RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 032994
(129 letters)
>3u5c_W 40S ribosomal protein S22-A; translation, ribosome, ribosomal,
ribosomal R ribosomal protein, eukaryotic ribosome,
RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB:
3izb_H 3o30_O 3o2z_O 3u5g_W 1s1h_H 3jyv_H* 3iz6_H 2zkq_h
Length = 130
Score = 140 bits (355), Expect = 2e-44
Identities = 60/123 (48%), Positives = 86/123 (69%)
Query: 6 LNDALRAIVNAERRGKATVELQPISTVMSSFLNIMKYRGYIKDFQLYDPHRVGKIKVELL 65
L DAL AI NAE+ GK V ++P S V+ FL +M+ GYI +F+ D HR GKI V+L
Sbjct: 7 LADALNAINNAEKTGKRQVLIRPSSKVIIKFLQVMQKHGYIGEFEYIDDHRSGKIVVQLN 66
Query: 66 GRVNDCRGLTYRQDVKAREIEGYTVHALPTRQWGYVVITTPDGVLDHEEALRRNVGGQVL 125
GR+N C ++ R +VK +IE +T + LP RQ+GYV++TT G++DHEEA R++V G++L
Sbjct: 67 GRLNKCGVISPRFNVKIGDIEKWTANLLPARQFGYVILTTSAGIMDHEEARRKHVSGKIL 126
Query: 126 GYF 128
G+
Sbjct: 127 GFV 129
>2xzm_H Ribosomal protein S8 containing protein; ribosome, translation;
3.93A {Tetrahymena thermophila} PDB: 2xzn_H
Length = 130
Score = 139 bits (354), Expect = 3e-44
Identities = 58/124 (46%), Positives = 86/124 (69%)
Query: 5 ILNDALRAIVNAERRGKATVELQPISTVMSSFLNIMKYRGYIKDFQLYDPHRVGKIKVEL 64
IL + L+ +VNAE+ GK V L+P+S V+ FL IM+ GYI +F++ D HR K+ VEL
Sbjct: 6 ILAECLKDLVNAEKMGKKQVLLRPVSKVVLKFLRIMQKNGYIGEFEVIDDHRSKKVVVEL 65
Query: 65 LGRVNDCRGLTYRQDVKAREIEGYTVHALPTRQWGYVVITTPDGVLDHEEALRRNVGGQV 124
+GR+N C ++ R DV + E +T + LP+RQ+G VV+TT G+L HEE +R+ GG++
Sbjct: 66 IGRINKCGVISPRYDVPLADFEKWTNNILPSRQFGNVVLTTTYGILTHEECRKRHTGGKI 125
Query: 125 LGYF 128
LG+F
Sbjct: 126 LGFF 129
>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 = 123 bits (311), Expect = 1e-37
Identities = 47/123 (38%), Positives = 72/123 (58%)
Query: 6 LNDALRAIVNAERRGKATVELQPISTVMSSFLNIMKYRGYIKDFQLYDPHRVGKIKVELL 65
L +AL I N ER GK V ++P S ++ L +M+ GYI +F+ + R G KVEL+
Sbjct: 7 LANALNHISNCERVGKKVVYIKPASKLIGRVLKVMQDNGYIGEFEFIEDGRAGIFKVELI 66
Query: 66 GRVNDCRGLTYRQDVKAREIEGYTVHALPTRQWGYVVITTPDGVLDHEEALRRNVGGQVL 125
G++N C + R VK E + LP R +G ++++T GV+ HEEA +R +GG++L
Sbjct: 67 GKINKCGAIKPRFPVKKFGYEKFEKRYLPARDFGILIVSTTQGVMSHEEAKKRGLGGRLL 126
Query: 126 GYF 128
Y
Sbjct: 127 AYV 129
>3bbn_H Ribosomal protein S8; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 134
Score = 49.8 bits (120), Expect = 5e-09
Identities = 22/131 (16%), Positives = 50/131 (38%), Gaps = 27/131 (20%)
Query: 13 IVNAERRGKATVELQPISTVMSSFLNIMKYRGYIKDFQLYDPHRVGKIKVELLGRVNDCR 72
I NA+ K TV + + + + + I+ G+I++ + + + +
Sbjct: 13 IRNADMNRKGTVRI-VSTNITENIVKILLREGFIENARKHQERNKYFLVLT--------- 62
Query: 73 GLTYRQDVKAREIEGYT--------------VHALPTRQWGY--VVITTPDGVLDHEEAL 116
L +R++ K + + +P G +++T G++ EA
Sbjct: 63 -LRHRRNKKGPYLNTFHLKRVSRPGLRIYSNYQRIPRILGGMGIAILSTSRGIMTDREAR 121
Query: 117 RRNVGGQVLGY 127
+GG++L Y
Sbjct: 122 LEGIGGEILCY 132
>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 = 49.1 bits (118), Expect = 1e-08
Identities = 28/135 (20%), Positives = 48/135 (35%), Gaps = 31/135 (22%)
Query: 13 IVNAERRGKATVELQPISTVMSSFLNIMKYRGYIKDFQLYDPHRVGKIKVELLGRVNDCR 72
I NA R K + ++ P S L I+ G+IK ++ D ++V
Sbjct: 13 IRNATRVYKESTDV-PASRFKEEILRILAREGFIKGYERVDVDGKPYLRVY--------- 62
Query: 73 GLTYRQDVKAREIEGYTV------------------HALPTRQWGY--VVITTPDGVLDH 112
L Y + + V +P + G +++T GVL
Sbjct: 63 -LKYGPRRQGPDPRPEQVIHHIRRISKPGRRVYVGVKEIPRVRRGLGIAILSTSKGVLTD 121
Query: 113 EEALRRNVGGQVLGY 127
EA + VGG+++
Sbjct: 122 REARKLGVGGELICE 136
>1sei_A Ribosomal protein S8; prokaryotic, rRNA-binding; 1.90A {Geobacillus
stearothermophilus} SCOP: d.140.1.1
Length = 130
Score = 48.6 bits (117), Expect = 1e-08
Identities = 33/130 (25%), Positives = 59/130 (45%), Gaps = 29/130 (22%)
Query: 13 IVNAERRGKATVELQPISTVMSSFLNIMKYRGYIKDFQLYDPHRVGKIKVEL-------- 64
I NA +E+ P S + I+K G+I+D++ + ++ G +++ L
Sbjct: 13 IRNANMVRHEKLEV-PASKIKREIAEILKREGFIRDYEYIEDNKQGILRIFLKYGPNERV 71
Query: 65 ---LGRVNDCRGLTYRQDVKAREIE----GYTVHALPTRQWGYVVITTPDGVLDHEEALR 117
L R++ GL R VKA E+ G G +++T GVL +EA +
Sbjct: 72 ITGLKRISKP-GL--RVYVKAHEVPRVLNGL----------GIAILSTSQGVLTDKEARQ 118
Query: 118 RNVGGQVLGY 127
+ GG+++ Y
Sbjct: 119 KGTGGEIIAY 128
>1s03_H 30S ribosomal protein S8; protein-RNA complex, SPC operon,
transcription-RN; 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 = 46.3 bits (111), Expect = 1e-07
Identities = 30/130 (23%), Positives = 57/130 (43%), Gaps = 30/130 (23%)
Query: 13 IVNAERRGKATVELQPISTVMSSFLNIMKYRGYIKDFQLYDPHRVGKIKVEL-------- 64
I N + KA V + P S + + N++K G+I+DF++ + ++++ L
Sbjct: 13 IRNGQAANKAAVTM-PSSKLKVAIANVLKEEGFIEDFKVEGDTK-PELELTLKYFQGKAV 70
Query: 65 ---LGRVNDCRGLTYRQDVKAREIE----GYTVHALPTRQWGYVVITTPDGVLDHEEALR 117
+ RV+ GL R + E+ G G V++T GV+ A +
Sbjct: 71 VESIQRVSRP-GL--RIYKRKDELPKVMAGL----------GIAVVSTSKGVMTDRAARQ 117
Query: 118 RNVGGQVLGY 127
+GG+++ Y
Sbjct: 118 AGLGGEIICY 127
>3rf2_A 30S ribosomal protein S8; RNA-binding protein, hyperthermophilic
bacterium, ribosome; 2.16A {Aquifex aeolicus}
Length = 168
Score = 41.3 bits (97), Expect = 2e-05
Identities = 26/159 (16%), Positives = 52/159 (32%), Gaps = 40/159 (25%)
Query: 8 DALRAIVNAERRGKATVELQPISTVMSSFLNIMKYRGYIKDFQLYDPHRVGKIKVELLGR 67
D AI NA R + + P S + L+++K G+I+D++ + + ++
Sbjct: 9 DMFSAIKNAIMRRDDFLYV-PSSKLKERILDVLKKEGFIQDWEALKGEKYEEEYKKMKEL 67
Query: 68 VNDCRGLTYRQDVKAREIEGYTVHA----------------------------------- 92
++ +K E
Sbjct: 68 AEKSPNPKMKRYLKQLEEYNKGTQYPIKIYLKYLDPKKRKSAITNIVKVSKGGRRVYAGV 127
Query: 93 --LPTRQWGY--VVITTPDGVLDHEEALRRNVGGQVLGY 127
+P + G +++T GV+ EA R GG+V+ +
Sbjct: 128 RTMPYVKRGLGIAIVSTDAGVMTDHEARRMRKGGEVIAF 166
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 29.1 bits (64), Expect = 0.43
Identities = 10/59 (16%), Positives = 21/59 (35%), Gaps = 6/59 (10%)
Query: 3 RRILNDALRAIVNAERRGKATVELQPISTVMSSFLNIMKYRGYIKDFQLYDPHRVGKIK 61
R + D R + R + +++++ + Y+ YI D DP +
Sbjct: 494 RMVFLD-FRFLEQKIRH--DSTAWNASGSILNTLQQLKFYKPYICD---NDPKYERLVN 546
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 27.7 bits (61), Expect = 1.4
Identities = 14/59 (23%), Positives = 19/59 (32%), Gaps = 18/59 (30%)
Query: 45 YIKDFQLYDP---HRVGKIKVELLGRVNDCRGLTYRQDVKAREIEGYTVHALPTRQWGY 100
+I DF P +G L R D G R I T+ P +G+
Sbjct: 500 HILDF---GPGGASGLGV----LTHRNKDGTG--------VRVIVAGTLDINPDDDYGF 543
>2yew_B E1 envelope glycoprotein; alphavirus, molecular dynamics; 5.00A
{Barmah forest virus}
Length = 427
Score = 27.3 bits (60), Expect = 1.6
Identities = 19/64 (29%), Positives = 29/64 (45%), Gaps = 8/64 (12%)
Query: 6 LNDALRAIVNAE---RRGKATVELQPISTVMSSFLNIMKYRG--YIKDFQLY---DPHRV 57
LN + VN + R ++ L PIS+ S F ++ YR Y +D+ Y R
Sbjct: 136 LNQTVDVFVNGDSPARIQQSKFILGPISSAWSPFDKVIVYRDEVYNEDYAPYGSGQAGRF 195
Query: 58 GKIK 61
G I+
Sbjct: 196 GDIQ 199
>1v31_A Hypothetical protein RAFL11-05-P19; SWI/SNF complex subunit,
structural genomics, riken structural
genomics/proteomics initiative, RSGI; NMR {Arabidopsis
thaliana} SCOP: a.42.1.1
Length = 93
Score = 25.1 bits (55), Expect = 4.1
Identities = 12/69 (17%), Positives = 20/69 (28%), Gaps = 10/69 (14%)
Query: 18 RRGKATVELQPISTVMSSFLN---------IMKYRGYIKDFQLYDPHRVGKIKV-ELLGR 67
E +ST + L I Y+K +L +P+ L +
Sbjct: 3 SGSSGVPEKFKLSTALMDVLGIEVETRPRIIAAIWHYVKARKLQNPNDPSFFNCDAALQK 62
Query: 68 VNDCRGLTY 76
V L +
Sbjct: 63 VFGEEKLKF 71
>3h8v_A Ubiquitin-like modifier-activating enzyme 5; rossman fold,
ATP-binding, UBL conjugation pathway, transfer
structural genomics consortium, SGC; HET: ATP; 2.00A
{Homo sapiens} PDB: 3guc_A*
Length = 292
Score = 25.3 bits (56), Expect = 5.9
Identities = 5/14 (35%), Positives = 8/14 (57%)
Query: 50 QLYDPHRVGKIKVE 63
+ PH+ G KV+
Sbjct: 79 LFFQPHQAGLSKVQ 92
>3rac_A Histidine-tRNA ligase; structural genomics, PSI-biology, midwest
center for structu genomics, MCSG, PSI-BIO; 2.30A
{Alicyclobacillus acidocaldarius subsp}
Length = 373
Score = 25.4 bits (56), Expect = 7.1
Identities = 5/27 (18%), Positives = 11/27 (40%), Gaps = 2/27 (7%)
Query: 96 RQWGYVVITTPDGVLDHEEALRRNVGG 122
GY +T+ + ++ + L R
Sbjct: 52 EDAGYEPVTSG--LFEYVDTLLRARSP 76
>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA
replication initation factor, cell cycle control factor;
HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11
c.37.1.20
Length = 389
Score = 25.1 bits (54), Expect = 8.8
Identities = 4/34 (11%), Positives = 13/34 (38%)
Query: 3 RRILNDALRAIVNAERRGKATVELQPISTVMSSF 36
R ++ R+ A++ G+ + + +
Sbjct: 241 RLAIDILYRSAYAAQQNGRKHIAPEDVRKSSKEV 274
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.323 0.141 0.421
Gapped
Lambda K H
0.267 0.0768 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,167,893
Number of extensions: 124285
Number of successful extensions: 285
Number of sequences better than 10.0: 1
Number of HSP's gapped: 284
Number of HSP's successfully gapped: 27
Length of query: 129
Length of database: 6,701,793
Length adjustment: 83
Effective length of query: 46
Effective length of database: 4,384,350
Effective search space: 201680100
Effective search space used: 201680100
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: 41 (22.0 bits)
S2: 52 (23.7 bits)