254780319

254780319

50S ribosomal protein L35

GeneID in NCBI database:8209304Locus tag:CLIBASIA_01020
Protein GI in NCBI database:254780319Protein Accession:YP_003064732.1
Gene range:-(211174, 211377)Protein Length:67aa
Gene description:50S ribosomal protein L35
COG prediction:[J] Ribosomal protein L35
KEGG prediction:rpmI; 50S ribosomal protein L35; K02916 large subunit ribosomal protein L35
SEED prediction:LSU ribosomal protein L35p
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
PHOBIUS1 TM-Helix
SignalP_HMMyes
SignalP_NNyes
COILScoiled coil
70% MSAconservation map
90% MSAconservation map
  
--------10--------20--------30--------40--------50--------60-------
MPKMKTNSSSKKRFSITATGKVRAQAAGKRHGMIKRSNKFIRNARGTMVLASADAKKVIRNYLPNGI
cccccccccccEEEEEcccccEEccccccccccccccHHHHHHHccccEEcHHHHHHHHHHHccccc
ccccccccHHHHEEEEEcccHEEEHHccccccccHcccHHHHHccccEEEccccHHHHHHHcccccc
mpkmktnssskkrfsiTATGKVRAQAagkrhgmikRSNKFIRNARGTMVLASADAKKVIRNYLPNGI
mpkmktnssskkrfsitatgkvraqaagkrhgmikrsnkfirnargtmvlasadakkvirnylpngi
MPKMKTNSSSKKRFSITATGKVRAQAAGKRHGMIKRSNKFIRNARGTMVLASADAKKVIRNYLPNGI
MPKMKTNSSSKKRFSITATGKVRAQAAGKR*G****************VLASADAKKVIRNYLPNGI
*******************************GMIKRSNKFIRNARGTMVLASADAKKVIRNYLPNGI
*****TNSSSKKRFSITATGKVRAQAAGKRHGMIKRSNKFIRNARGTMVLASADAKKVIRNYLPNGI
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iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooo
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
SSSSSSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooo
SSSSSSSSSSSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooo
SSSSSSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooo
MPKMKTNSSSKKRFSITATGKVRAQAAGKRHGMIKRSNKFIRNARGTMVLASADAKKVIRNYLPNGI
MPKMKTNSSSKKRFSITATGKVRAQAAGKRHGMIKRSNKFIRNARGTMVLASADAKKVIRNYLPNGI
MPKMKTNSSSKKRFSITATGKVRAQAAGKRHGMIKRSNKFIRNARGTMVLASADAKKVIRNYLPNGI

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 50S ribosomal protein L35 [Candidatus Liberibacter asia
31512225767 50S ribosomal protein L35 [Candidatus Liberibacter sola 1 3e-27
1596403667 50S ribosomal protein L35 [Sinorhizobium meliloti 1021] 1 8e-25
22214717167 50S ribosomal protein L35 [Agrobacterium vitis S4] Leng 1 1e-24
22782412667 50S ribosomal protein L35 [Sinorhizobium fredii NGR234] 1 2e-24
11625003567 50S ribosomal protein L35 [Rhizobium leguminosarum bv. 1 3e-24
1588760567 50S ribosomal protein L35 [Agrobacterium tumefaciens st 1 6e-24
19088992767 50S ribosomal protein L35 [Rhizobium etli CIAT 652] Len 1 7e-24
24120721467 50S ribosomal protein L35 [Rhizobium leguminosarum bv. 1 9e-24
31989827467 50S ribosomal protein L35 [Bartonella clarridgeiae 73] 1 1e-23
31940499367 50S ribosomal protein L35 [Bartonella sp. AR 15-3] Leng 1 1e-23
>gi|315122257|ref|YP_004062746.1| 50S ribosomal protein L35 [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 67 Back     alignment and organism information
 Score =  125 bits (313), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 60/67 (89%), Positives = 65/67 (97%)

Query: 1  MPKMKTNSSSKKRFSITATGKVRAQAAGKRHGMIKRSNKFIRNARGTMVLASADAKKVIR 60
          MPKMKTNSSSKKRFSITA+GKV+AQAAGKRHGMIKRSNKFIRNARG MVL +ADAKK+IR
Sbjct: 1  MPKMKTNSSSKKRFSITASGKVKAQAAGKRHGMIKRSNKFIRNARGAMVLGAADAKKIIR 60

Query: 61 NYLPNGI 67
          NYLPNG+
Sbjct: 61 NYLPNGL 67


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|15964036|ref|NP_384389.1| 50S ribosomal protein L35 [Sinorhizobium meliloti 1021] Length = 67 Back     alignment and organism information
>gi|222147171|ref|YP_002548128.1| 50S ribosomal protein L35 [Agrobacterium vitis S4] Length = 67 Back     alignment and organism information
>gi|227824126|ref|YP_002828099.1| 50S ribosomal protein L35 [Sinorhizobium fredii NGR234] Length = 67 Back     alignment and organism information
>gi|116250035|ref|YP_765873.1| 50S ribosomal protein L35 [Rhizobium leguminosarum bv. viciae 3841] Length = 67 Back     alignment and organism information
>gi|15887605|ref|NP_353286.1| 50S ribosomal protein L35 [Agrobacterium tumefaciens str. C58] Length = 67 Back     alignment and organism information
>gi|190889927|ref|YP_001976469.1| 50S ribosomal protein L35 [Rhizobium etli CIAT 652] Length = 67 Back     alignment and organism information
>gi|241207214|ref|YP_002978310.1| 50S ribosomal protein L35 [Rhizobium leguminosarum bv. trifolii WSM1325] Length = 67 Back     alignment and organism information
>gi|319898274|ref|YP_004158367.1| 50S ribosomal protein L35 [Bartonella clarridgeiae 73] Length = 67 Back     alignment and organism information
>gi|319404993|emb|CBI78602.1| 50S ribosomal protein L35 [Bartonella sp. AR 15-3] Length = 67 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 50S ribosomal protein L35 [Candidatus Liberibacter asia
PRK0017265 PRK00172, rpmI, 50S ribosomal protein L35; Reviewed 3e-14
TIGR0000163 TIGR00001, rpmI_bact, ribosomal protein L35 5e-09
pfam0163261 pfam01632, Ribosomal_L35p, Ribosomal protein L35 4e-06
CHL0010365 CHL00103, rpl35, ribosomal protein L35 6e-04
COG029165 COG0291, RpmI, Ribosomal protein L35 [Translation, ribo 3e-10
>gnl|CDD|178913 PRK00172, rpmI, 50S ribosomal protein L35; Reviewed Back     alignment and domain information
>gnl|CDD|129113 TIGR00001, rpmI_bact, ribosomal protein L35 Back     alignment and domain information
>gnl|CDD|145004 pfam01632, Ribosomal_L35p, Ribosomal protein L35 Back     alignment and domain information
>gnl|CDD|177032 CHL00103, rpl35, ribosomal protein L35 Back     alignment and domain information
>gnl|CDD|30639 COG0291, RpmI, Ribosomal protein L35 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 67 50S ribosomal protein L35 [Candidatus Liberibacter asia
TIGR0000164 rpmI_bact ribosomal protein L35; InterPro: IPR001706 Ri 99.96
PRK0017265 rpmI 50S ribosomal protein L35; Reviewed 99.95
CHL0010365 rpl35 ribosomal protein L35 99.95
COG029165 RpmI Ribosomal protein L35 [Translation, ribosomal stru 99.93
pfam0163261 Ribosomal_L35p Ribosomal protein L35. 99.89
pfam10196101 consensus 96.98
KOG4316172 consensus 95.12
>TIGR00001 rpmI_bact ribosomal protein L35; InterPro: IPR001706 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>PRK00172 rpmI 50S ribosomal protein L35; Reviewed Back     alignment and domain information
>CHL00103 rpl35 ribosomal protein L35 Back     alignment and domain information
>COG0291 RpmI Ribosomal protein L35 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>pfam01632 Ribosomal_L35p Ribosomal protein L35 Back     alignment and domain information
>pfam10196 consensus Back     alignment and domain information
>KOG4316 consensus Back     alignment and domain information

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

Homologous Structures Detected by PSI-BLAST against Nonredundant Database

IdentityAlignment graphLength Definition E-value
Target67 50S ribosomal protein L35 [Candidatus Liberibacter asia
3bbo_5159 Homology Model For The Spinach Chloroplast 50s Subu 3e-10
1vs6_365 Crystal Structure Of The Bacterial Ribosome From Es 8e-09
2j01_865 Structure Of The Thermus Thermophilus 70s Ribosome 2e-08
2aw4_364 Crystal Structure Of The Bacterial Ribosome From Es 4e-08
3fin_864 T. Thermophilus 70s Ribosome In Complex With Mrna, 1e-07
3pyo_563 Crystal Structure Of A Complex Containing Domain 3 2e-07
1nkw_364 Crystal Structure Of The Large Ribosomal Subunit Fr 2e-05
1sm1_366 Complex Of The Large Ribosomal Subunit From Deinoco 4e-05
1pnu_363 Crystal Structure Of A Streptomycin Dependent Ribos 1e-04
1nwx_365 Complex Of The Large Ribosomal Subunit From Deinoco 2e-04
gi|189096153|pdb|3BBO|5 Chain 5, Homology Model For The Spinach Chloroplast 50s Subunit Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome Length = 159 Back     alignment and structure
 Score = 68.4 bits (167), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 22/63 (34%), Positives = 34/63 (53%), Gaps = 1/63 (1%)

Query: 3   KMKTNSSSKKRFSITATGKVRAQAAGKRHGMIKRSNKFIRNARGTMVLASADAKKVIRNY 62
           KMKT+ +S KRF +T  GK+  + AGK+H + K++ K        + +  +D   VI   
Sbjct: 91  KMKTHKASAKRFRVTGKGKIVRRRAGKQHLLAKKNTKRKNRLSKLIQVDRSDYDNVIGA- 149

Query: 63  LPN 65
           LP 
Sbjct: 150 LPY 152


gi|116666598|pdb|1VS6|3 Chain 3, Crystal Structure Of The Bacterial Ribosome From Escherichia Coli In Complex With The Antibiotic Kasugamyin At 3.5a Resolution. This File Contains The 50s Subunit Of One 70s Ribosome. The Entire Crystal Structure Contains Two 70s Ribosomes And Is Described In Remark 400. Length = 65 Back     alignment and structure
gi|116668230|pdb|2J01|8 Chain 8, 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 = 65 Back     alignment and structure
>gi|83754089|pdb|2AW4|3 Chain 3, Crystal Structure Of The Bacterial Ribosome From Escherichia Coli At 3.5 A Resolution. This File Contains The 50s Subunit Of One 70s Ribosome. The Entire Crystal Structure Contains Two 70s Ribosomes And Is Described In Remark 400. Length = 64 Back     alignment and structure
>gi|224510777|pdb|3FIN|8 Chain 8, 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 = 64 Back     alignment and structure
>gi|322812602|pdb|3PYO|5 Chain 5, 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 = 63 Back     alignment and structure
>gi|28948947|pdb|1NKW|3 Chain 3, Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans Length = 64 Back     alignment and structure
gi|51247400|pdb|1SM1|3 Chain 3, Complex Of The Large Ribosomal Subunit From Deinococcus Radiodurans With Quinupristin And Dalfopristin Length = 66 Back     alignment and structure
>gi|34811582|pdb|1PNU|3 Chain 3, 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 = 63 Back     alignment and structure
>gi|29726815|pdb|1NWX|3 Chain 3, Complex Of The Large Ribosomal Subunit From Deinococcus Radiodurans With Abt-773 Length = 65 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target67 50S ribosomal protein L35 [Candidatus Liberibacter asia
2zjr_366 50S ribosomal protein L35; ribosome, large ribosomal su 7e-13
2j01_865 50S ribosomal protein L35; ribosome, tRNA, paromomycin, 3e-12
3i1n_365 50S ribosomal protein L35; ribosome structure, protein- 2e-11
3ofq_364 50S ribosomal protein L35; protein biosynthesis, riboso 3e-11
3bbo_5159 Ribosomal protein L35; large ribosomal subunit, spinach 2e-10
>2zjr_3 50S ribosomal protein L35; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: d.301.1.1 PDB: 2zjp_3* 1sm1_3 2zjq_3 3cf5_3* 3dll_3* 1nwy_3* 1nwx_3* 1xbp_3* 1nkw_3 1yl3_8 2b66_8 2b9n_8 2b9p_8 1pnu_3 1pny_3 1vor_5 1vou_5 1vow_5 1voy_5 1vp0_5 Length = 66 Back     alignment and structure
 Score = 67.3 bits (165), Expect = 7e-13
 Identities = 29/66 (43%), Positives = 37/66 (56%), Gaps = 1/66 (1%)

Query: 1  MPKMKTNSSSKKRFSITATGKVRAQAAGKRHGMIKRSNKFIRNARGTMVLASADAKKVIR 60
          MPKMKT+  +K+R  IT TGKV A  +GKRH    +S   IR      VLA A+  ++  
Sbjct: 1  MPKMKTHKMAKRRIKITGTGKVMAFKSGKRHQNTGKSGDEIRGKGKGFVLAKAEWARMKL 60

Query: 61 NYLPNG 66
            LP G
Sbjct: 61 -MLPRG 65


>2j01_8 50S ribosomal protein L35; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} SCOP: d.301.1.1 PDB: 1vsp_a 2hgj_7 2hgq_7 2hgu_7 1vsa_a 2j03_8 2jl6_8 2jl8_8 2v47_8 2v49_8 2wdi_8 2wdj_8 2wdl_8 2wdn_8 2wh2_8 2wh4_8 3d5b_8 3d5d_8 3f1f_8 3f1h_8 ... Length = 65 Back     alignment and structure
>3i1n_3 50S ribosomal protein L35; ribosome structure, protein-RNA complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA- binding, methylation; 3.19A {Escherichia coli k-12} PDB: 1vs8_3 1vs6_3 3i1p_3 3i1r_3 3i1t_3 3i20_3 3i22_3 2qam_3* 2awb_3 2aw4_3 2i2v_3 2j28_3 2i2t_3* 2qao_3* 2qba_3* 2qbc_3* 2qbe_3 2qbg_3 2qbi_3* 2qbk_3* ... Length = 65 Back     alignment and structure
>3ofq_3 50S ribosomal protein L35; protein biosynthesis, ribosomes, RNA, tRNA, transfer, antibi EXIT, peptidyl, ribosomal subunit, large; 3.10A {Escherichia coli} PDB: 2awb_3 2aw4_3 2i2v_3 2j28_3 2i2t_3* 2qao_3* 2qba_3* 2qbc_3* 2qbe_3 2qbg_3 2qbi_3* 2qbk_3* 2qov_3 2qox_3 2qoz_3* 2qp1_3* 2rdo_3 2vhm_3 2vhn_3 2wwq_7* ... Length = 64 Back     alignment and structure
>3bbo_5 Ribosomal protein L35; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Length = 159 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target67 50S ribosomal protein L35 [Candidatus Liberibacter asia
2zjr_366 50S ribosomal protein L35; ribosome, large ribosomal su 99.95
2j01_865 50S ribosomal protein L35; ribosome, tRNA, paromomycin, 99.94
3ofq_364 50S ribosomal protein L35; protein biosynthesis, riboso 99.93
3bbo_5159 Ribosomal protein L35; large ribosomal subunit, spinach 99.89
>2zjr_3 50S ribosomal protein L35; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: d.301.1.1 PDB: 2zjp_3* 1sm1_3 2zjq_3 3cf5_3* 3dll_3* 1nwy_3* 1nwx_3* 1xbp_3* 1nkw_3 1yl3_8 2b66_8 2b9n_8 2b9p_8 1pnu_3 1pny_3 1vor_5 1vou_5 1vow_5 1voy_5 1vp0_5 Back     alignment and structure
Probab=99.95  E-value=3.1e-29  Score=162.02  Aligned_cols=65  Identities=45%  Similarity=0.581  Sum_probs=63.6

Q ss_pred             CCCCCCCCHHHEEEEECCCCEEEECCCCCCCCCCCCCCHHHHHCCCCEEECHHHHHHHHHHHCCCC
Q ss_conf             987323301212257759980970324885254158804654146986837778999999858688
Q gi|254780319|r    1 MPKMKTNSSSKKRFSITATGKVRAQAAGKRHGMIKRSNKFIRNARGTMVLASADAKKVIRNYLPNG   66 (67)
Q Consensus         1 MPKmKT~k~akKRFk~T~sGKvkr~~agk~H~l~~Ks~krkR~lr~~~~v~~~~~~~i~r~llPYg   66 (67)
                      |||||||+||+|||++||||+|++++||++|+++++|++++|+|+++.+|+++|.++|.+ |||||
T Consensus         1 MPKmKT~k~akKRfkvT~sGKv~r~~a~k~H~l~~Ks~k~kR~lr~~~~v~~~~~k~ik~-lLPyg   65 (66)
T 2zjr_3            1 MPKMKTHKMAKRRIKITGTGKVMAFKSGKRHQNTGKSGDEIRGKGKGFVLAKAEWARMKL-MLPRG   65 (66)
T ss_pred             CCCCCCCHHHHHEEEECCCCCEEECCCCCCCCCCCCCHHHHHHCCCCEEECHHHHHHHHH-HCCCC
T ss_conf             997543122352057768987865537776665558888998657985478999999999-67899



>2j01_8 50S ribosomal protein L35; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} SCOP: d.301.1.1 PDB: 1vsp_a 2hgj_7 2hgq_7 2hgu_7 1vsa_a 2j03_8 2jl6_8 2jl8_8 2v47_8 2v49_8 2wdi_8 2wdj_8 2wdl_8 2wdn_8 2wh2_8 2wh4_8 2wrj_8 2wrl_8 2wro_8 2wrr_8 ... Back     alignment and structure
>3ofq_3 50S ribosomal protein L35; protein biosynthesis, ribosomes, RNA, tRNA, transfer, antibi EXIT, peptidyl, ribosomal subunit, large; 3.10A {Escherichia coli} PDB: 2awb_3 2aw4_3 2i2v_3 2j28_3 2i2t_3* 2qao_3* 2qba_3* 2qbc_3* 2qbe_3 2qbg_3 2qbi_3* 2qbk_3* 2qov_3 2qox_3 2qoz_3* 2qp1_3* 2rdo_3 2vhm_3 2vhn_3 2wwq_7* ... Back     alignment and structure
>3bbo_5 Ribosomal protein L35; 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

IdentityAlignment graphLength Definition E-value
Target 67 50S ribosomal protein L35 [Candidatus Liberibacter asia
d2j018164 d.301.1.1 (8:2-65) Ribosomal protein L35p {Thermus ther 6e-12
d2qam3164 d.301.1.1 (3:1-64) Ribosomal protein L35p {Escherichia 4e-11
>d2j0181 d.301.1.1 (8:2-65) Ribosomal protein L35p {Thermus thermophilus [TaxId: 274]} Length = 64 Back     information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: L35p-like
superfamily: L35p-like
family: Ribosomal protein L35p
domain: Ribosomal protein L35p
species: Thermus thermophilus [TaxId: 274]
 Score = 63.1 bits (154), Expect = 6e-12
 Identities = 27/59 (45%), Positives = 36/59 (61%)

Query: 2  PKMKTNSSSKKRFSITATGKVRAQAAGKRHGMIKRSNKFIRNARGTMVLASADAKKVIR 60
          PKMKT+  +KKR  ITA+GKV A   GKRH   ++S K IR      VLA  +A+++  
Sbjct: 1  PKMKTHKGAKKRVKITASGKVVAMKTGKRHLNWQKSGKEIRQKGRKFVLAKPEAERIKL 59


>d2qam31 d.301.1.1 (3:1-64) Ribosomal protein L35p {Escherichia coli [TaxId: 562]} Length = 64 Back     information, alignment and structure

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

IdentityAlignment graphLength Definition Probability
Target67 50S ribosomal protein L35 [Candidatus Liberibacter asia
d2qam3164 Ribosomal protein L35p {Escherichia coli [TaxId: 562]} 99.93
d2j018164 Ribosomal protein L35p {Thermus thermophilus [TaxId: 27 99.93
d2zjr3163 Ribosomal protein L35p {Deinococcus radiodurans [TaxId: 99.92
>d2qam31 d.301.1.1 (3:1-64) Ribosomal protein L35p {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: L35p-like
superfamily: L35p-like
family: Ribosomal protein L35p
domain: Ribosomal protein L35p
species: Escherichia coli [TaxId: 562]
Probab=99.93  E-value=2.1e-27  Score=151.89  Aligned_cols=64  Identities=33%  Similarity=0.449  Sum_probs=62.2

Q ss_pred             CCCCCCCHHHEEEEECCCCEEEECCCCCCCCCCCCCCHHHHHCCCCEEECHHHHHHHHHHHCCCC
Q ss_conf             87323301212257759980970324885254158804654146986837778999999858688
Q gi|254780319|r    2 PKMKTNSSSKKRFSITATGKVRAQAAGKRHGMIKRSNKFIRNARGTMVLASADAKKVIRNYLPNG   66 (67)
Q Consensus         2 PKmKT~k~akKRFk~T~sGKvkr~~agk~H~l~~Ks~krkR~lr~~~~v~~~~~~~i~r~llPYg   66 (67)
                      ||||||+||+|||++||||||++++||++|+|++||++++|+|+++.+|+++|.+.|.+ ||||.
T Consensus         1 PKmKT~k~akKRfkvT~sGKi~r~~agk~H~l~~Ks~krkR~lr~~~~v~~~d~k~ik~-lLPYa   64 (64)
T d2qam31           1 PKIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIA-CLPYA   64 (64)
T ss_dssp             CCCCCCTTTTTTCCCCSSSCCCBCCSSSSSCCTTSCHHHHHTTSSCBCCCSSSHHHHHH-HCTTC
T ss_pred             CCCCCCHHHHHHEEECCCCCEEECCCCCCCCCCCCCHHHHHHCCCCEEECHHHHHHHHH-HCCCC
T ss_conf             98765223464135778997863417777565458998998657981278999999998-68899



>d2j0181 d.301.1.1 (8:2-65) Ribosomal protein L35p {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d2zjr31 d.301.1.1 (3:2-64) Ribosomal protein L35p {Deinococcus radiodurans [TaxId: 1299]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 67 50S ribosomal protein L35 [Candidatus Liberibacter
3i1n_3_65 (3:) 50S ribosomal protein L35; ribosome structure 4e-12
2j01_8_65 (8:) 50S ribosomal protein L35; ribosome, tRNA, pa 6e-12
2zjr_3_66 (3:) 50S ribosomal protein L35; ribosome, large ri 8e-12
3bbo_5_159 (5:) Ribosomal protein L35; large ribosomal subuni 3e-10
>3i1n_3 (3:) 50S ribosomal protein L35; ribosome structure, protein-RNA complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA- binding, methylation; 3.19A {Escherichia coli k-12} PDB: 1vs8_3 1vs6_3 3i1p_3 3i1r_3 3i1t_3 3i20_3 3i22_3 2qam_3* 2awb_3 2aw4_3 2i2v_3 2j28_3 2i2t_3* 2qao_3* 2qba_3* 2qbc_3* 2qbe_3 2qbg_3 2qbi_3* 2qbk_3* ...Length = 65 Back     alignment and structure
 Score = 64.7 bits (158), Expect = 4e-12
 Identities = 22/66 (33%), Positives = 33/66 (50%), Gaps = 1/66 (1%)

Query: 1  MPKMKTNSSSKKRFSITATGKVRAQAAGKRHGMIKRSNKFIRNARGTMVLASADAKKVIR 60
          MPK+KT   + KRF  T  G  + + A  RH + K++ K  R+ R   +++  D   VI 
Sbjct: 1  MPKIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIA 60

Query: 61 NYLPNG 66
            LP  
Sbjct: 61 -CLPYA 65


>2j01_8 (8:) 50S ribosomal protein L35; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus}Length = 65 Back     alignment and structure
>2zjr_3 (3:) 50S ribosomal protein L35; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans}Length = 66 Back     alignment and structure
>3bbo_5 (5:) Ribosomal protein L35; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}Length = 159 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target67 50S ribosomal protein L35 [Candidatus Liberibacter asia
2zjr_3_66 50S ribosomal protein L35; ribosome, large ribosom 99.95
3i1n_3_65 50S ribosomal protein L35; ribosome structure, pro 99.95
2j01_8_65 50S ribosomal protein L35; ribosome, tRNA, paromom 99.94
3bbo_5_159 Ribosomal protein L35; large ribosomal subunit, sp 99.9
>2zjr_3 (3:) 50S ribosomal protein L35; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} Back     alignment and structure
Probab=99.95  E-value=1e-28  Score=160.28  Aligned_cols=65  Identities=45%  Similarity=0.581  Sum_probs=63.4

Q ss_pred             CCCCCCCCHHHEEEEECCCCEEEECCCCCCCCCCCCCCHHHHHCCCCEEECHHHHHHHHHHHCCCC
Q ss_conf             987323301212257759980970324885254158804654146986837778999999858688
Q gi|254780319|r    1 MPKMKTNSSSKKRFSITATGKVRAQAAGKRHGMIKRSNKFIRNARGTMVLASADAKKVIRNYLPNG   66 (67)
Q Consensus         1 MPKmKT~k~akKRFk~T~sGKvkr~~agk~H~l~~Ks~krkR~lr~~~~v~~~~~~~i~r~llPYg   66 (67)
                      |||||||+||+|||++||+|+|++++||++|+++++|++++|+|+++.+|+++|.++|.+ |||||
T Consensus         1 MPKmKT~k~akKRFk~T~sGKvkr~~agk~H~l~~Ks~k~kR~Lr~~~~v~~~~~k~ik~-~Lpy~   65 (66)
T 2zjr_3            1 MPKMKTHKMAKRRIKITGTGKVMAFKSGKRHQNTGKSGDEIRGKGKGFVLAKAEWARMKL-MLPRG   65 (66)
T ss_pred             CCCCCCCHHHHHHEEECCCCCEEECCCCCCCCCCCCCHHHHHHCCCCEEECHHHHHHHHH-HCCCC
T ss_conf             997643221353136778987860627776455337988998667985577999999999-67899



>3i1n_3 (3:) 50S ribosomal protein L35; ribosome structure, protein-RNA complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA- binding, methylation; 3.19A {Escherichia coli k-12} PDB: 1vs8_3 1vs6_3 3i1p_3 3i1r_3 3i1t_3 3i20_3 3i22_3 2qam_3* 2awb_3 2aw4_3 2i2v_3 2j28_3 2i2t_3* 2qao_3* 2qba_3* 2qbc_3* 2qbe_3 2qbg_3 2qbi_3* 2qbk_3* ... Back     alignment and structure
>2j01_8 (8:) 50S ribosomal protein L35; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} Back     alignment and structure
>3bbo_5 (5:) Ribosomal protein L35; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Back     alignment and structure