RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 033150
(126 letters)
>3bbn_M Ribosomal protein S13; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 145
Score = 117 bits (295), Expect = 4e-35
Identities = 48/100 (48%), Positives = 71/100 (71%), Gaps = 3/100 (3%)
Query: 5 LAMPVAPALSVICNGHNNNLLTNASLSFPVSKQPQYPGLSIQCARVGGVEIPNNKRIEYS 64
+++P+A + + ++ + S P + GL I+C R+GGVEIPN+KR+EYS
Sbjct: 7 VSVPIATSSLPLSARGRSS---SVSFPAPKKGGIGHGGLQIECIRIGGVEIPNHKRVEYS 63
Query: 65 LQYIHGVGRTRARQILVDLKMENKITKDMSEEELITIRDE 104
LQYIHG+GR+R+RQIL+DL +NK+TKD+SEEE+I +R E
Sbjct: 64 LQYIHGIGRSRSRQILLDLNFDNKVTKDLSEEEVIILRKE 103
>3r8n_M 30S ribosomal protein S13; protein biosynthesis, RNA, tRNA,
transfer RNA, 16S ribosomal subunit, RRF; 3.00A
{Escherichia coli} PDB: 2ykr_M 3oaq_M 3ofa_M 3ofx_M
3ofo_M 3r8o_M 4a2i_M 3i1m_M 1vs7_M* 3e1a_F 3e1c_F 1vs5_M
3i1o_M 3i1q_M 3i1s_M 3i1z_M 3i21_M 3iyx_M 3iyy_M 3izv_Q*
...
Length = 114
Score = 110 bits (278), Expect = 6e-33
Identities = 28/68 (41%), Positives = 48/68 (70%), Gaps = 1/68 (1%)
Query: 48 ARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKM-ENKITKDMSEEELITIRDEVS 106
AR+ G+ IP++K +L I+GVG+TR++ IL + E+ ++SE ++ T+RDEV+
Sbjct: 1 ARIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEVA 60
Query: 107 KYMIEGDL 114
K+++EGDL
Sbjct: 61 KFVVEGDL 68
>2vqe_M 30S ribosomal protein S13, 30S ribosomal protein S6; tRNA-binding,
rRNA-binding, metal-binding, zinc-finger, translation;
HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP:
a.156.1.1 PDB: 1gix_P* 1hnw_M* 1hnx_M* 1hnz_M* 1hr0_M
1ibk_M* 1ibl_M* 1ibm_M 1j5e_M 1jgo_P* 1jgp_P* 1jgq_P*
1mj1_P* 1ml5_P* 1n32_M* 1n33_M* 1n34_M 1n36_M 1xmo_M*
1xmq_M* ...
Length = 126
Score = 103 bits (259), Expect = 5e-30
Identities = 27/69 (39%), Positives = 46/69 (66%), Gaps = 2/69 (2%)
Query: 48 ARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKM-ENKITKDMSEEELITIRDEVS 106
AR+ GVEIP NKR++ +L YI+G+G+ RA++ L + KD++E E++ +R+ V
Sbjct: 2 ARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVE 61
Query: 107 K-YMIEGDL 114
+ +EG+L
Sbjct: 62 NTWKLEGEL 70
>2xzm_M RPS18E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB:
2xzn_M
Length = 155
Score = 73.1 bits (180), Expect = 1e-17
Identities = 18/76 (23%), Positives = 31/76 (40%), Gaps = 5/76 (6%)
Query: 48 ARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKM-ENKITKDMSEEELITIRDEVS 106
R+ I + +L I G+GR A I LK+ N ++E++ I D ++
Sbjct: 15 HRILNTNIDGKRITPIALTGIRGIGRRFAYIICKVLKIDPNARAGLLTEDQCNKITDLIA 74
Query: 107 KYMIEGDLVIIPYFFV 122
G IP + +
Sbjct: 75 DPEAHG----IPTWLL 86
>3iz6_M 40S ribosomal protein S18 (S13P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum}
Length = 152
Score = 72.3 bits (178), Expect = 2e-17
Identities = 17/76 (22%), Positives = 32/76 (42%), Gaps = 5/76 (6%)
Query: 48 ARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKM-ENKITKDMSEEELITIRDEVS 106
RV + ++I ++L I GVGR + + + NK ++S EE+ + V
Sbjct: 13 LRVLNTNVDGKQKIMFALTSIKGVGRRFSNIVCKKADIDMNKRAGELSAEEMDRLMAVVH 72
Query: 107 KYMIEGDLVIIPYFFV 122
+P +F+
Sbjct: 73 NPRQFK----VPDWFL 84
>3u5c_S 40S ribosomal protein S18-A, 40S ribosomal protein S17-A;
translation, ribosome, ribosomal, ribosomal R ribosomal
protein, eukaryotic ribosome, RNA-protein C; 3.00A
{Saccharomyces cerevisiae} PDB: 3izb_M 3o30_L 3o2z_L
3u5g_S 1s1h_M 3jyv_M* 2zkq_m
Length = 146
Score = 71.9 bits (177), Expect = 2e-17
Identities = 15/62 (24%), Positives = 28/62 (45%), Gaps = 1/62 (1%)
Query: 48 ARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKM-ENKITKDMSEEELITIRDEVS 106
R+ + N +I Y+L I GVGR + + + +K ++++EEL I +
Sbjct: 15 LRLLNTNVDGNIKIVYALTTIKGVGRRYSNLVCKKADVDLHKRAGELTQEELERIVQIMQ 74
Query: 107 KY 108
Sbjct: 75 NP 76
>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 = 31.6 bits (71), Expect = 0.055
Identities = 15/96 (15%), Positives = 30/96 (31%), Gaps = 24/96 (25%)
Query: 31 SFPVSK----------QPQYPGLSIQCARVGGVEIPNNKRIEYSLQYIH--GVGRTRARQ 78
+ ++ + Y G SI +I N + IH G R R+
Sbjct: 1638 TSKAAQDVWNRADNHFKDTY-GFSIL-------DIVINNPVNL---TIHFGGEKGKRIRE 1686
Query: 79 ILVDLKMENKITKDMSEEELITIRDEV-SKYMIEGD 113
+ E + + E++ +E + Y +
Sbjct: 1687 NYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSE 1722
Score = 25.4 bits (55), Expect = 7.1
Identities = 23/157 (14%), Positives = 39/157 (24%), Gaps = 59/157 (37%)
Query: 9 VAPALSVICNGHNNNLLTNASLSFPVSKQPQY--PGL---SIQCARV---GGVEIPNNKR 60
+ + LL+ Q+ P L G+ IP +
Sbjct: 1710 INEHSTSYTFRSEKGLLS----------ATQFTQPALTLMEKAAFEDLKSKGL-IPADAT 1758
Query: 61 I------EYS-LQYIHGV-------------GRTRARQILVD------LKM----ENKIT 90
EY+ L + V G T + D M ++
Sbjct: 1759 FAGHSLGEYAALASLADVMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVA 1818
Query: 91 KDMSEEELITIRDEVSK----------YMIEGDLVII 117
S+E L + + V K Y +E +
Sbjct: 1819 ASFSQEALQYVVERVGKRTGWLVEIVNYNVENQQYVA 1855
>1x2i_A HEF helicase/nuclease; alpha helix, helix-hairpin-helix DNA binding
domain, homodimer, hydrolase; 1.45A {Pyrococcus
furiosus} SCOP: a.60.2.5
Length = 75
Score = 26.9 bits (60), Expect = 0.81
Identities = 9/43 (20%), Positives = 19/43 (44%), Gaps = 1/43 (2%)
Query: 59 KRIEYSLQYIHGVGRTRARQILVDLKMENKITKDMSEEELITI 101
+R ++ + V T AR++L ++ S EL+ +
Sbjct: 10 ERQRLIVEGLPHVSATLARRLLKHFGSVERV-FTASVAELMKV 51
>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 = 27.9 bits (61), Expect = 1.1
Identities = 11/67 (16%), Positives = 24/67 (35%), Gaps = 13/67 (19%)
Query: 58 NKRIEYSLQYIHGVGRTRARQILVDLKMENKITKDMSEEELITIRDEVSKYMIEGDLVII 117
K+ + S I I ++LK++ + + ++ + K DL+
Sbjct: 418 EKQPKESTISIPS--------IYLELKVKLENEYAL-HRSIVD-HYNIPKTFDSDDLIPP 467
Query: 118 P---YFF 121
YF+
Sbjct: 468 YLDQYFY 474
Score = 26.0 bits (56), Expect = 4.9
Identities = 7/49 (14%), Positives = 22/49 (44%), Gaps = 12/49 (24%)
Query: 77 RQILVDLKM--EN-KIT--------KDMSEEELITIRDEVSKY-MIEGD 113
R++ L + + I D+ + +++ + +++ KY ++E
Sbjct: 372 RKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQ 420
>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces
cerevisiae}
Length = 1219
Score = 27.9 bits (62), Expect = 1.1
Identities = 13/41 (31%), Positives = 20/41 (48%), Gaps = 7/41 (17%)
Query: 52 GVEIPNNKRIEYS-----LQYIHGVGRTRARQILVDLKMEN 87
VE+ NK + + L+YI G G+ +A L L+ N
Sbjct: 700 SVEV--NKATDNNYYASALKYISGFGKRKAIDFLQSLQRLN 738
>2e7z_A Acetylene hydratase AHY; tungstoprotein, DMSO reductase family,
iron-sulfur-cluster, lyase; HET: MGD; 1.26A {Pelobacter
acetylenicus}
Length = 727
Score = 27.3 bits (61), Expect = 1.4
Identities = 4/32 (12%), Positives = 10/32 (31%), Gaps = 1/32 (3%)
Query: 10 APALSVICNGHNNNLLTNASLSF-PVSKQPQY 40
S ++ +L++ + P P
Sbjct: 685 ETGFSGAMLHNDAMVLSDDDWNLDPEQGLPNL 716
>3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces
cerevisiae}
Length = 1030
Score = 27.2 bits (60), Expect = 1.7
Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 9/55 (16%)
Query: 52 GVEIPNNKRIEYS-----LQYIHGVGRTRARQILVDLKMENKITKDMSEEELITI 101
VE+ NK + + L+YI G G+ +A L L+ N+ + ++LIT
Sbjct: 703 SVEV--NKATDNNYYASALKYISGFGKRKAIDFLQSLQRLNEPLL--ARQQLITH 753
>3mdm_A Cholesterol 24-hydroxylase; CYP46A1, P450 46A1, thioperamide,
monooxygenase, metab enzyme, oxidoreductase, heme,
cholesterol metabolism; HET: HEM FJZ; 1.60A {Homo
sapiens} PDB: 2q9g_A* 2q9f_A* 3mdr_A* 3mdt_A* 3mdv_A*
Length = 456
Score = 26.8 bits (60), Expect = 2.1
Identities = 12/67 (17%), Positives = 26/67 (38%), Gaps = 9/67 (13%)
Query: 55 IPNNKRIEYSLQYIHGVGRTRARQILVDLKMENKITKDM------SEEELIT---IRDEV 105
+ + S++++ VGR ++ LK ++ D+ +EE + D
Sbjct: 189 RKQLREVRESIRFLRQVGRDWVQRRREALKRGEEVPADILTQILKAEEGAQDDEGLLDNF 248
Query: 106 SKYMIEG 112
+ I G
Sbjct: 249 VTFFIAG 255
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 26.5 bits (57), Expect = 2.2
Identities = 5/21 (23%), Positives = 9/21 (42%), Gaps = 11/21 (52%)
Query: 10 APALSVICNGHNNNLLTNASL 30
APAL++ A++
Sbjct: 37 APALAI-----------KATM 46
>3s79_A Cytochrome P450 19A1; oxidoreductase; HET: HEM ASD; 2.75A {Homo
sapiens} PDB: 3eqm_A* 3s7s_A*
Length = 503
Score = 26.5 bits (59), Expect = 2.5
Identities = 8/72 (11%), Positives = 22/72 (30%), Gaps = 18/72 (25%)
Query: 56 PNNKRIEYSLQYIHGVG----RTRARQI-----------LVDLKMENKITKDMSEEELIT 100
K+ E S++ + + R+I + + D++ E
Sbjct: 239 WLYKKYEKSVKDLKDAIEVLIAEKRRRISTEEKLEECMDFATELILAEKRGDLTREN--- 295
Query: 101 IRDEVSKYMIEG 112
+ + + +I
Sbjct: 296 VNQCILEMLIAA 307
>1vq8_N 50S ribosomal protein L18P; ribosome 50S, protein-protein complex,
RNA-RNA complex, PROT complex, peptidyl transferase
reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A
{Haloarcula marismortui} SCOP: c.55.4.1 PDB: 1vq4_N*
1vq5_N* 1vq6_N* 1vq7_N* 1s72_N* 1vq9_N* 1vqk_N* 1vql_N*
1vqm_N* 1vqn_N* 1vqo_N* 1vqp_N* 1yhq_N* 1yi2_N* 1yij_N*
1yit_N* 1yj9_N* 1yjn_N* 1yjw_N* 2otj_N* ...
Length = 187
Score = 26.3 bits (58), Expect = 2.7
Identities = 15/67 (22%), Positives = 28/67 (41%), Gaps = 4/67 (5%)
Query: 48 ARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKMENKITKDMSEEELITIRDEVSK 107
A G++IP+N + Q G + L E + D +L DE+ +
Sbjct: 123 AIDAGLDIPHNDDVLADWQRTRGAHIAEYDEQL----EEPLYSGDFDAADLPEHFDELRE 178
Query: 108 YMIEGDL 114
+++GD+
Sbjct: 179 TLLDGDI 185
>2cru_A Programmed cell death protein 5; three helix bundle, apoptosis, DNA
binding, structural genomics, NPPSFA; NMR {Homo sapiens}
SCOP: a.5.6.1 PDB: 2k6b_A
Length = 118
Score = 26.0 bits (57), Expect = 2.8
Identities = 8/36 (22%), Positives = 21/36 (58%), Gaps = 3/36 (8%)
Query: 75 RARQI---LVDLKMENKITKDMSEEELITIRDEVSK 107
+ + + L+ + ++++ +SE+ LI I +VS+
Sbjct: 65 KTKAVENYLIQMARYGQLSEKVSEQGLIEILKKVSQ 100
>2qtc_A Pyruvate dehydrogenase E1 component; thiamin diphosphate,
glycolysis, MAG metal-binding, oxidoreductase, thiamine
pyrophosphate; HET: TDK; 1.77A {Escherichia coli} SCOP:
c.36.1.6 c.36.1.10 c.48.1.1 PDB: 2qta_A* 1l8a_A* 1rp7_A*
2g25_A* 2g28_A* 2g67_A 2iea_A* 3lpl_A* 3lq2_A* 3lq4_A*
Length = 886
Score = 26.7 bits (59), Expect = 2.8
Identities = 9/39 (23%), Positives = 17/39 (43%)
Query: 84 KMENKITKDMSEEELITIRDEVSKYMIEGDLVIIPYFFV 122
K K M+ + + IRD + + + D+ +PY
Sbjct: 403 KNIAHQVKKMNMDGVRHIRDRFNVPVSDADIEKLPYITF 441
>2k5e_A Uncharacterized protein; helix protein, structural genomic,
structural genomics, PSI-2, protein structure
initiative; NMR {Methanococcus jannaschii}
Length = 73
Score = 25.1 bits (55), Expect = 2.9
Identities = 7/27 (25%), Positives = 12/27 (44%)
Query: 85 MENKITKDMSEEELITIRDEVSKYMIE 111
M K TKDM+ + + V+ +
Sbjct: 1 MTQKFTKDMTFAQALQTHPGVAGVLRS 27
>2nap_A Protein (periplasmic nitrate reductase); nitrogenous acceptor,
dissimilatory nitrate reductase; HET: MGD MES; 1.90A
{Desulfovibrio desulfuricans} SCOP: b.52.2.2 c.81.1.1
PDB: 2jim_A* 2jir_A* 2jip_A* 2v45_A* 2v3v_A* 2jiq_A*
2jio_A*
Length = 723
Score = 26.4 bits (59), Expect = 3.4
Identities = 7/18 (38%), Positives = 11/18 (61%), Gaps = 1/18 (5%)
Query: 23 NLLTNASLSFPVSKQPQY 40
N L + PVS++P+Y
Sbjct: 697 NKLFLDATD-PVSREPEY 713
>1eij_A Hypothetical protein MTH1615; beta-helix, structural genomics, PSI,
protein structure initiative; NMR
{Methanothermobacterthermautotrophicus} SCOP: a.5.6.1
Length = 80
Score = 24.7 bits (54), Expect = 4.8
Identities = 7/36 (19%), Positives = 16/36 (44%), Gaps = 3/36 (8%)
Query: 75 RARQI---LVDLKMENKITKDMSEEELITIRDEVSK 107
QI L+ L ++ +++E+L + V+
Sbjct: 35 FVEQIELQLIQLAQMGRVRSKITDEQLKELLKRVAG 70
>2hvu_A PDCD5-like protein; YMR074CP, solution structure, unknown function;
NMR {Saccharomyces cerevisiae} PDB: 2jxn_A*
Length = 116
Score = 25.2 bits (55), Expect = 5.4
Identities = 10/36 (27%), Positives = 21/36 (58%), Gaps = 3/36 (8%)
Query: 75 RARQI---LVDLKMENKITKDMSEEELITIRDEVSK 107
RA+ + L L N +T ++E E+++I + ++K
Sbjct: 68 RAQAVETYLKKLIATNNVTHKITEAEIVSILNGIAK 103
>1ixr_A Holliday junction DNA helicase RUVA; heterooligomeric complex,
octameric RUVA, AAA-ATPase domain, complex with
nucleotide, hydrolase; HET: ANP; 3.30A {Thermus
thermophilus} SCOP: a.60.2.1 b.40.4.2
Length = 191
Score = 25.2 bits (56), Expect = 6.6
Identities = 12/44 (27%), Positives = 19/44 (43%), Gaps = 4/44 (9%)
Query: 64 SLQYIHGVGRTRARQILVDLKMENKITKDMSEEELI--TIRDEV 105
L GVGR A +I ++LK K+ + E + +E
Sbjct: 108 LLTSASGVGRRLAERIALELK--GKVPPHLLAGEKVESEAAEEA 149
>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA
helicase, DEAD-BOX, ATP-binding, HE hydrolase,
mitochondrion; HET: ANP; 1.90A {Saccharomyces
cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A*
Length = 563
Score = 25.1 bits (55), Expect = 9.0
Identities = 8/25 (32%), Positives = 13/25 (52%), Gaps = 6/25 (24%)
Query: 53 VEIPNNKRIEYSLQYIHGVGRT-RA 76
+ +P+ YIH +GRT R+
Sbjct: 417 IGVPSELA-----NYIHRIGRTARS 436
>3ml1_A NAPA, periplasmic nitrate reductase; heterodimer, oxidoreductase;
HET: MGD HEC; 1.60A {Ralstonia eutropha} PDB: 3o5a_A*
1ogy_A* 2nya_A*
Length = 802
Score = 25.1 bits (55), Expect = 9.3
Identities = 5/18 (27%), Positives = 9/18 (50%), Gaps = 1/18 (5%)
Query: 23 NLLTNASLSFPVSKQPQY 40
N +T + P+S Q +
Sbjct: 776 NKVTLDATC-PISLQTDF 792
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
0.321 0.137 0.394
Gapped
Lambda K H
0.267 0.0745 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,869,858
Number of extensions: 102076
Number of successful extensions: 291
Number of sequences better than 10.0: 1
Number of HSP's gapped: 284
Number of HSP's successfully gapped: 50
Length of query: 126
Length of database: 6,701,793
Length adjustment: 82
Effective length of query: 44
Effective length of database: 4,412,271
Effective search space: 194139924
Effective search space used: 194139924
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (23.4 bits)