RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy10356
(129 letters)
>3e1y_E Eukaryotic peptide chain release factor GTP-bindi ERF3A;
translation termination, peptide release, PTC, P
biosynthesis, GTP-binding; HET: ATP; 3.80A {Homo
sapiens}
Length = 204
Score = 146 bits (371), Expect = 7e-46
Identities = 77/100 (77%), Positives = 86/100 (86%)
Query: 30 IVILEHKSIICAGYSAVMHIHCVAEEVNVKALICLIDKKTGEKSKTRPRFVKQDQIAIMR 89
IVI+EHKSIIC GY+AV+HIH EEV + ALICL+DKK+GEKSKTRPRFVKQDQ+ I R
Sbjct: 102 IVIIEHKSIICPGYNAVLHIHTCIEEVEITALICLVDKKSGEKSKTRPRFVKQDQVCIAR 161
Query: 90 LEAAGVICLDQFKLFPQMGRFTLRDEGKTIAIGKVLKIVE 129
L AG ICL+ FK FPQMGRFTLRDEGKTIAIGKVLK+V
Sbjct: 162 LRTAGTICLETFKDFPQMGRFTLRDEGKTIAIGKVLKLVP 201
>1jny_A EF-1-alpha, elongation factor 1-alpha, EF-TU, TUF-1; GTPase,
alpha/beta structure, protein biosynthesis, translation;
HET: GDP; 1.80A {Sulfolobus solfataricus} SCOP: b.43.3.1
b.44.1.1 c.37.1.8 PDB: 1skq_A* 3agj_A*
Length = 435
Score = 137 bits (347), Expect = 5e-40
Identities = 30/100 (30%), Positives = 64/100 (64%)
Query: 30 IVILEHKSIICAGYSAVMHIHCVAEEVNVKALICLIDKKTGEKSKTRPRFVKQDQIAIMR 89
I+++ H + + GY+ V+H+H + V L+ +D +TG++++ P+F+KQ +AI++
Sbjct: 330 IIVVWHPTALANGYTPVLHVHTASVACRVSELVSKLDPRTGQEAEKNPQFLKQGDVAIVK 389
Query: 90 LEAAGVICLDQFKLFPQMGRFTLRDEGKTIAIGKVLKIVE 129
+ +C++++ FP +GRF +RD GKT+ +G ++ +
Sbjct: 390 FKPIKPLCVEKYNEFPPLGRFAMRDMGKTVGVGIIVDVKP 429
>1r5b_A Eukaryotic peptide chain release factor GTP-bindi subunit;
translation termination, peptide release, GTPase,
translatio; 2.35A {Schizosaccharomyces pombe} SCOP:
b.43.3.1 b.44.1.1 c.37.1.8 PDB: 1r5n_A* 1r5o_A* 3e20_A
Length = 467
Score = 136 bits (345), Expect = 1e-39
Identities = 47/100 (47%), Positives = 64/100 (64%), Gaps = 1/100 (1%)
Query: 30 IVILEHKSIICAGYSAVMHIHCVAEEVNVKALICLIDKKTGEKSKTRPRFVKQDQIAIMR 89
I ILE SI+ GYS VMHIH EEV+ L+ +DK T KSK P F + I
Sbjct: 369 IAILELPSILTTGYSCVMHIHTAVEEVSFAKLLHKLDK-TNRKSKKPPMFATKGMKIIAE 427
Query: 90 LEAAGVICLDQFKLFPQMGRFTLRDEGKTIAIGKVLKIVE 129
LE +C+++F+ + MGRFTLRD+G T+A+GKV+KI++
Sbjct: 428 LETQTPVCMERFEDYQYMGRFTLRDQGTTVAVGKVVKILD 467
>3izq_1 HBS1P, elongation factor 1 alpha-like protein; NO-GO mRNA decay,
ribosomal protein,hydrolase; 9.50A {Saccharomyces
cerevisiae}
Length = 611
Score = 136 bits (345), Expect = 5e-39
Identities = 27/103 (26%), Positives = 45/103 (43%), Gaps = 4/103 (3%)
Query: 30 IVILEHKSIICAGYSAVMHIHCVAEEVNVKALICLIDKKTGEKSKTRPRFVKQDQIAIMR 89
+ + + G ++ I + +K LI IDK SK + R + Q A +
Sbjct: 510 LTTFDMNRPLLPGTPFILFIGVKEQPARIKRLISFIDKGNT-ASKKKIRHLGSKQRAFVE 568
Query: 90 L---EAAGVICLDQFKLFPQMGRFTLRDEGKTIAIGKVLKIVE 129
+ E I L ++GR LR +G+TIA GK+ +I +
Sbjct: 569 IELIEVKRWIPLLTAHENDRLGRVVLRKDGRTIAAGKISEITQ 611
>3p26_A Elongation factor 1 alpha-like protein; GTP/GDP binding domain,
beta-barrel, translational GTPase, D structural
genomics; 2.50A {Saccharomyces cerevisiae} PDB: 3p27_A*
Length = 483
Score = 132 bits (334), Expect = 8e-38
Identities = 26/103 (25%), Positives = 44/103 (42%), Gaps = 4/103 (3%)
Query: 30 IVILEHKSIICAGYSAVMHIHCVAEEVNVKALICLIDKKTGEKSKTRPRFVKQDQIAIMR 89
+ + + G ++ I + +K LI IDK K + R + Q A +
Sbjct: 376 LTTFDMNRPLLPGTPFILFIGVKEQPARIKRLISFIDKGNTASKK-KIRHLGSKQRAFVE 434
Query: 90 L---EAAGVICLDQFKLFPQMGRFTLRDEGKTIAIGKVLKIVE 129
+ E I L ++GR LR +G+TIA GK+ +I +
Sbjct: 435 IELIEVKRWIPLLTAHENDRLGRVVLRKDGRTIAAGKISEITQ 477
>1f60_A Elongation factor EEF1A; protein-protein complex, translation;
1.67A {Saccharomyces cerevisiae} SCOP: b.43.3.1 b.44.1.1
c.37.1.8 PDB: 1g7c_A* 1ije_A* 1ijf_A* 2b7b_A* 2b7c_A
Length = 458
Score = 127 bits (321), Expect = 3e-36
Identities = 28/100 (28%), Positives = 56/100 (56%)
Query: 30 IVILEHKSIICAGYSAVMHIHCVAEEVNVKALICLIDKKTGEKSKTRPRFVKQDQIAIMR 89
+++L H I AGYS V+ H L+ D+++G+K + P+F+K A+++
Sbjct: 342 VIVLNHPGQISAGYSPVLDCHTAHIACRFDELLEKNDRRSGKKLEDHPKFLKSGDAALVK 401
Query: 90 LEAAGVICLDQFKLFPQMGRFTLRDEGKTIAIGKVLKIVE 129
+ +C++ F +P +GRF +RD +T+A+G + + +
Sbjct: 402 FVPSKPMCVEAFSEYPPLGRFAVRDMRQTVAVGVIKSVDK 441
>3mca_A HBS1, elongation factor 1 alpha-like protein; protein protein
complex, translation regulation; 2.74A
{Schizosaccharomyces pombe}
Length = 592
Score = 113 bits (285), Expect = 1e-30
Identities = 24/99 (24%), Positives = 43/99 (43%), Gaps = 10/99 (10%)
Query: 30 IVILEHKSIICAGYSAVMHIHCVAEEVNVKALICLIDKKTGEKSKTRPRFVKQDQIAIMR 89
I + I +G + V+H+ V++K + R R + + A++R
Sbjct: 502 IQTFDIHGPILSGSTLVLHLGRTVTSVSLK---------IVTVNNKRSRHIASRKRALVR 552
Query: 90 LE-AAGVICLDQFKLFPQMGRFTLRDEGKTIAIGKVLKI 127
+ G+ L + P +GRF LR G T+A G V ++
Sbjct: 553 ISFLDGLFPLCLAEECPALGRFILRRSGDTVAAGIVKEL 591
>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 = 38.5 bits (89), Expect = 3e-04
Identities = 26/140 (18%), Positives = 49/140 (35%), Gaps = 50/140 (35%)
Query: 10 KGEGM-----------LWQE----QRVIYGPSVIYIVILEHKSI-----------ICAGY 43
+G GM +W + YG S++ IVI ++ I Y
Sbjct: 1629 QGMGMDLYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIRENY 1688
Query: 44 SAVMHIHCVAEEVNVKALICLIDKKT------GEKSK-TRPRFVKQDQIAIMRLEAAGVI 96
SA++ V ++ + + I++ + EK + +F Q A+ +E A
Sbjct: 1689 SAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFT---QPALTLMEKA--- 1742
Query: 97 CLDQFKLFPQMGRFTLRDEG 116
F+ L+ +G
Sbjct: 1743 ---AFED--------LKSKG 1751
>2c78_A Elongation factor TU-A; hydrolase, GTPase, translation elongation
factor, protein synthesis, antibiotic, GTP-binding,
nucleotide-binding; HET: GNP PUL; 1.4A {Thermus
thermophilus} SCOP: b.43.3.1 b.44.1.1 c.37.1.8 PDB:
2y0u_Z* 2y0w_Z* 2y0y_Z* 2y10_Z* 2y12_Z* 2y14_Z* 2y16_Z*
2y18_Z* 2wrn_Z* 2wrq_Z* 2c77_A* 1aip_A 1exm_A* 1ha3_A*
2xqd_Z* 3fic_Z* 4abr_Z* 1b23_P* 1ob5_A* 1ttt_A* ...
Length = 405
Score = 31.0 bits (71), Expect = 0.085
Identities = 10/21 (47%), Positives = 15/21 (71%)
Query: 109 RFTLRDEGKTIAIGKVLKIVE 129
RF +R+ G+T+ G V KI+E
Sbjct: 385 RFAIREGGRTVGAGVVTKILE 405
>3avx_A Elongation factor TS, elongation factor TU, linke replicase; RNA
polymerase, translation, transferase-RNA complex; HET:
GH3; 2.41A {Escherichia coli O157} PDB: 3agq_A 3agp_A*
3avu_A 3avv_A 3avt_A* 3avw_A* 3avy_A* 3mmp_A* 3mmp_G*
1efu_B
Length = 1289
Score = 30.7 bits (69), Expect = 0.12
Identities = 8/21 (38%), Positives = 14/21 (66%)
Query: 109 RFTLRDEGKTIAIGKVLKIVE 129
RF +R+ G+T+ G V K++
Sbjct: 658 RFAIREGGRTVGAGVVAKVLS 678
>1zun_B Sulfate adenylate transferase, subunit 1/adenylylsulfate kinase;
beta barrel, switch domain, heterodimer, pyrophosphate,
G protein; HET: GDP AGS; 2.70A {Pseudomonas syringae PV}
SCOP: b.43.3.1 b.44.1.1 c.37.1.8
Length = 434
Score = 30.3 bits (69), Expect = 0.16
Identities = 13/72 (18%), Positives = 31/72 (43%), Gaps = 4/72 (5%)
Query: 56 VNVKALICLIDKKTGEKSKTRPRFVKQDQIAIMRLEAAGVICLDQFKLFPQMGRFTLRDE 115
++ ++ +D T E+ ++ ++I +++ I LD + G F + D
Sbjct: 364 GSIASITHRVDVNTLEEGP--ASSLQLNEIGRVKVSLDAPIALDGYSSNRTTGAFIVIDR 421
Query: 116 --GKTIAIGKVL 125
T+A G ++
Sbjct: 422 LTNGTVAAGMII 433
>1d2e_A Elongation factor TU (EF-TU); G-protein, beta-barrel, RNA binding
protein; HET: GDP; 1.94A {Bos taurus} SCOP: b.43.3.1
b.44.1.1 c.37.1.8 PDB: 1xb2_A* 2hcj_A* 2hdn_A*
Length = 397
Score = 29.9 bits (68), Expect = 0.21
Identities = 10/20 (50%), Positives = 11/20 (55%)
Query: 109 RFTLRDEGKTIAIGKVLKIV 128
RFTLRD +TI G V
Sbjct: 367 RFTLRDGNRTIGTGLVTDTP 386
>2dc0_A Probable amidase; structural genomics, NPPSFA, national project on
protein structural and functional analyses; 2.00A
{Thermus thermophilus}
Length = 434
Score = 29.1 bits (66), Expect = 0.39
Identities = 10/49 (20%), Positives = 18/49 (36%), Gaps = 5/49 (10%)
Query: 58 VKALICLIDKKTGEKSKTRPRFVKQDQIAIMRLEAAGVICL-----DQF 101
VK L + T +K + ++ A+ RL AG + +
Sbjct: 72 VKDLFPVKGMPTRAGTKAPLPPLPEEARAVRRLREAGALLFAKTNMHEI 120
>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 = 29.1 bits (64), Expect = 0.47
Identities = 9/52 (17%), Positives = 18/52 (34%), Gaps = 11/52 (21%)
Query: 75 TRPRFVKQDQIAIMRLEAAGVICLDQFKLFPQMGRFTLRDEGKTIAIGKVLK 126
+R + + + A++ L A + +D + GKT V
Sbjct: 132 SRLQPYLKLRQALLELRPAKNVLID------GVLGS-----GKTWVALDVCL 172
>2qmi_A PBP related beta-lactamase; PAB87, octamer, LU-HPDO3A, archaea,
hydrolase; HET: DO3; 2.20A {Pyrococcus abyssi}
Length = 447
Score = 25.2 bits (55), Expect = 8.7
Identities = 11/37 (29%), Positives = 15/37 (40%), Gaps = 7/37 (18%)
Query: 85 IAIMRLEAAGVICLDQ-------FKLFPQMGRFTLRD 114
+AIM+L G + LD KL P T+
Sbjct: 67 LAIMKLVEEGGLSLDDPVEKFVNIKLRPFGEPVTVHH 103
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
0.326 0.140 0.414
Gapped
Lambda K H
0.267 0.0690 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,972,540
Number of extensions: 109284
Number of successful extensions: 312
Number of sequences better than 10.0: 1
Number of HSP's gapped: 305
Number of HSP's successfully gapped: 22
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: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 52 (23.9 bits)