254780481

254780481

50S ribosomal protein L34

GeneID in NCBI database:8209470Locus tag:CLIBASIA_01830
Protein GI in NCBI database:254780481Protein Accession:YP_003064894.1
Gene range:+(403128, 403262)Protein Length:44aa
Gene description:50S ribosomal protein L34
COG prediction:[J] Ribosomal protein L34
KEGG prediction:rpmH; 50S ribosomal protein L34; K02914 large subunit ribosomal protein L34
SEED prediction:hypothetical protein
Pathway involved in KEGG:Ribosome [PATH:las03010]
Subsystem involved in SEED:- none -
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----
MKRTYNPSNIVRKRRCGFLARMSTRSGIRILNRRRSKGRKRLSA
cccccccccccHHHHHHHHHHHHcHHHHHHHHHHHHHcHHHHcc
ccccccccHHHEHHcccHHHHcccccHHHHHcccccccccEccc
mkrtynpsnivrkRRCGFLARMSTRSGIRILNRrrskgrkrlsa
mkrtynpsnivrkrrcgflarmstrsgirilnrrrskgrkrlsa
MKRTYNPSNIVRKRRCGFLARMSTRSGIRILNRRRSKGRKRLSA
*KRTY**SNIVRKRRCGFLARMSTRSGIRILNRRRSKGRKRLS*
MKRTYNPSNIVRKRRCGFLARMSTRSGIRILNRR**********
***TYNPSNIVRKRRCGFLARMS*********************
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oohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiii
iiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
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MKRTYNPSNIVRKRRCGFLARMSTRSGIRILNRRRSKGRKRLSA
MKRTYNPSNIVRKRRCGFLARMSTRSGIRILNRRRSKGRKRLSA
MKRTYNPSNIVRKRRCGFLARMSTRSGIRILNRRRSKGRKRLSA

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
Target44 50S ribosomal protein L34 [Candidatus Liberibacter asia
31512206344 50S ribosomal protein L34 [Candidatus Liberibacter sola 1 2e-12
8468536544 ribosomal protein L34 [Maritimibacter alkaliphilus HTCC 1 1e-08
5667718949 ribosomal protein L34 [Ruegeria pomeroyi DSS-3] Length 1 1e-08
8613581444 ribosomal protein L34 [Roseobacter sp. MED193] Length = 1 2e-08
12673706244 50S ribosomal protein L34 [Roseobacter sp. SK209-2-6] L 1 2e-08
8385492744 ribosomal protein L34 [Sulfitobacter sp. NAS-14.1] Leng 1 2e-08
25941613849 ribosomal protein L34 [Silicibacter sp. TrichCH4B] Leng 1 3e-08
12672491744 50S ribosomal protein L34 [Rhodobacterales bacterium HT 1 3e-08
8395004244 ribosomal protein L34 [Roseovarius nubinhibens ISM] Len 1 3e-08
32854524844 50S ribosomal protein L34 [polymorphum gilvum SL003B-26 1 3e-08
>gi|315122063|ref|YP_004062552.1| 50S ribosomal protein L34 [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 44 Back     alignment and organism information
 Score = 75.9 bits (185), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 38/43 (88%), Positives = 41/43 (95%)

Query: 1  MKRTYNPSNIVRKRRCGFLARMSTRSGIRILNRRRSKGRKRLS 43
          MKRTYNPSNIVRKRRCGFL RMSTRSGI+++ RRRSKGRKRLS
Sbjct: 1  MKRTYNPSNIVRKRRCGFLVRMSTRSGIKLMARRRSKGRKRLS 43


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|84685365|ref|ZP_01013263.1| ribosomal protein L34 [Maritimibacter alkaliphilus HTCC2654] Length = 44 Back     alignment and organism information
>gi|56677189|gb|AAV93855.1| ribosomal protein L34 [Ruegeria pomeroyi DSS-3] Length = 49 Back     alignment and organism information
>gi|86135814|ref|ZP_01054393.1| ribosomal protein L34 [Roseobacter sp. MED193] Length = 44 Back     alignment and organism information
>gi|126737062|ref|ZP_01752797.1| 50S ribosomal protein L34 [Roseobacter sp. SK209-2-6] Length = 44 Back     alignment and organism information
>gi|83854927|ref|ZP_00948457.1| ribosomal protein L34 [Sulfitobacter sp. NAS-14.1] Length = 44 Back     alignment and organism information
>gi|259416138|ref|ZP_05740058.1| ribosomal protein L34 [Silicibacter sp. TrichCH4B] Length = 49 Back     alignment and organism information
>gi|126724917|ref|ZP_01740760.1| 50S ribosomal protein L34 [Rhodobacterales bacterium HTCC2150] Length = 44 Back     alignment and organism information
>gi|83950042|ref|ZP_00958775.1| ribosomal protein L34 [Roseovarius nubinhibens ISM] Length = 44 Back     alignment and organism information
>gi|328545248|ref|YP_004305357.1| 50S ribosomal protein L34 [polymorphum gilvum SL003B-26A1] Length = 44 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
Target44 50S ribosomal protein L34 [Candidatus Liberibacter asia
PRK0039944 PRK00399, rpmH, 50S ribosomal protein L34; Reviewed 3e-06
KOG4612105 KOG4612, KOG4612, KOG4612, Mitochondrial ribosomal prot 0.001
pfam0046844 pfam00468, Ribosomal_L34, Ribosomal protein L34 1e-05
>gnl|CDD|179004 PRK00399, rpmH, 50S ribosomal protein L34; Reviewed Back     alignment and domain information
>gnl|CDD|39812 KOG4612, KOG4612, KOG4612, Mitochondrial ribosomal protein L34 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|144166 pfam00468, Ribosomal_L34, Ribosomal protein L34 Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 44 50S ribosomal protein L34 [Candidatus Liberibacter asia
PRK0039944 rpmH 50S ribosomal protein L34; Reviewed 99.91
COG023044 RpmH Ribosomal protein L34 [Translation, ribosomal stru 99.9
pfam0046844 Ribosomal_L34 Ribosomal protein L34. 99.89
TIGR0103044 rpmH_bact ribosomal protein L34; InterPro: IPR000271 Ri 99.82
KOG4612105 consensus 99.72
CHL0011546 rpl34 ribosomal protein L34; Reviewed 99.52
>PRK00399 rpmH 50S ribosomal protein L34; Reviewed Back     alignment and domain information
>COG0230 RpmH Ribosomal protein L34 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>pfam00468 Ribosomal_L34 Ribosomal protein L34 Back     alignment and domain information
>TIGR01030 rpmH_bact ribosomal protein L34; InterPro: IPR000271 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>KOG4612 consensus Back     alignment and domain information
>CHL00115 rpl34 ribosomal protein L34; Reviewed 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
Target44 50S ribosomal protein L34 [Candidatus Liberibacter asia
3mrz_448 Recognition Of The Amber Stop Codon By Release Fact 4e-05
2j01_749 Structure Of The Thermus Thermophilus 70s Ribosome 4e-05
1pnu_246 Crystal Structure Of A Streptomycin Dependent Ribos 5e-05
1nkw_247 Crystal Structure Of The Large Ribosomal Subunit Fr 5e-05
3bbo_4152 Homology Model For The Spinach Chloroplast 50s Subu 0.001
2ftc_Q38 Structural Model For The Large Subunit Of The Mamma 0.001
>gi|300508658|pdb|3MRZ|4 Chain 4, Recognition Of The Amber Stop Codon By Release Factor Rf1. This Entry 3mrz Contains 50s Ribosomal Subunit. The 30s Ribosomal Subunit Can Be Found In Pdb Entry 3ms0. Molecule A In The Same Asymmetric Unit Is Deposited As 3mr8 (50s) And 3ms1 (30s). Length = 48 Back     alignment and structure
 Score = 51.4 bits (123), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 22/43 (51%), Positives = 28/43 (65%)

Query: 1  MKRTYNPSNIVRKRRCGFLARMSTRSGIRILNRRRSKGRKRLS 43
          MKRT+ P+   R +  GF ARM T  G ++L RRR KGR RL+
Sbjct: 1  MKRTWQPNRRKRAKTHGFRARMRTPGGRKVLKRRRQKGRWRLT 43


gi|116668229|pdb|2J01|7 Chain 7, 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 = 49 Back     alignment and structure
>gi|34811581|pdb|1PNU|2 Chain 2, 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 = 46 Back     alignment and structure
gi|28948946|pdb|1NKW|2 Chain 2, Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans Length = 47 Back     alignment and structure
gi|189096152|pdb|3BBO|4 Chain 4, Homology Model For The Spinach Chloroplast 50s Subunit Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome Length = 152 Back     alignment and structure
>gi|99032323|pdb|2FTC|Q Chain Q, Structural Model For The Large Subunit Of The Mammalian Mitochondrial Ribosome Length = 38 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target44 50S ribosomal protein L34 [Candidatus Liberibacter asia
3ofq_246 50S ribosomal protein L34; protein biosynthesis, riboso 2e-05
3i1n_246 50S ribosomal protein L34; ribosome structure, protein- 7e-05
2j01_749 50S ribosomal protein L34; ribosome, tRNA, paromomycin, 7e-05
>3ofq_2 50S ribosomal protein L34; protein biosynthesis, ribosomes, RNA, tRNA, transfer, antibi EXIT, peptidyl, ribosomal subunit, large; 3.10A {Escherichia coli} PDB: 1vs8_2 1vs6_2 2aw4_2 2awb_2 1vt2_2 2i2v_2 2j28_2 2i2t_2* 2qao_2* 2qba_2* 2qbc_2* 2qbe_2 2qbg_2 2qbi_2* 2qbk_2* 2qov_2 2qox_2 2qoz_2* 2qp1_2* 2rdo_2 ... Length = 46 Back     alignment and structure
 Score = 42.7 bits (101), Expect = 2e-05
 Identities = 24/43 (55%), Positives = 33/43 (76%)

Query: 1  MKRTYNPSNIVRKRRCGFLARMSTRSGIRILNRRRSKGRKRLS 43
          MKRT+ PS + R R  GF ARM+T++G ++L RRR+KGR RL+
Sbjct: 1  MKRTFQPSVLKRNRSHGFRARMATKNGRQVLARRRAKGRARLT 43


>3i1n_2 50S ribosomal protein L34; ribosome structure, protein-RNA complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA- binding, methylation; 3.19A {Escherichia coli k-12} PDB: 1vs8_2 2aw4_2 2awb_2 1vs6_2 2i2v_2 2j28_2 2i2t_2* 2qao_2* 2qba_2* 2qbc_2* 2qbe_2 2qbg_2 2qbi_2* 2qbk_2* 2qov_2 2qox_2 2qoz_2* 2qp1_2* 2rdo_2 2vhm_2 ... Length = 46 Back     alignment and structure
>2j01_7 50S ribosomal protein L34; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} SCOP: j.118.1.1 PDB: 1vsp_Z 2hgj_6 2hgq_6 2hgu_6 1vsa_Z 2j03_7 2jl6_7 2jl8_7 2v47_7 2v49_7 2wdi_7 2wdj_7 2wdl_7 2wdn_7 2wh2_7 2wh4_7 3d5b_7 3d5d_7 3f1f_7 3f1h_7 ... Length = 49 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target44 50S ribosomal protein L34 [Candidatus Liberibacter asia
2j01_749 50S ribosomal protein L34; ribosome, tRNA, paromomycin, 99.91
3ofq_246 50S ribosomal protein L34; protein biosynthesis, riboso 99.9
2ftc_Q38 L34MT, MRP-L34, 39S ribosomal protein L34, mitochondria 99.78
3bbo_4152 Ribosomal protein L34; large ribosomal subunit, spinach 99.27
>2j01_7 50S ribosomal protein L34; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} SCOP: j.118.1.1 PDB: 1vsp_Z 2hgj_6 2hgq_6 2hgu_6 1vsa_Z 2j03_7 2jl6_7 2jl8_7 2v47_7 2v49_7 2wdi_7 2wdj_7 2wdl_7 2wdn_7 2wh2_7 2wh4_7 2wrj_7 2wrl_7 2wro_7 2wrr_7 ... Back     alignment and structure
Probab=99.91  E-value=1.1e-25  Score=137.46  Aligned_cols=44  Identities=50%  Similarity=0.795  Sum_probs=43.4

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCC
Q ss_conf             98876787841012332355415977799999999700265229
Q gi|254780481|r    1 MKRTYNPSNIVRKRRCGFLARMSTRSGIRILNRRRSKGRKRLSA   44 (44)
Q Consensus         1 mKrTyQPs~~kRkr~HGF~~Rm~T~~GRkvL~rRr~KGR~~Lsa   44 (44)
                      ||||||||+++|+++|||++||+|++||+||++|++|||+.|||
T Consensus         1 MKrTyqPs~~kRkr~HGFr~Rm~T~~GRkvl~rRR~KGR~~Ls~   44 (49)
T 2j01_7            1 MKRTWQPNRRKRAKTHGFRARMRTPGGRKVLKRRRQKGRWRLTP   44 (49)
T ss_dssp             CCCSCCCCHHHHHHHHSHHHHHHSHHHHHHHHHHHHHTCSCSSC
T ss_pred             CCCCCCCCCCEECHHHCHHHHCCCCCCHHHHHHHHHCCCCEEEE
T ss_conf             98776886320100004687706720099999999829958631



>3ofq_2 50S ribosomal protein L34; protein biosynthesis, ribosomes, RNA, tRNA, transfer, antibi EXIT, peptidyl, ribosomal subunit, large; 3.10A {Escherichia coli} PDB: 1vs8_2 1vs6_2 2aw4_2 2awb_2 1vt2_2 2i2v_2 2j28_2 2i2t_2* 2qao_2* 2qba_2* 2qbc_2* 2qbe_2 2qbg_2 2qbi_2* 2qbk_2* 2qov_2 2qox_2 2qoz_2* 2qp1_2* 2rdo_2 ... Back     alignment and structure
>2ftc_Q L34MT, MRP-L34, 39S ribosomal protein L34, mitochondrial; mitochondrial ribosome, large ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus} Back     alignment and structure
>3bbo_4 Ribosomal protein L34; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} 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

No hit with e-value below 0.005

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

No hit with probability above 90.00

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 44 50S ribosomal protein L34 [Candidatus Liberibacter
3i1n_2_46 (2:) 50S ribosomal protein L34; ribosome structure 3e-05
2j01_7_49 (7:) 50S ribosomal protein L34; ribosome, tRNA, pa 4e-05
3bbo_4_152 (4:) Ribosomal protein L34; large ribosomal subuni 0.002
>3i1n_2 (2:) 50S ribosomal protein L34; ribosome structure, protein-RNA complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA- binding, methylation; 3.19A {Escherichia coli k-12} PDB: 1vs8_2 2aw4_2 2awb_2 1vs6_2 2i2v_2 2j28_2 2i2t_2* 2qao_2* 2qba_2* 2qbc_2* 2qbe_2 2qbg_2 2qbi_2* 2qbk_2* 2qov_2 2qox_2 2qoz_2* 2qp1_2* 2rdo_2 2vhm_2 ...Length = 46 Back     alignment and structure
 Score = 42.3 bits (100), Expect = 3e-05
 Identities = 24/44 (54%), Positives = 33/44 (75%)

Query: 1  MKRTYNPSNIVRKRRCGFLARMSTRSGIRILNRRRSKGRKRLSA 44
          MKRT+ PS + R R  GF ARM+T++G ++L RRR+KGR RL+ 
Sbjct: 1  MKRTFQPSVLKRNRSHGFRARMATKNGRQVLARRRAKGRARLTV 44


>2j01_7 (7:) 50S ribosomal protein L34; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus}Length = 49 Back     alignment and structure
>3bbo_4 (4:) Ribosomal protein L34; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}Length = 152 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target44 50S ribosomal protein L34 [Candidatus Liberibacter asia
3i1n_2_46 50S ribosomal protein L34; ribosome structure, pro 99.92
2j01_7_49 50S ribosomal protein L34; ribosome, tRNA, paromom 99.91
3bbo_4_152 Ribosomal protein L34; large ribosomal subunit, sp 99.85
2ftc_Q_38 L34MT, MRP-L34, 39S ribosomal protein L34, mitocho 99.76
>3i1n_2 (2:) 50S ribosomal protein L34; ribosome structure, protein-RNA complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA- binding, methylation; 3.19A {Escherichia coli k-12} PDB: 1vs8_2 2aw4_2 2awb_2 1vs6_2 2i2v_2 2j28_2 2i2t_2* 2qao_2* 2qba_2* 2qbc_2* 2qbe_2 2qbg_2 2qbi_2* 2qbk_2* 2qov_2 2qox_2 2qoz_2* 2qp1_2* 2rdo_2 2vhm_2 ... Back     alignment and structure
Probab=99.92  E-value=3.7e-26  Score=140.38  Aligned_cols=44  Identities=55%  Similarity=0.909  Sum_probs=43.5

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCC
Q ss_conf             98876787841012332355415977799999999700265229
Q gi|254780481|r    1 MKRTYNPSNIVRKRRCGFLARMSTRSGIRILNRRRSKGRKRLSA   44 (44)
Q Consensus         1 mKrTyQPs~~kRkr~HGF~~Rm~T~~GRkvL~rRr~KGR~~Lsa   44 (44)
                      ||||||||+++|+++|||++||+|++||+||++|++|||+.|||
T Consensus         1 MkrTyQPs~~kRkr~HGF~~Rm~T~~GRkVl~rRr~KGR~~Ls~   44 (46)
T 3i1n_2            1 MKRTFQPSVLKRNRSHGFRARMATKNGRQVLARRRAKGRARLTV   44 (46)
T ss_dssp             CCCSCCCCHHHHHHHSSHHHHTTSHHHHHHHHHHHHHTCSCSSC
T ss_pred             CCCCCCCCCCEECCCCCHHHHCCCHHHHHHHHHHHHCCCCEEEE
T ss_conf             98776885211321004788706730199999999849806562



>2j01_7 (7:) 50S ribosomal protein L34; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} Back     alignment and structure
>3bbo_4 (4:) Ribosomal protein L34; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Back     alignment and structure
>2ftc_Q (Q:) L34MT, MRP-L34, 39S ribosomal protein L34, mitochondrial; mitochondrial ribosome, large ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus} Back     alignment and structure