization Of The Small Subunit Ribosomal Protein 2e-19
2zkq_c243 Structure Of A Mammalian Ribosomal 40s Subunit With 2e-18
2xzm_C243 Crystal Structure Of The Eukaryotic 40s Ribosomal S 1e-14
gi|116666550|pdb|1VS5|C Chain C, 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 = 233 Back     alignment and structure
 Score =  269 bits (689), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 113/230 (49%), Positives = 157/230 (68%), Gaps = 4/230 (1%)

Query: 1   MGQKINPILFRLGVNCTWNSRWFARGSEYGALLHEDLKIREYLQCHLKQAGVAKILIERT 60
           MGQK++P   RLG+   WNS WFA   E+   L  D K+R+YL   L +A V++I+IER 
Sbjct: 1   MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERP 60

Query: 61  HKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKPEINATLIAQSI 120
            K+ R+ +++ARPG++IGKKG D+EK+RK ++++      +++ EV KPE++A L+A SI
Sbjct: 61  AKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSI 120

Query: 121 AQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEGRVPLQTLRA 180
             QLERRV+FRRAMKRAVQ+AMR GA G+KV  SGRL GAE++RTE Y EGRVPL TLRA
Sbjct: 121 TSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRA 180

Query: 181 HIDYGTAVAETAYGSCGIKVYVSLRDEVSD----SDSTIPAAEHRVVEKD 226
            IDY T+ A T YG  G+KV++   + +           PAA+ +  ++ 
Sbjct: 181 DIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRK 230


>gi|33357880|pdb|1P6G|C Chain C, 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 = 232 Back     alignment and structure
>gi|116667412|pdb|2GY9|C Chain C, 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 = 206 Back     alignment and structure
gi|10835587|pdb|1FJG|C Chain C, Structure Of The Thermus Thermophilus 30s Ribosomal Subunit In Complex With The Antibiotics Streptomycin, Spectinomycin, And Paromomycin Length = 239 Back     alignment and structure
>gi|14278532|pdb|1I94|C Chain C, Crystal Structures Of The Small Ribosomal Subunit With Tetracycline, Edeine And If3 Length = 238 Back     alignment and structure
>gi|224510697|pdb|3FIC|C Chain C, 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 = 207 Back     alignment and structure
>gi|34811531|pdb|1PNS|C Chain C, 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 = 206 Back     alignment and structure
gi|188036204|pdb|3BBN|C Chain C, Homology Model For The Spinach Chloroplast 30s Subunit Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome. Length = 218 Back     alignment and structure
gi|313103665|pdb|3IZB|B Chain B, Localization Of The Small Subunit Ribosomal Proteins Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae Translating 80s Ribosome Length = 240 Back     alignment and structure
>gi|49258823|pdb|1S1H|C Chain C, 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 = 192 Back     alignment and structure
>gi|281500809|pdb|3JYV|C Chain C, 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 = 188 Back     alignment and structure
>gi|313103630|pdb|3IZ6|B Chain B, Localization Of The Small Subunit Ribosomal Proteins Into A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s Ribosome Length = 227 Back     alignment and structure
gi|187609257|pdb|2ZKQ|CC Chain c, 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 = 243 Back     alignment and structure
gi|319443358|pdb|2XZM|C Chain C, 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 = 243 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target227 30S ribosomal protein S3 [Candidatus Liberibacter asiat
3ofo_C206 30S ribosomal protein S3; protein biosynthesis, ribosom 1e-71
3i1m_C233 30S ribosomal protein S3; ribosome structure, protein-R 1e-62
3bbn_C218 Ribosomal protein S3; small ribosomal subunit, spinach 1e-57
2vqe_C239 30S ribosomal protein S3; tRNA-binding, rRNA-binding, m 3e-57
2zkq_c243 40S ribosomal protein S3E; protein-RNA complex, 40S rib 2e-43
1wh9_A92 40S ribosomal protein S3; KH domain, structural genomic 7e-14
>3ofo_C 30S ribosomal protein S3; protein biosynthesis, ribosomes, RNA, tRNA, transfer, eryThr ketolide, macrolide, antibiotic, EXIT, peptidyl; 3.10A {Escherichia coli} PDB: 2gyb_C 2gy9_C* 3fih_C* 2wwl_C 3ofp_C Length = 206 Back     alignment and structure
 Score =  264 bits (676), Expect = 1e-71
 Identities = 110/207 (53%), Positives = 150/207 (72%), Gaps = 1/207 (0%)

Query: 2   GQKINPILFRLGVNCTWNSRWFARGSEYGALLHEDLKIREYLQCHLKQAGVAKILIERTH 61
           GQK++P   RLG+   WNS WFA   E+   L  D K+R+YL   L +A V++I+IER  
Sbjct: 1   GQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERPA 60

Query: 62  KNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKPEINATLIAQSIA 121
           K+ R+ +++ARPG++IGKKG D+EK+RK ++++      +++ EV KPE++A L+A SI 
Sbjct: 61  KSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSIT 120

Query: 122 QQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEGRVPLQTLRAH 181
            QLERRV+FRRAMKRAVQ+AMR GA G+KV  SGRL GAE++RTE Y EGRVPL TLRA 
Sbjct: 121 SQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRAD 180

Query: 182 IDYGTAVAETAYGSCGIKVYVSLRDEV 208
           IDY T+ A T YG  G+KV++  + E+
Sbjct: 181 IDYNTSEAHTTYGVIGVKVWI-FKGEI 206


>3i1m_C 30S ribosomal protein S3; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_C* 3e1a_O 3e1c_O 1vs5_C 3i1o_C 3i1q_C 3i1s_C 3i1z_C 3i21_C 2qal_C* 1p6g_C 1p87_C 2aw7_C 2avy_C 2i2u_C 2i2p_C* 2qan_C* 2qb9_C* 2qbb_C* 2qbd_C ... Length = 233 Back     alignment and structure
>3bbn_C Ribosomal protein S3; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Length = 218 Back     alignment and structure
>2vqe_C 30S ribosomal protein S3; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} PDB: 1gix_F* 1hnw_C* 1hnx_C* 1hnz_C* 1hr0_C 1ibk_C* 1ibl_C* 1ibm_C 1j5e_C 1jgo_F* 1jgp_F* 1jgq_F* 1ml5_F* 1n32_C* 1n33_C* 1n34_C 1n36_C 1xmo_C* 1xmq_C* 1xnq_C* ... Length = 239 Back     alignment and structure
>2zkq_c 40S ribosomal protein S3E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} PDB: 1s1h_C Length = 243 Back     alignment and structure
>1wh9_A 40S ribosomal protein S3; KH domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, ribosome; NMR {Homo sapiens} SCOP: d.52.3.1 Length = 92 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target227 30S ribosomal protein S3 [Candidatus Liberibacter asiat
3i1m_C233 30S ribosomal protein S3; ribosome structure, protein-R 100.0
2vqe_C239 30S ribosomal protein S3; tRNA-binding, rRNA-binding, m 100.0
3ofo_C206 30S ribosomal protein S3; protein biosynthesis, ribosom 100.0
3bbn_C218 Ribosomal protein S3; small ribosomal subunit, spinach 100.0
2zkq_c243 40S ribosomal protein S3E; protein-RNA complex, 40S rib 100.0
1wh9_A92 40S ribosomal protein S3; KH domain, structural genomic 99.64
2pt7_G152 HP1451, hypothetical protein; ATPase, protein-protein c 95.55
3gku_A225 Probable RNA-binding protein; APC21302, structural geno 94.14
>3i1m_C 30S ribosomal protein S3; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_C* 3e1a_O 3e1c_O 1vs5_C 3i1o_C 3i1q_C 3i1s_C 3i1z_C 3i21_C 3kc4_C 2qal_C* 1p6g_C 1p87_C 2aw7_C 2avy_C 2i2u_C 2i2p_C* 2qan_C* 2qb9_C* 2qbb_C* ... Back     alignment and structure
Probab=100.00  E-value=0  Score=534.70  Aligned_cols=214  Identities=51%  Similarity=0.860  Sum_probs=207.9

Q ss_pred             CCCCCCCCEEEEEEECCCEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCEEEEEECCCCCCCCCC
Q ss_conf             98645785266503206215670273125799998999999999877422642215532588518999973741001356
Q gi|254780255|r    1 MGQKINPILFRLGVNCTWNSRWFARGSEYGALLHEDLKIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGKK   80 (227)
Q Consensus         1 MGQKvnP~g~RLg~~k~w~S~Wfa~~k~Y~~~L~eD~~IR~fi~k~l~~agis~i~I~Rt~~~i~I~I~~~kP~~iiGkk   80 (227)
                      |||||||+|||||++++|+|.|||++++|+++|+||++||+||.+++.++|+++++|+|+++.+.|.||+++|+.++|++
T Consensus         1 MGQKvnP~gfRlgi~k~w~S~Wfa~~k~Y~~~L~eD~~IR~fi~k~~~~agis~i~I~rt~~~~~I~I~~~~Pg~iig~k   80 (233)
T 3i1m_C            1 MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERPAKSIRVTIHTARPGIVIGKK   80 (233)
T ss_dssp             -CCCCCTTTTTTTSSCCCSBCCCCCHHHHHHHHHHHHHHHHHHHHHTGGGTEEEEEBCCCSSCBCCEEEESCHHHHHCST
T ss_pred             CCCCCCCCCCCCCCCCCCCCEECCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCEEEEEEECCCCEEECCC
T ss_conf             97987980311132479741787893334799889999999999987761443010574366469999934886487265


Q ss_pred             CHHHHHHHHHHHCCCCCEEEEEEEEECCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCC
Q ss_conf             53489989876403587057879981375533778799999998759636899999999853238855999970367864
Q gi|254780255|r   81 GTDIEKIRKKLSNMTNSEIHLSVNEVPKPEINATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGA  160 (227)
Q Consensus        81 g~~i~~l~~~L~~~~~~~v~i~v~ei~~p~~~A~~iA~~Ia~~Lekr~~fRr~~k~~i~~~~k~g~kGikI~isGRl~G~  160 (227)
                      |.++++|+..|++.++.+++|++.++++|+++|.++|++||++||+|++||++++++++++|++||+||||+||||||||
T Consensus        81 g~~i~~l~~~l~~~~~~~~~i~V~evk~p~l~A~~iA~~Ia~~Lekr~~fRr~~~~~~~~~~~~gakGikI~isGRL~Ga  160 (233)
T 3i1m_C           81 GEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSITSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGA  160 (233)
T ss_dssp             THHHHHHHHHHHHHHTSCBCCEEEECSSGGGCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHTTCCSEEEEEEESSTTSC
T ss_pred             CHHHHHHHHHHHHHHCCCEEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEECCCCHH
T ss_conf             35689999999984287316999994480034689999999999851357789999999998769967899981454402


Q ss_pred             CCCEEEEEEECCCCCCCEEEECEEEEEEEEECCCEEEEEEEEEECCCCCCCCCCC
Q ss_conf             2221578752553245200003056899995382667999973288537721134
Q gi|254780255|r  161 ELSRTECYLEGRVPLQTLRAHIDYGTAVAETAYGSCGIKVYVSLRDEVSDSDSTI  215 (227)
Q Consensus       161 e~Ar~e~~~~G~vpl~t~~a~idy~~~~a~T~~G~~GvKVwi~~~~~~~~~~~~~  215 (227)
                      ||||+|||++|+|||||++|+|||++++|+|+||+||||||||.+|+++ ++...
T Consensus       161 e~Ar~e~~~~G~vpl~tl~a~Idy~~~~a~T~yGv~GVKVwI~~~~~~~-~~~~~  214 (233)
T 3i1m_C          161 EIARTEWYREGRVPLHTLRADIDYNTSEAHTTYGVIGVKVWIFKGEILG-GMAAV  214 (233)
T ss_dssp             SSCCCCBCCEECCCTTCSSSEEEEEEECCEETTEECEEEEEEEEECC--------
T ss_pred             HHHEEEEEECCCCCCCCCCCCEEEEEEEEECCCEEEEEEEEEECCCCCC-CCCCC
T ss_conf             3111323536632356755406999999984886289999997786568-74344



>2vqe_C 30S ribosomal protein S3; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} PDB: 1gix_F* 1hnw_C* 1hnx_C* 1hnz_C* 1hr0_C 1ibk_C* 1ibl_C* 1ibm_C 1j5e_C 1jgo_F* 1jgp_F* 1jgq_F* 1ml5_F* 1n32_C* 1n33_C* 1n34_C 1n36_C 1xmo_C* 1xmq_C* 1xnq_C* ... Back     alignment and structure
>3ofo_C 30S ribosomal protein S3; protein biosynthesis, ribosomes, RNA, tRNA, transfer, eryThr ketolide, macrolide, antibiotic, EXIT, peptidyl; 3.10A {Escherichia coli} PDB: 2gyb_C 2gy9_C* 3fih_C* 2wwl_C 3ofp_C Back     alignment and structure
>3bbn_C Ribosomal protein S3; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Back     alignment and structure
>2zkq_c 40S ribosomal protein S3E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} PDB: 1s1h_C 3jyv_C* Back     alignment and structure
>1wh9_A 40S ribosomal protein S3; KH domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, ribosome; NMR {Homo sapiens} SCOP: d.52.3.1 Back     alignment and structure
>2pt7_G HP1451, hypothetical protein; ATPase, protein-protein complex, type IV secretion, hydrolase/protein binding complex; 2.40A {Helicobacter pylori 26695} Back     alignment and structure
>3gku_A Probable RNA-binding protein; APC21302, structural genomics, PSI-2, protein structure initiative; 2.95A {Clostridium symbiosum atcc 14940} 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 227 30S ribosomal protein S3 [Candidatus Liberibacter asiat
d2qalc1105 d.52.3.1 (C:1-105) Ribosomal protein S3 N-terminal doma 6e-34
d2uubc1105 d.52.3.1 (C:2-106) Ribosomal protein S3 N-terminal doma 5e-33
d2qalc2101 d.53.1.1 (C:106-206) Ribosomal protein S3 C-terminal do 7e-32
d2uubc2101 d.53.1.1 (C:107-207) Ribosomal protein S3 C-terminal do 3e-30
d1wh9a_92 d.52.3.1 (A:) Ribosomal protein S3 N-terminal domain {M 2e-14
>d2qalc1 d.52.3.1 (C:1-105) Ribosomal protein S3 N-terminal domain {Escherichia coli [TaxId: 562]} Length = 105 Back     information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: Alpha-lytic protease prodomain-like
superfamily: Prokaryotic type KH domain (KH-domain type II)
family: Prokaryotic type KH domain (KH-domain type II)
domain: Ribosomal protein S3 N-terminal domain
species: Escherichia coli [TaxId: 562]
 Score =  138 bits (348), Expect = 6e-34
 Identities = 45/105 (42%), Positives = 71/105 (67%)

Query: 2   GQKINPILFRLGVNCTWNSRWFARGSEYGALLHEDLKIREYLQCHLKQAGVAKILIERTH 61
           GQK++P   RLG+   WNS WFA   E+   L  D K+R+YL   L +A V++I+IER  
Sbjct: 1   GQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERPA 60

Query: 62  KNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEV 106
           K+ R+ +++ARPG++IGKKG D+EK+RK ++++      +++ EV
Sbjct: 61  KSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEV 105


>d2uubc1 d.52.3.1 (C:2-106) Ribosomal protein S3 N-terminal domain {Thermus thermophilus [TaxId: 274]} Length = 105 Back     information, alignment and structure
>d2qalc2 d.53.1.1 (C:106-206) Ribosomal protein S3 C-terminal domain {Escherichia coli [TaxId: 562]} Length = 101 Back     information, alignment and structure
>d2uubc2 d.53.1.1 (C:107-207) Ribosomal protein S3 C-terminal domain {Thermus thermophilus [TaxId: 274]} Length = 101 Back     information, alignment and structure
>d1wh9a_ d.52.3.1 (A:) Ribosomal protein S3 N-terminal domain {Mouse (Mus musculus) [TaxId: 10090]} Length = 92 Back     information, alignment and structure

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

IdentityAlignment graphLength Definition Probability
Target227 30S ribosomal protein S3 [Candidatus Liberibacter asiat
d2qalc2101 Ribosomal protein S3 C-terminal domain {Escherichia col 100.0
d2uubc2101 Ribosomal protein S3 C-terminal domain {Thermus thermop 100.0
d2uubc1105 Ribosomal protein S3 N-terminal domain {Thermus thermop 100.0
d2qalc1105 Ribosomal protein S3 N-terminal domain {Escherichia col 100.0
d1wh9a_92 Ribosomal protein S3 N-terminal domain {Mouse (Mus musc 99.64
d1egaa2113 GTPase Era C-terminal domain {Escherichia coli [TaxId: 90.83
>d2qalc2 d.53.1.1 (C:106-206) Ribosomal protein S3 C-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S3 C-terminal domain
superfamily: Ribosomal protein S3 C-terminal domain
family: Ribosomal protein S3 C-terminal domain
domain: Ribosomal protein S3 C-terminal domain
species: Escherichia coli [TaxId: 562]
Probab=100.00  E-value=9.3e-43  Score=264.30  Aligned_cols=101  Identities=63%  Similarity=0.954  Sum_probs=99.2

Q ss_pred             CCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCEEEEEEECCCCCCCEEEECEEEE
Q ss_conf             37553377879999999875963689999999985323885599997036786422215787525532452000030568
Q gi|254780255|r  107 PKPEINATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEGRVPLQTLRAHIDYGT  186 (227)
Q Consensus       107 ~~p~~~A~~iA~~Ia~~Lekr~~fRr~~k~~i~~~~k~g~kGikI~isGRl~G~e~Ar~e~~~~G~vpl~t~~a~idy~~  186 (227)
                      ++|++||+++|++||+|||+|++|||+++++++++|++||+||+|+|||||||+||||+|++++|++||||++++|||++
T Consensus         1 k~P~l~A~~vA~~IA~~LErr~~fRr~~~~~i~~~m~~ga~GikI~isGRl~gae~Ar~e~~~~G~ipl~t~~~~Idy~~   80 (101)
T d2qalc2           1 RKPELDAKLVADSITSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRADIDYNT   80 (101)
T ss_dssp             SCGGGCHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHSSCSEEEEEECSCGGGCSSCCCCCCEEECCCTTCGGGCEEEEE
T ss_pred             CCCCCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCHHEEEEEEECCCCCHHHHEEEEEEEECCCCCCCCEEEEEEE
T ss_conf             99886789999999999975508999999999987453420599998146660432116888894421456002677889


Q ss_pred             EEEEECCCEEEEEEEEEECCC
Q ss_conf             999953826679999732885
Q gi|254780255|r  187 AVAETAYGSCGIKVYVSLRDE  207 (227)
Q Consensus       187 ~~a~T~~G~~GvKVwi~~~~~  207 (227)
                      ++|+|+||++|||||||++|+
T Consensus        81 ~~a~t~~Gv~GVKVwI~~~ev  101 (101)
T d2qalc2          81 SEAHTTYGVIGVKVWIFKGEI  101 (101)
T ss_dssp             CCCCBTTBCCCEEEEEECCCC
T ss_pred             EEEECCCEEEEEEEEEECCCC
T ss_conf             999958600899999987989



>d2uubc2 d.53.1.1 (C:107-207) Ribosomal protein S3 C-terminal domain {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d2uubc1 d.52.3.1 (C:2-106) Ribosomal protein S3 N-terminal domain {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d2qalc1 d.52.3.1 (C:1-105) Ribosomal protein S3 N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1wh9a_ d.52.3.1 (A:) Ribosomal protein S3 N-terminal domain {Mouse (Mus musculus) [TaxId: 10090]} Back     information, alignment and structure
>d1egaa2 d.52.3.1 (A:183-295) GTPase Era C-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 227 30S ribosomal protein S3 [Candidatus Liberibacter
3i1m_C_1-109109 (C:1-109) 30S ribosomal protein S3; ribosome struc 4e-34
2vqe_C_1-109109 (C:1-109) 30S ribosomal protein S3; tRNA-binding, 6e-33
3bbn_C_1-121121 (C:1-121) Ribosomal protein S3; small ribosomal su 1e-30
2zkq_c_1-9494 (c:1-94) 40S ribosomal protein S3E; protein-RNA co 2e-24
1ega_A_182-284103 (A:182-284) Protein (GTP-binding protein ERA); GTP 3e-06
3i1m_C_110-233124 (C:110-233) 30S ribosomal protein S3; ribosome str 2e-28
2vqe_C_110-239130 (C:110-239) 30S ribosomal protein S3; tRNA-binding 5e-28
3bbn_C_122-21897 (C:122-218) Ribosomal protein S3; small ribosomal 1e-26
2zkq_c_95-243149 (c:95-243) 40S ribosomal protein S3E; protein-RNA 4e-22
1wh9_A_92 (A:) 40S ribosomal protein S3; KH domain, structur 5e-25
>3i1m_C (C:1-109) 30S ribosomal protein S3; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_C* 3e1a_O 3e1c_O 1vs5_C 3i1o_C 3i1q_C 3i1s_C 3i1z_C 3i21_C 2qal_C* 1p6g_C 1p87_C 2aw7_C 2avy_C 2i2u_C 2i2p_C* 2qan_C* 2qb9_C* 2qbb_C* 2qbd_C ...Length = 109 Back     alignment and structure
 Score =  139 bits (351), Expect = 4e-34
 Identities = 48/109 (44%), Positives = 74/109 (67%)

Query: 1   MGQKINPILFRLGVNCTWNSRWFARGSEYGALLHEDLKIREYLQCHLKQAGVAKILIERT 60
           MGQK++P   RLG+   WNS WFA   E+   L  D K+R+YL   L +A V++I+IER 
Sbjct: 1   MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERP 60

Query: 61  HKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKP 109
            K+ R+ +++ARPG++IGKKG D+EK+RK ++++      +++ EV KP
Sbjct: 61  AKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKP 109


>2vqe_C (C:1-109) 30S ribosomal protein S3; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} PDB: 1gix_F* 1hnw_C* 1hnx_C* 1hnz_C* 1hr0_C 1ibk_C* 1ibl_C* 1ibm_C 1j5e_C 1jgo_F* 1jgp_F* 1jgq_F* 1ml5_F* 1n32_C* 1n33_C* 1n34_C 1n36_C 1xmo_C* 1xmq_C* 1xnq_C* ...Length = 109 Back     alignment and structure
>3bbn_C (C:1-121) Ribosomal protein S3; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}Length = 121 Back     alignment and structure
>2zkq_c (c:1-94) 40S ribosomal protein S3E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} PDB: 1s1h_CLength = 94 Back     alignment and structure
>1ega_A (A:182-284) Protein (GTP-binding protein ERA); GTPase, RNA-binding, RAS-like, hydrolase; 2.40A {Escherichia coli}Length = 103 Back     alignment and structure
>3i1m_C (C:110-233) 30S ribosomal protein S3; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_C* 3e1a_O 3e1c_O 1vs5_C 3i1o_C 3i1q_C 3i1s_C 3i1z_C 3i21_C 2qal_C* 1p6g_C 1p87_C 2aw7_C 2avy_C 2i2u_C 2i2p_C* 2qan_C* 2qb9_C* 2qbb_C* 2qbd_C ...Length = 124 Back     alignment and structure
>2vqe_C (C:110-239) 30S ribosomal protein S3; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} PDB: 1gix_F* 1hnw_C* 1hnx_C* 1hnz_C* 1hr0_C 1ibk_C* 1ibl_C* 1ibm_C 1j5e_C 1jgo_F* 1jgp_F* 1jgq_F* 1ml5_F* 1n32_C* 1n33_C* 1n34_C 1n36_C 1xmo_C* 1xmq_C* 1xnq_C* ...Length = 130 Back     alignment and structure
>3bbn_C (C:122-218) Ribosomal protein S3; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}Length = 97 Back     alignment and structure
>2zkq_c (c:95-243) 40S ribosomal protein S3E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} PDB: 1s1h_CLength = 149 Back     alignment and structure
>1wh9_A (A:) 40S ribosomal protein S3; KH domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, ribosome; NMR {Homo sapiens}Length = 92 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target227 30S ribosomal protein S3 [Candidatus Liberibacter asiat
3i1m_C_110-233124 30S ribosomal protein S3; ribosome structure, prot 100.0
2vqe_C_110-239130 30S ribosomal protein S3; tRNA-binding, rRNA-bindi 100.0
2zkq_c_95-243149 40S ribosomal protein S3E; protein-RNA complex, 40 100.0
3bbn_C_122-21897 Ribosomal protein S3; small ribosomal subunit, spi 100.0
3i1m_C_1-109109 30S ribosomal protein S3; ribosome structure, prot 100.0
2vqe_C_1-109109 30S ribosomal protein S3; tRNA-binding, rRNA-bindi 100.0
3bbn_C_1-121121 Ribosomal protein S3; small ribosomal subunit, spi 100.0
2zkq_c_1-9494 40S ribosomal protein S3E; protein-RNA complex, 40 99.89
1wh9_A_92 40S ribosomal protein S3; KH domain, structural ge 99.82
1ega_A_182-284103 Protein (GTP-binding protein ERA); GTPase, RNA-bin 96.83
1wf3_A_180-301122 GTP-binding protein; GTPase, riken structural geno 90.79
3gku_A_61-14080 Probable RNA-binding protein; APC21302, structural 95.43
>3i1m_C (C:110-233) 30S ribosomal protein S3; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_C* 3e1a_O 3e1c_O 1vs5_C 3i1o_C 3i1q_C 3i1s_C 3i1z_C 3i21_C 2qal_C* 1p6g_C 1p87_C 2aw7_C 2avy_C 2i2u_C 2i2p_C* 2qan_C* 2qb9_C* 2qbb_C* 2qbd_C ... Back     alignment and structure
Probab=100.00  E-value=1.2e-40  Score=254.35  Aligned_cols=113  Identities=55%  Similarity=0.820  Sum_probs=104.8

Q ss_pred             CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCEEEEEEECCCCCCCEEEECEEEEEEE
Q ss_conf             53377879999999875963689999999985323885599997036786422215787525532452000030568999
Q gi|254780255|r  110 EINATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEGRVPLQTLRAHIDYGTAVA  189 (227)
Q Consensus       110 ~~~A~~iA~~Ia~~Lekr~~fRr~~k~~i~~~~k~g~kGikI~isGRl~G~e~Ar~e~~~~G~vpl~t~~a~idy~~~~a  189 (227)
                      ++||+++|++||.+||++++||++++++++++|++|++|+||+|||||+|+||||+|||++|++||||++++|||++.+|
T Consensus         1 el~A~~ia~~Ia~~Le~~~~frr~~~~~i~~~~~~gakGikI~isGRl~G~erAr~e~~~~G~ipl~t~~a~Idy~~~~a   80 (124)
T 3i1m_C            1 ELDAKLVADSITSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRADIDYNTSEA   80 (124)
T ss_dssp             GGCHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHTTCCSEEEEEEESSTTSCSSCCCCBCCEECCCTTCSSSEEEEEEECC
T ss_pred             CHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCEEEEEECCCCCCHHHHHEEHHHCCCCCCCCCCCEEEEEEEEE
T ss_conf             22478999999999972640899999999999875995699997355574132203321108888888362689999999


Q ss_pred             EECCCEEEEEEEEEECCCCCCCCCCCCCCHHHH
Q ss_conf             953826679999732885377211343320233
Q gi|254780255|r  190 ETAYGSCGIKVYVSLRDEVSDSDSTIPAAEHRV  222 (227)
Q Consensus       190 ~T~~G~~GvKVwi~~~~~~~~~~~~~~~~~~~~  222 (227)
                      +|+||+|||||||+++++.++........+...
T Consensus        81 ~tk~Gv~GIKVwI~~~~~~~~~~~~~~~~~~~~  113 (124)
T 3i1m_C           81 HTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAA  113 (124)
T ss_dssp             EETTEECEEEEEEEEECC---------------
T ss_pred             ECCCEEEEEEEEEECCCCCCCCCCCCCCCCCCC
T ss_conf             858575899999977862687333347556556



>2vqe_C (C:110-239) 30S ribosomal protein S3; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} PDB: 1gix_F* 1hnw_C* 1hnx_C* 1hnz_C* 1hr0_C 1ibk_C* 1ibl_C* 1ibm_C 1j5e_C 1jgo_F* 1jgp_F* 1jgq_F* 1ml5_F* 1n32_C* 1n33_C* 1n34_C 1n36_C 1xmo_C* 1xmq_C* 1xnq_C* ... Back     alignment and structure
>2zkq_c (c:95-243) 40S ribosomal protein S3E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} PDB: 1s1h_C Back     alignment and structure
>3bbn_C (C:122-218) Ribosomal protein S3; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Back     alignment and structure
>3i1m_C (C:1-109) 30S ribosomal protein S3; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_C* 3e1a_O 3e1c_O 1vs5_C 3i1o_C 3i1q_C 3i1s_C 3i1z_C 3i21_C 2qal_C* 1p6g_C 1p87_C 2aw7_C 2avy_C 2i2u_C 2i2p_C* 2qan_C* 2qb9_C* 2qbb_C* 2qbd_C ... Back     alignment and structure
>2vqe_C (C:1-109) 30S ribosomal protein S3; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} PDB: 1gix_F* 1hnw_C* 1hnx_C* 1hnz_C* 1hr0_C 1ibk_C* 1ibl_C* 1ibm_C 1j5e_C 1jgo_F* 1jgp_F* 1jgq_F* 1ml5_F* 1n32_C* 1n33_C* 1n34_C 1n36_C 1xmo_C* 1xmq_C* 1xnq_C* ... Back     alignment and structure
>3bbn_C (C:1-121) Ribosomal protein S3; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Back     alignment and structure
>2zkq_c (c:1-94) 40S ribosomal protein S3E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} PDB: 1s1h_C Back     alignment and structure
>1wh9_A (A:) 40S ribosomal protein S3; KH domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, ribosome; NMR {Homo sapiens} Back     alignment and structure
>1ega_A (A:182-284) Protein (GTP-binding protein ERA); GTPase, RNA-binding, RAS-like, hydrolase; 2.40A {Escherichia coli} Back     alignment and structure
>1wf3_A (A:180-301) GTP-binding protein; GTPase, riken structural genomics/proteomics initiative, RSGI, structural genomics, hydrolase; HET: GNP; 1.88A {Thermus thermophilus HB8} Back     alignment and structure
>3gku_A (A:61-140) Probable RNA-binding protein; APC21302, structural genomics, PSI-2, protein structure initiative; 2.95A {Clostridium symbiosum atcc 14940} Back     alignment and structure