254780647

254780647

50S ribosomal protein L27

GeneID in NCBI database:8209649Locus tag:CLIBASIA_02670
Protein GI in NCBI database:254780647Protein Accession:YP_003065060.1
Gene range:-(624887, 625159)Protein Length:90aa
Gene description:50S ribosomal protein L27
COG prediction:[J] Ribosomal protein L27
KEGG prediction:rpmA; 50S ribosomal protein L27; K02899 large subunit ribosomal protein L27
SEED prediction:LSU ribosomal protein L27p
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
MAHKKSGGSTQNGRDSAGQRLGLKKSGGQSVIAGNIIIRQRGTRYHPGLNVGLGKDHTIYALVDGHVRFFKKFSKGRAYVSVIPKIEDTQ
cccccccccccccccccccEEEEEEEcccEEEcccEEEEEcccEEEcccccEEccccEEEEEEccEEEEEEEcccccEEEEEEEcHHccc
ccHHHcccccccccccccHccccccccccEEccccEEEEccccEEccccccccccccEEEEEEccEEEEEEcccccccEEEEEccHHHcc
mahkksggstqngrdsagqrlglkksggqsviagniiirqrgtryhpglnvglgkdhtIYALVDGHVRFFKKfskgrayvsvipkiedtq
mahkksggstqngrdsagqrlglkksggqsvIAGNiiirqrgtryhPGLNVGLGKDHTIYALVDGHVRFFKkfskgrayvsvipkiedtq
MAHKKSGGSTQNGRDSAGQRLGLKKSGGQSVIAGNIIIRQRGTRYHPGLNVGLGKDHTIYALVDGHVRFFKKFSKGRAYVSVIPKIEDTQ
********************LGLKKSGGQSVIAGNIIIRQRGTRYHPGLNVGLGKDHTIYALVDGHVRFFKKFSKGRAYVSVIPKI****
*****************GQRLGLKKSGGQSVIAGNIIIRQRGTRYHPGLNVGLGKDHTIYALVDGHVRFFKKFSKGRAYVSVIPKIEDTQ
*******************RLGLKKSGGQSVIAGNIIIRQRGTRYHPGLNVGLGKDHTIYALVDGHVRFFKKFSKGRAYVSVIPKIE***
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MAHKKSGGSTQNGRDSAGQRLGLKKSGGQSVIAGNIIIRQRGTRYHPGLNVGLGKDHTIYALVDGHVRFFKKFSKGRAYVSVIPKIEDTQ
MAHKKSGGSTQNGRDSAGQRLGLKKSGGQSVIAGNIIIRQRGTRYHPGLNVGLGKDHTIYALVDGHVRFFKKFSKGRAYVSVIPKIEDTQ
MAHKKSGGSTQNGRDSAGQRLGLKKSGGQSVIAGNIIIRQRGTRYHPGLNVGLGKDHTIYALVDGHVRFFKKFSKGRAYVSVIPKIEDTQ

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
Target90 50S ribosomal protein L27 [Candidatus Liberibacter asia
31512216790 50S ribosomal protein L27 [Candidatus Liberibacter sola 1 7e-30
15039820189 50S ribosomal protein L27 [Sinorhizobium medicae WSM419 1 8e-28
15842571789 50S ribosomal protein L27 [Azorhizobium caulinodans ORS 1 4e-27
17074233993 50S ribosomal protein L27 [Methylobacterium sp. 4-46] L 1 5e-27
8905477289 50S ribosomal protein L27 [Jannaschia sp. CCS1] Length 1 8e-27
22208787389 ribosomal protein L27 [Agrobacterium radiobacter K84] L 1 9e-27
16386743789 50S ribosomal protein L27 [Bartonella tribocorum CIP 10 1 9e-27
21846294589 50S ribosomal protein L27 [Rhizobium etli Kim 5] Length 1 1e-26
17074655788 50S ribosomal protein L27 [Methylobacterium radiotolera 1 1e-26
28895916894 large subunit ribosomal protein L27 [Azospirillum sp. B 1 1e-26
>gi|315122167|ref|YP_004062656.1| 50S ribosomal protein L27 [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 90 Back     alignment and organism information
 Score =  133 bits (335), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 68/90 (75%), Positives = 77/90 (85%), Gaps = 1/90 (1%)

Query: 1  MAHKKSGGSTQNGRDSAGQRLGLKKSGGQSVIAGNIIIRQRGTRYHPGLNVGLGKDHTIY 60
          MAHKKSGGSTQNGRDSAG+RLGLKK GG+ V AGNII+RQRGTRYHPGLNVG+GKDHTI+
Sbjct: 1  MAHKKSGGSTQNGRDSAGRRLGLKKFGGEFVTAGNIIVRQRGTRYHPGLNVGIGKDHTIF 60

Query: 61 ALVDGHVRFFKKFSKGRAYVSVIPKIEDTQ 90
          ALVDG+V  FK  +KGR  VSVI   +D +
Sbjct: 61 ALVDGNVH-FKTIAKGRPRVSVIQNTKDAK 89


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|150398201|ref|YP_001328668.1| 50S ribosomal protein L27 [Sinorhizobium medicae WSM419] Length = 89 Back     alignment and organism information
>gi|158425717|ref|YP_001527009.1| 50S ribosomal protein L27 [Azorhizobium caulinodans ORS 571] Length = 89 Back     alignment and organism information
>gi|170742339|ref|YP_001770994.1| 50S ribosomal protein L27 [Methylobacterium sp. 4-46] Length = 93 Back     alignment and organism information
>gi|89054772|ref|YP_510223.1| 50S ribosomal protein L27 [Jannaschia sp. CCS1] Length = 89 Back     alignment and organism information
>gi|222087873|ref|YP_002546411.1| ribosomal protein L27 [Agrobacterium radiobacter K84] Length = 89 Back     alignment and organism information
>gi|163867437|ref|YP_001608634.1| 50S ribosomal protein L27 [Bartonella tribocorum CIP 105476] Length = 89 Back     alignment and organism information
>gi|218462945|ref|ZP_03503036.1| 50S ribosomal protein L27 [Rhizobium etli Kim 5] Length = 89 Back     alignment and organism information
>gi|170746557|ref|YP_001752817.1| 50S ribosomal protein L27 [Methylobacterium radiotolerans JCM 2831] Length = 88 Back     alignment and organism information
>gi|288959168|ref|YP_003449509.1| large subunit ribosomal protein L27 [Azospirillum sp. B510] Length = 94 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
Target90 50S ribosomal protein L27 [Candidatus Liberibacter asia
PRK0543582 PRK05435, rpmA, 50S ribosomal protein L27; Validated 6e-37
COG021187 COG0211, RpmA, Ribosomal protein L27 [Translation, ribo 4e-29
KOG4600144 KOG4600, KOG4600, KOG4600, Mitochondrial ribosomal prot 8e-28
TIGR0006283 TIGR00062, L27, ribosomal protein L27 2e-27
CHL0012186 CHL00121, rpl27, ribosomal protein L27; Reviewed 3e-26
pfam0101680 pfam01016, Ribosomal_L27, Ribosomal L27 protein 1e-32
>gnl|CDD|180080 PRK05435, rpmA, 50S ribosomal protein L27; Validated Back     alignment and domain information
>gnl|CDD|30560 COG0211, RpmA, Ribosomal protein L27 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|39800 KOG4600, KOG4600, KOG4600, Mitochondrial ribosomal protein MRP7 (L2) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>gnl|CDD|161685 TIGR00062, L27, ribosomal protein L27 Back     alignment and domain information
>gnl|CDD|177044 CHL00121, rpl27, ribosomal protein L27; Reviewed Back     alignment and domain information
>gnl|CDD|144560 pfam01016, Ribosomal_L27, Ribosomal L27 protein Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 90 50S ribosomal protein L27 [Candidatus Liberibacter asia
COG021187 RpmA Ribosomal protein L27 [Translation, ribosomal stru 100.0
CHL0012187 rpl27 ribosomal protein L27; Reviewed 100.0
PRK0543585 rpmA 50S ribosomal protein L27; Validated 100.0
KOG4600144 consensus 100.0
pfam0101680 Ribosomal_L27 Ribosomal L27 protein. 100.0
TIGR0006283 L27 ribosomal protein L27; InterPro: IPR001684 Ribosome 100.0
PRK09521 187 exosome complex RNA-binding protein Csl4; Provisional 94.62
PRK04163 232 exosome complex RNA-binding protein Rrp4; Provisional 94.39
COG1096 188 Predicted RNA-binding protein (consists of S1 domain an 93.37
pfam03961 450 DUF342 Protein of unknown function (DUF342). This famil 90.7
>COG0211 RpmA Ribosomal protein L27 [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>CHL00121 rpl27 ribosomal protein L27; Reviewed Back     alignment and domain information
>PRK05435 rpmA 50S ribosomal protein L27; Validated Back     alignment and domain information
>KOG4600 consensus Back     alignment and domain information
>pfam01016 Ribosomal_L27 Ribosomal L27 protein Back     alignment and domain information
>TIGR00062 L27 ribosomal protein L27; InterPro: IPR001684 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms Back     alignment and domain information
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional Back     alignment and domain information
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional Back     alignment and domain information
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis] Back     alignment and domain information
>pfam03961 DUF342 Protein of unknown function (DUF342) 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
Target90 50S ribosomal protein L27 [Candidatus Liberibacter asia
3bbo_X198 Homology Model For The Spinach Chloroplast 50s Subu 1e-33
1vs6_W85 Crystal Structure Of The Bacterial Ribosome From Es 8e-31
1v8q_A85 Crystal Structure Of Ribosomal Protein L27 From The 9e-30
1p85_U84 Real Space Refined Coordinates Of The 50s Subunit F 1e-29
1vsa_U85 Crystal Structure Of A 70s Ribosome-Trna Complex Re 1e-29
2v47_085 Structure Of The Ribosome Recycling Factor Bound To 2e-29
3mrz_W84 Recognition Of The Amber Stop Codon By Release Fact 2e-28
1nkw_U91 Crystal Structure Of The Large Ribosomal Subunit Fr 2e-27
3fik_W79 Ternary Complex-Bound E.Coli 70s Ribosome. This Ent 4e-27
1pnu_U86 Crystal Structure Of A Streptomycin Dependent Ribos 6e-26
3pyo_W76 Crystal Structure Of A Complex Containing Domain 3 9e-25
2ftc_O69 Structural Model For The Large Subunit Of The Mamma 2e-17
gi|189096146|pdb|3BBO|X Chain X, Homology Model For The Spinach Chloroplast 50s Subunit Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome Length = 198 Back     alignment and structure
 Score =  145 bits (368), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 50/84 (59%), Positives = 62/84 (73%), Gaps = 1/84 (1%)

Query: 2   AHKKSGGSTQNGRDSAGQRLGLKKSGGQSVIAGNIIIRQRGTRYHPGLNVGLGKDHTIYA 61
           AHKK  GST+NGRDS GQRLG+K  G Q    G II+RQRGT++H G NVG+GKDHTI++
Sbjct: 59  AHKKGAGSTKNGRDSPGQRLGVKIYGDQVAKPGAIIVRQRGTKFHAGKNVGIGKDHTIFS 118

Query: 62  LVDGHVRFFKKFSKGRAYVSVIPK 85
           L+DG V+F  KF   R  +SV P+
Sbjct: 119 LIDGLVKFE-KFGPDRKKISVYPR 141


gi|116666591|pdb|1VS6|W Chain W, Crystal Structure Of The Bacterial Ribosome From Escherichia Coli In Complex With The Antibiotic Kasugamyin At 3.5a Resolution. This File Contains The 50s Subunit Of One 70s Ribosome. The Entire Crystal Structure Contains Two 70s Ribosomes And Is Described In Remark 400. Length = 85 Back     alignment and structure
gi|51247910|pdb|1V8Q|A Chain A, Crystal Structure Of Ribosomal Protein L27 From Thermus Thermophilus Hb8 Length = 85 Back     alignment and structure
>gi|33357921|pdb|1P85|U Chain U, 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 = 84 Back     alignment and structure
gi|149240906|pdb|1VSA|U Chain U, Crystal Structure Of A 70s Ribosome-Trna Complex Reveals Functional Interactions And Rearrangements. This File, 1vsa, Contains The 50s Ribosome Subunit. 30s Ribosome Subunit Is In The File 2ow8 Length = 85 Back     alignment and structure
>gi|157836510|pdb|2V47|0 Chain 0, Structure Of The Ribosome Recycling Factor Bound To The Thermus Thermophilus 70s Ribosome With Mrna, Asl-Phe And Trna-Fmet (Part 2 Of 4). This File Contains The 50s Subunit For Molecule 1. Length = 85 Back     alignment and structure
>gi|300508651|pdb|3MRZ|W Chain W, Recognition Of The Amber Stop Codon By Release Factor Rf1. This Entry 3mrz Contains 50s Ribosomal Subunit. The 30s Ribosomal Subunit Can Be Found In Pdb Entry 3ms0. Molecule A In The Same Asymmetric Unit Is Deposited As 3mr8 (50s) And 3ms1 (30s). Length = 84 Back     alignment and structure
gi|28948940|pdb|1NKW|U Chain U, Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans Length = 91 Back     alignment and structure
>gi|224510752|pdb|3FIK|W Chain W, Ternary Complex-Bound E.Coli 70s Ribosome. This Entry Consists Of The 50s Subunit. Length = 79 Back     alignment and structure
>gi|34811574|pdb|1PNU|U Chain U, 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 = 86 Back     alignment and structure
>gi|322812594|pdb|3PYO|W Chain W, 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 = 76 Back     alignment and structure
>gi|99032321|pdb|2FTC|O Chain O, Structural Model For The Large Subunit Of The Mammalian Mitochondrial Ribosome Length = 69 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target90 50S ribosomal protein L27 [Candidatus Liberibacter asia
3bbo_X198 Ribosomal protein L27; large ribosomal subunit, spinach 9e-35
2zjr_T91 50S ribosomal protein L27; ribosome, large ribosomal su 2e-29
1v8q_A85 TT0826; structural genomics, proteomics, riken structur 3e-29
2qam_W84 50S ribosomal protein L27; RNA-protein complex, ribosom 9e-29
2ftc_O69 L27MT, MRP-L27, mitochondrial 39S ribosomal protein L27 4e-25
>3bbo_X Ribosomal protein L27; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Arabidopsis thaliana} SCOP: i.1.1.1 Length = 198 Back     alignment and structure
 Score =  140 bits (353), Expect = 9e-35
 Identities = 50/85 (58%), Positives = 63/85 (74%), Gaps = 1/85 (1%)

Query: 1   MAHKKSGGSTQNGRDSAGQRLGLKKSGGQSVIAGNIIIRQRGTRYHPGLNVGLGKDHTIY 60
            AHKK  GST+NGRDS GQRLG+K  G Q    G II+RQRGT++H G NVG+GKDHTI+
Sbjct: 58  SAHKKGAGSTKNGRDSPGQRLGVKIYGDQVAKPGAIIVRQRGTKFHAGKNVGIGKDHTIF 117

Query: 61  ALVDGHVRFFKKFSKGRAYVSVIPK 85
           +L+DG V+ F+KF   R  +SV P+
Sbjct: 118 SLIDGLVK-FEKFGPDRKKISVYPR 141


>2zjr_T 50S ribosomal protein L27; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: b.84.4.1 PDB: 1nwx_U* 1nwy_U* 1sm1_U* 1xbp_U* 1y69_U 1yl3_3 2b66_0 2b9n_0 2b9p_0 2zjp_T* 2zjq_T 1nkw_U 3cf5_T* 3dll_T* 1pnu_U 1pny_U 1vor_X 1vou_X 1vow_X 1voy_X ... Length = 91 Back     alignment and structure
>1v8q_A TT0826; structural genomics, proteomics, riken structural genomics/proteomics initiative, RSGI, translation; 2.80A {Thermus thermophilus} SCOP: b.84.4.1 PDB: 2hgj_Z 2hgq_Z 2hgu_Z 2j01_0 2j03_0 2jl6_0 2jl8_0 2wdi_0 2wdj_0 2wdl_0 2wdn_0 2wh2_0 2wh4_0 2wrj_0 2wrl_0 2wro_0 2wrr_0 3fin_0 3hux_0 3huz_0 ... Length = 85 Back     alignment and structure
>2qam_W 50S ribosomal protein L27; RNA-protein complex, ribosome; HET: NMY; 3.21A {Escherichia coli} SCOP: b.84.4.1 PDB: 1p85_U 1p86_U 2awb_W 2gya_U 2gyc_U 2aw4_W 2i2v_W 2j28_W 2i2t_W* 2qao_W* 2qba_W* 2qbc_W* 2qbe_W 2qbg_W 2qbi_W* 2qbk_W* 2qov_W 2qox_W 2qoz_W* 2qp1_W* ... Length = 84 Back     alignment and structure
>2ftc_O L27MT, MRP-L27, mitochondrial 39S ribosomal protein L27; mitochondrial ribosome, large ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus} PDB: 3iy9_O Length = 69 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target90 50S ribosomal protein L27 [Candidatus Liberibacter asia
1v8q_A85 TT0826; structural genomics, proteomics, riken structur 100.0
2zjr_T91 50S ribosomal protein L27; ribosome, large ribosomal su 100.0
2qam_W84 50S ribosomal protein L27; RNA-protein complex, ribosom 100.0
3bbo_X198 Ribosomal protein L27; large ribosomal subunit, spinach 100.0
2ftc_O69 L27MT, MRP-L27, mitochondrial 39S ribosomal protein L27 100.0
3m7n_A 179 Putative uncharacterized protein AF_0206; exosome, RNA, 93.11
2nn6_H 308 Exosome complex exonuclease RRP4; RNA, exosome, PM/SCL, 92.85
2nn6_I 209 3'-5' exoribonuclease CSL4 homolog; RNA, exosome, PM/SC 90.17
>1v8q_A TT0826; structural genomics, proteomics, riken structural genomics/proteomics initiative, RSGI, translation; 2.80A {Thermus thermophilus} SCOP: b.84.4.1 PDB: 2hgj_Z 2hgq_Z 2hgu_Z 2j01_0 2j03_0 2jl6_0 2jl8_0 2wdi_0 2wdj_0 2wdl_0 2wdn_0 2wh2_0 2wh4_0 2wrj_0 2wrl_0 2wro_0 2wrr_0 2x9s_0 2x9u_0 3fin_0 ... Back     alignment and structure
Probab=100.00  E-value=1.3e-44  Score=265.72  Aligned_cols=85  Identities=58%  Similarity=0.913  Sum_probs=81.9

Q ss_pred             CCCCCCCCCCCCCCCCCCCEEEEEEECCCEECCCCEEEECCCCEEECCCCEEECCCCEEEECCCCEEEEEEECCCCCCEE
Q ss_conf             96014567606789887425324542781953796899723888937766075686756352256899876368883289
Q gi|254780647|r    1 MAHKKSGGSTQNGRDSAGQRLGLKKSGGQSVIAGNIIIRQRGTRYHPGLNVGLGKDHTIYALVDGHVRFFKKFSKGRAYV   80 (90)
Q Consensus         1 mA~KK~gGStkNgrdS~~krLGvK~~~Gq~V~~G~IivRQRGtk~~PG~nVg~GkD~TLfA~~~G~V~f~~~~~~~r~~V   80 (90)
                      |||||++|||+|||||+|||||||+|+||+|.||+||||||||+||||+||+||+||||||+++|+|+|+++ .++|+||
T Consensus         1 MA~KK~~GStkNgrdS~~krLGvK~~ggq~V~aG~IivRQRGtk~hPG~NVg~GkD~TLfAl~~G~V~f~~~-~~~r~~V   79 (85)
T 1v8q_A            1 MAHKKGLGSTRNGRDSQAKRLGVKRYEGQVVRAGNILVRQRGTRFKPGKNVGMGRDFTLFALVDGVVEFQDR-GRLGRYV   79 (85)
T ss_dssp             -------------------CCEECSCTTCEECTTCEEEECSSCSSEECTTEEECTTCCEEESSSEEEEEEEC-GGGCEEE
T ss_pred             CCCCCCCCCCCCCCCCCCCCCEEEEECCEEECCCCEEEEECCCEEECCCCEEECCCCEEEEECCEEEEEEEC-CCCCEEE
T ss_conf             985346677788988988606778719989768858999277728188885687788098823579998593-8998799


Q ss_pred             EEECCC
Q ss_conf             976154
Q gi|254780647|r   81 SVIPKI   86 (90)
Q Consensus        81 ~V~P~~   86 (90)
                      ||+|.+
T Consensus        80 ~V~P~a   85 (85)
T 1v8q_A           80 HVRPLA   85 (85)
T ss_dssp             EEEECC
T ss_pred             EEEECC
T ss_conf             999689



>2zjr_T 50S ribosomal protein L27; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: b.84.4.1 PDB: 1nwx_U* 1nwy_U* 1sm1_U* 1xbp_U* 1y69_U 1yl3_3 2b66_0 2b9n_0 2b9p_0 2zjp_T* 2zjq_T 1nkw_U 3cf5_T* 3dll_T* 1pnu_U 1pny_U 1vor_X 1vou_X 1vow_X 1voy_X ... Back     alignment and structure
>2qam_W 50S ribosomal protein L27; RNA-protein complex, ribosome; HET: NMY; 3.21A {Escherichia coli} SCOP: b.84.4.1 PDB: 1p85_U 1p86_U 2awb_W 2gya_U 2gyc_U 2aw4_W 2i2v_W 2j28_W 2i2t_W* 2qao_W* 2qba_W* 2qbc_W* 2qbe_W 2qbg_W 2qbi_W* 2qbk_W* 2qov_W 2qox_W 2qoz_W* 2qp1_W* ... Back     alignment and structure
>3bbo_X Ribosomal protein L27; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Arabidopsis thaliana} SCOP: i.1.1.1 Back     alignment and structure
>2ftc_O L27MT, MRP-L27, mitochondrial 39S ribosomal protein L27; mitochondrial ribosome, large ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus} PDB: 3iy9_O Back     alignment and structure
>3m7n_A Putative uncharacterized protein AF_0206; exosome, RNA, exonuclease, hydrolase, nuclease, hydrolase-RN; 2.40A {Archaeoglobus fulgidus} PDB: 2ba1_A 3m85_A Back     alignment and structure
>2nn6_H Exosome complex exonuclease RRP4; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2 d.51.1.1 Back     alignment and structure
>2nn6_I 3'-5' exoribonuclease CSL4 homolog; RNA, exosome, PM/SCL, phosphorolytic, hydrolase/transferase complex; 3.35A {Homo sapiens} SCOP: b.40.4.5 b.84.4.2 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 90 50S ribosomal protein L27 [Candidatus Liberibacter asia
d2gycu184 b.84.4.1 (U:1-84) Ribosomal protein L27 {Escherichia co 2e-28
d2zjrt184 b.84.4.1 (T:2-85) Ribosomal protein L27 {Deinococcus ra 8e-28
d1v8qa_66 b.84.4.1 (A:) Ribosomal protein L27 {Thermus thermophil 4e-22
>d2gycu1 b.84.4.1 (U:1-84) Ribosomal protein L27 {Escherichia coli [TaxId: 562]} Length = 84 Back     information, alignment and structure

class: All beta proteins
fold: Barrel-sandwich hybrid
superfamily: Ribosomal L27 protein-like
family: Ribosomal L27 protein
domain: Ribosomal protein L27
species: Escherichia coli [TaxId: 562]
 Score =  117 bits (296), Expect = 2e-28
 Identities = 48/83 (57%), Positives = 66/83 (79%)

Query: 2  AHKKSGGSTQNGRDSAGQRLGLKKSGGQSVIAGNIIIRQRGTRYHPGLNVGLGKDHTIYA 61
          AHKK+GGST+NGRDS  +RLG+K+ GG+SV+AG+II+RQRGT++H G NVG G+DHT++A
Sbjct: 1  AHKKAGGSTRNGRDSEAKRLGVKRFGGESVLAGSIIVRQRGTKFHAGANVGCGRDHTLFA 60

Query: 62 LVDGHVRFFKKFSKGRAYVSVIP 84
            DG V+F  K  K R ++S+  
Sbjct: 61 KADGKVKFEVKGPKNRKFISIEA 83


>d2zjrt1 b.84.4.1 (T:2-85) Ribosomal protein L27 {Deinococcus radiodurans [TaxId: 1299]} Length = 84 Back     information, alignment and structure
>d1v8qa_ b.84.4.1 (A:) Ribosomal protein L27 {Thermus thermophilus [TaxId: 274]} Length = 66 Back     information, alignment and structure

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

IdentityAlignment graphLength Definition Probability
Target90 50S ribosomal protein L27 [Candidatus Liberibacter asia
d2zjrt184 Ribosomal protein L27 {Deinococcus radiodurans [TaxId: 100.0
d2gycu184 Ribosomal protein L27 {Escherichia coli [TaxId: 562]} 100.0
d1v8qa_66 Ribosomal protein L27 {Thermus thermophilus [TaxId: 274 99.97
d2ba0a251 Exosome complex RNA-binding protein 1, ECR1 {Archaeoglo 94.96
>d2zjrt1 b.84.4.1 (T:2-85) Ribosomal protein L27 {Deinococcus radiodurans [TaxId: 1299]} Back     information, alignment and structure
class: All beta proteins
fold: Barrel-sandwich hybrid
superfamily: Ribosomal L27 protein-like
family: Ribosomal L27 protein
domain: Ribosomal protein L27
species: Deinococcus radiodurans [TaxId: 1299]
Probab=100.00  E-value=1.7e-42  Score=252.74  Aligned_cols=83  Identities=53%  Similarity=0.908  Sum_probs=80.3

Q ss_pred             CCCCCCCCCCCCCCCCCCEEEEEEECCCEECCCCEEEECCCCEEECCCCEEECCCCEEEECCCCEEEEEEECCCCCCEEE
Q ss_conf             60145676067898874253245427819537968997238889377660756867563522568998763688832899
Q gi|254780647|r    2 AHKKSGGSTQNGRDSAGQRLGLKKSGGQSVIAGNIIIRQRGTRYHPGLNVGLGKDHTIYALVDGHVRFFKKFSKGRAYVS   81 (90)
Q Consensus         2 A~KK~gGStkNgrdS~~krLGvK~~~Gq~V~~G~IivRQRGtk~~PG~nVg~GkD~TLfA~~~G~V~f~~~~~~~r~~V~   81 (90)
                      ||||++|||+|+|||+|||||||+|+||+|.||+||||||||+||||+||+||+||||||+++|+|+|++. .++|++||
T Consensus         1 A~KK~~GSt~NgrdS~~krlGvK~~~Gq~V~~G~IivRQRGtk~hpG~nVg~GkD~TLfA~~~G~V~F~k~-~~~rk~V~   79 (84)
T d2zjrt1           1 AHKKGVGSSKNGRDSNPKYLGVKKFGGEVVKAGNILVRQRGTKFKAGQGVGMGRDHTLFALSDGKVVFINK-GKGARFIS   79 (84)
T ss_dssp             CCSSCSSCSSCCCCCCCCCCCCSSCTTCEECSSCEEECCSSSSSEECTTEECCTTSCEEESSCEEEEEEEE-TTTEEEEE
T ss_pred             CCCCCCCCCCCCCCCCCCCCEEEECCCEEEECCCEEEEECCCEECCCCCCCCCCCCCEEEEECEEEEEEEC-CCCCEEEE
T ss_conf             97456577788988987416578779978707858999447617287872336888688850339999895-89998989


Q ss_pred             EECC
Q ss_conf             7615
Q gi|254780647|r   82 VIPK   85 (90)
Q Consensus        82 V~P~   85 (90)
                      |+|+
T Consensus        80 V~p~   83 (84)
T d2zjrt1          80 IEAA   83 (84)
T ss_dssp             ECCC
T ss_pred             EEEC
T ss_conf             9968



>d2gycu1 b.84.4.1 (U:1-84) Ribosomal protein L27 {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1v8qa_ b.84.4.1 (A:) Ribosomal protein L27 {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d2ba0a2 b.84.4.2 (A:2-52) Exosome complex RNA-binding protein 1, ECR1 {Archaeoglobus fulgidus [TaxId: 2234]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 90 50S ribosomal protein L27 [Candidatus Liberibacter
2zjr_T_91 (T:) 50S ribosomal protein L27; ribosome, large ri 3e-30
1v8q_A_85 (A:) TT0826; structural genomics, proteomics, rike 5e-30
2qam_W_84 (W:) 50S ribosomal protein L27; RNA-protein comple 5e-30
2ftc_O_69 (O:) L27MT, MRP-L27, mitochondrial 39S ribosomal p 4e-24
3bbo_X_198 (X:) Ribosomal protein L27; large ribosomal subuni 1e-22
>2zjr_T (T:) 50S ribosomal protein L27; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans}Length = 91 Back     alignment and structure
 Score =  125 bits (315), Expect = 3e-30
 Identities = 45/84 (53%), Positives = 61/84 (72%), Gaps = 1/84 (1%)

Query: 1  MAHKKSGGSTQNGRDSAGQRLGLKKSGGQSVIAGNIIIRQRGTRYHPGLNVGLGKDHTIY 60
          MAHKK  GS++NGRDS  + LG+KK GG+ V AGNI++RQRGT++  G  VG+G+DHT++
Sbjct: 1  MAHKKGVGSSKNGRDSNPKYLGVKKFGGEVVKAGNILVRQRGTKFKAGQGVGMGRDHTLF 60

Query: 61 ALVDGHVRFFKKFSKGRAYVSVIP 84
          AL DG V F  K  KG  ++S+  
Sbjct: 61 ALSDGKVVFINK-GKGARFISIEA 83


>1v8q_A (A:) TT0826; structural genomics, proteomics, riken structural genomics/proteomics initiative, RSGI, translation; 2.80A {Thermus thermophilus}Length = 85 Back     alignment and structure
>2qam_W (W:) 50S ribosomal protein L27; RNA-protein complex, ribosome; HET: NMY; 3.21A {Escherichia coli}Length = 84 Back     alignment and structure
>2ftc_O (O:) L27MT, MRP-L27, mitochondrial 39S ribosomal protein L27; mitochondrial ribosome, large ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus} PDB: 3iy9_OLength = 69 Back     alignment and structure
>3bbo_X (X:) Ribosomal protein L27; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Arabidopsis thaliana}Length = 198 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target90 50S ribosomal protein L27 [Candidatus Liberibacter asia
2zjr_T_91 50S ribosomal protein L27; ribosome, large ribosom 100.0
1v8q_A_85 TT0826; structural genomics, proteomics, riken str 100.0
2qam_W_84 50S ribosomal protein L27; RNA-protein complex, ri 100.0
2ftc_O_69 L27MT, MRP-L27, mitochondrial 39S ribosomal protei 100.0
3bbo_X_198 Ribosomal protein L27; large ribosomal subunit, sp 99.78
2je6_I_1-7070 RRP4, exosome complex RNA-binding protein 1; nucle 93.19
2ba0_A_1-5353 Archeal exosome RNA binding protein RRP4; RNAse PH 91.3
>2zjr_T (T:) 50S ribosomal protein L27; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} Back     alignment and structure
Probab=100.00  E-value=8.4e-45  Score=267.54  Aligned_cols=88  Identities=51%  Similarity=0.876  Sum_probs=84.7

Q ss_pred             CCCCCCCCCCCCCCCCCCCEEEEEEECCCEECCCCEEEECCCCEEECCCCEEECCCCEEEECCCCEEEEEEECCCCCCEE
Q ss_conf             96014567606789887425324542781953796899723888937766075686756352256899876368883289
Q gi|254780647|r    1 MAHKKSGGSTQNGRDSAGQRLGLKKSGGQSVIAGNIIIRQRGTRYHPGLNVGLGKDHTIYALVDGHVRFFKKFSKGRAYV   80 (90)
Q Consensus         1 mA~KK~gGStkNgrdS~~krLGvK~~~Gq~V~~G~IivRQRGtk~~PG~nVg~GkD~TLfA~~~G~V~f~~~~~~~r~~V   80 (90)
                      |||||++|||+|||||+|||||||+|+||+|.||+||||||||+||||+||+||+||||||+++|+|+|+++ .++|+||
T Consensus         1 mA~KK~~GStkNgrdS~~krlGvK~~~gq~V~~G~IivRQRGtk~~PG~nVg~GkD~TL~Al~~G~V~f~~~-~~~r~~V   79 (91)
T 2zjr_T            1 MAHKKGVGSSKNGRDSNPKYLGVKKFGGEVVKAGNILVRQRGTKFKAGQGVGMGRDHTLFALSDGKVVFINK-GKGARFI   79 (91)
T ss_dssp             -CCSSCSSCSSCCCCCCCCCCCCSSCTTCEECSSCEEECCSSSSSEECTTEECCTTSCEEESSCEEEEEEEE-TTTEEEE
T ss_pred             CCCCCCCCCCCCCCCCCCCCCEEEECCCEEEECCCEEEEECCCCCCCCCCCCCCCCCCEEEECCEEEEEEEC-CCCCEEE
T ss_conf             984346678888988998728878779758716818999437607187872336888588850249999897-8999899


Q ss_pred             EEECCCCCC
Q ss_conf             976154235
Q gi|254780647|r   81 SVIPKIEDT   89 (90)
Q Consensus        81 ~V~P~~~~~   89 (90)
                      ||+|+.+++
T Consensus        80 ~V~p~~~~~   88 (91)
T 2zjr_T           80 SIEAAQTEV   88 (91)
T ss_dssp             EECCCC---
T ss_pred             EEEECCCCC
T ss_conf             998588302



>1v8q_A (A:) TT0826; structural genomics, proteomics, riken structural genomics/proteomics initiative, RSGI, translation; 2.80A {Thermus thermophilus} Back     alignment and structure
>2qam_W (W:) 50S ribosomal protein L27; RNA-protein complex, ribosome; HET: NMY; 3.21A {Escherichia coli} Back     alignment and structure
>2ftc_O (O:) L27MT, MRP-L27, mitochondrial 39S ribosomal protein L27; mitochondrial ribosome, large ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus} PDB: 3iy9_O Back     alignment and structure
>3bbo_X (X:) Ribosomal protein L27; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Arabidopsis thaliana} Back     alignment and structure
>2je6_I (I:1-70) RRP4, exosome complex RNA-binding protein 1; nuclease, hydrolase, exonuclease, phosphorolytic, exoribonuclease, RNA degradation; HET: 1PE; 1.6A {Sulfolobus solfataricus} Back     alignment and structure
>2ba0_A (A:1-53) Archeal exosome RNA binding protein RRP4; RNAse PH, RNA degradation, exoribonuclease, S1domain, KH domain, archaeal; 2.70A {Archaeoglobus fulgidus} Back     alignment and structure