254780261

254780261

50S ribosomal protein L3

GeneID in NCBI database:8209242Locus tag:CLIBASIA_00730
Protein GI in NCBI database:254780261Protein Accession:YP_003064674.1
Gene range:-(142391, 143056)Protein Length:221aa
Gene description:50S ribosomal protein L3
COG prediction:[J] Ribosomal protein L3
KEGG prediction:rplC; 50S ribosomal protein L3; K02906 large subunit ribosomal protein L3
SEED prediction:LSU ribosomal protein L3p (L3e)
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
TOPPRED1 TM-Helix
HMMTOPnone TM-Helix
MEMSATnone TM-Helix
MEMSAT_SVMnone TM-Helix
PHOBIUSnone TM-Helix
SignalP_HMMno
SignalP_NNyes
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-
MRSGVVARKLGMTCVYNIEGRRIPVTVLHLDNCQVVVHRTLDKNGYMAVQVGAGEAKVKNVSKPMRGFFSSVNVSPKKKLFEFRVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGFSGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKNLEVVSVDDKRGLILVKGCVPGAKKNSWILVRDSFKSAVNCKGKVS
ccccEEEEEEccEEEEcccccEEEEEEEEEccEEEEEEEcccccccEEEEEEcccccHHHccHHHHHHHHHcccccccEEEEEEEcccccccccccEEEEEEEccccEEEEEEEEcccccccEEEEEccccccccccccccccccEEEccccccccccccccccccccccEEEEEccEEEEEEccccEEEEEccccccccccEEEEEEccccccccccccc
cccEEEEEEcccEEEEEccccEEEEEEEEEcccEEEEEEEcccccEEEEEEEcccccccccccHcccccHHcccccccEEEEEEEcccccccccccEEEEHHcccccEEEEEEEEcccccccEEEEccccccccccccccccccccccccccccccccccccccccccccEEEEEEEEEEEEcccccEEEEEccccccccccEEEEEHHHHHccccccccc
MRSGVVARKLGMTCVyniegrripvtvlhldncQVVVHRTLDKNGYMAVQVGAgeakvknvskpmrgffssvnvspkkkLFEFrvqkdddllpvgsvfspsyftvgqlvdvtgmtigkgfsgamkrhnfgglrathgvsishrshgstgcrqdpgrvfknkkmagrmggnrvtvknlevvsvddkrglilvkgcvpgakknswiLVRDSFKSAVNCKGKVS
mrsgvvarklgmTCVYNIEGRRIPVTVLHLDNCQVVVHRTLDKNGYMAVQVGAGeakvknvskpmrgffssvnvspkKKLFEFRVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGFSGAMKRHNFGGLRATHGVsishrshgstgcrqdpgrVFKNKkmagrmggnrvtvknlevvsvddkrglilvkgcvpgakknswilvrdsfksavnckgkvs
MRSGVVARKLGMTCVYNIEGRRIPVTVLHLDNCQVVVHRTLDKNGYMAVQVGAGEAKVKNVSKPMRGFFSSVNVSPKKKLFEFRVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGFSGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKNLEVVSVDDKRGLILVKGCVPGAKKNSWILVRDSFKSAVNCKGKVS
*RSGVVARKLGMTCVYNIEGRRIPVTVLHLDNCQVVVHRTLDKNGYMAVQVGAGEAKVKNVSKPMRGFFSSVNVSPKKKLFEFRVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGFSGAMKRHNFG*********************QDPGRVFKNKKMAGRMGGNRVTVKNLEVVSVDDKRGLILVKGCVPGAKKNSWILVRDSF***********
MRSGVVARKLGMTCVYNIEGRRIPVTVLHLDNCQVVVHRTLDKNGYMAVQVGAGEAKVKNVSKPMRGFFSSVNVSPKKKLFEFRVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGFSGAMKRHNFGGLRATHGVS***********RQDPGRVFKNKKMAGRMGGNRVTVKNLEVVSVDDKRGLILVKGCVPGAKKNSWILVRDSFKS*********
*RSGVVARKLGMTCVYNIEGRRIPVTVLHLDNCQVVVHRTLDKNGYMAVQVGAGEAKVKNVSKPMRGFFSSVNVSPKKKLFEFRVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGFSGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKNLEVVSVDDKRGLILVKGCVPGAKKNSWILVRDSFKSA********
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xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxHHHHHHHHHHHHHHHHHHHHxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
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SSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
MRSGVVARKLGMTCVYNIEGRRIPVTVLHLDNCQVVVHRTLDKNGYMAVQVGAGEAKVKNVSKPMRGFFSSVNVSPKKKLFEFRVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGFSGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKNLEVVSVDDKRGLILVKGCVPGAKKNSWILVRDSFKSAVNCKGKVS
MRSGVVARKLGMTCVYNIEGRRIPVTVLHLDNCQVVVHRTLDKNGYMAVQVGAGEAKVKNVSKPMRGFFSSVNVSPKKKLFEFRVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGFSGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKNLEVVSVDDKRGLILVKGCVPGAKKNSWILVRDSFKSAVNCKGKVS
MRSGVVARKLGMTCVYNIEGRRIPVTVLHLDNCQVVVHRTLDKNGYMAVQVGAGEAKVKNVSKPMRGFFSSVNVSPKKKLFEFRVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGFSGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKNLEVVSVDDKRGLILVKGCVPGAKKNSWILVRDSFKSAVNCKGKVS

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
Target221 50S ribosomal protein L3 [Candidatus Liberibacter asiat
315122818221 50S ribosomal protein L3 [Candidatus Liberibacter solan 1 1e-108
86357305213 50S ribosomal protein L3 [Rhizobium etli CFN 42] Length 1 8e-81
222148366213 50S ribosomal protein L3 [Agrobacterium vitis S4] Lengt 1 8e-81
222085675219 50S ribosomal protein L3 [Agrobacterium radiobacter K84 1 8e-81
190891355213 50S ribosomal protein L3 [Rhizobium etli CIAT 652] Leng 1 1e-80
116251540213 50S ribosomal protein L3 [Rhizobium leguminosarum bv. v 1 3e-80
209548935213 50S ribosomal protein L3 [Rhizobium leguminosarum bv. t 1 5e-80
241204165213 50S ribosomal protein L3 [Rhizobium leguminosarum bv. t 1 6e-79
15965109228 50S ribosomal protein L3 [Sinorhizobium meliloti 1021] 1 3e-78
150396207228 50S ribosomal protein L3 [Sinorhizobium medicae WSM419] 1 5e-78
>gi|315122818|ref|YP_004063307.1| 50S ribosomal protein L3 [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 221 Back     alignment and organism information
 Score =  395 bits (1015), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 188/221 (85%), Positives = 206/221 (93%)

Query: 1   MRSGVVARKLGMTCVYNIEGRRIPVTVLHLDNCQVVVHRTLDKNGYMAVQVGAGEAKVKN 60
           MR GVVARKLGMTCVYN+EG+R+PVTVLHLDNCQVV HRTL KNGYMAVQVGAG+AK+KN
Sbjct: 1   MRPGVVARKLGMTCVYNLEGKRLPVTVLHLDNCQVVAHRTLQKNGYMAVQVGAGDAKIKN 60

Query: 61  VSKPMRGFFSSVNVSPKKKLFEFRVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGF 120
           VSKPMRGFFSSVN SPKK+L EFRVQK+D+LL +GSV SPS+F VGQLVDVTG+TIGKGF
Sbjct: 61  VSKPMRGFFSSVNASPKKRLSEFRVQKEDELLQIGSVLSPSHFNVGQLVDVTGVTIGKGF 120

Query: 121 SGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKNLEVV 180
           +GAMKRHNF GLRA+HGVSISHRS GSTGCRQDPGRVFKNKKMAG MGGNR+TVKNLEV+
Sbjct: 121 AGAMKRHNFAGLRASHGVSISHRSAGSTGCRQDPGRVFKNKKMAGHMGGNRITVKNLEVI 180

Query: 181 SVDDKRGLILVKGCVPGAKKNSWILVRDSFKSAVNCKGKVS 221
           S+DDKRGLI VKGCVPGAK +SWILVRDSFKSA N KGKV+
Sbjct: 181 SIDDKRGLIFVKGCVPGAKNDSWILVRDSFKSAANYKGKVA 221


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|86357305|ref|YP_469197.1| 50S ribosomal protein L3 [Rhizobium etli CFN 42] Length = 213 Back     alignment and organism information
>gi|222148366|ref|YP_002549323.1| 50S ribosomal protein L3 [Agrobacterium vitis S4] Length = 213 Back     alignment and organism information
>gi|222085675|ref|YP_002544205.1| 50S ribosomal protein L3 [Agrobacterium radiobacter K84] Length = 219 Back     alignment and organism information
>gi|190891355|ref|YP_001977897.1| 50S ribosomal protein L3 [Rhizobium etli CIAT 652] Length = 213 Back     alignment and organism information
>gi|116251540|ref|YP_767378.1| 50S ribosomal protein L3 [Rhizobium leguminosarum bv. viciae 3841] Length = 213 Back     alignment and organism information
>gi|209548935|ref|YP_002280852.1| 50S ribosomal protein L3 [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 213 Back     alignment and organism information
>gi|241204165|ref|YP_002975261.1| 50S ribosomal protein L3 [Rhizobium leguminosarum bv. trifolii WSM1325] Length = 213 Back     alignment and organism information
>gi|15965109|ref|NP_385462.1| 50S ribosomal protein L3 [Sinorhizobium meliloti 1021] Length = 228 Back     alignment and organism information
>gi|150396207|ref|YP_001326674.1| 50S ribosomal protein L3 [Sinorhizobium medicae WSM419] Length = 228 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
Target221 50S ribosomal protein L3 [Candidatus Liberibacter asiat
PRK00001210 PRK00001, rplC, 50S ribosomal protein L3; Validated 3e-83
TIGR03625202 TIGR03625, L3_bact, 50S ribosomal protein L3, bacterial 9e-80
KOG3141310 KOG3141, KOG3141, KOG3141, Mitochondrial/chloroplast ri 6e-61
CHL00143207 CHL00143, rpl3, ribosomal protein L3; Validated 3e-49
pfam00297199 pfam00297, Ribosomal_L3, Ribosomal protein L3 9e-45
COG0087218 COG0087, RplC, Ribosomal protein L3 [Translation, ribos 4e-65
TIGR03626330 TIGR03626, L3_arch, archaeal ribosomal protein L3 3e-11
PRK04231337 PRK04231, rpl3p, 50S ribosomal protein L3P; Reviewed 4e-08
>gnl|CDD|178784 PRK00001, rplC, 50S ribosomal protein L3; Validated Back     alignment and domain information
>gnl|CDD|163362 TIGR03625, L3_bact, 50S ribosomal protein L3, bacterial Back     alignment and domain information
>gnl|CDD|38351 KOG3141, KOG3141, KOG3141, Mitochondrial/chloroplast ribosomal protein L3 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|177065 CHL00143, rpl3, ribosomal protein L3; Validated Back     alignment and domain information
>gnl|CDD|144036 pfam00297, Ribosomal_L3, Ribosomal protein L3 Back     alignment and domain information
>gnl|CDD|30436 COG0087, RplC, Ribosomal protein L3 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|163363 TIGR03626, L3_arch, archaeal ribosomal protein L3 Back     alignment and domain information
>gnl|CDD|179795 PRK04231, rpl3p, 50S ribosomal protein L3P; Reviewed Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 221 50S ribosomal protein L3 [Candidatus Liberibacter asiat
PRK00001212 rplC 50S ribosomal protein L3; Validated 100.0
CHL00143207 rpl3 ribosomal protein L3; Validated 100.0
TIGR03625202 L3_bact 50S ribosomal protein L3, bacterial. This model 100.0
COG0087218 RplC Ribosomal protein L3 [Translation, ribosomal struc 100.0
KOG3141310 consensus 100.0
pfam00297199 Ribosomal_L3 Ribosomal protein L3. 100.0
TIGR03626330 L3_arch archaeal ribosomal protein L3. This model descr 100.0
PRK04231333 rpl3p 50S ribosomal protein L3P; Reviewed 100.0
PTZ00103393 60S ribosomal protein L3; Provisional 100.0
KOG0746384 consensus 99.93
>PRK00001 rplC 50S ribosomal protein L3; Validated Back     alignment and domain information
>CHL00143 rpl3 ribosomal protein L3; Validated Back     alignment and domain information
>TIGR03625 L3_bact 50S ribosomal protein L3, bacterial Back     alignment and domain information
>COG0087 RplC Ribosomal protein L3 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>KOG3141 consensus Back     alignment and domain information
>pfam00297 Ribosomal_L3 Ribosomal protein L3 Back     alignment and domain information
>TIGR03626 L3_arch archaeal ribosomal protein L3 Back     alignment and domain information
>PRK04231 rpl3p 50S ribosomal protein L3P; Reviewed Back     alignment and domain information
>PTZ00103 60S ribosomal protein L3; Provisional Back     alignment and domain information
>KOG0746 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
Target221 50S ribosomal protein L3 [Candidatus Liberibacter asiat
1p85_B209 Real Space Refined Coordinates Of The 50s Subunit F 3e-56
3fin_E205 T. Thermophilus 70s Ribosome In Complex With Mrna, 1e-50
2j01_E206 Structure Of The Thermus Thermophilus 70s Ribosome 1e-50
3pyo_D204 Crystal Structure Of A Complex Containing Domain 3 3e-50
1pnu_B205 Crystal Structure Of A Streptomycin Dependent Ribos 4e-49
1nkw_B211 Crystal Structure Of The Large Ribosomal Subunit Fr 3e-47
2ftc_C211 Structural Model For The Large Subunit Of The Mamma 1e-40
3bbo_F259 Homology Model For The Spinach Chloroplast 50s Subu 6e-34
1jj2_B337 Fully Refined Crystal Structure Of The Haloarcula M 3e-19
1ffk_B337 Crystal Structure Of The Large Ribosomal Subunit Fr 3e-19
1s72_B338 Refined Crystal Structure Of The Haloarcula Marismo 3e-19
1ml5_e338 Crystal Structure Of The Ribosome At 5.5 A Resoluti 1e-18
2zkr_b403 Structure Of A Mammalian Ribosomal 60s Subunit With 4e-07
3izr_C389 Localization Of The Large Subunit Ribosomal Protein 3e-06
3jyw_C362 Structure Of The 60s Proteins For Eukaryotic Riboso 2e-09
1s1i_C386 Structure Of The Ribosomal 80s-Eef2-Sordarin Comple 2e-09
3o58_C387 Yeast 80s Ribosome. This Entry Consists Of The 60s 2e-09
3izs_C388 Localization Of The Large Subunit Ribosomal Protein 2e-09
gi|33357903|pdb|1P85|B Chain B, 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 = 209 Back     alignment and structure
 Score =  222 bits (565), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 95/211 (45%), Positives = 133/211 (63%), Gaps = 2/211 (0%)

Query: 2   RSGVVARKLGMTCVYNIEGRRIPVTVLHLDNCQVVVHRTLDKNGYMAVQVGAGEAKVKNV 61
             G+V +K+GMT ++  +G  IPVTV+ ++  +V   + L  +GY A+QV  G  K   V
Sbjct: 1   MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRV 60

Query: 62  SKPMRGFFSSVNVSPKKKLFEFRVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGFS 121
           +KP  G F+   V   + L+EFR+ + ++   VG   S   F   + VDVTG + GKGF+
Sbjct: 61  TKPEAGHFAKAGVEAGRGLWEFRLAEGEE-FTVGQSISVELFADVKKVDVTGTSKGKGFA 119

Query: 122 GAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKNLEVVS 181
           G +KR NF    ATHG S+SHR  GS G  Q PG+VFK KKMAG+MG  RVTV++L+VV 
Sbjct: 120 GTVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVR 179

Query: 182 VDDKRGLILVKGCVPGAKKNSWILVRDSFKS 212
           VD +R L+LVKG VPGA   S ++V+ + K+
Sbjct: 180 VDAERNLLLVKGAVPGA-TGSDLIVKPAVKA 209


>gi|224510783|pdb|3FIN|E Chain E, 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 = 205 Back     alignment and structure
gi|116668236|pdb|2J01|E Chain E, 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 = 206 Back     alignment and structure
>gi|322812575|pdb|3PYO|D Chain D, 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 = 204 Back     alignment and structure
>gi|34811555|pdb|1PNU|B Chain B, 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 = 205 Back     alignment and structure
gi|28948921|pdb|1NKW|B Chain B, Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans Length = 211 Back     alignment and structure
>gi|99032309|pdb|2FTC|C Chain C, Structural Model For The Large Subunit Of The Mammalian Mitochondrial Ribosome Length = 211 Back     alignment and structure
gi|189096128|pdb|3BBO|F Chain F, Homology Model For The Spinach Chloroplast 50s Subunit Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome Length = 259 Back     alignment and structure
>gi|15825944|pdb|1JJ2|B Chain B, Fully Refined Crystal Structure Of The Haloarcula Marismortui Large Ribosomal Subunit At 2.4 Angstrom Resolution Length = 337 Back     alignment and structure
>gi|27066406|pdb|1FFK|B Chain B, Crystal Structure Of The Large Ribosomal Subunit From Haloarcula Marismortui At 2.4 Angstrom Resolution Length = 337 Back     alignment and structure
gi|50513471|pdb|1S72|B Chain B, Refined Crystal Structure Of The Haloarcula Marismortui Large Ribosomal Subunit At 2.4 Angstrom Resolution Length = 338 Back     alignment and structure
>gi|28373724|pdb|1ML5|EE Chain e, Structure Of The E. Coli Ribosomal Termination Complex With Release Factor 2 Length = 338 Back     alignment and structure
gi|187609300|pdb|2ZKR|BB Chain b, 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 = 403 Back     alignment and structure
>gi|315113296|pdb|3IZR|C Chain C, Localization Of The Large Subunit Ribosomal Proteins Into A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s Ribosome Length = 389 Back     alignment and structure
>gi|281500833|pdb|3JYW|C Chain C, Structure Of The 60s Proteins For Eukaryotic Ribosome Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome At 8.9a Resolution Length = 362 Back     alignment and structure
>gi|49258841|pdb|1S1I|C Chain C, 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 = 386 Back     alignment and structure
gi|315113528|pdb|3O58|C Chain C, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit Of The First 80s In The Asymmetric Unit. Length = 387 Back     alignment and structure
>gi|315113303|pdb|3IZS|C Chain C, Localization Of The Large Subunit Ribosomal Proteins Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae Translating 80s Ribosome Length = 388 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target221 50S ribosomal protein L3 [Candidatus Liberibacter asiat
3ofq_D209 50S ribosomal protein L3; protein biosynthesis, ribosom 2e-62
3bbo_F259 Ribosomal protein L3; large ribosomal subunit, spinach 7e-53
3i1n_D209 50S ribosomal protein L3; ribosome structure, protein-R 4e-47
2zjr_B211 50S ribosomal protein L3; ribosome, large ribosomal sub 2e-43
2j01_E206 50S ribosomal protein L3; ribosome, tRNA, paromomycin, 4e-43
2ftc_C211 L3MT, MRP-L3, mitochondrial 39S ribosomal protein L3; m 3e-42
3jyw_C362 60S ribosomal protein L3; eukaryotic ribosome, RACK1 pr 1e-33
2zkr_b403 60S ribosomal protein L3; protein-RNA complex, 60S ribo 8e-32
1vq8_B338 50S ribosomal protein L3P; ribosome 50S, protein-protei 2e-31
>3ofq_D 50S ribosomal protein L3; protein biosynthesis, ribosomes, RNA, tRNA, transfer, antibi EXIT, peptidyl, ribosomal subunit, large; 3.10A {Escherichia coli} PDB: 1p85_B 1p86_B 1vs8_D 1vs6_D 2aw4_D 2awb_D 2gya_B 2gyc_B 1vt2_D 2i2v_D 2j28_D 2i2t_D* 2qao_D* 2qba_D* 2qbc_D* 2qbe_D 2qbg_D 2qbi_D* 2qbk_D* 2qov_D ... Length = 209 Back     alignment and structure
 Score =  233 bits (596), Expect = 2e-62
 Identities = 95/209 (45%), Positives = 132/209 (63%), Gaps = 2/209 (0%)

Query: 4   GVVARKLGMTCVYNIEGRRIPVTVLHLDNCQVVVHRTLDKNGYMAVQVGAGEAKVKNVSK 63
           G+V +K+GMT ++  +G  IPVTV+ ++  +V   + L  +GY A+QV  G  K   V+K
Sbjct: 3   GLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRVTK 62

Query: 64  PMRGFFSSVNVSPKKKLFEFRVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGFSGA 123
           P  G F+   V   + L+EFR+  + +   VG   S   F   + VDVTG + GKGF+G 
Sbjct: 63  PEAGHFAKAGVEAGRGLWEFRLA-EGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAGT 121

Query: 124 MKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKNLEVVSVD 183
           +KR NF    ATHG S+SHR  GS G  Q PG+VFK KKMAG+MG  RVTV++L+VV VD
Sbjct: 122 VKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVRVD 181

Query: 184 DKRGLILVKGCVPGAKKNSWILVRDSFKS 212
            +R L+LVKG VPGA   S ++V+ + K+
Sbjct: 182 AERNLLLVKGAVPGA-TGSDLIVKPAVKA 209


>3bbo_F Ribosomal protein L3; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Nicotiana tabacum} Length = 259 Back     alignment and structure
>3i1n_D 50S ribosomal protein L3; ribosome structure, protein-RNA complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA- binding, methylation; 3.19A {Escherichia coli k-12} PDB: 1p85_B 1p86_B 1vs8_D 2aw4_D 2awb_D 2gya_B 2gyc_B 1vs6_D 2i2v_D 2j28_D 2i2t_D* 2qao_D* 2qba_D* 2qbc_D* 2qbe_D 2qbg_D 2qbi_D* 2qbk_D* 2qov_D 2qox_D ... Length = 209 Back     alignment and structure
>2zjr_B 50S ribosomal protein L3; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: b.43.3.2 PDB: 1nwx_B* 1nwy_B* 1sm1_B* 1xbp_B* 2ogm_B* 2ogn_B* 2ogo_B* 2zjp_B* 2zjq_B 1nkw_B 3cf5_B* 3dll_B* 1pnu_B 1pny_B 1vor_E 1vou_E 1vow_E 1voy_E 1vp0_E Length = 211 Back     alignment and structure
>2j01_E 50S ribosomal protein L3; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} SCOP: b.43.3.2 PDB: 1vsp_C 2hgj_E 2hgq_E 2hgu_E 1vsa_C 2j03_E 2jl6_E 2jl8_E 2v47_E 2v49_E 2wdi_E 2wdj_E 2wdl_E 2wdn_E 2wh2_E 2wh4_E 3d5b_E 3d5d_E 3f1f_E 3f1h_E ... Length = 206 Back     alignment and structure
>2ftc_C L3MT, MRP-L3, mitochondrial 39S ribosomal protein L3; mitochondrial ribosome, large ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus} Length = 211 Back     alignment and structure
>3jyw_C 60S ribosomal protein L3; eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus} PDB: 1s1i_C Length = 362 Back     alignment and structure
>2zkr_b 60S ribosomal protein L3; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Length = 403 Back     alignment and structure
>1vq8_B 50S ribosomal protein L3P; 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: b.43.3.2 PDB: 1vq4_B* 1vq5_B* 1vq6_B* 1vq7_B* 1s72_B* 1vq9_B* 1vqk_B* 1vql_B* 1vqm_B* 1vqn_B* 1vqo_B* 1vqp_B* 1yhq_B* 1yi2_B* 1yij_B* 1yit_B* 1yj9_B* 1yjn_B* 1yjw_B* 2otj_B* ... Length = 338 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target221 50S ribosomal protein L3 [Candidatus Liberibacter asiat
3ofq_D209 50S ribosomal protein L3; protein biosynthesis, ribosom 100.0
2ftc_C211 L3MT, MRP-L3, mitochondrial 39S ribosomal protein L3; m 100.0
3bbo_F259 Ribosomal protein L3; large ribosomal subunit, spinach 100.0
2zjr_B211 50S ribosomal protein L3; ribosome, large ribosomal sub 100.0
2j01_E206 50S ribosomal protein L3; ribosome, tRNA, paromomycin, 100.0
1vq8_B338 50S ribosomal protein L3P; ribosome 50S, protein-protei 100.0
3jyw_C362 60S ribosomal protein L3; eukaryotic ribosome, RACK1 pr 100.0
2zkr_b403 60S ribosomal protein L3; protein-RNA complex, 60S ribo 100.0
>3ofq_D 50S ribosomal protein L3; protein biosynthesis, ribosomes, RNA, tRNA, transfer, antibi EXIT, peptidyl, ribosomal subunit, large; 3.10A {Escherichia coli} PDB: 1p85_B 1p86_B 1vs8_D 1vs6_D 2aw4_D 2awb_D 2gya_B 2gyc_B 1vt2_D 2i2v_D 2j28_D 2i2t_D* 2qao_D* 2qba_D* 2qbc_D* 2qbe_D 2qbg_D 2qbi_D* 2qbk_D* 2qov_D ... Back     alignment and structure
Probab=100.00  E-value=0  Score=581.55  Aligned_cols=209  Identities=45%  Similarity=0.741  Sum_probs=203.4

Q ss_pred             CCCEEEEECCCCEEECCCCCEEEEEEEEECCCEEEEEEECCCCCCEEEEECCCCCCCCCCCCCHHHHHHHHCCCCCCEEE
Q ss_conf             44268996584516988987922689991797899997067788612564055556431571011257640356341036
Q gi|254780261|r    2 RSGVVARKLGMTCVYNIEGRRIPVTVLHLDNCQVVVHRTLDKNGYMAVQVGAGEAKVKNVSKPMRGFFSSVNVSPKKKLF   81 (221)
Q Consensus         2 r~Glig~KiGMT~if~e~G~~vpVTViev~~~~Vv~~kt~ekdGY~Avqvg~~~~k~k~~~Kp~~G~fkK~g~~pk~~l~   81 (221)
                      +.||||+|+||||+||+||+++||||||++||+|+|+||.|+|||+|+|+++++.++++++||++|||++++++|+++++
T Consensus         1 m~Glig~KvGMT~v~~~~G~~vPVTVie~~p~~V~~~kt~ekdgY~a~q~g~~~~~~k~~~Kp~~g~~~k~~~~~~~~l~   80 (209)
T 3ofq_D            1 MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRVTKPEAGHFAKAGVEAGRGLW   80 (209)
T ss_dssp             CCCEEEEECCCBCCCCSSCCCCCEEEEECCCBEEEECCCSSSSSCCEEEEECSCCCTTTCCHHHHHHHHHSCCCCCSCCE
T ss_pred             CCEEEEEECCCCEEECCCCEEEEEEEEEECCCEEEEEEEECCCCCEEEEEEEEECCCCCCCHHHHCCHHHCCCCCCCEEE
T ss_conf             91598997688448899990998799996598999998566789676898230012331685362563231667550489


Q ss_pred             EEECCCCHHHHHCCCCEEEEEECCCCEEEEEEEEECCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCC
Q ss_conf             53206511211003410001230253265789875343364057504421233357745434666555556752242267
Q gi|254780261|r   82 EFRVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGFSGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNK  161 (221)
Q Consensus        82 Efrv~~~~~~~~vG~~i~~~~F~~Gq~VDV~g~SkGKGFqGviKR~gf~g~~~sHG~sk~hR~~GsiG~~~~PgRV~kGk  161 (221)
                      |||+++++ .+++|++|++|+|++||+|||+|+||||||||+||||||+++|+|||+|++||+|||||++|+|||||||+
T Consensus        81 e~~~~~~~-~~~~G~~~~~~~F~~Gq~VDV~g~tkGKGFqGv~KR~gf~g~p~sHg~s~~hR~~Gs~G~~~~PgrV~kgk  159 (209)
T 3ofq_D           81 EFRLAEGE-EFTVGQSISVELFADVKKVDVTGTSKGKGFAGTVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGK  159 (209)
T ss_dssp             EEECSSCC-CCSSCCCBCGGGGSSCCCCCCEECCCCCBSCCTTTSSCCCCCCSSSSCCSCSSCCCCSSCSTTTCSCCTTC
T ss_pred             EEECCCHH-HCCCCCEEEEEEECCCCEEEEEEEECCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             97137655-41477632112244897689999981643444067644467985568985465887766789897388897


Q ss_pred             CCCCCCCCEEEEECCCEEEEEECCCCEEEEECCCCCCCCCEEEEEEECCCC
Q ss_conf             666523773336516589998076898999715745888709999603146
Q gi|254780261|r  162 KMAGRMGGNRVTVKNLEVVSVDDKRGLILVKGCVPGAKKNSWILVRDSFKS  212 (221)
Q Consensus       162 km~G~mG~~~~T~~nl~i~~id~e~n~i~vkGsVPG~~~~~~v~ir~a~k~  212 (221)
                      |||||||++++|++||+|++||+|+|||||||||||| ++++|+||+|+|+
T Consensus       160 kmaG~mG~~~~T~~Nl~Vv~id~e~n~i~vkGsVPG~-~~~~V~ir~aik~  209 (209)
T 3ofq_D          160 KMAGQMGNERVTVQSLDVVRVDAERNLLLVKGAVPGA-TGSDLIVKPAVKA  209 (209)
T ss_dssp             CCCCCBSCCCCCCTTCEEEEEETTTTEEEEESCCSSC-TTCEEEECCCSCC
T ss_pred             CCCCCCCCCEEEEECCEEEEEECCCCEEEEEECCCCC-CCCEEEEEECCCC
T ss_conf             2487458734987357999995889999997478789-9999998746359



>2ftc_C L3MT, MRP-L3, mitochondrial 39S ribosomal protein L3; mitochondrial ribosome, large ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus} Back     alignment and structure
>3bbo_F Ribosomal protein L3; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Nicotiana tabacum} Back     alignment and structure
>2zjr_B 50S ribosomal protein L3; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: b.43.3.2 PDB: 1nwx_B* 1nwy_B* 1sm1_B* 1xbp_B* 2ogm_B* 2ogn_B* 2ogo_B* 2zjp_B* 2zjq_B 1nkw_B 3cf5_B* 3dll_B* 1pnu_B 1pny_B 1vor_E 1vou_E 1vow_E 1voy_E 1vp0_E Back     alignment and structure
>2j01_E 50S ribosomal protein L3; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} SCOP: b.43.3.2 PDB: 1vsp_C 2hgj_E 2hgq_E 2hgu_E 1vsa_C 2j03_E 2jl6_E 2jl8_E 2v47_E 2v49_E 2wdi_E 2wdj_E 2wdl_E 2wdn_E 2wh2_E 2wh4_E 2wrj_E 2wrl_E 2wro_E 2wrr_E ... Back     alignment and structure
>1vq8_B 50S ribosomal protein L3P; 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: b.43.3.2 PDB: 1vq4_B* 1vq5_B* 1vq6_B* 1vq7_B* 1s72_B* 1vq9_B* 1vqk_B* 1vql_B* 1vqm_B* 1vqn_B* 1vqo_B* 1vqp_B* 1yhq_B* 1yi2_B* 1yij_B* 1yit_B* 1yj9_B* 1yjn_B* 1yjw_B* 2otj_B* ... Back     alignment and structure
>3jyw_C 60S ribosomal protein L3; eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus} PDB: 1s1i_C Back     alignment and structure
>2zkr_b 60S ribosomal protein L3; 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 221 50S ribosomal protein L3 [Candidatus Liberibacter asiat
d2gycb1209 b.43.3.2 (B:1-209) Ribosomal protein L3 {Escherichia co 2e-49
d2zjrb1205 b.43.3.2 (B:1-205) Ribosomal protein L3 {Deinococcus ra 1e-45
d2j01e1205 b.43.3.2 (E:1-205) Ribosomal protein L3 {Thermus thermo 8e-44
d1vqob1337 b.43.3.2 (B:1-337) Ribosomal protein L3 {Archaeon Haloa 9e-34
>d2gycb1 b.43.3.2 (B:1-209) Ribosomal protein L3 {Escherichia coli [TaxId: 562]} Length = 209 Back     information, alignment and structure

class: All beta proteins
fold: Reductase/isomerase/elongation factor common domain
superfamily: Translation proteins
family: Ribosomal protein L3
domain: Ribosomal protein L3
species: Escherichia coli [TaxId: 562]
 Score =  189 bits (480), Expect = 2e-49
 Identities = 95/209 (45%), Positives = 131/209 (62%), Gaps = 2/209 (0%)

Query: 4   GVVARKLGMTCVYNIEGRRIPVTVLHLDNCQVVVHRTLDKNGYMAVQVGAGEAKVKNVSK 63
           G+V +K+GMT ++  +G  IPVTV+ ++  +V   + L  +GY A+QV  G  K   V+K
Sbjct: 3   GLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRVTK 62

Query: 64  PMRGFFSSVNVSPKKKLFEFRVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGFSGA 123
           P  G F+   V   + L+EFR   + +   VG   S   F   + VDVTG + GKGF+G 
Sbjct: 63  PEAGHFAKAGVEAGRGLWEFR-LAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAGT 121

Query: 124 MKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKNLEVVSVD 183
           +KR NF    ATHG S+SHR  GS G  Q PG+VFK KKMAG+MG  RVTV++L+VV VD
Sbjct: 122 VKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVRVD 181

Query: 184 DKRGLILVKGCVPGAKKNSWILVRDSFKS 212
            +R L+LVKG VPGA   S ++V+ + K+
Sbjct: 182 AERNLLLVKGAVPGA-TGSDLIVKPAVKA 209


>d2zjrb1 b.43.3.2 (B:1-205) Ribosomal protein L3 {Deinococcus radiodurans [TaxId: 1299]} Length = 205 Back     information, alignment and structure
>d2j01e1 b.43.3.2 (E:1-205) Ribosomal protein L3 {Thermus thermophilus [TaxId: 274]} Length = 205 Back     information, alignment and structure
>d1vqob1 b.43.3.2 (B:1-337) Ribosomal protein L3 {Archaeon Haloarcula marismortui [TaxId: 2238]} Length = 337 Back     information, alignment and structure

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

IdentityAlignment graphLength Definition Probability
Target221 50S ribosomal protein L3 [Candidatus Liberibacter asiat
d2zjrb1205 Ribosomal protein L3 {Deinococcus radiodurans [TaxId: 1 100.0
d2gycb1209 Ribosomal protein L3 {Escherichia coli [TaxId: 562]} 100.0
d2j01e1205 Ribosomal protein L3 {Thermus thermophilus [TaxId: 274] 100.0
d1vqob1337 Ribosomal protein L3 {Archaeon Haloarcula marismortui [ 100.0
>d2zjrb1 b.43.3.2 (B:1-205) Ribosomal protein L3 {Deinococcus radiodurans [TaxId: 1299]} Back     information, alignment and structure
class: All beta proteins
fold: Reductase/isomerase/elongation factor common domain
superfamily: Translation proteins
family: Ribosomal protein L3
domain: Ribosomal protein L3
species: Deinococcus radiodurans [TaxId: 1299]
Probab=100.00  E-value=0  Score=565.22  Aligned_cols=205  Identities=43%  Similarity=0.725  Sum_probs=197.1

Q ss_pred             CCCEEEEECCCCEEECCCCCEEEEEEEEECCCEEEEEEECCCCCCEEEEECCCCCCCCCCCCCHHHHHHHHCCCCCCEEE
Q ss_conf             44268996584516988987922689991797899997067788612564055556431571011257640356341036
Q gi|254780261|r    2 RSGVVARKLGMTCVYNIEGRRIPVTVLHLDNCQVVVHRTLDKNGYMAVQVGAGEAKVKNVSKPMRGFFSSVNVSPKKKLF   81 (221)
Q Consensus         2 r~Glig~KiGMT~if~e~G~~vpVTViev~~~~Vv~~kt~ekdGY~Avqvg~~~~k~k~~~Kp~~G~fkK~g~~pk~~l~   81 (221)
                      +.||||+|+||||+||+ |.++||||||++||.|+++||.|+|||+|+||++++.++++++||++|||+|++++|++++.
T Consensus         1 m~Glig~KiGMT~i~~~-g~~vpVTVle~~p~~V~~~kt~ekdGY~avqvg~~~~~~k~~~K~~~g~~~k~~~~~~~~~~   79 (205)
T d2zjrb1           1 MKGILGTKIGMTQIWKN-DRAIPVTVVLAGPCPIVQRKTAQTDGYEAVQIGYAPKAERKVNKPMQGHFAKAGVAPTRILR   79 (205)
T ss_dssp             CCEEEEEEEEEEEEEET-TEEEEEEEEECCCEEEEEEECTTTTSSCEEEEECSCCCGGGCCHHHHHHHHTTTCCCCSCEE
T ss_pred             CCEEEEEECCCEEEEEC-CCEEEEEEEEECCCEEEEEEEECCCCCEEEEECCEEECCCCCCCCCCCCEECCCCCCCEEEE
T ss_conf             94698996255258859-99899899996788899988203579766430201411100132215606002444210232


Q ss_pred             EEECCCCHHHHHCCCCEEEEEECCCCEEEEEEEEECCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCC
Q ss_conf             53206511211003410001230253265789875343364057504421233357745434666555556752242267
Q gi|254780261|r   82 EFRVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGFSGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNK  161 (221)
Q Consensus        82 Efrv~~~~~~~~vG~~i~~~~F~~Gq~VDV~g~SkGKGFqGviKR~gf~g~~~sHG~sk~hR~~GsiG~~~~PgRV~kGk  161 (221)
                      |||.+.     +.|+++++|+|++||+|||+|+||||||||+||||||+++|+|||+|++||+|||||+|++|||||||+
T Consensus        80 ef~~~~-----~~g~~~~~~~F~~G~~VDV~g~sKGKGFqGv~KR~gf~g~p~sHG~s~~hR~~GsiG~~~~PgRV~kGk  154 (205)
T d2zjrb1          80 EFRGFA-----PDGDSVNVDIFAEGEKIDATGTSKGKGTQGVMKRWNFAGGPASHGSKKWHRRPGSIGQRKTPGRVYKGK  154 (205)
T ss_dssp             EETTCC-----CSSEECSTTTSCTTCEEEEEEECCEEEEECHHHHHCCCCCCSSSSCSSCSCSCCCCCCSSTTCSCCTTC
T ss_pred             ECCCCC-----CCCCEEEEEEECCCCEEEEEEEEECCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCC
T ss_conf             012345-----665166557530898899999860446666057611055753246875211565435667676595377


Q ss_pred             CCCCCCCCEEEEECCCEEEEEECCCCEEEEECCCCCCCCCEEEEEEECCCCC
Q ss_conf             6665237733365165899980768989997157458887099996031467
Q gi|254780261|r  162 KMAGRMGGNRVTVKNLEVVSVDDKRGLILVKGCVPGAKKNSWILVRDSFKSA  213 (221)
Q Consensus       162 km~G~mG~~~~T~~nl~i~~id~e~n~i~vkGsVPG~~~~~~v~ir~a~k~~  213 (221)
                      |||||||++++|++||+|++||+|+|||||||||||| +|++|+||||+|++
T Consensus       155 kMaG~mG~~~~Tv~nl~V~~id~e~nli~vkGsVPG~-~~~~V~ir~a~k~s  205 (205)
T d2zjrb1         155 RMAGHMGMERVTVQNLEVVEIRAGENLILVKGAIPGA-NGGLVVLRSAAKAS  205 (205)
T ss_dssp             CCCEEEECCEEEEEEEEEEEEETTTTEEEEESCCSSC-TTCEEEEEBCSSCC
T ss_pred             CCCCCCCCEEEEEECCEEEEEECCCCEEEEECCCCCC-CCCEEEEEECCCCC
T ss_conf             6688346607988377999995889999996067689-99899998442279



>d2gycb1 b.43.3.2 (B:1-209) Ribosomal protein L3 {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d2j01e1 b.43.3.2 (E:1-205) Ribosomal protein L3 {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1vqob1 b.43.3.2 (B:1-337) Ribosomal protein L3 {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 221 50S ribosomal protein L3 [Candidatus Liberibacter
3bbo_F_259 (F:) Ribosomal protein L3; large ribosomal subunit 4e-54
2j01_E_206 (E:) 50S ribosomal protein L3; ribosome, tRNA, par 2e-51
1vq8_B_338 (B:) 50S ribosomal protein L3P; ribosome 50S, prot 1e-39
2zjr_B_1-29_91-211150 (B:1-29,B:91-211) 50S ribosomal protein L3; riboso 9e-35
3i1n_D_1-30_102-209138 (D:1-30,D:102-209) 50S ribosomal protein L3; ribos 3e-33
2ftc_C_1-29_104-211137 (C:1-29,C:104-211) L3MT, MRP-L3, mitochondrial 39S 8e-31
2zkr_b_1-82_209-403277 (b:1-82,b:209-403) 60S ribosomal protein L3; prote 3e-27
3jyw_C_40-78_206-362196 (C:40-78,C:206-362) 60S ribosomal protein L3; euka 1e-22
3i1n_D_31-10171 (D:31-101) 50S ribosomal protein L3; ribosome stru 2e-18
2ftc_C_30-10374 (C:30-103) L3MT, MRP-L3, mitochondrial 39S ribosom 2e-17
2zjr_B_30-9061 (B:30-90) 50S ribosomal protein L3; ribosome, larg 6e-16
>3bbo_F (F:) Ribosomal protein L3; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Nicotiana tabacum}Length = 259 Back     alignment and structure
 Score =  205 bits (522), Expect = 4e-54
 Identities = 83/218 (38%), Positives = 117/218 (53%), Gaps = 3/218 (1%)

Query: 1   MRSGVVARKLGMTCVYNIEGRRIPVTVLHLDNCQVV-VHRTLDKNGYMAVQVGAGEAKVK 59
              GV+A KLGM   +   G  +PVTV+      +V   +T   +GY AVQVG    + +
Sbjct: 42  AGVGVMATKLGMMSFFEESGTVVPVTVVGFREGNIVTQIKTEATDGYNAVQVGYRRVRDR 101

Query: 60  NVSKPMRGFFSSVNVSPKKKLFEFRVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKG 119
            ++KP  G      + P + L EFR+Q  D       +     F  G LVDV+G TIGKG
Sbjct: 102 KLTKPEMGHLEKSGIIPLRHLQEFRLQSIDGFEVTQKLDFGELFKEGDLVDVSGTTIGKG 161

Query: 120 FSGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKNLEV 179
           F G +KRHNF   + THG S SHR  GS G    PGRV+K KKM GRMGG +  ++ L++
Sbjct: 162 FQGGIKRHNFKRGQMTHG-SKSHRQLGSIGAGTTPGRVYKGKKMPGRMGGTKRKIRKLKI 220

Query: 180 VSVDDKRGLILVKGCVPGAKKNSWILVRDSFKSAVNCK 217
           V +DD+  +I++KG +PG    + + +  +     N  
Sbjct: 221 VKIDDQLNIIMIKGALPGK-PGNLLRIAPAKIVGKNIP 257


>2j01_E (E:) 50S ribosomal protein L3; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus}Length = 206 Back     alignment and structure
>1vq8_B (B:) 50S ribosomal protein L3P; 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 = 338 Back     alignment and structure
>2zjr_B (B:1-29,B:91-211) 50S ribosomal protein L3; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans}Length = 150 Back     alignment and structure
>3i1n_D (D:1-30,D:102-209) 50S ribosomal protein L3; ribosome structure, protein-RNA complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA- binding, methylation; 3.19A {Escherichia coli k-12} PDB: 1p85_B 1p86_B 1vs8_D 2aw4_D 2awb_D 2gya_B 2gyc_B 1vs6_D 2i2v_D 2j28_D 2i2t_D* 2qao_D* 2qba_D* 2qbc_D* 2qbe_D 2qbg_D 2qbi_D* 2qbk_D* 2qov_D 2qox_D ...Length = 138 Back     alignment and structure
>2ftc_C (C:1-29,C:104-211) L3MT, MRP-L3, mitochondrial 39S ribosomal protein L3; mitochondrial ribosome, large ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus}Length = 137 Back     alignment and structure
>2zkr_b (b:1-82,b:209-403) 60S ribosomal protein L3; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris}Length = 277 Back     alignment and structure
>3jyw_C (C:40-78,C:206-362) 60S ribosomal protein L3; eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus} PDB: 1s1i_CLength = 196 Back     alignment and structure
>3i1n_D (D:31-101) 50S ribosomal protein L3; ribosome structure, protein-RNA complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA- binding, methylation; 3.19A {Escherichia coli k-12} PDB: 1p85_B 1p86_B 1vs8_D 2aw4_D 2awb_D 2gya_B 2gyc_B 1vs6_D 2i2v_D 2j28_D 2i2t_D* 2qao_D* 2qba_D* 2qbc_D* 2qbe_D 2qbg_D 2qbi_D* 2qbk_D* 2qov_D 2qox_D ...Length = 71 Back     alignment and structure
>2ftc_C (C:30-103) L3MT, MRP-L3, mitochondrial 39S ribosomal protein L3; mitochondrial ribosome, large ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus}Length = 74 Back     alignment and structure
>2zjr_B (B:30-90) 50S ribosomal protein L3; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans}Length = 61 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target221 50S ribosomal protein L3 [Candidatus Liberibacter asiat
3bbo_F_259 Ribosomal protein L3; large ribosomal subunit, spi 100.0
2j01_E_206 50S ribosomal protein L3; ribosome, tRNA, paromomy 100.0
1vq8_B_338 50S ribosomal protein L3P; ribosome 50S, protein-p 100.0
3i1n_D_1-30_102-209138 50S ribosomal protein L3; ribosome structure, prot 100.0
2zjr_B_1-29_91-211150 50S ribosomal protein L3; ribosome, large ribosoma 100.0
2ftc_C_1-29_104-211137 L3MT, MRP-L3, mitochondrial 39S ribosomal protein 100.0
2zkr_b_1-82_209-403277 60S ribosomal protein L3; protein-RNA complex, 60S 100.0
3jyw_C_40-78_206-362196 60S ribosomal protein L3; eukaryotic ribosome, RAC 100.0
3i1n_D_31-10171 50S ribosomal protein L3; ribosome structure, prot 99.87
2ftc_C_30-10374 L3MT, MRP-L3, mitochondrial 39S ribosomal protein 99.85
2zjr_B_30-9061 50S ribosomal protein L3; ribosome, large ribosoma 99.78
>3bbo_F (F:) Ribosomal protein L3; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Nicotiana tabacum} Back     alignment and structure
Probab=100.00  E-value=0  Score=553.41  Aligned_cols=215  Identities=39%  Similarity=0.639  Sum_probs=204.3

Q ss_pred             CCCCEEEEECCCCEEECCCCCEEEEEEEEECCCEEE-EEEECCCCCCEEEEECCCCCCCCCCCCCHHHHHHHHCCCCCCE
Q ss_conf             944268996584516988987922689991797899-9970677886125640555564315710112576403563410
Q gi|254780261|r    1 MRSGVVARKLGMTCVYNIEGRRIPVTVLHLDNCQVV-VHRTLDKNGYMAVQVGAGEAKVKNVSKPMRGFFSSVNVSPKKK   79 (221)
Q Consensus         1 mr~Glig~KiGMT~if~e~G~~vpVTViev~~~~Vv-~~kt~ekdGY~Avqvg~~~~k~k~~~Kp~~G~fkK~g~~pk~~   79 (221)
                      |++||||+|+||||+||+||.++||||||++||.|+ ++++.|+|||+|+|+|+++.++++++||++|||+|++++|+++
T Consensus        42 ~~~g~~g~K~GMt~i~~~~g~~~pvTvle~~p~~Vv~~~k~~e~~gy~a~~~g~~~~~~~~~~k~~~g~~~k~~~~~k~~  121 (259)
T 3bbo_F           42 AGVGVMATKLGMMSFFEESGTVVPVTVVGFREGNIVTQIKTEATDGYNAVQVGYRRVRDRKLTKPEMGHLEKSGIIPLRH  121 (259)
T ss_dssp             ---------------------------------------------------------CCSSCCHHHHTTCSSCCCCCSSC
T ss_pred             CCEEEEEEECCCCEEECCCCCEEEEEEEEECCCEEEEEEECCCCCCCEEEEEEEEECCCCCCCCCCCCCHHHCCCCCCEE
T ss_conf             53479999657867788899398679999689969988603566784368998887245344654466422227665212


Q ss_pred             EEEEECCCCHHHHHCCCCEEEEEECCCCEEEEEEEEECCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEC
Q ss_conf             36532065112110034100012302532657898753433640575044212333577454346665555567522422
Q gi|254780261|r   80 LFEFRVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGFSGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFK  159 (221)
Q Consensus        80 l~Efrv~~~~~~~~vG~~i~~~~F~~Gq~VDV~g~SkGKGFqGviKR~gf~g~~~sHG~sk~hR~~GsiG~~~~PgRV~k  159 (221)
                      +.|||+++.+..++.++.+.+|+|++||+|||+|+|||||||||||||||+++|+||| |++||++||||++++||||||
T Consensus       122 ~~ef~v~~~a~~~~g~~~~~~~~F~~Gq~VDV~g~tkGKGFqGviKR~gf~g~p~sHg-sk~hR~~GsiG~~~~PgRV~~  200 (259)
T 3bbo_F          122 LQEFRLQSIDGFEVTQKLDFGELFKEGDLVDVSGTTIGKGFQGGIKRHNFKRGQMTHG-SKSHRQLGSIGAGTTPGRVYK  200 (259)
T ss_dssp             CCCCCSCCCCTTTTCCCCSSCSSSCSSSCCCCCCBCCCCSSCCSSSSSCCCCCCSSSC-SSTTTSCCCCSCSSCCTTTTT
T ss_pred             EEEEECCCCCCCCCCCEECHHHHCCCCCEEEEEEEEECCCCCCHHHCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCEEEC
T ss_conf             1000024322224323012899534886687589984633566220435213455667-754304764256777874801


Q ss_pred             CCCCCCCCCCEEEEECCCEEEEEECCCCEEEEECCCCCCCCCEEEEEEECCCCCCCCC
Q ss_conf             6766652377333651658999807689899971574588870999960314677853
Q gi|254780261|r  160 NKKMAGRMGGNRVTVKNLEVVSVDDKRGLILVKGCVPGAKKNSWILVRDSFKSAVNCK  217 (221)
Q Consensus       160 Gkkm~G~mG~~~~T~~nl~i~~id~e~n~i~vkGsVPG~~~~~~v~ir~a~k~~~~~k  217 (221)
                      |+|||||||++++|++||+|++||+|+|||+|||||||| ++++|+||+|+|+..+..
T Consensus       201 g~km~G~mG~~~~T~~Nl~I~ki~~~~n~i~vkGsVPG~-~~~~V~ir~a~k~~~~~~  257 (259)
T 3bbo_F          201 GKKMPGRMGGTKRKIRKLKIVKIDDQLNIIMIKGALPGK-PGNLLRIAPAKIVGKNIP  257 (259)
T ss_dssp             TSCCCCCCCCCBCCCCCCCEEEEETTTTEEEECSCCSSC-SSSCCCCCCCCCC-----
T ss_pred             CCCCCCCCCCCEEEEECCEEEEECCCCCEEEEEECCCCC-CCCEEEEEECCCCCCCCC
T ss_conf             776587668854888467999983889889996168689-998899987875788999



>2j01_E (E:) 50S ribosomal protein L3; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} Back     alignment and structure
>1vq8_B (B:) 50S ribosomal protein L3P; 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
>3i1n_D (D:1-30,D:102-209) 50S ribosomal protein L3; ribosome structure, protein-RNA complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA- binding, methylation; 3.19A {Escherichia coli k-12} PDB: 1p85_B 1p86_B 1vs8_D 2aw4_D 2awb_D 2gya_B 2gyc_B 1vs6_D 2i2v_D 2j28_D 2i2t_D* 2qao_D* 2qba_D* 2qbc_D* 2qbe_D 2qbg_D 2qbi_D* 2qbk_D* 2qov_D 2qox_D ... Back     alignment and structure
>2zjr_B (B:1-29,B:91-211) 50S ribosomal protein L3; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} Back     alignment and structure
>2ftc_C (C:1-29,C:104-211) L3MT, MRP-L3, mitochondrial 39S ribosomal protein L3; mitochondrial ribosome, large ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus} Back     alignment and structure
>2zkr_b (b:1-82,b:209-403) 60S ribosomal protein L3; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Back     alignment and structure
>3jyw_C (C:40-78,C:206-362) 60S ribosomal protein L3; eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus} PDB: 1s1i_C Back     alignment and structure
>3i1n_D (D:31-101) 50S ribosomal protein L3; ribosome structure, protein-RNA complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA- binding, methylation; 3.19A {Escherichia coli k-12} PDB: 1p85_B 1p86_B 1vs8_D 2aw4_D 2awb_D 2gya_B 2gyc_B 1vs6_D 2i2v_D 2j28_D 2i2t_D* 2qao_D* 2qba_D* 2qbc_D* 2qbe_D 2qbg_D 2qbi_D* 2qbk_D* 2qov_D 2qox_D ... Back     alignment and structure
>2ftc_C (C:30-103) L3MT, MRP-L3, mitochondrial 39S ribosomal protein L3; mitochondrial ribosome, large ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus} Back     alignment and structure
>2zjr_B (B:30-90) 50S ribosomal protein L3; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} Back     alignment and structure