RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 030930
(169 letters)
>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 = 194 bits (495), Expect = 4e-65
Identities = 60/124 (48%), Positives = 85/124 (68%), Gaps = 2/124 (1%)
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-YMIEGDLRRFNALAIRRLKEIQCYRGIRHIQGLPCRGQHTKNNCRTLKGKRVAIAGKK 165
+ +EG+LR A I+RL +I CYRG+RH +GLP RGQ T+ N RT KG R +AGKK
Sbjct: 62 NTWKLEGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKTVAGKK 121
Query: 166 KAPR 169
KAPR
Sbjct: 122 KAPR 125
>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 = 183 bits (468), Expect = 4e-61
Identities = 53/112 (47%), Positives = 81/112 (72%), Gaps = 1/112 (0%)
Query: 48 ARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKM-ENKITKDMSEEELITIRDEVS 106
AR+ G+ IP++K +L I+GVG+TR++ IL + E+ ++SE ++ T+RDEV+
Sbjct: 1 ARIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEVA 60
Query: 107 KYMIEGDLRRFNALAIRRLKEIQCYRGIRHIQGLPCRGQHTKNNCRTLKGKR 158
K+++EGDLRR +++I+RL ++ CYRG+RH +GLP RGQ TK N RT KG R
Sbjct: 61 KFVVEGDLRREISMSIKRLMDLGCYRGLRHRRGLPVRGQRTKTNARTRKGPR 112
>3bbn_M Ribosomal protein S13; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 145
Score = 179 bits (456), Expect = 7e-59
Identities = 80/152 (52%), Positives = 106/152 (69%), Gaps = 13/152 (8%)
Query: 5 LAMPVAPALSVICNGHNNNLLTNASLSFPVSKQPQYPGLSIQCARVGGVEIPNNKRIEYS 64
+++P+A + + ++ + S P + GL I+C R+GGVEIPN+KR+EYS
Sbjct: 7 VSVPIATSSLPLSARGRSS---SVSFPAPKKGGIGHGGLQIECIRIGGVEIPNHKRVEYS 63
Query: 65 LQYIHGVGRTRARQILVDLKMENKITKDMSEEELITIRDEVSKYMIEGDLRRFNALAIRR 124
LQYIHG+GR+R+RQIL+DL +NK+TKD+SEEE+I +R +RFN +AI R
Sbjct: 64 LQYIHGIGRSRSRQILLDLNFDNKVTKDLSEEEVIILR----------KEKRFNRVAIER 113
Query: 125 LKEIQCYRGIRHIQGLPCRGQHTKNNCRTLKG 156
LKEI+CYRGIRH GLP RGQ TKNNCRTLKG
Sbjct: 114 LKEIRCYRGIRHKLGLPVRGQRTKNNCRTLKG 145
>2xzm_M RPS18E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB:
2xzn_M
Length = 155
Score = 135 bits (343), Expect = 1e-41
Identities = 37/143 (25%), Positives = 55/143 (38%), Gaps = 26/143 (18%)
Query: 48 ARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKM-ENKITKDMSEEELITIRDEVS 106
R+ I + +L I G+GR A I LK+ N ++E++ I D ++
Sbjct: 15 HRILNTNIDGKRITPIALTGIRGIGRRFAYIICKVLKIDPNARAGLLTEDQCNKITDLIA 74
Query: 107 KY-----------------------MIEGDLRRFNALAIRRLKEIQCYRGIRHIQGLPCR 143
M L + RLK+I+ +RG+RH GL R
Sbjct: 75 DPEAHGIPTWLLNRINDFKDGKNYQMASNTLDTKMREDLERLKKIKSHRGLRHFWGLKVR 134
Query: 144 GQHTKNNCRTLKGKRVAIAGKKK 166
GQHTK + R G + K K
Sbjct: 135 GQHTKTSGR--HGVVCGVVRKNK 155
>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 = 134 bits (339), Expect = 4e-41
Identities = 35/142 (24%), Positives = 59/142 (41%), Gaps = 26/142 (18%)
Query: 48 ARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKM-ENKITKDMSEEELITIRDEVS 106
RV + ++I ++L I GVGR + + + NK ++S EE+ + V
Sbjct: 13 LRVLNTNVDGKQKIMFALTSIKGVGRRFSNIVCKKADIDMNKRAGELSAEEMDRLMAVVH 72
Query: 107 -----------------------KYMIEGDLRRFNALAIRRLKEIQCYRGIRHIQGLPCR 143
++ + + RLK+I+ +RG+RH G+ R
Sbjct: 73 NPRQFKVPDWFLNRKKDYKDGRFSQVVSNAVDMKLRDDLERLKKIRNHRGLRHYWGVRVR 132
Query: 144 GQHTKNNCRTLKGKRVAIAGKK 165
GQHTK R GK V ++ K+
Sbjct: 133 GQHTKTTGRR--GKTVGVSKKR 152
>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 = 127 bits (322), Expect = 1e-38
Identities = 33/130 (25%), Positives = 54/130 (41%), Gaps = 24/130 (18%)
Query: 48 ARVGGVEIPNNKRIEYSLQYIHGVGRTRARQILVDLKM-ENKITKDMSEEELITIRDEVS 106
R+ + N +I Y+L I GVGR + + + +K ++++EEL I +
Sbjct: 15 LRLLNTNVDGNIKIVYALTTIKGVGRRYSNLVCKKADVDLHKRAGELTQEELERIVQIMQ 74
Query: 107 -----------------------KYMIEGDLRRFNALAIRRLKEIQCYRGIRHIQGLPCR 143
+ + ++ + RLK+I+ +RGIRH GL R
Sbjct: 75 NPTHYKIPAWFLNRQNDITDGKDYHTLANNVESKLRDDLERLKKIRAHRGIRHFWGLRVR 134
Query: 144 GQHTKNNCRT 153
GQHTK R
Sbjct: 135 GQHTKTTGRR 144
>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 = 34.3 bits (78), Expect = 0.018
Identities = 23/130 (17%), Positives = 40/130 (30%), Gaps = 41/130 (31%)
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---LRR--FN--AL-----AI-RR 124
+ E + + E++ +E + Y + L F AL A
Sbjct: 1687 NYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAAFED 1746
Query: 125 LKEIQCYRGI 134
LK +G+
Sbjct: 1747 LKS----KGL 1752
Score = 33.1 bits (75), Expect = 0.045
Identities = 29/197 (14%), Positives = 46/197 (23%), Gaps = 83/197 (42%)
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 KDMSEEELITIRDEVSKYMIEGDLRRFNALAIRRLKEIQCYRGIRHIQGLPCRGQHTKNN 150
S+E L + + V K L EI Y N
Sbjct: 1819 ASFSQEALQYVVERVGK-------------RTGWLVEIVNY------------------N 1847
Query: 151 CRTLKGKRVAIAGKKKA 167
++ AG +A
Sbjct: 1848 VE---NQQYVAAGDLRA 1861
>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 = 28.3 bits (62), Expect = 1.4
Identities = 11/87 (12%), Positives = 30/87 (34%), Gaps = 29/87 (33%)
Query: 77 RQILVDLKM--EN-KIT--------KDMSEEELITIRDEVSKY-MIEGDLRRF------- 117
R++ L + + I D+ + +++ + +++ KY ++E +
Sbjct: 372 RKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSI 431
Query: 118 ---------NALAIRRLKEIQCYRGIR 135
N A+ R + Y +
Sbjct: 432 YLELKVKLENEYALHR-SIVDHYNIPK 457
>3s79_A Cytochrome P450 19A1; oxidoreductase; HET: HEM ASD; 2.75A {Homo
sapiens} PDB: 3eqm_A* 3s7s_A*
Length = 503
Score = 27.3 bits (61), Expect = 2.9
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
>3psi_A Transcription elongation factor SPT6; nucleus; 3.30A {Saccharomyces
cerevisiae}
Length = 1219
Score = 27.5 bits (61), Expect = 3.0
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
>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 = 3.2
Identities = 5/21 (23%), Positives = 9/21 (42%), Gaps = 11/21 (52%)
Query: 10 APALSVICNGHNNNLLTNASL 30
APAL++ A++
Sbjct: 37 APALAI-----------KATM 46
>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 = 3.4
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
>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 = 3.6
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
>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 = 25.3 bits (56), Expect = 3.9
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
>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 = 4.7
Identities = 7/27 (25%), Positives = 12/27 (44%)
Query: 85 MENKITKDMSEEELITIRDEVSKYMIE 111
M K TKDM+ + + V+ +
Sbjct: 1 MTQKFTKDMTFAQALQTHPGVAGVLRS 27
>3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces
cerevisiae}
Length = 1030
Score = 26.8 bits (59), Expect = 4.9
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
>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 = 26.0 bits (58), Expect = 8.1
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
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 0.136 0.397
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: 2,547,038
Number of extensions: 149472
Number of successful extensions: 381
Number of sequences better than 10.0: 1
Number of HSP's gapped: 367
Number of HSP's successfully gapped: 29
Length of query: 169
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 82
Effective length of database: 4,272,666
Effective search space: 350358612
Effective search space used: 350358612
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 (21.9 bits)
S2: 54 (24.5 bits)