RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13246
(81 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 = 72.1 bits (178), Expect = 2e-18
Identities = 34/45 (75%), Positives = 38/45 (84%)
Query: 1 MVRVNVLSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHG 45
M R +VL+DAL +INNAEK GKRQVLIRP SKVI+KFL VM KHG
Sbjct: 1 MTRSSVLADALNAINNAEKTGKRQVLIRPSSKVIIKFLQVMQKHG 45
>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 = 70.2 bits (173), Expect = 1e-17
Identities = 19/45 (42%), Positives = 30/45 (66%)
Query: 1 MVRVNVLSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHG 45
M ++ L++AL I+N E+ GK+ V I+P SK+I + L VM +G
Sbjct: 1 MSLMDPLANALNHISNCERVGKKVVYIKPASKLIGRVLKVMQDNG 45
>2xzm_H Ribosomal protein S8 containing protein; ribosome, translation;
3.93A {Tetrahymena thermophila} PDB: 2xzn_H
Length = 130
Score = 68.7 bits (169), Expect = 6e-17
Identities = 27/45 (60%), Positives = 38/45 (84%)
Query: 1 MVRVNVLSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHG 45
MV+VN+L++ LK + NAEK GK+QVL+RP SKV++KFL +M K+G
Sbjct: 1 MVKVNILAECLKDLVNAEKMGKKQVLLRPVSKVVLKFLRIMQKNG 45
>3rf2_A 30S ribosomal protein S8; RNA-binding protein, hyperthermophilic
bacterium, ribosome; 2.16A {Aquifex aeolicus}
Length = 168
Score = 27.5 bits (61), Expect = 0.32
Identities = 12/39 (30%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 7 LSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHG 45
++D +I NA R + + P SK+ + L V+ K G
Sbjct: 7 IADMFSAIKNAIMRRDDFLYV-PSSKLKERILDVLKKEG 44
>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 = 26.6 bits (60), Expect = 0.52
Identities = 12/39 (30%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 7 LSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHG 45
++D L I N + K V + P SK+ V V+ + G
Sbjct: 6 IADMLTRIRNGQAANKAAVTM-PSSKLKVAIANVLKEEG 43
>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 = 26.3 bits (59), Expect = 0.72
Identities = 10/39 (25%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 7 LSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHG 45
++D L I NA + K + P S+ + L ++ + G
Sbjct: 6 IADMLTRIRNATRVYKESTDV-PASRFKEEILRILAREG 43
>1sei_A Ribosomal protein S8; prokaryotic, rRNA-binding; 1.90A
{Geobacillus stearothermophilus} SCOP: d.140.1.1
Length = 130
Score = 26.3 bits (59), Expect = 0.77
Identities = 9/39 (23%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 7 LSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHG 45
++D L +I NA ++ + P SK+ + ++ + G
Sbjct: 6 IADMLTAIRNANMVRHEKLEV-PASKIKREIAEILKREG 43
>1o2d_A Alcohol dehydrogenase, iron-containing; TM0920, structural
genomics, JCSG, PSI, protein structure initiative; HET:
MSE NAP TRS; 1.30A {Thermotoga maritima} SCOP: e.22.1.2
PDB: 1vhd_A*
Length = 371
Score = 26.8 bits (60), Expect = 0.82
Identities = 14/74 (18%), Positives = 27/74 (36%), Gaps = 17/74 (22%)
Query: 9 DALKSI-NNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGKLPEVFVIL---GIRTTVYCMI 64
L+ N + GKR ++V + K+G L ++ +L I ++
Sbjct: 27 KILEKRGNIIDLLGKR--------ALVVTGKSSSKKNGSLDDLKKLLDETEISYEIF--- 75
Query: 65 NWSGIKPNPIITLV 78
++ NP V
Sbjct: 76 --DEVEENPSFDNV 87
>3bbn_H Ribosomal protein S8; small ribosomal subunit, spinach
chloroplast ribosome, ribonucleoprotein particle,
macromolecular complex; 9.40A {Spinacea oleracea}
Length = 134
Score = 26.3 bits (59), Expect = 0.87
Identities = 8/39 (20%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 7 LSDALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHG 45
++D + I NA+ K V I + + + ++++ G
Sbjct: 6 IADIITCIRNADMNRKGTVRI-VSTNITENIVKILLREG 43
>3gty_S TF, 30S ribosomal protein S7; chaperone-client complex, cell
cycle, cell division, chapero isomerase, rotamase,
ribonucleoprotein, binding; 3.40A {Thermotoga maritima}
Length = 149
Score = 26.0 bits (58), Expect = 1.0
Identities = 7/27 (25%), Positives = 12/27 (44%), Gaps = 2/27 (7%)
Query: 22 KRQVLIRPC--SKVIVKFLTVMMKHGK 46
RQ+ P ++ K + +M GK
Sbjct: 2 GRQIPPDPVFGDVLVAKLINRVMWDGK 28
>3i1m_G 30S ribosomal protein S7; ribosome structure, protein-RNA
complex, ribonucleoprotein, ribosomal protein,
RNA-binding, rRNA-binding, antibiotic resistance; 3.19A
{Escherichia coli k-12} PDB: 1vs7_G* 3e1a_U 3e1c_U
1vs5_G 3i1o_G 3i1q_G 3i1s_G 3i1z_G 3i21_G 3izv_K*
3izw_K* 3kc4_G 3or9_G 3ora_G 3uoq_G* 2qal_G* 1p6g_G
1p87_G 2aw7_G 2avy_G ...
Length = 179
Score = 26.0 bits (58), Expect = 1.1
Identities = 9/27 (33%), Positives = 18/27 (66%), Gaps = 2/27 (7%)
Query: 22 KRQVLIRPC--SKVIVKFLTVMMKHGK 46
+R++L P S+++ KF+ ++M GK
Sbjct: 9 QRKILPDPKFGSELLAKFVNILMVDGK 35
>1rss_A Ribosomal protein S7; RNA-binding, translation; 1.90A {Thermus
thermophilus} SCOP: a.75.1.1 PDB: 1n32_G* 1i95_G*
1i96_G* 1i97_G* 1i94_G 1j5e_G* 1n33_G* 1n34_G 1n36_G
1pns_G 1pnx_G 1voq_G 1vos_G 1vov_G 1vox_G 1voz_G 2e5l_G
2zm6_G 3fic_G* 3mr8_G ...
Length = 151
Score = 26.0 bits (58), Expect = 1.2
Identities = 6/27 (22%), Positives = 12/27 (44%), Gaps = 2/27 (7%)
Query: 22 KRQVLIRPC--SKVIVKFLTVMMKHGK 46
RQ+ ++ F+ +M+ GK
Sbjct: 4 VRQLQPDLVYGDVLVTAFINKIMRDGK 30
>1hus_A Ribosomal protein S7; RNA-binding protein, decoding center,;
2.50A {Geobacillus stearothermophilus} SCOP: a.75.1.1
Length = 155
Score = 26.0 bits (58), Expect = 1.2
Identities = 10/27 (37%), Positives = 15/27 (55%), Gaps = 2/27 (7%)
Query: 22 KRQVLIRPC--SKVIVKFLTVMMKHGK 46
KR VL P SK++ + + +M GK
Sbjct: 8 KRDVLPDPIYNSKLVTRLINKIMIDGK 34
>1oj7_A Hypothetical oxidoreductase YQHD; structural genomics; HET: NZQ;
2.0A {Escherichia coli} SCOP: e.22.1.2
Length = 408
Score = 26.1 bits (58), Expect = 1.4
Identities = 16/71 (22%), Positives = 24/71 (33%), Gaps = 14/71 (19%)
Query: 9 DALKSINNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGKLPEVFVIL-GIRTTVYCMINWS 67
A+ + R VLI + K G L +V L G+ +
Sbjct: 38 GAIAGLREQIPHDAR-VLITYGGGSVKKT-------GVLDQVLDALKGMDVLEF-----G 84
Query: 68 GIKPNPIITLV 78
GI+PNP +
Sbjct: 85 GIEPNPAYETL 95
>3r8n_G 30S ribosomal protein S7; protein biosynthesis, RNA, tRNA,
transfer RNA, 16S ribosomal subunit, RRF; 3.00A
{Escherichia coli} PDB: 2ykr_G 3oaq_G 3ofa_G 3ofx_G
3ofo_G 3r8o_G 3sfs_G* 3ofp_G 3fih_G* 2wwl_G 3oar_G
3ofb_G 3ofy_G 4a2i_G 2gy9_G 2gyb_G
Length = 151
Score = 25.5 bits (57), Expect = 1.4
Identities = 9/27 (33%), Positives = 18/27 (66%), Gaps = 2/27 (7%)
Query: 22 KRQVLIRPC--SKVIVKFLTVMMKHGK 46
+R++L P S+++ KF+ ++M GK
Sbjct: 8 QRKILPDPKFGSELLAKFVNILMVDGK 34
>3bbn_G Ribosomal protein S7; small ribosomal subunit, spinach
chloroplast ribosome, ribonucleoprotein particle,
macromolecular complex; 9.40A {Spinacea oleracea} SCOP:
i.1.1.1
Length = 155
Score = 25.6 bits (57), Expect = 1.5
Identities = 5/27 (18%), Positives = 14/27 (51%), Gaps = 2/27 (7%)
Query: 22 KRQVLIRPC--SKVIVKFLTVMMKHGK 46
++ P ++++ + ++KHGK
Sbjct: 9 EKTAKSDPIYRNRLVNMLVNRILKHGK 35
>3ox4_A Alcohol dehydrogenase 2; iron, NAD, oxidoreductase; HET: NAD;
2.00A {Zymomonas mobilis} PDB: 3owo_A*
Length = 383
Score = 25.6 bits (57), Expect = 1.6
Identities = 21/74 (28%), Positives = 31/74 (41%), Gaps = 17/74 (22%)
Query: 9 DALKSI-NNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGKLPEVFVIL---GIRTTVYCMI 64
+L+ + G + LI V F M K G + +V +L GI + VY
Sbjct: 17 GSLEKAIKDLNGSGFKNALI-----VSDAF---MNKSGVVKQVADLLKAQGINSAVY--- 65
Query: 65 NWSGIKPNPIITLV 78
G+ PNP +T V
Sbjct: 66 --DGVMPNPTVTAV 77
>3bfj_A 1,3-propanediol oxidoreductase; opportunistic pathogens, decamer,
structural genomics,struct proteomics in europe, spine;
2.70A {Klebsiella pneumoniae}
Length = 387
Score = 25.6 bits (57), Expect = 1.9
Identities = 17/74 (22%), Positives = 31/74 (41%), Gaps = 15/74 (20%)
Query: 9 DALKSI-NNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGKLPEVFVIL---GIRTTVYCMI 64
+A+ + + G ++ L+ V K L +K G + + L GI ++
Sbjct: 19 NAISVVGERCQLLGGKKALL-----VTDKGLR-AIKDGAVDKTLHYLREAGIEVAIF--- 69
Query: 65 NWSGIKPNPIITLV 78
G++PNP T V
Sbjct: 70 --DGVEPNPKDTNV 81
>1rrm_A Lactaldehyde reductase; structural genomics, dehydrogenase, PSI,
protein structure initiative; HET: APR; 1.60A
{Escherichia coli} SCOP: e.22.1.2 PDB: 2bi4_A* 2bl4_A*
Length = 386
Score = 25.2 bits (56), Expect = 2.2
Identities = 18/74 (24%), Positives = 36/74 (48%), Gaps = 17/74 (22%)
Query: 9 DALKSI-NNAEKRGKRQVLIRPCSKVIVKFLTVMMKHGKLPEVFVIL---GIRTTVYCMI 64
A+ ++ + ++RG ++ LI V K +++ G + +V + G+ +Y
Sbjct: 17 GAVGALTDEVKRRGYQKALI-----VTDKT---LVQCGVVAKVTDKMDAAGLAWAIY--- 65
Query: 65 NWSGIKPNPIITLV 78
G+ PNP IT+V
Sbjct: 66 --DGVVPNPTITVV 77
>1vlj_A NADH-dependent butanol dehydrogenase; TM0820, structural G JCSG,
protein structure initiative, PSI, joint center for S
genomics; HET: NAP; 1.78A {Thermotoga maritima} SCOP:
e.22.1.2
Length = 407
Score = 25.3 bits (56), Expect = 2.6
Identities = 13/39 (33%), Positives = 19/39 (48%), Gaps = 8/39 (20%)
Query: 43 KHGKLPEVFVIL---GIRTTVYCMINWSGIKPNPIITLV 78
K+G +V L GI SG+KPNP+++ V
Sbjct: 57 KNGVYDQVVDSLKKHGIEWVEV-----SGVKPNPVLSKV 90
>1m56_C Cytochrome C oxidase; membrane protein, oxidoreductase; HET: HEA
PEH; 2.30A {Rhodobacter sphaeroides} SCOP: f.25.1.1
PDB: 1m57_C*
Length = 266
Score = 24.8 bits (55), Expect = 3.2
Identities = 8/27 (29%), Positives = 14/27 (51%), Gaps = 1/27 (3%)
Query: 40 VMMKHGKLPEVFVILGIRTTVYCMINW 66
V+ HG P + ++G+ +Y M W
Sbjct: 33 VLWMHGSGPWMG-LIGLVVVLYTMFGW 58
>1v54_C Cytochrome C oxidase polypeptide III; oxidoreductase; HET: FME
TPO HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus}
SCOP: f.25.1.1 PDB: 1v55_C* 2dyr_C* 2eij_C* 2eik_C*
2eil_C* 2eim_C* 2ein_C* 2y69_C* 2ybb_N* 2zxw_C* 3abk_C*
3abl_C* 3abm_C* 3ag1_C* 3ag2_C* 3ag3_C* 3ag4_C* 3asn_C*
3aso_C* 2occ_C* ...
Length = 261
Score = 24.0 bits (53), Expect = 6.0
Identities = 6/27 (22%), Positives = 11/27 (40%), Gaps = 1/27 (3%)
Query: 40 VMMKHGKLPEVFVILGIRTTVYCMINW 66
M H + ++G+ T + M W
Sbjct: 32 TMWFHFNSMTLL-MIGLTTNMLTMYQW 57
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
0.327 0.140 0.419
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: 1,234,984
Number of extensions: 61613
Number of successful extensions: 109
Number of sequences better than 10.0: 1
Number of HSP's gapped: 109
Number of HSP's successfully gapped: 22
Length of query: 81
Length of database: 6,701,793
Length adjustment: 50
Effective length of query: 31
Effective length of database: 5,305,743
Effective search space: 164478033
Effective search space used: 164478033
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (23.2 bits)