RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780755|ref|YP_003065168.1| octaprenyl-diphosphate
synthase protein [Candidatus Liberibacter asiaticus str. psy62]
(322 letters)
>3mzv_A Decaprenyl diphosphate synthase; transferase, structural genomics,
PSI-2, protein structure initiative; 1.90A {Rhodobacter
capsulatus}
Length = 341
Score = 283 bits (725), Expect = 4e-77
Identities = 145/319 (45%), Positives = 203/319 (63%), Gaps = 1/319 (0%)
Query: 4 LEDLTLKDMEKVNFLILKRICSD-VEMIPDVVKYLIFSGGKRLRPMLTLATALMLEYRGD 62
L +DM VN LI +R+ S+ IP+V +LI +GGKRLRPMLTLA A ++ Y G
Sbjct: 14 LAQALAEDMAAVNALIRERMSSEHAPRIPEVTAHLIEAGGKRLRPMLTLAAARLVGYGGP 73
Query: 63 NHVLLACAIEFIHTATLLHDDVVDDSALRRGKVAARLVWGNQTSVLVGDFLLSQAFCMVI 122
HV LA +EFIHTATLLHDDVVD+S RRG+ A L+W N++SVLVGD+L +++F ++
Sbjct: 74 FHVHLAATVEFIHTATLLHDDVVDESRQRRGRPTANLLWDNKSSVLVGDYLFARSFQLMT 133
Query: 123 ETKSQEALEALSLVACTLAEGELRQLSLSKNLDVTEEDYLHVIKSKTAVLFSAALEVSSL 182
+T + +E L+ + +AEGE+ QL+ ++NL TE+ YL VI+ KTA LFSAA EV +
Sbjct: 134 DTGNMRVMEILANASAVIAEGEVLQLTAAQNLATTEDIYLRVIRGKTAALFSAATEVGGI 193
Query: 183 IAGVQNSVRQALKSYGMNLGIAFQLVDDVLDYRGEVNEMGKNIGEDFRNGKPTLPVILAF 242
I G QAL YG LGIAFQ+VDD+LDY G+ E+GKN G+DFR K T+PVI A
Sbjct: 194 IGGAPEDQVQALFDYGDALGIAFQIVDDLLDYGGKSAEIGKNTGDDFRERKLTMPVIKAV 253
Query: 243 QRGTKREKNFWKSTINDGKISVENLKKAFIIMRENRALVDTEYRAYSYGQKAKDSLRCLP 302
+ E+ FWK I G +L+ A +M ++ L T A + A+ +L LP
Sbjct: 254 ALADEAERAFWKRVIEKGDQQDGDLEHAMALMTKHGTLEATRLAAIGWTDTARKALAKLP 313
Query: 303 DSSWKKSLMEVVDFCLQRL 321
D ++ L ++ D+ ++R+
Sbjct: 314 DHPLRQMLDDLADYVVERV 332
>3oyr_A Trans-isoprenyl diphosphate synthase; isoprenyl synthase, PSI,
protein structure initiative; HET: IPE; 2.00A
{Caulobacter crescentus}
Length = 345
Score = 281 bits (720), Expect = 1e-76
Identities = 150/317 (47%), Positives = 209/317 (65%)
Query: 4 LEDLTLKDMEKVNFLILKRICSDVEMIPDVVKYLIFSGGKRLRPMLTLATALMLEYRGDN 63
L L DM VN LI R+ SDV +IP + ++LI +GGKRLRP++T+A A + D+
Sbjct: 27 LVRLAEADMAGVNRLITDRMQSDVAIIPALAEHLIAAGGKRLRPLMTVAAARLAGADNDH 86
Query: 64 HVLLACAIEFIHTATLLHDDVVDDSALRRGKVAARLVWGNQTSVLVGDFLLSQAFCMVIE 123
LA A+EFIHTATLLHDDVVD S LRRGKVAA L+WG SVLVGDFL ++AF +++E
Sbjct: 87 FQKLAAAVEFIHTATLLHDDVVDGSQLRRGKVAAHLIWGGAQSVLVGDFLFARAFELMVE 146
Query: 124 TKSQEALEALSLVACTLAEGELRQLSLSKNLDVTEEDYLHVIKSKTAVLFSAALEVSSLI 183
T S +ALE L+ + +AEGE+ QL S +L++++ YL +I++KTA LF+AA E ++
Sbjct: 147 TNSMKALEILARASRVIAEGEVLQLMRSHDLNLSQAVYLEIIQAKTAELFAAASEAGAVS 206
Query: 184 AGVQNSVRQALKSYGMNLGIAFQLVDDVLDYRGEVNEMGKNIGEDFRNGKPTLPVILAFQ 243
AGV + +AL+ YG+NLG+AFQL DD LDY G +GKN G+DFR GK TLP++LA
Sbjct: 207 AGVDVAKSEALRDYGLNLGLAFQLADDALDYGGATETLGKNAGDDFREGKATLPLLLAIA 266
Query: 244 RGTKREKNFWKSTINDGKISVENLKKAFIIMRENRALVDTEYRAYSYGQKAKDSLRCLPD 303
R RE FW+ I + + + ++A ++ + AL T A Y KAK +L P
Sbjct: 267 RSGPREAEFWERAIGRREQTEADFRRARELIIGSGALDATLDLAADYADKAKAALAMFPA 326
Query: 304 SSWKKSLMEVVDFCLQR 320
+ W+++L E+ DF + R
Sbjct: 327 NDWREALEELADFAVSR 343
>3lmd_A Geranylgeranyl pyrophosphate synthase; isoprenyl diphosphate
synthase, structural genomics, PSI, protein structure
initiative, nysgrc; 1.90A {Corynebacterium glutamicum}
Length = 360
Score = 280 bits (717), Expect = 3e-76
Identities = 93/313 (29%), Positives = 157/313 (50%), Gaps = 4/313 (1%)
Query: 11 DMEKVNFLILKRICSDVEMIPDVVKYLIFSGGKRLRPMLTLATALMLEY-RGDNHVLLAC 69
M +V L+ + S + + D+V +L +GGKR RPM L + E +N + A
Sbjct: 43 AMVQVEELLHTELSSGEDFLVDIVMHLTRAGGKRFRPMFALLASEFGEKPLSENVIKAAV 102
Query: 70 AIEFIHTATLLHDDVVDDSALRRGKVAARLVWGNQTSVLVGDFLLSQAFCMVIETKSQEA 129
+E H ATL HDDV+D++++RRG +A W N ++L GD LL+ A ++ + + +
Sbjct: 103 VVEITHLATLYHDDVMDEASMRRGVPSANARWDNSVAILAGDILLAHASGLMSQLGT-DT 161
Query: 130 LEALSLVACTLAEGELRQLSLSKNLDVTEEDYLHVIKSKTAVLFSAALEVSSLIAGVQNS 189
+ + L G++R+ ++ D E Y +VI+ KT VL ++A + ++ AG
Sbjct: 162 VAHFAETFGELVTGQMRETVGPRDTD-PIEHYTNVIREKTGVLIASAGYLGAMHAGAAPE 220
Query: 190 VRQALKSYGMNLGIAFQLVDDVLDYRGEVNEMGKNIGEDFRNGKPTLPVILAFQRGTKRE 249
ALK++G +G+ FQ+VDD++D E +E GK G D R G TLPV+ A + T
Sbjct: 221 HIDALKNFGAAVGMIFQIVDDIIDIFSETHESGKTPGTDLREGVFTLPVLYALREDTPVG 280
Query: 250 KNFWKSTINDGKISVENLKKAFIIMRENRALVDTEYRAYSYGQKAKDSLRCLPDSSWKKS 309
+ + E + ++ ++ Y Y A L LPDS+ K++
Sbjct: 281 AE-LRDILTGPLEDDETVNHVLELLSQSGGRQAALDEVYRYMDIANAELDRLPDSTVKEA 339
Query: 310 LMEVVDFCLQRLN 322
L + F ++R+
Sbjct: 340 LRNLATFTVKRVG 352
>3n3d_A Geranylgeranyl pyrophosphate synthase; isoprenyl diphosphate
synthase, structural genomics, PSI, PR structure
initiative, nysgrc; 2.40A {Lactobacillus brevis}
Length = 335
Score = 257 bits (658), Expect = 2e-69
Identities = 84/313 (26%), Positives = 154/313 (49%), Gaps = 5/313 (1%)
Query: 10 KDMEKVNFLILKRICSDVEMIPDVVKYLIFSGGKRLRPMLTLATALMLEYRGDNHVL-LA 68
+ + +L+ + D + I + L+ SGGK LRP + + A
Sbjct: 16 PQLTALQDYLLRTVQLDNQPIHHKILALLKSGGKLLRPGYFYLFSTFGNAATPAQLQAGA 75
Query: 69 CAIEFIHTATLLHDDVVDDSALRRGKVAARLVWGNQTSVLVGDFLLSQAF-CMVIETKSQ 127
AIE +H TL+HDDV+DDS RRG ++ +G + ++ GDF+ + F ++ T +
Sbjct: 76 AAIEILHVGTLIHDDVIDDSPTRRGVRTIQMTYGQRNAIYAGDFMFTVYFDQVLKSTTDR 135
Query: 128 EALEALSLVACTLAEGELRQLSLSKNLDVTEEDYLHVIKSKTAVLFSAALEVSSLIAGVQ 187
++ + +GEL Q+ L+ D+T + YL+ I KTA LF+ + + +AG
Sbjct: 136 SLIQNHIDAMHRILQGELHQMDLNYREDITLDAYLNEIAGKTAELFALSCYQGAQLAGAP 195
Query: 188 NSVRQALKSYGMNLGIAFQLVDDVLDYRGEVNEMGKNIGEDFRNGKPTLPVILAFQRGTK 247
SV + G+ +G A+Q++DD+LDY G+ K + ED R+G +LP++L+ +
Sbjct: 196 QSVIDRTRDIGIAIGCAYQMLDDILDYAGDPKRTQKPVLEDLRSGVYSLPLLLSLSHAPR 255
Query: 248 REKNFWKSTINDGKISVENLKKAFIIMRENRALVDTEYRAYSYGQKAKDSLRCLPDSSWK 307
K +++E++K ++ + + + A Y +A ++ LP S +
Sbjct: 256 DFHKLLKK---KQAMTLEDIKHVQALVAQYDGVGAAKQLAQDYTDRALTLIQQLPVGSAQ 312
Query: 308 KSLMEVVDFCLQR 320
+SL ++ L+R
Sbjct: 313 QSLEQLTRLLLRR 325
>3aqb_B Component B of hexaprenyl diphosphate synthase; prenyltransferase,
transferase; 2.40A {Micrococcus luteus} PDB: 3aqc_B*
Length = 325
Score = 252 bits (645), Expect = 7e-68
Identities = 85/319 (26%), Positives = 164/319 (51%), Gaps = 1/319 (0%)
Query: 4 LEDLTLKDMEKVNFLILKRICSDVEMIPDVVKYLIFSGGKRLRPMLTLATALMLEYRGDN 63
+ + +V + + I SD E I +++ SGGKR+RPM L + + + + D+
Sbjct: 6 YKAFLNPYIIEVEKRLYECIQSDSETINKAAHHILSSGGKRVRPMFVLLSGFLNDTQKDD 65
Query: 64 HVLLACAIEFIHTATLLHDDVVDDSALRRGKVAARLVWGNQTSVLVGDFLLSQAFCMVIE 123
+ A ++E +H A+L+HDD +D+S +RRG + + + T++ G FLL++A +
Sbjct: 66 LIRTAVSLELVHMASLVHDDYIDNSDMRRGNTSVHIAFDKDTAIRTGHFLLARALQNIAT 125
Query: 124 TKSQEALEALSLVACTLAEGELRQLSLSKNLDVTEEDYLHVIKSKTAVLFSAALEVSSLI 183
+ + + S + GE Q++ N V+ YL I KTA+L A+ + +L
Sbjct: 126 INNSKFHQIFSKTILEVCFGEFDQMADRFNYPVSFTAYLRRINRKTAILIEASCHLGALS 185
Query: 184 AGVQNSVRQALKSYGMNLGIAFQLVDDVLDYRGEVNEMGKNIGEDFRNGKPTLPVILAFQ 243
+ + +K +G +G+++Q++DD+LDY + +GK +G D RNG T P++ A
Sbjct: 186 SQLDEQSTYHIKQFGHCIGMSYQIIDDILDYTSDEATLGKPVGSDIRNGHITYPLMAAIA 245
Query: 244 RGTKREKNFWKSTINDGKISVENLKKAFIIMR-ENRALVDTEYRAYSYGQKAKDSLRCLP 302
+++ + ++ + + ++ +I+ + + + E + YG KAK L L
Sbjct: 246 NLKEQDDDKLEAVVKHLTSTSDDEVYQYIVSQVKQYGIEPAELLSRKYGDKAKYHLSQLQ 305
Query: 303 DSSWKKSLMEVVDFCLQRL 321
DS+ K L E+ + L+R+
Sbjct: 306 DSNIKDYLEEIHEKMLKRV 324
>3nf2_A Putative polyprenyl synthetase; isoprenyl diphosphate synthase,
structural genomics, PSI, PR structure initiative,
nysgrc; 2.20A {Streptomyces coelicolor}
Length = 352
Score = 235 bits (600), Expect = 1e-62
Identities = 77/295 (26%), Positives = 127/295 (43%), Gaps = 10/295 (3%)
Query: 36 YLIFSGGKRLRPMLTLATALMLEYRGDNHVLLACAIEFIHTATLLHDDVVDDSALRRGKV 95
GGK +RP L + +A + + V A A+E +H +LLHDD++D RR +
Sbjct: 48 PADGDGGKAVRPALAVLSAEVTGAAPEVGVPGAVAVELVHNFSLLHDDLMDGDEQRRHRD 107
Query: 96 AARLVWGNQTSVLVGDFLLSQAFCMVIETKSQEALEALSLVACTLA---EGELRQLSLSK 152
V G ++LVGD L + A +++E + EA A + +G+ + +S
Sbjct: 108 TVWKVHGPAQAILVGDALFALANEVLLELGTVEAGRATRRLTKASRSLIDGQAQDISYEH 167
Query: 153 NLDVTEEDYLHVIKSKTAVLFSAALEVSSLIAGVQNSVRQALKSYGMNLGIAFQLVDDVL 212
V+ E+ L + +KT L + A + +++ G L+ YG +LG+AFQ VDD+L
Sbjct: 168 RDRVSVEECLEMEGNKTGALLACASSIGAVLGGADERTADTLEKYGYHLGLAFQAVDDLL 227
Query: 213 DYRGEVNEMGKNIGEDFRNGKPTLPVILAFQRGTKREKNFWKSTINDGK------ISVEN 266
G+ + GK D R K +LPV+ A G + + D K S E
Sbjct: 228 GIWGDPDATGKQTWSDLRQRKKSLPVVAALAAGGAASERLGEILTADAKASDFANFSEEE 287
Query: 267 LKKAFIIMRENRALVDTEYRAYSYGQKAKDSLRCLP-DSSWKKSLMEVVDFCLQR 320
++ E T A A ++L + + + DF + R
Sbjct: 288 FAARAALIEEAGGREWTADEARRQHTIAIEALDAVDMPDRVRDRFTALADFVVVR 342
>3lom_A Geranyltranstransferase; geranyltransferase, structural genomics,
PSI, protein structure initiative, nysgrc; 2.30A
{Legionella pneumophila subsp}
Length = 313
Score = 215 bits (549), Expect = 9e-57
Identities = 70/295 (23%), Positives = 122/295 (41%), Gaps = 18/295 (6%)
Query: 1 MKMLEDLTLKDMEKVNFLILKRICSDVEMIPDVVKYLIFSGGKRLRPMLTLATALMLEYR 60
K + D + E +L I I + Y +FSGGKR+RP+L +++
Sbjct: 9 NKQVIDKYTQRHELYLEQLLNEIIIPAPQIRSALHYALFSGGKRIRPILVYLAGDLIDVD 68
Query: 61 GDNHVLLACAIEFIHTATLLHDDV--VDDSALRRGKVAARLVWGNQTSVLVGDFLLSQAF 118
++A A+E H +L+HDD+ +D+ LRRGK + + T++LVGD + + A
Sbjct: 69 QGVLDIIAAALELTHCYSLIHDDLPAMDNDDLRRGKPSCHKAFDEATAILVGDGMQALAI 128
Query: 119 CMVIETKSQE----------ALEALSLVACTLAEGELRQLSLSKNLDVTEEDYLHVIKSK 168
+++ S + + + G+ LS VTEE + K
Sbjct: 129 EVLLMRLSPLLPAAQVVAITQVLVNASGISGMVSGQSLDLSELAKSSVTEEQLREIHLLK 188
Query: 169 TAVLFSAALEVSSLI-AGVQNSVRQALKSYGMNLGIAFQLVDDVLDYRGEVNEMGKNIGE 227
T L A E+ V ++ AL++YG ++G+ FQ+ DD LD +GK
Sbjct: 189 TGKLILACFEMVLAAQHEVSEQIKSALRTYGKHIGLVFQMQDDYLDLYAPTQILGKGRSS 248
Query: 228 DFRNGKPTLPVILAFQRGTKREKNFWKSTINDGKISVENLKK-----AFIIMREN 277
D N K T + Q+ + ++ ++ ++ + R N
Sbjct: 249 DQANQKTTFATLFNKQQLEEEIAVHYQIAMDSLRLFGSKAAALIELTKQLQNRSN 303
>3lk5_A Geranylgeranyl pyrophosphate synthase; structural genomics, protein
structure initiative; 1.90A {Corynebacterium glutamicum}
Length = 380
Score = 211 bits (539), Expect = 1e-55
Identities = 83/343 (24%), Positives = 133/343 (38%), Gaps = 31/343 (9%)
Query: 9 LKDMEKVNFLILKRICSDVEMIPDVVKYLIFSGGKRLRPMLTLATALMLEYRG------D 62
L L + I + V ++ + +GGKR+RP+ A L + +
Sbjct: 29 LTQFLDAQELTIADIGAPVTDAVAHLRSFVLNGGKRIRPLYAWAGFLAAQGHKNSSEKLE 88
Query: 63 NHVLLACAIEFIHTATLLHDDVVDDSALRRGKVAARLV----------------WGNQTS 106
+ + A ++EFI L+HDD++D S RRG +G S
Sbjct: 89 SVLDAAASLEFIQACALIHDDIIDSSDTRRGAPTVHRAVEADHRANNFEGDPEHFGVSVS 148
Query: 107 VLVGDFLLSQAFCMVIETKSQEALEALSLVACTLAEGELRQ-----LSLSKNLDVTEEDY 161
+L GD L A M+ ++ A + A E+ + L + + + E
Sbjct: 149 ILAGDMALVWAEDMLQDSGLSAEALARTRDAWRGMRTEVIGGQLLDIYLESHANESVELA 208
Query: 162 LHVIKSKTAVLFSAA-LEVSSLIAGVQNSVRQALKSYGMNLGIAFQLVDDVLDYRGEVNE 220
V + KTA A L + + IAG + AL YG ++GIAFQL DD+L G+
Sbjct: 209 DSVNRFKTAAYTIARPLHLGASIAGGSPQLIDALLHYGHDIGIAFQLRDDLLGVFGDPAI 268
Query: 221 MGKNIGEDFRNGKPTLPVILAFQRGTKREKNFWKS--TINDGKISVENLKKAFIIMRENR 278
GK G+D R GK T+ + LA QR K+ + S E++ +R
Sbjct: 269 TGKPAGDDIREGKRTVLLALALQRADKQSPEAATAIRAGVGKVTSPEDIAVITEHIRATG 328
Query: 279 ALVDTEYRAYSYGQKAKDSLRCLP-DSSWKKSLMEVVDFCLQR 320
A + E R + L + + L + +R
Sbjct: 329 AEEEVEQRISQLTESGLAHLDDVDIPDEVRAQLRALAIRSTER 371
>3p8l_A Geranyltranstransferase; isoprenyl synthase, structural genomics,
PSI, protein struct initiative, nysgrc; 2.00A
{Enterococcus faecalis}
Length = 302
Score = 195 bits (497), Expect = 1e-50
Identities = 77/293 (26%), Positives = 134/293 (45%), Gaps = 18/293 (6%)
Query: 4 LEDLTLKDMEKVNFLILKRI--CSDVEMIPDVVKYLIFSGGKRLRPMLTLATALMLEYRG 61
L + + + + V +++ I ++ E + + + Y I +GGKRLRP+L L T +
Sbjct: 10 LTNFSQQHLPLVEKVMVDFIAEYTENERLKEAMLYSIHAGGKRLRPLLVLTTVAAFQKEM 69
Query: 62 DNHVL-LACAIEFIHTATLLHDDVV--DDSALRRGKVAARLVWGNQTSVLVGDFLLSQAF 118
+ +A ++E IHT +L+HDD+ DD LRRGK V+G T++L GD LL+ AF
Sbjct: 70 ETQDYQVAASLEMIHTYSLIHDDLPAMDDDDLRRGKPTNHKVFGEATAILAGDGLLTGAF 129
Query: 119 CMVIETK---SQEALEALSLVACTLAEGELRQLSL---SKNLDVTEEDYLHVIKSKTAVL 172
++ ++ S++ L L +G + + + +T E+ V + KT L
Sbjct: 130 QLLSLSQLGLSEKVLLMQQLAKAAGNQGMVSGQMGDIEGEKVSLTLEELAAVHEKKTGAL 189
Query: 173 FSAALEVSSLIAGVQNSVRQALKSYGMNLGIAFQLVDDVLDYRGEVNEMGKNIGEDFRNG 232
AL ++A V L + + G+AFQ+ DD+LD ++GK +G D
Sbjct: 190 IEFALIAGGVLANQTEEVIGLLTQFAHHYGLAFQIRDDLLDATSTEADLGKKVGRDEALN 249
Query: 233 KPTLPVILAFQRGTKREKNF---WKSTINDGKISVENLKKA----FIIMRENR 278
K T P +L + + + K +V N + + + R
Sbjct: 250 KSTYPALLGIAGAKDALTHQLAEGSAVLEKIKANVPNFSEEHLANLLTQLQLR 302
>3llw_A Geranyltranstransferase (ISPA); structural genomics, PSI, protein
structure initiative, nysgrc; 2.30A {Helicobacter
pylori}
Length = 311
Score = 191 bits (487), Expect = 1e-49
Identities = 71/297 (23%), Positives = 140/297 (47%), Gaps = 25/297 (8%)
Query: 10 KDMEKVN-FL--ILKRICSDVEMIPDVVKYLIFSGGKRLRPMLTLATALML------EYR 60
+ E+ FL + S + ++ +GGKR RP L LA L +
Sbjct: 13 NECERFESFLKNHHLHLESFHPYLEKAFFEMVLNGGKRFRPKLFLAVLCALVGQKDYSNQ 72
Query: 61 GDNHVLLACAIEFIHTATLLHDDV--VDDSALRRGKVAARLVWGNQTSVLVGDFLLSQAF 118
+ +A +IE +HT +L+HDD+ +D++ALRR + T+VL+GD L + +F
Sbjct: 73 QTEYFKIALSIECLHTYSLIHDDLPCMDNAALRRNHPTLHAKYDETTAVLIGDALNTYSF 132
Query: 119 CMVIETKSQEALEALSLVACTLAEG------ELRQLSLSKNLDVTEEDYLHVIKSKTAVL 172
++ + + + + G +N + E + + KTA L
Sbjct: 133 ELLSNALLESHIIVELIKILSANGGIKGMILGQALDCYFENTPLNLEQLTFLHEHKTAKL 192
Query: 173 FSAALEVSSLIAGVQNS-VRQALKSYGMNLGIAFQLVDDVLDYRGEVNEMGKNIGEDFRN 231
SA+L + + +G+++ + + L+++G+ +G+ FQ++DD++D + E GK D +
Sbjct: 193 ISASLIMGLVASGIKDEELFKWLQAFGLKMGLCFQVLDDIIDVTQDEEESGKTTHLD--S 250
Query: 232 GKPTLPVILAFQRGTKREKNFWKSTINDGKISVENLKKAFIIMREN-RALVDTEYRA 287
K + +L +R + +ND ++ LK A+ +++EN AL++T ++
Sbjct: 251 AKNSFVNLLGLERANNYAQTLKTEVLND----LDALKPAYPLLQENLNALLNTLFKG 303
>3p8r_A Geranyltranstransferase; isoprenyl synthase, structural genomics,
PSI, protein struct initiative, nysgrc; 2.50A {Vibrio
cholerae}
Length = 302
Score = 190 bits (484), Expect = 3e-49
Identities = 74/294 (25%), Positives = 141/294 (47%), Gaps = 18/294 (6%)
Query: 1 MKMLEDLTLKDMEKVNFLILKRICSDVEMIPDVVKYLIFSGGKRLRPMLTLATALMLEYR 60
++ L ++ ++++ + + + +I + ++Y + GGKR RP L T ML
Sbjct: 10 LEALSSYQQRNNQQLDQWLNRIPFQTLPLI-EAMRYGLLLGGKRARPYLVYITGQMLGCE 68
Query: 61 GDNHVLLACAIEFIHTATLLHDDV--VDDSALRRGKVAARLVWGNQTSVLVGDFLLSQAF 118
+ A A+E IH +L+HDD+ +DD LRRGK + + T++L GD L + AF
Sbjct: 69 LSDLDTPASAVECIHAYSLIHDDLPAMDDDELRRGKPTCHIQFDEATAILTGDALQTLAF 128
Query: 119 CMVIETKSQEALEAL------SLVACTLAEGELRQLSL---SKNLDVTEEDYLHVIKSKT 169
++ E A E +L + A+G +L ++N ++ E+ + ++KT
Sbjct: 129 TILAEGDLSAAGETQRVAMLQALAEASGAQGMCLGQALDLAAENRLISLEELETIHRNKT 188
Query: 170 AVLFSAALEVSSLIAGVQN-SVRQALKSYGMNLGIAFQLVDDVLDYRGEVNEMGKNIGED 228
L A+ + +L AG + ++ L Y +G+AFQ+ DD+LD + +GK G D
Sbjct: 189 GALMRCAIRLGALAAGEKGRAMLPHLDRYAEAVGLAFQVQDDILDIISDTETLGKPQGSD 248
Query: 229 FRNGKPTLPVILAFQRGTKREKNFWK---STINDGKISVENLKKA--FIIMREN 277
K T P +L + ++ + + + E+L++ +++ R+N
Sbjct: 249 QELNKSTYPALLGLEGAQQKAHTLLQEALLALEAIPYNTEHLEEFARYVVERKN 302
>3lsn_A Geranyltranstransferase; structural genomics, protein structure
initiative, NEW YORK structural genomix research
consortium, nysgxrc; HET: MSE; 1.35A {Pseudomonas
fluorescens} PDB: 3lji_A*
Length = 304
Score = 189 bits (482), Expect = 6e-49
Identities = 70/276 (25%), Positives = 130/276 (47%), Gaps = 17/276 (6%)
Query: 19 ILKRICSDVEMIPDVVKYLIFSGGKRLRPMLTLATALMLEYRGDNHVLLACAIEFIHTAT 78
+ ++ + + ++Y + +GGKR+RP+L A L + + ACA+E IH +
Sbjct: 21 LFTAPSPELARLYEAMRYSVMNGGKRVRPLLAYAACEALGGKPEQANGAACAVELIHAYS 80
Query: 79 LLHDDV--VDDSALRRGKVAARLVWGNQTSVLVGDFLLSQAFCMVIETKSQEALEALSLV 136
L+HDD+ +DD LRRG+ + ++L GD L S AF +++ +A + L
Sbjct: 81 LVHDDLPAMDDDDLRRGQPTTHKAFDEACAILAGDGLQSLAFSALLDPALSDASAEIRLR 140
Query: 137 ACT---LAEGELRQL------SLSKNLDVTEEDYLHVIKSKTAVLFSAALEVSSLIAG-V 186
T A G + S L + ++ ++ + KT L A++ + +L +G
Sbjct: 141 MVTTLAQAAGPAGMVGGQAIDLGSVGLKLDQQALEYMHRHKTGALIEASVILGALASGRA 200
Query: 187 QNSVRQALKSYGMNLGIAFQLVDDVLDYRGEVNEMGKNIGEDFRNGKPTLPVILAFQRGT 246
+ +AL++Y +G+AFQ+ DD+LD + +GK G D KPT P +L
Sbjct: 201 EKGELKALQTYAQAIGLAFQVQDDILDVESDTATLGKRQGADIARDKPTYPALLGLAAAK 260
Query: 247 KREKNFWKSTINDGKI---SVENLKKA--FIIMREN 277
+ ++ + + E L++ +I+ R +
Sbjct: 261 EYALELRDQALHALRPFDAAAEPLRELARYIVERRS 296
>3lji_A Geranyltranstransferase; structural genomics, protein structure
initiative, NEW YORK structural genomix research
consortium, nysgxrc; HET: MSE; 1.39A {Pseudomonas
fluorescens}
Length = 304
Score = 183 bits (465), Expect = 5e-47
Identities = 69/276 (25%), Positives = 127/276 (46%), Gaps = 17/276 (6%)
Query: 19 ILKRICSDVEMIPDVVKYLIFSGGKRLRPMLTLATALMLEYRGDNHVLLACAIEFIHTAT 78
+ ++ + + ++Y + +GGKR+RP+L A L + + ACA+E IH +
Sbjct: 21 LFTAPSPELARLYEAMRYSVMNGGKRVRPLLAYAACEALGGKPEQANGAACAVELIHAYS 80
Query: 79 LLHDDV--VDDSALRRGKVAARLVWGNQTSVLVGDFLLSQAFCMVIETKSQEALEALSLV 136
L+HDD+ +DD LRRG+ + ++L GD L S AF +++ +A + L
Sbjct: 81 LVHDDLPAMDDDDLRRGQPTTHKAFDEACAILAGDGLQSLAFSALLDPALSDASAEIRLR 140
Query: 137 ACTL---AEGELRQL------SLSKNLDVTEEDYLHVIKSKTAVLFSAALEVSSLIAGVQ 187
T A G + S L + ++ ++ + KT L A++ + +L +G
Sbjct: 141 MVTTLAQAAGPAGMVGGQAIDLGSVGLKLDQQALEYMHRHKTGALIEASVILGALASGRA 200
Query: 188 NSVRQA-LKSYGMNLGIAFQLVDDVLDYRGEVNEMGKNIGEDFRNGKPTLPVILAFQRGT 246
L++Y +G+AFQ+ DD+LD + +GK G D KPT P +L
Sbjct: 201 EKGELKALQTYAQAIGLAFQVQDDILDVESDTATLGKRQGADIARDKPTYPALLGLAAAK 260
Query: 247 KREKNFWKSTINDGKI---SVENLKKA--FIIMREN 277
+ ++ + + E L++ +I+ R +
Sbjct: 261 EYALELRDQALHALRPFDAAAEPLRELARYIVERRS 296
>3pde_A Farnesyl-diphosphate synthase; isoprenyl diphosphate synthase,
structural genomics, PSI, PR structure initiative; HET:
IPE; 1.75A {Lactobacillus brevis} PDB: 3m9u_A*
Length = 309
Score = 183 bits (464), Expect = 7e-47
Identities = 77/332 (23%), Positives = 134/332 (40%), Gaps = 51/332 (15%)
Query: 4 LEDLTLKDMEKVNFLILKRICSDVE--MIPDVVKYLIFSGGKRLRPMLTLATALML--EY 59
L + + +N + + I +D + + + Y + +GGKRLRP+LT+AT L +
Sbjct: 8 LIAFEDQWVPALNAPLKQAILADSQDAQLAAAMTYSVLAGGKRLRPLLTVATMQSLGVTF 67
Query: 60 RGDNHVLLACAIEFIHTATLLHDDV--VDDSALRRGKVAARLVWGNQTSVLVGDFLLSQA 117
+ H A+E +HT +L+HDD+ +D+ ALRRG+ + +G + L GD LL+ A
Sbjct: 68 VPERHWRPVMALELLHTYSLIHDDLPAMDNDALRRGEPTNHVKFGAGMATLAGDGLLTLA 127
Query: 118 FCMVIETKSQEALEALSLVACTLAEGELRQL------SLSKNLDVTEEDYLHVIKSKTAV 171
F + T ++A + A A G + S+++++ + K KT
Sbjct: 128 FQWLTATDLPATMQAALVQALATAAGPSGMVAGQAKDIQSEHVNLPLSQLRVLHKEKTGA 187
Query: 172 LFSAALEVSSLIAGVQNSVRQALKSYGMNLGIAFQLVDDVLDYRGEVNEMGKNIGEDFRN 231
L A++ ++ + A + G+AFQ+ DD+LD EMGK +D
Sbjct: 188 LLHYAVQAGLILGQAPEAQWPAYLQFADAFGLAFQIYDDILDVVSSPAEMGKATQKDADE 247
Query: 232 GKPTLPVILAFQRGTKREKNFWKSTINDGKISVENLKKAFIIMRENRALVDTEYRAYSYG 291
K T P L + +
Sbjct: 248 AKNTYPGKLGLIGANQALID--------------------------------------TI 269
Query: 292 QKAKDSLRCLPDSSWKKSLMEVVD-FCLQRLN 322
+ +L+ LP S+ + L F +R+N
Sbjct: 270 HSGQAALQGLPTSTQRDDLAAFFSYFDTERVN 301
>3kra_B Geranyl diphosphate synthase small subunit; prenyltransferase,
isoprene biosynthesis, isoprenyl pyrophosphate synthase,
transferase; 1.90A {Mentha x piperita} PDB: 3krc_B*
3krf_B* 3kro_B* 3krp_B*
Length = 274
Score = 182 bits (462), Expect = 1e-46
Identities = 35/240 (14%), Positives = 84/240 (35%), Gaps = 26/240 (10%)
Query: 28 EMIPDVVKYLIFSGGKRLRPMLTLATALMLEYRGDNHVLLACAIEFIHTATLLHDDVVDD 87
E + + +L F+ L LA ++ + I +H A +H+ +
Sbjct: 26 ETVFGPMHHLTFAAPATAASTLCLAACELVGGDRSQAMXXXXXIHLVHAAAYVHEHLPLT 85
Query: 88 SA-LRRGKVAARLVWGNQTSVLVGDFLLSQAFCMVIETKSQEALEALSLVACTLAE---- 142
K A + +G +L GD ++ F ++ + + + + E
Sbjct: 86 DGSRPVSKPAIQHKYGPNVELLTGDGIVPFGFELLAGSVDPARTDDPDRILRVIIEISRA 145
Query: 143 -------GELRQLSLSKNLDVTEEDYLHVIKSKTAVLFSAALEVSSLIAGVQNSVRQALK 195
L + + + + + +V K K + + +++ G Q L+
Sbjct: 146 GGPEGMISGLHREEEIVDGNTSLDFIEYVCKKKYGEMHACGAACGAILGGAAEEEIQKLR 205
Query: 196 SYGMNLGI---------AFQLVDDVLDYRGE---VNEMGKNIGED--FRNGKPTLPVILA 241
++G+ G + QL+D+ + + + + E+G G++ + P + A
Sbjct: 206 NFGLYQGTLRGMMEMKNSHQLIDENIIGKLKELALEELGGFHGKNAELMSSLVAEPSLYA 265
>3npk_A Geranyltranstransferase; isoprene biosynthesis, SGX, structural
genomics protein structure initiative; 1.50A
{Campylobacter jejuni}
Length = 291
Score = 180 bits (457), Expect = 4e-46
Identities = 66/279 (23%), Positives = 126/279 (45%), Gaps = 16/279 (5%)
Query: 1 MKM-LEDLTLKDMEKVNFLILKRICSDVEMIPDVVKYLIFSGGKRLRPMLTLATALMLEY 59
M + L++L + +EK L ++ S + + ++ +GGK R L L+ +
Sbjct: 1 MSLNLKELFIHHLEK----NLPKVESFHPFFNEALALMLKAGGKHFRAQLLLSVVQSNKP 56
Query: 60 RGDNHVL-LACAIEFIHTATLLHDDV--VDDSALRRGKVAARLVWGNQTSVLVGDFLLSQ 116
N L +A A+EFIHT +L+HDD+ +D++ RRG + T++LVGD L ++
Sbjct: 57 ELLNQALDVALALEFIHTYSLIHDDLPAMDNADFRRGIPTLHKSYDETTAILVGDALNTE 116
Query: 117 AFCMVIETKSQEALEALSLVACTLAEGELRQL------SLSKNLDVTEEDYLHVIKSKTA 170
AF ++ ++ ++ + G + ++ ++ + + KTA
Sbjct: 117 AFLVLSHAHLKDEIKIKLIKTLAFNAGLNGMVIGQAIDCFFEDKRLSLNELEFLHTHKTA 176
Query: 171 VLFSAALEVSSLIAGVQNSVRQALKSYGMNLGIAFQLVDDVLDYRGEVNEMGKNIGEDFR 230
L +AAL++ I + N + G+ LG+ FQ+ DD++D + GK D
Sbjct: 177 RLIAAALKMGCEICELNNEESNQIYKLGLKLGLIFQINDDIIDVTTSQEQSGKPTNNDIH 236
Query: 231 NGKPTLPVILAFQRGTKREKNFWKSTINDGKISVENLKK 269
K + +L ++ K ++N D + E L +
Sbjct: 237 --KNSFVNLLGLEQAIKTKENLLNECEQDLEKLNEKLAQ 273
>3m0g_A Farnesyl diphosphate synthase; structural genomics, protein
structure initiative, NYSGXRC, isoprene biosynthesis,
transferase, PSI-2; 1.90A {Rhodobacter capsulatus} PDB:
3lvs_A
Length = 297
Score = 174 bits (441), Expect = 3e-44
Identities = 77/293 (26%), Positives = 127/293 (43%), Gaps = 22/293 (7%)
Query: 1 MKMLEDLTLKDMEKVNFLILKRICS-DVEMIPDVVKYLIFSGGKRLRPMLTLATALMLEY 59
M + E L + + V + I + D + Y GGKRLR L + +A +
Sbjct: 1 MSLSERLK-EVQDAVETAMAAAIGRLPAGDLRDAMAY-AAQGGKRLRAFLAIESAAIHGI 58
Query: 60 RGDNHVLLACAIEFIHTATLLHDDVV--DDSALRRGKVAARLVWGNQTSVLVGDFLLSQA 117
+ A A+E +H +L+HDD+ D+ LRRG W + T+VL GD L + A
Sbjct: 59 SMAQAMPAALAVEALHAYSLVHDDMPCMDNDDLRRGLPTVHKKWDDATAVLAGDALQTLA 118
Query: 118 FCMVIETKSQEALEALSLVA----CTLAEGELRQLSL-----SKNLDVTEEDYLHVIKSK 168
F + + A ++LVA + AEG + +L + + +T ++ + + K
Sbjct: 119 FELCTDPVLGSAENRVALVAALAQASGAEGMVYGQALDIAAETAAVPLTLDEIIRLQAGK 178
Query: 169 TAVLFSAALEVSSLIAGVQNSVRQALKSYGMNLGIAFQLVDDVLDYRGEVNEMGKNIGED 228
T L S A + +++AG R L +Y LG+AFQ+ DD+LD G GK +G+D
Sbjct: 179 TGALISFAAQAGAILAGAD---RGPLTAYATALGLAFQIADDILDVEGNEEAAGKRLGKD 235
Query: 229 FRNGKPTLPVILAFQRGTKREKNFWKSTINDGKI---SVENLKKA--FIIMRE 276
K T +L R + + L+ ++I R+
Sbjct: 236 AEAHKATFVSLLGLAGAKSRAADLVAEAEAALAPYGEAASTLRACARYVIERD 288
>3dyh_A Farnesyl pyrophosphate synthase; protein-bisphosphonate complex,
isoprene biosynthesis, transferase; HET: 721; 1.94A
{Trypanosoma brucei} PDB: 2ewg_A* 2i19_A* 2p1c_A*
3dyf_A* 3dyg_A* 2ogd_A* 3efq_A* 3egt_A*
Length = 390
Score = 167 bits (423), Expect = 3e-42
Identities = 66/358 (18%), Positives = 126/358 (35%), Gaps = 53/358 (14%)
Query: 13 EKVNFLILKRICSDVEMIPDVVKYL------IFSGGKRLRPMLTLATALMLEYRGDNH-- 64
+++ +L+ + +M P+ V+YL GGK R + + A L N+
Sbjct: 34 DEIQMFLLEELELKFDMDPNRVRYLRKMMDTTCLGGKYNRGLTVIDVAESLLSLSPNNNG 93
Query: 65 ---------------VLLACAIEFIHTATLLHDDVVDDSALRRGKVAARLVWGNQTSVLV 109
+ IEF+ L+ DD++D+S RRGK +
Sbjct: 94 EEDDGARRKRVLHDACVCGWMIEFLQAHYLVEDDIMDNSVTRRGKPCWYRHPDVTVQCAI 153
Query: 110 GDFLLSQAFCMVIETKS-------QEALEALSLVACTLAEG----------------ELR 146
D LL +++ ++ Q+ L + V T A G ++
Sbjct: 154 NDGLLLKSWTHMMAMHFFADRPFLQDLLCRFNRVDYTTAVGQLYDVTSMFDSNKLDPDVS 213
Query: 147 QLSLSKNLDVTEEDYLHVIKSKTAVLFSAALEVSSL--IAGVQNSVRQALKSYGMNLGIA 204
Q + + + T +Y ++K KTA V L + + M +G
Sbjct: 214 QPTTTDFAEFTLSNYKRIVKYKTAYYTYLLPLVMGLIVSEALPTVDMGVTEELAMLMGEY 273
Query: 205 FQLVDDVLDYRGEVNEMGKNIGEDFRNGKPTLPVILAFQRGTKREKNFWKSTINDGKISV 264
FQ+ DDV+D +GK G D ++ K + + + + + +K+ G
Sbjct: 274 FQVQDDVMDCFTPPERLGKV-GTDIQDAKCSWLAVTFLAKASSAQVAEFKANY--GSGDS 330
Query: 265 ENLKKAFIIMRENRALVDTEYRAYSYGQKAKDSLRCLPDSS--WKKSLMEVVDFCLQR 320
E + + E D + ++ K+ + L S + S+ + +R
Sbjct: 331 EKVATVRRLYEEADLQGDYVAYEAAVAEQVKELIEKLRLCSPGFAASVETLWGKTYKR 388
>2qis_A Farnesyl pyrophosphate synthetase; trans-prenyltransferase,
structural genomics, structural genomics consortium,
SGC; HET: RIS; 1.80A {Homo sapiens} PDB: 1yv5_A* 1yq7_A*
2opm_A* 2opn_A* 3cp6_A* 2rah_A* 2vf6_A* 1zw5_A* 3b7l_A*
2f94_F* 2f89_F* 2f7m_F* 2f8z_F* 2f8c_F* 2f92_F* 2f9k_F*
Length = 374
Score = 159 bits (403), Expect = 6e-40
Identities = 53/340 (15%), Positives = 105/340 (30%), Gaps = 32/340 (9%)
Query: 10 KDMEKVNFLILKRICSDV---EMIPDVVKYL------IFSGGKRLRPMLTLATALMLEYR 60
+D + I++ + D I D + L GGK R + + L
Sbjct: 36 QDFVQHFSQIVRVLTEDEMGHPEIGDAIARLKEVLEYNAIGGKYNRGLTVVVAFRELVEP 95
Query: 61 GDNH-------VLLACAIEFIHTATLLHDDVVDDSALRRGKVAARLVWGNQTS-VLVGDF 112
+ +E + L+ DD++D S RRG++ G + +
Sbjct: 96 RKQDADSLQRAWTVGWCVELLQAFFLVADDIMDSSLTRRGQICWYQKPGVGLDAINDANL 155
Query: 113 LLSQAFCM-----VIETKSQEALEALSLVACTLAEGELRQLSLSKN-----LDVTEEDYL 162
L + + + + +E + G+ L + + TE+ Y
Sbjct: 156 LEACIYRLLKLYCREQPYYLNLIELFLQSSYQTEIGQTLDLLTAPQGNVDLVRFTEKRYK 215
Query: 163 HVIKSKTAVLFSAALEVSSLIAG--VQNSVRQALKSYGMNLGIAFQLVDDVLDYRGEVNE 220
++K K+A +++ K + +G FQ+ DD LD G+ +
Sbjct: 216 SIVKYKSAFYSFYLPIAAAMYMAGIDGEKEHANAKKILLEMGEFFQIQDDYLDLFGDPSV 275
Query: 221 MGKNIGEDFRNGKPTLPVILAFQRGTKREKNFWKSTINDGKISVENLKKAFIIMRENRAL 280
IG D ++ K + V+ QR T + K G+ E + + + E
Sbjct: 276 T-GKIGTDIQDNKCSWLVVQCLQRATPEQYQILKENY--GQKEAEKVARVKALYEELDLP 332
Query: 281 VDTEYRAYSYGQKAKDSLRCLPDSSWKKSLMEVVDFCLQR 320
+ + + +R
Sbjct: 333 AVFLQYEEDSYSHIMALIEQYAAPLPPAVFLGLARKIYKR 372
>2ihi_A Pyrophosphate synthase; PV092040, structural genomics, structural
genomics consortium, SGC, transferase; 2.00A {Plasmodium
vivax sai-1} PDB: 3cc9_A* 3ez3_A*
Length = 395
Score = 156 bits (394), Expect = 7e-39
Identities = 56/315 (17%), Positives = 108/315 (34%), Gaps = 43/315 (13%)
Query: 41 GGKRLRPMLTLATALML------EYRGDNHVLLACAIEFIHTATLLHDDVVDDSALRRGK 94
GGK R +L + + + LA IE + A L+ DD++D +RR K
Sbjct: 78 GGKNNRGILVILIYEYVKNRDINSSEWEKAACLAWCIEILQAAFLVADDIMDKGEMRRNK 137
Query: 95 VAARLVWGNQTSVLVGDFLLSQAFCMVI-------ETKSQEALEALSLVACTLAEGELRQ 147
L+ +T V D LL + E+ + + G+
Sbjct: 138 YCWYLLKDVETKNAVNDVLLLYNSIYKLIEIYLRNESCYVDVIATFRDATLKTIIGQHLD 197
Query: 148 LSLSKNL------------------------DVTEEDYLHVIKSKTAVLF---SAALEVS 180
++ + + Y +++ KTA +
Sbjct: 198 TNIFSDKYSDAHREIDVNNINVPEQPVIDINMINFGVYKNIVIHKTAYYSFFLPIVCGML 257
Query: 181 SLIAGVQNSVRQALKSYGMNLGIAFQLVDDVLDYRGEVNEMGKNIGEDFRNGKPTLPVIL 240
V N + + ++ M +G FQ+ DD LD G+ + +G D +N K T P+I
Sbjct: 258 LAGIAVDNLIYKKIEDISMLMGEYFQIHDDYLDIFGDSTKT-GKVGSDIQNNKLTWPLIK 316
Query: 241 AFQRGTKREKNFWKSTINDGKISVENLKKAFIIMRENRALVDTEYRAYSYGQKAKDSLRC 300
F+ ++ +K GK ++ +K + + + E + K ++
Sbjct: 317 TFELCSEPDKIKIVKNY--GKNNLACVKVIDSLYEQYKIRKHYESYEKAQKAKILSAINE 374
Query: 301 LPDSSWKKSLMEVVD 315
L + L +++
Sbjct: 375 LHHEGIEYVLKYLLE 389
>1yhl_A Farnesyl pyrophosphate synthase; farnesyl diphosphate synthase,
bisphosphonate, dimethyl allyl pyrophosphate sulfate,
FPPS, transferase; HET: DMA RIS; 1.95A {Trypanosoma
cruzi} PDB: 1yhk_A* 1yhm_A*
Length = 362
Score = 155 bits (393), Expect = 9e-39
Identities = 63/364 (17%), Positives = 124/364 (34%), Gaps = 48/364 (13%)
Query: 1 MKMLEDLTLKDMEKVNFLILKRICSDVEMIPDVVKYL------IFSGGKRLRPMLTLATA 54
M +E L ++V +L ++ S E+ P+ +YL GGK R M + A
Sbjct: 1 MASMERF-LSVYDEVQAFLLDQLQSKYEIDPNRARYLRIMMDTTCLGGKYFRGMTVVNVA 59
Query: 55 LMLEYRGDNH-----------VLLACAIEFIHTATLLHDDVVDDSALRRGKVAARLVWGN 103
+ + IEF+ L+ DD++D S +RRGK G
Sbjct: 60 EGFLAVTQHDEATKERILHDACVGGWMIEFLQAHYLVEDDIMDGSVMRRGKPCWYRFPGV 119
Query: 104 QTSVLVGDFLLSQAFCMVIETKS-------QEALEALSLVACTLAEGELR---------- 146
T + D ++ +++ ++ ++ L V A G++
Sbjct: 120 TTQCAINDGIILKSWTQIMAWHYFADRPFLKDLLCLFQKVDYATAVGQMYDVTSMCDSNK 179
Query: 147 ------QLSLSKNLDVTEEDYLHVIKSKTAVLFSAALEVSSLIAGVQNSVRQA--LKSYG 198
Q + + T Y ++K KT V L + + ++
Sbjct: 180 LDPEVAQPMTTDFAEFTPAIYKRIVKYKTTFYTYLLPLVMGLFVSEAAASVEMNLVERVA 239
Query: 199 MNLGIAFQLVDDVLDYRGEVNEMGKNIGEDFRNGKPTLPVILAFQRGTKREKNFWKSTIN 258
+G FQ+ DDV+D ++GK G D + K + + + + +K+
Sbjct: 240 HLIGEYFQVQDDVMDCFTPPEQLGKV-GTDIEDAKCSWLAVTFLGKANAAQVAEFKANY- 297
Query: 259 DGKISVENLKKAFIIMRENRALVDTEYRAYSYGQKAKDSLRCL--PDSSWKKSLMEVVDF 316
G + + E D ++ + + L ++ +S+ V +
Sbjct: 298 -GDKDPAKVAVVKRLYSEANLQADFAAYEAEVVREVESLIEQLKVKSPTFAESVAVVWEK 356
Query: 317 CLQR 320
+R
Sbjct: 357 THKR 360
>1wy0_A Geranylgeranyl pyrophosphate synthetase; structural genomics, riken
structural genomics/proteomics initiative, RSGI,
transferase; 2.20A {Pyrococcus horikoshii OT3}
Length = 342
Score = 152 bits (383), Expect = 1e-37
Identities = 96/340 (28%), Positives = 162/340 (47%), Gaps = 20/340 (5%)
Query: 1 MKMLEDLT---LKDMEKVNFLILKRICS-DVEMIPDVVKYLIFSGGKRLRPMLTLATALM 56
M+ E+L + + ++ I + I D ++ + ++ +GGKR+RP + L +
Sbjct: 1 MEKYEELFARIKEKAKLIDEKIFELIPEKDPRVLYEAARHYPLAGGKRVRPFVVLTSTEA 60
Query: 57 LEYRGDNHVLLACAIEFIHTATLLHDDVVDDSALRRGKVAARLVWGNQTSVLVGDFLLSQ 116
+ + A AIE IH +L+HDD++D RRGK +WG ++L GD L S+
Sbjct: 61 VGGDPLRAIYPAVAIELIHNYSLVHDDIMDMDETRRGKPTVHRIWGVNMAILAGDLLFSK 120
Query: 117 AFCMVIETKSQEAL-----EALSLVACTLAEGELRQLSLSKNLDVTEEDYLHVIKSKTAV 171
AF V + E + + L EG+ R L K VT E+Y+ +I KT
Sbjct: 121 AFEAVARAEIPPEKKARVLEVIVKASNELCEGQARDLEFEKKSTVTIEEYMEMISGKTGA 180
Query: 172 LFSAALEVSSLIAGVQNSVRQALKSYGMNLGIAFQLVDDVLDYRGEVNEMGKNIGEDFRN 231
LF A+ +V +I +AL S+G N+GIAFQ+ DDVLD + ++GK +G D R
Sbjct: 181 LFEASAKVGGIIGTDNEEYIKALSSWGRNVGIAFQIWDDVLDLIADEKKLGKPVGSDIRK 240
Query: 232 GKPTLPVILAFQRGTKREKNFWKSTINDG-----------KISVENLKKAFIIMRENRAL 280
GK TL V F+ +++K + + ++ +A ++++ ++
Sbjct: 241 GKKTLIVAHFFENADEKDKQRFLKIFGKYAGDVKGRGIIEEDIKSDVMEAIDLLKKYGSI 300
Query: 281 VDTEYRAYSYGQKAKDSLRCLPDSSWKKSLMEVVDFCLQR 320
A +KA ++LR LP S + L + F ++R
Sbjct: 301 DYAAEIAKDMIKKANEALRILPKSKARMDLELLAKFIVER 340
>1uby_A FPS, farnesyl diphosphate synthase; transferase, isoprene
biosynthesis, cholesterol biosynthesis; HET: DMA; 2.40A
{Gallus gallus} SCOP: a.128.1.1 PDB: 1ubw_A* 1ubv_A*
1ubx_A* 1fps_A
Length = 367
Score = 149 bits (377), Expect = 8e-37
Identities = 63/327 (19%), Positives = 117/327 (35%), Gaps = 29/327 (8%)
Query: 20 LKRICSDVEMIPDVVKYL------IFSGGKRLRPMLTLATALMLEYRGDNH-------VL 66
L + D V L GGK R + +A L G +
Sbjct: 42 LTEDGIGHPEVGDAVARLKEVLQYNAPGGKCNRGLTVVAAYRELSGPGQKDAESLRCALA 101
Query: 67 LACAIEFIHTATLLHDDVVDDSALRRGKVAARLVWGNQTSVLVGDFLLSQAFCMVIETKS 126
+ IE A+L+ DD++D S RRG++ G + FLL + V++
Sbjct: 102 VGWCIELFQAASLVADDIMDQSLTRRGQLCWYKKEGVGLDAINDSFLLESSVYRVLKKYC 161
Query: 127 QEA---LEALSLVACTLAEGELRQL--------SLSKNLDVTEEDYLHVIKSKTAVLFSA 175
++ + L L T + EL Q+ S +EE Y ++K KTA
Sbjct: 162 RQRPYYVHLLELFLQTAYQTELGQMLDLITAPVSKVDLSHFSEERYKAIVKYKTAFYSFY 221
Query: 176 A--LEVSSLIAGVQNSVRQALKSYGMNLGIAFQLVDDVLDYRGEVNEMGKNIGEDFRNGK 233
++ + K+ + +G FQ+ DD LD G+ + +G D ++ K
Sbjct: 222 LPVAAAMYMVGIDSKEEHENAKAILLEMGEYFQIQDDYLDCFGD-PALTGAVGTDIQDNK 280
Query: 234 PTLPVILAFQRGTKREKNFWKSTINDGKISVENLKKAFIIMRENRALVDTEYRAYSYGQK 293
+ V+ QR T ++ + G+ E + K + + S ++
Sbjct: 281 CSWLVVQCLQRVTPEQRQLLEDNY--GRKEPEKVAKVKELYEAVGMRAAFQQYEESSYRR 338
Query: 294 AKDSLRCLPDSSWKKSLMEVVDFCLQR 320
++ + + K+ + + +R
Sbjct: 339 LQELIEKHSNRLPKEIFLGLAQKIYKR 365
>2h8o_A Geranyltranstransferase; geranyltransferase,agrobacterium
tumefaciens, structural genomics, PSI-2, protein
structure initiative; 1.60A {Agrobacterium tumefaciens
str}
Length = 335
Score = 147 bits (372), Expect = 2e-36
Identities = 69/261 (26%), Positives = 118/261 (45%), Gaps = 15/261 (5%)
Query: 32 DVVKYLIFSGGKRLRPMLTLATALMLEYRGDNHVLLACAIEFIHTATLLHDDV--VDDSA 89
+ +++ + +GGKRLRP L + + +L + + + A+E +H +L+HDD+ +DD
Sbjct: 75 EAMRHGVLNGGKRLRPFLVIESVALLGGDAEAGLHVGAALECLHCYSLVHDDLPAMDDDD 134
Query: 90 LRRGKVAARLVWGNQTSVLVGDFLLSQAFCMVIETKSQEALEALSLVACTLAEGELRQLS 149
LRRG+ + T++L GD LL+ AF ++ + A E + + +LA
Sbjct: 135 LRRGQPTVHRKFDEATAILAGDSLLTLAFDIIASDDNPLAAERKAALVISLARAAGIGGM 194
Query: 150 LSKNL--------DVTEEDYLHVIKSKTAVLFSAALEVSSLIAGVQNSVRQALKSYGMNL 201
E+ + + KT L A E ++IAG + RQ L+ +G +
Sbjct: 195 AGGQALDLAAEKKAPDEDGIITLQAMKTGALLRFACEAGAIIAGSNQAERQRLRLFGEKI 254
Query: 202 GIAFQLVDDVLDYRGEVNEMGKNIGEDFRNGKPTLPVILAFQRGTKREKNFWKSTINDGK 261
G++FQL DD+LD + MGK G+D GK TL + ++ +
Sbjct: 255 GLSFQLADDLLDLTADAATMGKATGKDAARGKGTLVALRGEAWAREKLQEQVAEASELLA 314
Query: 262 I---SVENLKKA--FIIMREN 277
L A FI R++
Sbjct: 315 PYGEKAAILIAAARFIAERKS 335
>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 = 144 bits (364), Expect = 3e-35
Identities = 56/326 (17%), Positives = 119/326 (36%), Gaps = 33/326 (10%)
Query: 12 MEKVNFLILKRICSDVEMIPDVVKYL------IFSGGKRLRPMLTLATALML----EYRG 61
+ + + +LK++ + E+ V++Y GK +R + + + + +
Sbjct: 35 FKVIVYNVLKKLPLNDEIRKPVIEYYLNCIDYNVKKGKHIRGKILVLISSLSSAYSNIKR 94
Query: 62 DNHVLLACAIEFIHTATLLHDDVVDDSALRRGKVAARLVWGNQTSVLVGDFLLSQAFCMV 121
D+ LL +E I L+ DD++D RRG +V G ++ FL + ++
Sbjct: 95 DSIYLLGWVVEAIQALILIADDIMDSGKFRRGAPCWYIVHGQSNAINDIFFLKMLSLSLI 154
Query: 122 IETKSQEALEALSLVACTLAE----GELRQL-----SLSKNLDVTEEDY-LHVIKSKTAV 171
E S + + + E L Q D E Y V +
Sbjct: 155 FELSSVFGNDIVMKIQKIYNESIFFTVLGQHLDLSYFDLSKADKISERYFSMVEMKTSRY 214
Query: 172 LFSAALEVSSLIAGVQNSV--RQALKSYGMNLGIAFQLVDDVLDYRGEVNEMGKNIGEDF 229
F + ++ +Q S +++ LG +Q+ +DV DY + +D
Sbjct: 215 TFYMPVFFGLTLSEIQVSSAQLNLIEAILYKLGEFYQVHNDVSDYL-----FNDSNADDI 269
Query: 230 RNGKPTLPVILAFQRGTKREKNFWKSTINDGKISVENLKKAFIIMRENRALVDTEYRAYS 289
K T P+ +F+ + K + +K + +++ N ++ + A
Sbjct: 270 CRFKLTWPLQKSFEIADEEMKLKISENYGK---NSSLVKDCYNLLKINEHYLEYQRNALD 326
Query: 290 YGQKAKDSLRCLPDSSWKKSLMEVVD 315
Y ++ + D S +K + ++
Sbjct: 327 Y---LIKLVKDITDDSLQKVFIHLIH 349
>1wmw_A Geranylgeranyl diphosphate synthetase; GGPP, prenyl diphosphate
synthase, structural genomics; 1.55A {Thermus
thermophilus HB8}
Length = 330
Score = 128 bits (321), Expect = 2e-30
Identities = 67/321 (20%), Positives = 125/321 (38%), Gaps = 15/321 (4%)
Query: 13 EKVNFLILKRICSDVEMIPDVVKYLIFSGGKRLRPMLTLATALMLEYRGDNHVLLACAIE 72
+ + +L R+ + D+++ GGK LR +LT+ +AL + + A A+E
Sbjct: 10 QALQERLLARLDHPDPLYRDLLQDYPRRGGKMLRGLLTVYSALAHGAPLEAGLEAATALE 69
Query: 73 FIHTATLLHDDVVDDSALRRGKVAARLVWGNQTSVLVGDFLLSQAFCMVIETKSQEALEA 132
L+HDD+ D S RRG+ A + ++ GD + ++ + ++ E ++
Sbjct: 70 LFQNWVLVHDDIEDGSEERRGRPALHRLHPMPLALNAGDAMHAEMWGLLAEGLARGLFPP 129
Query: 133 LSLVA-------CTLAEGELRQLSLSKNLDVTEEDYLHVIKSKTAVLFSAALEVSSLIAG 185
L+ + +L D+ EDY ++ K A ++A +
Sbjct: 130 EVLLEFHEVVRRTAYGQHLDLLWTLGGTFDLRPEDYFRMVAHKAA-YYTAVAPLRLGALL 188
Query: 186 VQNSVRQALKSYGMNLGIAFQLVDDVLDYRGEVNEMGKNIGEDFRNGKPTLPVILAFQRG 245
+ A + G+ LG AFQ+VDDVL+ G GK D GK TL ++ +
Sbjct: 189 AGKTPPAAYEEGGLRLGTAFQIVDDVLNLEGG-EAYGKERAGDLYEGKRTLILLRFLEEA 247
Query: 246 TKREKNFWKSTINDGK--ISVENLKKAFIIMRENRALVDTEYRAYSYGQKAKDSLR---- 299
E+ + + + + + +RAL + A + L
Sbjct: 248 PPEERARALALLALPREAKPEAEVGWLLERLLASRALAWAKAEAKRLQAEGLALLEAAFQ 307
Query: 300 CLPDSSWKKSLMEVVDFCLQR 320
LP L ++ ++R
Sbjct: 308 DLPGKEALDHLRGLLAALVER 328
>2q80_A Geranylgeranyl pyrophosphate synthetase; isoprenoid pathway,
isopentenyl transferase, structural genomics, structural
genomics consortium, SGC; HET: GRG; 2.70A {Homo sapiens}
SCOP: a.128.1.1
Length = 301
Score = 127 bits (319), Expect = 3e-30
Identities = 53/290 (18%), Positives = 112/290 (38%), Gaps = 6/290 (2%)
Query: 32 DVVKYLIFSGGKRLRPMLTLATALMLEYRGDNHVLLACAIEFIHTATLLHDDVVDDSALR 91
+ KYL+ GK++R L+ A L+ D ++ E +H A+LL DD+ D+S LR
Sbjct: 15 EPYKYLLQLPGKQVRTKLSQAFNHWLKVPEDKLQIIIEVTEMLHNASLLIDDIEDNSKLR 74
Query: 92 RGKVAARLVWGNQTSVLVGDFLLSQAFCMVIETKSQEALEALSLVACTLAEGELRQLSLS 151
RG A ++G + + +++ V+ +A++ + L +G+ +
Sbjct: 75 RGFPVAHSIYGIPSVINSANYVYFLGLEKVLTLDHPDAVKLFTRQLLELHQGQGLDIYWR 134
Query: 152 KNLDVTEEDYLHVIKSKTAVLFSAALEVSSLIAGVQNSVRQALKSYGMNLGIAFQLVDDV 211
N E+ + + ++ + + + ++ LK LG+ FQ+ DD
Sbjct: 135 DNYTCPTEEEYKAMVLQK---TGGLFGLAVGLMQLFSDYKEDLKPLLNTLGLFFQIRDDY 191
Query: 212 LDYRGEVNEMGKNIGEDFRNGKPTLPVILAFQRGTKREKNFWKSTINDGKISVENLKKAF 271
+ + K+ ED GK + P I A E ++ + +++ K
Sbjct: 192 ANLHSKEYSENKSFCEDLTEGKFSFPTIHAIWSR--PESTQVQNILRQRTENIDIKKYCV 249
Query: 272 IIMRENRALVDTEYRAYSYGQKAKDSLRCLPDSSWKKSLME-VVDFCLQR 320
+ + + T KA + + +L++ + +
Sbjct: 250 HYLEDVGSFEYTRNTLKELEAKAYKQIDARGGNPELVALVKHLSKMFKEE 299
>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 = 124 bits (312), Expect = 2e-29
Identities = 62/338 (18%), Positives = 137/338 (40%), Gaps = 20/338 (5%)
Query: 3 MLEDLTLKDMEKVNFLILKRICSDVEMIPDVVKYLIFSGGKRLRPMLTLATALMLEYRGD 62
M ++ ++++ + +I +++ GK R L + ++ D
Sbjct: 1 MTKNKMEAKIDELINNDPVWSSQNESLISKPYNHILLKPGKNFRLNLIVQINRVMNLPKD 60
Query: 63 NHVLLACAIEFIHTATLLHDDVVDDSALRRGKVAARLVWGNQTSVLVGDFLLSQAFCMVI 122
+++ +E +H ++LL DD+ D++ LRRG+ + L++G +++ +++ +A +V
Sbjct: 61 QLAIVSQIVELLHNSSLLIDDIEDNAPLRRGQTTSHLIFGVPSTINTANYMYFRAMQLVS 120
Query: 123 ETKSQEALEALSL-----VACTLAEG---ELRQLSLSKNLDVTEEDYLHVIKSKTAVLFS 174
+ ++E L + L G ++ + T+E YL+++ +KT LF
Sbjct: 121 QLTTKEPLYHNLITIFNEELINLHRGQGLDIYWRDFLPEIIPTQEMYLNMVMNKTGGLFR 180
Query: 175 AALEVSSLIAGVQNSVRQALKSYGMNLGIAFQLVDDVLDYRGEVNEMGKNIGEDFRNGKP 234
L + ++ + + LGI +Q+ DD L+ + K ED GK
Sbjct: 181 LTLRLMEALSPSSHHGHSLVPFIN-LLGIIYQIRDDYLNLKDFQMSSEKGFAEDITEGKL 239
Query: 235 TLPVILAFQ----RGTKREKNFWKSTINDGKISVENLKKAF-IIMRENRALVDTEYRAYS 289
+ P++ A +G + N + + K I+ + +L T+
Sbjct: 240 SFPIVHALNFTKTKGQTEQHNEILRILLLRTSDKDIKLKLIQILEFDTNSLAYTKNFINQ 299
Query: 290 YGQKAKDS--LRCLPD----SSWKKSLMEVVDFCLQRL 321
K+ + LPD S +L + + + + L
Sbjct: 300 LVNMIKNDNENKYLPDLASHSDTATNLHDELLYIIDHL 337
>3ipi_A Geranyltranstransferase; isoprene biosynthesis, helical bundle,
protein structure initiative II (PSI II), structural
genomics, nysgxrc; 1.90A {Methanosarcina mazei}
Length = 295
Score = 124 bits (311), Expect = 3e-29
Identities = 63/310 (20%), Positives = 129/310 (41%), Gaps = 39/310 (12%)
Query: 8 TLKDMEKVNFLILKRI-CSDVEMIPDVVKYLIFSGGKRLRPMLTLATALMLEYRGDNHVL 66
++ V I + I + + +V+++ SGGKR+RP++ L + + +
Sbjct: 7 EWEEYRYVEAGIKESITLIEDPGLKKMVEHVCHSGGKRIRPIILLLVSEICSGSYSRSLN 66
Query: 67 LACAIEFIHTATLLHDDVVDDSALRRGKVAARLVWGNQTSVLVGDFLLSQAFCMVIETKS 126
A A+E +H+A+L+HDD++D +RR +A +G ++L GD+L++++ +
Sbjct: 67 AALAVEMMHSASLIHDDLLDQGLVRRNLPSAPEKFGPSGALLCGDYLIAKSIAFISPYGE 126
Query: 127 QEALEALSLVACTLAEGELRQLSLSKNLDVTEEDYLHVIKSKTAVLFSAALEVSSLIAGV 186
+ + L ++ E DY I KTA LF+ + + + G
Sbjct: 127 KVIQDFGKAGMDMAEGEVLDL--KLEDESFGENDYFKCIYKKTASLFAISASIGAYTGGA 184
Query: 187 QNSVRQALKSYGMNLGIAFQLVDDVLDYRGEVNEMGKNIGEDFRNGKPTLPVILAFQRGT 246
+ + + +G LG A+Q+VDD+L++ + G++ + TLP I
Sbjct: 185 EEELAERFSHFGNALGTAYQIVDDILEF------LEVVEGKESKFTSETLPHIYMKSTSK 238
Query: 247 KREKNFWKSTINDGKISVENLKKAFIIMRENRALVDTEYRAYSYGQKAKDSLRCLPDSSW 306
+ LKK+ ++ + AK++L +
Sbjct: 239 EEA-----------------LKKSIDCVKL-------------HVAAAKETLETFRECPA 268
Query: 307 KKSLMEVVDF 316
+ L ++ D+
Sbjct: 269 RDKLFQITDY 278
>1rtr_A Geranyltranstransferase; 2.50A {Staphylococcus aureus} SCOP:
a.128.1.1
Length = 301
Score = 122 bits (307), Expect = 9e-29
Identities = 73/288 (25%), Positives = 140/288 (48%), Gaps = 20/288 (6%)
Query: 10 KDMEKVNFLILKRICSDV--EMIPDVVKYLIFSGGKRLRPMLTLATALMLEYRGDNHVLL 67
K +++VN + I V + + + Y + +GGKR+RP+L L T L + +
Sbjct: 8 KLIDEVNNELSVAINKSVMDTQLEESMLYSLNAGGKRIRPVLLLLTLDSLNTEYELGMKS 67
Query: 68 ACAIEFIHTATLLHDDVVDDSALRRGKV--AARLVWGNQTSVLVGDFLLSQAFCMVIETK 125
A A+E IHT +L+HDD+ + V+G T++L GD LL++AF ++
Sbjct: 68 AIALEMIHTYSLIHDDLPAMDNDDYRRGKLTNHKVYGEWTAILAGDALLTKAFELISSDD 127
Query: 126 SQ------EALEALSLVACT--LAEGELRQLSLSKNLDVTEEDYLHVIKSKTAVLFSAAL 177
+ L+ LS+ + + G++ + S+ + E + K+KT L + A+
Sbjct: 128 RLTDEVKIKVLQRLSIASGHVGMVGGQMLDMQ-SEGQPIDLETLEMIHKTKTGALLTFAV 186
Query: 178 EVSSLIAGVQNSVRQALKSYGMNLGIAFQLVDDVLDYRGEVNEMGKNIGEDFRNGKPTLP 237
++ IA V ++ ++ L+SY +LG+ FQ+ DD+LD G+ ++GK +G D N K T
Sbjct: 187 MSAADIANVDDTTKEHLESYSYHLGMMFQIKDDLLDCYGDEAKLGKKVGSDLENNKSTYV 246
Query: 238 VILAFQRGTKREKNFWKSTIN-----DGKISVENLKKA--FIIMRENR 278
+L + + ++ D + + ++L + R+++
Sbjct: 247 SLLGKDGAEDKLTYHRDAAVDELTQIDEQFNTKHLLEIVDLFYSRDHK 294
>1v4e_A Octoprenyl-diphosphate synthase; trans-type prenyltransferase,
thermophilic; 2.28A {Thermotoga maritima} SCOP:
a.128.1.1 PDB: 1v4j_A 1wkz_A 1vg2_A 1wl3_A 1wl0_A 1wl2_A
1v4h_A 1v4i_A 1v4k_A 2azl_A 1wl1_A 1vg4_A 1vg3_A 1vg6_A
1vg7_A
Length = 299
Score = 122 bits (305), Expect = 2e-28
Identities = 76/305 (24%), Positives = 144/305 (47%), Gaps = 22/305 (7%)
Query: 10 KDMEKVNFLILKRICSDVEMIPDVVKYLIFSGGKRLRPMLTLATALMLEYR-GDNHVLLA 68
++EKV I + + + P+ + + GK LR L++ + G++ +
Sbjct: 11 YELEKVKERIEQIL---SQFFPEQIMKDLPLYGKMLRVRLSILSFKNRGVEIGEDAISSL 67
Query: 69 CAIEFIHTATLLHDDVVDDSALRRGKVAARLVWGNQTSVLVGDFLLSQAFCMVIETKSQE 128
A+E +H A+LLHDDV+D + RRGK ++G++ +V GD +L AF V E + +
Sbjct: 68 AALELVHLASLLHDDVIDGARFRRGKETINFMYGDKAAVAAGDLVLVSAFHTVEEIGNNK 127
Query: 129 ALEALSLVACTLAEGELRQLSLSKNLDVTEEDYLHVIKSKTAVLFSAALEVSSLIAGVQN 188
A V ++E E LS+ +T+E+YL +++ K+ LF AL++ +L+ +
Sbjct: 128 LRRAFLNVIGKMSEAE-LIEQLSRYKPITKEEYLRIVEGKSGALFGLALQLPALL---EG 183
Query: 189 SVRQALKSYGMNLGIAFQLVDDVLDYRGEVNEMGKNIGEDFRNGKPTLPVILAFQRGTKR 248
+ + L + G+ +G +Q+ DD++D+ G ++GK+ D +NG + P++ A ++ +
Sbjct: 184 ELGEDLYNLGVTIGTIYQMFDDIMDFAGM-EKIGKDGFLDLKNGVASFPLVTAMEKFPEA 242
Query: 249 EKNFWKSTINDGKISVENLKKAFIIMRENRALVDTEYRAYSYGQKA---KDSLRCLPDSS 305
+ F + MRE L + E + LR D
Sbjct: 243 RQMFEN----------RDWSGLMSFMREKGILKECEETLKVLVKNVIIENSWLRDFVDGI 292
Query: 306 WKKSL 310
+K +
Sbjct: 293 FKIKI 297
>1rqj_A Geranyltranstransferase; bisphosphonate, isoprenyl synthase; HET:
IPR RIS; 1.95A {Escherichia coli} SCOP: a.128.1.1 PDB:
1rqi_A* 2for_A*
Length = 299
Score = 118 bits (297), Expect = 1e-27
Identities = 74/294 (25%), Positives = 132/294 (44%), Gaps = 19/294 (6%)
Query: 2 KMLEDLTLKDMEKVNFLILKRICSDVEMIPDVVKYLIFSGGKRLRPMLTLATALMLEYRG 61
+ LE + + ++ I + ++ + ++Y GGKRLRP L AT M
Sbjct: 5 QQLEACVKQANQALSRFIAPLPFQNTPVV-ETMQYGALLGGKRLRPFLVYATGHMFGVST 63
Query: 62 DNHVLLACAIEFIHTATLLHDDVVDDSALRR--GKVAARLVWGNQTSVLVGDFLLSQAFC 119
+ A A+E IH +L+HDD+ G + +G ++L GD L + AF
Sbjct: 64 NTLDAPAAAVECIHAYSLIHDDLPAMDDDDLRRGLPTCHVKFGEANAILAGDALQTLAFS 123
Query: 120 MVIETKSQEA-----LEALSLVACT-----LAEGELRQLSLSKNLDVTEEDYLHVIKSKT 169
++ + E + +S +A + G+ L ++ V + + + KT
Sbjct: 124 ILSDADMPEVSDRDRISMISELASASGIAGMCGGQALDLD-AEGKHVPLDALERIHRHKT 182
Query: 170 AVLFSAALEVSSLIAGVQNSVRQ-ALKSYGMNLGIAFQLVDDVLDYRGEVNEMGKNIGED 228
L AA+ + +L AG + L Y ++G+AFQ+ DD+LD G+ +GK G D
Sbjct: 183 GALIRAAVRLGALSAGDKGRRALPVLDKYAESIGLAFQVQDDILDVVGDTATLGKRQGAD 242
Query: 229 FRNGKPTLPVILAFQRGTKREKNFWKSTINDGKISVENLKKAFIIMRENRALVD 282
+ GK T P +L ++ K+ ++ I+D + S++ L + + AL D
Sbjct: 243 QQLGKSTYPALLGLEQARKKARDL----IDDARQSLKQLAEQSLDTSALEALAD 292
>2j1p_A Geranylgeranyl pyrophosphate synthetase; transferase, isoprene
biosynthesis, multifunctional enzyme, carotenoid
biosynthesis; HET: GRG; 1.8A {Sinapis alba} PDB: 2j1o_A
Length = 293
Score = 118 bits (297), Expect = 1e-27
Identities = 70/290 (24%), Positives = 121/290 (41%), Gaps = 35/290 (12%)
Query: 9 LKDMEKVNFLILKRICSDV-EMIPDVVKYLIFSGGKRLRPMLTLATALMLEYRGDNHVLL 67
++ + VN + + I + ++Y + +GGKR+RP+L +A ++ +
Sbjct: 18 IRKADSVNKALDSAVPLREPLKIHEAMRYSLLAGGKRVRPVLCIAACELVGGEESLAMPA 77
Query: 68 ACAIEFIHTATLLHDDVV--DDSALRRGKVAARLVWGNQTSVLVGDFLLSQAFCMVIETK 125
ACA+E IHT +L+HDD+ D+ LRRGK V+G +VL GD LLS AF +
Sbjct: 78 ACAVEMIHTMSLIHDDLPCMDNDDLRRGKPTNHKVYGEDVAVLAGDALLSFAFEHLASAT 137
Query: 126 S-----QEALEALSLVACTLAEGELRQLSL-------SKNLDVTEEDYLHVIKSKTAVLF 173
S + A+ +A + L + +V E + KTA L
Sbjct: 138 SSEVSPARVVRAVGELAKAIGTEGLVAGQVVDISSEGLDLNNVGLEHLKFIHLHKTAALL 197
Query: 174 SAALEVSSLIAGVQNSVRQALKSYGMNLGIAFQLVDDVLDYRGEVNEMGKNIGEDFRNGK 233
A+ + +I G + + L+ + +G+ FQ+VDD+LD K
Sbjct: 198 EASAVLGGIIGGGSDEEIERLRKFARCIGLLFQVVDDILDVTKS--------------SK 243
Query: 234 PTLPVILAFQRGTKREKNFWKSTIND----GKISVENLKKA--FIIMREN 277
T P ++ ++ + + + V L +I R+N
Sbjct: 244 LTYPKLMGLEKSREFAEKLNTEARDQLLGFDSDKVAPLLALANYIANRQN 293
>2azj_A Geranylgeranyl pyrophosphate synthetase; hexpps,
trans-prenyltransferase; 2.40A {Sulfolobus solfataricus}
PDB: 2azk_A
Length = 289
Score = 112 bits (279), Expect = 1e-25
Identities = 68/281 (24%), Positives = 122/281 (43%), Gaps = 15/281 (5%)
Query: 1 MKMLEDLTLKDMEKVNFLILKRICSDVE-MIPDVVKYLIFSGGKRLRPMLTLATALMLEY 59
M ++E + ++ LI + + S+ + + D+ Y I GKR R L + + L
Sbjct: 9 MSIIEFWL-EAKATIDRLIEQFLNSNRDWDLVDISSY-ILKDGKRFRGTLNMFFTVALGG 66
Query: 60 RGDNHVLLACAIEFIHTATLLHDDVVDDSALRRGKVAARLVWGNQTSVLVGDFLLSQAFC 119
+ A AIE +H+A+L D+VD A RRG AA +V+GN+ + + ++L+ A
Sbjct: 67 DIKDSYGGALAIEILHSASLALCDIVDLDATRRGDKAAWVVYGNRKVIFITNYLIPTALR 126
Query: 120 MVIETKSQEALEALSLVACTLAEGELRQLSLSKNLDVTEEDYLHVIKSKTAVLFSAALEV 179
++ + +AL + + G LR DY+ I+ KT LF + +
Sbjct: 127 IIQTSYGDDALNTSIELWKDTSVGALRD-------MYDNSDYIRTIELKTGSLFKLSTVL 179
Query: 180 SSLIAGVQNSVRQALKSYGMNLGIAFQLVDDVLDYRGEVNE----MGKNIGEDFRNGKPT 235
S+ + N+ +Q L G LGI +Q++DD +DY+ + E K + + +R GK
Sbjct: 180 SAYASKHYNTKQQMLD-VGKYLGIIYQVIDDFVDYKTKKVEEIDGSAKQLFKYYREGKLE 238
Query: 236 LPVILAFQRGTKREKNFWKSTINDGKISVENLKKAFIIMRE 276
V + ++ + K E +
Sbjct: 239 EYVRSVYLEYKQKYDELISNIPFQSKYLSEIRSLPEFLANG 279
>2ftz_A Geranyltranstransferase; TM0161, structural genomics, joint center
for structural genomics, JCSG, protein structure
initiative, PSI; HET: MLY; 1.90A {Thermotoga maritima
MSB8}
Length = 284
Score = 101 bits (251), Expect = 3e-22
Identities = 47/267 (17%), Positives = 90/267 (33%), Gaps = 9/267 (3%)
Query: 13 EKVNFLILKRICSDVEMI-PDVVKYLIFSGGKRLRPMLTLATALMLEYRGDNHVLLACAI 71
E V I + + +++ + + Y GG R+RP+L L L + + +A A+
Sbjct: 16 EXVEERIREILRPGWDLLTEEAMLYSATVGGXRIRPLLVLTLGEDLGVEEEXLLDVAVAV 75
Query: 72 EFIHTATLLHDDVVDDSALRRGKVAARLVWGNQTSVLVGDFLLSQAFCMVIETKSQEALE 131
E HTA+L+HDD+ + + + + +
Sbjct: 76 ELFHTASLIHDDLPPIDNADFRRGXPSCHRTYGEDIALLAGDGLFFLAFSQISXIGNSXI 135
Query: 132 ALSLVACTLAEGELRQLSLSKNLDVTEEDYLHVIKSKTAVLFSAALEVSSLIAGVQ--NS 189
+ + E V + + AL A
Sbjct: 136 FEEFSETAYXLLLGEAMDVEFERRXMEVSQEMVERMYA--FXTGALFAFCFSAPFILXGX 193
Query: 190 VRQALKSYGMNLGIAFQLVDDVLDYRGEVNEMGKNIGEDFRNGKPTLPVILAFQRGTKRE 249
+ G G+AFQ+ DD+ D G ++GK++G+D TL + Q +
Sbjct: 194 DHTXMXLLGEXFGVAFQIYDDLXDILGSFEKVGKDLGKD--TEXVTLVXXVGIQXAREMA 251
Query: 250 KNFWKSTINDGKISVENLKKAFIIMRE 276
+++ + I E L + ++ E
Sbjct: 252 DXYYEEVL--XGIESEGLFRTLFLLXE 276
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl reductase,
beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces
cerevisiae}
Length = 2006
Score = 34.9 bits (80), Expect = 0.026
Identities = 38/172 (22%), Positives = 60/172 (34%), Gaps = 73/172 (42%)
Query: 186 VQNSVRQALK-SYGMNLGIAFQLVDDVLDYRGEVN-------EMGKNIGEDFRNGKPTLP 237
V N K +YG F ++D V++ VN E GK I E++
Sbjct: 1645 VWNRADNHFKDTYG------FSILDIVIN--NPVNLTIHFGGEKGKRIRENYS------- 1689
Query: 238 VILAFQRGTKREKNFWKSTINDGKISVENLKK--------------------------AF 271
+ F+ TI DGK+ E + K A
Sbjct: 1690 -AMIFE------------TIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPAL 1736
Query: 272 IIMR-------ENRALV--DTEYRAYSYGQKAKDSLRCLPDSSWKKSLMEVV 314
+M +++ L+ D + +S G+ A +L L D +SL+EVV
Sbjct: 1737 TLMEKAAFEDLKSKGLIPADATFAGHSLGEYA--ALASLADVMSIESLVEVV 1786
Score = 31.5 bits (71), Expect = 0.29
Identities = 22/175 (12%), Positives = 49/175 (28%), Gaps = 51/175 (29%)
Query: 130 LEALSLVACTLAEGELRQLSLSKNLDVTEEDYLHVIKSKTAVLFSAAL-EVSSLIAG--V 186
++A S TL+ G L L V + + + F+ L E + A
Sbjct: 1 MDAYSTRPLTLSHGSLEH-VLL----VPTASFFIASQLQEQ--FNKILPEPTEGFAADDE 53
Query: 187 QNSVRQALKSYGMNLG-IAFQLVDDVLDYRGEVNEMGKNIGEDFRNGKPTLPVIL-AFQR 244
+ + + + LG ++ + + +V L + L F+
Sbjct: 54 PTTPAELVGKF---LGYVSSLVEPSKVGQFDQV-----------------LNLCLTEFEN 93
Query: 245 GTKREKNFWKSTIN------DGKISVENLKKAFIIMRENRALVDTEYRAYSYGQK 293
+ I+ + +K +I + A ++
Sbjct: 94 CYLEGND-----IHALAAKLLQENDTTLVKTKELI----KNY----ITARIMAKR 135
>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 = 30.7 bits (68), Expect = 0.39
Identities = 11/41 (26%), Positives = 16/41 (39%), Gaps = 15/41 (36%)
Query: 276 ENRALVDTEYRAYSYGQKAKDSLRCLPDSSWK----KSLME 312
E +AL +K + SL+ D S K+ ME
Sbjct: 18 EKQAL-----------KKLQASLKLYADDSAPALAIKATME 47
Score = 28.8 bits (63), Expect = 1.5
Identities = 8/21 (38%), Positives = 11/21 (52%), Gaps = 5/21 (23%)
Query: 191 RQALKSYGMNLGIAFQL-VDD 210
+QALK L + +L DD
Sbjct: 19 KQALKK----LQASLKLYADD 35
>1ezf_A Farnesyl-diphosphate farnesyltransferase; isoprenoid synthase fold,
all alpha-helix; HET: IN0; 2.15A {Homo sapiens} SCOP:
a.128.1.2
Length = 340
Score = 29.9 bits (67), Expect = 0.82
Identities = 30/233 (12%), Positives = 66/233 (28%), Gaps = 37/233 (15%)
Query: 82 DDVVDDSALRRGKVAARLVW---------GNQTSVLVGDFLLSQAFCMVIETKSQEALEA 132
D + DD + K L D + + F + A +
Sbjct: 50 DTLEDDMTISVEKKVPLLHNFHSFLYQPDWRFMESKEKDRQVLEDFPTISLEFRNLAEKY 109
Query: 133 LSLVACTLAEGELRQLSLSKNLDVTEEDYLHVIKSKTAVLFSAALEVSSLIAGVQNSVRQ 192
+++A + +E+++ ++ + S + ++ +
Sbjct: 110 QTVIADICRRMGIGMAEFLDKHVTSEQEWDKYCHYVAGLVGIGLSRLFS-ASEFEDPLVG 168
Query: 193 ALKSYGMNLGIAFQLVDDVLDYRGEVNEMGKNIGEDFRNGKPTLPVILAFQRGTKREKNF 252
++G+ Q + + D ED + G+ P + + K +F
Sbjct: 169 EDTERANSMGLFLQKTNIIRD-----------YLEDQQGGREFWPQEVWSRYVKKLG-DF 216
Query: 253 WKSTINDGKISVENLKKAFIIMRENRALVDTEYRAYSYGQKAKDSLRCLPDSS 305
K EN+ A + E L+ A + L L + S
Sbjct: 217 AKP---------ENIDLAVQCLNE---LIT---NALHHIPDVITYLSRLRNQS 254
>3dxl_A Allergen AED A 2; odorant-binding protein, all-helical, secreted;
1.30A {Aedes aegypti} PDB: 3dy9_A 3dye_A* 3dzt_A*
Length = 303
Score = 28.8 bits (64), Expect = 1.5
Identities = 13/64 (20%), Positives = 29/64 (45%), Gaps = 6/64 (9%)
Query: 259 DGKISVENLKKAFIIMRENRALVD------TEYRAYSYGQKAKDSLRCLPDSSWKKSLME 312
D ++ VE +K+ F ++ ++ ++ + +K+ +CL +SS K E
Sbjct: 203 DNQLDVEEVKRDFKLVNKDTKALEEVLNDCKSKEPSNAKEKSWHYYKCLVESSVKDDFKE 262
Query: 313 VVDF 316
D+
Sbjct: 263 AFDY 266
>1gtt_A 4-hydroxyphenylacetate degradation bifunctional
isomerase/decarboxylase; lyase, bifunctional enzyme,
multifunctional enzyme decarboxylase; 1.7A {Escherichia
coli} SCOP: d.177.1.1 d.177.1.1 PDB: 1i7o_A
Length = 429
Score = 28.7 bits (64), Expect = 1.8
Identities = 4/28 (14%), Positives = 11/28 (39%)
Query: 212 LDYRGEVNEMGKNIGEDFRNGKPTLPVI 239
L++R +++ + + P V
Sbjct: 10 LNHRSQLDAWQEAFQQSPYKAPPKTAVW 37
>1g9k_A Serralysin; beta jelly roll, hydrolase; 1.96A {Pseudomonas} SCOP:
b.80.7.1 d.92.1.6 PDB: 1o0q_A 1o0t_A 1om6_A 1om7_A
1om8_A 1omj_A 1h71_P
Length = 463
Score = 28.0 bits (61), Expect = 2.6
Identities = 5/32 (15%), Positives = 11/32 (34%)
Query: 179 VSSLIAGVQNSVRQALKSYGMNLGIAFQLVDD 210
S A + + +L+S+ + F
Sbjct: 78 FSQFSALQKEQAKLSLESWADVAKVTFTEGPA 109
>1u6t_A SH3 domain-binding glutamic acid-rich-like protein; SH3-binding,
glutaredoxin, thioredoxin fold, crystallography, protein
binding; HET: CIT; 1.90A {Homo sapiens} PDB: 1wry_A
Length = 121
Score = 28.0 bits (62), Expect = 3.2
Identities = 13/71 (18%), Positives = 21/71 (29%), Gaps = 5/71 (7%)
Query: 171 VLFSAALEVSSLIAGVQNSVRQALKSYGMNLGIAFQLVDDVLDYRGEVNEMGKNIGED-F 229
++ A+ S+ I Q V L++ I F+ D +
Sbjct: 3 RVYIASSSGSTAIKKKQQDVLGFLEAN----KIGFEEKDIAANEENRKWMRENVPENSRP 58
Query: 230 RNGKPTLPVIL 240
G P P I
Sbjct: 59 ATGYPLPPQIF 69
>1itw_A Isocitrate dehydrogenase; greece KEY motif, oxidoreductase; HET:
ICT; 1.95A {Azotobacter vinelandii} SCOP: c.77.1.2 PDB:
1j1w_A*
Length = 741
Score = 27.0 bits (60), Expect = 5.9
Identities = 6/25 (24%), Positives = 11/25 (44%)
Query: 293 KAKDSLRCLPDSSWKKSLMEVVDFC 317
K D+ +PD + V++ C
Sbjct: 369 KLHDTKAVIPDRCYAGVYQVVIEDC 393
>2b0t_A NADP isocitrate dehydrogenase; monomeric, IDH, oxidoreductase;
1.75A {Corynebacterium glutamicum}
Length = 738
Score = 27.0 bits (60), Expect = 6.5
Identities = 8/25 (32%), Positives = 15/25 (60%)
Query: 293 KAKDSLRCLPDSSWKKSLMEVVDFC 317
+ +D+L +PDSS+ V++ C
Sbjct: 365 QEQDTLAIIPDSSYAGVYQTVIEDC 389
Database: pdb70
Posted date: Jan 26, 2011 11:21 AM
Number of letters in database: 5,693,230
Number of sequences in database: 24,244
Lambda K H
0.321 0.136 0.384
Gapped
Lambda K H
0.267 0.0493 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 2,632,263
Number of extensions: 117788
Number of successful extensions: 524
Number of sequences better than 10.0: 1
Number of HSP's gapped: 442
Number of HSP's successfully gapped: 52
Length of query: 322
Length of database: 5,693,230
Length adjustment: 93
Effective length of query: 229
Effective length of database: 3,438,538
Effective search space: 787425202
Effective search space used: 787425202
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: 57 (26.3 bits)