254780187

254780187

30S ribosomal protein S4

GeneID in NCBI database:8209167Locus tag:CLIBASIA_00350
Protein GI in NCBI database:254780187Protein Accession:YP_003064600.1
Gene range:-(72701, 73321)Protein Length:206aa
Gene description:30S ribosomal protein S4
COG prediction:none
KEGG prediction:rpsD; 30S ribosomal protein S4; K02986 small subunit ribosomal protein S4
SEED prediction:SSU ribosomal protein S4p (S9e)
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------
MSKRESSKHKIDRRIGENLWGRPKSPVNTRSYGPGLHGQRRKSKPSYFGLQLRAKQKMKKYYGDISEKKFRSIFKEADRSRGDTSHNLISFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSKQLASVLEASQLAERDVPEYISVNHDNMVATFVRIPSSLKDVPYPVIMQPNLVVEFYSR
ccccccccHHccHHHccccccccccHHHccccccccccccccccccHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHccccccHHHHHHHcccccEEEccEEEcccccccccccEEEEccHHHHHHHHHHHHHHcccccccEEEEccccEEEEEEEcccHHHcccccccccccEEEEEEcc
ccccccHHHHHHHHccccccccccccccccccHHHHHHHcccccccHEEccHHHHHHHHHHcccccHHHHHHHHHHHHHHcccHHHHHHHHHHHcccHHHHHcccccccccHHHHHcccEEEEccccEcccccccccccEEEcccccHHHHHHHHHHHHHHHcccccccccHHHHcccHccccHHHcHHHHcHHHHHHEEEEHccc
mskresskhKIDRrigenlwgrpkspvntrsygpglhgqrrkskpsyfglQLRAKQKMKKYYGDISEKKFRSIFKEadrsrgdtshNLISFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLvngrsvnigsyrckegdviEVKQKSKQLASVLEASQlaerdvpeyisvnhDNMVATFVripsslkdvpypvimqpnlVVEFYSR
mskresskhkidrrigenlwgrpkspvntrsygpglhgqrrkskpsyfglqLRAKQKMKKYYGDISEKKFRSIFkeadrsrgdtshnlISFLESRLDTIVYRAKFVPTIFAArqfvnhrhvlvngrsvnigsyrCKEGDVIEVKQKSKQLASVLEASQLAERDVPEYISVNHDNMVATFVRIPsslkdvpypvimqpnlvvefysr
MSKRESSKHKIDRRIGENLWGRPKSPVNTRSYGPGLHGQRRKSKPSYFGLQLRAKQKMKKYYGDISEKKFRSIFKEADRSRGDTSHNLISFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSKQLASVLEASQLAERDVPEYISVNHDNMVATFVRIPSSLKDVPYPVIMQPNLVVEFYSR
*SKRESSKHKIDRRIGENLWGRPKSPVNTRSY*************SYFGLQLRAKQKMKKYYGDISEKKFRSIFKEADRSRGDTSHNLISFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSKQLASVLEASQLAERDVPEYISVNHDNMVATFVRIPSSLKDVPYPVIMQPNLVVEFYSR
***********DRRIGENLWGRPKSPVNTRSY*************SYFGLQLRAKQKMKKYYGDISEKKFRSIFKEADRSRGDTSHNLISFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSKQLASVLEASQLAERDVPEYISVNHDNMVATFVRIPSSLKDVPYPVIMQPNLVVEFYSR
**KRESSKHKIDRRIGENLWGRPKSPVNTRSYGPGLHGQRRKSKPSYFGLQLRAKQKMKKYYGDISEKKFRSIFKEADRSRGDTSHNLISFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSKQLASVLEASQLAERDVPEYISVNHDNMVATFVRIPSSLKDVPYPVIMQPNLVVEFYSR
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MSKRESSKHKIDRRIGENLWGRPKSPVNTRSYGPGLHGQRRKSKPSYFGLQLRAKQKMKKYYGDISEKKFRSIFKEADRSRGDTSHNLISFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSKQLASVLEASQLAERDVPEYISVNHDNMVATFVRIPSSLKDVPYPVIMQPNLVVEFYSR
MSKRESSKHKIDRRIGENLWGRPKSPVNTRSYGPGLHGQRRKSKPSYFGLQLRAKQKMKKYYGDISEKKFRSIFKEADRSRGDTSHNLISFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSKQLASVLEASQLAERDVPEYISVNHDNMVATFVRIPSSLKDVPYPVIMQPNLVVEFYSR
MSKRESSKHKIDRRIGENLWGRPKSPVNTRSYGPGLHGQRRKSKPSYFGLQLRAKQKMKKYYGDISEKKFRSIFKEADRSRGDTSHNLISFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSKQLASVLEASQLAERDVPEYISVNHDNMVATFVRIPSSLKDVPYPVIMQPNLVVEFYSR

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
Target206 30S ribosomal protein S4 [Candidatus Liberibacter asiat
315122617206 30S ribosomal protein S4 [Candidatus Liberibacter solan 1 1e-103
227822183205 30S ribosomal protein S4 [Sinorhizobium fredii NGR234] 1 1e-89
15965540205 30S ribosomal protein S4 [Sinorhizobium meliloti 1021] 1 1e-89
150396726205 30S ribosomal protein S4 [Sinorhizobium medicae WSM419] 1 4e-89
190891998205 30S ribosomal protein S4 [Rhizobium etli CIAT 652] Leng 1 6e-89
222148432205 30S ribosomal protein S4 [Agrobacterium vitis S4] Lengt 1 6e-89
15889161205 30S ribosomal protein S4 [Agrobacterium tumefaciens str 1 1e-88
209549541205 30S ribosomal protein S4 [Rhizobium leguminosarum bv. t 1 2e-88
116252370205 30S ribosomal protein S4 [Rhizobium leguminosarum bv. v 1 3e-88
241204876205 30S ribosomal protein S4 [Rhizobium leguminosarum bv. t 1 4e-88
>gi|315122617|ref|YP_004063106.1| 30S ribosomal protein S4 [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 206 Back     alignment and organism information
 Score =  379 bits (972), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 180/206 (87%), Positives = 192/206 (93%)

Query: 1   MSKRESSKHKIDRRIGENLWGRPKSPVNTRSYGPGLHGQRRKSKPSYFGLQLRAKQKMKK 60
           MSKRESSKHKIDRRI ENLWGRPKSPVN RSYGPGLHGQRRKSKPSYFGLQLRAKQKMKK
Sbjct: 1   MSKRESSKHKIDRRISENLWGRPKSPVNVRSYGPGLHGQRRKSKPSYFGLQLRAKQKMKK 60

Query: 61  YYGDISEKKFRSIFKEADRSRGDTSHNLISFLESRLDTIVYRAKFVPTIFAARQFVNHRH 120
           YYGD+ EK+FRSIFKEADR +GDTS NLISFLESRLDTIVYRAKFVPT+FAARQFVNHRH
Sbjct: 61  YYGDVGEKQFRSIFKEADRCKGDTSQNLISFLESRLDTIVYRAKFVPTVFAARQFVNHRH 120

Query: 121 VLVNGRSVNIGSYRCKEGDVIEVKQKSKQLASVLEASQLAERDVPEYISVNHDNMVATFV 180
           VLVNG SVNIGSYRCK GDVIEVK KSK+L SVL + QL ERDVPEYIS +H+NMVATFV
Sbjct: 121 VLVNGFSVNIGSYRCKAGDVIEVKSKSKKLTSVLGSVQLPERDVPEYISADHENMVATFV 180

Query: 181 RIPSSLKDVPYPVIMQPNLVVEFYSR 206
           +IP+SL +VPYPVIM+PNLVVEFYSR
Sbjct: 181 KIPTSLSEVPYPVIMEPNLVVEFYSR 206



Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|227822183|ref|YP_002826154.1| 30S ribosomal protein S4 [Sinorhizobium fredii NGR234] Length = 205 Back     alignment and organism information
>gi|15965540|ref|NP_385893.1| 30S ribosomal protein S4 [Sinorhizobium meliloti 1021] Length = 205 Back     alignment and organism information
>gi|150396726|ref|YP_001327193.1| 30S ribosomal protein S4 [Sinorhizobium medicae WSM419] Length = 205 Back     alignment and organism information
>gi|190891998|ref|YP_001978540.1| 30S ribosomal protein S4 [Rhizobium etli CIAT 652] Length = 205 Back     alignment and organism information
>gi|222148432|ref|YP_002549389.1| 30S ribosomal protein S4 [Agrobacterium vitis S4] Length = 205 Back     alignment and organism information
>gi|15889161|ref|NP_354842.1| 30S ribosomal protein S4 [Agrobacterium tumefaciens str. C58] Length = 205 Back     alignment and organism information
>gi|209549541|ref|YP_002281458.1| 30S ribosomal protein S4 [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 205 Back     alignment and organism information
>gi|116252370|ref|YP_768208.1| 30S ribosomal protein S4 [Rhizobium leguminosarum bv. viciae 3841] Length = 205 Back     alignment and organism information
>gi|241204876|ref|YP_002975972.1| 30S ribosomal protein S4 [Rhizobium leguminosarum bv. trifolii WSM1325] Length = 205 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
Target206 30S ribosomal protein S4 [Candidatus Liberibacter asiat
PRK05327203 PRK05327, rpsD, 30S ribosomal protein S4; Validated 1e-79
TIGR01017200 TIGR01017, rpsD_bact, ribosomal protein S4, bacterial/o 1e-57
CHL00113201 CHL00113, rps4, ribosomal protein S4; Reviewed 1e-36
COG0522205 COG0522, RpsD, Ribosomal protein S4 and related protein 6e-49
pfam0147948 pfam01479, S4, S4 domain 2e-12
cd0016570 cd00165, S4, S4/Hsp/ tRNA synthetase RNA-binding domain 4e-12
smart0036360 smart00363, S4, S4 RNA-binding domain 6e-12
PRK04051177 PRK04051, rps4p, 30S ribosomal protein S4P; Validated 1e-08
KOG3301183 KOG3301, KOG3301, KOG3301, Ribosomal protein S4 [Transl 3e-07
TIGR01018162 TIGR01018, rpsD_arch, ribosomal protein S4(archaeal typ 4e-07
PLN00189194 PLN00189, PLN00189, 40S ribosomal protein S9; Provision 9e-05
PTZ00155181 PTZ00155, PTZ00155, 40S ribosomal protein S9; Provision 0.002
pfam0016394 pfam00163, Ribosomal_S4, Ribosomal protein S4/S9 N-term 9e-08
>gnl|CDD|180018 PRK05327, rpsD, 30S ribosomal protein S4; Validated Back     alignment and domain information
>gnl|CDD|130089 TIGR01017, rpsD_bact, ribosomal protein S4, bacterial/organelle type Back     alignment and domain information
>gnl|CDD|177038 CHL00113, rps4, ribosomal protein S4; Reviewed Back     alignment and domain information
>gnl|CDD|30868 COG0522, RpsD, Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|144902 pfam01479, S4, S4 domain Back     alignment and domain information
>gnl|CDD|29105 cd00165, S4, S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes Back     alignment and domain information
>gnl|CDD|128657 smart00363, S4, S4 RNA-binding domain Back     alignment and domain information
>gnl|CDD|179730 PRK04051, rps4p, 30S ribosomal protein S4P; Validated Back     alignment and domain information
>gnl|CDD|38511 KOG3301, KOG3301, KOG3301, Ribosomal protein S4 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|130090 TIGR01018, rpsD_arch, ribosomal protein S4(archaeal type)/S9(eukaryote cytosolic type) Back     alignment and domain information
>gnl|CDD|177783 PLN00189, PLN00189, 40S ribosomal protein S9; Provisional Back     alignment and domain information
>gnl|CDD|185484 PTZ00155, PTZ00155, 40S ribosomal protein S9; Provisional Back     alignment and domain information
>gnl|CDD|143931 pfam00163, Ribosomal_S4, Ribosomal protein S4/S9 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 206 30S ribosomal protein S4 [Candidatus Liberibacter asiat
TIGR01017217 rpsD_bact ribosomal protein S4; InterPro: IPR005709 Rib 100.0
PRK05327201 rpsD 30S ribosomal protein S4; Validated 100.0
PRK12565197 30S ribosomal protein S4; Provisional 100.0
CHL00113201 rps4 ribosomal protein S4; Reviewed 100.0
COG0522205 RpsD Ribosomal protein S4 and related proteins [Transla 100.0
pfam0016394 Ribosomal_S4 Ribosomal protein S4/S9 N-terminal domain. 99.95
KOG3301183 consensus 99.82
TIGR01018170 rpsD_arch ribosomal protein S4; InterPro: IPR005710 Rib 99.72
PRK04051177 rps4p 30S ribosomal protein S4; Validated 99.67
PTZ00155188 40S ribosomal protein S9; Provisional 99.59
smart0036360 S4 S4 RNA-binding domain. 99.22
pfam0147948 S4 S4 domain. The S4 domain is a small domain consistin 99.21
cd0016570 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The doma 99.13
COG1189 245 Predicted rRNA methylase [Translation, ribosomal struct 98.49
COG1188100 Ribosome-associated heat shock protein implicated in th 98.38
TIGR00478 240 tly hemolysin A; InterPro: IPR004538 Hemolysins are exo 98.34
TIGR03069257 PS_II_S4 photosystem II S4 domain protein. Members of t 98.31
PRK10348133 ribosome-associated heat shock protein Hsp15; Provision 98.19
PRK10839 231 16S rRNA pseudouridylate synthase A; Provisional 98.18
COG2302257 Uncharacterized conserved protein, contains S4-like dom 98.11
PRK11180 325 rluD 23S rRNA pseudouridine synthase D; Provisional 97.76
PRK11025 317 23S rRNA pseudouridylate synthase C; Provisional 97.6
KOG4655181 consensus 97.56
COG0564 289 RluA Pseudouridylate synthases, 23S RNA-specific [Trans 97.52
PRK10475 290 23S rRNA pseudouridine synthase F; Provisional 97.49
COG1187 248 RsuA 16S rRNA uridine-516 pseudouridylate synthase and 97.08
PRK10700 291 23S rRNA pseudouridylate synthase B; Provisional 96.64
PRK1150770 hypothetical protein; Provisional 96.52
TIGR0298860 YaaA_near_RecF S4 domain protein YaaA; InterPro: IPR014 96.44
PRK04313237 30S ribosomal protein S4e; Validated 96.37
PTZ00223 273 40S ribosomal protein S4; Provisional 96.37
PTZ00118 262 40S ribosomal protein S4; Provisional 96.21
COG250173 S4-like RNA binding protein [Replication, recombination 96.16
COG1471241 RPS4A Ribosomal protein S4E [Translation, ribosomal str 95.42
PRK13354405 tyrosyl-tRNA synthetase; Provisional 96.7
PRK05912402 tyrosyl-tRNA synthetase; Validated 95.73
COG0162401 TyrS Tyrosyl-tRNA synthetase [Translation, ribosomal st 93.92
TIGR00005 337 rluA_subfam pseudouridine synthase, RluA family; InterP 95.82
>TIGR01017 rpsD_bact ribosomal protein S4; InterPro: IPR005709 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>PRK05327 rpsD 30S ribosomal protein S4; Validated Back     alignment and domain information
>PRK12565 30S ribosomal protein S4; Provisional Back     alignment and domain information
>CHL00113 rps4 ribosomal protein S4; Reviewed Back     alignment and domain information
>COG0522 RpsD Ribosomal protein S4 and related proteins [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>pfam00163 Ribosomal_S4 Ribosomal protein S4/S9 N-terminal domain Back     alignment and domain information
>KOG3301 consensus Back     alignment and domain information
>TIGR01018 rpsD_arch ribosomal protein S4; InterPro: IPR005710 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>PRK04051 rps4p 30S ribosomal protein S4; Validated Back     alignment and domain information
>PTZ00155 40S ribosomal protein S9; Provisional Back     alignment and domain information
>smart00363 S4 S4 RNA-binding domain Back     alignment and domain information
>pfam01479 S4 S4 domain Back     alignment and domain information
>cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes Back     alignment and domain information
>COG1189 Predicted rRNA methylase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>TIGR00478 tly hemolysin A; InterPro: IPR004538 Hemolysins are exotoxins that attack blood cell membranes and cause cell rupture Back     alignment and domain information
>TIGR03069 PS_II_S4 photosystem II S4 domain protein Back     alignment and domain information
>PRK10348 ribosome-associated heat shock protein Hsp15; Provisional Back     alignment and domain information
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional Back     alignment and domain information
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown] Back     alignment and domain information
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional Back     alignment and domain information
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional Back     alignment and domain information
>KOG4655 consensus Back     alignment and domain information
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK10475 23S rRNA pseudouridine synthase F; Provisional Back     alignment and domain information
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional Back     alignment and domain information
>PRK11507 hypothetical protein; Provisional Back     alignment and domain information
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA; InterPro: IPR014330 This small protein has a single S4 domain (IPR002942 from INTERPRO); it is also found in bacterial S4 ribosomal proteins, some pseudouridine synthases and tyrosyl-tRNA synthetases Back     alignment and domain information
>PRK04313 30S ribosomal protein S4e; Validated Back     alignment and domain information
>PTZ00223 40S ribosomal protein S4; Provisional Back     alignment and domain information
>PTZ00118 40S ribosomal protein S4; Provisional Back     alignment and domain information
>COG2501 S4-like RNA binding protein [Replication, recombination, and repair] Back     alignment and domain information
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>PRK13354 tyrosyl-tRNA synthetase; Provisional Back     alignment and domain information
>PRK05912 tyrosyl-tRNA synthetase; Validated Back     alignment and domain information
>COG0162 TyrS Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family; InterPro: IPR006225 This is the RluD subfamily of pseudouridine synthases 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
Target206 30S ribosomal protein S4 [Candidatus Liberibacter asiat
1vs5_D206 Crystal Structure Of The Bacterial Ribosome From Es 4e-55
1fka_D209 Structure Of Functionally Activated Small Ribosomal 9e-55
1fjg_D209 Structure Of The Thermus Thermophilus 30s Ribosomal 2e-54
1p6g_D205 Real Space Refined Coordinates Of The 30s Subunit F 6e-54
1i94_D208 Crystal Structures Of The Small Ribosomal Subunit W 9e-54
2gy9_D204 Structure Of The 30s Subunit Of A Pre-Translocation 3e-53
3bbn_D201 Homology Model For The Spinach Chloroplast 30s Subu 2e-47
1qd7_C159 Partial Model For 30s Ribosomal Subunit Length = 15 2e-39
gi|116666551|pdb|1VS5|D Chain D, 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 = 206 Back     alignment and structure 
 Score =  218 bits (555), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 81/211 (38%), Positives = 127/211 (60%), Gaps = 10/211 (4%)

Query: 1   MSKRESSKHKIDRRIGENLWGRPK-SPVNTRSY---GPGLHGQRRKSKPSYFGLQLRAKQ 56
           M++    K K+ RR G +L+ +     ++T+      PG HG  RK + S +G+QLR KQ
Sbjct: 1   MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGA-RKPRLSDYGVQLREKQ 59

Query: 57  KMKKYYGDISEKKFRSIFKEADRSRGDTSHNLISFLESRLDTIVYRAKFVPTIFAARQFV 116
           K+++ YG + E++FR+ +KEA R +G+T  NL++ LE RLD +VYR  F  T   ARQ V
Sbjct: 60  KVRRIYGVL-ERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLV 118

Query: 117 NHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSKQLASVLEASQLAE-RDVPEYISVNHDNM 175
           +H+ ++VNGR VNI SY+    DV+ +++K+K+ + V  A +LAE R+ P ++ V+   M
Sbjct: 119 SHKAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKM 178

Query: 176 VATFVRIPSSLKDVPYPVIMQPNLVVEFYSR 206
             TF R P           +  +L+VE YS+
Sbjct: 179 EGTFKRKPERSD---LSADINEHLIVELYSK 206
gi|10120567|pdb|1FKA|D Chain D, Structure Of Functionally Activated Small Ribosomal Subunit At 3.3 A Resolution Length = 209 Back     alignment and structure
>gi|10835588|pdb|1FJG|D Chain D, Structure Of The Thermus Thermophilus 30s Ribosomal Subunit In Complex With The Antibiotics Streptomycin, Spectinomycin, And Paromomycin Length = 209 Back     alignment and structure
>gi|33357881|pdb|1P6G|D Chain D, 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 = 205 Back     alignment and structure
>gi|14278533|pdb|1I94|D Chain D, Crystal Structures Of The Small Ribosomal Subunit With Tetracycline, Edeine And If3 Length = 208 Back     alignment and structure
>gi|116667413|pdb|2GY9|D Chain D, 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 = 204 Back     alignment and structure
gi|188036205|pdb|3BBN|D Chain D, Homology Model For The Spinach Chloroplast 30s Subunit Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome. Length = 201 Back     alignment and structure
>gi|6137687|pdb|1QD7|C Chain C, Partial Model For 30s Ribosomal Subunit Length = 159 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
Target206 30S ribosomal protein S4 [Candidatus Liberibacter asiat
3ofo_D205 30S ribosomal protein S4; protein biosynthesis, ribosom 8e-55
3i1m_D206 30S ribosomal protein S4; ribosome structure, protein-R 3e-49
2vqe_D209 30S ribosomal protein S4; tRNA-binding, rRNA-binding, m 8e-48
3bbn_D201 Ribosomal protein S4; small ribosomal subunit, spinach 1e-41
1c05_A159 Ribosomal protein S4 delta 41; two subdomains, unique t 1e-39
3jyv_D158 40S ribosomal protein S9(A); eukaryotic ribosome, RACK1 2e-22
1s1h_D179 40S ribosomal protein S9-A; 80S ribosome, 40S ribosomal 1e-16
2cqj_A71 BRMS2, U3 small nucleolar ribonucleoprotein protein IMP 4e-15
1p9k_A79 ORF, hypothetical protein; alfal motif, RNA-binding pro 3e-08
1dm9_A133 Hypothetical 15.5 KD protein in MRCA-PCKA intergenic re 9e-06
2k6p_A92 Uncharacterized protein HP_1423; alpha-L motif, RNA-bin 8e-05
>3ofo_D 30S ribosomal protein S4; protein biosynthesis, ribosomes, RNA, tRNA, transfer, eryThr ketolide, macrolide, antibiotic, EXIT, peptidyl; 3.10A {Escherichia coli} PDB: 1p6g_D 1p87_D 2aw7_D 2avy_D 2i2u_D 2i2p_D* 2qan_D* 2qb9_D* 2qbb_D* 2qbd_D 2qbf_D 2qbh_D* 2qbj_D* 2qou_D* 2qow_D* 2qoy_D* 2qp0_D* 2vho_D 2vhp_D 2wwl_D* ... Length = 205 Back     alignment and structure
 Score =  208 bits (531), Expect = 8e-55
 Identities = 79/204 (38%), Positives = 122/204 (59%), Gaps = 10/204 (4%)

Query: 8   KHKIDRRIGENLWGRPKSPV----NTRSYGPGLHGQRRKSKPSYFGLQLRAKQKMKKYYG 63
           K K+ RR G +L+ +               PG HG R+  + S +G+QLR KQK+++ YG
Sbjct: 7   KLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKP-RLSDYGVQLREKQKVRRIYG 65

Query: 64  DISEKKFRSIFKEADRSRGDTSHNLISFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLV 123
            + E++FR+ +KEA R +G+T  NL++ LE RLD +VYR  F  T   ARQ V+H+ ++V
Sbjct: 66  -VLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSHKAIMV 124

Query: 124 NGRSVNIGSYRCKEGDVIEVKQKSKQLASVLEASQLAE-RDVPEYISVNHDNMVATFVRI 182
           NGR VNI SY+    DV+ +++K+K+ + V  A +LAE R+ P ++ V+   M  TF R 
Sbjct: 125 NGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEGTFKRK 184

Query: 183 PSSLKDVPYPVIMQPNLVVEFYSR 206
           P    D+   +    +L+VE YS+
Sbjct: 185 PER-SDLSADI--NEHLIVELYSK 205
>3i1m_D 30S ribosomal protein S4; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_D* 3e1a_R 3e1c_R 1vs5_D 3i1o_D 3i1q_D 3i1s_D 3i1z_D 3i21_D 2qal_D* 1p6g_D 1p87_D 2aw7_D 2avy_D 2i2u_D 2i2p_D* 2qan_D* 2qb9_D* 2qbb_D* 2qbd_D ... Length = 206 Back     alignment and structure
>2vqe_D 30S ribosomal protein S4; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: d.66.1.2 PDB: 1hnw_D* 1hnx_D* 1hnz_D* 1ibk_D* 1fka_D* 1ibm_D 1xmo_D* 1ibl_D* 1xnq_D* 1xnr_D* 1yl4_G 2b64_D* 2b9m_D* 2b9o_D* 2hgi_G 2hgp_G 2hgr_G 2hhh_D* 1xmq_D* 2j02_D* ... Length = 209 Back     alignment and structure
>3bbn_D Ribosomal protein S4; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Length = 201 Back     alignment and structure
>1c05_A Ribosomal protein S4 delta 41; two subdomains, unique topology, possible helix-turn-helix motif; NMR {Bacillus stearothermophilus} SCOP: d.66.1.2 PDB: 1c06_A 1eg0_A 1qd7_C Length = 159 Back     alignment and structure
>3jyv_D 40S ribosomal protein S9(A); eukaryotic ribosome, RACK1 protein, flexible fitting; HET: 2MG H2U M2G OMC OMG YYG PSU 5MC 7MG 5MU 1MA; 8.90A {Thermomyces lanuginosus} Length = 158 Back     alignment and structure
>1s1h_D 40S ribosomal protein S9-A; 80S ribosome, 40S ribosomal subunit, EEF2, tRNA translocation, sordarin, cryo-EM; 11.70A {Saccharomyces cerevisiae} SCOP: i.1.1.1 Length = 179 Back     alignment and structure
>2cqj_A BRMS2, U3 small nucleolar ribonucleoprotein protein IMP3 homolog; S4 domain, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 71 Back     alignment and structure
>1p9k_A ORF, hypothetical protein; alfal motif, RNA-binding protein, E.coli, montreal-kingston bacterial structural genomics initiative, BSGI; NMR {Escherichia coli K12} SCOP: d.66.1.6 Length = 79 Back     alignment and structure
>1dm9_A Hypothetical 15.5 KD protein in MRCA-PCKA intergenic region; heat shock proteins, protein-RNA interactions, ribosome, structural genomics; 2.00A {Escherichia coli} SCOP: d.66.1.3 PDB: 3bbu_A Length = 133 Back     alignment and structure
>2k6p_A Uncharacterized protein HP_1423; alpha-L motif, RNA-binding, unknown function; NMR {Helicobacter pylori} Length = 92 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

Original result of HHsearch against PDB70 database

IdentityAlignment graphLength Definition Probability
Target206 30S ribosomal protein S4 [Candidatus Liberibacter asiat
2vqe_D209 30S ribosomal protein S4; tRNA-binding, rRNA-binding, m 100.0
3ofo_D205 30S ribosomal protein S4; protein biosynthesis, ribosom 100.0
3bbn_D201 Ribosomal protein S4; small ribosomal subunit, spinach 100.0
1c05_A159 Ribosomal protein S4 delta 41; two subdomains, unique t 100.0
3jyv_D158 40S ribosomal protein S9(A); eukaryotic ribosome, RACK1 99.94
1s1h_D179 40S ribosomal protein S9-A; 80S ribosome, 40S ribosomal 99.85
2cqj_A71 BRMS2, U3 small nucleolar ribonucleoprotein protein IMP 99.69
1p9k_A79 ORF, hypothetical protein; alfal motif, RNA-binding pro 98.84
1dm9_A133 Hypothetical 15.5 KD protein in MRCA-PCKA intergenic re 98.74
2k6p_A92 Uncharacterized protein HP_1423; alpha-L motif, RNA-bin 98.48
3hp7_A 291 Hemolysin, putative; structural genomics, APC64019, PSI 98.38
1ksk_A 234 Ribosomal small subunit pseudouridine synthase A; RSUA, 98.22
3dh3_A 290 Ribosomal large subunit pseudouridine synthase F; prote 98.1
1vio_A 243 Ribosomal small subunit pseudouridine synthase A; struc 97.98
1v9f_A 325 Ribosomal large subunit pseudouridine synthase D; RNA b 97.25
1h3f_A432 Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA synthet 96.61
3kbg_A213 30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR28, NE 96.53
2jan_A432 Tyrosyl-tRNA synthetase; protein biosynthesis, aminoacy 96.42
1jil_A420 Tyrrs, tyrosyl-tRNA synthetase, tyrosyl-transfer; trunc 94.68
2ts1_A419 Tyrosyl-tRNA synthetase; ligase (synthetase); 2.30A {Ge 94.24
>2vqe_D 30S ribosomal protein S4; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: d.66.1.2 PDB: 1hnw_D* 1hnx_D* 1hnz_D* 1ibk_D* 1fka_D* 1ibm_D 1xmo_D* 1ibl_D* 1xnq_D* 1xnr_D* 1yl4_G 2b64_D* 2b9m_D* 2b9o_D* 2hgi_G 2hgp_G 2hgr_G 2hhh_D* 1xmq_D* 2j02_D* ... Back     alignment and structure
Probab=100.00  E-value=0  Score=527.58  Aligned_cols=202  Identities=40%  Similarity=0.713  Sum_probs=191.7

Q ss_pred             CCCCCCCEEEEEEECCCCCCCC------CCCCHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHH
Q ss_conf             9764487123520058888888------8770001368998776544334135899999988485551565479999999
Q gi|254780187|r    1 MSKRESSKHKIDRRIGENLWGR------PKSPVNTRSYGPGLHGQRRKSKPSYFGLQLRAKQKMKKYYGDISEKKFRSIF   74 (206)
Q Consensus         1 M~r~~gpk~K~~RrlG~~l~~~------~k~~~~~r~~~pGqhg~~r~~k~S~yg~qL~eKQKlr~~YG~~~ekq~~~~~   74 (206)
                      ||||+|||+|+|||||++||++      +|+++++|+++|||||+++++|.|+||+||+||||+||+|| |+|+||++||
T Consensus         1 MaRy~GPk~Ki~RRlG~~l~~~~~~~~~~K~~l~kr~~~PGqhG~~r~~k~S~Yg~qL~EKQKlr~~YG-l~EkQf~~~~   79 (209)
T 2vqe_D            1 MGRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRPSDYAVRLREKQKLRRIYG-ISERQFRNLF   79 (209)
T ss_dssp             -CCCCSCCHHHHHHHSSCCCTTSTTSSSTTCSGGGCCSCSSTTTTSCCCCCCHHHHHHHHHHHHHHHHT-CCHHHHHHHH
T ss_pred             CCCCCCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCC-CCHHHHHHHH
T ss_conf             986547687885207998667786667876500037899986666678763489999999999987518-8789999999


Q ss_pred             HHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECCHHHHHHHHH
Q ss_conf             87530334430268999998888899862121247887887624978788889413534833884788611002269999
Q gi|254780187|r   75 KEADRSRGDTSHNLISFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSKQLASVL  154 (206)
Q Consensus        75 ~~A~~~~g~t~~~ll~~LE~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~ksk~~~~i~  154 (206)
                      ++|.+++|+||++||++||+||||+|||+|||+|+++|||||+||||+|||++||||||.|+|||+|++++++++...+.
T Consensus        80 ~~A~k~~G~tg~~ll~lLE~RlD~vv~r~g~a~s~~~ARQ~v~Hghv~vng~~v~ips~~~k~gd~i~~~~k~~~~~~v~  159 (209)
T 2vqe_D           80 EEASKKKGVTGSVFLGLLESRLDNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAVAEKSRNLELIR  159 (209)
T ss_dssp             HHHHHSSSCHHHHHHHHHHTBHHHHHHHTTSSSSHHHHHHHHHTTCEEETTEECCCTTCBCCTTCEEEECGGGTTCHHHH
T ss_pred             HHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCEECCCEEECCCCEECCCCCEEEECCCCCCHHHHH
T ss_conf             99985689789999999999889999834751799999999873073219979735886827999998610211549999


Q ss_pred             HHHHH-CCCCCCCEEEECCCCCEEEEEECCCCCCCCCCCCCCCCCEEEEEECC
Q ss_conf             87752-16899962788124318999967884211246753466316775049
Q gi|254780187|r  155 EASQL-AERDVPEYISVNHDNMVATFVRIPSSLKDVPYPVIMQPNLVVEFYSR  206 (206)
Q Consensus       155 ~~~~~-~~~~~P~wLevd~~~l~g~v~~~P~r~e~i~~p~~ine~LVVEyYSR  206 (206)
                      ++++. ....+|+||++|.++|+|++++.|++ +|  +|+.+||+||||||||
T Consensus       160 ~~~~~~~~~~vp~wL~~d~~~l~g~v~~~P~r-~~--i~~~ine~lVVEyYSR  209 (209)
T 2vqe_D          160 QNLEAMKGRKVGPWLSLDVEGMKGKFLRLPDR-ED--LALPVNEQLVIEFYSR  209 (209)
T ss_dssp             HHHHHTTTCCCCTTCCEETTTTEEECCSCCCG-GG--CCCSCCHHHHHHHTTC
T ss_pred             HHHHHHCCCCCCCCEEECCHHCEEEEEECCCH-HH--CCCCCCCCEEEEECCC
T ss_conf             99986152788886164251089999945478-87--8988773579986069
>3ofo_D 30S ribosomal protein S4; protein biosynthesis, ribosomes, RNA, tRNA, transfer, eryThr ketolide, macrolide, antibiotic, EXIT, peptidyl; 3.10A {Escherichia coli} PDB: 1p6g_D 1p87_D 2aw7_D 2avy_D 2i2u_D 2i2p_D* 2qan_D* 2qb9_D* 2qbb_D* 2qbd_D 2qbf_D 2qbh_D* 2qbj_D* 2qou_D* 2qow_D* 2qoy_D* 2qp0_D* 2vho_D 2vhp_D 2wwl_D* ... Back     alignment and structure
>3bbn_D Ribosomal protein S4; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Back     alignment and structure
>1c05_A Ribosomal protein S4 delta 41; two subdomains, unique topology, possible helix-turn-helix motif, ribosome; NMR {Geobacillus stearothermophilus} SCOP: d.66.1.2 PDB: 1c06_A 1eg0_A 1qd7_C Back     alignment and structure
>3jyv_D 40S ribosomal protein S9(A); eukaryotic ribosome, RACK1 protein, flexible fitting; HET: 2MG H2U M2G OMC OMG YYG PSU 5MC 7MG 5MU 1MA; 8.90A {Thermomyces lanuginosus} Back     alignment and structure
>1s1h_D 40S ribosomal protein S9-A; 80S ribosome, 40S ribosomal subunit, EEF2, tRNA translocation, sordarin, cryo-EM; 11.70A {Saccharomyces cerevisiae} SCOP: i.1.1.1 Back     alignment and structure
>2cqj_A BRMS2, U3 small nucleolar ribonucleoprotein protein IMP3 homolog; S4 domain, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>1p9k_A ORF, hypothetical protein; alfal motif, RNA-binding protein, E.coli, montreal-kingston bacterial structural genomics initiative, BSGI; NMR {Escherichia coli K12} SCOP: d.66.1.6 Back     alignment and structure
>1dm9_A Hypothetical 15.5 KD protein in MRCA-PCKA intergenic region; heat shock proteins, protein-RNA interactions, ribosome, structural genomics; 2.00A {Escherichia coli} SCOP: d.66.1.3 PDB: 3bbu_A Back     alignment and structure
>2k6p_A Uncharacterized protein HP_1423; alpha-L motif, RNA-binding, unknown function; NMR {Helicobacter pylori} Back     alignment and structure
>3hp7_A Hemolysin, putative; structural genomics, APC64019, PSI-2, protein structure initiative; HET: MSE; 1.53A {Streptococcus thermophilus lmg 18311} Back     alignment and structure
>1ksk_A Ribosomal small subunit pseudouridine synthase A; RSUA, lyase; 2.00A {Escherichia coli} SCOP: d.265.1.3 d.66.1.5 PDB: 1ksl_A 1ksv_A* Back     alignment and structure
>3dh3_A Ribosomal large subunit pseudouridine synthase F; protein-RNA complex, S4 domain, alpha/beta protein, isomerase, RNA-binding, rRNA processing; HET: FHU; 3.00A {Escherichia coli} Back     alignment and structure
>1vio_A Ribosomal small subunit pseudouridine synthase A; structural genomics, lyase; 1.59A {Haemophilus influenzae} SCOP: d.265.1.3 d.66.1.5 Back     alignment and structure
>1v9f_A Ribosomal large subunit pseudouridine synthase D; RNA binding, lyase; 1.70A {Escherichia coli} SCOP: d.265.1.3 PDB: 2ist_A 1qyu_A 1prz_A Back     alignment and structure
>1h3f_A Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA synthetase; HET: TYB; 2.0A {Thermus thermophilus} SCOP: c.26.1.1 d.66.1.4 PDB: 1h3e_A* Back     alignment and structure
>3kbg_A 30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR28, NESG, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.75A {Thermoplasma acidophilum} Back     alignment and structure
>2jan_A Tyrosyl-tRNA synthetase; protein biosynthesis, aminoacyl-tRNA synthetase, tyrrs, ligase, tyrosine, RNA-binding, ATP-binding; 2.9A {Mycobacterium tuberculosis} Back     alignment and structure
>1jil_A Tyrrs, tyrosyl-tRNA synthetase, tyrosyl-transfer; truncation, structure based inhibitor design, ligase; HET: 485; 2.20A {Staphylococcus aureus} SCOP: c.26.1.1 PDB: 1jij_A* 1jii_A* 1jik_A* Back     alignment and structure
>2ts1_A Tyrosyl-tRNA synthetase; ligase (synthetase); 2.30A {Geobacillus stearothermophilus} SCOP: c.26.1.1 PDB: 3ts1_A* 1tyd_E* 1tya_E* 1tyc_A 1tyb_E* 4ts1_A* 1jh3_A 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 206 30S ribosomal protein S4 [Candidatus Liberibacter asiat
d2gy9d1204 d.66.1.2 (D:2-205) Ribosomal protein S4 {Escherichia co 7e-49
d2uubd1208 d.66.1.2 (D:2-209) Ribosomal protein S4 {Thermus thermo 6e-46
d1c06a_159 d.66.1.2 (A:) Ribosomal protein S4 {Bacillus stearother 3e-40
d1dm9a_104 d.66.1.3 (A:) Heat shock protein 15 kD {Escherichia col 1e-09
d1vioa258 d.66.1.5 (A:0-57) Pseudouridine synthase RsuA N-termina 1e-06
d1p9ka_79 d.66.1.6 (A:) Hypothetical protein YbcJ {Escherichia co 1e-04
d1kska359 d.66.1.5 (A:1-59) Pseudouridine synthase RsuA N-termina 1e-04
>d2gy9d1 d.66.1.2 (D:2-205) Ribosomal protein S4 {Escherichia coli [TaxId: 562]} Length = 204 Back     information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Ribosomal protein S4
domain: Ribosomal protein S4
species: Escherichia coli [TaxId: 562]

 Score =  187 bits (475), Expect = 7e-49
 Identities = 79/204 (38%), Positives = 122/204 (59%), Gaps = 10/204 (4%)

Query: 8   KHKIDRRIGENLWGRPK----SPVNTRSYGPGLHGQRRKSKPSYFGLQLRAKQKMKKYYG 63
           K K+ RR G +L+ +               PG HG R+  + S +G+QLR KQK+++ YG
Sbjct: 6   KLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKP-RLSDYGVQLREKQKVRRIYG 64

Query: 64  DISEKKFRSIFKEADRSRGDTSHNLISFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLV 123
            + E++FR+ +KEA R +G+T  NL++ LE RLD +VYR  F  T   ARQ V+H+ ++V
Sbjct: 65  -VLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSHKAIMV 123

Query: 124 NGRSVNIGSYRCKEGDVIEVKQKSKQLASVLEASQLAE-RDVPEYISVNHDNMVATFVRI 182
           NGR VNI SY+    DV+ +++K+K+ + V  A +LAE R+ P ++ V+   M  TF R 
Sbjct: 124 NGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEGTFKRK 183

Query: 183 PSSLKDVPYPVIMQPNLVVEFYSR 206
           P    D+   +    +L+VE YS+
Sbjct: 184 PER-SDLSADI--NEHLIVELYSK 204
>d2uubd1 d.66.1.2 (D:2-209) Ribosomal protein S4 {Thermus thermophilus [TaxId: 274]} Length = 208 Back     information, alignment and structure
>d1c06a_ d.66.1.2 (A:) Ribosomal protein S4 {Bacillus stearothermophilus [TaxId: 1422]} Length = 159 Back     information, alignment and structure
>d1dm9a_ d.66.1.3 (A:) Heat shock protein 15 kD {Escherichia coli [TaxId: 562]} Length = 104 Back     information, alignment and structure
>d1vioa2 d.66.1.5 (A:0-57) Pseudouridine synthase RsuA N-terminal domain {Haemophilus influenzae [TaxId: 727]} Length = 58 Back     information, alignment and structure
>d1p9ka_ d.66.1.6 (A:) Hypothetical protein YbcJ {Escherichia coli [TaxId: 562]} Length = 79 Back     information, alignment and structure
>d1kska3 d.66.1.5 (A:1-59) Pseudouridine synthase RsuA N-terminal domain {Escherichia coli [TaxId: 562]} Length = 59 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
Target206 30S ribosomal protein S4 [Candidatus Liberibacter asiat
d2uubd1208 Ribosomal protein S4 {Thermus thermophilus [TaxId: 274] 100.0
d2gy9d1204 Ribosomal protein S4 {Escherichia coli [TaxId: 562]} 100.0
d1c06a_159 Ribosomal protein S4 {Bacillus stearothermophilus [TaxI 100.0
d1dm9a_104 Heat shock protein 15 kD {Escherichia coli [TaxId: 562] 99.28
d1vioa258 Pseudouridine synthase RsuA N-terminal domain {Haemophi 98.87
d1kska359 Pseudouridine synthase RsuA N-terminal domain {Escheric 98.86
d1p9ka_79 Hypothetical protein YbcJ {Escherichia coli [TaxId: 562 98.62
d1h3fa281 Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain {The 97.35
d1jh3a_99 Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain {Bac 96.71
>d2uubd1 d.66.1.2 (D:2-209) Ribosomal protein S4 {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Alpha-L RNA-binding motif
superfamily: Alpha-L RNA-binding motif
family: Ribosomal protein S4
domain: Ribosomal protein S4
species: Thermus thermophilus [TaxId: 274]

Probab=100.00  E-value=0  Score=524.75  Aligned_cols=201  Identities=39%  Similarity=0.710  Sum_probs=189.8

Q ss_pred             CCCCCCEEEEEEECCCCCCCC------CCCCHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Q ss_conf             764487123520058888888------87700013689987765443341358999999884855515654799999998
Q gi|254780187|r    2 SKRESSKHKIDRRIGENLWGR------PKSPVNTRSYGPGLHGQRRKSKPSYFGLQLRAKQKMKKYYGDISEKKFRSIFK   75 (206)
Q Consensus         2 ~r~~gpk~K~~RrlG~~l~~~------~k~~~~~r~~~pGqhg~~r~~k~S~yg~qL~eKQKlr~~YG~~~ekq~~~~~~   75 (206)
                      .||+||++|+|||+|++||++      +|+++++|++||||||+++++|+|+||+||+||||+||+|| |+|+||++||+
T Consensus         1 gRy~GPk~K~~RRlG~~l~~~g~~~~~~k~~~~kr~~~PG~hg~~r~~k~S~Yg~qL~EKQKlr~~YG-v~EkQfr~~~~   79 (208)
T d2uubd1           1 GRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRPSDYAVRLREKQKLRRIYG-ISERQFRNLFE   79 (208)
T ss_dssp             CCCCSCCHHHHHHHTSCCCSSSTTSSSTTSSSSSCCSCSSTTSSSCCCCCCHHHHHHHHHHHHHHHHT-CCHHHHHHHHH
T ss_pred             CCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHC-CCHHHHHHHHH
T ss_conf             98667465641127898677785667877500048899987777678755578999999999999818-46188999999


Q ss_pred             HHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECCHHHHHHHHHH
Q ss_conf             75303344302689999988888998621212478878876249787888894135348338847886110022699998
Q gi|254780187|r   76 EADRSRGDTSHNLISFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSKQLASVLE  155 (206)
Q Consensus        76 ~A~~~~g~t~~~ll~~LE~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~ksk~~~~i~~  155 (206)
                      +|.+++|+||++||++||+||||||||+|||+|+++|||||+||||+|||++||||||.|+|||+|+++++++++..+.+
T Consensus        80 ~A~~~~G~tg~~ll~lLE~Rld~vv~r~g~a~t~~~ARQ~v~Hg~i~vNg~~v~ips~~~~~gd~I~vreksk~~~~i~~  159 (208)
T d2uubd1          80 EASKKKGVTGSVFLGLLESRLDNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAVAEKSRNLELIRQ  159 (208)
T ss_dssp             HHHHSSSCHHHHHHHHHHTBHHHHHHHTTSSSSHHHHHHHHHTTCEEETTEECCCTTCBCCTTCEEEECGGGTTCHHHHH
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCEECCCEEEEECCEEECCCCEEEHHHCCCHHHHHHH
T ss_conf             99854798367899999999999998536201289888998735742288399862679428862001110001899999


Q ss_pred             HHHH-CCCCCCCEEEECCCCCEEEEEECCCCCCCCCCCCCCCCCEEEEEECC
Q ss_conf             7752-16899962788124318999967884211246753466316775049
Q gi|254780187|r  156 ASQL-AERDVPEYISVNHDNMVATFVRIPSSLKDVPYPVIMQPNLVVEFYSR  206 (206)
Q Consensus       156 ~~~~-~~~~~P~wLevd~~~l~g~v~~~P~r~e~i~~p~~ine~LVVEyYSR  206 (206)
                      +++. ....+|+||++|.++|+|+|++.|++ +|  +|+.+||+||||||||
T Consensus       160 ~le~~~~~~~P~wLevd~~~l~g~v~~~P~r-ee--i~~~ine~LIVEyYSR  208 (208)
T d2uubd1         160 NLEAMKGRKVGPWLSLDVEGMKGKFLRLPDR-ED--LALPVNEQLVIEFYSR  208 (208)
T ss_dssp             HHHHHTTCCCCTTEEEETTTTEEEECSCCCG-GG--CCCSCCHHHHHHHHHC
T ss_pred             HHHHHCCCCCCCCEEEECCCCEEEEEECCCH-HH--CCCCCCCCEEEEECCC
T ss_conf             9986222789898674051188999944577-87--7988772579986069
>d2gy9d1 d.66.1.2 (D:2-205) Ribosomal protein S4 {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1c06a_ d.66.1.2 (A:) Ribosomal protein S4 {Bacillus stearothermophilus [TaxId: 1422]} Back     information, alignment and structure
>d1dm9a_ d.66.1.3 (A:) Heat shock protein 15 kD {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1vioa2 d.66.1.5 (A:0-57) Pseudouridine synthase RsuA N-terminal domain {Haemophilus influenzae [TaxId: 727]} Back     information, alignment and structure
>d1kska3 d.66.1.5 (A:1-59) Pseudouridine synthase RsuA N-terminal domain {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1p9ka_ d.66.1.6 (A:) Hypothetical protein YbcJ {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1h3fa2 d.66.1.4 (A:352-432) Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1jh3a_ d.66.1.4 (A:) Tyrosyl-tRNA synthetase (TyrRS), C-terminal domain {Bacillus stearothermophilus [TaxId: 1422]} 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 206 30S ribosomal protein S4 [Candidatus Liberibacter
3bbn_D_82-201120 (D:82-201) Ribosomal protein S4; small ribosomal s 2e-30
3i1m_D_97-19094 (D:97-190) 30S ribosomal protein S4; ribosome stru 3e-24
2vqe_D_100-19394 (D:100-193) 30S ribosomal protein S4; tRNA-binding 2e-21
2k6p_A_92 (A:) Uncharacterized protein HP_1423; alpha-L moti 2e-11
1dm9_A_133 (A:) Hypothetical 15.5 KD protein in MRCA-PCKA int 5e-10
1s1h_D_81-17999 (D:81-179) 40S ribosomal protein S9-A; 80S ribosom 4e-23
2cqj_A_71 (A:) BRMS2, U3 small nucleolar ribonucleoprotein p 4e-20
1h3f_A_350-43283 (A:350-432) Tyrosyl-tRNA synthetase; ligase, amino 8e-18
1p9k_A_79 (A:) ORF, hypothetical protein; alfal motif, RNA-b 2e-15
3hp7_A_1-6565 (A:1-65) Hemolysin, putative; structural genomics, 5e-14
1vio_A_1-5757 (A:1-57) Ribosomal small subunit pseudouridine syn 2e-12
1ksk_A_1-5858 (A:1-58) Ribosomal small subunit pseudouridine syn 6e-12
3dh3_A_1-6363 (A:1-63) Ribosomal large subunit pseudouridine syn 1e-07
1c05_A_77-15983 (A:77-159) Ribosomal protein S4 delta 41; two subd 1e-19
2vqe_D_1-99_194-209115 (D:1-99,D:194-209) 30S ribosomal protein S4; tRNA- 4e-19
3i1m_D_1-96_191-206112 (D:1-96,D:191-206) 30S ribosomal protein S4; ribos 4e-17
1c05_A_22-7655 (A:22-76) Ribosomal protein S4 delta 41; two subdo 2e-17
>3bbn_D (D:82-201) Ribosomal protein S4; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}Length = 120 Back     alignment and structure
 Score =  126 bits (318), Expect = 2e-30
 Identities = 48/120 (40%), Positives = 69/120 (57%), Gaps = 4/120 (3%)

Query: 88  LISFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKS 147
           L+  LE RLD I++R    PTI  ARQ VNHRH+LVNGR V+I SYRCK  D I  + + 
Sbjct: 2   LLQLLEMRLDNILFRLGMAPTIPGARQLVNHRHILVNGRIVDIPSYRCKPQDTIMARDEQ 61

Query: 148 KQLASVLEASQLAE-RDVPEYISVNHDNMVATFVRIPSSLKDVPYPVIMQPNLVVEFYSR 206
           K +A +  +  L+   ++P+++++N         +I    K V     +   LVVE+YSR
Sbjct: 62  KSIALIQNSLDLSPREELPKHLTLNPFPYKGLVNQII-DSKWVGLK--INELLVVEYYSR 118
>3i1m_D (D:97-190) 30S ribosomal protein S4; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_D* 3e1a_R 3e1c_R 1vs5_D 3i1o_D 3i1q_D 3i1s_D 3i1z_D 3i21_D 2qal_D* 1p6g_D 1p87_D 2aw7_D 2avy_D 2i2u_D 2i2p_D* 2qan_D* 2qb9_D* 2qbb_D* 2qbd_D ...Length = 94 Back     alignment and structure
>2vqe_D (D:100-193) 30S ribosomal protein S4; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus}Length = 94 Back     alignment and structure
>2k6p_A (A:) Uncharacterized protein HP_1423; alpha-L motif, RNA-binding, unknown function; NMR {Helicobacter pylori}Length = 92 Back     alignment and structure
>1dm9_A (A:) Hypothetical 15.5 KD protein in MRCA-PCKA intergenic region; heat shock proteins, protein-RNA interactions, ribosome, structural genomics; 2.00A {Escherichia coli}Length = 133 Back     alignment and structure
>1s1h_D (D:81-179) 40S ribosomal protein S9-A; 80S ribosome, 40S ribosomal subunit, EEF2, tRNA translocation, sordarin, cryo-EM; 11.70A {Saccharomyces cerevisiae}Length = 99 Back     alignment and structure
>2cqj_A (A:) BRMS2, U3 small nucleolar ribonucleoprotein protein IMP3 homolog; S4 domain, structural genomics, NPPSFA; NMR {Homo sapiens}Length = 71 Back     alignment and structure
>1h3f_A (A:350-432) Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA synthetase; HET: TYB; 2.0A {Thermus thermophilus}Length = 83 Back     alignment and structure
>1p9k_A (A:) ORF, hypothetical protein; alfal motif, RNA-binding protein, E.coli, montreal-kingston bacterial structural genomics initiative, BSGI; NMR {Escherichia coli K12}Length = 79 Back     alignment and structure
>3hp7_A (A:1-65) Hemolysin, putative; structural genomics, APC64019, PSI-2, protein structure initiative; HET: MSE; 1.53A {Streptococcus thermophilus lmg 18311}Length = 65 Back     alignment and structure
>1vio_A (A:1-57) Ribosomal small subunit pseudouridine synthase A; structural genomics, lyase; 1.59A {Haemophilus influenzae}Length = 57 Back     alignment and structure
>1ksk_A (A:1-58) Ribosomal small subunit pseudouridine synthase A; RSUA, lyase; 2.00A {Escherichia coli}Length = 58 Back     alignment and structure
>3dh3_A (A:1-63) Ribosomal large subunit pseudouridine synthase F; protein-RNA complex, S4 domain, alpha/beta protein, isomerase, RNA-binding, rRNA processing; HET: FHU; 3.00A {Escherichia coli}Length = 63 Back     alignment and structure
>1c05_A (A:77-159) Ribosomal protein S4 delta 41; two subdomains, unique topology, possible helix-turn-helix motif; NMR {Bacillus stearothermophilus}Length = 83 Back     alignment and structure
>2vqe_D (D:1-99,D:194-209) 30S ribosomal protein S4; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus}Length = 115 Back     alignment and structure
>3i1m_D (D:1-96,D:191-206) 30S ribosomal protein S4; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_D* 3e1a_R 3e1c_R 1vs5_D 3i1o_D 3i1q_D 3i1s_D 3i1z_D 3i21_D 2qal_D* 1p6g_D 1p87_D 2aw7_D 2avy_D 2i2u_D 2i2p_D* 2qan_D* 2qb9_D* 2qbb_D* 2qbd_D ...Length = 112 Back     alignment and structure
>1c05_A (A:22-76) Ribosomal protein S4 delta 41; two subdomains, unique topology, possible helix-turn-helix motif; NMR {Bacillus stearothermophilus}Length = 55 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

Original result of HHsearch against MMDB70 database

IdentityAlignment graphLength Definition Probability
Target206 30S ribosomal protein S4 [Candidatus Liberibacter asiat
3bbn_D_82-201120 Ribosomal protein S4; small ribosomal subunit, spi 100.0
3i1m_D_97-19094 30S ribosomal protein S4; ribosome structure, prot 99.94
2vqe_D_100-19394 30S ribosomal protein S4; tRNA-binding, rRNA-bindi 99.91
2vqe_D_1-99_194-209115 30S ribosomal protein S4; tRNA-binding, rRNA-bindi 100.0
3i1m_D_1-96_191-206112 30S ribosomal protein S4; ribosome structure, prot 99.97
1s1h_D_81-17999 40S ribosomal protein S9-A; 80S ribosome, 40S ribo 99.91
1c05_A_77-15983 Ribosomal protein S4 delta 41; two subdomains, uni 99.91
1c05_A_22-7655 Ribosomal protein S4 delta 41; two subdomains, uni 99.84
1jil_A_247-420174 Tyrrs, tyrosyl-tRNA synthetase, tyrosyl-transfer; 97.63
2ts1_A_246-419174 Tyrosyl-tRNA synthetase; ligase (synthetase); 2.30 96.89
2cqj_A_71 BRMS2, U3 small nucleolar ribonucleoprotein protei 99.72
3hp7_A_1-6565 Hemolysin, putative; structural genomics, APC64019 99.41
1h3f_A_350-43283 Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA sy 99.26
1p9k_A_79 ORF, hypothetical protein; alfal motif, RNA-bindin 99.1
1vio_A_1-5757 Ribosomal small subunit pseudouridine synthase A; 99.02
1ksk_A_1-5858 Ribosomal small subunit pseudouridine synthase A; 98.96
1dm9_A_133 Hypothetical 15.5 KD protein in MRCA-PCKA intergen 98.83
2k6p_A_92 Uncharacterized protein HP_1423; alpha-L motif, RN 98.67
3dh3_A_1-6363 Ribosomal large subunit pseudouridine synthase F; 98.34
2jan_A_345-43288 Tyrosyl-tRNA synthetase; protein biosynthesis, ami 97.56
3kbg_A_1-8181 30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR2 96.84
1v9f_A_ 325 Ribosomal large subunit pseudouridine synthase D; 95.53
>3bbn_D (D:82-201) Ribosomal protein S4; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Back     alignment and structure
Probab=100.00  E-value=4.1e-39  Score=274.00  Aligned_cols=117  Identities=40%  Similarity=0.614  Sum_probs=109.4

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCEEECCEEEECCCEEECCCCEEEECCHHHHHHHHHHHHHHC-CCCCC
Q ss_conf             68999998888899862121247887887624978788889413534833884788611002269999877521-68999
Q gi|254780187|r   87 NLISFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSKQLASVLEASQLA-ERDVP  165 (206)
Q Consensus        87 ~ll~~LE~RLD~~v~r~g~a~t~~~Arq~v~hg~i~vng~~v~~ps~~~k~gd~I~~~~ksk~~~~i~~~~~~~-~~~~P  165 (206)
                      .|+++||+|||++|||+|||+|+++|||+|+||||+|||++|++|||+|++||+|++++++++...+..+.+.. ...+|
T Consensus         1 ~ll~~LE~RLD~~l~R~gfa~s~~~ARqlI~hghV~VNg~~v~~ps~~v~~gD~i~~~~~~~~~~~~~~~~~~~~~~~~p   80 (120)
T 3bbn_D            1 VLLQLLEMRLDNILFRLGMAPTIPGARQLVNHRHILVNGRIVDIPSYRCKPQDTIMARDEQKSIALIQNSLDLSPREELP   80 (120)
T ss_dssp             TTTHHHHSBTTTTTTTTTSSSSSHHHHHHHHTTCEEETTEECCCTTCBCCTTEEEEECSSTTSCHHHHHHSSSTTTSCCC
T ss_pred             HHHHHHHHHHHHEEEECCCCCCHHHHHHHHHHHCEECCCEEECCCCEECCHHHHHHHCCHHHHHHHHHHHHHHHCCCCCC
T ss_conf             79998987531035505733576888899987513615489816572546166300100131499999999852658999


Q ss_pred             CEEEECCCCCEEEEEECCCCCCCCCCCCCCCCCEEEEEECC
Q ss_conf             62788124318999967884211246753466316775049
Q gi|254780187|r  166 EYISVNHDNMVATFVRIPSSLKDVPYPVIMQPNLVVEFYSR  206 (206)
Q Consensus       166 ~wLevd~~~l~g~v~~~P~r~e~i~~p~~ine~LVVEyYSR  206 (206)
                      +||++|+++++|++++.|++.+   +|..+||+||||||||
T Consensus        81 ~~Levd~~~~~~~~~~~P~r~e---i~~~i~e~lVvE~Ysr  118 (120)
T 3bbn_D           81 KHLTLNPFPYKGLVNQIIDSKW---VGLKINELLVVEYYSR  118 (120)
T ss_dssp             TTEEEETTTTEEEECSCCCGGG---CCCSCCHHHHTTTSCC
T ss_pred             CEEEEECCCCEEEEECCCCHHH---CCCCCCCCEEEEECCC
T ss_conf             8699874448899973777300---8999874479997677
>3i1m_D (D:97-190) 30S ribosomal protein S4; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_D* 3e1a_R 3e1c_R 1vs5_D 3i1o_D 3i1q_D 3i1s_D 3i1z_D 3i21_D 2qal_D* 1p6g_D 1p87_D 2aw7_D 2avy_D 2i2u_D 2i2p_D* 2qan_D* 2qb9_D* 2qbb_D* 2qbd_D ... Back     alignment and structure
>2vqe_D (D:100-193) 30S ribosomal protein S4; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} Back     alignment and structure
>2vqe_D (D:1-99,D:194-209) 30S ribosomal protein S4; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} Back     alignment and structure
>3i1m_D (D:1-96,D:191-206) 30S ribosomal protein S4; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_D* 3e1a_R 3e1c_R 1vs5_D 3i1o_D 3i1q_D 3i1s_D 3i1z_D 3i21_D 2qal_D* 1p6g_D 1p87_D 2aw7_D 2avy_D 2i2u_D 2i2p_D* 2qan_D* 2qb9_D* 2qbb_D* 2qbd_D ... Back     alignment and structure
>1s1h_D (D:81-179) 40S ribosomal protein S9-A; 80S ribosome, 40S ribosomal subunit, EEF2, tRNA translocation, sordarin, cryo-EM; 11.70A {Saccharomyces cerevisiae} Back     alignment and structure
>1c05_A (A:77-159) Ribosomal protein S4 delta 41; two subdomains, unique topology, possible helix-turn-helix motif; NMR {Bacillus stearothermophilus} Back     alignment and structure
>1c05_A (A:22-76) Ribosomal protein S4 delta 41; two subdomains, unique topology, possible helix-turn-helix motif; NMR {Bacillus stearothermophilus} Back     alignment and structure
>1jil_A (A:247-420) Tyrrs, tyrosyl-tRNA synthetase, tyrosyl-transfer; truncation, structure based inhibitor design, ligase; HET: 485; 2.20A {Staphylococcus aureus} Back     alignment and structure
>2ts1_A (A:246-419) Tyrosyl-tRNA synthetase; ligase (synthetase); 2.30A {Geobacillus stearothermophilus} Back     alignment and structure
>2cqj_A (A:) BRMS2, U3 small nucleolar ribonucleoprotein protein IMP3 homolog; S4 domain, structural genomics, NPPSFA; NMR {Homo sapiens} Back     alignment and structure
>3hp7_A (A:1-65) Hemolysin, putative; structural genomics, APC64019, PSI-2, protein structure initiative; HET: MSE; 1.53A {Streptococcus thermophilus lmg 18311} Back     alignment and structure
>1h3f_A (A:350-432) Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA synthetase; HET: TYB; 2.0A {Thermus thermophilus} Back     alignment and structure
>1p9k_A (A:) ORF, hypothetical protein; alfal motif, RNA-binding protein, E.coli, montreal-kingston bacterial structural genomics initiative, BSGI; NMR {Escherichia coli K12} Back     alignment and structure
>1vio_A (A:1-57) Ribosomal small subunit pseudouridine synthase A; structural genomics, lyase; 1.59A {Haemophilus influenzae} Back     alignment and structure
>1ksk_A (A:1-58) Ribosomal small subunit pseudouridine synthase A; RSUA, lyase; 2.00A {Escherichia coli} Back     alignment and structure
>1dm9_A (A:) Hypothetical 15.5 KD protein in MRCA-PCKA intergenic region; heat shock proteins, protein-RNA interactions, ribosome, structural genomics; 2.00A {Escherichia coli} Back     alignment and structure
>2k6p_A (A:) Uncharacterized protein HP_1423; alpha-L motif, RNA-binding, unknown function; NMR {Helicobacter pylori} Back     alignment and structure
>3dh3_A (A:1-63) Ribosomal large subunit pseudouridine synthase F; protein-RNA complex, S4 domain, alpha/beta protein, isomerase, RNA-binding, rRNA processing; HET: FHU; 3.00A {Escherichia coli} Back     alignment and structure
>2jan_A (A:345-432) Tyrosyl-tRNA synthetase; protein biosynthesis, aminoacyl-tRNA synthetase, tyrrs, ligase, tyrosine, RNA-binding, ATP-binding; 2.9A {Mycobacterium tuberculosis} Back     alignment and structure
>3kbg_A (A:1-81) 30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR28, NESG, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.75A {Thermoplasma acidophilum} Back     alignment and structure
>1v9f_A (A:) Ribosomal large subunit pseudouridine synthase D; RNA binding, lyase; 1.70A {Escherichia coli} Back     alignment and structure