RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3887
(250 letters)
>2q80_A Geranylgeranyl pyrophosphate synthetase; isoprenoid pathway,
isopentenyl transferase, structural GENO structural
genomics consortium, SGC; HET: GRG; 2.70A {Homo sapiens}
SCOP: a.128.1.1
Length = 301
Score = 60.3 bits (147), Expect = 5e-11
Identities = 25/37 (67%), Positives = 31/37 (83%)
Query: 177 ALSQIAEQLLELHRGQGMEIYWRDNYTCPSEEEYRTM 213
A+ QLLELH+GQG++IYWRDNYTCP+EEEY+ M
Sbjct: 112 AVKLFTRQLLELHQGQGLDIYWRDNYTCPTEEEYKAM 148
>2e8v_A Geranylgeranyl pyrophosphate synthetase; prenyltransferase,
farnesyl pyrophosphate, bisphosphonate; HET: GRG; 1.80A
{Saccharomyces cerevisiae} PDB: 2e8t_A* 2e8u_A* 2dh4_A*
2e8w_A* 2e8x_A* 2e90_A* 2e91_A* 2e92_A* 2e93_A* 2e94_A*
2e95_A* 2z4v_A* 2z4w_A* 2z4x_A* 2z4y_A* 2z4z_A* 2z50_A*
2z52_A* 2z78_A* 2z7h_A* ...
Length = 340
Score = 55.9 bits (135), Expect = 2e-09
Identities = 17/39 (43%), Positives = 25/39 (64%), Gaps = 2/39 (5%)
Query: 177 ALSQIAEQLLELHRGQGMEIYWRDNY--TCPSEEEYRTM 213
++ E+L+ LHRGQG++IYWRD P++E Y M
Sbjct: 132 LITIFNEELINLHRGQGLDIYWRDFLPEIIPTQEMYLNM 170
>2her_A Fragment, farnesyl pyrophosphate synthase; farnesyl diphosphate
synthase, structural genomics, structural genomics
consortium, SGC; HET: ZOL; 2.37A {Cryptosporidium
parvum} PDB: 2o1o_A* 2q58_A*
Length = 368
Score = 44.8 bits (106), Expect = 1e-05
Identities = 11/69 (15%), Positives = 25/69 (36%), Gaps = 4/69 (5%)
Query: 146 LSGIALSQIALKVGLSLYESSLLLSRPLSGIALSQIAEQLLELHRGQGMEIYWRD-NYTC 204
L ++L + ++E S + + E + GQ +++ + D +
Sbjct: 141 NDIFFLKMLSLSL---IFELSSVFGNDIVMKIQKIYNESIFFTVLGQHLDLSYFDLSKAD 197
Query: 205 PSEEEYRTM 213
E Y +M
Sbjct: 198 KISERYFSM 206
>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 = 42.0 bits (98), Expect = 2e-04
Identities = 54/268 (20%), Positives = 74/268 (27%), Gaps = 117/268 (43%)
Query: 29 GFV----EAVYGFSHRLCLRVDTALQSDKTFEKYRERILEPN------ASLLRSGD--LA 76
G+V E L L FE LE N A LL+ D L
Sbjct: 66 GYVSSLVEPSKVGQFDQVLN--LCLTE---FE---NCYLEGNDIHALAAKLLQENDTTLV 117
Query: 77 KVHISI--------VINRPTTIMRLVRTEDSKKKLVALTWVMFQSHRAGKMRTDGIF--- 125
K I + RP + +S AL F++ G + IF
Sbjct: 118 KTKELIKNYITARIMAKRPFD-----KKSNS-----AL----FRAVGEGNAQLVAIFGGQ 163
Query: 126 ----LFL--LRLLDPEINRFKKYRRPLSGIALSQIALKVGLSLYESSLLLSRPLSGIALS 179
+ LR LY++ L G +
Sbjct: 164 GNTDDYFEELR------------------------------DLYQTY----HVLVGDLIK 189
Query: 180 QIAEQLLELHR---------GQGMEIY-W-RDNYTCPSEEEYRTMTIRTVGRSVGYPTIR 228
AE L EL R QG+ I W + P ++Y + ++ S P I
Sbjct: 190 FSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPD-KDY----LLSIPISC--PLI- 241
Query: 229 TSKGGASSQVQTYAV--------PGNSR 248
G Q+ Y V PG R
Sbjct: 242 ----GV-IQLAHYVVTAKLLGFTPGELR 264
Score = 27.3 bits (60), Expect = 5.8
Identities = 16/69 (23%), Positives = 25/69 (36%), Gaps = 24/69 (34%)
Query: 152 SQIALKVG--LSLYESS-----------LLLSRPLSGIALSQIAEQ---LLELHRG--QG 193
SQ + G + LY++S G ++ I L +H G +G
Sbjct: 1626 SQ---EQGMGMDLYKTSKAAQDVWNRADNHFKDTY-GFSILDIVINNPVNLTIHFGGEKG 1681
Query: 194 MEIYWRDNY 202
I R+NY
Sbjct: 1682 KRI--RENY 1688
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 29.1 bits (64), Expect = 0.71
Identities = 10/25 (40%), Positives = 13/25 (52%), Gaps = 4/25 (16%)
Query: 155 ALKVGLSLYESSLLLSRPLSGIALS 179
ALK L ++SL L S AL+
Sbjct: 21 ALK---KL-QASLKLYADDSAPALA 41
>3kb9_A EPI-isozizaene synthase; terpenoid cyclase, alpha-helical fold,
farnesyl diphosphate, metal-binding, lyase, magnesium;
HET: BTM; 1.60A {Streptomyces coelicolor} PDB: 3kbk_A
3lgk_A 3lg5_A*
Length = 382
Score = 30.1 bits (67), Expect = 0.73
Identities = 11/62 (17%), Positives = 18/62 (29%)
Query: 158 VGLSLYESSLLLSRPLSGIALSQIAEQLLELHRGQGMEIYWRDNYTCPSEEEYRTMTIRT 217
+ +S L L ++ A + E + R P EEY + T
Sbjct: 159 LVAGFADSVRRLYAFLPATWNARFARHFHTVIEAYDREFHNRTRGIVPGVEEYLELRRLT 218
Query: 218 VG 219
Sbjct: 219 FA 220
>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 = 29.8 bits (66), Expect = 1.0
Identities = 27/197 (13%), Positives = 58/197 (29%), Gaps = 46/197 (23%)
Query: 16 VHSPHRVDAVNRRGFVEAVYGFSHRLCLRVDTALQSDKTF-----EKYR-ERILEPNASL 69
V+ H+ V ++ E+ + L + L+++ + Y + + + +
Sbjct: 408 VNKLHKYSLVEKQPK-ESTISI-PSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLI 465
Query: 70 LRSGD------LAKVHISIVINRPTTIMRLVRTEDSKKKLVALTWVMFQSHRAGKMRTDG 123
D + H+ I R + + ++ K+R D
Sbjct: 466 PPYLDQYFYSHIGH-HLK-------NIEHPERMTLFRMVFLDFRFL------EQKIRHDS 511
Query: 124 IFLFLLRLLDPEINRFKKYRR------PLSGIALSQIA---LKVGLSLYES---SLL--- 168
+ + + K Y+ P ++ I K+ +L S LL
Sbjct: 512 TAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIA 571
Query: 169 LSRPLSGI---ALSQIA 182
L I A Q+
Sbjct: 572 LMAEDEAIFEEAHKQVQ 588
>1ps1_A Pentalenene synthase; antibiotic biosynthesis, sesquiterpene
cyclase, lyase; 2.60A {Streptomyces SP} SCOP: a.128.1.4
PDB: 1hm7_A 1hm4_A
Length = 337
Score = 29.3 bits (65), Expect = 1.2
Identities = 11/64 (17%), Positives = 19/64 (29%), Gaps = 1/64 (1%)
Query: 157 KVGLSLYESSLLLSRPLSGIALSQIAEQLLELHRGQGMEIYWRD-NYTCPSEEEYRTMTI 215
+ + ++ ++ A G E R N C S +Y M
Sbjct: 115 PIAHGFADIWRRTCEGMTPAWCARSARHWRNYFDGYVDEAESRFWNAPCDSAAQYLAMRR 174
Query: 216 RTVG 219
T+G
Sbjct: 175 HTIG 178
>2i2w_A Phosphoheptose isomerase; lipopolysaccharide biosynthesis; 1.95A
{Escherichia coli} PDB: 2i22_A 1x94_A
Length = 212
Score = 28.1 bits (63), Expect = 2.1
Identities = 5/21 (23%), Positives = 11/21 (52%)
Query: 136 INRFKKYRRPLSGIALSQIAL 156
R+++ R IA+S ++
Sbjct: 87 TGRYRENRPGYPAIAISDVSH 107
>3sdr_A Alpha-bisabolene synthase; lyase, terpene synthase; HET: 210; 1.86A
{Abies grandis} PDB: 3sdq_A 3sae_A* 3sdt_A* 3sdu_A*
3sdv_A*
Length = 817
Score = 28.0 bits (61), Expect = 3.7
Identities = 9/42 (21%), Positives = 16/42 (38%)
Query: 178 LSQIAEQLLELHRGQGMEIYWRDNYTCPSEEEYRTMTIRTVG 219
+S + + G E W P+ +EY I ++G
Sbjct: 627 VSFFRKGWEDYLLGYYEEAEWLAAEYVPTLDEYIKNGITSIG 668
>2xbl_A Phosphoheptose isomerase; capsule; HET: M7P PGE PG4; 1.62A
{Burkholderia pseudomallei} PDB: 2x3y_A
Length = 198
Score = 27.3 bits (61), Expect = 3.9
Identities = 6/18 (33%), Positives = 10/18 (55%)
Query: 136 INRFKKYRRPLSGIALSQ 153
++RF R L +AL+
Sbjct: 71 VSRFAFDRPGLPAVALTT 88
>1tk9_A Phosphoheptose isomerase 1; lipopolysaccharide biosynthesis,
structural genomics, NYSGXRC, LPC1_camje, PSI, protein
structure initiative; 2.10A {Campylobacter jejuni} SCOP:
c.80.1.3
Length = 188
Score = 27.3 bits (61), Expect = 4.5
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 136 INRFKKYRRPLSGIALSQ 153
R+KK R+ L+GIAL+
Sbjct: 65 SGRYKKERKALAGIALTT 82
>1x92_A APC5045, phosphoheptose isomerase; midwest centre for structural
genomics, SIS domain, A/B protein, lipopolysaccharide
biosynthesis, PSI; HET: M7P; 2.30A {Pseudomonas
aeruginosa} SCOP: c.80.1.3 PDB: 3bjz_A
Length = 199
Score = 26.9 bits (60), Expect = 4.7
Identities = 7/18 (38%), Positives = 12/18 (66%)
Query: 136 INRFKKYRRPLSGIALSQ 153
+NRF++ R L +AL+
Sbjct: 68 LNRFERERPSLPAVALTT 85
>3trj_A Phosphoheptose isomerase; lipopolysaccharide biosynthesis; 2.80A
{Francisella tularensis subsp}
Length = 201
Score = 26.9 bits (60), Expect = 5.1
Identities = 8/18 (44%), Positives = 11/18 (61%)
Query: 136 INRFKKYRRPLSGIALSQ 153
+N F+ R PL IAL+
Sbjct: 69 LNHFEMERPPLPAIALTG 86
>3g4d_A (+)-delta-cadinene synthase isozyme XC1; cyclase, lyase, magnesium,
metal-binding; 2.40A {Gossypium arboreum} PDB: 3g4f_A*
Length = 554
Score = 27.1 bits (59), Expect = 6.2
Identities = 9/42 (21%), Positives = 17/42 (40%)
Query: 178 LSQIAEQLLELHRGQGMEIYWRDNYTCPSEEEYRTMTIRTVG 219
+ ++ L + +E W PS EE++ + T G
Sbjct: 368 VEYAKNAMIRLAQSYLVEAKWTLQNYKPSFEEFKANALPTCG 409
>2yva_A DNAA initiator-associating protein DIAA; intermolecular disulfide
bonding, putative phosphosugar BIND protein, DNAA
binding protein; 1.85A {Escherichia coli}
Length = 196
Score = 26.5 bits (59), Expect = 6.2
Identities = 9/18 (50%), Positives = 11/18 (61%)
Query: 136 INRFKKYRRPLSGIALSQ 153
INRF+ R L IAL+
Sbjct: 64 INRFETERPSLPAIALNT 81
>3e6u_A LANC-like protein 1; alpha barrel, cytoplasm, signaling protein;
2.60A {Homo sapiens} PDB: 3e73_A*
Length = 411
Score = 27.1 bits (59), Expect = 6.5
Identities = 8/17 (47%), Positives = 8/17 (47%)
Query: 123 GIFLFLLRLLDPEINRF 139
G FL LL P RF
Sbjct: 390 GTIYFLADLLVPTKARF 406
>3v1v_A 2-MIB synthase, 2-methylisoborneol synthase; class I terpenoid
cyclase fold, DDXXXXD motif, NDXXSXXXE MOT
methylisoborneol biosynthesis; HET: GST; 1.80A
{Streptomyces coelicolor} PDB: 3v1x_A*
Length = 433
Score = 26.6 bits (58), Expect = 8.2
Identities = 10/45 (22%), Positives = 13/45 (28%)
Query: 169 LSRPLSGIALSQIAEQLLELHRGQGMEIYWRDNYTCPSEEEYRTM 213
R + + + LH G E W P EY M
Sbjct: 248 FVRAATPSQSDRYRHDMARLHLGYLAEGAWAQTGHVPEVWEYLAM 292
>3s9v_A Abietadiene synthase, chloroplastic; alpha bundle/barrel, lyase,
isomerase; 2.30A {Abies grandis}
Length = 785
Score = 26.7 bits (58), Expect = 8.6
Identities = 8/42 (19%), Positives = 11/42 (26%)
Query: 178 LSQIAEQLLELHRGQGMEIYWRDNYTCPSEEEYRTMTIRTVG 219
L I E W + PS EY ++
Sbjct: 599 LGYIQNVWKVQLEAYTKEAEWSEAKYVPSFNEYIENASVSIA 640
>1n1b_A (+)-bornyl diphosphate synthase; terpene synthase fold, isomerase;
2.00A {Salvia officinalis} SCOP: a.102.4.1 a.128.1.3
PDB: 1n1z_A* 1n20_A* 1n21_A* 1n22_A* 1n23_A* 1n24_A*
Length = 549
Score = 26.7 bits (58), Expect = 9.9
Identities = 9/42 (21%), Positives = 18/42 (42%)
Query: 178 LSQIAEQLLELHRGQGMEIYWRDNYTCPSEEEYRTMTIRTVG 219
L + + +++L E W + PS +EY + +V
Sbjct: 363 LQYLRKSVVDLVEAYFHEAKWYHSGYTPSLDEYLNIAKISVA 404
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
0.322 0.137 0.399
Gapped
Lambda K H
0.267 0.0507 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,758,386
Number of extensions: 218214
Number of successful extensions: 390
Number of sequences better than 10.0: 1
Number of HSP's gapped: 386
Number of HSP's successfully gapped: 28
Length of query: 250
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 159
Effective length of database: 4,160,982
Effective search space: 661596138
Effective search space used: 661596138
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 (21.9 bits)
S2: 56 (25.9 bits)