RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 033139
(126 letters)
>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 = 185 bits (471), Expect = 8e-62
Identities = 102/118 (86%), Positives = 113/118 (95%)
Query: 1 MSLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELS 60
MSL+A E+FQHILRVLNTNVDGKQKIMFALTSIKG+GRR +NIVCKKAD+DMNKRAGELS
Sbjct: 1 MSLIAGEEFQHILRVLNTNVDGKQKIMFALTSIKGVGRRFSNIVCKKADIDMNKRAGELS 60
Query: 61 AAELDQLMVVVANPRQFKIPDWFLNRQKDYKDGRYSQVVSNALDMKLRDDLERLKKIR 118
A E+D+LM VV NPRQFK+PDWFLNR+KDYKDGR+SQVVSNA+DMKLRDDLERLKKIR
Sbjct: 61 AEEMDRLMAVVHNPRQFKVPDWFLNRKKDYKDGRFSQVVSNAVDMKLRDDLERLKKIR 118
>2xzm_M RPS18E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB:
2xzn_M
Length = 155
Score = 177 bits (452), Expect = 7e-59
Identities = 60/120 (50%), Positives = 82/120 (68%), Gaps = 2/120 (1%)
Query: 1 MSLVA--NEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGE 58
MS V DF++I R+LNTN+DGK+ ALT I+GIGRR A I+CK +D N RAG
Sbjct: 1 MSFVIEKESDFKYIHRILNTNIDGKRITPIALTGIRGIGRRFAYIICKVLKIDPNARAGL 60
Query: 59 LSAAELDQLMVVVANPRQFKIPDWFLNRQKDYKDGRYSQVVSNALDMKLRDDLERLKKIR 118
L+ + +++ ++A+P IP W LNR D+KDG+ Q+ SN LD K+R+DLERLKKI+
Sbjct: 61 LTEDQCNKITDLIADPEAHGIPTWLLNRINDFKDGKNYQMASNTLDTKMREDLERLKKIK 120
>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 = 176 bits (449), Expect = 2e-58
Identities = 74/120 (61%), Positives = 96/120 (80%), Gaps = 2/120 (1%)
Query: 1 MSLVANE--DFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGE 58
MSLV E FQHILR+LNTNVDG KI++ALT+IKG+GRR +N+VCKKADVD++KRAGE
Sbjct: 1 MSLVVQEQGSFQHILRLLNTNVDGNIKIVYALTTIKGVGRRYSNLVCKKADVDLHKRAGE 60
Query: 59 LSAAELDQLMVVVANPRQFKIPDWFLNRQKDYKDGRYSQVVSNALDMKLRDDLERLKKIR 118
L+ EL++++ ++ NP +KIP WFLNRQ D DG+ ++N ++ KLRDDLERLKKIR
Sbjct: 61 LTQEELERIVQIMQNPTHYKIPAWFLNRQNDITDGKDYHTLANNVESKLRDDLERLKKIR 120
>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 = 53.2 bits (129), Expect = 1e-10
Identities = 17/60 (28%), Positives = 30/60 (50%)
Query: 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVAN 73
R+ N+ + + ALTSI G+G+ + + A + + + ELS ++D L VA
Sbjct: 2 RIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEVAK 61
>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 = 52.1 bits (126), Expect = 6e-10
Identities = 17/60 (28%), Positives = 30/60 (50%)
Query: 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVAN 73
R+ + +++ ALT I GIG+ A +K ++ R +L+ AE+ +L V N
Sbjct: 3 RIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYVEN 62
>3bbn_M Ribosomal protein S13; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 145
Score = 48.1 bits (115), Expect = 3e-08
Identities = 14/54 (25%), Positives = 26/54 (48%), Gaps = 1/54 (1%)
Query: 14 RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQL 67
R+ + +++ ++L I GIGR + + + D NK +LS E+ L
Sbjct: 48 RIGGVEIPNHKRVEYSLQYIHGIGRSRSRQILLDLNFD-NKVTKDLSEEEVIIL 100
>2i0z_A NAD(FAD)-utilizing dehydrogenases; structural genomics, PSI-2,
protein structure initiative, midwest center for
structural genomics, MCSG; HET: FAD; 1.84A {Bacillus
cereus} SCOP: c.3.1.8 e.74.1.1
Length = 447
Score = 34.4 bits (80), Expect = 0.005
Identities = 13/59 (22%), Positives = 30/59 (50%), Gaps = 4/59 (6%)
Query: 9 FQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQL 67
FQ +L+ + + K+ I L + R + +K ++D +++AG++S ++ L
Sbjct: 308 FQRMLKQMKED--PKKGIKNVLKGY--VPERYFLFLLEKNEIDGSEQAGQVSHEKIRAL 362
>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 = 33.9 bits (77), Expect = 0.009
Identities = 21/130 (16%), Positives = 47/130 (36%), Gaps = 39/130 (30%)
Query: 1 MSLVANEDFQHI---LRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAG 57
M ++N + + + N+++ +++ +L G + N+V +G
Sbjct: 338 MLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLV----NGAK--NLVV----------SG 381
Query: 58 ELSAAELDQLMVVV------ANPRQFKIPDWFLNRQKDYKDGRY--------SQVVSNAL 103
L L + + + Q +IP F R+ + R+ S ++ A
Sbjct: 382 --PPQSLYGLNLTLRKAKAPSGLDQSRIP--FSERKLKF-SNRFLPVASPFHSHLLVPAS 436
Query: 104 DMKLRDDLER 113
D + DL +
Sbjct: 437 D-LINKDLVK 445
Score = 30.8 bits (69), Expect = 0.12
Identities = 14/69 (20%), Positives = 24/69 (34%), Gaps = 30/69 (43%)
Query: 12 ILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVV 71
++ ++N NV+ +Q V AG+L A LD + V+
Sbjct: 1840 LVEIVNYNVENQQ------------------YVA----------AGDLRA--LDTVTNVL 1869
Query: 72 ANPRQFKIP 80
+ KI
Sbjct: 1870 NFIKLQKID 1878
>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 = 32.1 bits (72), Expect = 0.038
Identities = 20/135 (14%), Positives = 42/135 (31%), Gaps = 35/135 (25%)
Query: 2 SLVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCK------KADVD--MN 53
S+++ E+ HI+ + +F K +V K + + M+
Sbjct: 44 SILSKEEIDHIIMS--KDAVSGTLRLFWTLLSKQ-----EEMVQKFVEEVLRINYKFLMS 96
Query: 54 KRAGELSAAELDQLMVVVANPRQF----KIPDWFLNRQKDYKDGRYSQVVSNALDMKLRD 109
E + M + R + + ++R + Y KLR
Sbjct: 97 PIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYL--------------KLRQ 142
Query: 110 DLERLKKIRYGLVVL 124
L L+ + V++
Sbjct: 143 ALLELRPAKN--VLI 155
Score = 28.7 bits (63), Expect = 0.54
Identities = 20/127 (15%), Positives = 36/127 (28%), Gaps = 43/127 (33%)
Query: 33 IKGIGRRLANIVC-----KKADVDMNKRAGELSAAELD--------QLMVVVANPRQFKI 79
+ I + + + K + D E S L+ + V P I
Sbjct: 330 LSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVF--PPSAHI 387
Query: 80 PD------W--------------FLNR---QKDYKDGRYSQVVSNALDMKL-RDDLERL- 114
P W +K K+ S + S L++K+ ++ L
Sbjct: 388 PTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTIS-IPSIYLELKVKLENEYALH 446
Query: 115 KKI--RY 119
+ I Y
Sbjct: 447 RSIVDHY 453
>4dcm_A Ribosomal RNA large subunit methyltransferase G; 23S rRNA
(guanine1835-N2)-methyltransferase; HET: SAM; 2.30A
{Escherichia coli}
Length = 375
Score = 27.9 bits (62), Expect = 0.94
Identities = 13/68 (19%), Positives = 25/68 (36%), Gaps = 6/68 (8%)
Query: 36 IGRRLANIVCKKA--DVDMNKRAGELSAAELDQLMVVVANPRQFKIPDWFLNRQKDYKDG 93
IG L + + VD + A S ++ M + +F I + +
Sbjct: 236 IGLTLLDKNPQAKVVFVDESPMAVASSRLNVETNMPEALDRCEFMINNAL----SGVEPF 291
Query: 94 RYSQVVSN 101
R++ V+ N
Sbjct: 292 RFNAVLCN 299
>2hnh_A DNA polymerase III alpha subunit; DNA replication,
nucleotidyltransferase, beta, PHP, transferase; HET:
DNA; 2.30A {Escherichia coli} PDB: 2hqa_A*
Length = 910
Score = 27.8 bits (63), Expect = 0.99
Identities = 12/56 (21%), Positives = 24/56 (42%), Gaps = 17/56 (30%)
Query: 20 VDGKQKIMFALTSIKGIGRR-LANIV---------------CKKADV-DMNKRAGE 58
V+ +I++ + +IKG+G + I+ C + D +N+R E
Sbjct: 825 VNDDGEIVYGIGAIKGVGEGPIEAIIEARNKGGYFRELFDLCARTDTKKLNRRVLE 880
>3f2b_A DNA-directed DNA polymerase III alpha chain; DNA polymerase C, DNA
polymerase III; HET: DGT; 2.39A {Geobacillus
kaustophilus} PDB: 3f2c_A* 3f2d_A*
Length = 1041
Score = 27.3 bits (61), Expect = 1.8
Identities = 10/54 (18%), Positives = 20/54 (37%), Gaps = 18/54 (33%)
Query: 20 VDGKQKIMFALTSIKGIGRRLA-NIV--------------CKKADVDMNKRAGE 58
+DG ++ +I G+G +A IV ++ + +K E
Sbjct: 960 IDGN-SLIPPFNAIPGLGTNVAQAIVRAREEGEFLSKEDLQQRGKL--SKTLLE 1010
>3doa_A Fibrinogen binding protein; structural genomics, MCSG., protein
structure initiative, midwest center for structural
genomics; 2.81A {Staphylococcus aureus subsp}
Length = 288
Score = 26.1 bits (57), Expect = 4.0
Identities = 7/62 (11%), Positives = 20/62 (32%), Gaps = 2/62 (3%)
Query: 6 NEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELD 65
+ +L+ ++ N K + L +G + N + + + E +
Sbjct: 173 DITGAEVLKYIDFNAGNIAKQL--LNQFEGFSPLITNEIVSRRQFMTSSTLPEAFDEVMA 230
Query: 66 QL 67
+
Sbjct: 231 ET 232
>1o6e_A Capsid protein P40; proteinase, beta-barrel, hydrolase, serine
protease, structu proteomics in europe, spine,
structural genomics; 2.3A {Human herpesvirus 4} SCOP:
b.57.1.1
Length = 235
Score = 25.2 bits (55), Expect = 7.3
Identities = 22/109 (20%), Positives = 40/109 (36%), Gaps = 11/109 (10%)
Query: 13 LRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVD-MNKRAGELSAAELDQLMVVV 71
+ T DG + F SI +GRR D+ + K +L + Q+
Sbjct: 122 PDIPQTTADGGKLSFFDHVSICALGRRRGTTAVYGTDLAWVLKHFSDLEPSIAAQIENDA 181
Query: 72 ANP-RQFKIPDWFLNRQKDYKDGRYSQVVSNALD-MKLRDDLERLKKIR 118
R+ P+ +++ A+D LR+ +E L++ R
Sbjct: 182 NAAKRESGCPEDHPLPLTK--------LIAKAIDAGFLRNRVETLRQDR 222
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 0.138 0.389
Gapped
Lambda K H
0.267 0.0600 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,942,503
Number of extensions: 108409
Number of successful extensions: 333
Number of sequences better than 10.0: 1
Number of HSP's gapped: 332
Number of HSP's successfully gapped: 30
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 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 51 (23.7 bits)