RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780247|ref|YP_003064660.1| 30S ribosomal protein S8
[Candidatus Liberibacter asiaticus str. psy62]
(129 letters)
>1i6u_A 30S ribosomal protein S8P; protein-RNA interactions, ribosome, RNA,
X-RAY crystallography; 2.60A {Methanocaldococcus
jannaschii} SCOP: d.140.1.1
Length = 130
Score = 138 bits (349), Expect = 4e-34
Identities = 40/127 (31%), Positives = 61/127 (48%), Gaps = 4/127 (3%)
Query: 4 LGDMLTRIRNANLRYKPSVVI-PFSRLHARVLDVLKTEGYIGEYCEIDAGKGRIQLKVDL 62
L + L I N K V I P S+L RVL V++ GYIGE+ I+ G+ I +
Sbjct: 7 LANALNHISNCERVGKKVVYIKPASKLIGRVLKVMQDNGYIGEFEFIEDGRAGIFKVELI 66
Query: 63 KYHNGASVIRKIDCVSKPGRRLYSSFKDIPQVCNGLGIMIVTTSKGVMAGHQARECKVGG 122
N I+ V K G + GI+IV+T++GVM+ +A++ +GG
Sbjct: 67 GKINKCGAIKPRFPVKKFGYEKFEKRYLPA---RDFGILIVSTTQGVMSHEEAKKRGLGG 123
Query: 123 EVLCSVF 129
+L V+
Sbjct: 124 RLLAYVY 130
>2vqe_H 30S ribosomal protein S8, 30S ribosomal protein S6; tRNA-binding,
rRNA-binding, metal-binding, zinc-finger, translation;
HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP:
d.140.1.1 PDB: 1eg0_E* 1fka_H 1gix_K* 1hnw_H* 1hnx_H*
1hnz_H* 1hr0_H 1ibk_H* 1ibl_H* 1ibm_H 1j5e_H 1jgo_K*
1jgp_K* 1jgq_K* 1ml5_K* 1n32_H* 1n33_H* 1n34_H 1n36_H
1pns_H ...
Length = 138
Score = 136 bits (344), Expect = 1e-33
Identities = 54/133 (40%), Positives = 74/133 (55%), Gaps = 7/133 (5%)
Query: 4 LGDMLTRIRNANLRYKPSVVIPFSRLHARVLDVLKTEGYIGEYCEIDAGK-------GRI 56
+ DMLTRIRNA YK S +P SR +L +L EG+I Y +D +
Sbjct: 6 IADMLTRIRNATRVYKESTDVPASRFKEEILRILAREGFIKGYERVDVDGKPYLRVYLKY 65
Query: 57 QLKVDLKYHNGASVIRKIDCVSKPGRRLYSSFKDIPQVCNGLGIMIVTTSKGVMAGHQAR 116
+ VI I +SKPGRR+Y K+IP+V GLGI I++TSKGV+ +AR
Sbjct: 66 GPRRQGPDPRPEQVIHHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLTDREAR 125
Query: 117 ECKVGGEVLCSVF 129
+ VGGE++C V+
Sbjct: 126 KLGVGGELICEVW 138
>1s03_H 30S ribosomal protein S8; protein-RNA complex, SPC operon,
transcription/RNA complex; 2.70A {Escherichia coli}
SCOP: d.140.1.1 PDB: 1p6g_H 1p87_H 2avy_H 2aw7_H 2i2p_H
2i2u_H 2qal_H* 2qan_H* 2qb9_H* 2qbb_H* 2qbd_H 2qbf_H
2qbh_H* 2qbj_H* 2qou_H* 2qow_H* 2qoy_H* 2qp0_H* 2vho_H
2vhp_H ...
Length = 129
Score = 134 bits (338), Expect = 7e-33
Identities = 52/125 (41%), Positives = 77/125 (61%), Gaps = 2/125 (1%)
Query: 4 LGDMLTRIRNANLRYKPSVVIPFSRLHARVLDVLKTEGYIGEYCEIDAGKGRIQLKVDLK 63
+ DMLTRIRN K +V +P S+L + +VLK EG+I ++ K + ++ LK
Sbjct: 6 IADMLTRIRNGQAANKAAVTMPSSKLKVAIANVLKEEGFIEDFKVEGDTKPEL--ELTLK 63
Query: 64 YHNGASVIRKIDCVSKPGRRLYSSFKDIPQVCNGLGIMIVTTSKGVMAGHQARECKVGGE 123
Y G +V+ I VS+PG R+Y ++P+V GLGI +V+TSKGVM AR+ +GGE
Sbjct: 64 YFQGKAVVESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQAGLGGE 123
Query: 124 VLCSV 128
++C V
Sbjct: 124 IICYV 128
>3bbn_H Ribosomal protein S8; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 134
Score = 131 bits (331), Expect = 5e-32
Identities = 39/129 (30%), Positives = 75/129 (58%), Gaps = 3/129 (2%)
Query: 4 LGDMLTRIRNANLRYKPSVVIPFSRLHARVLDVLKTEGYIGEYCEIDAG-KGRIQLKVDL 62
+ D++T IRNA++ K +V I + + ++ +L EG+I + K + L +
Sbjct: 6 IADIITCIRNADMNRKGTVRIVSTNITENIVKILLREGFIENARKHQERNKYFLVLTLRH 65
Query: 63 KYHNGASVIR--KIDCVSKPGRRLYSSFKDIPQVCNGLGIMIVTTSKGVMAGHQARECKV 120
+ + + + VS+PG R+YS+++ IP++ G+GI I++TS+G+M +AR +
Sbjct: 66 RRNKKGPYLNTFHLKRVSRPGLRIYSNYQRIPRILGGMGIAILSTSRGIMTDREARLEGI 125
Query: 121 GGEVLCSVF 129
GGE+LC ++
Sbjct: 126 GGEILCYIW 134
>1sei_A Ribosomal protein S8; prokaryotic, rRNA-binding; 1.90A {Geobacillus
stearothermophilus} SCOP: d.140.1.1
Length = 130
Score = 129 bits (326), Expect = 2e-31
Identities = 50/125 (40%), Positives = 78/125 (62%), Gaps = 1/125 (0%)
Query: 4 LGDMLTRIRNANLRYKPSVVIPFSRLHARVLDVLKTEGYIGEYCEIDAGKGRIQLKVDLK 63
+ DMLT IRNAN+ + +P S++ + ++LK EG+I +Y I+ K I L++ LK
Sbjct: 6 IADMLTAIRNANMVRHEKLEVPASKIKREIAEILKREGFIRDYEYIEDNKQGI-LRIFLK 64
Query: 64 YHNGASVIRKIDCVSKPGRRLYSSFKDIPQVCNGLGIMIVTTSKGVMAGHQARECKVGGE 123
Y VI + +SKPG R+Y ++P+V NGLGI I++TS+GV+ +AR+ GGE
Sbjct: 65 YGPNERVITGLKRISKPGLRVYVKAHEVPRVLNGLGIAILSTSQGVLTDKEARQKGTGGE 124
Query: 124 VLCSV 128
++ V
Sbjct: 125 IIAYV 129
>2zkq_h 40S ribosomal protein S15AE; protein-RNA complex, 40S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris} PDB: 1s1h_H
Length = 130
Score = 108 bits (270), Expect = 5e-25
Identities = 39/130 (30%), Positives = 57/130 (43%), Gaps = 4/130 (3%)
Query: 1 MSCLGDMLTRIRNANLRYKPSVVI-PFSRLHARVLDVLKTEGYIGEYCEIDAGKGRIQLK 59
M+ L D L I NA R K V+I P S++ R L V+ GYIGE+ ID + +
Sbjct: 4 MNVLADALKSINNAEKRGKRQVLIRPCSKVIVRFLTVMMKHGYIGEFEIIDDHRAGKIVV 63
Query: 60 VDLKYHNGASVIRKIDCVSKPGRRLYSSFKDIPQVCNGLGIMIVTTSKGVMAGHQARECK 119
N VI V + + + G +++TTS G+M +AR
Sbjct: 64 NLTGRLNKCGVISPRFDVQLKDLEKWQNNLLPSR---QFGFIVLTTSAGIMDHEEARRKH 120
Query: 120 VGGEVLCSVF 129
GG++L F
Sbjct: 121 TGGKILGFFF 130
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl reductase,
beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 2006
Score = 33.4 bits (76), Expect = 0.016
Identities = 27/159 (16%), Positives = 46/159 (28%), Gaps = 76/159 (47%)
Query: 13 NANLR--YKPSVV----IPFS----RLHARVL---------------DVLKTEGYIGEYC 47
N LR PS + IPFS + R L D++ + +
Sbjct: 390 NLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLIN-KDLVKNNV 448
Query: 48 EIDAGKGRIQLKV---------DLKYHNGASVIRK-IDCV-SKPGRRLYSSFKDIPQVCN 96
+A +++ DL+ S+ + +DC+ P
Sbjct: 449 SFNAK----DIQIPVYDTFDGSDLR-VLSGSISERIVDCIIRLP--------VKWETTTQ 495
Query: 97 ---------------GLGIMIVTTSK-----GV---MAG 112
GLG++ T + GV +AG
Sbjct: 496 FKATHILDFGPGGASGLGVL---THRNKDGTGVRVIVAG 531
Score = 25.3 bits (55), Expect = 3.8
Identities = 11/45 (24%), Positives = 18/45 (40%), Gaps = 13/45 (28%)
Query: 1 MSCLGDMLTRIRNAN-LRYKPSVVIPFSRLHARVLDV-LKTE-GY 42
S LG + R ++ +R VI A LD+ + G+
Sbjct: 509 ASGLGVLTHRNKDGTGVR-----VI-----VAGTLDINPDDDYGF 543
>2g40_A Conserved hypothetical protein; 6459694, structural genomics,
PSI, protein structure initiative, joint center for
structural genomics; 1.70A {Deinococcus radiodurans}
SCOP: c.124.1.7
Length = 224
Score = 24.9 bits (54), Expect = 5.4
Identities = 11/52 (21%), Positives = 18/52 (34%), Gaps = 6/52 (11%)
Query: 6 DMLTRIRNANLRYKPSVVIPFSRLHAR----VLDVLKT--EGYIGEYCEIDA 51
+MLT I A +P + P+ +L + Y Y + A
Sbjct: 25 EMLTTINRAIAGSRPEALPPYPVPAPLSRAEILHQFEDRILDYGAAYTHVSA 76
>1m1h_A Transcription antitermination protein NUSG; transcription
termination, RNP motif, immunoglobulin fold, nucleic
acid interaction; 1.95A {Aquifex aeolicus} SCOP:
b.114.1.1 d.58.42.1 PDB: 1m1g_A 1npp_A 1npr_A
Length = 248
Score = 24.3 bits (52), Expect = 8.1
Identities = 3/23 (13%), Positives = 10/23 (43%)
Query: 40 EGYIGEYCEIDAGKGRIQLKVDL 62
+ G E+ K ++ + + +
Sbjct: 209 MNFTGTVEEVHPEKRKLTVMISI 231
Database: pdb70
Posted date: Jan 26, 2011 11:21 AM
Number of letters in database: 5,693,230
Number of sequences in database: 24,244
Lambda K H
0.324 0.141 0.426
Gapped
Lambda K H
0.267 0.0573 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,107,446
Number of extensions: 47392
Number of successful extensions: 157
Number of sequences better than 10.0: 1
Number of HSP's gapped: 148
Number of HSP's successfully gapped: 14
Length of query: 129
Length of database: 5,693,230
Length adjustment: 82
Effective length of query: 47
Effective length of database: 3,705,222
Effective search space: 174145434
Effective search space used: 174145434
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 51 (23.8 bits)