RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy140
(184 letters)
>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 = 53.1 bits (128), Expect = 7e-09
Identities = 25/117 (21%), Positives = 44/117 (37%), Gaps = 21/117 (17%)
Query: 2 VMVSPALNPVAVWEFEGEILVLHHPTTISSRYQAMVHCGSIRQTASILSMSAECLRTGDK 61
V+ S A F +I +L P+ +++ Y ++H + + S + + +T K
Sbjct: 351 VLTSTKNPVHATTRFIAQIAILELPSILTTGYSCVMHIHTAVEEVSFAKLLHKLDKTNRK 410
Query: 62 AAVHFRFIK------------HP-------EYLRAGQRMVFR-EGRTKAVGNVTKVL 98
+ F P +Y + R R +G T AVG V K+L
Sbjct: 411 SKKPPMFATKGMKIIAELETQTPVCMERFEDY-QYMGRFTLRDQGTTVAVGKVVKIL 466
>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 = 49.9 bits (120), Expect = 9e-08
Identities = 23/127 (18%), Positives = 39/127 (30%), Gaps = 25/127 (19%)
Query: 2 VMVSPALNPV-AVWEFEGEILVLHHPTTISSRYQAMVHCGSIRQTASI------------ 48
+ S + + + F E+ + ++ G Q A I
Sbjct: 357 LAASVDYSSIHSAQCFVLELTTFDMNRPLLPGTPFILFIGVKEQPARIKRLISFIDKGNT 416
Query: 49 -LSMSAECLRTGDKAAVHFRFI---------KHPEYLRAGQRMVFR-EGRTKAVGNVTKV 97
L + +A V I E R G R+V R +GRT A G ++++
Sbjct: 417 ASKKKIRHLGSKQRAFVEIELIEVKRWIPLLTAHENDRLG-RVVLRKDGRTIAAGKISEI 475
Query: 98 LPPSGHQ 104
H
Sbjct: 476 TQHHHHH 482
>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 = 49.2 bits (118), Expect = 1e-07
Identities = 30/119 (25%), Positives = 49/119 (41%), Gaps = 22/119 (18%)
Query: 2 VMVSPALNPVAVWEFEGEILVLHHPTTISSRYQAMVHCGSIRQTASILSMSAE------- 54
V+ P P EF I+V+ HPT +++ Y ++H + + + ++
Sbjct: 312 VVGHPNNPPTVADEFTARIIVVWHPTALANGYTPVLHVHTASVACRVSELVSKLDPRTGQ 371
Query: 55 -------CLRTGDKAAVHFRFIK------HPEYLRAGQRMVFR-EGRTKAVGNVTKVLP 99
L+ GD A V F+ IK + E+ G R R G+T VG + V P
Sbjct: 372 EAEKNPQFLKQGDVAIVKFKPIKPLCVEKYNEFPPLG-RFAMRDMGKTVGVGIIVDVKP 429
>3izq_1 HBS1P, elongation factor 1 alpha-like protein; NO-GO mRNA decay,
ribosomal protein,hydrolase; 9.50A {Saccharomyces
cerevisiae}
Length = 611
Score = 49.3 bits (118), Expect = 2e-07
Identities = 22/121 (18%), Positives = 41/121 (33%), Gaps = 25/121 (20%)
Query: 2 VMVSPALNPV-AVWEFEGEILVLHHPTTISSRYQAMVHCGSIRQTASILSMSA------- 53
+ S + + + F E+ + ++ G Q A I + +
Sbjct: 491 LAASVDYSSIHSAQCFVLELTTFDMNRPLLPGTPFILFIGVKEQPARIKRLISFIDKGNT 550
Query: 54 ------ECLRTGDKAAVHFRFIK--HP-------EYLRAGQRMVFR-EGRTKAVGNVTKV 97
L + +A V I+ E R G R+V R +GRT A G ++++
Sbjct: 551 ASKKKIRHLGSKQRAFVEIELIEVKRWIPLLTAHENDRLG-RVVLRKDGRTIAAGKISEI 609
Query: 98 L 98
Sbjct: 610 T 610
>3mca_A HBS1, elongation factor 1 alpha-like protein; protein protein
complex, translation regulation; 2.74A
{Schizosaccharomyces pombe}
Length = 592
Score = 49.4 bits (118), Expect = 2e-07
Identities = 20/109 (18%), Positives = 37/109 (33%), Gaps = 14/109 (12%)
Query: 2 VMVSPALNPVAVWEFEGEILVLHHPTTISSRYQAMVHCGS-----IRQTASILSMSAECL 56
++ + V F EI I S ++H G + ++ + + +
Sbjct: 484 ILSNYENPVRRVRSFVAEIQTFDIHGPILSGSTLVLHLGRTVTSVSLKIVTVNNKRSRHI 543
Query: 57 RTGDKAAVHFRFIKHP-------EYLRAGQRMVFR-EGRTKAVGNVTKV 97
+ +A V F+ E A R + R G T A G V ++
Sbjct: 544 ASRKRALVRISFLDGLFPLCLAEEC-PALGRFILRRSGDTVAAGIVKEL 591
>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 = 44.9 bits (107), Expect = 3e-06
Identities = 19/116 (16%), Positives = 39/116 (33%), Gaps = 29/116 (25%)
Query: 9 NPV-AVWEFEGEILVLHHPTTISSRYQAMVHCGSIRQTASILSMSAE------------- 54
N + F+ +I+++ H + I Y A++H T
Sbjct: 90 NLCHSGRTFDAQIVIIEHKSIICPGYNAVLHI----HTCIEEVEITALICLVDKKSGEKS 145
Query: 55 -----CLRTGDKAAVHFRFIK------HPEYLRAGQRMVFREGRTKAVGNVTKVLP 99
++ R ++ + G+ + EG+T A+G V K++P
Sbjct: 146 KTRPRFVKQDQVCIARLRTAGTICLETFKDFPQMGRFTLRDEGKTIAIGKVLKLVP 201
>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 = 39.6 bits (93), Expect = 3e-04
Identities = 30/114 (26%), Positives = 42/114 (36%), Gaps = 28/114 (24%)
Query: 10 PVAVWEFEGEILVLHHPTTISSRYQAMVHCGSIRQTASILSMSAECL-----RTGDKAAV 64
P F ++VL+HP IS+ Y ++ C TA I E L R+G K
Sbjct: 332 PKGCASFNATVIVLNHPGQISAGYSPVLDC----HTAHIACRFDELLEKNDRRSGKKLED 387
Query: 65 HFRFIKH-------------------PEYLRAGQRMVFREGRTKAVGNVTKVLP 99
H +F+K EY G+ V +T AVG + V
Sbjct: 388 HPKFLKSGDAALVKFVPSKPMCVEAFSEYPPLGRFAVRDMRQTVAVGVIKSVDK 441
>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 = 31.8 bits (72), Expect = 0.14
Identities = 22/72 (30%), Positives = 26/72 (36%), Gaps = 9/72 (12%)
Query: 59 GDKAAVHFRFIKHPEYLRAGQRMVFREG-RTKAVGNVTKVLPP-------SGHQGNYSHL 110
GD + I HP + G R REG RT G V KVL G G S
Sbjct: 638 GDNIKMVVTLI-HPIAMDDGLRFAIREGGRTVGAGVVAKVLSGASGAAGGGGSGGGGSMS 696
Query: 111 SRTKANKMLSHR 122
+ LS +
Sbjct: 697 KTASSRNSLSAQ 708
>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 = 30.6 bits (70), Expect = 0.23
Identities = 13/43 (30%), Positives = 16/43 (37%), Gaps = 2/43 (4%)
Query: 59 GDKAAVHFRFIKHPEYLRAGQRMVFREG-RTKAVGNVTKVLPP 100
G+ + P L GQR R+G RT G VT
Sbjct: 347 GEDLKLTLILR-QPMILEKGQRFTLRDGNRTIGTGLVTDTPAM 388
>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 = 30.4 bits (68), Expect = 0.39
Identities = 32/195 (16%), Positives = 58/195 (29%), Gaps = 54/195 (27%)
Query: 25 HPTTISSRYQAMVHCGSIRQTASILSM--SAECLRTGDKAAVHFRFIKHPEYLRAGQRMV 82
P + S + TA ++ S E + A+ F ++ G R
Sbjct: 259 TPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLF-----FI--GVR-- 309
Query: 83 FREGRTKAVGNVTKVLPPSGHQGNYSHLSRTKANKMLS-----------HRAQPNKTWAL 131
+A N + LPPS + + + + + MLS + + N
Sbjct: 310 ----CYEAYPNTS--LPPSILEDSLEN-NEGVPSPMLSISNLTQEQVQDYVNKTNSH--- 359
Query: 132 SPVTEK--------PE--VKT--PRDLDRAGQAGAKRGGVEGAEPSETK--TRQPILEAG 177
P ++ + V + P+ L K G + S R+
Sbjct: 360 LPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNR 419
Query: 178 --PIS------LLRP 184
P++ LL P
Sbjct: 420 FLPVASPFHSHLLVP 434
>2k5n_A Putative cold-shock protein; GFT protein structure, PSI, nesgc, OB
fold, cold shock structural genomics; NMR
{Pectobacterium atrosepticum}
Length = 74
Score = 27.7 bits (62), Expect = 0.62
Identities = 12/55 (21%), Positives = 20/55 (36%), Gaps = 8/55 (14%)
Query: 59 GDKAAVHFRFIKHPEYLRAGQRMVFREGRTK----AVGNVTKVLPPSGHQGNYSH 109
GD H + +P+ ++ + F A V KV+P H + H
Sbjct: 24 GDNRYFHVIKVANPDLIKKDAAVTFEPTTNNKGLSAY-AV-KVVPLEHHH--HHH 74
>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 = 29.4 bits (65), Expect = 0.77
Identities = 13/73 (17%), Positives = 27/73 (36%), Gaps = 17/73 (23%)
Query: 43 RQTASI----LSMSAECLRTGDKAAVHFRFIKHPEYLRAGQRMVFREGRTKAVGNVTKVL 98
R+ + LS+ AE +R + + + V + T + + VL
Sbjct: 320 REVLTTNPRRLSIIAESIR---------DGLATWDNWK----HVNCDKLTTIIESSLNVL 366
Query: 99 PPSGHQGNYSHLS 111
P+ ++ + LS
Sbjct: 367 EPAEYRKMFDRLS 379
>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 = 28.3 bits (64), Expect = 1.6
Identities = 17/41 (41%), Positives = 18/41 (43%), Gaps = 2/41 (4%)
Query: 59 GDKAAVHFRFIKHPEYLRAGQRMVFREG-RTKAVGNVTKVL 98
GD I P L G R REG RT G VTK+L
Sbjct: 365 GDNVTFTVELI-KPVALEEGLRFAIREGGRTVGAGVVTKIL 404
>1wdi_A Hypothetical protein TT0907; structural genomics, riken
structural genomics/proteomics initiative, RSGI,
unknown function; HET: CIT; 2.10A {Thermus
thermophilus} SCOP: e.53.1.1
Length = 345
Score = 27.4 bits (62), Expect = 2.5
Identities = 15/43 (34%), Positives = 19/43 (44%), Gaps = 9/43 (20%)
Query: 57 RTGDKAAVHFRFIKHPEYLRAGQRMVFREGRTKAVGNVTKVLP 99
R G H R PE+LR G +VF N +KV+P
Sbjct: 34 REGPFRVAHKRVRDLPEFLRPGDVLVF---------NESKVIP 67
>1wb1_A Translation elongation factor SELB; selenocysteine, protein
synthesis, selenium, ribosome; HET: GDP DXC; 3.0A
{Methanococcus maripaludis} SCOP: b.43.3.1 b.43.3.1
b.44.1.1 c.37.1.8 PDB: 1wb2_A* 1wb3_A*
Length = 482
Score = 27.8 bits (62), Expect = 2.7
Identities = 12/119 (10%), Positives = 34/119 (28%), Gaps = 21/119 (17%)
Query: 2 VMVSPALNPVAVWEFEGEILVL-HHPTTISSRYQAMVHCGSIRQTASI------------ 48
++ S V + +I + ++ + + ++ G + A
Sbjct: 279 ILTSKDTKLQTVDKIVAKIKISDIFKYNLTPKMKVHLNVGMLIVPAVAVPFKKVTFGKTE 338
Query: 49 LSMSAECLRTGDKAAVHFRFIKHPEYLRAGQRMVFRE-------GRTKAVGNVTKVLPP 100
++ + +G++ F G R++ R G + + P
Sbjct: 339 ENIILNEVISGNEXYXAFELE-EKVLAEVGDRVLITRLDLPPTTLRIXGHGLIEEFKPI 396
>1yy3_A S-adenosylmethionine:tRNA ribosyltransferase- isomerase;
beta-barrel, QUEA, quein queuosine, tRNA- modification;
2.88A {Bacillus subtilis}
Length = 346
Score = 27.0 bits (61), Expect = 4.1
Identities = 9/35 (25%), Positives = 13/35 (37%), Gaps = 11/35 (31%)
Query: 65 HFRFIKHPEYLRAGQRMVFREGRTKAVGNVTKVLP 99
F+ I + G +V N T+VLP
Sbjct: 46 SFKHI--ISFFNEGDCLVL---------NNTRVLP 69
>1vky_A S-adenosylmethionine:tRNA ribosyltransferase-ISOM; TM0574, struct
genomics, JCSG, protein structure initiative, PSI;
2.00A {Thermotoga maritima} SCOP: e.53.1.1
Length = 347
Score = 26.7 bits (60), Expect = 4.7
Identities = 12/35 (34%), Positives = 16/35 (45%), Gaps = 9/35 (25%)
Query: 65 HFRFIKHPEYLRAGQRMVFREGRTKAVGNVTKVLP 99
H F + EYL G +V NV+KV+P
Sbjct: 52 HRIFREIIEYLEPGDLLVL---------NVSKVIP 77
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
0.317 0.131 0.388
Gapped
Lambda K H
0.267 0.0763 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,727,155
Number of extensions: 149821
Number of successful extensions: 262
Number of sequences better than 10.0: 1
Number of HSP's gapped: 255
Number of HSP's successfully gapped: 18
Length of query: 184
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 96
Effective length of database: 4,244,745
Effective search space: 407495520
Effective search space used: 407495520
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (24.5 bits)