RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 032980
(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 = 139 bits (354), Expect = 3e-44
Identities = 57/123 (46%), Positives = 85/123 (69%)
Query: 6 LNNALRAIVNAERRGKATVELQPISTVMSSFLNIMKYRGYVKDFQVYDPHRVGKIKVELL 65
L +AL AI NAE+ GK V ++P S V+ FL +M+ GY+ +F+ D HR GKI V+L
Sbjct: 7 LADALNAINNAEKTGKRQVLIRPSSKVIIKFLQVMQKHGYIGEFEYIDDHRSGKIVVQLN 66
Query: 66 GRVNDCRALTYRQDIKASEIEGYTVRALPTRQWGYVVITTPDGVLDHEEALRRNVGGQVL 125
GR+N C ++ R ++K +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 = 138 bits (349), Expect = 2e-43
Identities = 57/124 (45%), Positives = 85/124 (68%)
Query: 5 ILNNALRAIVNAERRGKATVELQPISTVMSSFLNIMKYRGYVKDFQVYDPHRVGKIKVEL 64
IL L+ +VNAE+ GK V L+P+S V+ FL IM+ GY+ +F+V D HR K+ VEL
Sbjct: 6 ILAECLKDLVNAEKMGKKQVLLRPVSKVVLKFLRIMQKNGYIGEFEVIDDHRSKKVVVEL 65
Query: 65 LGRVNDCRALTYRQDIKASEIEGYTVRALPTRQWGYVVITTPDGVLDHEEALRRNVGGQV 124
+GR+N C ++ R D+ ++ 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 = 9e-38
Identities = 48/123 (39%), Positives = 74/123 (60%)
Query: 6 LNNALRAIVNAERRGKATVELQPISTVMSSFLNIMKYRGYVKDFQVYDPHRVGKIKVELL 65
L NAL I N ER GK V ++P S ++ L +M+ GY+ +F+ + R G KVEL+
Sbjct: 7 LANALNHISNCERVGKKVVYIKPASKLIGRVLKVMQDNGYIGEFEFIEDGRAGIFKVELI 66
Query: 66 GRVNDCRALTYRQDIKASEIEGYTVRALPTRQWGYVVITTPDGVLDHEEALRRNVGGQVL 125
G++N C A+ R +K E + R 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 = 21/131 (16%), Positives = 52/131 (39%), Gaps = 27/131 (20%)
Query: 13 IVNAERRGKATVELQPISTVMSSFLNIMKYRGYVKDFQVYDPHRVGKIKVELLGRVNDCR 72
I NA+ K TV + + + + + I+ G++++ + + + + L
Sbjct: 13 IRNADMNRKGTVRI-VSTNITENIVKILLREGFIENARKHQERNKYFLVLTL-------- 63
Query: 73 ALTYRQDIKASEIEGYTVR--------------ALPTRQWGY--VVITTPDGVLDHEEAL 116
+R++ K + + ++ +P G +++T G++ EA
Sbjct: 64 --RHRRNKKGPYLNTFHLKRVSRPGLRIYSNYQRIPRILGGMGIAILSTSRGIMTDREAR 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 = 48.3 bits (116), Expect = 2e-08
Identities = 27/135 (20%), Positives = 49/135 (36%), Gaps = 31/135 (22%)
Query: 13 IVNAERRGKATVELQPISTVMSSFLNIMKYRGYVKDFQVYDPHRVGKIKVELLGRVNDCR 72
I NA R K + ++ P S L I+ G++K ++ D ++V
Sbjct: 13 IRNATRVYKESTDV-PASRFKEEILRILAREGFIKGYERVDVDGKPYLRVY--------- 62
Query: 73 ALTYRQDIKASEIEGYTV------------------RALPTRQWGY--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 = 46.3 bits (111), Expect = 1e-07
Identities = 27/129 (20%), Positives = 52/129 (40%), Gaps = 27/129 (20%)
Query: 13 IVNAERRGKATVELQPISTVMSSFLNIMKYRGYVKDFQVYDPHRVGKIKVELLGRVNDCR 72
I NA +E+ P S + I+K G+++D++ + ++ G +++
Sbjct: 13 IRNANMVRHEKLEV-PASKIKREIAEILKREGFIRDYEYIEDNKQGILRIF--------- 62
Query: 73 ALTYRQDIKASEIEG-----------YT-VRALPTRQWGY--VVITTPDGVLDHEEALRR 118
L Y I G Y +P G +++T GVL +EA ++
Sbjct: 63 -LKYGP--NERVITGLKRISKPGLRVYVKAHEVPRVLNGLGIAILSTSQGVLTDKEARQK 119
Query: 119 NVGGQVLGY 127
GG+++ Y
Sbjct: 120 GTGGEIIAY 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 = 43.6 bits (104), Expect = 1e-06
Identities = 29/129 (22%), Positives = 53/129 (41%), Gaps = 28/129 (21%)
Query: 13 IVNAERRGKATVELQPISTVMSSFLNIMKYRGYVKDFQVYDPHRVGKIKVELLGRVNDCR 72
I N + KA V + P S + + N++K G+++DF+V + ++++
Sbjct: 13 IRNGQAANKAAVTM-PSSKLKVAIANVLKEEGFIEDFKVEGDTK-PELELT--------- 61
Query: 73 ALTYRQDIKASEIEG-----------YT-VRALPTRQWGY--VVITTPDGVLDHEEALRR 118
L Y Q +E Y LP G V++T GV+ A +
Sbjct: 62 -LKYFQGKAV--VESIQRVSRPGLRIYKRKDELPKVMAGLGIAVVSTSKGVMTDRAARQA 118
Query: 119 NVGGQVLGY 127
+GG+++ Y
Sbjct: 119 GLGGEIICY 127
>3rf2_A 30S ribosomal protein S8; RNA-binding protein, hyperthermophilic
bacterium, ribosome; 2.16A {Aquifex aeolicus}
Length = 168
Score = 39.0 bits (91), Expect = 1e-04
Identities = 29/154 (18%), Positives = 53/154 (34%), Gaps = 40/154 (25%)
Query: 13 IVNAERRGKATVELQPISTVMSSFLNIMKYRGYVKDFQVYDPHRVGKIKVELLGRVNDCR 72
I NA R + + P S + L+++K G+++D++ + + ++
Sbjct: 14 IKNAIMRRDDFLYV-PSSKLKERILDVLKKEGFIQDWEALKGEKYEEEYKKMKELAEKSP 72
Query: 73 ------------------------ALTYRQDIK-ASEIEG-----------YT-VRALPT 95
L Y K S I Y VR +P
Sbjct: 73 NPKMKRYLKQLEEYNKGTQYPIKIYLKYLDPKKRKSAITNIVKVSKGGRRVYAGVRTMPY 132
Query: 96 RQWGY--VVITTPDGVLDHEEALRRNVGGQVLGY 127
+ G +++T GV+ EA R GG+V+ +
Sbjct: 133 VKRGLGIAIVSTDAGVMTDHEARRMRKGGEVIAF 166
>2yew_B E1 envelope glycoprotein; alphavirus, molecular dynamics; 5.00A
{Barmah forest virus}
Length = 427
Score = 27.7 bits (61), Expect = 1.3
Identities = 19/64 (29%), Positives = 29/64 (45%), Gaps = 8/64 (12%)
Query: 6 LNNALRAIVNAE---RRGKATVELQPISTVMSSFLNIMKYRG--YVKDFQVY---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
>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 = 25.9 bits (56), Expect = 4.6
Identities = 4/34 (11%), Positives = 13/34 (38%)
Query: 3 RRILNNALRAIVNAERRGKATVELQPISTVMSSF 36
R ++ R+ A++ G+ + + +
Sbjct: 241 RLAIDILYRSAYAAQQNGRKHIAPEDVRKSSKEV 274
>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 = 25.7 bits (57), Expect = 5.1
Identities = 14/67 (20%), Positives = 23/67 (34%), Gaps = 7/67 (10%)
Query: 50 QVYDPHRVGKIKVE----LLGRVN-DCRALTYRQDIKASEIEGYTVRALPTRQWGYVVIT 104
+ PH+ G KV+ L +N D + +I + +E + G
Sbjct: 79 LFFQPHQAGLSKVQAAEHTLRNINPDVLFEVHNYNI--TTVENFQHFMDRISNGGLEEGK 136
Query: 105 TPDGVLD 111
D VL
Sbjct: 137 PVDLVLS 143
>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 = 26.0 bits (56), Expect = 5.1
Identities = 8/58 (13%), Positives = 19/58 (32%), Gaps = 12/58 (20%)
Query: 4 RILNNALRAIVNAERRGKATVELQPISTVMSSFLNIMKYRGYVKDFQVYDPHRVGKIK 61
R L +R + +++++ + Y+ Y+ D DP +
Sbjct: 501 RFLEQKIR---------HDSTAWNASGSILNTLQQLKFYKPYICD---NDPKYERLVN 546
>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 = 6.1
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
>2ovk_B RLC, myosin regulatory light chain LC-2, mantle muscle; rigor-like,
squid, contractIle protein; 2.60A {Todarodes pacificus}
PDB: 2ekv_B 2ekw_B 2oy6_B* 3i5f_B* 3i5g_B 3i5h_B 3i5i_B
Length = 153
Score = 25.2 bits (56), Expect = 6.2
Identities = 8/41 (19%), Positives = 14/41 (34%), Gaps = 8/41 (19%)
Query: 36 FLNIMKYRGYVKD--------FQVYDPHRVGKIKVELLGRV 68
FL + + D F ++D G I + L +
Sbjct: 70 FLTLFGEKVSGTDPEDALRNAFSMFDEDGQGFIPEDYLKDL 110
>3j04_B Myosin regulatory light chain 2, smooth muscle MA isoform;
phosphorylation, 2D crystalline arrays, myosin
regulation, M light chains, structural protein; 20.00A
{Gallus gallus}
Length = 143
Score = 25.1 bits (56), Expect = 6.6
Identities = 8/41 (19%), Positives = 13/41 (31%), Gaps = 8/41 (19%)
Query: 36 FLNIMKYRGYVKD--------FQVYDPHRVGKIKVELLGRV 68
FL + + D F +D G I + L +
Sbjct: 61 FLTMFGEKLNGTDPEDVIRNAFACFDEEASGFIHEDHLREL 101
>2mys_B Myosin; muscle protein, motor protein; HET: MLY; 2.80A {Gallus
gallus} SCOP: a.39.1.5 PDB: 1i84_U* 1m8q_B* 1mvw_B*
1o18_E* 1o19_B* 1o1a_B* 1o1b_B* 1o1c_B* 1o1d_B* 1o1e_B*
1o1f_B* 1o1g_B* 2w4a_B 2w4g_B 2w4h_B
Length = 166
Score = 24.9 bits (55), Expect = 8.4
Identities = 11/41 (26%), Positives = 15/41 (36%), Gaps = 8/41 (19%)
Query: 36 FLNIMKYRGYVKD--------FQVYDPHRVGKIKVELLGRV 68
FL + + D F+V DP G IK L +
Sbjct: 80 FLTMFGEKLKGADPEDVIMGAFKVLDPDGKGSIKKSFLEEL 120
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 0.140 0.411
Gapped
Lambda K H
0.267 0.0834 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,138,625
Number of extensions: 122857
Number of successful extensions: 260
Number of sequences better than 10.0: 1
Number of HSP's gapped: 259
Number of HSP's successfully gapped: 26
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: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (23.6 bits)