254780292

254780292

50S ribosomal protein L13

GeneID in NCBI database:8209274Locus tag:CLIBASIA_00885
Protein GI in NCBI database:254780292Protein Accession:YP_003064705.1
Gene range:+(183368, 183835)Protein Length:155aa
Gene description:50S ribosomal protein L13
COG prediction:[J] Ribosomal protein L13
KEGG prediction:rplM; 50S ribosomal protein L13; K02871 large subunit ribosomal protein L13
SEED prediction:LSU ribosomal protein L13p (L13Ae)
Pathway involved in KEGG:Ribosome [PATH:las03010]
Subsystem involved in SEED:Ribosome LSU bacterial
sequencesequence profile

Prediction of Local Sequence Properties

SourceSummaryResult
scaler
NCBI Databasesequence
PSIPREDsecondary structure
SSPROsecondary structure
DISEMBLcoil and loop
DISEMBLflexible loop
SEGlow complexity
DISOPREDdisordered
DISEMBLmissing residues
DISPROdisordered
TMHMMnone TM-Helix
TOPPREDnone TM-Helix
HMMTOPnone TM-Helix
MEMSATnone TM-Helix
MEMSAT_SVMnone TM-Helix
PHOBIUSnone TM-Helix
SignalP_HMMno
SignalP_NNno
COILScoiled coil
70% MSAconservation map
90% MSAconservation map
  
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-----
MIPTFFQKSSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHIYAEDHHPHEAQKPVFMDIAKMNPKNSRRT
ccccccccHHHccEEEEEEEcccccHHHHHHHHHHHHccccccccccccccccEEEEEEHHHEEEccHHHHHHHHHHHcccccccccccHHHHHccccHHHHHHHHHHccccccHHHHHHHHccEEEccccccHHHHccEEEEcccccccccccc
ccccccccHHHcEccEEEEEcccccHHHHHHHHHHHHccccccccccccccccEEEEEEccEEEEEcccccccEEEEccccccccccccHHHHHHccccHHHHHHHHHcccccccHHHHHHHHcEEccccccccHcccccEEEHHcccccccccc
MIPTFFQKSSEVEKKWILVDAKGLIVGRLASQIALRLrgknkptytpsaddgdhvVIINASKvafsgkkydqktyyrhtgypggikkttakeilagasptNILKKAIARMlprgplarKQMKNLHIyaedhhpheaqkpvfmdiakmnpknsrrt
miptffqkssevekkwilvdakgliVGRLASQIALRlrgknkptytpsaddgdhvVIINASkvafsgkkydqktyyrhtgypggikkTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHIYAEDHhpheaqkpvfmdiakmnpknsrrt
MIPTFFQKSSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHIYAEDHHPHEAQKPVFMDIAKMNPKNSRRT
**PTFFQKSSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHIYAEDHHPHEAQKPVFMDI****P******
********SSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHIYAEDHHPHEAQKPVFMDIAKMNPKNSRRT
****FFQKSSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHIYAEDHHPHEAQKPVFMDIAKM********
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MIPTFFQKSSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHIYAEDHHPHEAQKPVFMDIAKMNPKNSRRT
MIPTFFQKSSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHIYAEDHHPHEAQKPVFMDIAKMNPKNSRRT
MIPTFFQKSSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHIYAEDHHPHEAQKPVFMDIAKMNPKNSRRT

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
Target155 50S ribosomal protein L13 [Candidatus Liberibacter asia
315122853154 50S ribosomal protein L13 [Candidatus Liberibacter sola 1 7e-70
222085551154 ribosomal protein L13 [Agrobacterium radiobacter K84] L 1 6e-54
15964996154 50S ribosomal protein L13 [Sinorhizobium meliloti 1021] 1 7e-54
150396085154 50S ribosomal protein L13 [Sinorhizobium medicae WSM419 1 9e-54
222148254154 50S ribosomal protein L13 [Agrobacterium vitis S4] Leng 1 1e-53
190891252154 50S ribosomal protein L13 [Rhizobium etli CIAT 652] Len 1 1e-53
218662851154 50S ribosomal protein L13 [Rhizobium etli IE4771] Lengt 1 2e-53
116251439154 50S ribosomal protein L13 [Rhizobium leguminosarum bv. 1 2e-53
218682703154 50S ribosomal protein L13 [Rhizobium etli CIAT 894] Len 1 3e-53
227821595154 50S ribosomal protein L13 [Sinorhizobium fredii NGR234] 1 3e-53
>gi|315122853|ref|YP_004063342.1| 50S ribosomal protein L13 [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 154 Back     alignment and organism information
 Score =  266 bits (680), Expect = 7e-70,   Method: Compositional matrix adjust.
 Identities = 122/154 (79%), Positives = 141/154 (91%)

Query: 2   IPTFFQKSSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINAS 61
           +P+FFQKSSEVEKKWIL+DAKGLIVGRLA+QIALRLRGK+KPTYTPS DDG +VVIINA+
Sbjct: 1   MPSFFQKSSEVEKKWILIDAKGLIVGRLAAQIALRLRGKDKPTYTPSVDDGSYVVIINAA 60

Query: 62  KVAFSGKKYDQKTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQM 121
           KV FSG KYD+K YY HTGYPGGIKK TA+EI+ G+SP N+LKKAI RMLP+GPLARKQ+
Sbjct: 61  KVVFSGNKYDKKVYYHHTGYPGGIKKATAREIIEGSSPINVLKKAIERMLPKGPLARKQL 120

Query: 122 KNLHIYAEDHHPHEAQKPVFMDIAKMNPKNSRRT 155
           KNLHIYAE++HPHEAQKP+ +D+AKMN KNSRR 
Sbjct: 121 KNLHIYAEENHPHEAQKPMLIDVAKMNIKNSRRN 154


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|222085551|ref|YP_002544081.1| ribosomal protein L13 [Agrobacterium radiobacter K84] Length = 154 Back     alignment and organism information
>gi|15964996|ref|NP_385349.1| 50S ribosomal protein L13 [Sinorhizobium meliloti 1021] Length = 154 Back     alignment and organism information
>gi|150396085|ref|YP_001326552.1| 50S ribosomal protein L13 [Sinorhizobium medicae WSM419] Length = 154 Back     alignment and organism information
>gi|222148254|ref|YP_002549211.1| 50S ribosomal protein L13 [Agrobacterium vitis S4] Length = 154 Back     alignment and organism information
>gi|190891252|ref|YP_001977794.1| 50S ribosomal protein L13 [Rhizobium etli CIAT 652] Length = 154 Back     alignment and organism information
>gi|218662851|ref|ZP_03518781.1| 50S ribosomal protein L13 [Rhizobium etli IE4771] Length = 154 Back     alignment and organism information
>gi|116251439|ref|YP_767277.1| 50S ribosomal protein L13 [Rhizobium leguminosarum bv. viciae 3841] Length = 154 Back     alignment and organism information
>gi|218682703|ref|ZP_03530304.1| 50S ribosomal protein L13 [Rhizobium etli CIAT 894] Length = 154 Back     alignment and organism information
>gi|227821595|ref|YP_002825565.1| 50S ribosomal protein L13 [Sinorhizobium fredii NGR234] Length = 154 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
Target155 50S ribosomal protein L13 [Candidatus Liberibacter asia
PRK09216144 PRK09216, rplM, 50S ribosomal protein L13; Reviewed 5e-63
TIGR01066140 TIGR01066, rplM_bact, ribosomal protein L13, bacterial 4e-49
COG0102148 COG0102, RplM, Ribosomal protein L13 [Translation, ribo 9e-48
CHL00159143 CHL00159, rpl13, ribosomal protein L13; Validated 5e-40
cd00392114 cd00392, Ribosomal_L13, Ribosomal protein L13 1e-37
KOG3203165 KOG3203, KOG3203, KOG3203, Mitochondrial/chloroplast ri 4e-35
PLN00205191 PLN00205, PLN00205, ribisomal protein L13 family protei 9e-29
PRK06394146 PRK06394, rpl13p, 50S ribosomal protein L13P; Reviewed 3e-10
TIGR01077142 TIGR01077, L13_A_E, ribosomal protein L13, archaeal/euk 3e-07
pfam00572128 pfam00572, Ribosomal_L13, Ribosomal protein L13 7e-49
>gnl|CDD|181703 PRK09216, rplM, 50S ribosomal protein L13; Reviewed Back     alignment and domain information
>gnl|CDD|162186 TIGR01066, rplM_bact, ribosomal protein L13, bacterial type Back     alignment and domain information
>gnl|CDD|30451 COG0102, RplM, Ribosomal protein L13 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|177072 CHL00159, rpl13, ribosomal protein L13; Validated Back     alignment and domain information
>gnl|CDD|88313 cd00392, Ribosomal_L13, Ribosomal protein L13 Back     alignment and domain information
>gnl|CDD|38413 KOG3203, KOG3203, KOG3203, Mitochondrial/chloroplast ribosomal protein L13 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|177795 PLN00205, PLN00205, ribisomal protein L13 family protein; Provisional Back     alignment and domain information
>gnl|CDD|180552 PRK06394, rpl13p, 50S ribosomal protein L13P; Reviewed Back     alignment and domain information
>gnl|CDD|162192 TIGR01077, L13_A_E, ribosomal protein L13, archaeal/eukaryotic Back     alignment and domain information
>gnl|CDD|144239 pfam00572, Ribosomal_L13, Ribosomal protein L13 Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 155 50S ribosomal protein L13 [Candidatus Liberibacter asia
TIGR01066145 rplM_bact ribosomal protein L13; InterPro: IPR005823 Ri 100.0
CHL00159143 rpl13 ribosomal protein L13; Validated 100.0
PRK09216144 rplM 50S ribosomal protein L13; Reviewed 100.0
COG0102148 RplM Ribosomal protein L13 [Translation, ribosomal stru 100.0
pfam00572128 Ribosomal_L13 Ribosomal protein L13. 100.0
KOG3203165 consensus 100.0
cd00392114 Ribosomal_L13 Ribosomal protein L13. Protein L13, a lar 100.0
PRK06394143 rpl13p 50S ribosomal protein L13P; Reviewed 100.0
TIGR01077144 L13_A_E ribosomal protein L13; InterPro: IPR005755 Ribo 99.96
PTZ00068201 60S ribosomal protein L13a; Provisional 99.92
KOG3204197 consensus 99.57
>TIGR01066 rplM_bact ribosomal protein L13; InterPro: IPR005823 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>CHL00159 rpl13 ribosomal protein L13; Validated Back     alignment and domain information
>PRK09216 rplM 50S ribosomal protein L13; Reviewed Back     alignment and domain information
>COG0102 RplM Ribosomal protein L13 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>pfam00572 Ribosomal_L13 Ribosomal protein L13 Back     alignment and domain information
>KOG3203 consensus Back     alignment and domain information
>cd00392 Ribosomal_L13 Ribosomal protein L13 Back     alignment and domain information
>PRK06394 rpl13p 50S ribosomal protein L13P; Reviewed Back     alignment and domain information
>TIGR01077 L13_A_E ribosomal protein L13; InterPro: IPR005755 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>PTZ00068 60S ribosomal protein L13a; Provisional Back     alignment and domain information
>KOG3204 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
Target155 50S ribosomal protein L13 [Candidatus Liberibacter asia
1p85_H142 Real Space Refined Coordinates Of The 50s Subunit F 8e-45
2j28_J140 Model Of E. Coli Srp Bound To 70s Rncs Length = 140 1e-43
1vsa_H163 Crystal Structure Of A 70s Ribosome-Trna Complex Re 4e-42
2j01_N140 Structure Of The Thermus Thermophilus 70s Ribosome 5e-42
3fin_N139 T. Thermophilus 70s Ribosome In Complex With Mrna, 1e-41
1vsp_H140 Interactions And Dynamics Of The Shine-Dalgarno Hel 2e-41
3mrz_J139 Recognition Of The Amber Stop Codon By Release Fact 3e-41
1nkw_H174 Crystal Structure Of The Large Ribosomal Subunit Fr 9e-41
3pyo_J137 Crystal Structure Of A Complex Containing Domain 3 3e-40
1pnu_H143 Crystal Structure Of A Streptomycin Dependent Ribos 1e-39
3bbo_L250 Homology Model For The Spinach Chloroplast 50s Subu 4e-39
2ftc_H148 Structural Model For The Large Subunit Of The Mamma 1e-30
1s1i_M146 Structure Of The Ribosomal 80s-Eef2-Sordarin Comple 2e-14
3izs_K199 Localization Of The Large Subunit Ribosomal Protein 5e-14
3jyw_M178 Structure Of The 60s Proteins For Eukaryotic Riboso 7e-14
1j3a_A142 Crystal Structure Of Ribosomal Protein L13 From Pyr 1e-12
3izr_K206 Localization Of The Large Subunit Ribosomal Protein 2e-12
2zkr_j203 Structure Of A Mammalian Ribosomal 60s Subunit With 2e-11
3g4s_J142 Co-Crystal Structure Of Tiamulin Bound To The Large 8e-10
1ffk_G145 Crystal Structure Of The Large Ribosomal Subunit Fr 8e-10
gi|33357909|pdb|1P85|H Chain H, 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 = 142 Back     alignment and structure
 Score =  183 bits (464), Expect = 8e-45,   Method: Composition-based stats.
 Identities = 65/143 (45%), Positives = 95/143 (66%), Gaps = 1/143 (0%)

Query: 2   IPTFFQKSSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINAS 61
           + TF  K   V++ W +VDA G  +GRLA+++A RLRGK+K  YTP  D GD+++++NA 
Sbjct: 1   MKTFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNAD 60

Query: 62  KVAFSGKKYDQKTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQM 121
           KVA +G K   K YY HTG+ GGIK+ T +E++A   P  +++ A+  MLP+GPL R   
Sbjct: 61  KVAVTGNKRTDKVYYHHTGHIGGIKQATFEEMIAR-RPERVIEIAVKGMLPKGPLGRAMF 119

Query: 122 KNLHIYAEDHHPHEAQKPVFMDI 144
           + L +YA + H H AQ+P  +DI
Sbjct: 120 RKLKVYAGNEHNHAAQQPQVLDI 142


>gi|119390354|pdb|2J28|J Chain J, Model Of E. Coli Srp Bound To 70s Rncs Length = 140 Back     alignment and structure
>gi|149240893|pdb|1VSA|H Chain H, 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 = 163 Back     alignment and structure
gi|116668245|pdb|2J01|N Chain N, 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 = 140 Back     alignment and structure
>gi|224510789|pdb|3FIN|N Chain N, 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 = 139 Back     alignment and structure
>gi|160285435|pdb|1VSP|H Chain H, Interactions And Dynamics Of The Shine-Dalgarno Helix In The 70s Ribosome. This File, 1vsp, Contains The 50s Ribosome Subunit. 30s Ribosome Subunit Is In The File 2qnh Length = 140 Back     alignment and structure
>gi|300508638|pdb|3MRZ|J Chain J, 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 = 139 Back     alignment and structure
gi|28948927|pdb|1NKW|H Chain H, Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans Length = 174 Back     alignment and structure
>gi|322812581|pdb|3PYO|J Chain J, 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 = 137 Back     alignment and structure
>gi|34811561|pdb|1PNU|H Chain H, 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 = 143 Back     alignment and structure
gi|189096134|pdb|3BBO|L Chain L, Homology Model For The Spinach Chloroplast 50s Subunit Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome Length = 250 Back     alignment and structure
>gi|99032314|pdb|2FTC|H Chain H, Structural Model For The Large Subunit Of The Mammalian Mitochondrial Ribosome Length = 148 Back     alignment and structure
>gi|49258851|pdb|1S1I|M Chain M, 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 = 146 Back     alignment and structure
>gi|315113310|pdb|3IZS|K Chain K, Localization Of The Large Subunit Ribosomal Proteins Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae Translating 80s Ribosome Length = 199 Back     alignment and structure
>gi|281500843|pdb|3JYW|M Chain M, Structure Of The 60s Proteins For Eukaryotic Ribosome Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome At 8.9a Resolution Length = 178 Back     alignment and structure
gi|28373434|pdb|1J3A|A Chain A, Crystal Structure Of Ribosomal Protein L13 From Pyrococcus Horikoshii Length = 142 Back     alignment and structure
>gi|315113298|pdb|3IZR|K Chain K, Localization Of The Large Subunit Ribosomal Proteins Into A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s Ribosome Length = 206 Back     alignment and structure
>gi|187609308|pdb|2ZKR|JJ Chain j, 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 = 203 Back     alignment and structure
>gi|228312151|pdb|3G4S|J Chain J, Co-Crystal Structure Of Tiamulin Bound To The Large Ribosomal Subunit Length = 142 Back     alignment and structure
gi|10120926|pdb|1FFK|G Chain G, Crystal Structure Of The Large Ribosomal Subunit From Haloarcula Marismortui At 2.4 Angstrom Resolution Length = 145 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target155 50S ribosomal protein L13 [Candidatus Liberibacter asia
3ofq_J142 50S ribosomal protein L13; protein biosynthesis, riboso 2e-46
3f1f_N163 50S ribosomal protein L13; RF2, ribosome, termination, 2e-45
3bbo_L250 Ribosomal protein L13; large ribosomal subunit, spinach 6e-43
2zjr_G174 50S ribosomal protein L13; ribosome, large ribosomal su 4e-38
3i1n_J142 50S ribosomal protein L13; ribosome structure, protein- 5e-36
3jyw_M178 60S ribosomal protein L16(A); eukaryotic ribosome, RACK 9e-36
2j01_N140 50S ribosomal protein L13; ribosome, tRNA, paromomycin, 2e-35
2ftc_H148 L13MT, MRP-L13, 39S ribosomal protein L13, mitochondria 7e-34
1j3a_A142 50S ribosomal protein L13P; rRNA binding, ribosomal ass 2e-28
2zkr_j203 60S ribosomal protein L13A; protein-RNA complex, 60S ri 8e-28
1vq8_J145 50S ribosomal protein L13P; ribosome 50S, protein-prote 1e-25
>3ofq_J 50S ribosomal protein L13; protein biosynthesis, ribosomes, RNA, tRNA, transfer, antibi EXIT, peptidyl, ribosomal subunit, large; 3.10A {Escherichia coli} PDB: 1p85_H 1p86_H 1vs8_J 1vs6_J 2aw4_J 2awb_J 2gya_H 2gyc_H 1vt2_J 2i2v_J 2i2t_J* 2qao_J* 2qba_J* 2qbc_J* 2qbe_J 2qbg_J 2qbi_J* 2qbk_J* 2qov_J 2qox_J ... Length = 142 Back     alignment and structure
 Score =  179 bits (456), Expect = 2e-46
 Identities = 65/141 (46%), Positives = 94/141 (66%), Gaps = 1/141 (0%)

Query: 4   TFFQKSSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKV 63
           TF  K   V++ W +VDA G  +GRLA+++A RLRGK+K  YTP  D GD+++++NA KV
Sbjct: 3   TFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNADKV 62

Query: 64  AFSGKKYDQKTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKN 123
           A +G K   K YY HTG+ GGIK+ T +E++A   P  +++ A+  MLP+GPL R   + 
Sbjct: 63  AVTGNKRTDKVYYHHTGHIGGIKQATFEEMIA-RRPERVIEIAVKGMLPKGPLGRAMFRK 121

Query: 124 LHIYAEDHHPHEAQKPVFMDI 144
           L +YA + H H AQ+P  +DI
Sbjct: 122 LKVYAGNEHNHAAQQPQVLDI 142


>3f1f_N 50S ribosomal protein L13; RF2, ribosome, termination, tRNA; 3.00A {Thermus thermophilus} PDB: 1vsa_H 3d5d_N 3d5b_N 3f1h_N Length = 163 Back     alignment and structure
>3bbo_L Ribosomal protein L13; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1 Length = 250 Back     alignment and structure
>2zjr_G 50S ribosomal protein L13; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: c.21.1.1 PDB: 1nwx_H* 1nwy_H* 1sm1_H* 1xbp_H* 2zjp_G* 2zjq_G 1nkw_H 3cf5_G* 3dll_G* 1pnu_H 1pny_H 1vor_K 1vou_K 1vow_K 1voy_K 1vp0_K Length = 174 Back     alignment and structure
>3i1n_J 50S ribosomal protein L13; ribosome structure, protein-RNA complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA- binding, methylation; 3.19A {Escherichia coli k-12} PDB: 1p85_H 1p86_H 1vs8_J 2aw4_J 2awb_J 2gya_H 2gyc_H 1vs6_J 2i2v_J 2i2t_J* 2qao_J* 2qba_J* 2qbc_J* 2qbe_J 2qbg_J 2qbi_J* 2qbk_J* 2qov_J 2qox_J 2qoz_J* ... Length = 142 Back     alignment and structure
>3jyw_M 60S ribosomal protein L16(A); eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus} PDB: 1s1i_M Length = 178 Back     alignment and structure
>2j01_N 50S ribosomal protein L13; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} SCOP: c.21.1.1 PDB: 2hgq_M 2hgj_M 2hgu_M 2j03_N 2jl6_N 2jl8_N 2v47_N 2v49_N 2wdi_N 2wdj_N 2wdl_N 2wdn_N 2wh2_N 2wh4_N 3hux_N 3huz_N 3fin_N 1vsp_H Length = 140 Back     alignment and structure
>2ftc_H L13MT, MRP-L13, 39S ribosomal protein L13, mitochondrial; mitochondrial ribosome, large ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus} Length = 148 Back     alignment and structure
>1j3a_A 50S ribosomal protein L13P; rRNA binding, ribosomal assembly, ribosome; 1.60A {Pyrococcus horikoshii} SCOP: c.21.1.1 Length = 142 Back     alignment and structure
>2zkr_j 60S ribosomal protein L13A; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Length = 203 Back     alignment and structure
>1vq8_J 50S ribosomal protein L13P; 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.21.1.1 PDB: 1giy_M 1jj2_I 1k73_K* 1k8a_K* 1k9m_K* 1kc8_K* 1kd1_K* 1kqs_I* 1m1k_K* 1m90_K* 1ml5_m* 1n8r_K* 1nji_K* 1q7y_K* 1q81_K* 1q82_K* 1q86_K* 1qvf_I 1qvg_I 1s72_J* ... Length = 145 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target155 50S ribosomal protein L13 [Candidatus Liberibacter asia
3ofq_J142 50S ribosomal protein L13; protein biosynthesis, riboso 100.0
3f1f_N163 50S ribosomal protein L13; RF2, ribosome, termination, 100.0
3bbo_L250 Ribosomal protein L13; large ribosomal subunit, spinach 100.0
2j01_N140 50S ribosomal protein L13; ribosome, tRNA, paromomycin, 100.0
2zjr_G174 50S ribosomal protein L13; ribosome, large ribosomal su 100.0
2ftc_H148 L13MT, MRP-L13, 39S ribosomal protein L13, mitochondria 100.0
1j3a_A142 50S ribosomal protein L13P; rRNA binding, ribosomal ass 100.0
3jyw_M178 60S ribosomal protein L16(A); eukaryotic ribosome, RACK 100.0
1vq8_J145 50S ribosomal protein L13P; ribosome 50S, protein-prote 100.0
2zkr_j203 60S ribosomal protein L13A; protein-RNA complex, 60S ri 100.0
>3ofq_J 50S ribosomal protein L13; protein biosynthesis, ribosomes, RNA, tRNA, transfer, antibi EXIT, peptidyl, ribosomal subunit, large; 3.10A {Escherichia coli} PDB: 1p85_H 1p86_H 1vs8_J 1vs6_J 2aw4_J 2awb_J 2gya_H 2gyc_H 1vt2_J 2i2v_J 2i2t_J* 2qao_J* 2qba_J* 2qbc_J* 2qbe_J 2qbg_J 2qbi_J* 2qbk_J* 2qov_J 2qox_J ... Back     alignment and structure
Probab=100.00  E-value=0  Score=402.58  Aligned_cols=142  Identities=45%  Similarity=0.832  Sum_probs=139.4

Q ss_pred             CEEEECCHHHCCEEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHCCCC
Q ss_conf             51132684360200699978987457679999999846565210345566888999751010015601211333311575
Q gi|254780292|r    2 IPTFFQKSSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYRHTGY   81 (155)
Q Consensus         2 ~kT~~~k~~~~~r~W~iiDA~~~~lGRlAs~iA~~L~GKhKp~y~P~~d~GD~VvViNa~ki~~tG~K~~~k~y~~htgy   81 (155)
                      |+||++++++++|+||+|||+||+||||||.||++|+|||||+|+|++||||+||||||++|++||+||.+|.||+||||
T Consensus         1 Mkt~~~k~~~~~r~W~liDA~~~~lGRlAs~iA~~L~GK~kp~y~p~~d~Gd~VvViNa~ki~~tG~K~~~k~y~~hsgy   80 (142)
T 3ofq_J            1 MKTFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNADKVAVTGNKRTDKVYYHHTGH   80 (142)
T ss_dssp             CCCCCCCSSSCCCCEEECCCSSSCSSHHHHHHHHHHTTTTSSCCCTTSCCCCEEECCBGGGCCCCSSCTTTCCCCEECSS
T ss_pred             CCCCCCCHHHCCCCEEEEECCCCCHHHHHHHHHHHHHCCCCCCHHHCCCCCCEEEEEECHHEEECCCCHHCEEEEEEEEC
T ss_conf             97505884452664799968999468889999999843788630103578867999831465861861120466784105


Q ss_pred             CCCCEEEECCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCCHHHCCCEEEEH
Q ss_conf             576336302000012487999999997308998547899962701078999713208547616
Q gi|254780292|r   82 PGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHIYAEDHHPHEAQKPVFMDI  144 (155)
Q Consensus        82 pGG~k~~~~~~~~~~~~P~~il~~aV~gMLPkn~lgr~~lkrL~vy~g~~Hph~aq~P~~l~~  144 (155)
                      |||+++.++.+++ +++|++||++||+||||+|++|+.+|+||+||+|++|||+||+|+.||+
T Consensus        81 pGg~k~~~~~~~~-~k~P~~il~~aV~gMLPkn~lgr~~~krLkvy~g~~hp~~aq~P~~l~i  142 (142)
T 3ofq_J           81 IGGIKQATFEEMI-ARRPERVIEIAVKGMLPKGPLGRAMFRKLKVYAGNEHNHAAQQPQVLDI  142 (142)
T ss_dssp             SSCEECCCHHHHS-SSCGGGHHHHTTTTTSCCSTTHHHHHTTEECCBSSCCSCGGGCCCCCCC
T ss_pred             CCCCCCCCHHHHH-HHCHHHHHHHHHHHHCCCCHHHHHHHHCCEEECCCCCCCCCCCCEEECC
T ss_conf             9998678989998-5287899999998817998359999848889698999965679877169



>3f1f_N 50S ribosomal protein L13; RF2, ribosome, termination, tRNA; 3.00A {Thermus thermophilus} PDB: 1vsa_H 3d5d_N 3d5b_N 3f1h_N Back     alignment and structure
>3bbo_L Ribosomal protein L13; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1 Back     alignment and structure
>2j01_N 50S ribosomal protein L13; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} SCOP: c.21.1.1 PDB: 2hgq_M 2hgj_M 2hgu_M 2j03_N 2jl6_N 2jl8_N 2v47_N 2v49_N 2wdi_N 2wdj_N 2wdl_N 2wdn_N 2wh2_N 2wh4_N 2wrj_N 2wrl_N 2wro_N 2wrr_N 2x9s_N 2x9u_N ... Back     alignment and structure
>2zjr_G 50S ribosomal protein L13; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: c.21.1.1 PDB: 1nwx_H* 1nwy_H* 1sm1_H* 1xbp_H* 2zjp_G* 2zjq_G 1nkw_H 3cf5_G* 3dll_G* 1pnu_H 1pny_H 1vor_K 1vou_K 1vow_K 1voy_K 1vp0_K Back     alignment and structure
>2ftc_H L13MT, MRP-L13, 39S ribosomal protein L13, mitochondrial; mitochondrial ribosome, large ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus} Back     alignment and structure
>1j3a_A 50S ribosomal protein L13P; rRNA binding, ribosomal assembly, ribosome; 1.60A {Pyrococcus horikoshii} SCOP: c.21.1.1 Back     alignment and structure
>3jyw_M 60S ribosomal protein L16(A); eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus} PDB: 1s1i_M Back     alignment and structure
>1vq8_J 50S ribosomal protein L13P; 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.21.1.1 PDB: 1giy_M 1jj2_I 1k73_K* 1k8a_K* 1k9m_K* 1kc8_K* 1kd1_K* 1kqs_I* 1m1k_K* 1m90_K* 1ml5_m* 1n8r_K* 1nji_K* 1q7y_K* 1q81_K* 1q82_K* 1q86_K* 1qvf_I 1qvg_I 1s72_J* ... Back     alignment and structure
>2zkr_j 60S ribosomal protein L13A; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} 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 155 50S ribosomal protein L13 [Candidatus Liberibacter asia
d2zjrg1142 c.21.1.1 (G:30-171) Ribosomal protein L13 {Deinococcus 2e-37
d2gych1140 c.21.1.1 (H:1-140) Ribosomal protein L13 {Escherichia c 3e-35
d2j01n1139 c.21.1.1 (N:1-139) Ribosomal protein L13 {Thermus therm 2e-34
d1vqoj1142 c.21.1.1 (J:4-145) Ribosomal protein L13 {Archaeon Halo 7e-26
d1j3aa_142 c.21.1.1 (A:) Ribosomal protein L13 {Archaeon Pyrococcu 2e-22
>d2zjrg1 c.21.1.1 (G:30-171) Ribosomal protein L13 {Deinococcus radiodurans [TaxId: 1299]} Length = 142 Back     information, alignment and structure

class: Alpha and beta proteins (a/b)
fold: Ribosomal protein L13
superfamily: Ribosomal protein L13
family: Ribosomal protein L13
domain: Ribosomal protein L13
species: Deinococcus radiodurans [TaxId: 1299]
 Score =  148 bits (375), Expect = 2e-37
 Identities = 64/144 (44%), Positives = 93/144 (64%), Gaps = 3/144 (2%)

Query: 4   TFFQKSSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKV 63
           T+  K    E+ W++VDA G+ +GRLA+ IA R+RGK++P +TP+   GD VV+INA++V
Sbjct: 2   TYIPK--NDEQNWVVVDASGVPLGRLATLIASRIRGKHRPDFTPNMIQGDFVVVINAAQV 59

Query: 64  AFSGKKYDQKTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKN 123
           A +GKK D K Y R+TGY GG+K  TA+E L+   P  +++ A+  MLP+G   R     
Sbjct: 60  ALTGKKLDDKVYTRYTGYQGGLKTETAREALSK-HPERVIEHAVFGMLPKGRQGRAMHTR 118

Query: 124 LHIYAEDHHPHEAQKPVFMDIAKM 147
           L +YA + HPH AQKP  +    +
Sbjct: 119 LKVYAGETHPHSAQKPQVLKTQPL 142


>d2gych1 c.21.1.1 (H:1-140) Ribosomal protein L13 {Escherichia coli [TaxId: 562]} Length = 140 Back     information, alignment and structure
>d2j01n1 c.21.1.1 (N:1-139) Ribosomal protein L13 {Thermus thermophilus [TaxId: 274]} Length = 139 Back     information, alignment and structure
>d1vqoj1 c.21.1.1 (J:4-145) Ribosomal protein L13 {Archaeon Haloarcula marismortui [TaxId: 2238]} Length = 142 Back     information, alignment and structure
>d1j3aa_ c.21.1.1 (A:) Ribosomal protein L13 {Archaeon Pyrococcus horikoshii [TaxId: 53953]} Length = 142 Back     information, alignment and structure

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

IdentityAlignment graphLength Definition Probability
Target155 50S ribosomal protein L13 [Candidatus Liberibacter asia
d2zjrg1142 Ribosomal protein L13 {Deinococcus radiodurans [TaxId: 100.0
d2j01n1139 Ribosomal protein L13 {Thermus thermophilus [TaxId: 274 100.0
d2gych1140 Ribosomal protein L13 {Escherichia coli [TaxId: 562]} 100.0
d1j3aa_142 Ribosomal protein L13 {Archaeon Pyrococcus horikoshii [ 100.0
d1vqoj1142 Ribosomal protein L13 {Archaeon Haloarcula marismortui 100.0
>d2zjrg1 c.21.1.1 (G:30-171) Ribosomal protein L13 {Deinococcus radiodurans [TaxId: 1299]} Back     information, alignment and structure
class: Alpha and beta proteins (a/b)
fold: Ribosomal protein L13
superfamily: Ribosomal protein L13
family: Ribosomal protein L13
domain: Ribosomal protein L13
species: Deinococcus radiodurans [TaxId: 1299]
Probab=100.00  E-value=0  Score=385.90  Aligned_cols=142  Identities=45%  Similarity=0.811  Sum_probs=137.1

Q ss_pred             EEEECCHHHCCEEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHHCCCCC
Q ss_conf             11326843602006999789874576799999998465652103455668889997510100156012113333115755
Q gi|254780292|r    3 PTFFQKSSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYRHTGYP   82 (155)
Q Consensus         3 kT~~~k~~~~~r~W~iiDA~~~~lGRlAs~iA~~L~GKhKp~y~P~~d~GD~VvViNa~ki~~tG~K~~~k~y~~htgyp   82 (155)
                      |||+++.  ++|+||||||+||+||||||.||++|+|||||+|+|++||||+||||||+++.+||+||.+|+|++|||||
T Consensus         1 kt~~~k~--~~r~W~viDA~~~~lGRlAs~iAk~L~GK~kp~y~p~~d~Gd~ViViNa~ki~~tG~K~~~k~y~~htg~p   78 (142)
T d2zjrg1           1 KTYIPKN--DEQNWVVVDASGVPLGRLATLIASRIRGKHRPDFTPNMIQGDFVVVINAAQVALTGKKLDDKVYTRYTGYQ   78 (142)
T ss_dssp             CCCCCCC--SCCCEEEEECTTSBHHHHHHHHHHHHHCSSCSSCCSSSCCCCEEEEECCTTCBCSSCSSSSCEEEECCSSC
T ss_pred             CCCCCCC--CCCCEEEEECCCCCHHHHHHHHHHHHHCCCCCCEEECCCCCCEEEECCCCEEEECCCCHHHHEEHHHCCCC
T ss_conf             9627877--77658999799995688999999998557665255235678779974873358727535531000110344


Q ss_pred             CCCEEEECCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCCHHHCCCEEEEHHHC
Q ss_conf             76336302000012487999999997308998547899962701078999713208547616652
Q gi|254780292|r   83 GGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHIYAEDHHPHEAQKPVFMDIAKM  147 (155)
Q Consensus        83 GG~k~~~~~~~~~~~~P~~il~~aV~gMLPkn~lgr~~lkrL~vy~g~~Hph~aq~P~~l~~~~~  147 (155)
                      ||+++.++.+++ +++|++||++||+||||+|++|+.+|+||+||+|++|||+||+|+.|+++++
T Consensus        79 gg~k~~~~~~~~-~r~P~~ii~~aV~gMLPkn~lgr~~lkrLkvy~G~~hp~~~q~P~~l~~~~l  142 (142)
T d2zjrg1          79 GGLKTETAREAL-SKHPERVIEHAVFGMLPKGRQGRAMHTRLKVYAGETHPHSAQKPQVLKTQPL  142 (142)
T ss_dssp             SSCCEEEESTTT-TSCHHHHHHHHHGGGSCCSHHHHHHHTTCEECSCSTGGGGSCCSCCCCCCCC
T ss_pred             CCCCCCCHHHHH-CCCHHHHHHHHHHHCCCCCHHHHHHHHCCEEECCCCCCCCCCCCCEECCCCC
T ss_conf             554422288875-1166789999997248998659999858868698999810159806504359



>d2j01n1 c.21.1.1 (N:1-139) Ribosomal protein L13 {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d2gych1 c.21.1.1 (H:1-140) Ribosomal protein L13 {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1j3aa_ c.21.1.1 (A:) Ribosomal protein L13 {Archaeon Pyrococcus horikoshii [TaxId: 53953]} Back     information, alignment and structure
>d1vqoj1 c.21.1.1 (J:4-145) Ribosomal protein L13 {Archaeon Haloarcula marismortui [TaxId: 2238]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 155 50S ribosomal protein L13 [Candidatus Liberibacter
2zjr_G_174 (G:) 50S ribosomal protein L13; ribosome, large ri 6e-44
3i1n_J_142 (J:) 50S ribosomal protein L13; ribosome structure 4e-43
3bbo_L_250 (L:) Ribosomal protein L13; large ribosomal subuni 1e-42
3f1f_N_163 (N:) 50S ribosomal protein L13; RF2, ribosome, ter 3e-42
2ftc_H_17-148132 (H:17-148) L13MT, MRP-L13, 39S ribosomal protein L 1e-41
3jyw_M_1-141141 (M:1-141) 60S ribosomal protein L16(A); eukaryotic 3e-32
1vq8_J_145 (J:) 50S ribosomal protein L13P; ribosome 50S, pro 7e-31
1j3a_A_142 (A:) 50S ribosomal protein L13P; rRNA binding, rib 2e-29
2j01_N_1-63_93-140111 (N:1-63,N:93-140) 50S ribosomal protein L13; ribos 4e-28
2zkr_j_203 (j:) 60S ribosomal protein L13A; protein-RNA compl 2e-27
2j01_N_64-9229 (N:64-92) 50S ribosomal protein L13; ribosome, tRN 0.004
>2zjr_G (G:) 50S ribosomal protein L13; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans}Length = 174 Back     alignment and structure
 Score =  170 bits (433), Expect = 6e-44
 Identities = 63/147 (42%), Positives = 91/147 (61%), Gaps = 1/147 (0%)

Query: 4   TFFQKSSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKV 63
                    E+ W++VDA G+ +GRLA+ IA R+RGK++P +TP+   GD VV+INA++V
Sbjct: 29  VKTYIPKNDEQNWVVVDASGVPLGRLATLIASRIRGKHRPDFTPNMIQGDFVVVINAAQV 88

Query: 64  AFSGKKYDQKTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKN 123
           A +GKK D K Y R+TGY GG+K  TA+E L+   P  +++ A+  MLP+G   R     
Sbjct: 89  ALTGKKLDDKVYTRYTGYQGGLKTETAREALSKH-PERVIEHAVFGMLPKGRQGRAMHTR 147

Query: 124 LHIYAEDHHPHEAQKPVFMDIAKMNPK 150
           L +YA + HPH AQKP  +    +  K
Sbjct: 148 LKVYAGETHPHSAQKPQVLKTQPLEVK 174


>3i1n_J (J:) 50S ribosomal protein L13; ribosome structure, protein-RNA complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA- binding, methylation; 3.19A {Escherichia coli k-12} PDB: 1p85_H 1p86_H 1vs8_J 2aw4_J 2awb_J 2gya_H 2gyc_H 1vs6_J 2i2v_J 2i2t_J* 2qao_J* 2qba_J* 2qbc_J* 2qbe_J 2qbg_J 2qbi_J* 2qbk_J* 2qov_J 2qox_J 2qoz_J* ...Length = 142 Back     alignment and structure
>3bbo_L (L:) Ribosomal protein L13; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}Length = 250 Back     alignment and structure
>3f1f_N (N:) 50S ribosomal protein L13; RF2, ribosome, termination, tRNA; 3.00A {Thermus thermophilus} PDB: 1vsa_H 3d5d_N 3d5b_N 3f1h_NLength = 163 Back     alignment and structure
>2ftc_H (H:17-148) L13MT, MRP-L13, 39S ribosomal protein L13, mitochondrial; mitochondrial ribosome, large ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus}Length = 132 Back     alignment and structure
>3jyw_M (M:1-141) 60S ribosomal protein L16(A); eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus} PDB: 1s1i_MLength = 141 Back     alignment and structure
>1vq8_J (J:) 50S ribosomal protein L13P; 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 = 145 Back     alignment and structure
>1j3a_A (A:) 50S ribosomal protein L13P; rRNA binding, ribosomal assembly, ribosome; 1.60A {Pyrococcus horikoshii}Length = 142 Back     alignment and structure
>2j01_N (N:1-63,N:93-140) 50S ribosomal protein L13; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus}Length = 111 Back     alignment and structure
>2zkr_j (j:) 60S ribosomal protein L13A; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris}Length = 203 Back     alignment and structure
>2j01_N (N:64-92) 50S ribosomal protein L13; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus}Length = 29 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target155 50S ribosomal protein L13 [Candidatus Liberibacter asia
3bbo_L_250 Ribosomal protein L13; large ribosomal subunit, sp 100.0
2zjr_G_174 50S ribosomal protein L13; ribosome, large ribosom 100.0
3i1n_J_142 50S ribosomal protein L13; ribosome structure, pro 100.0
3f1f_N_163 50S ribosomal protein L13; RF2, ribosome, terminat 100.0
2ftc_H_17-148132 L13MT, MRP-L13, 39S ribosomal protein L13, mitocho 100.0
1j3a_A_142 50S ribosomal protein L13P; rRNA binding, ribosoma 100.0
1vq8_J_145 50S ribosomal protein L13P; ribosome 50S, protein- 100.0
2j01_N_1-63_93-140111 50S ribosomal protein L13; ribosome, tRNA, paromom 100.0
2zkr_j_203 60S ribosomal protein L13A; protein-RNA complex, 6 100.0
3jyw_M_1-141141 60S ribosomal protein L16(A); eukaryotic ribosome, 100.0
2j01_N_64-9229 50S ribosomal protein L13; ribosome, tRNA, paromom 97.29
>3bbo_L (L:) Ribosomal protein L13; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Back     alignment and structure
Probab=100.00  E-value=0  Score=398.74  Aligned_cols=152  Identities=43%  Similarity=0.752  Sum_probs=146.9

Q ss_pred             CCEEEECCHHH---CCEEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCCCCHHHHHHHHH
Q ss_conf             95113268436---020069997898745767999999984656521034556688899975101001560121133331
Q gi|254780292|r    1 MIPTFFQKSSE---VEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYR   77 (155)
Q Consensus         1 ~~kT~~~k~~~---~~r~W~iiDA~~~~lGRlAs~iA~~L~GKhKp~y~P~~d~GD~VvViNa~ki~~tG~K~~~k~y~~   77 (155)
                      ||+||+++.++   ++|+||||||+||+||||||.||++|+|||||+|||++||||+||||||++|++||+||.+|.||+
T Consensus        96 ~~~t~~~k~~~~~~~~r~W~vIDA~~~~LGRLAs~IAk~L~GKhKp~ytP~~d~Gd~VIVVNa~ki~itG~k~~~k~y~~  175 (250)
T 3bbo_L           96 WNTTWYPKSADHVPTDKKWYVVDATDLILGRMASTIAIHIRGKNLASYTPSVDMGAFVIVVNADKVAVSGKKRTQKLYRR  175 (250)
T ss_dssp             ----------------CCCCEECCSSCCSSTTHHHHTTTTTTTTTTCCCTTSCCSCCCEESCCSSCCCCSGGGGTCCCBC
T ss_pred             CCCCCCCCCCCCCCCCCCEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEECCHHEEECCCHHHHHEEEE
T ss_conf             15441367566666576489995899946888999999980477775066767785699835501050560333210011


Q ss_pred             CCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCCCCCHHHCCCEEEEHHHCCCCCCC
Q ss_conf             1575576336302000012487999999997308998547899962701078999713208547616652813123
Q gi|254780292|r   78 HTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHIYAEDHHPHEAQKPVFMDIAKMNPKNSR  153 (155)
Q Consensus        78 htgypGG~k~~~~~~~~~~~~P~~il~~aV~gMLPkn~lgr~~lkrL~vy~g~~Hph~aq~P~~l~~~~~~~kn~~  153 (155)
                      |||||||+++.++.+++ .++|++||++||+||||+|++|+.+|+||+||+|++|||++|+|+.+++.++++++.+
T Consensus       176 htg~pGg~k~~~~~~~~-~r~P~~Ii~~aVrgMLPkn~lgr~~lkrLkvy~g~~hp~~~qkp~~l~~~~~~~~~kr  250 (250)
T 3bbo_L          176 HSGRPGGLKEETFDQLQ-KRIPERIIEHAVRGMLPKGRLGRYLFNHLKVYKGAEHPHQAQQPIDLPLRDKRIRVEK  250 (250)
T ss_dssp             CCSSSSCCCBCCHHHHT-TSCTTHHHHHHHHTTSCSSSSHHHHHTTCCCCSSSCCSCTTSCC--------------
T ss_pred             ECCCCCCCCCCCCCCCC-CCCHHHHHHHHHHHCCCCCHHHHHHHHCCEEECCCCCCCCCCCCEECCHHHHHHHHCC
T ss_conf             11333445543223224-5688899999987418998459999749789689999712359715366674443049



>2zjr_G (G:) 50S ribosomal protein L13; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} Back     alignment and structure
>3i1n_J (J:) 50S ribosomal protein L13; ribosome structure, protein-RNA complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA- binding, methylation; 3.19A {Escherichia coli k-12} PDB: 1p85_H 1p86_H 1vs8_J 2aw4_J 2awb_J 2gya_H 2gyc_H 1vs6_J 2i2v_J 2i2t_J* 2qao_J* 2qba_J* 2qbc_J* 2qbe_J 2qbg_J 2qbi_J* 2qbk_J* 2qov_J 2qox_J 2qoz_J* ... Back     alignment and structure
>3f1f_N (N:) 50S ribosomal protein L13; RF2, ribosome, termination, tRNA; 3.00A {Thermus thermophilus} PDB: 1vsa_H 3d5d_N 3d5b_N 3f1h_N Back     alignment and structure
>2ftc_H (H:17-148) L13MT, MRP-L13, 39S ribosomal protein L13, mitochondrial; mitochondrial ribosome, large ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus} Back     alignment and structure
>1j3a_A (A:) 50S ribosomal protein L13P; rRNA binding, ribosomal assembly, ribosome; 1.60A {Pyrococcus horikoshii} Back     alignment and structure
>1vq8_J (J:) 50S ribosomal protein L13P; 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
>2j01_N (N:1-63,N:93-140) 50S ribosomal protein L13; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} Back     alignment and structure
>2zkr_j (j:) 60S ribosomal protein L13A; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Back     alignment and structure
>3jyw_M (M:1-141) 60S ribosomal protein L16(A); eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus} PDB: 1s1i_M Back     alignment and structure
>2j01_N (N:64-92) 50S ribosomal protein L13; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} Back     alignment and structure