254780260

254780260

50S ribosomal protein L4

GeneID in NCBI database:8209241Locus tag:CLIBASIA_00725
Protein GI in NCBI database:254780260Protein Accession:YP_003064673.1
Gene range:-(141771, 142394)Protein Length:207aa
Gene description:50S ribosomal protein L4
COG prediction:[J] Ribosomal protein L4
KEGG prediction:rplD; 50S ribosomal protein L4; K02926 large subunit ribosomal protein L4
SEED prediction:LSU ribosomal protein L4p (L1e)
Pathway involved in KEGG:Ribosome [PATH:las03010]
Subsystem involved in SEED:Ribosome LSU 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-------
MIELSVRNLDGEDKGVISVSEDIFALKPQQGILARVLRWQSWRKRIGCSKSKGRSEVAYTGSKMYVQKGTGRARHSSKSVSQFRGGGKAFGPVPIIGVHALPKKVRSLALRHALSDKFCSNDIMVIDNLVSKECKTKYLVTRFRALDLSNALIIDGCQLDRNFQLAARNIPNINLLPVQGINVYDILRCSKLVLSKSAIEALEDRFK
ccccEEEcccccEEEEEEccHHHHcccccHHHHHHHHHHHHHHcccccHHHcccccccccccccccccccccccccccccccccccEEEcccccccccccccHHHHHHHHHHHHHHHHHcccEEEEEccccccccHHHHHHHHHHccccccEEEEcccccHHHHHHHccccccEEEEHHHccHHHHHccccEEEEHHHHHHHHHHHc
ccEEEEEEccccccEEEEEcHHHccccccHHHHHHHHHHHHHHHHccccccccHHHHccccccccccccccccccccccccccccccEEcccccccHHccccHHHHHHHHHHHHHHHHHcccEEEEEccccccccHHHHHHHHHHcccccEEEEEcccccHHHHHHHHcccccEEEEcccccHHHHHccccEEEcHHHHHHHHHHHc
MIELSvrnldgedkgvisvsedifalkpQQGILARVLRWQSWrkrigcskskgrsevayTGSKMYvqkgtgrarhssksvsqfrgggkafgpvpiigvhalpKKVRSLALRHAlsdkfcsndimVIDNLVSKECKTKYLVTRFRALDLSNALIIDGCQLDRNFQLAarnipninllpvqginvyDILRCSKLVLSKSAIEALEDRFK
mielsvrnldgedkgviSVSEdifalkpqqgiLARVLRWqswrkrigcskskgrsevaytgskmyvqkgtgrarhssksvsqfrgggkafgpvpIIGVHALPKKVRSLALRHALsdkfcsndimVIDNLVSKECKTKYLVTRFRALDLSNALIIDGCQLDRNFQLAARNIpninllpvqGINVYDILRCSKLVLSksaiealedrfk
MIELSVRNLDGEDKGVISVSEDIFALKPQQGILARVLRWQSWRKRIGCSKSKGRSEVAYTGSKMYVQKGTGRARHSSKSVSQFRGGGKAFGPVPIIGVHALPKKVRSLALRHALSDKFCSNDIMVIDNLVSKECKTKYLVTRFRALDLSNALIIDGCQLDRNFQLAARNIPNINLLPVQGINVYDILRCSKLVLSKSAIEALEDRFK
*IELSVRNLDGEDKGVISVSEDIFALKPQQGILARVLRWQSWRKRIGCSKSKGRSEVAYTGSKMYVQKGTGRARHSSKSVSQFRGGGKAFGPVPIIGVHALPKKVRSLALRHALSDKFCSNDIMVIDNLVSKECKTKYLVTRFRALDLSNALIIDGCQLDRNFQLAARNIPNINLLPVQGINVYDILRCSKLVLSKSAIEALEDRFK
MIELSVRNLDGEDKGVISVSEDIFALKPQQGILARVLRWQSWRKRIG*********VAYTGSKMYVQ*****************GGGKAFGPVPIIGVHALPKKVRSLALRHALSDKFCSNDIMVIDNLVSKECKTKYLVTRFRALDLSNALIIDGCQLDRNFQLAARNIPNINLLPVQGINVYDILRCSKLVLSKSAIEALEDRFK
*IELSVRNLDGEDKGVISVSEDIFALKPQQGILARVLRWQSWRKRI********************************SVSQFRGGGKAFGPVPIIGVHALPKKVRSLALRHALSDKFCSNDIMVIDNLVSKECKTKYLVTRFRALDLSNALIIDGCQLDRNFQLAARNIPNINLLPVQGINVYDILRCSKLVLSKSAIEALEDRFK
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MIELSVRNLDGEDKGVISVSEDIFALKPQQGILARVLRWQSWRKRIGCSKSKGRSEVAYTGSKMYVQKGTGRARHSSKSVSQFRGGGKAFGPVPIIGVHALPKKVRSLALRHALSDKFCSNDIMVIDNLVSKECKTKYLVTRFRALDLSNALIIDGCQLDRNFQLAARNIPNINLLPVQGINVYDILRCSKLVLSKSAIEALEDRFK
MIELSVRNLDGEDKGVISVSEDIFALKPQQGILARVLRWQSWRKRIGCSKSKGRSEVAYTGSKMYVQKGTGRARHSSKSVSQFRGGGKAFGPVPIIGVHALPKKVRSLALRHALSDKFCSNDIMVIDNLVSKECKTKYLVTRFRALDLSNALIIDGCQLDRNFQLAARNIPNINLLPVQGINVYDILRCSKLVLSKSAIEALEDRFK
MIELSVRNLDGEDKGVISVSEDIFALKPQQGILARVLRWQSWRKRIGCSKSKGRSEVAYTGSKMYVQKGTGRARHSSKSVSQFRGGGKAFGPVPIIGVHALPKKVRSLALRHALSDKFCSNDIMVIDNLVSKECKTKYLVTRFRALDLSNALIIDGCQLDRNFQLAARNIPNINLLPVQGINVYDILRCSKLVLSKSAIEALEDRFK

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
Target207 50S ribosomal protein L4 [Candidatus Liberibacter asiat
315122817207 50S ribosomal protein L4 [Candidatus Liberibacter solan 1 1e-100
86357306206 50S ribosomal protein L4 [Rhizobium etli CFN 42] Length 1 1e-69
218460209206 50S ribosomal protein L4 [Rhizobium etli Kim 5] Length 1 1e-69
218672011206 50S ribosomal protein L4 [Rhizobium etli GR56] Length = 1 2e-69
190891356206 50S ribosomal protein L4 [Rhizobium etli CIAT 652] Leng 1 2e-69
325293335206 50S ribosomal protein L4 [Agrobacterium sp. H13-3] Leng 1 1e-68
116251541206 50S ribosomal protein L4 [Rhizobium leguminosarum bv. v 1 1e-68
15889241206 50S ribosomal protein L4 [Agrobacterium tumefaciens str 1 1e-68
241204166206 50S ribosomal protein L4 [Rhizobium leguminosarum bv. t 1 2e-68
15965110206 50S ribosomal protein L4 [Sinorhizobium meliloti 1021] 1 6e-68
>gi|315122817|ref|YP_004063306.1| 50S ribosomal protein L4 [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 207 Back     alignment and organism information
 Score =  367 bits (941), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 179/207 (86%), Positives = 189/207 (91%)

Query: 1   MIELSVRNLDGEDKGVISVSEDIFALKPQQGILARVLRWQSWRKRIGCSKSKGRSEVAYT 60
           MIELSVR+LDG DKGVISVSE IFALKPQQGILARVLRWQSWR+  GCSKSKGRSE+AYT
Sbjct: 1   MIELSVRDLDGADKGVISVSEGIFALKPQQGILARVLRWQSWRRSKGCSKSKGRSEIAYT 60

Query: 61  GSKMYVQKGTGRARHSSKSVSQFRGGGKAFGPVPIIGVHALPKKVRSLALRHALSDKFCS 120
           G+KMY QKGTGRARHSSKS  QFRGGGKAFGPVP  G H LPKK+RSLALRHALSDKF S
Sbjct: 61  GAKMYTQKGTGRARHSSKSAPQFRGGGKAFGPVPGNGAHDLPKKIRSLALRHALSDKFSS 120

Query: 121 NDIMVIDNLVSKECKTKYLVTRFRALDLSNALIIDGCQLDRNFQLAARNIPNINLLPVQG 180
           NDI+VID+LVSKE KTKYL  RFRAL+LSNALIIDG QLDRNFQLAARNIPNINLL VQG
Sbjct: 121 NDILVIDSLVSKELKTKYLAERFRALNLSNALIIDGVQLDRNFQLAARNIPNINLLSVQG 180

Query: 181 INVYDILRCSKLVLSKSAIEALEDRFK 207
           INVYDILRCSKL+LSKSA+EALE RFK
Sbjct: 181 INVYDILRCSKLILSKSAVEALEGRFK 207



Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|86357306|ref|YP_469198.1| 50S ribosomal protein L4 [Rhizobium etli CFN 42] Length = 206 Back     alignment and organism information
>gi|218460209|ref|ZP_03500300.1| 50S ribosomal protein L4 [Rhizobium etli Kim 5] Length = 206 Back     alignment and organism information
>gi|218672011|ref|ZP_03521680.1| 50S ribosomal protein L4 [Rhizobium etli GR56] Length = 206 Back     alignment and organism information
>gi|190891356|ref|YP_001977898.1| 50S ribosomal protein L4 [Rhizobium etli CIAT 652] Length = 206 Back     alignment and organism information
>gi|325293335|ref|YP_004279199.1| 50S ribosomal protein L4 [Agrobacterium sp. H13-3] Length = 206 Back     alignment and organism information
>gi|116251541|ref|YP_767379.1| 50S ribosomal protein L4 [Rhizobium leguminosarum bv. viciae 3841] Length = 206 Back     alignment and organism information
>gi|15889241|ref|NP_354922.1| 50S ribosomal protein L4 [Agrobacterium tumefaciens str. C58] Length = 206 Back     alignment and organism information
>gi|241204166|ref|YP_002975262.1| 50S ribosomal protein L4 [Rhizobium leguminosarum bv. trifolii WSM1325] Length = 206 Back     alignment and organism information
>gi|15965110|ref|NP_385463.1| 50S ribosomal protein L4 [Sinorhizobium meliloti 1021] Length = 206 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
Target207 50S ribosomal protein L4 [Candidatus Liberibacter asiat
PRK05319205 PRK05319, rplD, 50S ribosomal protein L4; Provisional 4e-65
COG0088214 COG0088, RplD, Ribosomal protein L4 [Translation, ribos 3e-45
KOG1624290 KOG1624, KOG1624, KOG1624, Mitochondrial/chloroplast ri 2e-41
PRK14547298 PRK14547, rplD, 50S ribosomal protein L4; Provisional 7e-27
CHL00147215 CHL00147, rpl4, ribosomal protein L4; Validated 6e-22
pfam00573190 pfam00573, Ribosomal_L4, Ribosomal protein L4/L1 family 1e-52
PRK14907295 PRK14907, rplD, 50S ribosomal protein L4; Provisional 2e-20
>gnl|CDD|180011 PRK05319, rplD, 50S ribosomal protein L4; Provisional Back     alignment and domain information
>gnl|CDD|30437 COG0088, RplD, Ribosomal protein L4 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|36837 KOG1624, KOG1624, KOG1624, Mitochondrial/chloroplast ribosomal protein L4 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|184735 PRK14547, rplD, 50S ribosomal protein L4; Provisional Back     alignment and domain information
>gnl|CDD|177068 CHL00147, rpl4, ribosomal protein L4; Validated Back     alignment and domain information
>gnl|CDD|144240 pfam00573, Ribosomal_L4, Ribosomal protein L4/L1 family Back     alignment and domain information
>gnl|CDD|184900 PRK14907, rplD, 50S ribosomal protein L4; Provisional 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 207 50S ribosomal protein L4 [Candidatus Liberibacter asiat
CHL00147214 rpl4 ribosomal protein L4; Validated 100.0
PRK05319206 rplD 50S ribosomal protein L4; Provisional 100.0
pfam00573190 Ribosomal_L4 Ribosomal protein L4/L1 family. This famil 100.0
COG0088214 RplD Ribosomal protein L4 [Translation, ribosomal struc 100.0
KOG1624290 consensus 100.0
TIGR03672251 rpl4p_arch 50S ribosomal protein L4P. One of the primar 100.0
PRK04042254 rpl4lp 50S ribosomal protein L4P; Provisional 100.0
KOG1475363 consensus 99.96
>CHL00147 rpl4 ribosomal protein L4; Validated Back     alignment and domain information
>PRK05319 rplD 50S ribosomal protein L4; Provisional Back     alignment and domain information
>pfam00573 Ribosomal_L4 Ribosomal protein L4/L1 family Back     alignment and domain information
>COG0088 RplD Ribosomal protein L4 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>KOG1624 consensus Back     alignment and domain information
>TIGR03672 rpl4p_arch 50S ribosomal protein L4P Back     alignment and domain information
>PRK04042 rpl4lp 50S ribosomal protein L4P; Provisional Back     alignment and domain information
>KOG1475 consensus Back     alignment and domain information

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

Homologous Structures Detected by PSI-BLAST against Nonredundant Database

Original result of PSI-BLAST

IdentityAlignment graphLength Definition E-value
Target207 50S ribosomal protein L4 [Candidatus Liberibacter asiat
1p85_C201 Real Space Refined Coordinates Of The 50s Subunit F 2e-43
2gya_C198 Structure Of The 50s Subunit Of A Pre-Translocation 1e-42
1dmg_A225 Crystal Structure Of Ribosomal Protein L4 Length = 5e-40
3pyo_E202 Crystal Structure Of A Complex Containing Domain 3 5e-39
3d5b_F210 Structural Basis For Translation Termination On The 5e-39
1vsa_D205 Crystal Structure Of A 70s Ribosome-Trna Complex Re 5e-39
3fin_F208 T. Thermophilus 70s Ribosome In Complex With Mrna, 2e-38
2j01_F210 Structure Of The Thermus Thermophilus 70s Ribosome 2e-38
1vor_F198 Crystal Structure Of Five 70s Ribosomes From Escher 9e-37
1pnu_C197 Crystal Structure Of A Streptomycin Dependent Ribos 9e-37
1jzx_K205 Structural Basis For The Interaction Of Antibiotics 4e-36
1nwx_C204 Complex Of The Large Ribosomal Subunit From Deinoco 8e-35
3bbo_G293 Homology Model For The Spinach Chloroplast 50s Subu 9e-35
1ffk_C246 Crystal Structure Of The Large Ribosomal Subunit Fr 8e-17
3izr_D 405 Localization Of The Large Subunit Ribosomal Protein 1e-16
1jj2_C246 Fully Refined Crystal Structure Of The Haloarcula M 1e-16
3cc2_C246 The Refined Crystal Structure Of The Haloarcula Mar 2e-16
2zkr_c 421 Structure Of A Mammalian Ribosomal 60s Subunit With 2e-15
3jyw_D257 Structure Of The 60s Proteins For Eukaryotic Riboso 2e-12
1s1i_D361 Structure Of The Ribosomal 80s-Eef2-Sordarin Comple 3e-12
3izs_D362 Localization Of The Large Subunit Ribosomal Protein 3e-12
2ww9_H362 Cryo-Em Structure Of The Active Yeast Ssh1 Complex 3e-12
2ftc_D175 Structural Model For The Large Subunit Of The Mamma 4e-26
gi|33357904|pdb|1P85|C Chain C, Real Space Refined Coordinates Of The 50s Subunit Fitted Into The Low Resolution Cryo-Em Map Of The Ef-G.Gtp State Of E. Coli 70s Ribosome Length = 201 Back     alignment and structure 
 Score =  179 bits (454), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 59/205 (28%), Positives = 104/205 (50%), Gaps = 5/205 (2%)

Query: 2   IELSVRNLDGEDKGVISVSEDIFALKPQQGILARVLRWQSWRKRIGCSKSKGRSEVAYTG 61
           +EL +++        ++VSE  F     + ++ +V+   +   R G    K R+EV  +G
Sbjct: 1   MELVLKDAQ----SALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSG 56

Query: 62  SKMYVQKGTGRARHSSKSVSQFRGGGKAFGPVPIIGVHALPKKVRSLALRHALSDKFCSN 121
            K + QKGTGRAR  S     +R GG  F   P      + KK+   AL+  LS+    +
Sbjct: 57  KKPWRQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQD 116

Query: 122 DIMVIDNLVSKECKTKYLVTRFRALDLSNALIIDGCQLDRNFQLAARNIPNINLLPVQGI 181
            ++V++    +  KTK L  + + + L + LII G +LD N  LAARN+  +++    GI
Sbjct: 117 RLIVVEKFSVEAPKTKLLAQKLKDMALEDVLIITG-ELDENLFLAARNLHKVDVRDATGI 175

Query: 182 NVYDILRCSKLVLSKSAIEALEDRF 206
           +   ++   K+V++  A++ +E+  
Sbjct: 176 DPVSLIAFDKVVMTADAVKQVEEML 200
>gi|116667437|pdb|2GYA|C Chain C, Structure Of The 50s 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 = 198 Back     alignment and structure
>gi|12084410|pdb|1DMG|A Chain A, Crystal Structure Of Ribosomal Protein L4 Length = 225 Back     alignment and structure
>gi|322812576|pdb|3PYO|E Chain E, Crystal Structure Of A Complex Containing Domain 3 From The Psiv Igr Ires Rna Bound To The 70s Ribosome. This File Contains The 50s Subunit Of The First 70s Ribosome. Length = 202 Back     alignment and structure
>gi|209156522|pdb|3D5B|F Chain F, Structural Basis For Translation Termination On The 70s Ribosome. This File Contains The 50s Subunit Of One 70s Ribosome. The Entire Crystal Structure Contains Two 70s Ribosomes As Described In Remark 400. Length = 210 Back     alignment and structure
gi|149240889|pdb|1VSA|D Chain D, Crystal Structure Of A 70s Ribosome-Trna Complex Reveals Functional Interactions And Rearrangements. This File, 1vsa, Contains The 50s Ribosome Subunit. 30s Ribosome Subunit Is In The File 2ow8 Length = 205 Back     alignment and structure
>gi|224510784|pdb|3FIN|F Chain F, 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 50s Subunit Length = 208 Back     alignment and structure
gi|116668237|pdb|2J01|F Chain F, Structure Of The Thermus Thermophilus 70s Ribosome Complexed With Mrna, Trna And Paromomycin (Part 2 Of 4). This File Contains The 50s Subunit From Molecule I. Length = 210 Back     alignment and structure
>gi|56966348|pdb|1VOR|F Chain F, Crystal Structure Of Five 70s Ribosomes From Escherichia Coli In Complex With Protein Y. This File Contains The 50s Subunit Of One 70s Ribosome. The Entire Crystal Structure Contains Five 70s Ribosomes And Is Described In Remark 400. Length = 198 Back     alignment and structure
>gi|34811556|pdb|1PNU|C Chain C, Crystal Structure Of A Streptomycin Dependent Ribosome From Escherichia Coli, 50s Subunit Of 70s Ribosome. This File, 1pnu, Contains Only Molecules Of The 50s Ribosomal Subunit. The 30s Subunit, Mrna, P-Site Trna, And A-Site Trna Are In The Pdb File 1pns. Length = 197 Back     alignment and structure
gi|16975049|pdb|1JZX|K Chain K, Structural Basis For The Interaction Of Antibiotics With The Peptidyl Transferase Center In Eubacteria Length = 205 Back     alignment and structure
>gi|29726790|pdb|1NWX|C Chain C, Complex Of The Large Ribosomal Subunit From Deinococcus Radiodurans With Abt-773 Length = 204 Back     alignment and structure
gi|189096129|pdb|3BBO|G Chain G, Homology Model For The Spinach Chloroplast 50s Subunit Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome Length = 293 Back     alignment and structure
>gi|10120922|pdb|1FFK|C Chain C, Crystal Structure Of The Large Ribosomal Subunit From Haloarcula Marismortui At 2.4 Angstrom Resolution Length = 246 Back     alignment and structure
>gi|315113297|pdb|3IZR|D Chain D, Localization Of The Large Subunit Ribosomal Proteins Into A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s Ribosome Length = 405 Back     alignment and structure
>gi|15825945|pdb|1JJ2|C Chain C, Fully Refined Crystal Structure Of The Haloarcula Marismortui Large Ribosomal Subunit At 2.4 Angstrom Resolution Length = 246 Back     alignment and structure
gi|188596004|pdb|3CC2|C Chain C, The Refined Crystal Structure Of The Haloarcula Marismortui Large Ribosomal Subunit At 2.4 Angstrom Resolution With Rrna Sequence For The 23s Rrna And Genome-Derived Sequences For R-Proteins Length = 246 Back     alignment and structure
gi|187609301|pdb|2ZKR|CC Chain c, Structure Of A Mammalian Ribosomal 60s Subunit Within An 80s Complex Obtained By Docking Homology Models Of The Rna And Proteins Into An 8.7 A Cryo-Em Map Length = 421 Back     alignment and structure
>gi|281500834|pdb|3JYW|D Chain D, Structure Of The 60s Proteins For Eukaryotic Ribosome Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome At 8.9a Resolution Length = 257 Back     alignment and structure
>gi|49258842|pdb|1S1I|D Chain D, 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, 1s1i, Contains 60s Subunit. The 40s Ribosomal Subunit Is In File 1s1h Length = 361 Back     alignment and structure
>gi|315113348|pdb|3IZS|D Chain D, Localization Of The Large Subunit Ribosomal Proteins Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae Translating 80s Ribosome Length = 362 Back     alignment and structure
gi|270346345|pdb|2WW9|H Chain H, Cryo-Em Structure Of The Active Yeast Ssh1 Complex Bound To The Yeast 80s Ribosome Length = 362 Back     alignment and structure
>gi|99032310|pdb|2FTC|D Chain D, Structural Model For The Large Subunit Of The Mammalian Mitochondrial Ribosome Length = 175 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
Target207 50S ribosomal protein L4 [Candidatus Liberibacter asiat
3ofq_E201 50S ribosomal protein L4; protein biosynthesis, ribosom 3e-48
3bbo_G293 Ribosomal protein L4; large ribosomal subunit, spinach 4e-44
3i1n_E201 50S ribosomal protein L4; ribosome structure, protein-R 3e-38
2zjr_C205 50S ribosomal protein L4; ribosome, large ribosomal sub 1e-37
1dmg_A225 Ribosomal protein L4; alpha-beta, ribosome, RNA, S10 op 1e-34
2wwb_H362 60S ribosomal protein L4-B; ribosome, protein EXIT tunn 2e-34
2j01_F210 50S ribosomal protein L4; ribosome, tRNA, paromomycin, 2e-32
1vq8_C246 50S ribosomal protein L4E; ribosome 50S, protein-protei 2e-31
2zkr_c 421 60S ribosomal protein L4; protein-RNA complex, 60S ribo 3e-26
2ftc_D175 Mitochondrial ribosomal protein L4 isoform A, mitochond 2e-34
>3ofq_E 50S ribosomal protein L4; protein biosynthesis, ribosomes, RNA, tRNA, transfer, antibi EXIT, peptidyl, ribosomal subunit, large; 3.10A {Escherichia coli} PDB: 1p85_C 1p86_C 1vs8_E 1vs6_E 2aw4_E 2awb_E 1vt2_E 2i2v_E 2j28_E 2i2t_E* 2qao_E* 2qba_E* 2qbc_E* 2qbe_E 2qbg_E 2qbi_E* 2qbk_E* 2qov_E 2qox_E 2qoz_E* ... Length = 201 Back     alignment and structure
 Score =  186 bits (474), Expect = 3e-48
 Identities = 59/205 (28%), Positives = 105/205 (51%), Gaps = 5/205 (2%)

Query: 2   IELSVRNLDGEDKGVISVSEDIFALKPQQGILARVLRWQSWRKRIGCSKSKGRSEVAYTG 61
           +EL +++     +  ++VSE  F     + ++ +V+   +   R G    K R+EV  +G
Sbjct: 1   MELVLKD----AQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSG 56

Query: 62  SKMYVQKGTGRARHSSKSVSQFRGGGKAFGPVPIIGVHALPKKVRSLALRHALSDKFCSN 121
            K + QKGTGRAR  S     +R GG  F   P      + KK+   AL+  LS+    +
Sbjct: 57  KKPWRQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQD 116

Query: 122 DIMVIDNLVSKECKTKYLVTRFRALDLSNALIIDGCQLDRNFQLAARNIPNINLLPVQGI 181
            ++V++    +  KTK L  + + + L + LII G +LD N  LAARN+  +++    GI
Sbjct: 117 RLIVVEKFSVEAPKTKLLAQKLKDMALEDVLIITG-ELDENLFLAARNLHKVDVRDATGI 175

Query: 182 NVYDILRCSKLVLSKSAIEALEDRF 206
           +   ++   K+V++  A++ +E+  
Sbjct: 176 DPVSLIAFDKVVMTADAVKQVEEML 200
>3bbo_G Ribosomal protein L4; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Length = 293 Back     alignment and structure
>3i1n_E 50S ribosomal protein L4; ribosome structure, protein-RNA complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA- binding, methylation; 3.19A {Escherichia coli k-12} PDB: 1p85_C 1p86_C 1vs8_E 2aw4_E 2awb_E 1vs6_E 2i2v_E 2j28_E 2i2t_E* 2qao_E* 2qba_E* 2qbc_E* 2qbe_E 2qbg_E 2qbi_E* 2qbk_E* 2qov_E 2qox_E 2qoz_E* 2qp1_E* ... Length = 201 Back     alignment and structure
>2zjr_C 50S ribosomal protein L4; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: c.22.1.1 PDB: 1j5a_K* 1jzy_K* 1jzz_K* 1k01_K* 1nkw_C 1sm1_C* 2zjp_C* 2zjq_C 1jzx_K 3cf5_C* 3dll_C* 1nwy_C* 1nwx_C* 1xbp_C* 1pnu_C 1pny_C 1vor_F 1vou_F 1vow_F 1voy_F ... Length = 205 Back     alignment and structure
>1dmg_A Ribosomal protein L4; alpha-beta, ribosome, RNA, S10 operon; HET: CIT; 1.70A {Thermotoga maritima} SCOP: c.22.1.1 Length = 225 Back     alignment and structure
>2wwb_H 60S ribosomal protein L4-B; ribosome, protein EXIT tunnel, cotranslational protein translocation, protein conducting channel; 6.48A {Triticum aestivum} PDB: 2wwa_H 2ww9_H 1s1i_D Length = 362 Back     alignment and structure
>2j01_F 50S ribosomal protein L4; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} SCOP: c.22.1.1 PDB: 2hgq_F 2hgj_F 2hgu_F 2j03_F 2jl6_F 2jl8_F 2v47_F 2v49_F 2wdi_F 2wdj_F 2wdl_F 2wdn_F 2wh2_F 2wh4_F 3hux_F 3huz_F 3f1f_F 3d5d_F 3d5b_F 3f1h_F ... Length = 210 Back     alignment and structure
>1vq8_C 50S ribosomal protein L4E; ribosome 50S, protein-protein complex, RNA-RNA complex, protein-RNA complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: c.22.1.1 PDB: 1k73_E* 1k8a_E* 1k9m_E* 1kc8_E* 1kd1_E* 1kqs_C* 1m1k_E* 1m90_E* 1n8r_E* 1nji_E* 1q7y_E* 1q81_E* 1q82_E* 1q86_E* 1qvf_C 1qvg_C 1s72_C* 1vq4_C* 1vq5_C* 1vq6_C* ... Length = 246 Back     alignment and structure
>2zkr_c 60S ribosomal protein L4; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Length = 421 Back     alignment and structure
>2ftc_D Mitochondrial ribosomal protein L4 isoform A, mitochondrial 39S ribosomal protein L3; mitochondrial ribosome, large ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus} PDB: 3iy9_D Length = 175 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

Original result of HHsearch against PDB70 database

IdentityAlignment graphLength Definition Probability
Target207 50S ribosomal protein L4 [Candidatus Liberibacter asiat
3bbo_G293 Ribosomal protein L4; large ribosomal subunit, spinach 100.0
1dmg_A225 Ribosomal protein L4; alpha-beta, ribosome, RNA, S10 op 100.0
2zjr_C205 50S ribosomal protein L4; ribosome, large ribosomal sub 100.0
3ofq_E201 50S ribosomal protein L4; protein biosynthesis, ribosom 100.0
2j01_F210 50S ribosomal protein L4; ribosome, tRNA, paromomycin, 100.0
1vq8_C246 50S ribosomal protein L4E; ribosome 50S, protein-protei 100.0
2wwb_H362 60S ribosomal protein L4-B; ribosome, protein EXIT tunn 100.0
2zkr_c 421 60S ribosomal protein L4; protein-RNA complex, 60S ribo 100.0
2ftc_D175 Mitochondrial ribosomal protein L4 isoform A, mitochond 100.0
>3bbo_G Ribosomal protein L4; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Back     alignment and structure
Probab=100.00  E-value=0  Score=493.18  Aligned_cols=206  Identities=29%  Similarity=0.383  Sum_probs=198.6

Q ss_pred             CCEEEEECCCCCEEEEEEECHHHHCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             96226554688645568609779398766899999999999727886200136212148988764558875542365311
Q gi|254780260|r    1 MIELSVRNLDGEDKGVISVSEDIFALKPQQGILARVLRWQSWRKRIGCSKSKGRSEVAYTGSKMYVQKGTGRARHSSKSV   80 (207)
Q Consensus         1 mm~~~v~~~~g~~~~~i~l~~~vf~~~~~~~li~~~v~~~~~~~R~gta~tk~r~ev~gs~kK~~~QKGtGrAR~Gs~rs   80 (207)
                      ||+++|||++|+++|+++||++||+.++|.||||++|+||++|+|||||+||+|+||+|||+|||+||||||||+|++||
T Consensus        52 ~M~~~V~n~~G~~~g~ieL~~~vF~~~~~~dllh~aV~~~~an~RqGta~tKtRsEV~GsgrKp~~QKGTGrAR~Gs~rs  131 (293)
T 3bbo_G           52 LIPLPILNFSGEKVGETFLNLKTAPPEKARAVVHRGLITHLQNKRRGTASTLTRAEVRGGGRKPYPQKKTGRARRGSQGS  131 (293)
T ss_dssp             CEEEECCCSSSCCCSEEEECSSSSSSCCCTTTTTTHHHHHHHHHCCCCCCCCSSTTCSSSCCCCCCCSSSCSCSCCSSSC
T ss_pred             CEEEEEECCCCCCCCEEECCHHHHCCCCCHHHHHHHHHHHHHHCCCCCCCCCCHHCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             13666874889881059849889489861889999999999861056777985110268889877889998768778879


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCEEEEECCCCCCCCHHHHHHHHHHCCCC---CEEEEECC
Q ss_conf             101057742277875320000159999999998787650595899514337877818999984113556---32786157
Q gi|254780260|r   81 SQFRGGGKAFGPVPIIGVHALPKKVRSLALRHALSDKFCSNDIMVIDNLVSKECKTKYLVTRFRALDLS---NALIIDGC  157 (207)
Q Consensus        81 p~~rgGg~afgp~pr~~~~klnkK~~~lAl~saLs~k~~~~~l~Vvd~~~~~~~KTK~~~~~L~~l~~~---~~llv~~~  157 (207)
                      |+|||||++|||+||+|++++|||++++||++|||.++.++.|+++|++.++.+|||+++++|+++++.   +.|||+ .
T Consensus       132 P~~rGGG~afgPkpr~y~~klnKK~rrlALrsALS~k~~~~~Ivv~d~~~~~~pKTK~~~~~L~~lgl~~~~k~LiV~-~  210 (293)
T 3bbo_G          132 PLRPGGGVIFGPKPRDWTIKMNKKERRLALSTAIASAVGNSFVVEEFAENFEKPKTKDFIAAMQRWGLDPAEKSLFFL-M  210 (293)
T ss_dssp             SSSSSSCCSSCCCSCCCCCCCCSHHHHHHHHHHHHHHHHTTCCCCCCGGGTTCCSSHHHHTTHHHHSCSSCSSSCCEE-C
T ss_pred             CCCCCCEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCHHHHHHHHHHCCCCCCCCEEEEE-C
T ss_conf             978888570799864230036799999999999985204760688622445676699999999851755656259996-5


Q ss_pred             CCCHHHHHHHCCCCCCEEEEHHCCCHHHHEECCCEEEEHHHHHHHHHHHC
Q ss_conf             75178999962788956842402887571005908984999999999739
Q gi|254780260|r  158 QLDRNFQLAARNIPNINLLPVQGINVYDILRCSKLVLSKSAIEALEDRFK  207 (207)
Q Consensus       158 ~~d~n~~~s~rNi~~v~v~~~~~lnv~dll~~~~iVit~~Ai~~l~e~lk  207 (207)
                      +.++|+++|+||||+|+++++++|||||||++++||||++||+.|+|||-
T Consensus       211 ~~~enl~~A~RNI~~V~vl~~~~LNVyDLLk~~~LViT~~AL~~Leerlg  260 (293)
T 3bbo_G          211 DLVENVEKSGRNIRTLKLLTPRSLNLFDVLNAEKLVFTEGTIQYLNQRYG  260 (293)
T ss_dssp             CCSSSCCTTTSSSSSCEECCSSCCCHHHHHHSSCEECCTTHHHHHHHHSC
T ss_pred             CCCHHHHHHHHCCCCCEEEECCCEEHHHHHCCCCEEEEHHHHHHHHHHHC
T ss_conf             66189999983889975864597019998379819987899999999958
>1dmg_A Ribosomal protein L4; alpha-beta, ribosome, RNA, S10 operon, gene regulation; HET: CIT; 1.70A {Thermotoga maritima} SCOP: c.22.1.1 Back     alignment and structure
>2zjr_C 50S ribosomal protein L4; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: c.22.1.1 PDB: 1j5a_K* 1jzy_K* 1jzz_K* 1k01_K* 1nkw_C 1sm1_C* 2zjp_C* 2zjq_C 1jzx_K 3cf5_C* 3dll_C* 1nwy_C* 1nwx_C* 1xbp_C* 1pnu_C 1pny_C 1vor_F 1vou_F 1vow_F 1voy_F ... Back     alignment and structure
>3ofq_E 50S ribosomal protein L4; protein biosynthesis, ribosomes, RNA, tRNA, transfer, antibi EXIT, peptidyl, ribosomal subunit, large; 3.10A {Escherichia coli} PDB: 1p85_C 1p86_C 1vs8_E 1vs6_E 2aw4_E 2awb_E 1vt2_E 2i2v_E 2j28_E 2i2t_E* 2qao_E* 2qba_E* 2qbc_E* 2qbe_E 2qbg_E 2qbi_E* 2qbk_E* 2qov_E 2qox_E 2qoz_E* ... Back     alignment and structure
>2j01_F 50S ribosomal protein L4; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} SCOP: c.22.1.1 PDB: 2hgq_F 2hgj_F 2hgu_F 2j03_F 2jl6_F 2jl8_F 2v47_F 2v49_F 2wdi_F 2wdj_F 2wdl_F 2wdn_F 2wh2_F 2wh4_F 2wrj_F 2wrl_F 2wro_F 2wrr_F 2x9s_F 2x9u_F ... Back     alignment and structure
>1vq8_C 50S ribosomal protein L4E; ribosome 50S, protein-protein complex, RNA-RNA complex, protein-RNA complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: c.22.1.1 PDB: 1k73_E* 1k8a_E* 1k9m_E* 1kc8_E* 1kd1_E* 1kqs_C* 1m1k_E* 1m90_E* 1n8r_E* 1nji_E* 1q7y_E* 1q81_E* 1q82_E* 1q86_E* 1qvf_C 1qvg_C 1s72_C* 1vq4_C* 1vq5_C* 1vq6_C* ... Back     alignment and structure
>2wwb_H 60S ribosomal protein L4-B; ribosome, protein EXIT tunnel, cotranslational protein translocation, protein conducting channel; 6.48A {Triticum aestivum} PDB: 2wwa_H 2ww9_H 1s1i_D Back     alignment and structure
>2zkr_c 60S ribosomal protein L4; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Back     alignment and structure
>2ftc_D Mitochondrial ribosomal protein L4 isoform A, mitochondrial 39S ribosomal protein L3; mitochondrial ribosome, large ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus} PDB: 3iy9_D 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 207 50S ribosomal protein L4 [Candidatus Liberibacter asiat
d2gycc1198 c.22.1.1 (C:1-198) Ribosomal protein L4 {Escherichia co 6e-39
d2zjrc1197 c.22.1.1 (C:2-198) Ribosomal protein L4 {Deinococcus ra 9e-37
d1dmga_225 c.22.1.1 (A:) Ribosomal protein L4 {Thermotoga maritima 9e-35
d2j01f1208 c.22.1.1 (F:1-208) Ribosomal protein L4 {Thermus thermo 8e-33
d1vqoc1246 c.22.1.1 (C:1-246) Ribosomal protein L4 {Archaeon Haloa 1e-31
>d2gycc1 c.22.1.1 (C:1-198) Ribosomal protein L4 {Escherichia coli [TaxId: 562]} Length = 198 Back     information, alignment and structure

class: Alpha and beta proteins (a/b)
fold: Ribosomal protein L4
superfamily: Ribosomal protein L4
family: Ribosomal protein L4
domain: Ribosomal protein L4
species: Escherichia coli [TaxId: 562]

 Score =  154 bits (390), Expect = 6e-39
 Identities = 59/203 (29%), Positives = 105/203 (51%), Gaps = 5/203 (2%)

Query: 2   IELSVRNLDGEDKGVISVSEDIFALKPQQGILARVLRWQSWRKRIGCSKSKGRSEVAYTG 61
           +EL +++     +  ++VSE  F     + ++ +V+   +   R G    K R+EV  +G
Sbjct: 1   MELVLKD----AQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSG 56

Query: 62  SKMYVQKGTGRARHSSKSVSQFRGGGKAFGPVPIIGVHALPKKVRSLALRHALSDKFCSN 121
            K + QKGTGRAR  S     +R GG  F   P      + KK+   AL+  LS+    +
Sbjct: 57  KKPWRQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQD 116

Query: 122 DIMVIDNLVSKECKTKYLVTRFRALDLSNALIIDGCQLDRNFQLAARNIPNINLLPVQGI 181
            ++V++    +  KTK L  + + + L + LII G +LD N  LAARN+  +++    GI
Sbjct: 117 RLIVVEKFSVEAPKTKLLAQKLKDMALEDVLIITG-ELDENLFLAARNLHKVDVRDATGI 175

Query: 182 NVYDILRCSKLVLSKSAIEALED 204
           +   ++   K+V++  A++ +E+
Sbjct: 176 DPVSLIAFDKVVMTADAVKQVEE 198
>d2zjrc1 c.22.1.1 (C:2-198) Ribosomal protein L4 {Deinococcus radiodurans [TaxId: 1299]} Length = 197 Back     information, alignment and structure
>d1dmga_ c.22.1.1 (A:) Ribosomal protein L4 {Thermotoga maritima [TaxId: 2336]} Length = 225 Back     information, alignment and structure
>d2j01f1 c.22.1.1 (F:1-208) Ribosomal protein L4 {Thermus thermophilus [TaxId: 274]} Length = 208 Back     information, alignment and structure
>d1vqoc1 c.22.1.1 (C:1-246) Ribosomal protein L4 {Archaeon Haloarcula marismortui [TaxId: 2238]} Length = 246 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
Target207 50S ribosomal protein L4 [Candidatus Liberibacter asiat
d1dmga_225 Ribosomal protein L4 {Thermotoga maritima [TaxId: 2336] 100.0
d2gycc1198 Ribosomal protein L4 {Escherichia coli [TaxId: 562]} 100.0
d2j01f1208 Ribosomal protein L4 {Thermus thermophilus [TaxId: 274] 100.0
d2zjrc1197 Ribosomal protein L4 {Deinococcus radiodurans [TaxId: 1 100.0
d1vqoc1246 Ribosomal protein L4 {Archaeon Haloarcula marismortui [ 100.0
d1vqoc1246 Ribosomal protein L4 {Archaeon Haloarcula marismortui [ 90.95
>d1dmga_ c.22.1.1 (A:) Ribosomal protein L4 {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
class: Alpha and beta proteins (a/b)
fold: Ribosomal protein L4
superfamily: Ribosomal protein L4
family: Ribosomal protein L4
domain: Ribosomal protein L4
species: Thermotoga maritima [TaxId: 2336]

Probab=100.00  E-value=0  Score=464.00  Aligned_cols=205  Identities=34%  Similarity=0.525  Sum_probs=194.2

Q ss_pred             CEEEEECCCCCEEEEEEECHHHHCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             62265546886455686097793987668999999999997278862001362121489887645588755423653111
Q gi|254780260|r    2 IELSVRNLDGEDKGVISVSEDIFALKPQQGILARVLRWQSWRKRIGCSKSKGRSEVAYTGSKMYVQKGTGRARHSSKSVS   81 (207)
Q Consensus         2 m~~~v~~~~g~~~~~i~l~~~vf~~~~~~~li~~~v~~~~~~~R~gta~tk~r~ev~gs~kK~~~QKGtGrAR~Gs~rsp   81 (207)
                      ++++|||++|+++|+++||++||+.|+|.||||++|+||++|+|||||+||+|+||+|||+|||+||||||||+|++|+|
T Consensus         1 ~~v~v~~~~g~~~g~i~L~~~vF~~~~r~dli~~~v~~~~~~~Rqgt~~tk~rsev~g~gkK~~~QKGtG~AR~Gs~~sp   80 (225)
T d1dmga_           1 AQVDLLNVKGEKVGTLEISDFVFNIDPNYDVMWRYVDMQLSNRRAGTASTKTRGEVSGGGRKPWPQKHTGRARHGSIRSP   80 (225)
T ss_dssp             CEEEEECTTSCEEEEEECCHHHHSSCCCHHHHHHHHHHHHC---------------------------------------
T ss_pred             CEEEEECCCCCEEEEEEECHHHHCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             91578758998812798298995998569999999999998451676666633266403445556678676654532000


Q ss_pred             CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCEEEEECCCCCCCCHHHHHHHHHHCCCC--CEEEEECC--
Q ss_conf             01057742277875320000159999999998787650595899514337877818999984113556--32786157--
Q gi|254780260|r   82 QFRGGGKAFGPVPIIGVHALPKKVRSLALRHALSDKFCSNDIMVIDNLVSKECKTKYLVTRFRALDLS--NALIIDGC--  157 (207)
Q Consensus        82 ~~rgGg~afgp~pr~~~~klnkK~~~lAl~saLs~k~~~~~l~Vvd~~~~~~~KTK~~~~~L~~l~~~--~~llv~~~--  157 (207)
                      +|||||+||||+||+|+++||||++++|+++|||.++++++|+|||+|.++++|||++.++|+++++.  +.++|+..  
T Consensus        81 ~~~gGg~a~gp~pr~~~~klnkK~r~~Al~~aLs~k~~~~~l~VVd~~~~~~~KTK~~~~~l~~l~~~~~~~llv~~~~~  160 (225)
T d1dmga_          81 IWRHGGVVHGPKPRDWSKKLNKKMKKLALRSALSVKYRENKLLVLDDLKLERPKTKSLKEILQNLQLSDKKTLIVLPWKE  160 (225)
T ss_dssp             --------------CHHHHHHHHHHHHHHHHHHHHHHHTTCEEEESCCCCSSCCHHHHHHHHHHTTCTTSCEEEEECCCS
T ss_pred             EEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEECCCCCCCCCHHHHHHHHHHHCCCCCCEEEEECCCC
T ss_conf             44114456688871241008899999999999999861587077224434665638999987440334552345412533


Q ss_pred             CCCHHHHHHHCCCCCCEEEEHHC---------------CCHHHHEECCCEEEEHHHHHHHHHHH
Q ss_conf             75178999962788956842402---------------88757100590898499999999973
Q gi|254780260|r  158 QLDRNFQLAARNIPNINLLPVQG---------------INVYDILRCSKLVLSKSAIEALEDRF  206 (207)
Q Consensus       158 ~~d~n~~~s~rNi~~v~v~~~~~---------------lnv~dll~~~~iVit~~Ai~~l~e~l  206 (207)
                      +.++|+++|+||||+|+++.+++               +||||||++++||||++||+.|||+|
T Consensus       161 e~~~n~~~s~rNlp~v~v~~~~~~~~~~~~~~~~~~~~lNvydlL~~~~lVit~~Al~~lee~L  224 (225)
T d1dmga_         161 EGYMNVKLSGRNLPDVKVIIADNPNNSKNGEKAVRIDGLNVFDMLKYDYLVLTRDMVSKIEEVL  224 (225)
T ss_dssp             HHHHHHHHHHTTCTTEEEEECCCCSSCCSSCCCCCCTTCCHHHHHHSSEEEEEHHHHHHHHHHH
T ss_pred             CHHHHHHHHHCCCCCCEEEECCCCCCCCCCCCCCCCCCCCHHHHHCCCEEEEEHHHHHHHHHHC
T ss_conf             1037799997178995476346633211233346657854999834881998599999999970
>d2gycc1 c.22.1.1 (C:1-198) Ribosomal protein L4 {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2j01f1 c.22.1.1 (F:1-208) Ribosomal protein L4 {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d2zjrc1 c.22.1.1 (C:2-198) Ribosomal protein L4 {Deinococcus radiodurans [TaxId: 1299]} Back     information, alignment and structure
>d1vqoc1 c.22.1.1 (C:1-246) Ribosomal protein L4 {Archaeon Haloarcula marismortui [TaxId: 2238]} Back     information, alignment and structure
>d1vqoc1 c.22.1.1 (C:1-246) Ribosomal protein L4 {Archaeon Haloarcula marismortui [TaxId: 2238]} 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 207 50S ribosomal protein L4 [Candidatus Liberibacter
2j01_F_210 (F:) 50S ribosomal protein L4; ribosome, tRNA, par 2e-51
2zjr_C_205 (C:) 50S ribosomal protein L4; ribosome, large rib 5e-47
1dmg_A_225 (A:) Ribosomal protein L4; alpha-beta, ribosome, R 7e-45
2wwb_H_1-138138 (H:1-138) 60S ribosomal protein L4-B; ribosome, pr 2e-24
3i1n_E_20-11697 (E:20-116) 50S ribosomal protein L4; ribosome stru 2e-22
3bbo_G_77-17195 (G:77-171) Ribosomal protein L4; large ribosomal s 7e-21
1vq8_C_24-132109 (C:24-132) 50S ribosomal protein L4E; ribosome 50S 4e-20
2zkr_c_29-146118 (c:29-146) 60S ribosomal protein L4; protein-RNA c 6e-18
3i1n_E_1-19_117-201104 (E:1-19,E:117-201) 50S ribosomal protein L4; ribos 6e-21
3bbo_G_172-293122 (G:172-293) Ribosomal protein L4; large ribosomal 8e-16
2ftc_D_104-17572 (D:104-175) Mitochondrial ribosomal protein L4 iso 2e-15
1vq8_C_1-23_133-246137 (C:1-23,C:133-246) 50S ribosomal protein L4E; ribo 5e-14
>2j01_F (F:) 50S ribosomal protein L4; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus}Length = 210 Back     alignment and structure
 Score =  196 bits (499), Expect = 2e-51
 Identities = 65/206 (31%), Positives = 102/206 (49%)

Query: 1   MIELSVRNLDGEDKGVISVSEDIFALKPQQGILARVLRWQSWRKRIGCSKSKGRSEVAYT 60
           M E++V  +                 +    +L  V+RWQ  ++R G + +K R EVAY+
Sbjct: 1   MKEVAVYQIPVLSPSGRRELAADLPAEINPHLLWEVVRWQLAKRRRGTASTKTRGEVAYS 60

Query: 61  GSKMYVQKGTGRARHSSKSVSQFRGGGKAFGPVPIIGVHALPKKVRSLALRHALSDKFCS 120
           G K++ QK TGRARH       F GGG  FGP P    + LPKKVR   L  A++D+   
Sbjct: 61  GRKIWPQKHTGRARHGDIGAPIFVGGGVVFGPKPRDYSYTLPKKVRKKGLAMAVADRARE 120

Query: 121 NDIMVIDNLVSKECKTKYLVTRFRALDLSNALIIDGCQLDRNFQLAARNIPNINLLPVQG 180
             +++++       KTK  +   +   L  +  +     +   + AARN+P +  L  +G
Sbjct: 121 GKLLLVEAFAGVNGKTKEFLAWAKEAGLDGSESVLLVTGNELVRRAARNLPWVVTLAPEG 180

Query: 181 INVYDILRCSKLVLSKSAIEALEDRF 206
           +NVYDI+R  +LV+   A E  ++R 
Sbjct: 181 LNVYDIVRTERLVMDLDAWEVFQNRI 206
>2zjr_C (C:) 50S ribosomal protein L4; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans}Length = 205 Back     alignment and structure
>1dmg_A (A:) Ribosomal protein L4; alpha-beta, ribosome, RNA, S10 operon; HET: CIT; 1.70A {Thermotoga maritima}Length = 225 Back     alignment and structure
>2wwb_H (H:1-138) 60S ribosomal protein L4-B; ribosome, protein EXIT tunnel, cotranslational protein translocation, protein conducting channel; 6.48A {Triticum aestivum} PDB: 2wwa_H 2ww9_H 1s1i_DLength = 138 Back     alignment and structure
>3i1n_E (E:20-116) 50S ribosomal protein L4; ribosome structure, protein-RNA complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA- binding, methylation; 3.19A {Escherichia coli k-12} PDB: 1p85_C 1p86_C 1vs8_E 2aw4_E 2awb_E 1vs6_E 2i2v_E 2j28_E 2i2t_E* 2qao_E* 2qba_E* 2qbc_E* 2qbe_E 2qbg_E 2qbi_E* 2qbk_E* 2qov_E 2qox_E 2qoz_E* 2qp1_E* ...Length = 97 Back     alignment and structure
>3bbo_G (G:77-171) Ribosomal protein L4; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}Length = 95 Back     alignment and structure
>1vq8_C (C:24-132) 50S ribosomal protein L4E; ribosome 50S, protein-protein complex, RNA-RNA complex, protein-RNA complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui}Length = 109 Back     alignment and structure
>2zkr_c (c:29-146) 60S ribosomal protein L4; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris}Length = 118 Back     alignment and structure
>3i1n_E (E:1-19,E:117-201) 50S ribosomal protein L4; ribosome structure, protein-RNA complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA- binding, methylation; 3.19A {Escherichia coli k-12} PDB: 1p85_C 1p86_C 1vs8_E 2aw4_E 2awb_E 1vs6_E 2i2v_E 2j28_E 2i2t_E* 2qao_E* 2qba_E* 2qbc_E* 2qbe_E 2qbg_E 2qbi_E* 2qbk_E* 2qov_E 2qox_E 2qoz_E* 2qp1_E* ...Length = 104 Back     alignment and structure
>3bbo_G (G:172-293) Ribosomal protein L4; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}Length = 122 Back     alignment and structure
>2ftc_D (D:104-175) Mitochondrial ribosomal protein L4 isoform A, mitochondrial 39S ribosomal protein L3; mitochondrial ribosome, large ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus} PDB: 3iy9_DLength = 72 Back     alignment and structure
>1vq8_C (C:1-23,C:133-246) 50S ribosomal protein L4E; ribosome 50S, protein-protein complex, RNA-RNA complex, protein-RNA complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui}Length = 137 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

Original result of HHsearch against MMDB70 database

IdentityAlignment graphLength Definition Probability
Target207 50S ribosomal protein L4 [Candidatus Liberibacter asiat
2j01_F_210 50S ribosomal protein L4; ribosome, tRNA, paromomy 100.0
1dmg_A_225 Ribosomal protein L4; alpha-beta, ribosome, RNA, S 100.0
2zjr_C_205 50S ribosomal protein L4; ribosome, large ribosoma 100.0
2wwb_H_1-138138 60S ribosomal protein L4-B; ribosome, protein EXIT 100.0
3i1n_E_20-11697 50S ribosomal protein L4; ribosome structure, prot 100.0
3bbo_G_77-17195 Ribosomal protein L4; large ribosomal subunit, spi 100.0
2zkr_c_29-146118 60S ribosomal protein L4; protein-RNA complex, 60S 100.0
1vq8_C_24-132109 50S ribosomal protein L4E; ribosome 50S, protein-p 100.0
3i1n_E_1-19_117-201104 50S ribosomal protein L4; ribosome structure, prot 99.84
1vq8_C_1-23_133-246137 50S ribosomal protein L4E; ribosome 50S, protein-p 99.8
3bbo_G_172-293122 Ribosomal protein L4; large ribosomal subunit, spi 99.77
2ftc_D_104-17572 Mitochondrial ribosomal protein L4 isoform A, mito 99.59
2wwb_H_139-362224 60S ribosomal protein L4-B; ribosome, protein EXIT 99.32
2zkr_c_1-28_147-421 303 60S ribosomal protein L4; protein-RNA complex, 60S 98.96
>2j01_F (F:) 50S ribosomal protein L4; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} Back     alignment and structure
Probab=100.00  E-value=0  Score=477.18  Aligned_cols=207  Identities=31%  Similarity=0.448  Sum_probs=201.7

Q ss_pred             CCEEEEECCCCCEEEEEEECHHHHCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             96226554688645568609779398766899999999999727886200136212148988764558875542365311
Q gi|254780260|r    1 MIELSVRNLDGEDKGVISVSEDIFALKPQQGILARVLRWQSWRKRIGCSKSKGRSEVAYTGSKMYVQKGTGRARHSSKSV   80 (207)
Q Consensus         1 mm~~~v~~~~g~~~~~i~l~~~vf~~~~~~~li~~~v~~~~~~~R~gta~tk~r~ev~gs~kK~~~QKGtGrAR~Gs~rs   80 (207)
                      |++++|||++|++.++++++|++|+.|+|+|+||++|+||++|+|||||+||+|+||+|||+|||+||||||||+||+++
T Consensus         1 M~~~~v~~~~g~~~~~~~~~~~vF~~~~r~dii~~~v~~~~~~~R~gta~tk~r~ev~gsgrK~~~QKgtGrAR~Gs~~s   80 (210)
T 2j01_F            1 MKEVAVYQIPVLSPSGRRELAADLPAEINPHLLWEVVRWQLAKRRRGTASTKTRGEVAYSGRKIWPQKHTGRARHGDIGA   80 (210)
T ss_dssp             CCCCCCCCCCSSSCCCCCCCSTTSSSCCCHHHHHHHHHHHHHHTCCCCCCCCCTTTSCCCCCCSSCSSSSSSCCCCCTTS
T ss_pred             CCCEEEEEEEEECCCCCEECCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             98226874335368888801551565237999999999999746378777775340146676567543355335555401


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCEEEEECCCCCCCCHHHHHHHHHHCCCCCEEEEECCCCC
Q ss_conf             10105774227787532000015999999999878765059589951433787781899998411355632786157751
Q gi|254780260|r   81 SQFRGGGKAFGPVPIIGVHALPKKVRSLALRHALSDKFCSNDIMVIDNLVSKECKTKYLVTRFRALDLSNALIIDGCQLD  160 (207)
Q Consensus        81 p~~rgGg~afgp~pr~~~~klnkK~~~lAl~saLs~k~~~~~l~Vvd~~~~~~~KTK~~~~~L~~l~~~~~llv~~~~~d  160 (207)
                      |+|+|||+||||+||+|+++||||++++|+++|||.|+++++|+|||++.++++|||++.++|+.+++.+..+++..+.|
T Consensus        81 P~~~gGg~a~gpkpr~~~~klnkK~~~lal~~aLs~k~~~~~l~vVd~~~~~~~kTk~~~~~l~~l~~~~~~liv~~~~~  160 (210)
T 2j01_F           81 PIFVGGGVVFGPKPRDYSYTLPKKVRKKGLAMAVADRAREGKLLLVEAFAGVNGKTKEFLAWAKEAGLDGSESVLLVTGN  160 (210)
T ss_dssp             TTSTTSCCSSCCCCCCCCCCCCHHHHHHHHHHHHHHHHHTTCEEEECCCCCCSSCHHHHHHHHHHHTCCSSSCEEEECSC
T ss_pred             CCCCCCEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCH
T ss_conf             21266456526420257888999999999999999974458725304433456662888888877512354543555512


Q ss_pred             HHHHHHHCCCCCCEEEEHHCCCHHHHEECCCEEEEHHHHHHHHHHHC
Q ss_conf             78999962788956842402887571005908984999999999739
Q gi|254780260|r  161 RNFQLAARNIPNINLLPVQGINVYDILRCSKLVLSKSAIEALEDRFK  207 (207)
Q Consensus       161 ~n~~~s~rNi~~v~v~~~~~lnv~dll~~~~iVit~~Ai~~l~e~lk  207 (207)
                      +|+++|+||||+|+++++++||+||||++++||||++|++.|+|+|-
T Consensus       161 ~n~~~a~rNi~~v~v~~~~~lnv~dll~~~~ivit~~Al~~l~e~~~  207 (210)
T 2j01_F          161 ELVRRAARNLPWVVTLAPEGLNVYDIVRTERLVMDLDAWEVFQNRIG  207 (210)
T ss_dssp             HHHHHHHTTCTTEEEECGGGCCHHHHHHSSEEEEEHHHHHHHHHTCC
T ss_pred             HHHHHHHHCCCCCEEEECCCCCHHHHHCCCCEEEEHHHHHHHHHHHC
T ss_conf             68999984768967863388129998668949987899999999966
>1dmg_A (A:) Ribosomal protein L4; alpha-beta, ribosome, RNA, S10 operon; HET: CIT; 1.70A {Thermotoga maritima} Back     alignment and structure
>2zjr_C (C:) 50S ribosomal protein L4; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} Back     alignment and structure
>2wwb_H (H:1-138) 60S ribosomal protein L4-B; ribosome, protein EXIT tunnel, cotranslational protein translocation, protein conducting channel; 6.48A {Triticum aestivum} PDB: 2wwa_H 2ww9_H 1s1i_D Back     alignment and structure
>3i1n_E (E:20-116) 50S ribosomal protein L4; ribosome structure, protein-RNA complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA- binding, methylation; 3.19A {Escherichia coli k-12} PDB: 1p85_C 1p86_C 1vs8_E 2aw4_E 2awb_E 1vs6_E 2i2v_E 2j28_E 2i2t_E* 2qao_E* 2qba_E* 2qbc_E* 2qbe_E 2qbg_E 2qbi_E* 2qbk_E* 2qov_E 2qox_E 2qoz_E* 2qp1_E* ... Back     alignment and structure
>3bbo_G (G:77-171) Ribosomal protein L4; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Back     alignment and structure
>2zkr_c (c:29-146) 60S ribosomal protein L4; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Back     alignment and structure
>1vq8_C (C:24-132) 50S ribosomal protein L4E; ribosome 50S, protein-protein complex, RNA-RNA complex, protein-RNA complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} Back     alignment and structure
>3i1n_E (E:1-19,E:117-201) 50S ribosomal protein L4; ribosome structure, protein-RNA complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA- binding, methylation; 3.19A {Escherichia coli k-12} PDB: 1p85_C 1p86_C 1vs8_E 2aw4_E 2awb_E 1vs6_E 2i2v_E 2j28_E 2i2t_E* 2qao_E* 2qba_E* 2qbc_E* 2qbe_E 2qbg_E 2qbi_E* 2qbk_E* 2qov_E 2qox_E 2qoz_E* 2qp1_E* ... Back     alignment and structure
>1vq8_C (C:1-23,C:133-246) 50S ribosomal protein L4E; ribosome 50S, protein-protein complex, RNA-RNA complex, protein-RNA complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} Back     alignment and structure
>3bbo_G (G:172-293) Ribosomal protein L4; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Back     alignment and structure
>2ftc_D (D:104-175) Mitochondrial ribosomal protein L4 isoform A, mitochondrial 39S ribosomal protein L3; mitochondrial ribosome, large ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus} PDB: 3iy9_D Back     alignment and structure
>2wwb_H (H:139-362) 60S ribosomal protein L4-B; ribosome, protein EXIT tunnel, cotranslational protein translocation, protein conducting channel; 6.48A {Triticum aestivum} PDB: 2wwa_H 2ww9_H 1s1i_D Back     alignment and structure
>2zkr_c (c:1-28,c:147-421) 60S ribosomal protein L4; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Back     alignment and structure