254780253

254780253

ribosomal protein L29

GeneID in NCBI database:8209234Locus tag:CLIBASIA_00690
Protein GI in NCBI database:254780253Protein Accession:YP_003064666.1
Gene range:-(138518, 138721)Protein Length:67aa
Gene description:ribosomal protein L29
COG prediction:[J] Ribosomal protein L29
KEGG prediction:ribosomal protein L29; K02904 large subunit ribosomal protein L29
SEED prediction:LSU ribosomal protein L29p (L35e)
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-------
MLKFKDISVMSIDQLTEKLIQLKKDQMSLRFQKASGQIEKPFRMREVSRDIARIKTMMNSRVFKNNS
cccHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHccc
cccHHHHHHccHHHHHHHHHHHHHHHHcHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHcccc
mlkfkdisVMSIDQLTEKLIQLKKDQMSLRFQkasgqiekpfrmrEVSRDIARIKTMMNsrvfknns
mlkfkdisvmsIDQLTEKLIQLKKDQMSLRFqkasgqiekpfrmrevSRDIARiktmmnsrvfknns
MLKFKDISVMSIDQLTEKLIQLKKDQMSLRFQKASGQIEKPFRMREVSRDIARIKTMMNSRVFKNNS
*LKFKDISVMSIDQLTEKLIQLKKDQMSLRFQ*************EVSRDIARIKTMM**R******
MLKFKDISVMSIDQLTEKLIQLKKDQMSLRFQKASGQIEKPFRMREVSRDIARIKTMMNSRVFKNNS
****KDISVMSIDQLTEKLIQLKKDQMSLRFQKASGQIEKPFRMREVSRDIARIKTMMNSRV*****
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MLKFKDISVMSIDQLTEKLIQLKKDQMSLRFQKASGQIEKPFRMREVSRDIARIKTMMNSRVFKNNS
MLKFKDISVMSIDQLTEKLIQLKKDQMSLRFQKASGQIEKPFRMREVSRDIARIKTMMNSRVFKNNS
MLKFKDISVMSIDQLTEKLIQLKKDQMSLRFQKASGQIEKPFRMREVSRDIARIKTMMNSRVFKNNS

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

No hits with e-value below 0.05

Close Homologs Detected BLAST or PSI-BLAST in the First 2 Iterations

IdentityAlignment graphLength Definition Round E-value
Target67 ribosomal protein L29 [Candidatus Liberibacter asiaticu
31512281067 ribosomal protein L29 [Candidatus Liberibacter solanace 1 8e-22
20996404869 50S ribosomal protein L29 [Rhodospirillum centenum SW] 1 3e-12
8537445768 50S ribosomal protein L29 [Erythrobacter litoralis HTCC 1 4e-11
22092190771 ribosomal protein L29 [Methylobacterium nodulans ORS 20 1 8e-11
16376080766 50S ribosomal protein L29 [Hoeflea phototrophica DFL-43 1 1e-10
17073869571 ribosomal protein L29 [Methylobacterium sp. 4-46] Lengt 1 1e-10
15842417073 50S ribosomal protein L29 [Azorhizobium caulinodans ORS 1 1e-10
32638820568 50S ribosomal protein L29 [Novosphingobium nitrogenifig 1 2e-10
19710470464 50S ribosomal protein L29 [Phenylobacterium zucineum HL 1 3e-10
16764558664 50S ribosomal protein L29 [Caulobacter sp. K31] Length 1 3e-10
>gi|315122810|ref|YP_004063299.1| ribosomal protein L29 [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 67 Back     alignment and organism information
 Score =  106 bits (265), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 49/67 (73%), Positives = 62/67 (92%)

Query: 1  MLKFKDISVMSIDQLTEKLIQLKKDQMSLRFQKASGQIEKPFRMREVSRDIARIKTMMNS 60
          MLKFKDIS+M+ DQL E+L+QLK++QMSLRFQKA+GQ+EKPFRMR ++RDIAR+KTMMNS
Sbjct: 1  MLKFKDISIMNADQLREQLVQLKREQMSLRFQKATGQLEKPFRMRGINRDIARVKTMMNS 60

Query: 61 RVFKNNS 67
          + F+N S
Sbjct: 61 KSFENKS 67


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|209964048|ref|YP_002296963.1| 50S ribosomal protein L29 [Rhodospirillum centenum SW] Length = 69 Back     alignment and organism information
>gi|85374457|ref|YP_458519.1| 50S ribosomal protein L29 [Erythrobacter litoralis HTCC2594] Length = 68 Back     alignment and organism information
>gi|220921907|ref|YP_002497208.1| ribosomal protein L29 [Methylobacterium nodulans ORS 2060] Length = 71 Back     alignment and organism information
>gi|163760807|ref|ZP_02167886.1| 50S ribosomal protein L29 [Hoeflea phototrophica DFL-43] Length = 66 Back     alignment and organism information
>gi|170738695|ref|YP_001767350.1| ribosomal protein L29 [Methylobacterium sp. 4-46] Length = 71 Back     alignment and organism information
>gi|158424170|ref|YP_001525462.1| 50S ribosomal protein L29 [Azorhizobium caulinodans ORS 571] Length = 73 Back     alignment and organism information
>gi|326388205|ref|ZP_08209808.1| 50S ribosomal protein L29 [Novosphingobium nitrogenifigens DSM 19370] Length = 68 Back     alignment and organism information
>gi|197104704|ref|YP_002130081.1| 50S ribosomal protein L29 [Phenylobacterium zucineum HLK1] Length = 64 Back     alignment and organism information
>gi|167645586|ref|YP_001683249.1| 50S ribosomal protein L29 [Caulobacter sp. K31] Length = 64 Back     alignment and organism information

Conserved Domains in CDD Database
Detected by RPS-BLAST and HHsearch

Conserved Domains in CDD Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target67 ribosomal protein L29 [Candidatus Liberibacter asiaticu
PRK0030666 PRK00306, PRK00306, 50S ribosomal protein L29; Reviewed 3e-12
cd0042757 cd00427, Ribosomal_L29_HIP, Ribosomal L29 protein/HIP 1e-09
COG025569 COG0255, RpmC, Ribosomal protein L29 [Translation, ribo 2e-09
TIGR0001255 TIGR00012, L29, ribosomal protein L29 1e-08
PRK0046187 PRK00461, rpmC, 50S ribosomal protein L29; Reviewed 3e-07
PRK1454969 PRK14549, PRK14549, 50S ribosomal protein L29P; Provisi 1e-06
pfam0083158 pfam00831, Ribosomal_L29, Ribosomal L29 protein 3e-11
>gnl|CDD|178971 PRK00306, PRK00306, 50S ribosomal protein L29; Reviewed Back     alignment and domain information
>gnl|CDD|88602 cd00427, Ribosomal_L29_HIP, Ribosomal L29 protein/HIP Back     alignment and domain information
>gnl|CDD|30604 COG0255, RpmC, Ribosomal protein L29 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|129124 TIGR00012, L29, ribosomal protein L29 Back     alignment and domain information
>gnl|CDD|179037 PRK00461, rpmC, 50S ribosomal protein L29; Reviewed Back     alignment and domain information
>gnl|CDD|184737 PRK14549, PRK14549, 50S ribosomal protein L29P; Provisional Back     alignment and domain information
>gnl|CDD|144430 pfam00831, Ribosomal_L29, Ribosomal L29 protein Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 67 ribosomal protein L29 [Candidatus Liberibacter asiaticu
PRK00461122 rpmC 50S ribosomal protein L29; Reviewed 99.87
PRK0030666 50S ribosomal protein L29; Reviewed 99.8
PRK0145071 rpmC 50S ribosomal protein L29; Provisional 99.79
COG025569 RpmC Ribosomal protein L29 [Translation, ribosomal stru 99.77
TIGR0001257 L29 ribosomal protein L29; InterPro: IPR001854 Ribosome 99.75
cd0042757 Ribosomal_L29_HIP Ribosomal L29 protein/HIP. L29 is a p 99.71
pfam0083158 Ribosomal_L29 Ribosomal L29 protein. 99.71
CHL0015467 rpl29 ribosomal protein L29; Validated 99.49
KOG3436123 consensus 99.24
KOG3331213 consensus 98.03
pfam0698487 MRP-L47 Mitochondrial 39-S ribosomal protein L47 (MRP-L 97.86
>PRK00461 rpmC 50S ribosomal protein L29; Reviewed Back     alignment and domain information
>PRK00306 50S ribosomal protein L29; Reviewed Back     alignment and domain information
>PRK01450 rpmC 50S ribosomal protein L29; Provisional Back     alignment and domain information
>COG0255 RpmC Ribosomal protein L29 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>TIGR00012 L29 ribosomal protein L29; InterPro: IPR001854 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>cd00427 Ribosomal_L29_HIP Ribosomal L29 protein/HIP Back     alignment and domain information
>pfam00831 Ribosomal_L29 Ribosomal L29 protein Back     alignment and domain information
>CHL00154 rpl29 ribosomal protein L29; Validated Back     alignment and domain information
>KOG3436 consensus Back     alignment and domain information
>KOG3331 consensus Back     alignment and domain information
>pfam06984 MRP-L47 Mitochondrial 39-S ribosomal protein L47 (MRP-L47) Back     alignment and domain information

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

Homologous Structures Detected by PSI-BLAST against Nonredundant Database

IdentityAlignment graphLength Definition E-value
Target67 ribosomal protein L29 [Candidatus Liberibacter asiaticu
3g4s_V65 Co-Crystal Structure Of Tiamulin Bound To The Large 9e-09
1r73_A66 Solution Structure Of Tm1492, The L29 Ribosomal Pro 1e-08
1ffk_S70 Crystal Structure Of The Large Ribosomal Subunit Fr 2e-08
1s72_V71 Refined Crystal Structure Of The Haloarcula Marismo 3e-08
1p85_W63 Real Space Refined Coordinates Of The 50s Subunit F 2e-07
3bbo_Z173 Homology Model For The Spinach Chloroplast 50s Subu 3e-07
2go5_5124 Structure Of Signal Recognition Particle Receptor ( 4e-07
2gya_W60 Structure Of The 50s Subunit Of A Pre-Translocation 3e-06
1nkw_W67 Crystal Structure Of The Large Ribosomal Subunit Fr 4e-06
2zkr_v123 Structure Of A Mammalian Ribosomal 60s Subunit With 6e-06
2j01_272 Structure Of The Thermus Thermophilus 70s Ribosome 7e-06
2hgj_167 Crystal Structure Of The 70s Thermus Thermophilus R 8e-06
1pnu_W65 Crystal Structure Of A Streptomycin Dependent Ribos 2e-05
3jyw_X86 Structure Of The 60s Proteins For Eukaryotic Riboso 3e-05
1s1i_X120 Structure Of The Ribosomal 80s-Eef2-Sordarin Comple 9e-05
3fin_251 T. Thermophilus 70s Ribosome In Complex With Mrna, 5e-04
3pyo_Y62 Crystal Structure Of A Complex Containing Domain 3 0.001
>gi|228312163|pdb|3G4S|V Chain V, Co-Crystal Structure Of Tiamulin Bound To The Large Ribosomal Subunit Length = 65 Back     alignment and structure
 Score = 63.8 bits (155), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 19/57 (33%), Positives = 32/57 (56%), Gaps = 1/57 (1%)

Query: 5  KDISVMSIDQLTEKLIQLKKDQMSLR-FQKASGQIEKPFRMREVSRDIARIKTMMNS 60
          ++I  M+  +   +L  LK + ++ R  Q A G  E P R++E+ + IARIKT+   
Sbjct: 6  QEIRDMTPAEREAELDDLKTELLNARAVQAAGGAPENPGRIKELRKAIARIKTIQGE 62


gi|253723088|pdb|1R73|A Chain A, Solution Structure Of Tm1492, The L29 Ribosomal Protein From Thermotoga Maritima Length = 66 Back     alignment and structure
>gi|10120938|pdb|1FFK|S Chain S, Crystal Structure Of The Large Ribosomal Subunit From Haloarcula Marismortui At 2.4 Angstrom Resolution Length = 70 Back     alignment and structure
gi|50513491|pdb|1S72|V Chain V, Refined Crystal Structure Of The Haloarcula Marismortui Large Ribosomal Subunit At 2.4 Angstrom Resolution Length = 71 Back     alignment and structure
gi|33357922|pdb|1P85|W Chain W, 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 = 63 Back     alignment and structure
gi|189096148|pdb|3BBO|Z Chain Z, Homology Model For The Spinach Chloroplast 50s Subunit Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome Length = 173 Back     alignment and structure
gi|110590378|pdb|2GO5|5 Chain 5, Structure Of Signal Recognition Particle Receptor (Sr) In Complex With Signal Recognition Particle (Srp) And Ribosome Nascent Chain Complex Length = 124 Back     alignment and structure
>gi|116667455|pdb|2GYA|W Chain W, 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 = 60 Back     alignment and structure
gi|28948941|pdb|1NKW|W Chain W, Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans Length = 67 Back     alignment and structure
gi|187609321|pdb|2ZKR|VV Chain v, 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 = 123 Back     alignment and structure
gi|116668224|pdb|2J01|2 Chain 2, 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 = 72 Back     alignment and structure
gi|119389757|pdb|2HGJ|1 Chain 1, Crystal Structure Of The 70s Thermus Thermophilus Ribosome Showing How The 16s 3'-End Mimicks Mrna E And P Codons. This Entry 2hgj Contains 50s Ribosomal Subunit. The 30s Ribosomal Subunit Can Be Found In Pdb Entry 2hgi. Length = 67 Back     alignment and structure
>gi|34811576|pdb|1PNU|W Chain W, 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 = 65 Back     alignment and structure
>gi|281500854|pdb|3JYW|X Chain X, Structure Of The 60s Proteins For Eukaryotic Ribosome Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome At 8.9a Resolution Length = 86 Back     alignment and structure
gi|49258863|pdb|1S1I|X Chain X, 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 = 120 Back     alignment and structure
>gi|224510771|pdb|3FIN|2 Chain 2, 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 = 51 Back     alignment and structure
>gi|322812596|pdb|3PYO|Y Chain Y, 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 = 62 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target67 ribosomal protein L29 [Candidatus Liberibacter asiaticu
3jyw_X86 60S ribosomal protein L35; eukaryotic ribosome, RACK1 p 8e-13
3bbo_Z173 Ribosomal protein L29; large ribosomal subunit, spinach 7e-12
3i1n_Y63 50S ribosomal protein L29; ribosome structure, protein- 2e-11
3ofq_Y63 50S ribosomal protein L29; protein biosynthesis, riboso 3e-11
1r73_A66 TM1492, 50S ribosomal protein L29; ribosome, structural 3e-11
2zjr_V67 50S ribosomal protein L29; ribosome, large ribosomal su 1e-10
2j01_272 50S ribosomal protein L29; ribosome, tRNA, paromomycin, 2e-10
2go5_5124 Ribosomal protein L35; SR, SRP, ribosome, translation/R 6e-10
1vq8_V71 50S ribosomal protein L29P; ribosome 50S, protein-prote 9e-10
2zkr_v123 60S ribosomal protein L35; protein-RNA complex, 60S rib 3e-09
2wwb_N120 60S ribosomal protein L35; ribosome, protein EXIT tunne 5e-09
>3jyw_X 60S ribosomal protein L35; eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus} Length = 86 Back     alignment and structure
 Score = 67.3 bits (165), Expect = 8e-13
 Identities = 17/59 (28%), Positives = 32/59 (54%), Gaps = 2/59 (3%)

Query: 1  MLKFKDISVMSIDQLTEKLIQLKKDQMSLRFQKASGQIEKPFRMREVSRDIARIKTMMN 59
           +K  ++   S +QL  +L+ LKK+   L+ QK S       +++ V + IA + T++N
Sbjct: 2  GVKAYELRTKSKEQLASQLVDLKKELAELKVQKLSRP--SLPKIKTVRKSIACVLTVIN 58


>3bbo_Z Ribosomal protein L29; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Arabidopsis thaliana} Length = 173 Back     alignment and structure
>3i1n_Y 50S ribosomal protein L29; ribosome structure, protein-RNA complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA- binding, methylation; 3.19A {Escherichia coli k-12} PDB: 1p85_W 1p86_W 1vs8_X 2aw4_X 2awb_X 1vs6_X 2i2v_Y 2j28_X 2i2t_Y* 2qao_X* 2qba_X* 2qbc_X* 2qbe_X 2qbg_X 2qbi_X* 2qbk_X* 2qov_X 2qox_X 2qoz_X* 2qp1_X* ... Length = 63 Back     alignment and structure
>3ofq_Y 50S ribosomal protein L29; protein biosynthesis, ribosomes, RNA, tRNA, transfer, antibi EXIT, peptidyl, ribosomal subunit, large; 3.10A {Escherichia coli} PDB: 1p85_W 1p86_W 1vs8_X 1vs6_X 2aw4_X 2awb_X 1vt2_Y 2i2v_Y 2j28_X 2i2t_Y* 2qao_X* 2qba_X* 2qbc_X* 2qbe_X 2qbg_X 2qbi_X* 2qbk_X* 2qov_X 2qox_X 2qoz_X* ... Length = 63 Back     alignment and structure
>1r73_A TM1492, 50S ribosomal protein L29; ribosome, structural genomics, PSI, protein structure initiative, joint center for structural genomics; NMR {Thermotoga maritima} SCOP: a.2.2.1 Length = 66 Back     alignment and structure
>2zjr_V 50S ribosomal protein L29; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: a.2.2.1 PDB: 1nwx_W* 1nwy_W* 1sm1_W* 1xbp_W* 2aar_W 2d3o_W 2zjp_V* 2zjq_V 1nkw_W 3cf5_V* 3dll_V* 1pnu_W 1pny_W 1vor_Y 1vou_Y 1vow_Y 1voy_Y 1vp0_Y Length = 67 Back     alignment and structure
>2j01_2 50S ribosomal protein L29; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} SCOP: a.2.2.1 PDB: 1vsp_W 1vsa_W 2j03_2 2jl6_2 2jl8_2 2v47_2 2v49_2 2wdi_2 2wdj_2 2wdl_2 2wdn_2 2wh2_2 2wh4_2 3d5b_2 3d5d_2 3f1f_2 3f1h_2 3hux_2 3huz_2 2hgu_1 ... Length = 72 Back     alignment and structure
>2go5_5 Ribosomal protein L35; SR, SRP, ribosome, translation/RNA complex; 7.40A {Triticum SP} PDB: 2j37_5 Length = 124 Back     alignment and structure
>1vq8_V 50S ribosomal protein L29P; 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: a.2.2.1 PDB: 1vq4_V* 1vq5_V* 1vq6_V* 1vq7_V* 1s72_V* 1vq9_V* 1vqk_V* 1vql_V* 1vqm_V* 1vqn_V* 1vqo_V* 1vqp_V* 1yhq_V* 1yi2_V* 1yij_V* 1yit_V* 1yj9_V* 1yjn_V* 1yjw_V* 2otj_V* ... Length = 71 Back     alignment and structure
>2zkr_v 60S ribosomal protein L35; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Length = 123 Back     alignment and structure
>2wwb_N 60S ribosomal protein L35; ribosome, protein EXIT tunnel, cotranslational protein translocation, protein conducting channel; 6.48A {Triticum aestivum} PDB: 1s1i_X 2wwa_N 2ww9_N Length = 120 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target67 ribosomal protein L29 [Candidatus Liberibacter asiaticu
1vq8_V71 50S ribosomal protein L29P; ribosome 50S, protein-prote 99.81
1r73_A66 TM1492, 50S ribosomal protein L29; ribosome, structural 99.79
2go5_5124 Ribosomal protein L35; SR, SRP, ribosome, translation/R 99.79
2zjr_V67 50S ribosomal protein L29; ribosome, large ribosomal su 99.78
2zkr_v123 60S ribosomal protein L35; protein-RNA complex, 60S rib 99.76
3bbo_Z173 Ribosomal protein L29; large ribosomal subunit, spinach 99.75
3ofq_Y63 50S ribosomal protein L29; protein biosynthesis, riboso 99.72
3jyw_X86 60S ribosomal protein L35; eukaryotic ribosome, RACK1 p 99.71
2wwb_N120 60S ribosomal protein L35; ribosome, protein EXIT tunne 99.69
2j01_272 50S ribosomal protein L29; ribosome, tRNA, paromomycin, 99.62
>1vq8_V 50S ribosomal protein L29P; 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: a.2.2.1 PDB: 1vq4_V* 1vq5_V* 1vq6_V* 1vq7_V* 1s72_V* 1vq9_V* 1vqk_V* 1vql_V* 1vqm_V* 1vqn_V* 1vqo_V* 1vqp_V* 1yhq_V* 1yi2_V* 1yij_V* 1yit_V* 1yj9_V* 1yjn_V* 1yjw_V* 2otj_V* ... Back     alignment and structure
Probab=99.81  E-value=7e-20  Score=138.04  Aligned_cols=66  Identities=30%  Similarity=0.405  Sum_probs=63.3

Q ss_pred             CCCHHHHHHCCHHHHHHHHHHHHHHHHHHH-HHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             988899972999999999999999999999-999537865469999999999999999999998532
Q gi|254780253|r    1 MLKFKDISVMSIDQLTEKLIQLKKDQMSLR-FQKASGQIEKPFRMREVSRDIARIKTMMNSRVFKNN   66 (67)
Q Consensus         1 mmk~~elr~~s~~eL~~~l~~l~~el~~lr-fq~~~gql~np~~ir~~Rk~IARi~Tvl~er~~~~~   66 (67)
                      |||++|||++|.+||.+++.++++|||+|| ||+++||++|||+|+.+||+||||+||++|+..++.
T Consensus         3 ~mk~~elR~~s~eeL~~~l~elk~el~~LR~~q~~~gql~~~~~ir~~Rk~IARi~Til~Ek~~~~~   69 (71)
T 1vq8_V            3 VLHVQEIRDMTPAEREAELDDLKTELLNARAVQAAGGAPENPGRIKELRKAIARIKTIQGEEGDLQE   69 (71)
T ss_dssp             CSCHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHTTCCCCCHHHHHHHHHHHHHHHHHHHHHTC---
T ss_pred             CCCHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             6879999869999999999999999999999999818877708999999999999999999986250



>1r73_A TM1492, 50S ribosomal protein L29; ribosome, structural genomics, PSI, protein structure initiative, joint center for structural genomics; NMR {Thermotoga maritima} SCOP: a.2.2.1 Back     alignment and structure
>2go5_5 Ribosomal protein L35; SR, SRP, ribosome, translation/RNA complex; 7.40A {Triticum SP} PDB: 2j37_5 Back     alignment and structure
>2zjr_V 50S ribosomal protein L29; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: a.2.2.1 PDB: 1nwx_W* 1nwy_W* 1sm1_W* 1xbp_W* 2aar_W 2d3o_W 2zjp_V* 2zjq_V 1nkw_W 3cf5_V* 3dll_V* 1pnu_W 1pny_W 1vor_Y 1vou_Y 1vow_Y 1voy_Y 1vp0_Y Back     alignment and structure
>2zkr_v 60S ribosomal protein L35; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Back     alignment and structure
>3bbo_Z Ribosomal protein L29; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Arabidopsis thaliana} Back     alignment and structure
>3ofq_Y 50S ribosomal protein L29; protein biosynthesis, ribosomes, RNA, tRNA, transfer, antibi EXIT, peptidyl, ribosomal subunit, large; 3.10A {Escherichia coli} PDB: 1p85_W 1p86_W 1vs8_X 1vs6_X 2aw4_X 2awb_X 1vt2_Y 2i2v_Y 2j28_X 2i2t_Y* 2qao_X* 2qba_X* 2qbc_X* 2qbe_X 2qbg_X 2qbi_X* 2qbk_X* 2qov_X 2qox_X 2qoz_X* ... Back     alignment and structure
>3jyw_X 60S ribosomal protein L35; eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus} Back     alignment and structure
>2wwb_N 60S ribosomal protein L35; ribosome, protein EXIT tunnel, cotranslational protein translocation, protein conducting channel; 6.48A {Triticum aestivum} PDB: 1s1i_X 2wwa_N 2ww9_N Back     alignment and structure
>2j01_2 50S ribosomal protein L29; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} SCOP: a.2.2.1 PDB: 1vsp_W 1vsa_W 2j03_2 2jl6_2 2jl8_2 2v47_2 2v49_2 2wdi_2 2wdj_2 2wdl_2 2wdn_2 2wh2_2 2wh4_2 2wrj_2 2wrl_2 2wro_2 2wrr_2 2x9s_2 2x9u_2 2xg0_2 ... Back     alignment and structure

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

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

IdentityAlignment graphLength Definition E-value
Target 67 ribosomal protein L29 [Candidatus Liberibacter asiaticu
d1r73a_66 a.2.2.1 (A:) Ribosomal protein L29 (L29p) {Thermotoga m 1e-11
d2gycw160 a.2.2.1 (W:1-60) Ribosomal protein L29 (L29p) {Escheric 2e-11
d1vqov165 a.2.2.1 (V:1-65) Ribosomal protein L29 (L29p) {Archaeon 6e-11
d2zjrv166 a.2.2.1 (V:1-66) Ribosomal protein L29 (L29p) {Deinococ 6e-11
d2j012151 a.2.2.1 (2:12-62) Ribosomal protein L29 (L29p) {Thermus 9e-11
>d1r73a_ a.2.2.1 (A:) Ribosomal protein L29 (L29p) {Thermotoga maritima [TaxId: 2336]} Length = 66 Back     information, alignment and structure

class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Ribosomal protein L29 (L29p)
family: Ribosomal protein L29 (L29p)
domain: Ribosomal protein L29 (L29p)
species: Thermotoga maritima [TaxId: 2336]
 Score = 61.9 bits (151), Expect = 1e-11
 Identities = 21/59 (35%), Positives = 34/59 (57%)

Query: 3  KFKDISVMSIDQLTEKLIQLKKDQMSLRFQKASGQIEKPFRMREVSRDIARIKTMMNSR 61
          K  ++   + ++L   L + K+  M LRFQ A GQ++    ++   RDIARIKT++  R
Sbjct: 2  KASELRNYTDEELKNLLEEKKRQLMELRFQLAMGQLKNTSLIKLTKRDIARIKTILRER 60


>d2gycw1 a.2.2.1 (W:1-60) Ribosomal protein L29 (L29p) {Escherichia coli [TaxId: 562]} Length = 60 Back     information, alignment and structure
>d1vqov1 a.2.2.1 (V:1-65) Ribosomal protein L29 (L29p) {Archaeon Haloarcula marismortui [TaxId: 2238]} Length = 65 Back     information, alignment and structure
>d2zjrv1 a.2.2.1 (V:1-66) Ribosomal protein L29 (L29p) {Deinococcus radiodurans [TaxId: 1299]} Length = 66 Back     information, alignment and structure
>d2j0121 a.2.2.1 (2:12-62) Ribosomal protein L29 (L29p) {Thermus thermophilus [TaxId: 274]} Length = 51 Back     information, alignment and structure

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

IdentityAlignment graphLength Definition Probability
Target67 ribosomal protein L29 [Candidatus Liberibacter asiaticu
d1vqov165 Ribosomal protein L29 (L29p) {Archaeon Haloarcula maris 99.79
d1r73a_66 Ribosomal protein L29 (L29p) {Thermotoga maritima [TaxI 99.79
d2zjrv166 Ribosomal protein L29 (L29p) {Deinococcus radiodurans [ 99.79
d2gycw160 Ribosomal protein L29 (L29p) {Escherichia coli [TaxId: 99.77
d2j012151 Ribosomal protein L29 (L29p) {Thermus thermophilus [Tax 99.34
>d1vqov1 a.2.2.1 (V:1-65) Ribosomal protein L29 (L29p) {Archaeon Haloarcula marismortui [TaxId: 2238]} Back     information, alignment and structure
class: All alpha proteins
fold: Long alpha-hairpin
superfamily: Ribosomal protein L29 (L29p)
family: Ribosomal protein L29 (L29p)
domain: Ribosomal protein L29 (L29p)
species: Archaeon Haloarcula marismortui [TaxId: 2238]
Probab=99.79  E-value=1.4e-19  Score=134.84  Aligned_cols=62  Identities=32%  Similarity=0.457  Sum_probs=60.5

Q ss_pred             CCCHHHHHHCCHHHHHHHHHHHHHHHHHHH-HHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             988899972999999999999999999999-99953786546999999999999999999999
Q gi|254780253|r    1 MLKFKDISVMSIDQLTEKLIQLKKDQMSLR-FQKASGQIEKPFRMREVSRDIARIKTMMNSRV   62 (67)
Q Consensus         1 mmk~~elr~~s~~eL~~~l~~l~~el~~lr-fq~~~gql~np~~ir~~Rk~IARi~Tvl~er~   62 (67)
                      |||++|||+||.+||.+++.++++|||+|| ||+++||++|||+|+.+||+||||+||++|+.
T Consensus         2 ~mK~~elr~ls~~eL~~~l~elk~El~~LR~~q~~~gql~~~~~ik~~Rk~IARi~Tvl~ek~   64 (65)
T d1vqov1           2 VLHVQEIRDMTPAEREAELDDLKTELLNARAVQAAGGAPENPGRIKELRKAIARIKTIQGEEG   64 (65)
T ss_dssp             CSCHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             747899986899999999999999999999999980887761899999999999999998726



>d1r73a_ a.2.2.1 (A:) Ribosomal protein L29 (L29p) {Thermotoga maritima [TaxId: 2336]} Back     information, alignment and structure
>d2zjrv1 a.2.2.1 (V:1-66) Ribosomal protein L29 (L29p) {Deinococcus radiodurans [TaxId: 1299]} Back     information, alignment and structure
>d2gycw1 a.2.2.1 (W:1-60) Ribosomal protein L29 (L29p) {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2j0121 a.2.2.1 (2:12-62) Ribosomal protein L29 (L29p) {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 67 ribosomal protein L29 [Candidatus Liberibacter asi
2zjr_V_67 (V:) 50S ribosomal protein L29; ribosome, large ri 4e-11
1r73_A_66 (A:) TM1492, 50S ribosomal protein L29; ribosome, 6e-11
3i1n_Y_63 (Y:) 50S ribosomal protein L29; ribosome structure 7e-11
2j01_2_72 (2:) 50S ribosomal protein L29; ribosome, tRNA, pa 1e-10
3bbo_Z_173 (Z:) Ribosomal protein L29; large ribosomal subuni 2e-10
3jyw_X_86 (X:) 60S ribosomal protein L35; eukaryotic ribosom 1e-09
2go5_5_124 (5:) Ribosomal protein L35; SR, SRP, ribosome, tra 1e-09
1vq8_V_71 (V:) 50S ribosomal protein L29P; ribosome 50S, pro 1e-09
2zkr_v_123 (v:) 60S ribosomal protein L35; protein-RNA comple 4e-09
2wwb_N_120 (N:) 60S ribosomal protein L35; ribosome, protein 1e-08
>2zjr_V (V:) 50S ribosomal protein L29; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans}Length = 67 Back     alignment and structure
 Score = 61.5 bits (150), Expect = 4e-11
 Identities = 17/60 (28%), Positives = 36/60 (60%)

Query: 2  LKFKDISVMSIDQLTEKLIQLKKDQMSLRFQKASGQIEKPFRMREVSRDIARIKTMMNSR 61
          +K  ++  +      +++   KK+ M LRFQ A+GQ+ +P R+R++ R++A++ T+    
Sbjct: 1  MKPSEMRNLQATDFAKEIDARKKELMELRFQAAAGQLAQPHRVRQLRREVAQLNTVKAEL 60


>1r73_A (A:) TM1492, 50S ribosomal protein L29; ribosome, structural genomics, PSI, protein structure initiative, joint center for structural genomics; NMR {Thermotoga maritima}Length = 66 Back     alignment and structure
>3i1n_Y (Y:) 50S ribosomal protein L29; ribosome structure, protein-RNA complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA- binding, methylation; 3.19A {Escherichia coli k-12} PDB: 1p85_W 1p86_W 1vs8_X 2aw4_X 2awb_X 1vs6_X 2i2v_Y 2j28_X 2i2t_Y* 2qao_X* 2qba_X* 2qbc_X* 2qbe_X 2qbg_X 2qbi_X* 2qbk_X* 2qov_X 2qox_X 2qoz_X* 2qp1_X* ...Length = 63 Back     alignment and structure
>2j01_2 (2:) 50S ribosomal protein L29; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus}Length = 72 Back     alignment and structure
>3bbo_Z (Z:) Ribosomal protein L29; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Arabidopsis thaliana}Length = 173 Back     alignment and structure
>3jyw_X (X:) 60S ribosomal protein L35; eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus}Length = 86 Back     alignment and structure
>2go5_5 (5:) Ribosomal protein L35; SR, SRP, ribosome, translation/RNA complex; 7.40A {Triticum SP} PDB: 2j37_5Length = 124 Back     alignment and structure
>1vq8_V (V:) 50S ribosomal protein L29P; 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 = 71 Back     alignment and structure
>2zkr_v (v:) 60S ribosomal protein L35; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris}Length = 123 Back     alignment and structure
>2wwb_N (N:) 60S ribosomal protein L35; ribosome, protein EXIT tunnel, cotranslational protein translocation, protein conducting channel; 6.48A {Triticum aestivum} PDB: 1s1i_X 2wwa_N 2ww9_NLength = 120 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target67 ribosomal protein L29 [Candidatus Liberibacter asiaticu
1r73_A_66 TM1492, 50S ribosomal protein L29; ribosome, struc 99.81
1vq8_V_71 50S ribosomal protein L29P; ribosome 50S, protein- 99.81
3bbo_Z_173 Ribosomal protein L29; large ribosomal subunit, sp 99.8
2zjr_V_67 50S ribosomal protein L29; ribosome, large ribosom 99.8
2go5_5_124 Ribosomal protein L35; SR, SRP, ribosome, translat 99.78
2zkr_v_123 60S ribosomal protein L35; protein-RNA complex, 60 99.76
3i1n_Y_63 50S ribosomal protein L29; ribosome structure, pro 99.76
3jyw_X_86 60S ribosomal protein L35; eukaryotic ribosome, RA 99.68
2wwb_N_120 60S ribosomal protein L35; ribosome, protein EXIT 99.64
2j01_2_72 50S ribosomal protein L29; ribosome, tRNA, paromom 99.64
>1r73_A (A:) TM1492, 50S ribosomal protein L29; ribosome, structural genomics, PSI, protein structure initiative, joint center for structural genomics; NMR {Thermotoga maritima} Back     alignment and structure
Probab=99.81  E-value=5.2e-20  Score=139.71  Aligned_cols=65  Identities=32%  Similarity=0.455  Sum_probs=63.3

Q ss_pred             CCHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             88899972999999999999999999999999537865469999999999999999999998532
Q gi|254780253|r    2 LKFKDISVMSIDQLTEKLIQLKKDQMSLRFQKASGQIEKPFRMREVSRDIARIKTMMNSRVFKNN   66 (67)
Q Consensus         2 mk~~elr~~s~~eL~~~l~~l~~el~~lrfq~~~gql~np~~ir~~Rk~IARi~Tvl~er~~~~~   66 (67)
                      ||++|||++|.+||.+++.+++++||+||||+++||++|||+|+.+||+||||+||++|++.++.
T Consensus         1 MK~~elr~~s~~EL~~~l~~lk~elf~Lr~q~~~~~l~np~~ir~~Rk~IARi~Tvl~ek~~~~~   65 (66)
T 1r73_A            1 MKASELRNYTDEELKNLLEEKKRQLMELRFQLAMGQLKNTSLIKLTKRDIARIKTILRERELGIR   65 (66)
T ss_dssp             CCCSHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHHHHHHHHHHTTT
T ss_pred             CCHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             98898874899999999999999999999999878886728999989999999999999986667



>1vq8_V (V:) 50S ribosomal protein L29P; 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_Z (Z:) Ribosomal protein L29; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Arabidopsis thaliana} Back     alignment and structure
>2zjr_V (V:) 50S ribosomal protein L29; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} Back     alignment and structure
>2go5_5 (5:) Ribosomal protein L35; SR, SRP, ribosome, translation/RNA complex; 7.40A {Triticum SP} PDB: 2j37_5 Back     alignment and structure
>2zkr_v (v:) 60S ribosomal protein L35; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Back     alignment and structure
>3i1n_Y (Y:) 50S ribosomal protein L29; ribosome structure, protein-RNA complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA- binding, methylation; 3.19A {Escherichia coli k-12} PDB: 1p85_W 1p86_W 1vs8_X 2aw4_X 2awb_X 1vs6_X 2i2v_Y 2j28_X 2i2t_Y* 2qao_X* 2qba_X* 2qbc_X* 2qbe_X 2qbg_X 2qbi_X* 2qbk_X* 2qov_X 2qox_X 2qoz_X* 2qp1_X* ... Back     alignment and structure
>3jyw_X (X:) 60S ribosomal protein L35; eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus} Back     alignment and structure
>2wwb_N (N:) 60S ribosomal protein L35; ribosome, protein EXIT tunnel, cotranslational protein translocation, protein conducting channel; 6.48A {Triticum aestivum} PDB: 1s1i_X 2wwa_N 2ww9_N Back     alignment and structure
>2j01_2 (2:) 50S ribosomal protein L29; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} Back     alignment and structure