RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy732
(119 letters)
>3pm9_A Putative oxidoreductase; putative D-2-hydroxyglutarate
dehydrogenase, putative D-LACT dehydrogenase; HET: FAD;
2.57A {Rhodopseudomonas palustris}
Length = 476
Score = 89.9 bits (224), Expect = 2e-22
Identities = 25/95 (26%), Positives = 40/95 (42%), Gaps = 1/95 (1%)
Query: 9 LGSCVDHDAEKLNTFLQDGIENNIILDAVMCSEESKIQKIWPLRERIVESCLKDGYIYNY 68
L S D L + L+ G E+ I++DA + + + Q W LRE I + +G +
Sbjct: 295 LSSPRDDARAALESILERGFEDGIVVDAAIANSVQQQQAFWKLREEISPAQKPEGGSIKH 354
Query: 69 DISLSLKDFYSIIPIMKERLKDQ-PVVTVCGYGHL 102
DIS+ + I + P +GHL
Sbjct: 355 DISVPVAAVPQFIEQANAAVVALIPGARPVPFGHL 389
>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 = 37.7 bits (87), Expect = 4e-04
Identities = 25/121 (20%), Positives = 43/121 (35%), Gaps = 25/121 (20%)
Query: 14 DHDAEKLNTFLQDGIENNIILDAVMCSEESKIQKIWPLRER----IVESCLKDGYIY--- 66
+H + + D + NN + + E K ++I RE I E+ + DG +
Sbjct: 1651 NHFKDTYGFSILDIVINNPVNLTIHFGGE-KGKRI---RENYSAMIFETIV-DGKLKTEK 1705
Query: 67 ---NYDISLSLKDFYSIIPIMKERLKD----QPVVTVCGYGHLERLKDQPVVTVCGY--G 117
+ + F S K L QP +T+ E LK + ++ G
Sbjct: 1706 IFKEINEHSTSYTFRS--E--KGLLSATQFTQPALTLMEKAAFEDLKSKGLIPADATFAG 1761
Query: 118 H 118
H
Sbjct: 1762 H 1762
>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 = 30.2 bits (67), Expect = 0.15
Identities = 13/75 (17%), Positives = 28/75 (37%), Gaps = 17/75 (22%)
Query: 11 SCVDHDAEKLNTFL---QDGIENNIILDAVMCSEESKIQKIWPLRERIVES--------- 58
S V KL+ + + E+ I + ++ + K++ + L IV+
Sbjct: 402 SDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDS 461
Query: 59 --CLK---DGYIYNY 68
+ D Y Y++
Sbjct: 462 DDLIPPYLDQYFYSH 476
Score = 29.8 bits (66), Expect = 0.21
Identities = 21/140 (15%), Positives = 38/140 (27%), Gaps = 48/140 (34%)
Query: 20 LNTFLQDGIEN---NIILD---AVMCSEE--------SKIQK----IWPLR-------ER 54
L+ F ++N + D +++ EE + W L ++
Sbjct: 22 LSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQK 81
Query: 55 IVESCLKDGY-------------------IYNYDISLSLKDFYSIIPIMKERLKDQPVVT 95
VE L+ Y +Y D RL+ P +
Sbjct: 82 FVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQ--PYLK 139
Query: 96 VCGYGHLERLKDQPVVTVCG 115
+ L L+ V + G
Sbjct: 140 L--RQALLELRPAKNVLIDG 157
Score = 28.7 bits (63), Expect = 0.44
Identities = 22/135 (16%), Positives = 36/135 (26%), Gaps = 35/135 (25%)
Query: 16 DAEKLNTFLQDGIENNIILDA-------VMCS---EESKI-----QKIWP-----LRERI 55
+ +KL T ++ + L+ S + I IW +
Sbjct: 351 NCDKLTTIIESSLNV---LEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVV 407
Query: 56 VESCL---------KDGYIYNYDISLSLKDFYSIIPIMKERLKDQ--PVVTVCGYGHLER 104
V K+ I I L LK + + D T +
Sbjct: 408 VNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPP 467
Query: 105 LKDQPVVTVCGYGHL 119
DQ + G+ HL
Sbjct: 468 YLDQYFYSHIGH-HL 481
>2f1z_A Ubiquitin carboxyl-terminal hydrolase 7; hausp, USP7, UBP,
deubiquitinating enzyme, substrate recognition; 3.20A
{Homo sapiens}
Length = 522
Score = 28.4 bits (63), Expect = 0.50
Identities = 19/71 (26%), Positives = 30/71 (42%), Gaps = 9/71 (12%)
Query: 15 HDAEKLNTFLQDGIENNIILDAVMCSEESKIQKIWPLRERIVESCLKDGYIYN-----YD 69
HD ++L L D +EN + E I K++ + C + Y + YD
Sbjct: 256 HDVQELCRVLLDNVENKM----KGTCVEGTIPKLFRGKMVSYIQCKEVDYRSDRREDYYD 311
Query: 70 ISLSLKDFYSI 80
I LS+K +I
Sbjct: 312 IQLSIKGKKNI 322
>3dcy_A Regulator protein; OMIM 610775, C12ORF5, tigar, TP53-induced
glycolysis and apoptosis regulator, CAsp target,
structural genomics medical relevance; HET: MSE; 1.75A
{Homo sapiens}
Length = 275
Score = 26.7 bits (59), Expect = 1.8
Identities = 6/24 (25%), Positives = 12/24 (50%)
Query: 31 NIILDAVMCSEESKIQKIWPLRER 54
+ IL+ ++ ++ LRER
Sbjct: 72 HGILERSKFCKDMTVKYDSRLRER 95
>1mzh_A Deoxyribose-phosphate aldolase; alpha-beta barrel, structural
genomics, PSI, protein structure initiative; 2.00A
{Aquifex aeolicus} SCOP: c.1.10.1
Length = 225
Score = 26.0 bits (58), Expect = 3.2
Identities = 5/30 (16%), Positives = 10/30 (33%), Gaps = 6/30 (20%)
Query: 76 DFYSI------IPIMKERLKDQPVVTVCGY 99
Y++ + + K V V G+
Sbjct: 33 GIYAVCVNPYHVKLASSIAKKVKVCCVIGF 62
>1vcv_A Probable deoxyribose-phosphate aldolase; DERA, hyperthermophIle,
archaea, lyase; 2.00A {Pyrobaculum aerophilum} SCOP:
c.1.10.1
Length = 226
Score = 25.7 bits (57), Expect = 3.5
Identities = 3/29 (10%), Positives = 9/29 (31%), Gaps = 6/29 (20%)
Query: 76 DFYSI------IPIMKERLKDQPVVTVCG 98
+ P+++ L+ + V
Sbjct: 30 GVAAYCVNPIYAPVVRPLLRKVKLCVVAD 58
>3cw2_C Translation initiation factor 2 subunit alpha; AIF2, intact AIF2,
initiation factor 2 alpha subunit, initiation factor 2
beta subunit; 2.80A {Sulfolobus solfataricus} PDB:
2aho_B 3v11_B*
Length = 266
Score = 25.3 bits (55), Expect = 6.1
Identities = 11/83 (13%), Positives = 30/83 (36%), Gaps = 13/83 (15%)
Query: 38 MCSEESKIQKIWPLRERI------VESCLKDGYIYNYDISLSLKDFYSIIPIMKERLKDQ 91
+ +++ Q W L + +E +K+G D + ++ + +++
Sbjct: 116 LSEKDAWEQVAWKLEAKYGDPITAIEKAVKEGEKILIDAGVPEIWVKPLLEEASKHAEER 175
Query: 92 PV-------VTVCGYGHLERLKD 107
V V +E++K+
Sbjct: 176 KVKMSGLITVRTNEPLGVEKIKE 198
>1nb8_A Ubiquitin carboxyl-terminal hydrolase 7; UBP, deubiquitination,
hausp, P53 binding; 2.30A {Homo sapiens} SCOP: d.3.1.9
PDB: 1nbf_A
Length = 353
Score = 25.2 bits (55), Expect = 6.4
Identities = 20/73 (27%), Positives = 31/73 (42%), Gaps = 13/73 (17%)
Query: 15 HDAEKLNTFLQDGIENNIILDAVMCSEESKIQKIW--PLRERIVESCLKDGYIYN----- 67
HD ++L L D +EN + E I K++ + I C + Y +
Sbjct: 87 HDVQELCRVLLDNVENKM----KGTCVEGTIPKLFRGKMVSYIQ--CKEVDYRSDRREDY 140
Query: 68 YDISLSLKDFYSI 80
YDI LS+K +I
Sbjct: 141 YDIQLSIKGKKNI 153
>3h0g_E DNA-directed RNA polymerases I, II, and III subunit rpabc1;
transcription, multi-protein complex, DNA- binding,
magnesium; 3.65A {Schizosaccharomyces pombe}
Length = 210
Score = 25.0 bits (54), Expect = 6.6
Identities = 11/61 (18%), Positives = 24/61 (39%), Gaps = 1/61 (1%)
Query: 38 MCSEESKIQKIWPLRERIVESCLKDGY-IYNYDISLSLKDFYSIIPIMKERLKDQPVVTV 96
M +EE I +++ + + GY + ++ L+L F ++ M L +
Sbjct: 1 MSAEEKNIVRVFRAWKTAHQLVHDRGYGVSQAELDLTLDQFKAMHCGMGRNLDRTTLSFY 60
Query: 97 C 97
Sbjct: 61 A 61
>3fz2_A Minor tail protein U; mixed alpha-beta fold, viral protein; 2.70A
{Enterobacteria phage lambda} PDB: 3fzb_A 1z1z_A
Length = 134
Score = 24.7 bits (53), Expect = 7.2
Identities = 11/36 (30%), Positives = 15/36 (41%)
Query: 34 LDAVMCSEESKIQKIWPLRERIVESCLKDGYIYNYD 69
LDA M S + P ++ S + GY Y D
Sbjct: 80 LDAWMESRIYPVMSDIPALSDLITSMVASGYDYRRD 115
>2rdo_7 EF-G, elongation factor G; elongation factor G, EF-G, RRF, GDPNP,
50S subunit, cryo-EM, REAL-space refinement,
ribonucleoprotein; 9.10A {Escherichia coli} PDB: 3j0e_H
Length = 704
Score = 24.8 bits (55), Expect = 9.6
Identities = 6/19 (31%), Positives = 10/19 (52%)
Query: 76 DFYSIIPIMKERLKDQPVV 94
+F ++ +K RL PV
Sbjct: 150 NFLKVVNQIKTRLGANPVP 168
>1dar_A EF-G, elongation factor G; ribosomal translocase, translational
GTPase; HET: GDP; 2.40A {Thermus thermophilus} SCOP:
b.43.3.1 c.37.1.8 d.14.1.1 d.58.11.1 PDB: 1elo_A 1ktv_A
2om7_L* 2wri_Y* 2wrk_Y* 2xsy_Y* 2xuy_Y* 2j7k_A* 2efg_A*
1jqm_B 1efg_A* 1fnm_A* 1pn6_A 2bm1_A* 2bm0_A* 2bv3_A*
3izp_E 1zn0_B 1jqs_C 2bcw_C ...
Length = 691
Score = 24.8 bits (55), Expect = 9.9
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 76 DFYSIIPIMKERLKDQPVV 94
D + +I M+ERL +PVV
Sbjct: 145 DLWLVIRTMQERLGARPVV 163
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
0.325 0.144 0.460
Gapped
Lambda K H
0.267 0.0799 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,935,248
Number of extensions: 103865
Number of successful extensions: 342
Number of sequences better than 10.0: 1
Number of HSP's gapped: 337
Number of HSP's successfully gapped: 23
Length of query: 119
Length of database: 6,701,793
Length adjustment: 81
Effective length of query: 38
Effective length of database: 4,440,192
Effective search space: 168727296
Effective search space used: 168727296
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (23.3 bits)