RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy14785
(211 letters)
>4a17_C RPL4, ribosomal protein L3; eukaryotic ribosome, ribosome,
eukaryotic initiation factor 60S, translation, large
ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB:
4a1a_C 4a1c_C 4a1e_C
Length = 410
Score = 84.5 bits (208), Expect = 2e-19
Identities = 30/111 (27%), Positives = 51/111 (45%), Gaps = 1/111 (0%)
Query: 1 MMANTDLARLLKSEEIKKVLRRPIRGVRRASRKLNPLTNKRMMLRLNPFAQVTIRSAIIS 60
++AN D+AR++ S E++ V++ RK NPLTN + +LNP A++ A +
Sbjct: 289 LLANADIARIINSNEVQSVVK-VAGTTETHERKKNPLTNNNALFKLNPAAKIVKEQAKKA 347
Query: 61 EEKRKLAREAKLAEKRGVSTTSKSLLGVPRSAIISEEKRKLAREAKLAEKR 111
E K R+A L R + T K +A + +A+ +
Sbjct: 348 AEASKAKRQATLKANRKAAKTHKKGSQAWIAAFNKANEEAIAKARQEDADF 398
>3iz5_D 60S ribosomal protein L4 (L4P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_D
Length = 405
Score = 78.7 bits (193), Expect = 2e-17
Identities = 28/84 (33%), Positives = 49/84 (58%)
Query: 1 MMANTDLARLLKSEEIKKVLRRPIRGVRRASRKLNPLTNKRMMLRLNPFAQVTIRSAIIS 60
MAN DL R++ S+E++ V++ + V+R ++ NPL N +L+LNP+ + A ++
Sbjct: 288 KMANADLGRIINSDEVQSVVKPLNKEVKRREKRKNPLKNVAAVLKLNPYFGTARKMATLA 347
Query: 61 EEKRKLAREAKLAEKRGVSTTSKS 84
E R AR+ KL KR + ++
Sbjct: 348 EAARIKARKEKLDSKRTKLSPEEA 371
>2wwb_H 60S ribosomal protein L4-B; ribosome, protein EXIT tunnel,
cotranslational protein translocation, protein
conducting channel; 6.48A {Triticum aestivum} PDB:
2wwa_H 2ww9_H 3izc_D 3izs_D 3o58_D 3o5h_D 3u5e_C 3u5i_C
1s1i_D 3jyw_D
Length = 362
Score = 76.0 bits (186), Expect = 1e-16
Identities = 21/80 (26%), Positives = 44/80 (55%), Gaps = 2/80 (2%)
Query: 1 MMANTDLARLLKSEEIKKVLRRPIRGVRRAS--RKLNPLTNKRMMLRLNPFAQVTIRSAI 58
+++ +D+ R++ S EI+ +R + ++ + K NPL NK+++LRLNP+A+V +
Sbjct: 280 IISTSDVTRIINSSEIQSAIRPAGQATQKRTHVLKKNPLKNKQVLLRLNPYAKVFAAEKL 339
Query: 59 ISEEKRKLAREAKLAEKRGV 78
S++ K + +
Sbjct: 340 GSKKAEKTGTKPAAVFAETL 359
>2zkr_c 60S ribosomal protein L4; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 421
Score = 71.1 bits (173), Expect = 1e-14
Identities = 35/118 (29%), Positives = 55/118 (46%)
Query: 1 MMANTDLARLLKSEEIKKVLRRPIRGVRRASRKLNPLTNKRMMLRLNPFAQVTIRSAIIS 60
M NTDL+R+LK + LR P + + R K NPL N R+ML+LNP+A+ R+ I+
Sbjct: 283 KMLNTDLSRILKMPRDPRALRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILR 342
Query: 61 EEKRKLAREAKLAEKRGVSTTSKSLLGVPRSAIISEEKRKLAREAKLAEKRGVSTTSK 118
+ K R K A + K + G ++ + + K + + T K
Sbjct: 343 QAKNHKLRMDKAAAALEAKSEEKGVPGKKPRRKKGKKTVGVKKPKKPVVGKKAAATKK 400
>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 = 45.2 bits (106), Expect = 8e-06
Identities = 29/194 (14%), Positives = 57/194 (29%), Gaps = 51/194 (26%)
Query: 12 KSEEI-KKVLRRPIRGVRRASRKLNPLT-------NKRMMLRLNPFAQV------TIRSA 57
+ + + K L + + R NP + + + + V TI +
Sbjct: 302 EVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIES 361
Query: 58 II----SEEKRKLAREAKLAEKRGVSTTSKSLLGVPRSAIISEEKRKLARE---AKLAEK 110
+ E RK+ + + LL + +I + + + L EK
Sbjct: 362 SLNVLEPAEYRKMFDRLSVFPP-SAHIPTI-LLSLIWFDVIKSDVMVVVNKLHKYSLVEK 419
Query: 111 RGVSTTSKYLVGVPATFYLHH-YLYTRGGQTGNRGSHHRN--RGYAAIRKQVYPSDS--- 164
+ +T + YL + + N + HR+ Y + + SD
Sbjct: 420 QPKEST----------ISIPSIYLELKV-KLENEYALHRSIVDHYNIPKT--FDSDDLIP 466
Query: 165 -EED--------HH 169
D HH
Sbjct: 467 PYLDQYFYSHIGHH 480
Score = 37.9 bits (87), Expect = 0.002
Identities = 44/232 (18%), Positives = 78/232 (33%), Gaps = 68/232 (29%)
Query: 6 DLAR-LLKSEEIKKVLRRPIRGVRRASRKLNPLTNKRM---------MLRLN-PFAQVTI 54
D+ + +L EEI ++ V R L +K+ +LR+N F +
Sbjct: 40 DMPKSILSKEEIDHIIMSKDA-VSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKF----L 94
Query: 55 RSAIISEEKRKLAREAKLAEKRGVSTTSKSLLG---VPRSAIISEEKRKLAREAKLAEKR 111
S I +E+++ E+R + V R + KL R+A L E R
Sbjct: 95 MSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSR----LQPYLKL-RQA-LLELR 148
Query: 112 GVSTTSKYLVGVPATFYLHHYLYTRGGQTGNRGSHHRNRGYAAIRKQVYPSDSEEDH--H 169
+K ++ + G GS G K D +
Sbjct: 149 ----PAKNVL-------ID----------GVLGS-----G-----KTWVALDVCLSYKVQ 177
Query: 170 KTGNCKV-W-NVKN-----GIGKLLQR---ALGSETHFRVDPLTPDCLELEN 211
+ K+ W N+KN + ++LQ+ + R D + L + +
Sbjct: 178 CKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHS 229
>3idf_A USP-like protein; universal, stress, PSI, MCSG, structural
genomics, midwest center for structural genomics
structure initiative; 2.00A {Wolinella succinogenes}
Length = 138
Score = 28.7 bits (65), Expect = 0.85
Identities = 7/45 (15%), Positives = 16/45 (35%)
Query: 54 IRSAIISEEKRKLAREAKLAEKRGVSTTSKSLLGVPRSAIISEEK 98
I + K + + ++G++ G P ++ E K
Sbjct: 56 IEMKEEEKAKLLTQKFSTFFTEKGINPFVVIKEGEPVEMVLEEAK 100
>1mjh_A Protein (ATP-binding domain of protein MJ0577); hypothetical
protein, structural genomics, functional assignment;
HET: ATP; 1.70A {Methanocaldococcus jannaschii} SCOP:
c.26.2.4
Length = 162
Score = 28.1 bits (63), Expect = 1.6
Identities = 14/60 (23%), Positives = 24/60 (40%), Gaps = 11/60 (18%)
Query: 54 IRSAIISEEKRKLAREAKLAEKRGVSTTSKSLLGVPRSAIISEEKRKLAREAKLAEKRGV 113
+++ + E K K+ K E G ++G+P I+ K+AE GV
Sbjct: 73 LKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIV-----------KIAEDEGV 121
Score = 26.1 bits (58), Expect = 6.6
Identities = 15/77 (19%), Positives = 29/77 (37%)
Query: 50 AQVTIRSAIISEEKRKLAREAKLAEKRGVSTTSKSLLGVPRSAIISEEKRKLAREAKLAE 109
+V + I E +K + L G++ + + ++ + E K K+ K E
Sbjct: 34 EEVILLHVIDEREIKKRDIFSLLLGVAGLNKSVEEFENELKNKLTEEAKNKMENIKKELE 93
Query: 110 KRGVSTTSKYLVGVPAT 126
G +VG+P
Sbjct: 94 DVGFKVKDIIVVGIPHE 110
>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 = 28.5 bits (63), Expect = 2.2
Identities = 18/96 (18%), Positives = 29/96 (30%), Gaps = 39/96 (40%)
Query: 50 AQVTIRSAIISEEKRKLAR---EAKLAEKRGVSTTSKSLLGVPRSAIISEEKRKLAREAK 106
A++ + + ++L + A++ KR S S L R+ A+
Sbjct: 106 AKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALF--RAV--------GEGNAQ 155
Query: 107 LAEKRGVSTTSKYLVGVPATFYLHHYLYTRGGQTGN 142
L A F GGQ GN
Sbjct: 156 LV----------------AIF---------GGQ-GN 165
>3fdx_A Putative filament protein / universal stress PROT; structural
genomics, APC60640.1, universal protein F, PSI-2; HET:
MSE ATP; 1.58A {Klebsiella pneumoniae subsp} PDB:
3fh0_A*
Length = 143
Score = 26.4 bits (59), Expect = 5.0
Identities = 9/59 (15%), Positives = 18/59 (30%), Gaps = 5/59 (8%)
Query: 46 LNPFAQVTIRSAIISEEKRKLAREAKLAEKRGVSTTSKSLLGVPRSAIISEEKRKLARE 104
+ A++ + + +L AK G P+ I+ LA+
Sbjct: 51 MAYTAELPGMDELREGSETQLKEIAKKFSIPEDRMHFHVAEGSPKDKIL-----ALAKS 104
>2gm3_A Unknown protein; AT3G01520, putative ethylene-responsive protein,
USP domain, nucleotide binding domain, AMP; HET: MSE
AMP; 2.46A {Arabidopsis thaliana} SCOP: c.26.2.4
Length = 175
Score = 25.9 bits (57), Expect = 8.7
Identities = 10/46 (21%), Positives = 17/46 (36%)
Query: 54 IRSAIISEEKRKLAREAKLAEKRGVSTTSKSLLGVPRSAIISEEKR 99
+R + ++ L + GV + G P+ I E KR
Sbjct: 77 MRQSNKAKGLHLLEFFVNKCHEIGVGCEAWIKTGDPKDVICQEVKR 122
>1gh6_A Large T antigen; tumor suppressor, oncoprotein, antitumor protein;
3.20A {Simian virus 40} SCOP: a.2.3.1
Length = 114
Score = 25.2 bits (55), Expect = 9.9
Identities = 8/25 (32%), Positives = 11/25 (44%), Gaps = 5/25 (20%)
Query: 85 LLGVPRSAIISEEK-----RKLARE 104
LLG+ RSA + K +E
Sbjct: 13 LLGLERSAWGNIPLMRKAYLKKCKE 37
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 0.132 0.371
Gapped
Lambda K H
0.267 0.0485 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,284,754
Number of extensions: 193028
Number of successful extensions: 505
Number of sequences better than 10.0: 1
Number of HSP's gapped: 499
Number of HSP's successfully gapped: 26
Length of query: 211
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 122
Effective length of database: 4,216,824
Effective search space: 514452528
Effective search space used: 514452528
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: 55 (25.6 bits)