254780146

254780146

50S ribosomal protein L1

GeneID in NCBI database:8209121Locus tag:CLIBASIA_00125
Protein GI in NCBI database:254780146Protein Accession:YP_003064559.1
Gene range:-(29578, 30276)Protein Length:232aa
Gene description:50S ribosomal protein L1
COG prediction:[J] Ribosomal protein L1
KEGG prediction:rplA; 50S ribosomal protein L1; K02863 large subunit ribosomal protein L1
SEED prediction:LSU ribosomal protein L1p (L10Ae)
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-------160-------170-------180-------190-------200-------210-------220-------230--
MVSKISKRMQQISQGIDRSALYGLSDAVVMLKERATARFDETVEIAMNLGIDPRHANQMVRGVVTMPNGTGVNVRVAVFATSSKADEAREAGADIVGGEDLFEIVKGGQIDFDRCIATPDMMPLVGRLGRILGPRGIMPNLRVGTVTTDVATAVRESKSGAVDFRSEKAGIIHAGIGKVSFENKKIEENVLAFVSAVVKAKPSVAKGDYVKRVTLSSTMGCGIKVDLSSFSV
cccHHHHHHHHHHHHccccccccHHHHHHHHHHccccccccEEEEEEEccccccccccEEEEEEEcccccccccEEEEEEccHHHHHHHHccccEEcHHHHHHHHHcccccccEEEEcHHHHHHHHHHcccccccccccccccccccHHHHHHHHHHHccEEEEEEEcccEEEEEEEcccccHHHHHHHHHHHHHHHHHcccccccccEEEEEEEEEcccccEEEcHHHHcc
cHHHHHcccccccccccccccEcHHHHHHHHHcccccccccEEEEEEEEccccccHHHccEEEEEccccccccccEEEEcccHHHHHHHHccccEEEcHHHHHHHHcccccccEEEEcHHHHHHHHHHHHHHHHHccccccccccEcccHHHHHHHHHccEEEEEcccccEEEEEEEEccccHHHHHHHHHHHHHHHHcccccccccccEEEEEEEccccccEEEccccccc
MVSKISKRMQQISQGIDRSALYGLSDAVVMLKERATARFDETVEIAMNlgidprhanqmvrgvvtmpngtgVNVRVAVFATSSKADEAReagadivggEDLFEIVkggqidfdrciatpdmmplvgrlgrilgprgimpnlrvgtvTTDVATAVResksgavdfrsekagiihagigkvsfenkKIEENVLAFVSAVVKakpsvakgdyvkrvtlsstmgcgikvdlssfsv
MVSKISKRMQQIsqgidrsalyGLSDAVVMLKERATARFDETVEIAMNlgidprhaNQMVRGVVTMPNGTGVNVRVAVFATSSKADEAREAGADIVGGEDLFEIVKGGQIDFDRCIATPDMMPLVGRLGRILGPRGIMPNLRVGTVTTDVATAVresksgavdfrsekaGIIHAgigkvsfenKKIEENVLAFVSAVvkakpsvakgdyvkrvtlsstmgcgikvdlssfsv
MVSKISKRMQQISQGIDRSALYGLSDAVVMLKERATARFDETVEIAMNLGIDPRHANQMVRGVVTMPNGTGVNVRVAVFATSSKADEAREAGADIVGGEDLFEIVKGGQIDFDRCIATPDMMplvgrlgrilgprgiMPNLRvgtvttdvatavRESKSGAVDFRSEKAGIIHAGIGKVSFENKKIEENVLafvsavvkakpsvakGDYVKRVTLSSTMGCGIKVDLSSFSV
***********ISQGIDRSALYGLSDAVVMLKERATARFDETVEIAMNLGIDPRHANQMVRGVVTMPNGTGVNVRVAVFATSSKADEAREAGADIVGGEDLFEIVKGGQIDFDRCIATPDMMPLVGRLGRILGPRGIMPNLRVGTVTTDVATAVRESKSGAVDFRSEKAGIIHAGIGKVSFENKKIEENVLAFVSAVVKAKPSVAKGDYVKRVTLSSTMGCGIKVDLSSF**
************SQGIDRSALYGLSDAVVMLKERATARFDETVEIAMNLGIDPRHANQMVRGVVTMPNGTGVNVRVAVFATSSKADEAREAGADIVGGEDLFEIVKGGQIDFDRCIATPDMMPLVGRLGRILGPRGIMPNLRVGTVTTDVATAVRESKSGAVDFRSEKAGIIHAGIGKVSFENKKIEENVLAFVSAVVKAKPSVAKGDYVKRVTLSSTMGCGIKVDLSSFSV
********MQQISQGIDRSALYGLSDAVVMLKERATARFDETVEIAMNLGIDPRHANQMVRGVVTMPNGTGVNVRVAVFATSSKADEAREAGADIVGGEDLFEIVKGGQIDFDRCIATPDMMPLVGRLGRILGPRGIMPNLRVGTVTTDVATAVRESKSGAVDFRSEKAGIIHAGIGKVSFENKKIEENVLAFVSAVVKAKPSVAKGDYVKRVTLSSTMGCGIKVDLS****
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MVSKISKRMQQISQGIDRSALYGLSDAVVMLKERATARFDETVEIAMNLGIDPRHANQMVRGVVTMPNGTGVNVRVAVFATSSKADEAREAGADIVGGEDLFEIVKGGQIDFDRCIATPDMMPLVGRLGRILGPRGIMPNLRVGTVTTDVATAVRESKSGAVDFRSEKAGIIHAGIGKVSFENKKIEENVLAFVSAVVKAKPSVAKGDYVKRVTLSSTMGCGIKVDLSSFSV
MVSKISKRMQQISQGIDRSALYGLSDAVVMLKERATARFDETVEIAMNLGIDPRHANQMVRGVVTMPNGTGVNVRVAVFATSSKADEAREAGADIVGGEDLFEIVKGGQIDFDRCIATPDMMPLVGRLGRILGPRGIMPNLRVGTVTTDVATAVRESKSGAVDFRSEKAGIIHAGIGKVSFENKKIEENVLAFVSAVVKAKPSVAKGDYVKRVTLSSTMGCGIKVDLSSFSV
MVSKISKRMQQISQGIDRSALYGLSDAVVMLKERATARFDETVEIAMNLGIDPRHANQMVRGVVTMPNGTGVNVRVAVFATSSKADEAREAGADIVGGEDLFEIVKGGQIDFDRCIATPDMMPLVGRLGRILGPRGIMPNLRVGTVTTDVATAVRESKSGAVDFRSEKAGIIHAGIGKVSFENKKIEENVLAFVSAVVKAKPSVAKGDYVKRVTLSSTMGCGIKVDLSSFSV

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

Original result of BLAST against C. L. asiaticus genome

No hits with e-value below 0.05

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

Original result of PSI-BLAST first 2 iterations

IdentityAlignment graphLength Definition Round E-value
Target232 50S ribosomal protein L1 [Candidatus Liberibacter asiat
157704381232 50S ribosomal subunit protein L1 [Candidatus Liberibact 1 1e-129
78355045232 putative 50S ribosomal subunit protein L1 [Candidatus L 1 1e-129
133872304231 50S ribosomal subunit protein L1 [Candidatus Liberibact 1 1e-116
133872297232 50S ribosomal subunit protein L1 [Candidatus Liberibact 1 1e-104
315122748232 50S ribosomal protein L1 [Candidatus Liberibacter solan 1 1e-103
222148354231 50S ribosomal protein L1 [Agrobacterium vitis S4] Lengt 1 2e-92
150396196232 50S ribosomal protein L1 [Sinorhizobium medicae WSM419] 1 3e-92
227821744232 50S ribosomal protein L1 [Sinorhizobium fredii NGR234] 1 4e-92
15965098232 50S ribosomal protein L1 [Sinorhizobium meliloti 1021] 1 2e-91
163759403232 50S ribosomal protein L1 [Hoeflea phototrophica DFL-43] 1 8e-91
>gi|157704381|gb|ABV68880.1| 50S ribosomal subunit protein L1 [Candidatus Liberibacter asiaticus] Length = 232 Back     alignment and organism information
 Score =  463 bits (1192), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 231/232 (99%), Positives = 231/232 (99%)

Query: 1   MVSKISKRMQQISQGIDRSALYGLSDAVVMLKERATARFDETVEIAMNLGIDPRHANQMV 60
           MVSKISKRMQQISQGIDRSALYGLSDAVVMLKERATARFDETVEIAMNLGIDPRHANQMV
Sbjct: 1   MVSKISKRMQQISQGIDRSALYGLSDAVVMLKERATARFDETVEIAMNLGIDPRHANQMV 60

Query: 61  RGVVTMPNGTGVNVRVAVFATSSKADEAREAGADIVGGEDLFEIVKGGQIDFDRCIATPD 120
           RGVVTMPNGTGVNVRVAVFATSSKADEAREAGADIVGGEDLFEIVKGGQIDFDRCIATPD
Sbjct: 61  RGVVTMPNGTGVNVRVAVFATSSKADEAREAGADIVGGEDLFEIVKGGQIDFDRCIATPD 120

Query: 121 MMPLVGRLGRILGPRGIMPNLRVGTVTTDVATAVRESKSGAVDFRSEKAGIIHAGIGKVS 180
           MMPLVGRLGRILGPRGIMPNLRVGTVTTDVATAVRESKSGAVDFRSEKAGIIHAGIGKVS
Sbjct: 121 MMPLVGRLGRILGPRGIMPNLRVGTVTTDVATAVRESKSGAVDFRSEKAGIIHAGIGKVS 180

Query: 181 FENKKIEENVLAFVSAVVKAKPSVAKGDYVKRVTLSSTMGCGIKVDLSSFSV 232
           FENKKIEENVLAFVSAVVKAKPSVAKGDYVKRVTLSS MGCGIKVDLSSFSV
Sbjct: 181 FENKKIEENVLAFVSAVVKAKPSVAKGDYVKRVTLSSHMGCGIKVDLSSFSV 232



Species: Candidatus Liberibacter asiaticus
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|78355045|gb|ABB40597.1| putative 50S ribosomal subunit protein L1 [Candidatus Liberibacter asiaticus] Length = 232 Back     alignment and organism information
>gi|133872304|gb|ABO40223.1| 50S ribosomal subunit protein L1 [Candidatus Liberibacter africanus] Length = 231 Back     alignment and organism information
>gi|133872297|gb|ABO40217.1| 50S ribosomal subunit protein L1 [Candidatus Liberibacter americanus] Length = 232 Back     alignment and organism information
>gi|315122748|ref|YP_004063237.1| 50S ribosomal protein L1 [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 232 Back     alignment and organism information
>gi|222148354|ref|YP_002549311.1| 50S ribosomal protein L1 [Agrobacterium vitis S4] Length = 231 Back     alignment and organism information
>gi|150396196|ref|YP_001326663.1| 50S ribosomal protein L1 [Sinorhizobium medicae WSM419] Length = 232 Back     alignment and organism information
>gi|227821744|ref|YP_002825714.1| 50S ribosomal protein L1 [Sinorhizobium fredii NGR234] Length = 232 Back     alignment and organism information
>gi|15965098|ref|NP_385451.1| 50S ribosomal protein L1 [Sinorhizobium meliloti 1021] Length = 232 Back     alignment and organism information
>gi|163759403|ref|ZP_02166489.1| 50S ribosomal protein L1 [Hoeflea phototrophica DFL-43] Length = 232 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

Original result of RPS-BLAST against CDD database part I

Original result of RPS-BLASTagainst CDD database part II

IdentityAlignment graphLength Definition E-value
Target232 50S ribosomal protein L1 [Candidatus Liberibacter asiat
PRK05424230 PRK05424, rplA, 50S ribosomal protein L1; Validated 1e-106
TIGR01169227 TIGR01169, rplA_bact, ribosomal protein L1, bacterial/c 8e-93
COG0081228 COG0081, RplA, Ribosomal protein L1 [Translation, ribos 6e-77
CHL00129229 CHL00129, rpl1, ribosomal protein L1; Reviewed 1e-69
cd00403208 cd00403, Ribosomal_L1, Ribosomal protein L1 2e-52
KOG1569323 KOG1569, KOG1569, KOG1569, 50S ribosomal protein L1 [Tr 5e-38
PRK04203215 PRK04203, rpl1P, 50S ribosomal protein L1P; Reviewed 8e-25
PTZ00029216 PTZ00029, PTZ00029, 60S ribosomal protein L10a; Provisi 4e-08
PTZ00225214 PTZ00225, PTZ00225, 60S ribosomal protein L10a; Provisi 0.003
pfam00687203 pfam00687, Ribosomal_L1, Ribosomal protein L1p/L10e fam 2e-79
TIGR01170141 TIGR01170, rplA_mito, ribosomal protein L1, mitochondri 2e-19
>gnl|CDD|180071 PRK05424, rplA, 50S ribosomal protein L1; Validated Back     alignment and domain information
>gnl|CDD|162232 TIGR01169, rplA_bact, ribosomal protein L1, bacterial/chloroplast Back     alignment and domain information
>gnl|CDD|30430 COG0081, RplA, Ribosomal protein L1 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|177051 CHL00129, rpl1, ribosomal protein L1; Reviewed Back     alignment and domain information
>gnl|CDD|88601 cd00403, Ribosomal_L1, Ribosomal protein L1 Back     alignment and domain information
>gnl|CDD|36782 KOG1569, KOG1569, KOG1569, 50S ribosomal protein L1 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|179783 PRK04203, rpl1P, 50S ribosomal protein L1P; Reviewed Back     alignment and domain information
>gnl|CDD|185405 PTZ00029, PTZ00029, 60S ribosomal protein L10a; Provisional Back     alignment and domain information
>gnl|CDD|140252 PTZ00225, PTZ00225, 60S ribosomal protein L10a; Provisional Back     alignment and domain information
>gnl|CDD|144329 pfam00687, Ribosomal_L1, Ribosomal protein L1p/L10e family Back     alignment and domain information
>gnl|CDD|162233 TIGR01170, rplA_mito, ribosomal protein L1, mitochondrial Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

Original result of HHsearch against CDD database

IdentityAlignment graphLength Definition Probability
Target 232 50S ribosomal protein L1 [Candidatus Liberibacter asiat
TIGR01169227 rplA_bact ribosomal protein L1; InterPro: IPR005878 Rib 100.0
PRK05424232 rplA 50S ribosomal protein L1; Validated 100.0
CHL00129229 rpl1 ribosomal protein L1; Reviewed 100.0
COG0081228 RplA Ribosomal protein L1 [Translation, ribosomal struc 100.0
pfam00687203 Ribosomal_L1 Ribosomal protein L1p/L10e family. This fa 100.0
PRK04203216 rpl1P 50S ribosomal protein L1P; Reviewed 100.0
PTZ00029217 60S ribosomal protein L1/L10a; Provisional 100.0
PTZ00225214 60S ribosomal protein L10a; Provisional 100.0
cd00403208 Ribosomal_L1 Ribosomal protein L1. The L1 protein, loca 100.0
KOG1569323 consensus 100.0
KOG1570218 consensus 99.93
TIGR01170155 rplA_mito ribosomal protein L1, mitochondrial; InterPro 99.97
KOG1685343 consensus 99.0
PTZ00029217 60S ribosomal protein L1/L10a; Provisional 93.48
>TIGR01169 rplA_bact ribosomal protein L1; InterPro: IPR005878 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>PRK05424 rplA 50S ribosomal protein L1; Validated Back     alignment and domain information
>CHL00129 rpl1 ribosomal protein L1; Reviewed Back     alignment and domain information
>COG0081 RplA Ribosomal protein L1 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>pfam00687 Ribosomal_L1 Ribosomal protein L1p/L10e family Back     alignment and domain information
>PRK04203 rpl1P 50S ribosomal protein L1P; Reviewed Back     alignment and domain information
>PTZ00029 60S ribosomal protein L1/L10a; Provisional Back     alignment and domain information
>PTZ00225 60S ribosomal protein L10a; Provisional Back     alignment and domain information
>cd00403 Ribosomal_L1 Ribosomal protein L1 Back     alignment and domain information
>KOG1569 consensus Back     alignment and domain information
>KOG1570 consensus Back     alignment and domain information
>TIGR01170 rplA_mito ribosomal protein L1, mitochondrial; InterPro: IPR005879 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>KOG1685 consensus Back     alignment and domain information
>PTZ00029 60S ribosomal protein L1/L10a; Provisional 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

Original result of PSI-BLAST

IdentityAlignment graphLength Definition E-value
Target232 50S ribosomal protein L1 [Candidatus Liberibacter asiat
2j01_C229 Structure Of The Thermus Thermophilus 70s Ribosome 3e-62
2hgj_C229 Fitting Of Components With Known Structure Into An 6e-62
1ml5_c228 Crystal Structure Of The Ribosome At 5.5 A Resoluti 5e-61
2v49_C229 Structure Of The Ribosome Recycling Factor Bound To 8e-61
1ad2_A228 Ribosomal Protein L1 Mutant With Serine 179 Replace 2e-60
1zho_A228 The Structure Of A Ribosomal Protein L1 In Complex 1e-59
2hw8_A228 Structure Of Ribosomal Protein L1-Mrna Complex At 2 2e-59
487d_H224 Seven Ribosomal Proteins Fitted To A Cryo-Electron 8e-59
3fik_5234 Ternary Complex-Bound E.Coli 70s Ribosome. This Ent 6e-55
2rdo_9233 50s Subunit With Ef-G(Gdpnp) And Rrf Bound Length = 5e-54
2gya_2222 Structure Of The 50s Subunit Of A Pre-Translocation 2e-51
3bbo_D352 Homology Model For The Spinach Chloroplast 50s Subu 8e-49
3fin_C191 T. Thermophilus 70s Ribosome In Complex With Mrna, 3e-42
2zkr_5212 Structure Of A Mammalian Ribosomal 60s Subunit With 9e-18
1dwu_A213 Ribosomal Protein L1 Length = 213 2e-17
1cjs_A219 Crystal Structure Of Ribosomal Protein L1 From Meth 1e-15
1mzp_A217 Structure Of The L1 Protuberance In The Ribosome Le 1e-14
1u63_A219 The Structure Of A Ribosomal Protein L1-Mrna Comple 4e-14
2noq_G213 Structure Of Ribosome-Bound Cricket Paralysis Virus 1e-13
3e1b_Z213 Structure Of The 50s Subunit Of E. Coli Ribosome In 1e-13
1s1i_A217 Structure Of The Ribosomal 80s-Eef2-Sordarin Comple 3e-13
2ov7_A137 The First Domain Of The Ribosomal Protein L1 From T 2e-16
2ov7_A137 The First Domain Of The Ribosomal Protein L1 From T 2e-16
2ftc_A189 Structural Model For The Large Subunit Of The Mamma 6e-16
3izr_A216 Localization Of The Large Subunit Ribosomal Protein 1e-13
gi|116668234|pdb|2J01|C Chain C, 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 = 229 Back     alignment and structure 
 Score =  242 bits (617), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 101/229 (44%), Positives = 155/229 (67%), Gaps = 1/229 (0%)

Query: 2   VSKISKRMQQISQGIDRSALYGLSDAVVMLKERATARFDETVEIAMNLGIDPRHANQMVR 61
           + K  KR + + + +D + +Y + +A  ++KE ATA+FDETVE+   LGIDPR ++Q VR
Sbjct: 1   MPKHGKRYRALLEKVDPNKVYTIDEAARLVKELATAKFDETVEVHAKLGIDPRRSDQNVR 60

Query: 62  GVVTMPNGTGVNVRVAVFATSSKADEAREAGADIVGGEDLFEIVKGGQIDFDRCIATPDM 121
           G V++P+G G  VRV   A   K  EA EAGAD VGGE++ + +  G +DFD  +ATPD+
Sbjct: 61  GTVSLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVGGEEIIQKILDGWMDFDAVVATPDV 120

Query: 122 MPLV-GRLGRILGPRGIMPNLRVGTVTTDVATAVRESKSGAVDFRSEKAGIIHAGIGKVS 180
           M  V  +LGRILGPRG++PN + GTV  ++   +RE K+G ++FR++K G IHA +GK S
Sbjct: 121 MGAVGSKLGRILGPRGLLPNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKAS 180

Query: 181 FENKKIEENVLAFVSAVVKAKPSVAKGDYVKRVTLSSTMGCGIKVDLSS 229
           F  +K+ +N+ AF+ A+   KP  AKG +++ V +++TMG  ++++  S
Sbjct: 181 FPPEKLADNIRAFIRALEAHKPEGAKGTFLRSVYVTTTMGPSVRINPHS 229
>gi|119389735|pdb|2HGJ|C Chain C, 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 = 229 Back     alignment and structure
>gi|28373722|pdb|1ML5|CC Chain c, Structure Of The E. Coli Ribosomal Termination Complex With Release Factor 2 Length = 228 Back     alignment and structure
>gi|157836577|pdb|2V49|C Chain C, Structure Of The Ribosome Recycling Factor Bound To The Thermus Thermophilus 70s Ribosome With Mrna, Asl-Phe And Trna-Fmet (Part 4 Of 4). This File Contains The 50s Subunit Of Molecule 2 Length = 229 Back     alignment and structure
>gi|157829807|pdb|1AD2|A Chain A, Ribosomal Protein L1 Mutant With Serine 179 Replaced By Cysteine Length = 228 Back     alignment and structure
>gi|109156960|pdb|1ZHO|A Chain A, The Structure Of A Ribosomal Protein L1 In Complex With Mrna Length = 228 Back     alignment and structure
>gi|122920476|pdb|2HW8|A Chain A, Structure Of Ribosomal Protein L1-Mrna Complex At 2.1 Resolution Length = 228 Back     alignment and structure
>gi|7767184|pdb|487D|H Chain H, Seven Ribosomal Proteins Fitted To A Cryo-Electron Microscopic Map Of The Large 50s Subunit At 7.5 Angstroms Resolution Length = 224 Back     alignment and structure
gi|224510737|pdb|3FIK|5 Chain 5, Ternary Complex-Bound E.Coli 70s Ribosome. This Entry Consists Of The 50s Subunit. Length = 234 Back     alignment and structure
>gi|169404633|pdb|2RDO|9 Chain 9, 50s Subunit With Ef-G(Gdpnp) And Rrf Bound Length = 233 Back     alignment and structure
>gi|116667432|pdb|2GYA|2 Chain 2, 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 = 222 Back     alignment and structure
gi|189096126|pdb|3BBO|D Chain D, Homology Model For The Spinach Chloroplast 50s Subunit Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome Length = 352 Back     alignment and structure
>gi|224510781|pdb|3FIN|C Chain C, 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 = 191 Back     alignment and structure
gi|187609331|pdb|2ZKR|5 Chain 5, 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 = 212 Back     alignment and structure
gi|12084594|pdb|1DWU|A Chain A, Ribosomal Protein L1 Length = 213 Back     alignment and structure
gi|8569324|pdb|1CJS|A Chain A, Crystal Structure Of Ribosomal Protein L1 From Methanococcus Jannaschii Length = 219 Back     alignment and structure
>gi|28373823|pdb|1MZP|A Chain A, Structure Of The L1 Protuberance In The Ribosome Length = 217 Back     alignment and structure
>gi|66360220|pdb|1U63|A Chain A, The Structure Of A Ribosomal Protein L1-Mrna Complex Length = 219 Back     alignment and structure
>gi|119390529|pdb|2NOQ|G Chain G, Structure Of Ribosome-Bound Cricket Paralysis Virus Ires Rna Length = 213 Back     alignment and structure
>gi|256032398|pdb|3E1B|Z Chain Z, Structure Of The 50s Subunit Of E. Coli Ribosome In Pre- Accommodation State Length = 213 Back     alignment and structure
gi|49258839|pdb|1S1I|A Chain A, 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 = 217 Back     alignment and structure
>gi|163930938|pdb|2OV7|A Chain A, The First Domain Of The Ribosomal Protein L1 From Thermus Thermophilus Length = 137 Back     alignment and structure
>gi|163930938|pdb|2OV7|A Chain A, The First Domain Of The Ribosomal Protein L1 From Thermus Thermophilus Length = 137 Back     alignment and structure
>gi|99032307|pdb|2FTC|A Chain A, Structural Model For The Large Subunit Of The Mammalian Mitochondrial Ribosome Length = 189 Back     alignment and structure
>gi|315113249|pdb|3IZR|A Chain A, Localization Of The Large Subunit Ribosomal Proteins Into A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s Ribosome Length = 216 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

IdentityAlignment graphLength Definition E-value
Target232 50S ribosomal protein L1 [Candidatus Liberibacter asiat
2wwq_5234 50S ribosomal protein L1; ribosomal protein, ribonucleo 5e-71
1ad2_A228 TL2, ribosomal protein L1; RNA binding, protein synthes 3e-65
3bbo_D352 Ribosomal protein L1; large ribosomal subunit, spinach 3e-64
3fik_5234 50S ribosomal protein L1; ribosome, decoding, tRNA, EF- 5e-63
1mzp_A217 50S ribosomal protein L1P; ribosome, RNA-protein comple 1e-49
1i2a_A219 50S ribosomal protein L1P; primary rRNA-binding protein 1e-47
2noq_G213 60S ribosomal protein L1; IRES RNA, ribosome, translati 9e-42
2zkr_5212 60S ribosomal protein L10A; protein-RNA complex, 60S ri 5e-33
2ftc_A189 Mitochondrial ribosomal protein L1; mitochondrial ribos 7e-41
2ov7_A137 50S ribosomal protein L1; 2.30A {Thermus thermophilus} 1e-24
2ov7_A137 50S ribosomal protein L1; 2.30A {Thermus thermophilus} 2e-18
>2wwq_5 50S ribosomal protein L1; ribosomal protein, ribonucleoprotein, nucleotide-binding, protein biosynthesis, translation, zinc-finger; HET: 5MU; 5.80A {Escherichia coli} PDB: 3fik_5 3kcr_5 2rdo_9 2gya_2 2gyc_2 Length = 234 Back     alignment and structure
 Score =  262 bits (670), Expect = 5e-71
 Identities = 115/229 (50%), Positives = 175/229 (76%)

Query: 3   SKISKRMQQISQGIDRSALYGLSDAVVMLKERATARFDETVEIAMNLGIDPRHANQMVRG 62
           +K++KRM+ I + +D +  Y +++A+ +LKE ATA+F E+V++A+NLGID R ++Q VRG
Sbjct: 2   AKLTKRMRVIREKVDATKQYDINEAIALLKELATAKFVESVDVAVNLGIDARKSDQNVRG 61

Query: 63  VVTMPNGTGVNVRVAVFATSSKADEAREAGADIVGGEDLFEIVKGGQIDFDRCIATPDMM 122
              +P+GTG +VRVAVF   + A+ A+ AGA++VG EDL + +K G+++FD  IA+PD M
Sbjct: 62  ATVLPHGTGRSVRVAVFTQGANAEAAKAAGAELVGMEDLADQIKKGEMNFDVVIASPDAM 121

Query: 123 PLVGRLGRILGPRGIMPNLRVGTVTTDVATAVRESKSGAVDFRSEKAGIIHAGIGKVSFE 182
            +VG+LG++LGPRG+MPN +VGTVT +VA AV+ +K+G V +R++K GIIH  IGKV F+
Sbjct: 122 RVVGQLGQVLGPRGLMPNPKVGTVTPNVAEAVKNAKAGQVRYRNDKNGIIHTTIGKVDFD 181

Query: 183 NKKIEENVLAFVSAVVKAKPSVAKGDYVKRVTLSSTMGCGIKVDLSSFS 231
             K++EN+ A + A+ KAKP+ AKG Y+K+V++S+TMG G+ VD +  S
Sbjct: 182 ADKLKENLEALLVALKKAKPTQAKGVYIKKVSISTTMGAGVAVDQAGLS 230
>1ad2_A TL2, ribosomal protein L1; RNA binding, protein synthesis, mutant; 1.90A {Thermus thermophilus} SCOP: e.24.1.1 PDB: 1eg0_N 1vsa_A 1vsp_A 2hgj_C 2hgq_C 2hgu_C 1zho_A 1ml5_c* 1yl3_C 1giy_C 2hw8_A 2j01_C 2j03_C 2jl6_C 2jl8_C 2om7_K* 2v47_C 2wdi_C 2wdj_C 2wdl_C ... Length = 228 Back     alignment and structure
>3bbo_D Ribosomal protein L1; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Length = 352 Back     alignment and structure
>3fik_5 50S ribosomal protein L1; ribosome, decoding, tRNA, EF-TU, ternary complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding; 6.70A {Escherichia coli} PDB: 2rdo_9 2gya_2 2gyc_2 Length = 234 Back     alignment and structure
>1mzp_A 50S ribosomal protein L1P; ribosome, RNA-protein complex; 2.65A {Sulfolobus acidocaldarius} SCOP: e.24.1.1 PDB: 1pnu_5 1pny_5 1vor_7 1vou_7 1vow_7 1voy_7 1vp0_7 3e1b_Z 3e1d_Z Length = 217 Back     alignment and structure
>1i2a_A 50S ribosomal protein L1P; primary rRNA-binding protein, translational repressor, ribosome; 1.85A {Methanocaldococcus jannaschii} SCOP: e.24.1.1 PDB: 1cjs_A 1u63_A 1dwu_A Length = 219 Back     alignment and structure
>2noq_G 60S ribosomal protein L1; IRES RNA, ribosome, translation, internal initiation; 7.30A {Saccharomyces cerevisiae} PDB: 1s1i_A Length = 213 Back     alignment and structure
>2zkr_5 60S ribosomal protein L10A; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Length = 212 Back     alignment and structure
>2ftc_A Mitochondrial ribosomal protein L1; mitochondrial ribosome, large ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus} Length = 189 Back     alignment and structure
>2ov7_A 50S ribosomal protein L1; 2.30A {Thermus thermophilus} PDB: 2oum_A 2vpl_A Length = 137 Back     alignment and structure
>2ov7_A 50S ribosomal protein L1; 2.30A {Thermus thermophilus} PDB: 2oum_A 2vpl_A Length = 137 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

Original result of HHsearch against PDB70 database

IdentityAlignment graphLength Definition Probability
Target232 50S ribosomal protein L1 [Candidatus Liberibacter asiat
2wwq_5234 50S ribosomal protein L1; ribosomal protein, ribonucleo 100.0
3bbo_D352 Ribosomal protein L1; large ribosomal subunit, spinach 100.0
1ad2_A228 TL2, ribosomal protein L1; RNA binding, protein synthes 100.0
1i2a_A219 50S ribosomal protein L1P; primary rRNA-binding protein 100.0
1mzp_A217 50S ribosomal protein L1P; ribosome, RNA-protein comple 100.0
2zkr_5212 60S ribosomal protein L10A; protein-RNA complex, 60S ri 100.0
2noq_G213 60S ribosomal protein L1; IRES RNA, ribosome, translati 100.0
2ov7_A137 50S ribosomal protein L1; 2.30A {Thermus thermophilus} 100.0
2ftc_A189 Mitochondrial ribosomal protein L1; mitochondrial ribos 100.0
>2wwq_5 50S ribosomal protein L1; ribosomal protein, ribonucleoprotein, nucleotide-binding, protein biosynthesis, translation, zinc-finger; HET: 5MU; 5.80A {Escherichia coli} PDB: 3fik_5 3kcr_5 2rdo_9 2gya_2 2gyc_2 Back     alignment and structure
Probab=100.00  E-value=0  Score=497.26  Aligned_cols=230  Identities=50%  Similarity=0.862  Sum_probs=227.3

Q ss_pred             CCCCCHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCCCCCCEEEEEECCCCCCCCCEEEEEC
Q ss_conf             74223437989851384768898999999986087899862999999537876454430137995277886540699975
Q gi|254780146|r    2 VSKISKRMQQISQGIDRSALYGLSDAVVMLKERATARFDETVEIAMNLGIDPRHANQMVRGVVTMPNGTGVNVRVAVFAT   81 (232)
Q Consensus         2 m~k~~Kr~~~~~~~~~~~~~ysi~eAi~~lk~~~~~kf~esvel~i~L~id~~k~~~~irg~v~LPh~~gk~~kV~Vf~~   81 (232)
                      |+|+||||+.+.+.+|..+.|+++||++++|+.+.++|+||+|++|+|++|++|++++|||++.|||++|++.+|||||+
T Consensus         1 m~k~~kr~k~~~~~~d~~k~y~i~eAi~~lk~~~~~kF~etvel~i~L~~d~~k~~~~i~g~v~LP~~~~k~~ki~v~a~   80 (234)
T 2wwq_5            1 MAKLTKRMRVIREKVDATKQYDINEAIALLKELATAKFVESVDVAVNLGIDARKSDQNVRGATVLPHGTGRSVRVAVFTQ   80 (234)
T ss_dssp             CCCCCHHHHHHHTTSCCSSEECHHHHHHHHHHTCCCSSCCEEEEEEEECSCCCSSTTSCCEEEECSSCCSSCCCEEEECS
T ss_pred             CCCCCHHHHHHHHHCCCCCCCCHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCCCCCEECCEEECCCCCCCCEEEEEECC
T ss_conf             99536899998861553566699999999997177998764899999788777666302213304678986259999738


Q ss_pred             HHHHHHHHHCCCCCCCHHHHHHHHHCCCCCCCEEEECHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHCCC
Q ss_conf             04457687412000027899999751753334688644677888864332001001742233566655799999986011
Q gi|254780146|r   82 SSKADEAREAGADIVGGEDLFEIVKGGQIDFDRCIATPDMMPLVGRLGRILGPRGIMPNLRVGTVTTDVATAVRESKSGA  161 (232)
Q Consensus        82 ~~~~~~Ak~aGa~~vg~~eli~~i~~~~~~fd~~iAt~~~m~~i~klgriLGPkglMPn~k~GTv~~di~~~i~~~k~g~  161 (232)
                      ++.+++|+++||+++|++||+++|+++|++||+|+|||++|+++++||++||||||||||+.||+++|+.++|+++++|+
T Consensus        81 ~~~~~~Ak~aGa~~vg~~dLi~~Ik~~~~~~d~~ia~~~~m~~l~klg~iLGprGlMP~pk~GTv~~d~~~~i~~~k~g~  160 (234)
T 2wwq_5           81 GANAEAAKAAGAELVGMEDLADQIKKGEMNFDVVIASPDAMRVVGQLGQVLGPRGLMPNPKVGTVTPNVAEAVKNAKAGQ  160 (234)
T ss_dssp             SSCHHHHHHHTCSEECSHHHHHHHHHTCCCSSEEEECHHHHHHTTSSCSCCCSSCCSCCTTTTCBCSCSHHHHHHHHHHE
T ss_pred             CHHHHHHHHCCCCEECHHHHHHHHHCCCCCCCEEECCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCE
T ss_conf             15799998769989753776655424551026332377788888876541564568999998976704999999985786


Q ss_pred             CCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEECCCCCEEEECHHCC
Q ss_conf             1022357526787531577898999999999999998608662544337799999238972774001005
Q gi|254780146|r  162 VDFRSEKAGIIHAGIGKVSFENKKIEENVLAFVSAVVKAKPSVAKGDYVKRVTLSSTMGCGIKVDLSSFS  231 (232)
Q Consensus       162 i~~r~~k~g~i~~~IG~~~m~~e~i~eNi~~~~~~i~~~kp~~~kg~~Ik~v~lssTmGp~i~id~~~~~  231 (232)
                      ++||.++.|++|++||+++|+++||.||+.+++++|.+++|.+.+|.||+++|||||||||++||+.+|+
T Consensus       161 v~~r~~k~g~i~~~IG~~~m~~e~L~eNi~a~l~~i~~~~p~~~kg~~Ik~v~lksTMGp~i~id~~~~~  230 (234)
T 2wwq_5          161 VRYRNDKNGIIHTTIGKVDFDADKLKENLEALLVALKKAKPTQAKGVYIKKVSISTTMGAGVAVDQAGLS  230 (234)
T ss_dssp             EEECCSSSCEEEEEEEETTSCHHHHHHHHHHHHHHHHHSCCSSCCSCCEEEEEEEESSSCEEEESSSCCC
T ss_pred             EEEEECCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEECCCCCCEEEEHHHHH
T ss_conf             9994167755887753456898999999999999999739653467458899998998998898868956
>3bbo_D Ribosomal protein L1; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Back     alignment and structure
>1ad2_A TL2, ribosomal protein L1; RNA binding, protein synthesis, mutant; 1.90A {Thermus thermophilus} SCOP: e.24.1.1 PDB: 1vsa_A 1eg0_N 1vsp_A 2hgj_C 2hgq_C 2hgu_C 1zho_A 1ml5_c* 1yl3_C 1giy_C 2hw8_A 2j01_C 2j03_C 2jl6_C 2jl8_C 2om7_K* 2v47_C 2wdi_C 2wdj_C 2wdl_C ... Back     alignment and structure
>1i2a_A 50S ribosomal protein L1P; primary rRNA-binding protein, translational repressor, ribosome; 1.85A {Methanocaldococcus jannaschii} SCOP: e.24.1.1 PDB: 1cjs_A 1u63_A 1dwu_A Back     alignment and structure
>1mzp_A 50S ribosomal protein L1P; ribosome, RNA-protein complex; 2.65A {Sulfolobus acidocaldarius} SCOP: e.24.1.1 PDB: 1pnu_5 1pny_5 1vor_7 1vou_7 1vow_7 1voy_7 1vp0_7 3e1b_Z 3e1d_Z Back     alignment and structure
>2zkr_5 60S ribosomal protein L10A; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Back     alignment and structure
>2noq_G 60S ribosomal protein L1; IRES RNA, ribosome, translation, internal initiation; 7.30A {Saccharomyces cerevisiae} PDB: 3jyw_A 1s1i_A Back     alignment and structure
>2ov7_A 50S ribosomal protein L1; 2.30A {Thermus thermophilus} PDB: 2oum_A 2vpl_A Back     alignment and structure
>2ftc_A Mitochondrial ribosomal protein L1; mitochondrial ribosome, large ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus} 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

Original result of RPS-BLAST against SCOP70(version1.75) database

IdentityAlignment graphLength Definition E-value
Target 232 50S ribosomal protein L1 [Candidatus Liberibacter asiat
d1ad2a_224 e.24.1.1 (A:) Ribosomal protein L1 {Thermus thermophilu 4e-63
d1i2aa_212 e.24.1.1 (A:) Ribosomal protein L1 {Archaeon Methanococ 1e-38
d1mzpa_217 e.24.1.1 (A:) Ribosomal protein L1 {Archaeon Sulfolobus 2e-38
>d1ad2a_ e.24.1.1 (A:) Ribosomal protein L1 {Thermus thermophilus [TaxId: 274]} Length = 224 Back     information, alignment and structure

class: Multi-domain proteins (alpha and beta)
fold: Ribosomal protein L1
superfamily: Ribosomal protein L1
family: Ribosomal protein L1
domain: Ribosomal protein L1
species: Thermus thermophilus [TaxId: 274]

 Score =  234 bits (599), Expect = 4e-63
 Identities = 100/224 (44%), Positives = 152/224 (67%), Gaps = 1/224 (0%)

Query: 7   KRMQQISQGIDRSALYGLSDAVVMLKERATARFDETVEIAMNLGIDPRHANQMVRGVVTM 66
           KR + + + +D + +Y + +A  ++KE ATA+FDETVE+   LGIDPR ++Q VRG V++
Sbjct: 1   KRYRALLEKVDPNKIYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSL 60

Query: 67  PNGTGVNVRVAVFATSSKADEAREAGADIVGGEDLFEIVKGGQIDFDRCIATPDMMPLVG 126
           P+G G  VRV   A   K  EA EAGAD VGGE++ + +  G +DFD  +ATPD+M  VG
Sbjct: 61  PHGLGKQVRVLAIAKGEKIKEAEEAGADYVGGEEIIQKILDGWMDFDAVVATPDVMGAVG 120

Query: 127 R-LGRILGPRGIMPNLRVGTVTTDVATAVRESKSGAVDFRSEKAGIIHAGIGKVSFENKK 185
             LGRILGPRG++PN + GTV  ++   +RE K+G ++FR++K G IHA +GK  F  +K
Sbjct: 121 SKLGRILGPRGLLPNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKACFPPEK 180

Query: 186 IEENVLAFVSAVVKAKPSVAKGDYVKRVTLSSTMGCGIKVDLSS 229
           + +N+ AF+ A+   KP  AKG +++ V +++TMG  ++++  S
Sbjct: 181 LADNIRAFIRALEAHKPEGAKGTFLRSVYVTTTMGPSVRINPHS 224
>d1i2aa_ e.24.1.1 (A:) Ribosomal protein L1 {Archaeon Methanococcus jannaschii [TaxId: 2190]} Length = 212 Back     information, alignment and structure
>d1mzpa_ e.24.1.1 (A:) Ribosomal protein L1 {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]} Length = 217 Back     information, alignment and structure

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

Original result of HHsearch against SCOP70(version1.75) database

IdentityAlignment graphLength Definition Probability
Target232 50S ribosomal protein L1 [Candidatus Liberibacter asiat
d1ad2a_224 Ribosomal protein L1 {Thermus thermophilus [TaxId: 274] 100.0
d1mzpa_217 Ribosomal protein L1 {Archaeon Sulfolobus acidocaldariu 100.0
d1i2aa_212 Ribosomal protein L1 {Archaeon Methanococcus jannaschii 100.0
>d1ad2a_ e.24.1.1 (A:) Ribosomal protein L1 {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
class: Multi-domain proteins (alpha and beta)
fold: Ribosomal protein L1
superfamily: Ribosomal protein L1
family: Ribosomal protein L1
domain: Ribosomal protein L1
species: Thermus thermophilus [TaxId: 274]

Probab=100.00  E-value=0  Score=484.29  Aligned_cols=223  Identities=45%  Similarity=0.796  Sum_probs=218.9

Q ss_pred             HHHHHHHHHCCCCCCCCHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCCCCCCEEEEEECCCCCCCCCEEEEECHHHHH
Q ss_conf             43798985138476889899999998608789986299999953787645443013799527788654069997504457
Q gi|254780146|r    7 KRMQQISQGIDRSALYGLSDAVVMLKERATARFDETVEIAMNLGIDPRHANQMVRGVVTMPNGTGVNVRVAVFATSSKAD   86 (232)
Q Consensus         7 Kr~~~~~~~~~~~~~ysi~eAi~~lk~~~~~kf~esvel~i~L~id~~k~~~~irg~v~LPh~~gk~~kV~Vf~~~~~~~   86 (232)
                      |||+++.+.+|..+.|+++||+++||+.+.++|+||||++++|++|++|++++|||+|.|||++|++.+|||||+++.++
T Consensus         1 kr~~~~~~~~d~~k~ysi~EAi~~lk~~~~~kF~esvel~i~L~~~~~k~~~~i~g~v~LP~~~~k~~ki~v~~~~e~~~   80 (224)
T d1ad2a_           1 KRYRALLEKVDPNKIYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIK   80 (224)
T ss_dssp             CCCTTTTTSCCTTCCBCHHHHHHHHHTTCCSSSCCEEEEEEEESSCTTCGGGCCEEEEECSSSCSTTSCEEEECCTHHHH
T ss_pred             CCHHHHHHCCCCCCCCCHHHHHHHHHHCCCCCCCCEEEEEEEECCCCCCCCCCCCEEEEECCCCCCCEEEEEECCHHHHH
T ss_conf             94677765067667769999999999718899995299999974566655554312677414666640378854637799


Q ss_pred             HHHHCCCCCCCHHHHHHHHHCCCCCCCEEEECHHHHHHHH-HHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHCCCCCCC
Q ss_conf             6874120000278999997517533346886446778888-643320010017422335666557999999860111022
Q gi|254780146|r   87 EAREAGADIVGGEDLFEIVKGGQIDFDRCIATPDMMPLVG-RLGRILGPRGIMPNLRVGTVTTDVATAVRESKSGAVDFR  165 (232)
Q Consensus        87 ~Ak~aGa~~vg~~eli~~i~~~~~~fd~~iAt~~~m~~i~-klgriLGPkglMPn~k~GTv~~di~~~i~~~k~g~i~~r  165 (232)
                      +|+++||++||++|++++|+++|++||+|||||+||++++ +|||+||||||||||+.||+++|+.++|+++++|+++||
T Consensus        81 ~Ak~aGa~~vg~~eli~ki~~~~~~fd~~ia~~~~m~~v~~~lgriLGprGlMP~pk~Gtv~~di~~~v~~~k~g~v~~r  160 (224)
T d1ad2a_          81 EAEEAGADYVGGEEIIQKILDGWMDFDAVVATPDVMGAVGSKLGRILGPRGLLPNPKAGTVGFNIGEIIREIKAGRIEFR  160 (224)
T ss_dssp             HHHHTTCSEEECGGGHHHHHTTCCCCSEEEECGGGHHHHHHHHHHHHHHHTCSCCTTTTCBCSCHHHHHHHHHTTEEEEE
T ss_pred             HHHHCCCCCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCEEEEE
T ss_conf             98766762007377888875577530068868999999998640204765679987778866449999999868848986


Q ss_pred             CCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEECCCCCEEEECHH
Q ss_conf             3575267875315778989999999999999986086625443377999992389727740010
Q gi|254780146|r  166 SEKAGIIHAGIGKVSFENKKIEENVLAFVSAVVKAKPSVAKGDYVKRVTLSSTMGCGIKVDLSS  229 (232)
Q Consensus       166 ~~k~g~i~~~IG~~~m~~e~i~eNi~~~~~~i~~~kp~~~kg~~Ik~v~lssTmGp~i~id~~~  229 (232)
                      +++.|++|++||+++|+++||.||+.+++++|.+++|.+.+|.||+++|||||||||++||.+|
T Consensus       161 ~~k~g~i~~~IG~~~m~~e~i~eNi~~~i~~i~~~~p~~~k~~~ik~v~l~sTmGp~~~id~~s  224 (224)
T d1ad2a_         161 NDKTGAIHAPVGKACFPPEKLADNIRAFIRALEAHKPEGAKGTFLRSVYVTTTMGPSVRINPHS  224 (224)
T ss_dssp             CCTTSEEEEEEEETTSCHHHHHHHHHHHHHHHHTTCCTTCCSCSEEEEEEECTTSCCEEECTTC
T ss_pred             ECCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEECCCCCCEEECCCC
T ss_conf             4787545102210248989999999999999998495645787486999989999897839999
>d1mzpa_ e.24.1.1 (A:) Ribosomal protein L1 {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]} Back     information, alignment and structure
>d1i2aa_ e.24.1.1 (A:) Ribosomal protein L1 {Archaeon Methanococcus jannaschii [TaxId: 2190]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

Original result of RPS-BLAST against MMDB70 database

IdentityAlignment graphLength Definition E-value
Target 232 50S ribosomal protein L1 [Candidatus Liberibacter
2ftc_A_189 (A:) Mitochondrial ribosomal protein L1; mitochond 1e-48
2ov7_A_18-137120 (A:18-137) 50S ribosomal protein L1; 2.30A {Thermu 3e-33
3fik_5_1-71_134-234172 (5:1-71,5:134-234) 50S ribosomal protein L1; ribos 3e-27
3bbo_D_184-27188 (D:184-271) Ribosomal protein L1; large ribosomal 8e-32
1ad2_A_69-15991 (A:69-159) TL2, ribosomal protein L1; RNA binding, 5e-28
1i2a_A_55-14894 (A:55-148) 50S ribosomal protein L1P; primary rRNA 2e-25
2zkr_5_55-14793 (5:55-147) 60S ribosomal protein L10A; protein-RNA 2e-25
2noq_G_57-14993 (G:57-149) 60S ribosomal protein L1; IRES RNA, rib 8e-25
1mzp_A_59-15294 (A:59-152) 50S ribosomal protein L1P; ribosome, RN 4e-24
3fik_5_72-13362 (5:72-133) 50S ribosomal protein L1; ribosome, dec 8e-24
3fik_5_1-71_134-234172 (5:1-71,5:134-234) 50S ribosomal protein L1; ribos 3e-22
3bbo_D_1-183_272-352264 (D:1-183,D:272-352) Ribosomal protein L1; large ri 4e-22
1ad2_A_1-68_160-228137 (A:1-68,A:160-228) TL2, ribosomal protein L1; RNA 1e-22
1i2a_A_1-54_149-219125 (A:1-54,A:149-219) 50S ribosomal protein L1P; prim 3e-13
1mzp_A_1-58_153-217123 (A:1-58,A:153-217) 50S ribosomal protein L1P; ribo 1e-13
2zkr_5_1-54_148-212119 (5:1-54,5:148-212) 60S ribosomal protein L10A; pro 5e-13
3bbo_D_1-183_272-352264 (D:1-183,D:272-352) Ribosomal protein L1; large ri 1e-23
1ad2_A_1-68_160-228137 (A:1-68,A:160-228) TL2, ribosomal protein L1; RNA 1e-22
1i2a_A_1-54_149-219125 (A:1-54,A:149-219) 50S ribosomal protein L1P; prim 2e-19
2noq_G_1-56_150-213120 (G:1-56,G:150-213) 60S ribosomal protein L1; IRES 3e-18
1mzp_A_1-58_153-217123 (A:1-58,A:153-217) 50S ribosomal protein L1P; ribo 1e-17
2zkr_5_1-54_148-212119 (5:1-54,5:148-212) 60S ribosomal protein L10A; pro 2e-17
>2ftc_A (A:) Mitochondrial ribosomal protein L1; mitochondrial ribosome, large ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus}Length = 189 Back     alignment and structure
 Score =  187 bits (476), Expect = 1e-48
 Identities = 36/191 (18%), Positives = 82/191 (42%), Gaps = 6/191 (3%)

Query: 43  VEIAMNLGIDPRHANQMVRGVVTMPNGTGVNVRVAVFAT--SSKADEAREAGADIVGGED 100
           +++ +++ +  +   +    V+++P      +      T  +S+   A E GA   GG  
Sbjct: 1   LDLTLDMALGKKKNVEPFTSVLSLPYPFASEINKVAVFTENASEVKIAEENGAAFAGGTS 60

Query: 101 LFEIVKGGQIDFDRCIATPDMMPLVGRLGRILGPRGIMPNLRVGTVTTDVATAVRESKSG 160
           L + +   +I  D  +A P++MP + RL + L  +    +    ++  D+   +   K+G
Sbjct: 61  LIQKIWDDEIVADFYVAVPEIMPELNRLRKKLNKKYPKLS--RNSIGRDIPKMLELFKNG 118

Query: 161 -AVDFRSEKAGIIHAGIGKVSFENKKIEENVLAFVSAVVKAKPSVAKGDYVKRVTLSSTM 219
             +    E+   +   I  +   + +I  N+ A ++ V + +P    G +V R  L S+ 
Sbjct: 119 HEIKVDEERENFLQTKIATLDMSSDQIAANLQAVINEVCRHRPL-NLGPFVVRAFLRSST 177

Query: 220 GCGIKVDLSSF 230
             G+ + +   
Sbjct: 178 SEGLLLKIDPL 188
>2ov7_A (A:18-137) 50S ribosomal protein L1; 2.30A {Thermus thermophilus} PDB: 2oum_A 2vpl_ALength = 120 Back     alignment and structure
>3fik_5 (5:1-71,5:134-234) 50S ribosomal protein L1; ribosome, decoding, tRNA, EF-TU, ternary complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding; 6.70A {Escherichia coli} PDB: 2rdo_9 2gya_2 2gyc_2Length = 172 Back     alignment and structure
>3bbo_D (D:184-271) Ribosomal protein L1; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}Length = 88 Back     alignment and structure
>1ad2_A (A:69-159) TL2, ribosomal protein L1; RNA binding, protein synthesis, mutant; 1.90A {Thermus thermophilus}Length = 91 Back     alignment and structure
>1i2a_A (A:55-148) 50S ribosomal protein L1P; primary rRNA-binding protein, translational repressor, ribosome; 1.85A {Methanocaldococcus jannaschii}Length = 94 Back     alignment and structure
>2zkr_5 (5:55-147) 60S ribosomal protein L10A; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris}Length = 93 Back     alignment and structure
>2noq_G (G:57-149) 60S ribosomal protein L1; IRES RNA, ribosome, translation, internal initiation; 7.30A {Saccharomyces cerevisiae} PDB: 1s1i_ALength = 93 Back     alignment and structure
>1mzp_A (A:59-152) 50S ribosomal protein L1P; ribosome, RNA-protein complex; 2.65A {Sulfolobus acidocaldarius}Length = 94 Back     alignment and structure
>3fik_5 (5:72-133) 50S ribosomal protein L1; ribosome, decoding, tRNA, EF-TU, ternary complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding; 6.70A {Escherichia coli} PDB: 2rdo_9 2gya_2 2gyc_2Length = 62 Back     alignment and structure
>3fik_5 (5:1-71,5:134-234) 50S ribosomal protein L1; ribosome, decoding, tRNA, EF-TU, ternary complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding; 6.70A {Escherichia coli} PDB: 2rdo_9 2gya_2 2gyc_2Length = 172 Back     alignment and structure
>3bbo_D (D:1-183,D:272-352) Ribosomal protein L1; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}Length = 264 Back     alignment and structure
>1ad2_A (A:1-68,A:160-228) TL2, ribosomal protein L1; RNA binding, protein synthesis, mutant; 1.90A {Thermus thermophilus}Length = 137 Back     alignment and structure
>1i2a_A (A:1-54,A:149-219) 50S ribosomal protein L1P; primary rRNA-binding protein, translational repressor, ribosome; 1.85A {Methanocaldococcus jannaschii}Length = 125 Back     alignment and structure
>1mzp_A (A:1-58,A:153-217) 50S ribosomal protein L1P; ribosome, RNA-protein complex; 2.65A {Sulfolobus acidocaldarius}Length = 123 Back     alignment and structure
>2zkr_5 (5:1-54,5:148-212) 60S ribosomal protein L10A; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris}Length = 119 Back     alignment and structure
>3bbo_D (D:1-183,D:272-352) Ribosomal protein L1; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}Length = 264 Back     alignment and structure
>1ad2_A (A:1-68,A:160-228) TL2, ribosomal protein L1; RNA binding, protein synthesis, mutant; 1.90A {Thermus thermophilus}Length = 137 Back     alignment and structure
>1i2a_A (A:1-54,A:149-219) 50S ribosomal protein L1P; primary rRNA-binding protein, translational repressor, ribosome; 1.85A {Methanocaldococcus jannaschii}Length = 125 Back     alignment and structure
>2noq_G (G:1-56,G:150-213) 60S ribosomal protein L1; IRES RNA, ribosome, translation, internal initiation; 7.30A {Saccharomyces cerevisiae} PDB: 1s1i_ALength = 120 Back     alignment and structure
>1mzp_A (A:1-58,A:153-217) 50S ribosomal protein L1P; ribosome, RNA-protein complex; 2.65A {Sulfolobus acidocaldarius}Length = 123 Back     alignment and structure
>2zkr_5 (5:1-54,5:148-212) 60S ribosomal protein L10A; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris}Length = 119 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

Original result of HHsearch against MMDB70 database

IdentityAlignment graphLength Definition Probability
Target232 50S ribosomal protein L1 [Candidatus Liberibacter asiat
2ftc_A_189 Mitochondrial ribosomal protein L1; mitochondrial 100.0
2zkr_5_1-54_148-212119 60S ribosomal protein L10A; protein-RNA complex, 6 99.96
1i2a_A_1-54_149-219125 50S ribosomal protein L1P; primary rRNA-binding pr 99.96
2noq_G_1-56_150-213120 60S ribosomal protein L1; IRES RNA, ribosome, tran 99.85
3fik_5_1-71_134-234172 50S ribosomal protein L1; ribosome, decoding, tRNA 100.0
3bbo_D_1-183_272-352264 Ribosomal protein L1; large ribosomal subunit, spi 100.0
1ad2_A_1-68_160-228137 TL2, ribosomal protein L1; RNA binding, protein sy 100.0
1mzp_A_1-58_153-217123 50S ribosomal protein L1P; ribosome, RNA-protein c 99.96
1ad2_A_69-15991 TL2, ribosomal protein L1; RNA binding, protein sy 99.97
3bbo_D_184-27188 Ribosomal protein L1; large ribosomal subunit, spi 99.97
1mzp_A_59-15294 50S ribosomal protein L1P; ribosome, RNA-protein c 99.94
1i2a_A_55-14894 50S ribosomal protein L1P; primary rRNA-binding pr 99.94
2zkr_5_55-14793 60S ribosomal protein L10A; protein-RNA complex, 6 99.94
2noq_G_57-14993 60S ribosomal protein L1; IRES RNA, ribosome, tran 99.93
2ov7_A_18-137120 50S ribosomal protein L1; 2.30A {Thermus thermophi 99.93
3fik_5_72-13362 50S ribosomal protein L1; ribosome, decoding, tRNA 99.78
>2ftc_A (A:) Mitochondrial ribosomal protein L1; mitochondrial ribosome, large ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus} Back     alignment and structure
Probab=100.00  E-value=0  Score=394.02  Aligned_cols=185  Identities=22%  Similarity=0.452  Sum_probs=178.2

Q ss_pred             EEEEEEECCCCCCCCCCCEEEEEECCCCCCCC-CEEEEECH-HHHHHHHHCCCCCCCHHHHHHHHHCCCCCCCEEEECHH
Q ss_conf             99999953787645443013799527788654-06999750-44576874120000278999997517533346886446
Q gi|254780146|r   43 VEIAMNLGIDPRHANQMVRGVVTMPNGTGVNV-RVAVFATS-SKADEAREAGADIVGGEDLFEIVKGGQIDFDRCIATPD  120 (232)
Q Consensus        43 vel~i~L~id~~k~~~~irg~v~LPh~~gk~~-kV~Vf~~~-~~~~~Ak~aGa~~vg~~eli~~i~~~~~~fd~~iAt~~  120 (232)
                      ||++++|+++++|+++++||+|.|||+++++. ||||||++ +.+++|++|||++||++|||++|++||++||+|||||+
T Consensus         1 idl~l~l~~~~kk~~~~~rg~v~LPh~~~k~~~kv~Vfa~~~~~~~~A~~aGA~~vG~~eli~kI~~g~~~~D~~ia~~~   80 (189)
T 2ftc_A            1 LDLTLDMALGKKKNVEPFTSVLSLPYPFASEINKVAVFTENASEVKIAEENGAAFAGGTSLIQKIWDDEIVADFYVAVPE   80 (189)
T ss_pred             CEEEEEECCCCCCCCCCEEEEEECCCCCCCCEEEEEEECCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCEEECHH
T ss_conf             95999917787667663678997789999843699998488256999985565201367788898726622450023177


Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHCC-CCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             7788886433200100174223356665579999998601-110223575267875315778989999999999999986
Q gi|254780146|r  121 MMPLVGRLGRILGPRGIMPNLRVGTVTTDVATAVRESKSG-AVDFRSEKAGIIHAGIGKVSFENKKIEENVLAFVSAVVK  199 (232)
Q Consensus       121 ~m~~i~klgriLGPkglMPn~k~GTv~~di~~~i~~~k~g-~i~~r~~k~g~i~~~IG~~~m~~e~i~eNi~~~~~~i~~  199 (232)
                      |||+|++|||+||||  |||||.||+++|+.++|+++++| +++||.++.|++|++||+++|+++||.||+.+++++|++
T Consensus        81 ~m~~l~klg~iLGpk--mP~~k~gTv~~di~~~i~~~k~g~~~~~r~~k~g~i~~~IG~~~m~~e~l~eNi~~~i~~i~~  158 (189)
T 2ftc_A           81 IMPELNRLRKKLNKK--YPKLSRNSIGRDIPKMLELFKNGHEIKVDEERENFLQTKIATLDMSSDQIAANLQAVINEVCR  158 (189)
T ss_pred             HHHHHHHHHHHHCCC--CCCCCCCCCCCCHHHHHHHHHCCCEEEEECCCCCEEEECCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             899899999875235--888776656754899999973694566503544168851366667889999999999999997


Q ss_pred             CCCCCCCCCEEEEEEEEECCCCCEEEECHHC
Q ss_conf             0866254433779999923897277400100
Q gi|254780146|r  200 AKPSVAKGDYVKRVTLSSTMGCGIKVDLSSF  230 (232)
Q Consensus       200 ~kp~~~kg~~Ik~v~lssTmGp~i~id~~~~  230 (232)
                      ++|.+. |+||+++|||||||||++||+++|
T Consensus       159 ~kp~~~-g~~i~~~~i~stmgp~~~i~~~~~  188 (189)
T 2ftc_A          159 HRPLNL-GPFVVRAFLRSSTSEGLLLKIDPL  188 (189)
T ss_pred             HCCCCC-CCCEEEEEEECCCCCCEEEECCCC
T ss_conf             287456-872889999898999721546878
>2zkr_5 (5:1-54,5:148-212) 60S ribosomal protein L10A; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Back     alignment and structure
>1i2a_A (A:1-54,A:149-219) 50S ribosomal protein L1P; primary rRNA-binding protein, translational repressor, ribosome; 1.85A {Methanocaldococcus jannaschii} Back     alignment and structure
>2noq_G (G:1-56,G:150-213) 60S ribosomal protein L1; IRES RNA, ribosome, translation, internal initiation; 7.30A {Saccharomyces cerevisiae} PDB: 1s1i_A Back     alignment and structure
>3fik_5 (5:1-71,5:134-234) 50S ribosomal protein L1; ribosome, decoding, tRNA, EF-TU, ternary complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding; 6.70A {Escherichia coli} PDB: 2rdo_9 2gya_2 2gyc_2 Back     alignment and structure
>3bbo_D (D:1-183,D:272-352) Ribosomal protein L1; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Back     alignment and structure
>1ad2_A (A:1-68,A:160-228) TL2, ribosomal protein L1; RNA binding, protein synthesis, mutant; 1.90A {Thermus thermophilus} Back     alignment and structure
>1mzp_A (A:1-58,A:153-217) 50S ribosomal protein L1P; ribosome, RNA-protein complex; 2.65A {Sulfolobus acidocaldarius} Back     alignment and structure
>1ad2_A (A:69-159) TL2, ribosomal protein L1; RNA binding, protein synthesis, mutant; 1.90A {Thermus thermophilus} Back     alignment and structure
>3bbo_D (D:184-271) Ribosomal protein L1; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Back     alignment and structure
>1mzp_A (A:59-152) 50S ribosomal protein L1P; ribosome, RNA-protein complex; 2.65A {Sulfolobus acidocaldarius} Back     alignment and structure
>1i2a_A (A:55-148) 50S ribosomal protein L1P; primary rRNA-binding protein, translational repressor, ribosome; 1.85A {Methanocaldococcus jannaschii} Back     alignment and structure
>2zkr_5 (5:55-147) 60S ribosomal protein L10A; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Back     alignment and structure
>2noq_G (G:57-149) 60S ribosomal protein L1; IRES RNA, ribosome, translation, internal initiation; 7.30A {Saccharomyces cerevisiae} PDB: 1s1i_A Back     alignment and structure
>2ov7_A (A:18-137) 50S ribosomal protein L1; 2.30A {Thermus thermophilus} PDB: 2oum_A 2vpl_A Back     alignment and structure
>3fik_5 (5:72-133) 50S ribosomal protein L1; ribosome, decoding, tRNA, EF-TU, ternary complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding; 6.70A {Escherichia coli} PDB: 2rdo_9 2gya_2 2gyc_2 Back     alignment and structure