254780260
50S ribosomal protein L4
GeneID in NCBI database: | 8209241 | Locus tag: | CLIBASIA_00725 |
Protein GI in NCBI database: | 254780260 | Protein 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 | ||
sequence | sequence profile |
Prediction of Local Sequence Properties
Source | Summary | Result |
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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
Identity | Alignment graph | Length | Definition | Round | E-value |
Target | 207 | 50S ribosomal protein L4 [Candidatus Liberibacter asiat | |||
315122817 | 207 | 50S ribosomal protein L4 [Candidatus Liberibacter solan | 1 | 1e-100 | |
86357306 | 206 | 50S ribosomal protein L4 [Rhizobium etli CFN 42] Length | 1 | 1e-69 | |
218460209 | 206 | 50S ribosomal protein L4 [Rhizobium etli Kim 5] Length | 1 | 1e-69 | |
218672011 | 206 | 50S ribosomal protein L4 [Rhizobium etli GR56] Length = | 1 | 2e-69 | |
190891356 | 206 | 50S ribosomal protein L4 [Rhizobium etli CIAT 652] Leng | 1 | 2e-69 | |
325293335 | 206 | 50S ribosomal protein L4 [Agrobacterium sp. H13-3] Leng | 1 | 1e-68 | |
116251541 | 206 | 50S ribosomal protein L4 [Rhizobium leguminosarum bv. v | 1 | 1e-68 | |
15889241 | 206 | 50S ribosomal protein L4 [Agrobacterium tumefaciens str | 1 | 1e-68 | |
241204166 | 206 | 50S ribosomal protein L4 [Rhizobium leguminosarum bv. t | 1 | 2e-68 | |
15965110 | 206 | 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 |
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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 |
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>gi|218460209|ref|ZP_03500300.1| 50S ribosomal protein L4 [Rhizobium etli Kim 5] Length = 206 | Back alignment and organism information |
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>gi|218672011|ref|ZP_03521680.1| 50S ribosomal protein L4 [Rhizobium etli GR56] Length = 206 | Back alignment and organism information |
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>gi|190891356|ref|YP_001977898.1| 50S ribosomal protein L4 [Rhizobium etli CIAT 652] Length = 206 | Back alignment and organism information |
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>gi|325293335|ref|YP_004279199.1| 50S ribosomal protein L4 [Agrobacterium sp. H13-3] Length = 206 | Back alignment and organism information |
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>gi|116251541|ref|YP_767379.1| 50S ribosomal protein L4 [Rhizobium leguminosarum bv. viciae 3841] Length = 206 | Back alignment and organism information |
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>gi|15889241|ref|NP_354922.1| 50S ribosomal protein L4 [Agrobacterium tumefaciens str. C58] Length = 206 | Back alignment and organism information |
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>gi|241204166|ref|YP_002975262.1| 50S ribosomal protein L4 [Rhizobium leguminosarum bv. trifolii WSM1325] Length = 206 | Back alignment and organism information |
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>gi|15965110|ref|NP_385463.1| 50S ribosomal protein L4 [Sinorhizobium meliloti 1021] Length = 206 | Back alignment and organism information |
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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
Identity | Alignment graph | Length | Definition | E-value |
Target | 207 | 50S ribosomal protein L4 [Candidatus Liberibacter asiat | ||
PRK05319 | 205 | PRK05319, rplD, 50S ribosomal protein L4; Provisional | 4e-65 | |
COG0088 | 214 | COG0088, RplD, Ribosomal protein L4 [Translation, ribos | 3e-45 | |
KOG1624 | 290 | KOG1624, KOG1624, KOG1624, Mitochondrial/chloroplast ri | 2e-41 | |
PRK14547 | 298 | PRK14547, rplD, 50S ribosomal protein L4; Provisional | 7e-27 | |
CHL00147 | 215 | CHL00147, rpl4, ribosomal protein L4; Validated | 6e-22 | |
pfam00573 | 190 | pfam00573, Ribosomal_L4, Ribosomal protein L4/L1 family | 1e-52 | |
PRK14907 | 295 | PRK14907, rplD, 50S ribosomal protein L4; Provisional | 2e-20 |
>gnl|CDD|180011 PRK05319, rplD, 50S ribosomal protein L4; Provisional | Back alignment and domain information |
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>gnl|CDD|30437 COG0088, RplD, Ribosomal protein L4 [Translation, ribosomal structure and biogenesis] | Back alignment and domain information |
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>gnl|CDD|36837 KOG1624, KOG1624, KOG1624, Mitochondrial/chloroplast ribosomal protein L4 [Translation, ribosomal structure and biogenesis] | Back alignment and domain information |
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>gnl|CDD|184735 PRK14547, rplD, 50S ribosomal protein L4; Provisional | Back alignment and domain information |
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>gnl|CDD|177068 CHL00147, rpl4, ribosomal protein L4; Validated | Back alignment and domain information |
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>gnl|CDD|144240 pfam00573, Ribosomal_L4, Ribosomal protein L4/L1 family | Back alignment and domain information |
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>gnl|CDD|184900 PRK14907, rplD, 50S ribosomal protein L4; Provisional | Back alignment and domain information |
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Conserved Domains in CDD Database Detected by HHsearch
Original result of HHsearch against CDD database
Identity | Alignment graph | Length | Definition | Probability |
Target | 207 | 50S ribosomal protein L4 [Candidatus Liberibacter asiat | ||
CHL00147 | 214 | rpl4 ribosomal protein L4; Validated | 100.0 | |
PRK05319 | 206 | rplD 50S ribosomal protein L4; Provisional | 100.0 | |
pfam00573 | 190 | Ribosomal_L4 Ribosomal protein L4/L1 family. This famil | 100.0 | |
COG0088 | 214 | RplD Ribosomal protein L4 [Translation, ribosomal struc | 100.0 | |
KOG1624 | 290 | consensus | 100.0 | |
TIGR03672 | 251 | rpl4p_arch 50S ribosomal protein L4P. One of the primar | 100.0 | |
PRK04042 | 254 | rpl4lp 50S ribosomal protein L4P; Provisional | 100.0 | |
KOG1475 | 363 | consensus | 99.96 |
>CHL00147 rpl4 ribosomal protein L4; Validated | Back alignment and domain information |
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>PRK05319 rplD 50S ribosomal protein L4; Provisional | Back alignment and domain information |
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>pfam00573 Ribosomal_L4 Ribosomal protein L4/L1 family | Back alignment and domain information |
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>COG0088 RplD Ribosomal protein L4 [Translation, ribosomal structure and biogenesis] | Back alignment and domain information |
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>KOG1624 consensus | Back alignment and domain information |
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>TIGR03672 rpl4p_arch 50S ribosomal protein L4P | Back alignment and domain information |
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>PRK04042 rpl4lp 50S ribosomal protein L4P; Provisional | Back alignment and domain information |
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>KOG1475 consensus | Back alignment and domain information |
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Homologous Structures in PDB Database
Detected by PSI-BLAST, RPS-BLAST and HHsearch
Homologous Structures Detected by PSI-BLAST against Nonredundant Database
Identity | Alignment graph | Length | Definition | E-value |
Target | 207 | 50S ribosomal protein L4 [Candidatus Liberibacter asiat | ||
1p85_C | 201 | Real Space Refined Coordinates Of The 50s Subunit F | 2e-43 | |
2gya_C | 198 | Structure Of The 50s Subunit Of A Pre-Translocation | 1e-42 | |
1dmg_A | 225 | Crystal Structure Of Ribosomal Protein L4 Length = | 5e-40 | |
3pyo_E | 202 | Crystal Structure Of A Complex Containing Domain 3 | 5e-39 | |
3d5b_F | 210 | Structural Basis For Translation Termination On The | 5e-39 | |
1vsa_D | 205 | Crystal Structure Of A 70s Ribosome-Trna Complex Re | 5e-39 | |
3fin_F | 208 | T. Thermophilus 70s Ribosome In Complex With Mrna, | 2e-38 | |
2j01_F | 210 | Structure Of The Thermus Thermophilus 70s Ribosome | 2e-38 | |
1vor_F | 198 | Crystal Structure Of Five 70s Ribosomes From Escher | 9e-37 | |
1pnu_C | 197 | Crystal Structure Of A Streptomycin Dependent Ribos | 9e-37 | |
1jzx_K | 205 | Structural Basis For The Interaction Of Antibiotics | 4e-36 | |
1nwx_C | 204 | Complex Of The Large Ribosomal Subunit From Deinoco | 8e-35 | |
3bbo_G | 293 | Homology Model For The Spinach Chloroplast 50s Subu | 9e-35 | |
1ffk_C | 246 | Crystal Structure Of The Large Ribosomal Subunit Fr | 8e-17 | |
3izr_D | 405 | Localization Of The Large Subunit Ribosomal Protein | 1e-16 | |
1jj2_C | 246 | Fully Refined Crystal Structure Of The Haloarcula M | 1e-16 | |
3cc2_C | 246 | The Refined Crystal Structure Of The Haloarcula Mar | 2e-16 | |
2zkr_c | 421 | Structure Of A Mammalian Ribosomal 60s Subunit With | 2e-15 | |
3jyw_D | 257 | Structure Of The 60s Proteins For Eukaryotic Riboso | 2e-12 | |
1s1i_D | 361 | Structure Of The Ribosomal 80s-Eef2-Sordarin Comple | 3e-12 | |
3izs_D | 362 | Localization Of The Large Subunit Ribosomal Protein | 3e-12 | |
2ww9_H | 362 | Cryo-Em Structure Of The Active Yeast Ssh1 Complex | 3e-12 | |
2ftc_D | 175 | 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
Identity | Alignment graph | Length | Definition | E-value |
Target | 207 | 50S ribosomal protein L4 [Candidatus Liberibacter asiat | ||
3ofq_E | 201 | 50S ribosomal protein L4; protein biosynthesis, ribosom | 3e-48 | |
3bbo_G | 293 | Ribosomal protein L4; large ribosomal subunit, spinach | 4e-44 | |
3i1n_E | 201 | 50S ribosomal protein L4; ribosome structure, protein-R | 3e-38 | |
2zjr_C | 205 | 50S ribosomal protein L4; ribosome, large ribosomal sub | 1e-37 | |
1dmg_A | 225 | Ribosomal protein L4; alpha-beta, ribosome, RNA, S10 op | 1e-34 | |
2wwb_H | 362 | 60S ribosomal protein L4-B; ribosome, protein EXIT tunn | 2e-34 | |
2j01_F | 210 | 50S ribosomal protein L4; ribosome, tRNA, paromomycin, | 2e-32 | |
1vq8_C | 246 | 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_D | 175 | 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 |
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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 |
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>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 |
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>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 |
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>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 |
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>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 |
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>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 |
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>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 |
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>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 |
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>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 |
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Homologous Structures in PDB70 Database Detected by HHsearch
Original result of HHsearch against PDB70 database
Identity | Alignment graph | Length | Definition | Probability |
Target | 207 | 50S ribosomal protein L4 [Candidatus Liberibacter asiat | ||
3bbo_G | 293 | Ribosomal protein L4; large ribosomal subunit, spinach | 100.0 | |
1dmg_A | 225 | Ribosomal protein L4; alpha-beta, ribosome, RNA, S10 op | 100.0 | |
2zjr_C | 205 | 50S ribosomal protein L4; ribosome, large ribosomal sub | 100.0 | |
3ofq_E | 201 | 50S ribosomal protein L4; protein biosynthesis, ribosom | 100.0 | |
2j01_F | 210 | 50S ribosomal protein L4; ribosome, tRNA, paromomycin, | 100.0 | |
1vq8_C | 246 | 50S ribosomal protein L4E; ribosome 50S, protein-protei | 100.0 | |
2wwb_H | 362 | 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_D | 175 | 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 |
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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 |
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>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 |
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>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 |
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>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 |
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>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 |
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>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 |
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>2zkr_c 60S ribosomal protein L4; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} | Back alignment and structure |
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>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 |
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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
Identity | Alignment graph | Length | Definition | E-value |
207 | 50S ribosomal protein L4 [Candidatus Liberibacter asiat | |||
d2gycc1 | 198 | c.22.1.1 (C:1-198) Ribosomal protein L4 {Escherichia co | 6e-39 | |
d2zjrc1 | 197 | 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 | |
d2j01f1 | 208 | c.22.1.1 (F:1-208) Ribosomal protein L4 {Thermus thermo | 8e-33 | |
d1vqoc1 | 246 | 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 |
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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 |
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>d1dmga_ c.22.1.1 (A:) Ribosomal protein L4 {Thermotoga maritima [TaxId: 2336]} Length = 225 | Back information, alignment and structure |
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>d2j01f1 c.22.1.1 (F:1-208) Ribosomal protein L4 {Thermus thermophilus [TaxId: 274]} Length = 208 | Back information, alignment and structure |
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>d1vqoc1 c.22.1.1 (C:1-246) Ribosomal protein L4 {Archaeon Haloarcula marismortui [TaxId: 2238]} Length = 246 | Back information, alignment and structure |
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Homologous Domains in SCOP70 (Version 1.75) Database Detected by HHsearch
Original result of HHsearch against SCOP70(version1.75) database
Identity | Alignment graph | Length | Definition | Probability |
Target | 207 | 50S ribosomal protein L4 [Candidatus Liberibacter asiat | ||
d1dmga_ | 225 | Ribosomal protein L4 {Thermotoga maritima [TaxId: 2336] | 100.0 | |
d2gycc1 | 198 | Ribosomal protein L4 {Escherichia coli [TaxId: 562]} | 100.0 | |
d2j01f1 | 208 | Ribosomal protein L4 {Thermus thermophilus [TaxId: 274] | 100.0 | |
d2zjrc1 | 197 | Ribosomal protein L4 {Deinococcus radiodurans [TaxId: 1 | 100.0 | |
d1vqoc1 | 246 | Ribosomal protein L4 {Archaeon Haloarcula marismortui [ | 100.0 | |
d1vqoc1 | 246 | 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 |
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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 |
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>d2j01f1 c.22.1.1 (F:1-208) Ribosomal protein L4 {Thermus thermophilus [TaxId: 274]} | Back information, alignment and structure |
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>d2zjrc1 c.22.1.1 (C:2-198) Ribosomal protein L4 {Deinococcus radiodurans [TaxId: 1299]} | Back information, alignment and structure |
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>d1vqoc1 c.22.1.1 (C:1-246) Ribosomal protein L4 {Archaeon Haloarcula marismortui [TaxId: 2238]} | Back information, alignment and structure |
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>d1vqoc1 c.22.1.1 (C:1-246) Ribosomal protein L4 {Archaeon Haloarcula marismortui [TaxId: 2238]} | Back information, alignment and structure |
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Homologous Domains in MMDB70 Database Detected by RPS-BLAST
Original result of RPS-BLAST against MMDB70 database
Identity | Alignment graph | Length | 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_1-138 | 138 | (H:1-138) 60S ribosomal protein L4-B; ribosome, pr | 2e-24 | |
3i1n_E_20-116 | 97 | (E:20-116) 50S ribosomal protein L4; ribosome stru | 2e-22 | |
3bbo_G_77-171 | 95 | (G:77-171) Ribosomal protein L4; large ribosomal s | 7e-21 | |
1vq8_C_24-132 | 109 | (C:24-132) 50S ribosomal protein L4E; ribosome 50S | 4e-20 | |
2zkr_c_29-146 | 118 | (c:29-146) 60S ribosomal protein L4; protein-RNA c | 6e-18 | |
3i1n_E_1-19_117-201 | 104 | (E:1-19,E:117-201) 50S ribosomal protein L4; ribos | 6e-21 | |
3bbo_G_172-293 | 122 | (G:172-293) Ribosomal protein L4; large ribosomal | 8e-16 | |
2ftc_D_104-175 | 72 | (D:104-175) Mitochondrial ribosomal protein L4 iso | 2e-15 | |
1vq8_C_1-23_133-246 | 137 | (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 |
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>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 |
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>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 |
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>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 |
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>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 |
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>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 |
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>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 |
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>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 |
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>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
Identity | Alignment graph | Length | Definition | Probability |
Target | 207 | 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_1-138 | 138 | 60S ribosomal protein L4-B; ribosome, protein EXIT | 100.0 | |
3i1n_E_20-116 | 97 | 50S ribosomal protein L4; ribosome structure, prot | 100.0 | |
3bbo_G_77-171 | 95 | Ribosomal protein L4; large ribosomal subunit, spi | 100.0 | |
2zkr_c_29-146 | 118 | 60S ribosomal protein L4; protein-RNA complex, 60S | 100.0 | |
1vq8_C_24-132 | 109 | 50S ribosomal protein L4E; ribosome 50S, protein-p | 100.0 | |
3i1n_E_1-19_117-201 | 104 | 50S ribosomal protein L4; ribosome structure, prot | 99.84 | |
1vq8_C_1-23_133-246 | 137 | 50S ribosomal protein L4E; ribosome 50S, protein-p | 99.8 | |
3bbo_G_172-293 | 122 | Ribosomal protein L4; large ribosomal subunit, spi | 99.77 | |
2ftc_D_104-175 | 72 | Mitochondrial ribosomal protein L4 isoform A, mito | 99.59 | |
2wwb_H_139-362 | 224 | 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 |
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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 |
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>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 |
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>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 |
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>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 |
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>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 |
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>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 |
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>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 |
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>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 |
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>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 |
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>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 |
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>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 |
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>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 |
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>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 |
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