RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy9255
(127 letters)
>3ir9_A Peptide chain release factor subunit 1; structural genomics,
APC36528.1, C-terminal domain, PSI-2, protein structure
initiative; 2.21A {Methanosarcina mazei}
Length = 166
Score = 72.0 bits (176), Expect = 3e-17
Identities = 21/106 (19%), Positives = 40/106 (37%), Gaps = 2/106 (1%)
Query: 11 YLGRYPAVQDLVGKYEILNYERDMDLLFNNIGKYFDEISQDTGKYCFGVEDTLRALELGS 70
Y + +LV + ++ N + +F E+ D+GK +G LE+ S
Sbjct: 4 YTDES-GLSELVNAAGEKLQDLELMGQKNAVRDFFKELIADSGKVAYGESQVRANLEINS 62
Query: 71 VETLICWENLDIQRYVLKNHSTS-EDRVLHLTPEQEKDKSHFTDKE 115
V+ L+ E+L +R K E++ E + +
Sbjct: 63 VDVLLLSEDLRAERVTTKCSVCGYENKWTRRWKPGEPAPAAGNCPK 108
>1dt9_A ERF1, protein (eukaryotic peptide chain release factor subunit 1);
tRNA mimicry, protein sythesis, STOP codon recognition,
peptidyl-tRNA hydrolysis; 2.70A {Homo sapiens} SCOP:
c.55.4.2 d.79.3.2 d.91.1.1 PDB: 3e1y_A* 2ktu_A 2ktv_A
2lgt_A 2hst_A
Length = 437
Score = 74.3 bits (181), Expect = 7e-17
Identities = 58/90 (64%), Positives = 68/90 (75%)
Query: 31 ERDMDLLFNNIGKYFDEISQDTGKYCFGVEDTLRALELGSVETLICWENLDIQRYVLKNH 90
IG+YFDEISQDTGKYCFGVEDTL+ALE+G+VE LI +ENLDI RYVL
Sbjct: 277 NVKFIQEKKLIGRYFDEISQDTGKYCFGVEDTLKALEMGAVEILIVYENLDIMRYVLHCQ 336
Query: 91 STSEDRVLHLTPEQEKDKSHFTDKEMLTDL 120
T E+++L+LTPEQEKDKSHFTDKE +
Sbjct: 337 GTEEEKILYLTPEQEKDKSHFTDKETGQEH 366
>3e20_C Eukaryotic peptide chain release factor subunit 1; SUP35, SUP45,
translation termination, peptide release, GTP-
nucleotide-binding; 3.50A {Schizosaccharomyces pombe}
Length = 441
Score = 64.3 bits (155), Expect = 2e-13
Identities = 38/122 (31%), Positives = 56/122 (45%), Gaps = 2/122 (1%)
Query: 1 MRKYFKDKHKYLGRYPAVQDLVGKYEILNYERDMDLLFNNIGKYFDEISQDTGKYCFGVE 60
+ K G + I ++FDEIS D+GKYCFGV
Sbjct: 252 QSRIIKTVDVSYGGDAGFNQAIELAADTLSNVKYVQEKKLIQRFFDEISLDSGKYCFGVV 311
Query: 61 DTLRALELGSVETLICWENLDIQRYVLKNHSTSEDRVLHLTPEQEKD--KSHFTDKEMLT 118
DT+ AL+ G+VETL+C+ +LD+ RY KN + ++EKD S DK+
Sbjct: 312 DTMNALQEGAVETLLCFADLDMIRYEFKNSEGNPVITYMTKEQEEKDSTNSFLLDKDTGA 371
Query: 119 DL 120
++
Sbjct: 372 EM 373
>1x52_A Pelota homolog, CGI-17; ERF1_3 domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: d.79.3.2
Length = 124
Score = 55.1 bits (133), Expect = 4e-11
Identities = 8/65 (12%), Positives = 26/65 (40%), Gaps = 7/65 (10%)
Query: 16 PAVQDLVGKYEILNYERDMDLLFNNIGKYFDEISQDTGKYCFGVEDTLRALELGSVETLI 75
V + + + +D ++ + + + +G++ +A E +++TL+
Sbjct: 7 GTVASRLSDTKAAGEVKALD-------DFYKMLQHEPDRAFYGLKQVEKANEAMAIDTLL 59
Query: 76 CWENL 80
+ L
Sbjct: 60 ISDEL 64
>3agk_A Peptide chain release factor subunit 1; translation; 2.10A
{Aeropyrum pernix}
Length = 373
Score = 46.9 bits (110), Expect = 3e-07
Identities = 18/90 (20%), Positives = 44/90 (48%)
Query: 17 AVQDLVGKYEILNYERDMDLLFNNIGKYFDEISQDTGKYCFGVEDTLRALELGSVETLIC 76
+++ V K E + + N + ++ +++ TG +G +D ALE+G+V+TL+
Sbjct: 262 GLKEAVMKAEKVVEAQMYRDAVNAMEEFKLHLAKGTGMIVYGEKDVEAALEMGAVKTLLI 321
Query: 77 WENLDIQRYVLKNHSTSEDRVLHLTPEQEK 106
E+ + ++ +S +V+ + +
Sbjct: 322 HESREDLEEWVEKAKSSGAQVIVVPESLAE 351
>2vgn_A DOM34; translation termination factor, protein biosynthesis,
translation regulation, cell division, mRNA degradation;
2.5A {Saccharomyces cerevisiae} SCOP: b.38.4.1 c.55.4.2
d.79.3.2 PDB: 2vgm_A 3izq_0 3j16_A*
Length = 386
Score = 47.0 bits (111), Expect = 3e-07
Identities = 10/67 (14%), Positives = 28/67 (41%), Gaps = 7/67 (10%)
Query: 14 RYPAVQDLVGKYEILNYERDMDLLFNNIGKYFDEISQDTGKYCFGVEDTLRALELGSVET 73
+ P + + MD ++ +++D K +G ++ ++A E G++
Sbjct: 264 KNPLYASKLQDTKYSKEIMVMD-------EFLLHLNKDDDKAWYGEKEVVKAAEYGAISY 316
Query: 74 LICWENL 80
L+ + +
Sbjct: 317 LLLTDKV 323
>3mca_B Protein DOM34, elongation factor 1 alpha-like protein; protein
protein complex, translation regulation; 2.74A
{Schizosaccharomyces pombe}
Length = 390
Score = 45.9 bits (108), Expect = 6e-07
Identities = 16/68 (23%), Positives = 35/68 (51%), Gaps = 7/68 (10%)
Query: 14 RYPAVQDLVGKYEILNYERDMDLLFNNIGKYFDEISQDTGKYCFGVEDTLRALELGSVET 73
+ PAV+ + + + R ++ K++D +++D K +G L+A ELG++
Sbjct: 258 KDPAVESKLADTKYVQEIRVLN-------KFYDVMNEDDRKAWYGPNHVLKAFELGAIGE 310
Query: 74 LICWENLD 81
L+ ++L
Sbjct: 311 LLISDSLF 318
>3obw_A Protein pelota homolog; SM fold, hydrolase; 2.60A {Sulfolobus
solfataricus}
Length = 364
Score = 44.0 bits (103), Expect = 3e-06
Identities = 17/91 (18%), Positives = 38/91 (41%), Gaps = 13/91 (14%)
Query: 16 PAVQDLVGKYEILNYERDMDLLFNNIGKYFDEISQDTGKYCFGVEDTLRALELGSVETLI 75
+ ++ YEI + M+ K + +++ +G+E A+E+G+VET++
Sbjct: 254 DIIDKIMTDYEIAIGAKKME-------KAMELLAKQPELVTYGLEQVKNAIEMGAVETVL 306
Query: 76 CWENLDIQRYVLKNHSTSEDRVLHLTPEQEK 106
E+L L + + + + E
Sbjct: 307 VIEDL------LSSDEQERLTIERMLEDIEN 331
>3j15_A Protein pelota; ribosome recycling, ribosome, archaea,
translation-transport complex; HET: ADP; 6.60A
{Pyrococcus furiosus}
Length = 357
Score = 43.2 bits (101), Expect = 5e-06
Identities = 13/80 (16%), Positives = 32/80 (40%), Gaps = 7/80 (8%)
Query: 16 PAVQDLVGKYEILNYERDMDLLFNNIGKYFDEISQDTGKYCFGVEDTLRALELGSVETLI 75
V + + + + ++ K + I+++ G +G+++ A+ G+VETL+
Sbjct: 249 GVVDRVYQENRVAKEVQLVE-------KVLENIARNNGLVAYGLKEVEEAVNYGAVETLL 301
Query: 76 CWENLDIQRYVLKNHSTSED 95
+ L K +
Sbjct: 302 VLDELLKGELREKVEELMDA 321
>3agj_B Protein pelota homolog; GTP binding, translation-hydrolase complex;
HET: GTP; 2.30A {Aeropyrum pernix}
Length = 358
Score = 42.8 bits (100), Expect = 7e-06
Identities = 9/65 (13%), Positives = 28/65 (43%), Gaps = 7/65 (10%)
Query: 16 PAVQDLVGKYEILNYERDMDLLFNNIGKYFDEISQDTGKYCFGVEDTLRALELGSVETLI 75
+V ++ + I+ E ++ ++ I++ + + L +G+V+T++
Sbjct: 241 ESVTRILRELSIVEAEGVLE-------EFLRRIAKSRDTVAYTPGEVLAVARMGAVDTVL 293
Query: 76 CWENL 80
+ L
Sbjct: 294 LVDTL 298
>2qi2_A Pelota, cell division protein pelota related protein; DOM34, cell
cycle; 2.90A {Thermoplasma acidophilum} SCOP: b.38.4.1
c.55.4.2 d.79.3.2
Length = 347
Score = 35.5 bits (81), Expect = 0.002
Identities = 15/75 (20%), Positives = 31/75 (41%), Gaps = 13/75 (17%)
Query: 16 PAVQDLVGKYEILNYERDMDLLFNNIGKYFDEISQDTGKYCFGVEDTLRALELGSVETLI 75
L+ I + +D ++ + +D G Y G + T AL++G++ LI
Sbjct: 236 ADGAKLLSNERIARDKEIVD-------EFLVAVKKDMGVY--GRDQTESALQMGALSDLI 286
Query: 76 CWENL----DIQRYV 86
+ + D +R +
Sbjct: 287 ITDEMFRTEDGRRSL 301
>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 = 35.8 bits (82), Expect = 0.002
Identities = 18/93 (19%), Positives = 29/93 (31%), Gaps = 31/93 (33%)
Query: 19 QDLVGKYEILNYERDMDLLFNNIGKYFDEISQDTGKYCF-GVEDTLR-------ALELGS 70
+ + Y + +E +D K F EI++ + Y F + L AL L
Sbjct: 1682 KRIRENYSAMIFETIVDG-KLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLME 1740
Query: 71 VETLICWENLDIQRYVLKN------------HS 91
+E LK+ HS
Sbjct: 1741 K---AAFE-------DLKSKGLIPADATFAGHS 1763
Score = 35.4 bits (81), Expect = 0.003
Identities = 23/138 (16%), Positives = 39/138 (28%), Gaps = 53/138 (38%)
Query: 2 RKYFKDKHKYLGR----------YPAVQDLVGKYEILNYERDMDLLFN---NIGKYFDEI 48
+ Y + R + AV + G ++ +F N YF+E+
Sbjct: 124 KNYITARI-MAKRPFDKKSNSALFRAVGE--GNAQL--V-----AIFGGQGNTDDYFEEL 173
Query: 49 SQDTGKYCFGVEDTLRALELGSVETLICWENLDIQRYVLKNHSTSEDRVLHLTPEQEKDK 108
+D Y T L V LI S + + L +
Sbjct: 174 -RDL--Y-----QTYHVL----VGDLI---------------KFSAETLSELIRTTLDAE 206
Query: 109 SHFTDKEMLTDLLSLLQQ 126
FT ++L L+
Sbjct: 207 KVFTQG---LNILEWLEN 221
>3oby_A Protein pelota homolog; SM fold, hydrolase; 2.90A {Archaeoglobus
fulgidus}
Length = 352
Score = 35.5 bits (81), Expect = 0.002
Identities = 9/65 (13%), Positives = 26/65 (40%), Gaps = 8/65 (12%)
Query: 16 PAVQDLVGKYEILNYERDMDLLFNNIGKYFDEISQDTGKYCFGVEDTLRALELGSVETLI 75
V +VG+ + +D + + I++ + +G+++ A ++E L+
Sbjct: 235 RVVDKIVGEVRLAEEAEYID-------RLLEGIAKG-ERVAYGLDEVREAHNYRAIEVLL 286
Query: 76 CWENL 80
+
Sbjct: 287 VADEF 291
>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 = 0.46
Identities = 27/135 (20%), Positives = 55/135 (40%), Gaps = 24/135 (17%)
Query: 4 YFKDKHKYLGRYPAVQDLVGKYEIL-NYERDMDLLFNNIGKYFDEISQDTGKYCFGVEDT 62
Y + K K Y + +V Y I ++ D DL+ + +YF Y +
Sbjct: 432 YLELKVKLENEYALHRSIVDHYNIPKTFDSD-DLIPPYLDQYF---------YSH-IGHH 480
Query: 63 LRALELGSVETLICWENLDIQRYV---LKNHSTSEDR---VLHLTPEQEKDKSHFTDKE- 115
L+ +E TL LD R++ +++ ST+ + +L+ + + K + D +
Sbjct: 481 LKNIEHPERMTLFRMVFLDF-RFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDP 539
Query: 116 ----MLTDLLSLLQQ 126
++ +L L +
Sbjct: 540 KYERLVNAILDFLPK 554
Score = 26.0 bits (56), Expect = 4.3
Identities = 12/57 (21%), Positives = 24/57 (42%), Gaps = 4/57 (7%)
Query: 51 DTGKYCFGVEDTLRALELGSVETLICWENLDIQRYVLKNHSTSE-DRVLHLTPEQEK 106
+TG++ + +D L E V+ C + D+ + +L S E D ++
Sbjct: 10 ETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSIL---SKEEIDHIIMSKDAVSG 63
>1w41_A 50S ribosomal protein L30E; electrostatic interactions,
thermostability, protein engineering; 1.7A
{Thermococcus celer} SCOP: d.79.3.1 PDB: 3n4y_A 3lfo_A
1w40_A 1go0_A 1go1_A 1h7m_A 1w42_A 1w3e_X 3ra6_A 3ra5_A
3n4z_A 2bo1_A
Length = 101
Score = 26.3 bits (58), Expect = 1.6
Identities = 9/35 (25%), Positives = 16/35 (45%)
Query: 50 QDTGKYCFGVEDTLRALELGSVETLICWENLDIQR 84
QDTGK G +++ ++G + +I N
Sbjct: 12 QDTGKIVMGARKSIQYAKMGGAKLIIVARNARPDI 46
>3ks9_A Mglur1, metabotropic glutamate receptor 1; glutamate receptors,
dimerization, glutamic acid BIN structural genomics,
structural genomics consortium; HET: Z99 NAG; 1.90A
{Homo sapiens} PDB: 1ewk_A* 1ewt_A* 1ewv_A 1isr_A*
1iss_A* 3lmk_A*
Length = 496
Score = 26.7 bits (59), Expect = 2.4
Identities = 6/27 (22%), Positives = 14/27 (51%), Gaps = 2/27 (7%)
Query: 20 DLVGKYEILNYERDMD--LLFNNIGKY 44
D G+Y+I+N + + ++G +
Sbjct: 447 DAPGRYDIMNLQYTEANRYDYVHVGTW 473
>3mq4_A Mglur7, metabotropic glutamate receptor 7; glutamate receptors,
dimerization, glutamic acid BIN structural genomics,
structural genomics consortium; HET: Z99; 2.80A {Homo
sapiens} PDB: 2e4z_A*
Length = 481
Score = 26.4 bits (58), Expect = 3.3
Identities = 9/32 (28%), Positives = 16/32 (50%), Gaps = 2/32 (6%)
Query: 20 DLVGKYEILNYERDMD--LLFNNIGKYFDEIS 49
D G+Y+I Y+ + IG++ DE+
Sbjct: 440 DAPGRYDIFQYQTTNTSNPGYRLIGQWTDELQ 471
>1a2o_A CHEB methylesterase; bacterial chemotaxis, adaptation, serine
hydrolase; 2.40A {Salmonella typhimurium} SCOP: c.23.1.1
c.40.1.1
Length = 349
Score = 25.9 bits (58), Expect = 4.4
Identities = 10/15 (66%), Positives = 13/15 (86%)
Query: 58 GVEDTLRALELGSVE 72
G E TLRALELG+++
Sbjct: 89 GSEVTLRALELGAID 103
>3t8y_A CHEB, chemotaxis response regulator protein-glutamate
methylesterase; CHEA, hydrolase; 1.90A {Thermotoga
maritima}
Length = 164
Score = 25.3 bits (56), Expect = 6.0
Identities = 6/15 (40%), Positives = 9/15 (60%)
Query: 58 GVEDTLRALELGSVE 72
G T+ AL G+V+
Sbjct: 111 GAAITIEALRNGAVD 125
>3kyj_B CHEY6 protein, putative histidine protein kinase; protein-protein
interaction, histidine kinase, response regulator,
phosphorylation; 1.40A {Rhodobacter sphaeroides} PDB:
3kyi_B*
Length = 145
Score = 24.9 bits (55), Expect = 7.1
Identities = 6/15 (40%), Positives = 7/15 (46%)
Query: 58 GVEDTLRALELGSVE 72
G RA ELG+
Sbjct: 100 GSPHAARARELGADG 114
>3mqm_A Probable histone-lysine N-methyltransferase ASH1L; KIAA1420,
absent small and homeotic disks prote homolog, lysine
N-methyltransferase 2H, KMT2H; 2.54A {Homo sapiens}
Length = 126
Score = 24.2 bits (53), Expect = 9.5
Identities = 9/29 (31%), Positives = 15/29 (51%), Gaps = 1/29 (3%)
Query: 23 GKYEILN-YERDMDLLFNNIGKYFDEISQ 50
G Y+ + ++ DM +F N KY+ S
Sbjct: 68 GYYKTVEAFDADMLKVFRNAEKYYGRKSP 96
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
0.319 0.138 0.403
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: 1,928,383
Number of extensions: 106816
Number of successful extensions: 243
Number of sequences better than 10.0: 1
Number of HSP's gapped: 242
Number of HSP's successfully gapped: 38
Length of query: 127
Length of database: 6,701,793
Length adjustment: 83
Effective length of query: 44
Effective length of database: 4,384,350
Effective search space: 192911400
Effective search space used: 192911400
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 (21.7 bits)
S2: 51 (23.4 bits)