RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 018156
(360 letters)
>3apz_A Geranyl diphosphate synthase; prenyltransferase, all alpha-helices
fold, chroloplast, TRAN isoprenoid biosynthetic process;
2.60A {Arabidopsis thaliana} PDB: 3aq0_A*
Length = 348
Score = 362 bits (932), Expect = e-125
Identities = 215/347 (61%), Positives = 264/347 (76%), Gaps = 27/347 (7%)
Query: 41 NENKKHLDPFSLVGDELSLISMRLRSMVVAEVPELASAAGYFFKEGVEGKKLCPTVILLM 100
+ ++ LDPFSLV DELSL+S +LR MV+AEVP+LASAA YFFK GV+GK+ T++LLM
Sbjct: 2 SLVEEELDPFSLVADELSLLSNKLREMVLAEVPKLASAAEYFFKRGVQGKQFRSTILLLM 61
Query: 101 ATALNVCTPELSPNVLGNTLILDLRRRQQCIAEITEMIHVASLIHDDVLDDADTRRGIGS 160
ATAL+V PE + + +LR RQ+ IAEITEMIHVASL+HDDVLDDADTRRG+GS
Sbjct: 62 ATALDVRVPEALIGESTDIVTSELRVRQRGIAEITEMIHVASLLHDDVLDDADTRRGVGS 121
Query: 161 LSSVMGNKLAILAGDLLISRALVALASLKHTEVI-------------------------- 194
L+ VMGNK+++LAGD L+SRA ALA+LK+TEV+
Sbjct: 122 LNVVMGNKMSVLAGDFLLSRACGALAALKNTEVVALLATAVEHLVTGETMEITSSTEQRY 181
Query: 195 -MECYMQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTG 253
M+ YMQKTY KTA+L+SNSCKAVA L+GQ EVA LAFEYG+NLGLA+QLIDDILDFTG
Sbjct: 182 SMDYYMQKTYYKTASLISNSCKAVAVLTGQTAEVAVLAFEYGRNLGLAFQLIDDILDFTG 241
Query: 254 TSASLGKASLTDLRNGIITAPILFAMEEFPQLRAFINSSSDNPANVDVILEYLGKSHGIQ 313
TSASLGK SL+D+R+G+ITAPILFAMEEFPQLR ++ +P NVD+ LEYLGKS GIQ
Sbjct: 242 TSASLGKGSLSDIRHGVITAPILFAMEEFPQLREVVDQVEKDPRNVDIALEYLGKSKGIQ 301
Query: 314 RTTELALKHASLAAAAIDSLPETHDVDATNARTALVHITQKIITRNK 360
R ELA++HA+LAAAAI SLPET + D +R AL+ +T ++ITRNK
Sbjct: 302 RARELAMEHANLAAAAIGSLPETDNEDVKRSRRALIDLTHRVITRNK 348
>3pko_A Geranylgeranyl pyrophosphate synthase; isoprenyl diphosphate
synthase, structural genomics, PSI, PR structure
initiative, nysgrc; HET: CIT; 1.98A {Lactobacillus
brevis} PDB: 3n3d_A
Length = 334
Score = 239 bits (611), Expect = 7e-77
Identities = 81/347 (23%), Positives = 141/347 (40%), Gaps = 54/347 (15%)
Query: 43 NKKHLDPFSLVGDELSLISMRLRSMVVAEVPELASAAGYFFKEGVEGKKLCPTVILLMAT 102
+++ F V +L+ + L V + + K G GK L P L +T
Sbjct: 11 DRQLWRQFPQVEPQLTALQDYLLRTVQLDNQPIHHKILALLKSG--GKLLRPGYFYLFST 68
Query: 103 ALNVCTPELSPNVLGNTLILDLRRRQQCIAEITEMIHVASLIHDDVLDDADTRRGIGSLS 162
N TP + Q A E++HV +LIHDDV+DD+ TRRG+ ++
Sbjct: 69 FGNAATPA----------------QLQAGAAAIEILHVGTLIHDDVIDDSPTRRGVRTIQ 112
Query: 163 SVMGNKLAILAGDLLISRALVALA----------------------------SLKHTEVI 194
G + AI AGD + + + ++
Sbjct: 113 MTYGQRNAIYAGDFMFTVYFDQVLKSTTDRSLIQNHIDAMHRILQGELHQMDLNYREDIT 172
Query: 195 MECYMQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGT 254
++ Y+ + KTA L + SC A L+G + V + G +G AYQ++DDILD+ G
Sbjct: 173 LDAYLNEIAGKTAELFALSCYQGAQLAGAPQSVIDRTRDIGIAIGCAYQMLDDILDYAGD 232
Query: 255 SASLGKASLTDLRNGIITAPILFAMEEFP--QLRAFINSSSDNPANVDVILEYLGKSHGI 312
K L DLR+G+ + P+L ++ P + + ++ + + + G+
Sbjct: 233 PKRTQKPVLEDLRSGVYSLPLLLSLSHAPRDFHKLLKKKQAMTLEDIKHVQALVAQYDGV 292
Query: 313 QRTTELALKHASLAAAAIDSLPETHDVDATNARTALVHITQKIITRN 359
+LA + A I LP +A+ +L +T+ ++ R+
Sbjct: 293 GAAKQLAQDYTDRALTLIQQLPV------GSAQQSLEQLTRLLLRRD 333
>3aqb_B Component B of hexaprenyl diphosphate synthase; prenyltransferase,
transferase; 2.40A {Micrococcus luteus} PDB: 3aqc_B*
Length = 325
Score = 228 bits (583), Expect = 8e-73
Identities = 84/348 (24%), Positives = 151/348 (43%), Gaps = 58/348 (16%)
Query: 45 KHLDPFSLVGDELSLISMRLRSMVVAEVPELASAAGYFFKEGVEGKKLCPTVILLMATAL 104
L + + + + RL + ++ + AA + G GK++ P +LL
Sbjct: 2 IALSYKAFLNPYIIEVEKRLYECIQSDSETINKAAHHILSSG--GKRVRPMFVLLSGFLN 59
Query: 105 NVCTPELSPNVLGNTLILDLRRRQQCIAEITEMIHVASLIHDDVLDDADTRRGIGSLSSV 164
+ +L A E++H+ASL+HDD +D++D RRG S+
Sbjct: 60 DTQKDDLIR-----------------TAVSLELVHMASLVHDDYIDNSDMRRGNTSVHIA 102
Query: 165 MGNKLAILAGDLLISRALVALASLKHTEVI---------------------------MEC 197
AI G L++RAL +A++ +++
Sbjct: 103 FDKDTAIRTGHFLLARALQNIATINNSKFHQIFSKTILEVCFGEFDQMADRFNYPVSFTA 162
Query: 198 YMQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSAS 257
Y+++ KTA L+ SC A S E+ ++G +G++YQ+IDDILD+T A+
Sbjct: 163 YLRRINRKTAILIEASCHLGALSSQLDEQSTYHIKQFGHCIGMSYQIIDDILDYTSDEAT 222
Query: 258 LGKASLTDLRNGIITAPILFAM-----EEFPQLRAFI-NSSSDNPANVDVILEYLGKSHG 311
LGK +D+RNG IT P++ A+ ++ +L A + + +S + V + K +G
Sbjct: 223 LGKPVGSDIRNGHITYPLMAAIANLKEQDDDKLEAVVKHLTSTSDDEVYQYIVSQVKQYG 282
Query: 312 IQRTTELALKHASLAAAAIDSLPETHDVDATNARTALVHITQKIITRN 359
I+ L+ K+ A + L + +N + L I +K++ R
Sbjct: 283 IEPAELLSRKYGDKAKYHLSQLQD------SNIKDYLEEIHEKMLKRV 324
>3rmg_A Octaprenyl-diphosphate synthase; structural genomics, protein
structure initiative, isoprene biosynthesis,
transferase; 2.30A {Bacteroides thetaiotaomicron}
Length = 334
Score = 219 bits (561), Expect = 2e-69
Identities = 80/343 (23%), Positives = 138/343 (40%), Gaps = 58/343 (16%)
Query: 50 FSLVGDELSLISMRLRSMVVAEVPELASAAGYFFKEGVEGKKLCPTVILLMATALNVCTP 109
+ + EL + + L S + K GK + P ++LL+A TP
Sbjct: 10 KTPIEAELEDFKALFDTPLSDSNALLDSVITHIRKRN--GKMMRPILVLLVARLYGAVTP 67
Query: 110 ELSPNVLGNTLILDLRRRQQCIAEITEMIHVASLIHDDVLDDADTRRGIGSLSSVMGNKL 169
A E++H ASL+HDDV+D++ RRG S++++ NK+
Sbjct: 68 -----------------ATLHAAVSLELLHTASLVHDDVVDESTERRGQLSVNAIFNNKV 110
Query: 170 AILAGDLLISRALVALASLKHTEVI---------------------------MECYMQKT 202
++LAGD L++ +LV + E+I E Y
Sbjct: 111 SVLAGDYLLATSLVHAEQTNNYEIIRLVSSLGQKLAEGELLQLSNVSNHSFSEEVYFDVI 170
Query: 203 YNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASLGKAS 262
KTAAL + +A A EE A G+ +G+ +Q+ DDI D+ S +GK +
Sbjct: 171 RKKTAALFAACAEAAALSVQVGEEEVAFARLLGEYIGICFQIKDDIFDYFD-SKKIGKPT 229
Query: 263 LTDLRNGIITAPILFAM-----EEFPQLRAFINSSSDNPANVDVILEYLGKSHGIQRTTE 317
D+ G +T P L+A+ Q+ + + P + ++E+ + GI+
Sbjct: 230 GNDMLEGKLTLPALYALNTTKDAWAEQIAFKVKEGTATPDEIVRLIEFTKDNGGIEYACR 289
Query: 318 LALKHASLAAAAIDSLPETHDVDATNARTALVHITQKIITRNK 360
++ A + +LP+ +N AL ++ R K
Sbjct: 290 TIEQYKKKAFDLLAALPD------SNICLALRTYLDYVVAREK 326
>3oyr_A Trans-isoprenyl diphosphate synthase; isoprenyl synthase, PSI,
protein structure initiative; HET: IPE; 2.00A
{Caulobacter crescentus}
Length = 345
Score = 220 bits (562), Expect = 2e-69
Identities = 79/341 (23%), Positives = 132/341 (38%), Gaps = 57/341 (16%)
Query: 50 FSLVGDELSLISMRLRSMVVAEVPELASAAGYFFKEGVEGKKLCPTVILLMATALNVCTP 109
L +++ ++ + + ++V + + A + G GK+L P + + A
Sbjct: 28 VRLAEADMAGVNRLITDRMQSDVAIIPALAEHLIAAG--GKRLRPLMTVAAARLAGADND 85
Query: 110 ELSPNVLGNTLILDLRRRQQCIAEITEMIHVASLIHDDVLDDADTRRGIGSLSSVMGNKL 169
+A E IH A+L+HDDV+D + RRG + + G
Sbjct: 86 HFQK-----------------LAAAVEFIHTATLLHDDVVDGSQLRRGKVAAHLIWGGAQ 128
Query: 170 AILAGDLLISRALVALASLKHTEVI---------------------------MECYMQKT 202
++L GD L +RA + + + Y++
Sbjct: 129 SVLVGDFLFARAFELMVETNSMKALEILARASRVIAEGEVLQLMRSHDLNLSQAVYLEII 188
Query: 203 YNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASLGKAS 262
KTA L + + +A A +G + +YG NLGLA+QL DD LD+ G + +LGK +
Sbjct: 189 QAKTAELFAAASEAGAVSAGVDVAKSEALRDYGLNLGLAFQLADDALDYGGATETLGKNA 248
Query: 263 LTDLRNGIITAPILFAM-----EEFPQLRAFINSSSDNPANVDVILEYLGKSHGIQRTTE 317
D R G T P+L A+ E I A+ E + S + T +
Sbjct: 249 GDDFREGKATLPLLLAIARSGPREAEFWERAIGRREQTEADFRRARELIIGSGALDATLD 308
Query: 318 LALKHASLAAAAIDSLPETHDVDATNARTALVHITQKIITR 358
LA +A A AA+ P + R AL + ++R
Sbjct: 309 LAADYADKAKAALAMFPA------NDWREALEELADFAVSR 343
>3lmd_A Geranylgeranyl pyrophosphate synthase; isoprenyl diphosphate
synthase, structural genomics, PSI, protein structure
initiative, nysgrc; 1.90A {Corynebacterium glutamicum}
PDB: 3q2q_A*
Length = 360
Score = 218 bits (557), Expect = 2e-68
Identities = 82/338 (24%), Positives = 145/338 (42%), Gaps = 53/338 (15%)
Query: 50 FSLVGDELSLISMRLRSMVVAEVPELASAAGYFFKEGVEGKKLCPTVILLMATALNVCTP 109
+ + D + + L + + + L + + G GK+ P LL +
Sbjct: 37 TARINDAMVQVEELLHTELSSGEDFLVDIVMHLTRAG--GKRFRPMFALLAS---EFGEK 91
Query: 110 ELSPNVLGNTLILDLRRRQQCIAEITEMIHVASLIHDDVLDDADTRRGIGSLSSVMGNKL 169
LS NV+ A + E+ H+A+L HDDV+D+A RRG+ S ++ N +
Sbjct: 92 PLSENVIK-------------AAVVVEITHLATLYHDDVMDEASMRRGVPSANARWDNSV 138
Query: 170 AILAGDLLISRALVALASLKHTEV-------------------------IMECYMQKTYN 204
AILAGD+L++ A ++ L V +E Y
Sbjct: 139 AILAGDILLAHASGLMSQLGTDTVAHFAETFGELVTGQMRETVGPRDTDPIEHYTNVIRE 198
Query: 205 KTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASLGKASLT 264
KT L++++ A +G E +G +G+ +Q++DDI+D + GK T
Sbjct: 199 KTGVLIASAGYLGAMHAGAAPEHIDALKNFGAAVGMIFQIVDDIIDIFSETHESGKTPGT 258
Query: 265 DLRNGIITAPILFAM----EEFPQLRAFINSSSDNPANVDVILEYLGKSHGIQRTTELAL 320
DLR G+ T P+L+A+ +LR + ++ V+ +LE L +S G Q +
Sbjct: 259 DLREGVFTLPVLYALREDTPVGAELRDILTGPLEDDETVNHVLELLSQSGGRQAALDEVY 318
Query: 321 KHASLAAAAIDSLPETHDVDATNARTALVHITQKIITR 358
++ +A A +D LP+ + + AL ++ + R
Sbjct: 319 RYMDIANAELDRLPD------STVKEALRNLATFTVKR 350
>3mzv_A Decaprenyl diphosphate synthase; transferase, structural genomics,
PSI-2, protein structure initiative; 1.90A {Rhodobacter
capsulatus}
Length = 341
Score = 209 bits (535), Expect = 2e-65
Identities = 80/358 (22%), Positives = 146/358 (40%), Gaps = 64/358 (17%)
Query: 39 NSNENKKHLDPFSLVGDELS----LISMRLRSMVVAEVPELASAAGYFFKEGVEGKKLCP 94
+ K H + ++++ LI R+ S +PE+ + + + G GK+L P
Sbjct: 4 DDKATKPHDRLAQALAEDMAAVNALIRERMSSEHAPRIPEVTA---HLIEAG--GKRLRP 58
Query: 95 TVILLMATALNVCTPELSPNVLGNTLILDLRRRQQCIAEITEMIHVASLIHDDVLDDADT 154
+ L A + P +A E IH A+L+HDDV+D++
Sbjct: 59 MLTLAAARLVGYGGPFHVH-----------------LAATVEFIHTATLLHDDVVDESRQ 101
Query: 155 RRGIGSLSSVMGNKLAILAGDLLISRALVALASLKHTEVI-------------------- 194
RRG + + + NK ++L GD L +R+ + + V+
Sbjct: 102 RRGRPTANLLWDNKSSVLVGDYLFARSFQLMTDTGNMRVMEILANASAVIAEGEVLQLTA 161
Query: 195 -------MECYMQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDD 247
+ Y++ KTAAL S + + + G E+ F+YG LG+A+Q++DD
Sbjct: 162 AQNLATTEDIYLRVIRGKTAALFSAATEVGGIIGGAPEDQVQALFDYGDALGIAFQIVDD 221
Query: 248 ILDFTGTSASLGKASLTDLRNGIITAPILFAM-----EEFPQLRAFINSSSDNPANVDVI 302
+LD+ G SA +GK + D R +T P++ A+ E + I +++
Sbjct: 222 LLDYGGKSAEIGKNTGDDFRERKLTMPVIKAVALADEAERAFWKRVIEKGDQQDGDLEHA 281
Query: 303 LEYLGKSHGIQRTTELALKHASLAAAAIDSLPETHDVDATNARTALVHITQKIITRNK 360
+ + K ++ T A+ A A+ LP+ R L + ++ R +
Sbjct: 282 MALMTKHGTLEATRLAAIGWTDTARKALAKLPD------HPLRQMLDDLADYVVERVR 333
>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 = 200 bits (510), Expect = 3e-62
Identities = 67/327 (20%), Positives = 125/327 (38%), Gaps = 56/327 (17%)
Query: 47 LDPFSLVGDELSLISMRLRSMVVAEVPELASAAGYFFKEGVEGKKLCPTVILLMATALNV 106
+ + EL + R+ ++ PE GK L + +L V
Sbjct: 3 KNKLNQNSYELEKVKERIEQILSQFFPEQIM---KDLPLY--GKMLRVRLSILSFKNRGV 57
Query: 107 CTPELSPNVLGNTLILDLRRRQQCIAEITEMIHVASLIHDDVLDDADTRRGIGSLSSVMG 166
++ E++H+ASL+HDDV+D A RRG +++ + G
Sbjct: 58 ----------------EIGEDAISSLAALELVHLASLLHDDVIDGARFRRGKETINFMYG 101
Query: 167 NKLAILAGDLLISRALVALASLKHTEVI--------------------------MECYMQ 200
+K A+ AGDL++ A + + + ++ E Y++
Sbjct: 102 DKAAVAAGDLVLVSAFHTVEEIGNNKLRRAFLNVIGKMSEAELIEQLSRYKPITKEEYLR 161
Query: 201 KTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASLGK 260
K+ AL + + A L G+ E + G +G YQ+ DDI+DF G +GK
Sbjct: 162 IVEGKSGALFGLALQLPALLEGELGED---LYNLGVTIGTIYQMFDDIMDFAGM-EKIGK 217
Query: 261 ASLTDLRNGIITAPILFAMEEFPQLRAFINSSSDNPANVDVILEYLGKSHGIQRTTELAL 320
DL+NG+ + P++ AME+FP+ R + + ++ ++ + ++ E
Sbjct: 218 DGFLDLKNGVASFPLVTAMEKFPEARQMFEN-----RDWSGLMSFMREKGILKECEETLK 272
Query: 321 KHASLAAAAIDSLPETHDVDATNARTA 347
L + D ++
Sbjct: 273 VLVKNVIIENSWLRDFVDGIFKIKISS 299
>3tc1_A Octaprenyl pyrophosphate synthase; all alpha-helices fold,
transferase; 2.00A {Helicobacter pylori}
Length = 315
Score = 199 bits (508), Expect = 1e-61
Identities = 71/338 (21%), Positives = 130/338 (38%), Gaps = 62/338 (18%)
Query: 52 LVGDELSLISMRLRS-MVVAEVPELASAAGYFFKEGVEGKKLCPTVILLMATALNVCTPE 110
+ +L I ++ S + E + + + LL + +
Sbjct: 1 MQEKQLKAIQNKIASWIKEIESGFIDELFSKIGPSK--MLRSKLMLALLNEKTDAILLDK 58
Query: 111 LSPNVLGNTLILDLRRRQQCIAEITEMIHVASLIHDDVLDDADTRRGIGSLSSVMGNKLA 170
+ I EMI ASL+HDDV+D A RR + S++++ GN A
Sbjct: 59 ALN-----------------LCTIVEMIQTASLLHDDVIDKATMRRKLPSINALFGNFNA 101
Query: 171 ILAGDLLISRALVALASL--------------------------KHTEVIMECYMQKTYN 204
++ GD+ S+A L+ + + + Y + +
Sbjct: 102 VMLGDVFYSKAFFELSKMGELIAQALSNAVLRLSRGEIEDVFVGECFNSDKQKYWRILED 161
Query: 205 KTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASLGKASLT 264
KTA + S K++A L + ++ ++G N G+A+Q+IDD+LD T + +LGK + +
Sbjct: 162 KTAHFIEASLKSMAILLNKDAKI---YADFGLNFGMAFQIIDDLLDITQDAKTLGKPNFS 218
Query: 265 DLRNGIITAPILFAMEEF-PQLRAFINS--SSDNPANVDVILEYLGKSHGIQRTTELALK 321
D + G T P L E+ + + S D+ ++ E + I+ T + A
Sbjct: 219 DFKEGKTTLPYLLLYEKLNQHDQGLLISYFKQDSHEIIEWTKEKFKQYGIIEETLKTAQV 278
Query: 322 HASLAAAAIDSLPETHDVDATNARTALVHITQKIITRN 359
++ A AI L + Q +I+R
Sbjct: 279 YSKKALEAIKGEN----------NLILEKLAQDVISRT 306
>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 = 184 bits (469), Expect = 5e-56
Identities = 61/329 (18%), Positives = 107/329 (32%), Gaps = 61/329 (18%)
Query: 64 LRSMVVAEVPELASAAGYFFKEGVEGKKLCPTVILLMATALNVCTPELSPNVLGNTLILD 123
+ L Y + GK++ + L V +L
Sbjct: 2 MEKTQETVQRILLEPYKYLLQLP--GKQVRTKLSQAFNHWLKVPEDKLQI---------- 49
Query: 124 LRRRQQCIAEITEMIHVASLIHDDVLDDADTRRGIGSLSSVMGNKLAILAGDLLISRALV 183
I E+TEM+H ASL+ DD+ D++ RRG S+ G I + + + L
Sbjct: 50 -------IIEVTEMLHNASLLIDDIEDNSKLRRGFPVAHSIYGIPSVINSANYVYFLGLE 102
Query: 184 ALASLKHTEVI----------------------------MECYMQKTYNKTAALVSNSCK 215
+ +L H + + E Y KT L +
Sbjct: 103 KVLTLDHPDAVKLFTRQLLELHQGQGLDIYWRDNYTCPTEEEYKAMVLQKTGGLFGLAVG 162
Query: 216 AVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASLGKASLTDLRNGIITAPI 275
+ S +E++ LGL +Q+ DD + S K+ DL G + P
Sbjct: 163 LMQLFSDYKEDLK----PLLNTLGLFFQIRDDYANLHSKEYSENKSFCEDLTEGKFSFPT 218
Query: 276 LFAMEEFP---QLRAFINSSSDNPANVDVILEYLGKSHGIQRTTELALKHASLAAAAIDS 332
+ A+ P Q++ + ++N + YL + T + + A ID+
Sbjct: 219 IHAIWSRPESTQVQNILRQRTENIDIKKYCVHYLEDVGSFEYTRNTLKELEAKAYKQIDA 278
Query: 333 LPETHDVDATNARTALVH-ITQKIITRNK 360
ALV +++ N+
Sbjct: 279 RGGNP------ELVALVKHLSKMFKEENE 301
>1wy0_A Geranylgeranyl pyrophosphate synthetase; pyrococcus horikosh
structural genomics, riken structural
genomics/proteomics initiative, RSGI; 2.20A {Pyrococcus
horikoshii}
Length = 342
Score = 182 bits (465), Expect = 6e-55
Identities = 86/365 (23%), Positives = 143/365 (39%), Gaps = 74/365 (20%)
Query: 44 KKHLDPFSLVGDELSLISMRLRS-MVVAEVPELASAAGYFFKEGVEGKKLCPTVILLMAT 102
+K+ + F+ + ++ LI ++ + + L AA ++ G GK++ P V+L
Sbjct: 2 EKYEELFARIKEKAKLIDEKIFELIPEKDPRVLYEAARHYPLAG--GKRVRPFVVLTSTE 59
Query: 103 ALNVCTPELSPNVLGNTLILDLRRRQQCIAEITEMIHVASLIHDDVLDDADTRRGIGSLS 162
A+ A E+IH SL+HDD++D +TRRG ++
Sbjct: 60 AVGGDPLRAIY-----------------PAVAIELIHNYSLVHDDIMDMDETRRGKPTVH 102
Query: 163 SVMGNKLAILAGDLLISRALVALASL--------------------------------KH 190
+ G +AILAGDLL S+A A+A K
Sbjct: 103 RIWGVNMAILAGDLLFSKAFEAVARAEIPPEKKARVLEVIVKASNELCEGQARDLEFEKK 162
Query: 191 TEVIMECYMQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILD 250
+ V +E YM+ KT AL S K + EE +G+N+G+A+Q+ DD+LD
Sbjct: 163 STVTIEEYMEMISGKTGALFEASAKVGGIIGTDNEEYIKALSSWGRNVGIAFQIWDDVLD 222
Query: 251 FTGTSASLGKASLTDLRNGIITAPILFAME-----EFPQLRAFINSSSDNP--------- 296
LGK +D+R G T + E + + + +
Sbjct: 223 LIADEKKLGKPVGSDIRKGKKTLIVAHFFENADEKDKQRFLKIFGKYAGDVKGRGIIEED 282
Query: 297 --ANVDVILEYLGKSHGIQRTTELALKHASLAAAAIDSLPETHDVDATNARTALVHITQK 354
++V ++ L K I E+A A A+ LP+ + AR L + +
Sbjct: 283 IKSDVMEAIDLLKKYGSIDYAAEIAKDMIKKANEALRILPK------SKARMDLELLAKF 336
Query: 355 IITRN 359
I+ R
Sbjct: 337 IVERE 341
>3ipi_A Geranyltranstransferase; isoprene biosynthesis, helical bundle,
protein structure initiative II (PSI II), structural
genomics, nysgxrc; 1.90A {Methanosarcina mazei}
Length = 295
Score = 180 bits (459), Expect = 1e-54
Identities = 71/330 (21%), Positives = 117/330 (35%), Gaps = 82/330 (24%)
Query: 55 DELSLISMRLRS-MVVAEVPELASAAGYFFKEGVEGKKLCPTVILLMATALNVCTPELSP 113
+E + ++ + + E P L + G GK++ P ++LL++ +
Sbjct: 9 EEYRYVEAGIKESITLIEDPGLKKMVEHVCHSG--GKRIRPIILLLVSEICSGSYSRSLN 66
Query: 114 NVLGNTLILDLRRRQQCIAEITEMIHVASLIHDDVLDDADTRRGIGSLSSVMGNKLAILA 173
A EM+H ASLIHDD+LD RR + S G A+L
Sbjct: 67 -----------------AALAVEMMHSASLIHDDLLDQGLVRRNLPSAPEKFGPSGALLC 109
Query: 174 GDLLISRALVALASL-------------------------KHTEVIMECYMQKTYNKTAA 208
GD LI++++ ++ + Y + Y KTA+
Sbjct: 110 GDYLIAKSIAFISPYGEKVIQDFGKAGMDMAEGEVLDLKLEDESFGENDYFKCIYKKTAS 169
Query: 209 LVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASLGKASLTDLRN 268
L + S AY G EE+A +G LG AYQ++DDIL+F GK + +
Sbjct: 170 LFAISASIGAYTGGAEEELAERFSHFGNALGTAYQIVDDILEFLEVVE--GK----ESKF 223
Query: 269 GIITAPILFAMEEFPQLRAFINSSSDNPANVDVILEYLGKSHGIQRTTELALKHASLAAA 328
T P ++ K ++++ + H + A
Sbjct: 224 TSETLPHIYMKST-------------------------SKEEALKKSIDCVKLHVAAAKE 258
Query: 329 AIDSLPETHDVDATNARTALVHITQKIITR 358
+++ E AR L IT I
Sbjct: 259 TLETFRE------CPARDKLFQITDYITVD 282
>4dhd_A Polyprenyl synthetase; isoprenoid synthesis, isoprenoid diphosphate
synthase, trans; 1.65A {Pyrobaculum calidifontis}
Length = 358
Score = 175 bits (446), Expect = 5e-52
Identities = 69/356 (19%), Positives = 115/356 (32%), Gaps = 75/356 (21%)
Query: 51 SLVGDELSLISMRLRSMVVAEVPE-LASAAGYFFKEGVEGKKLCPTVILLMATALNVCTP 109
L + + L + + E A Y K G GK+L P + L A A++
Sbjct: 8 RLHQKYGAEVEKALVRYLSIGLAEDFREAVLYQVKTG--GKRLRPLLTLAAAEAVSGQWR 65
Query: 110 ELSPNVLGNTLILDLRRRQQCIAEITEMIHVASLIHDDVLDDADTRRGIGSLSSVMGNKL 169
P A I E+IH SLI+DD++D D RRG+ ++ G+
Sbjct: 66 PALP-----------------AAAIVELIHNYSLIYDDIIDRGDVRRGLPTVRKAFGDNA 108
Query: 170 AILAGDLLISRALVALASLKHTEVIMEC-------------------------------- 197
AIL G A+ + +
Sbjct: 109 AILVGIWYREAIEEAVLDTPKPTLFAKEVAEVIKAIDEGERLDILFEAAGRSDPYFVQAR 168
Query: 198 --------YMQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDIL 249
Y++ KT AL++ + K +A A+ +G G+A+Q+IDD+L
Sbjct: 169 WREVTLDDYIKMVSLKTGALIAAAAKWGVLSVSDDRGLAEAAWNFGMAAGVAFQIIDDVL 228
Query: 250 DFTGTSASLGKASLTDLRNGIITAPILFAM------EEFPQLRAFINSSSDNPANVDVIL 303
D G GK D++ ++ E +L + A+V +
Sbjct: 229 DIYGDPKKFGKEIGKDIKEHKRGNAVVAVALSHLGEGERRRLLEILAREVVEEADVREAV 288
Query: 304 EYLGKSHGIQRTTELALKHASLAAAAIDSLPETHDVDATNARTALVHITQKIITRN 359
L + LA ++ A + +P L + I+ R
Sbjct: 289 ALLDSVGAREEALRLAARYREEAERHLAKIPN---------NGTLKELLDFIVARE 335
>2azj_A Geranylgeranyl pyrophosphate synthetase; hexpps,
trans-prenyltransferase; 2.40A {Sulfolobus solfataricus}
PDB: 2azk_A
Length = 289
Score = 169 bits (429), Expect = 3e-50
Identities = 53/302 (17%), Positives = 99/302 (32%), Gaps = 48/302 (15%)
Query: 40 SNENKKHLDPFSLVGDELSLISMRLRSMVVAEVPELASAAGYFFKEGVEGKKLCPTVILL 99
++ + H+ + + I + + + + + GK+ T+ +
Sbjct: 2 AHHHHHHMSIIEFWLEAKATIDRLIEQFLNSNRDWDLVDISSYILKD--GKRFRGTLNMF 59
Query: 100 MATALNVCTPELSPNVLGNTLILDLRRRQQCIAEITEMIHVASLIHDDVLDDADTRRGIG 159
AL + A E++H ASL D++D TRRG
Sbjct: 60 FTVALGGDIKDSYG-----------------GALAIEILHSASLALCDIVDLDATRRGDK 102
Query: 160 SLSSVMGNKLAILAGDLLISRALVALASLKHTEVI--------------------MECYM 199
+ V GN+ I + LI AL + + + + Y+
Sbjct: 103 AAWVVYGNRKVIFITNYLIPTALRIIQTSYGDDALNTSIELWKDTSVGALRDMYDNSDYI 162
Query: 200 QKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSA--- 256
+ KT +L S AY S + + GK LG+ YQ+IDD +D+
Sbjct: 163 RTIELKTGSLFKLSTVLSAYASKHYNTKQQML-DVGKYLGIIYQVIDDFVDYKTKKVEEI 221
Query: 257 -SLGKASLTDLRNGIITAPILFAMEEF-PQLRAFINS---SSDNPANVDVILEYLGKSHG 311
K R G + + E+ + I++ S + + + E+L
Sbjct: 222 DGSAKQLFKYYREGKLEEYVRSVYLEYKQKYDELISNIPFQSKYLSEIRSLPEFLANGLL 281
Query: 312 IQ 313
+
Sbjct: 282 KE 283
>3nf2_A Putative polyprenyl synthetase; isoprenyl diphosphate synthase,
structural genomics, PSI, PR structure initiative,
nysgrc; 2.20A {Streptomyces coelicolor}
Length = 352
Score = 170 bits (432), Expect = 5e-50
Identities = 66/339 (19%), Positives = 125/339 (36%), Gaps = 65/339 (19%)
Query: 63 RLRSMVVAEVPELASAAGYFFKEGVEGKKLCPTVILLMATALNVCTPELSPNVLGNTLIL 122
+ ++ + + +G GK + P + +L A P
Sbjct: 30 PMDTVAAYHFGWIDAQGNPADGDG--GKAVRPALAVLSAEVTGAAPEVGVP--------- 78
Query: 123 DLRRRQQCIAEITEMIHVASLIHDDVLDDADTRRGIGSLSSVMGNKLAILAGDLLISRA- 181
A E++H SL+HDD++D + RR ++ V G AIL GD L + A
Sbjct: 79 --------GAVAVELVHNFSLLHDDLMDGDEQRRHRDTVWKVHGPAQAILVGDALFALAN 130
Query: 182 --LVALASLKHTEVI---------------------------MECYMQKTYNKTAALVSN 212
L+ L +++ +E ++ NKT AL++
Sbjct: 131 EVLLELGTVEAGRATRRLTKASRSLIDGQAQDISYEHRDRVSVEECLEMEGNKTGALLAC 190
Query: 213 SCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASLGKASLTDLRNGIIT 272
+ A L G E A +YG +LGLA+Q +DD+L G + GK + +DLR +
Sbjct: 191 ASSIGAVLGGADERTADTLEKYGYHLGLAFQAVDDLLGIWGDPDATGKQTWSDLRQRKKS 250
Query: 273 APILFAMEE-FPQLRAFI----------NSSSDNPANVDVILEYLGKSHGIQRTTELALK 321
P++ A+ + ++ + + ++ G + T + A +
Sbjct: 251 LPVVAALAAGGAASERLGEILTADAKASDFANFSEEEFAARAALIEEAGGREWTADEARR 310
Query: 322 HASLAAAAIDSLPETHDVDATNARTALVHITQKIITRNK 360
++A A+D++ R + ++ R +
Sbjct: 311 QHTIAIEALDAVDMPDR-----VRDRFTALADFVVVRKR 344
>4fp4_A Polyprenyl synthetase; isoprenoid synthesis, isoprenoid diphosphate
synthase, trans; HET: GER UNL; 2.00A {Pyrobaculum
calidifontis}
Length = 285
Score = 155 bits (395), Expect = 2e-45
Identities = 60/303 (19%), Positives = 107/303 (35%), Gaps = 51/303 (16%)
Query: 50 FSLVGDELSLISMRLRSMVVAEVPE-LASAAGYFFKEGVEGKKLCPTVILLMATALNVCT 108
V L + RL + P L A ++ + GK L P ++L +++
Sbjct: 7 PPEVLAALERVKARLNKVGEELEPISLRKAVRHYIETP--GKLLRPLLLLTFTYSID-RR 63
Query: 109 PELSPNVLGNTLILDLRRRQQCIAEITEMIHVASLIHDDVLDDADTRRGIGSLSSVMGNK 168
+ P +L A I E++HV SL+ DDV+D D RRGI + ++ G+
Sbjct: 64 SIMDPRILE-------------AAAIVELLHVVSLLQDDVMDQHDQRRGIKTPRAMYGDG 110
Query: 169 LAILAGDLLISRALVALASL---------KHTEVI--------MECYMQKTYNKTAALVS 211
AI+A D LI+ ++ +L + + + KTA L+
Sbjct: 111 RAIVASDWLIAESIKMAVNLGADVVTYLADVAQRLSVGQALDLEGERDKAAEFKTAPLIE 170
Query: 212 NSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASLGKASLTDLRNGII 271
+ + G+RE + T + G LG+ YQ DD D K+ ++ G
Sbjct: 171 AALVMPLVILGRRELIETAK-KLGTKLGILYQYSDDYSDENVERPE-TKSIANEI--GRY 226
Query: 272 TAPILFAM-----EEFPQLRAFINSSSDNPANVDVILEYLGKSHGIQRTTELALKHASLA 326
I + ++ I + + V + + + H
Sbjct: 227 LLKIKEHVGDAIAPFERLIKYLIGKALEGTLTVSRTIA--------ENLYFQSHHHHHHW 278
Query: 327 AAA 329
+
Sbjct: 279 SHP 281
>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 = 153 bits (389), Expect = 6e-44
Identities = 53/353 (15%), Positives = 115/353 (32%), Gaps = 65/353 (18%)
Query: 51 SLVGDELSLISMRLRSMVVAEVPELASAAGYFFKEGVEGKKLCPTVILLMATALNVCTPE 110
+ + ++ + ++ + + GK +I+ + +N+ +
Sbjct: 4 NKMEAKIDELINNDPVWSSQNESLISKPYNHILLKP--GKNFRLNLIVQINRVMNLPKDQ 61
Query: 111 LSPNVLGNTLILDLRRRQQCIAEITEMIHVASLIHDDVLDDADTRRGIGSLSSVMGNKLA 170
L+ +++I E++H +SL+ DD+ D+A RRG + + G
Sbjct: 62 LAI-----------------VSQIVELLHNSSLLIDDIEDNAPLRRGQTTSHLIFGVPST 104
Query: 171 ILAGDLLISRALVALASLKH-----------------------------------TEVIM 195
I + + RA+ ++ L
Sbjct: 105 INTANYMYFRAMQLVSQLTTKEPLYHNLITIFNEELINLHRGQGLDIYWRDFLPEIIPTQ 164
Query: 196 ECYMQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTS 255
E Y+ NKT L + + + LS +L + LG+ YQ+ DD L+
Sbjct: 165 EMYLNMVMNKTGGLFRLTLRLMEALSPSSHHGHSLV-PFINLLGIIYQIRDDYLNLKDFQ 223
Query: 256 ASLGKASLTDLRNGIITAPILFAME------EFPQLRAFINSSSDNPANVDV---ILEYL 306
S K D+ G ++ PI+ A+ + Q + ++ D+ +++ L
Sbjct: 224 MSSEKGFAEDITEGKLSFPIVHALNFTKTKGQTEQHNEILRILLLRTSDKDIKLKLIQIL 283
Query: 307 GKSHG-IQRTTELALKHASLAAAAIDSLPETHDVDATNARTALVHITQKIITR 358
+ T + ++ ++ ++ T L II
Sbjct: 284 EFDTNSLAYTKNFINQLVNMIKNDNENKYLPDLASHSDTATNLHDELLYIIDH 336
>1wmw_A Geranylgeranyl diphosphate synthetase; GGPP, prenyl diphosphate
synthase, structural genom riken structural
genomics/proteomics initiative; 1.55A {Thermus
thermophilus}
Length = 330
Score = 152 bits (386), Expect = 2e-43
Identities = 68/338 (20%), Positives = 113/338 (33%), Gaps = 66/338 (19%)
Query: 63 RLRSMVVAEVPELASAAGYFFKEGVEGKKLCPTVILLMATALNVCTPELSPNVLGNTLIL 122
RL + + P + + G GK L + + A A
Sbjct: 15 RLLARLDHPDPLYRDLLQDYPRRG--GKMLRGLLTVYSALAHGAPLEAGLE--------- 63
Query: 123 DLRRRQQCIAEITEMIHVASLIHDDVLDDADTRRGIGSLSSVMGNKLAILAGDLLISRAL 182
A E+ L+HDD+ D ++ RRG +L + LA+ AGD + +
Sbjct: 64 --------AATALELFQNWVLVHDDIEDGSEERRGRPALHRLHPMPLALNAGDAMHAEMW 115
Query: 183 VALASLKH----------------------------------TEVIMECYMQKTYNKTAA 208
LA ++ E Y + +K A
Sbjct: 116 GLLAEGLARGLFPPEVLLEFHEVVRRTAYGQHLDLLWTLGGTFDLRPEDYFRMVAHKAAY 175
Query: 209 L-VSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASLGKASLTDLR 267
+ A L+G+ A E G LG A+Q++DD+L+ G A GK DL
Sbjct: 176 YTAVAPLRLGALLAGKTPPAA--YEEGGLRLGTAFQIVDDVLNLEGGEA-YGKERAGDLY 232
Query: 268 NGIITAPILFAME-----EFPQLRAFINSSSDN--PANVDVILEYLGKSHGIQRTTELAL 320
G T +L +E E + A + + A V +LE L S + A
Sbjct: 233 EGKRTLILLRFLEEAPPEERARALALLALPREAKPEAEVGWLLERLLASRALAWAKAEAK 292
Query: 321 KHASLAAAAIDSLPETHDVDATNARTALVHITQKIITR 358
+ + A +++ + D+ A L + ++ R
Sbjct: 293 RLQAEGLALLEAAFQ--DLPGKEALDHLRGLLAALVER 328
>3lk5_A Geranylgeranyl pyrophosphate synthase; structural genomics, protein
structure initiative, geranylge pyrophosphate synthase;
1.90A {Corynebacterium glutamicum} PDB: 3qqv_A*
Length = 380
Score = 150 bits (380), Expect = 4e-42
Identities = 72/350 (20%), Positives = 120/350 (34%), Gaps = 76/350 (21%)
Query: 68 VVAEVPELASAAGYFFKEGVEGKKLCPTVILLMATALNVCTPELSPNVLGNTLILDLRRR 127
+ A V + + F G GK++ P A G+ +
Sbjct: 43 IGAPVTDAVAHLRSFVLNG--GKRIRPLYAWAGFLA-----------AQGHKNSSEKLES 89
Query: 128 QQCIAEITEMIHVASLIHDDVLDDADTRRG----------------IGSLSSVMGNKLAI 171
A E I +LIHDD++D +DTRRG G ++I
Sbjct: 90 VLDAAASLEFIQACALIHDDIIDSSDTRRGAPTVHRAVEADHRANNFEGDPEHFGVSVSI 149
Query: 172 LAGDLLISRALVALASLKH----------------TEVI----------------MECYM 199
LAGD+ + A L TEVI +E
Sbjct: 150 LAGDMALVWAEDMLQDSGLSAEALARTRDAWRGMRTEVIGGQLLDIYLESHANESVELAD 209
Query: 200 QKTYNKTAA-LVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASL 258
KTAA ++ A ++G ++ YG ++G+A+QL DD+L G A
Sbjct: 210 SVNRFKTAAYTIARPLHLGASIAGGSPQLIDALLHYGHDIGIAFQLRDDLLGVFGDPAIT 269
Query: 259 GKASLTDLRNGIITAPILFAM--------EEFPQLRAFINSSSDNPANVDVILEYLGKSH 310
GK + D+R G T + A+ E +RA + + P ++ VI E++ +
Sbjct: 270 GKPAGDDIREGKRTVLLALALQRADKQSPEAATAIRAGVGKVTS-PEDIAVITEHIRATG 328
Query: 311 GIQRTTELALKHASLAAAAIDSLPETHDVDATNARTALVHITQKIITRNK 360
+ + + A +D + + R L + + R +
Sbjct: 329 AEEEVEQRISQLTESGLAHLDDVDIPDE-----VRAQLRALAIRSTERRE 373
>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 = 133 bits (336), Expect = 5e-36
Identities = 56/363 (15%), Positives = 104/363 (28%), Gaps = 64/363 (17%)
Query: 41 NENKKHLDPFSLVGDELSLISMRLRSMVVAEVPELASAAGYFFKEGVEGKKLCPTVILLM 100
E ++ + F + +L + V + + G GK ++
Sbjct: 26 REREEFVGFFPQIVRDL--TEDGIGHPEVGDAVARLKEVLQYNAPG--GKCNRGLTVVAA 81
Query: 101 ATALNVCTPELSPNVLGNTLILDLRRRQQCIAEITEMIHVASLIHDDVLDDADTRRGIGS 160
L+ + + ++ R + E+ ASL+ DD++D + TRRG
Sbjct: 82 YRELSGPGQKDAESL----------RCALAVGWCIELFQAASLVADDIMDQSLTRRGQLC 131
Query: 161 LSSVMGNKLAILAGDLLISRA-----------------LVALASLKHTEVI--------- 194
G L + L+ + L+ L +
Sbjct: 132 WYKKEGVGLDAINDSFLLESSVYRVLKKYCRQRPYYVHLLELFLQTAYQTELGQMLDLIT 191
Query: 195 ------------MECYMQKTYNKTAAL--VSNSCKAVAYLSGQREEVATLAFEYGKNLGL 240
E Y KTA A+ + +E A +G
Sbjct: 192 APVSKVDLSHFSEERYKAIVKYKTAFYSFYLPVAAAMYMVGIDSKEEHENAKAILLEMGE 251
Query: 241 AYQLIDDILDFTGTSASLGKASLTDLRNGIITAPILFAMEEF-PQLRAFI--NSSSDNPA 297
+Q+ DD LD G A G TD+++ + ++ ++ P+ R + N P
Sbjct: 252 YFQIQDDYLDCFGDPALTGAVG-TDIQDNKCSWLVVQCLQRVTPEQRQLLEDNYGRKEPE 310
Query: 298 NVDVILEYLGKSHGIQRTTELALKHASLAAAAIDSLPETHDVDATNARTALVHITQKIIT 357
V + E + I+ + + + QKI
Sbjct: 311 KVAKVKELYEAVGMRAAFQQYEESSYRRLQELIEKHSN------RLPKEIFLGLAQKIYK 364
Query: 358 RNK 360
R K
Sbjct: 365 RQK 367
>2qis_A Farnesyl pyrophosphate synthetase; trans-prenyltransferase,
structural genomics, structural GEN consortium, SGC,
transferase; HET: RIS; 1.80A {Homo sapiens} PDB: 4dem_F*
1yv5_A* 1yq7_A* 2opm_A* 2opn_A* 3cp6_A* 2rah_A* 2vf6_A*
1zw5_A* 3b7l_A* 3s4j_A* 3rye_A* 3n45_F* 2f89_F* 2f7m_F*
2f8z_F* 2f8c_F* 2f92_F* 2f9k_F* 3n1v_F* ...
Length = 374
Score = 120 bits (303), Expect = 3e-31
Identities = 50/315 (15%), Positives = 89/315 (28%), Gaps = 60/315 (19%)
Query: 89 GKKLCPTVILLMATALNVCTPELSPNVLGNTLILDLRRRQQCIAEITEMIHVASLIHDDV 148
GK +++ L V D +R + E++ L+ DD+
Sbjct: 77 GKYNRGLTVVVAFREL----------VEPRKQDADSLQRAWTVGWCVELLQAFFLVADDI 126
Query: 149 LDDADTRRGIGSLSSVMGNKL-AILAGDLLISRALVALASLK----------------HT 191
+D + TRRG G L AI +LL + L
Sbjct: 127 MDSSLTRRGQICWYQKPGVGLDAINDANLLEACIYRLLKLYCREQPYYLNLIELFLQSSY 186
Query: 192 EVI---------------------MECYMQKTYNKTAALVSNSCKAVAYLSGQ--REEVA 228
+ + Y K+A A A E+
Sbjct: 187 QTEIGQTLDLLTAPQGNVDLVRFTEKRYKSIVKYKSAFYSFYLPIAAAMYMAGIDGEKEH 246
Query: 229 TLAFEYGKNLGLAYQLIDDILDFTGTSASLGKASLTDLRNGIITAPILFAMEEF-PQLRA 287
A + +G +Q+ DD LD G + GK TD+++ + ++ ++ P+
Sbjct: 247 ANAKKILLEMGEFFQIQDDYLDLFGDPSVTGKIG-TDIQDNKCSWLVVQCLQRATPEQYQ 305
Query: 288 FI--NSSSDNPANVDVILEYLGKSHGIQRTTELALKHASLAAAAIDSLPETHDVDATNAR 345
+ N V + + + S A I+
Sbjct: 306 ILKENYGQKEAEKVARVKALYEELDLPAVFLQYEEDSYSHIMALIEQYAAPL------PP 359
Query: 346 TALVHITQKIITRNK 360
+ + +KI R K
Sbjct: 360 AVFLGLARKIYKRRK 374
>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 = 116 bits (293), Expect = 9e-30
Identities = 43/327 (13%), Positives = 88/327 (26%), Gaps = 60/327 (18%)
Query: 89 GKKLCPTVILLMATALNVCTPELSPNVLGNTLILDLRRRQQCIAEITEMIHVASLIHDDV 148
GK ++ +A +L +P + + + E + L+ DD+
Sbjct: 69 GKYNRGLTVIDVAESLLSLSPNNNGEEDDGARRKRVLHDACVCGWMIEFLQAHYLVEDDI 128
Query: 149 LDDADTRRGIGSLSSVMGNKLAILAGDLLISRALVALASLKH------------------ 190
+D++ TRRG + D L+ ++ + ++
Sbjct: 129 MDNSVTRRGKPCWYRHPDVTVQCAINDGLLLKSWTHMMAMHFFADRPFLQDLLCRFNRVD 188
Query: 191 --------------------------------TEVIMECYMQKTYNKTAAL-VSNSCKAV 217
E + Y + KTA
Sbjct: 189 YTTAVGQLYDVTSMFDSNKLDPDVSQPTTTDFAEFTLSNYKRIVKYKTAYYTYLLPLVMG 248
Query: 218 AYLSGQR-EEVATLAFEYGKNLGLAYQLIDDILDFTGTSASLGKASLTDLRNGIITAPIL 276
+S + E +G +Q+ DD++D LGK TD+++ + +
Sbjct: 249 LIVSEALPTVDMGVTEELAMLMGEYFQVQDDVMDCFTPPERLGKVG-TDIQDAKCSWLAV 307
Query: 277 FAMEEF-PQLRAFI--NSSSDNPANVDVILEYLGKSHGIQRTTELALKHASLAAAAIDSL 333
+ + A N S + V + ++ A I+ L
Sbjct: 308 TFLAKASSAQVAEFKANYGSGDSEKVATVRRLYEEADLQGDYVAYEAAVAEQVKELIEKL 367
Query: 334 PETHDVDATNARTALVHITQKIITRNK 360
++ + K R K
Sbjct: 368 RLCSP----GFAASVETLWGKTYKRQK 390
>1yhl_A Farnesyl pyrophosphate synthase; farnesyl diphosphate synthase,
bisphosphonate, dimethyl ALLY pyrophosphate sulfate,
FPPS, transferase; HET: DMA RIS; 1.95A {Trypanosoma
cruzi} PDB: 1yhk_A* 1yhm_A* 3iba_A* 3ick_A* 3icm_A*
3icn_A* 3icz_A* 3id0_A*
Length = 362
Score = 115 bits (290), Expect = 1e-29
Identities = 43/348 (12%), Positives = 88/348 (25%), Gaps = 68/348 (19%)
Query: 68 VVAEVPELASAAGYFFKEGVEGKKLCPTVILLMATALNVCTPELSPNVLGNTLILDLRRR 127
+ G GK ++ +A L+ +
Sbjct: 28 IDPNRARYLRIMMDTTCLG--GKYFRGMTVVNVAEGF------LAVTQHDEATKERILHD 79
Query: 128 QQCIAEITEMIHVASLIHDDVLDDADTRRGIGSLSSVMGNKLAILAGDLLISRALVALAS 187
+ E + L+ DD++D + RRG G D +I ++ + +
Sbjct: 80 ACVGGWMIEFLQAHYLVEDDIMDGSVMRRGKPCWYRFPGVTTQCAINDGIILKSWTQIMA 139
Query: 188 LKH--------------------------------------------------TEVIMEC 197
+ E
Sbjct: 140 WHYFADRPFLKDLLCLFQKVDYATAVGQMYDVTSMCDSNKLDPEVAQPMTTDFAEFTPAI 199
Query: 198 YMQKTYNKTAAL-VSNSCKAVAYLSGQ-REEVATLAFEYGKNLGLAYQLIDDILDFTGTS 255
Y + KT ++S L +G +Q+ DD++D
Sbjct: 200 YKRIVKYKTTFYTYLLPLVMGLFVSEAAASVEMNLVERVAHLIGEYFQVQDDVMDCFTPP 259
Query: 256 ASLGKASLTDLRNGIITAPILFAMEEF-PQLRAFI--NSSSDNPANVDVILEYLGKSHGI 312
LGK TD+ + + + + + A N +PA V V+ +++
Sbjct: 260 EQLGKVG-TDIEDAKCSWLAVTFLGKANAAQVAEFKANYGDKDPAKVAVVKRLYSEANLQ 318
Query: 313 QRTTELALKHASLAAAAIDSLPETHDVDATNARTALVHITQKIITRNK 360
+ + I+ L + ++ + +K R K
Sbjct: 319 ADFAAYEAEVVREVESLIEQLKV----KSPTFAESVAVVWEKTHKRKK 362
>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 = 115 bits (290), Expect = 2e-29
Identities = 54/378 (14%), Positives = 103/378 (27%), Gaps = 69/378 (18%)
Query: 27 SHRRYGHQPTFRNSN-ENKKHLDPFSLVGDELSLISMRLRSMVVAEVPELASAAGYFFK- 84
SH + H N + + F D+ +I + + Y+
Sbjct: 4 SHHHHHHSSGRENLYFQGEYDYTDFINYYDKFKVIVYNVLKKLPLNDEIRKPVIEYYLNC 63
Query: 85 ---EGVEGKKLCPTVILLMATALNVCTPELSPNVLGNTLILDLRRRQQCIAEITEMIHVA 141
+GK + +++L+++ + + ++ + + E I
Sbjct: 64 IDYNVKKGKHIRGKILVLISSLSSAYSNIKRDSIY-------------LLGWVVEAIQAL 110
Query: 142 SLIHDDVLDDADTRRGIGSLSSVMGNKLAILAGDLLISRALVALASLKH----------- 190
LI DD++D RRG V G AI L +L + L
Sbjct: 111 ILIADDIMDSGKFRRGAPCWYIVHGQSNAINDIFFLKMLSLSLIFELSSVFGNDIVMKIQ 170
Query: 191 -------------------------TEVIMECYMQKTYNKTAAL-VSNSCKAVAYLSGQR 224
+ I E Y KT+ LS +
Sbjct: 171 KIYNESIFFTVLGQHLDLSYFDLSKADKISERYFSMVEMKTSRYTFYMPVFFGLTLSEIQ 230
Query: 225 --EEVATLAFEYGKNLGLAYQLIDDILDFTGTSASLGKASLTDLRNGIITAPILFAMEEF 282
L LG YQ+ +D+ D+ ++ D+ +T P+ + E
Sbjct: 231 VSSAQLNLIEAILYKLGEFYQVHNDVSDYLF-----NDSNADDICRFKLTWPLQKSFEIA 285
Query: 283 P--QLRAFINSSSDNPANVDVILEYLGKSHGIQRTTELALKHASLAAAAIDSLPETHDVD 340
+ N + V L + AL + + + + D
Sbjct: 286 DEEMKLKISENYGKNSSLVKDCYNLLKINEHYLEYQRNALDYLI---KLVKDITD--DSL 340
Query: 341 ATNARTALVHITQKIITR 358
+ I++ I
Sbjct: 341 QKVFIHLIHQISELITNS 358
>3uca_A Geranyltranstransferase; isoprenoid synthesis, isoprenoid
diphosphate synthase; 2.00A {Clostridium perfringens}
Length = 324
Score = 105 bits (265), Expect = 3e-26
Identities = 54/185 (29%), Positives = 78/185 (42%), Gaps = 41/185 (22%)
Query: 136 EMIHVASLIHDDV--LDDADTRRGIGSLSSVMGNKLAILAGDLLISRA--LVALASLKHT 191
EMIH SLIHDD+ +D+ D RRG + V G +A+LAGD L++ A ++ SL+
Sbjct: 104 EMIHTYSLIHDDLPCMDNDDLRRGKPTNHKVFGEAIAVLAGDALLNEAMKILVDYSLEEG 163
Query: 192 EVIMEC-----------------------------------YMQKTYNKTAALVSNSCKA 216
+ ++ YM KT L+ S +
Sbjct: 164 KSALKATKIIADAAGSDGMIGGQIVDIINEDKEEISLKELDYMHL--KKTGELIKASIMS 221
Query: 217 VAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASLGKASLTDLRNGIITAPIL 276
A L+ E +G LGLA+Q+ DDILD G + LGK D + +
Sbjct: 222 GAVLAEASEGDIKKLEGFGYKLGLAFQIKDDILDVVGNAKDLGKNVHKDQESNKNNYITI 281
Query: 277 FAMEE 281
F +EE
Sbjct: 282 FGLEE 286
>2h8o_A Geranyltranstransferase; geranyltransferase,agrobacterium
tumefaciens, structural GEN PSI-2, protein structure
initiative; 1.60A {Agrobacterium tumefaciens}
Length = 335
Score = 103 bits (260), Expect = 2e-25
Identities = 50/185 (27%), Positives = 80/185 (43%), Gaps = 41/185 (22%)
Query: 136 EMIHVASLIHDDV--LDDADTRRGIGSLSSVMGNKLAILAGDLLISRALVALASLKHT-- 191
E +H SL+HDD+ +DD D RRG ++ AILAGD L++ A +AS +
Sbjct: 115 ECLHCYSLVHDDLPAMDDDDLRRGQPTVHRKFDEATAILAGDSLLTLAFDIIASDDNPLA 174
Query: 192 -----EVIMEC------------------------------YMQKTYNKTAALVSNSCKA 216
+++ +Q KT AL+ +C+A
Sbjct: 175 AERKAALVISLARAAGIGGMAGGQALDLAAEKKAPDEDGIITLQA--MKTGALLRFACEA 232
Query: 217 VAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASLGKASLTDLRNGIITAPIL 276
A ++G + +G+ +GL++QL DD+LD T +A++GKA+ D G T L
Sbjct: 233 GAIIAGSNQAERQRLRLFGEKIGLSFQLADDLLDLTADAATMGKATGKDAARGKGTLVAL 292
Query: 277 FAMEE 281
Sbjct: 293 RGEAW 297
>1rtr_A Geranyltranstransferase; 2.50A {Staphylococcus aureus} SCOP:
a.128.1.1
Length = 301
Score = 103 bits (258), Expect = 2e-25
Identities = 52/184 (28%), Positives = 78/184 (42%), Gaps = 40/184 (21%)
Query: 136 EMIHVASLIHDDV--LDDADTRRGIGSLSSVMGNKLAILAGDLLISRA--LVALASLKHT 191
EMIH SLIHDD+ +D+ D RRG + V G AILAGD L+++A L++
Sbjct: 72 EMIHTYSLIHDDLPAMDNDDYRRGKLTNHKVYGEWTAILAGDALLTKAFELISSDDRLTD 131
Query: 192 EVIMEC----------------------------------YMQKTYNKTAALVSNSCKAV 217
EV ++ + K KT AL++ + +
Sbjct: 132 EVKIKVLQRLSIASGHVGMVGGQMLDMQSEGQPIDLETLEMIHK--TKTGALLTFAVMSA 189
Query: 218 AYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASLGKASLTDLRNGIITAPILF 277
A ++ + Y +LG+ +Q+ DD+LD G A LGK +DL N T L
Sbjct: 190 ADIANVDDTTKEHLESYSYHLGMMFQIKDDLLDCYGDEAKLGKKVGSDLENNKSTYVSLL 249
Query: 278 AMEE 281
+
Sbjct: 250 GKDG 253
>3p8l_A Geranyltranstransferase; isoprenyl synthase, structural genomics,
PSI, protein struct initiative, nysgrc; 2.00A
{Enterococcus faecalis}
Length = 302
Score = 102 bits (257), Expect = 3e-25
Identities = 68/230 (29%), Positives = 97/230 (42%), Gaps = 55/230 (23%)
Query: 89 GKKLCPTVILLMATALNVCTPELSPNVLGNTLILDLRRRQQCIAEITEMIHVASLIHDDV 148
GK+L P +L++ T D + +A EMIH SLIHDD+
Sbjct: 50 GKRLRP--LLVLTTV------AA---FQKEMETQDYQ-----VAASLEMIHTYSLIHDDL 93
Query: 149 --LDDADTRRGIGSLSSVMGNKLAILAGDLLISRA--LVALASLKHTEVI---------- 194
+DD D RRG + V G AILAGD L++ A L++L+ L +E +
Sbjct: 94 PAMDDDDLRRGKPTNHKVFGEATAILAGDGLLTGAFQLLSLSQLGLSEKVLLMQQLAKAA 153
Query: 195 ------------MEC-----------YMQKTYNKTAALVSNSCKAVAYLSGQREEVATLA 231
+E + + KT AL+ + A L+ Q EEV L
Sbjct: 154 GNQGMVSGQMGDIEGEKVSLTLEELAAVHE--KKTGALIEFALIAGGVLANQTEEVIGLL 211
Query: 232 FEYGKNLGLAYQLIDDILDFTGTSASLGKASLTDLRNGIITAPILFAMEE 281
++ + GLA+Q+ DD+LD T T A LGK D T P L +
Sbjct: 212 TQFAHHYGLAFQIRDDLLDATSTEADLGKKVGRDEALNKSTYPALLGIAG 261
>4f62_A Geranyltranstransferase; enzyme function initiative, structural
genomics; 2.10A {Marinomonas SP}
Length = 317
Score = 101 bits (254), Expect = 8e-25
Identities = 52/186 (27%), Positives = 78/186 (41%), Gaps = 43/186 (23%)
Query: 136 EMIHVASLIHDDV--LDDADTRRGIGSLSSVMGNKLAILAGDLLISRALVALASLKHT-- 191
E IH SLIHDD+ +D+ + RRG + AILAGD L + A L++
Sbjct: 75 ESIHAYSLIHDDLPAMDNDELRRGKPTCHIQFDEATAILAGDALQTFAFELLSNPTSAQP 134
Query: 192 EVIMEC----------------------------------YMQKTYNKTAALVSNSCKAV 217
E+ ++ M +KT AL+ S +
Sbjct: 135 ELAIKLIQELVVASGRNGMITGQMIDLSSENKNISLAELEQMHV--HKTGALIKASVRMG 192
Query: 218 AYLSGQ--REEVATLAFEYGKNLGLAYQLIDDILDFTGTSASLGKASLTDLRNGIITAPI 275
A +GQ E++A L Y +GLA+Q+ DDI+D T + +LGK +D T P
Sbjct: 193 ALSTGQVKPEQLAKLD-AYAHAIGLAFQVQDDIIDLTSDTETLGKTQFSDAEANKATYPK 251
Query: 276 LFAMEE 281
L ++
Sbjct: 252 LLGLDG 257
>3lsn_A Geranyltranstransferase; structural genomics, protein structure
initiative, NEW YORK structural genomix research
consortium, nysgxrc; HET: MSE; 1.35A {Pseudomonas
fluorescens} PDB: 3lji_A* 3p41_A*
Length = 304
Score = 100 bits (252), Expect = 1e-24
Identities = 56/188 (29%), Positives = 77/188 (40%), Gaps = 45/188 (23%)
Query: 136 EMIHVASLIHDDV--LDDADTRRGIGSLSSVMGNKLAILAGDLLISRALVALASLKHTEV 193
E+IH SL+HDD+ +DD D RRG + AILAGD L S A AL ++
Sbjct: 74 ELIHAYSLVHDDLPAMDDDDLRRGQPTTHKAFDEACAILAGDGLQSLAFSALLDPALSDA 133
Query: 194 IMEC--------------------------------------YMQKTYNKTAALVSNSCK 215
E YM + +KT AL+ S
Sbjct: 134 SAEIRLRMVTTLAQAAGPAGMVGGQAIDLGSVGLKLDQQALEYMHR--HKTGALIEASVI 191
Query: 216 AVAYLSGQ--REEVATLAFEYGKNLGLAYQLIDDILDFTGTSASLGKASLTDLRNGIITA 273
A SG+ + E+ L Y + +GLA+Q+ DDILD +A+LGK D+ T
Sbjct: 192 LGALASGRAEKGELKALQ-TYAQAIGLAFQVQDDILDVESDTATLGKRQGADIARDKPTY 250
Query: 274 PILFAMEE 281
P L +
Sbjct: 251 PALLGLAA 258
>3m0g_A Farnesyl diphosphate synthase; structural genomics, protein
structure initiative, NYSGXRC, biosynthesis,
transferase, PSI-2; 1.90A {Rhodobacter capsulatus} PDB:
3lvs_A
Length = 297
Score = 100 bits (251), Expect = 2e-24
Identities = 61/265 (23%), Positives = 87/265 (32%), Gaps = 86/265 (32%)
Query: 136 EMIHVASLIHDDV--LDDADTRRGIGSLSSVMGNKLAILAGDLLISRA--LVALASLKHT 191
E +H SL+HDD+ +D+ D RRG+ ++ + A+LAGD L + A L L
Sbjct: 71 EALHAYSLVHDDMPCMDNDDLRRGLPTVHKKWDDATAVLAGDALQTLAFELCTDPVLGSA 130
Query: 192 EVIMEC------------------------------------YMQKTYNKTAALVSNSCK 215
E + +Q KT AL+S + +
Sbjct: 131 ENRVALVAALAQASGAEGMVYGQALDIAAETAAVPLTLDEIIRLQA--GKTGALISFAAQ 188
Query: 216 AVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASLGKASLTDLRNGIITAPI 275
A A L+G T Y LGLA+Q+ DDILD G + GK D T
Sbjct: 189 AGAILAGADRGPLT---AYATALGLAFQIADDILDVEGNEEAAGKRLGKDAEAHKAT--- 242
Query: 276 LFAMEEFPQLRAFINSSSDNPANVDVILEYLGKSHGIQRTTELALKHASLAAAAIDSLPE 335
F L G+ A + A AA+ E
Sbjct: 243 ------FVSL------------------------LGLAGAKSRAADLVAEAEAALAPYGE 272
Query: 336 THDVDATNARTALVHITQKIITRNK 360
L + +I R+K
Sbjct: 273 AAS--------TLRACARYVIERDK 289
>3ts7_A Geranyltranstransferase; isoprenoid synthesis, farnesyl diphosphate
synthase; 1.94A {Methylococcus capsulatus}
Length = 324
Score = 100 bits (251), Expect = 3e-24
Identities = 53/188 (28%), Positives = 67/188 (35%), Gaps = 45/188 (23%)
Query: 136 EMIHVASLIHDDV--LDDADTRRGIGSLSSVMGNKLAILAGDLLISRALVALASLKHTEV 193
E IHV SLIHDD+ +DD D RRG + AILAGD L + A LA V
Sbjct: 80 EFIHVYSLIHDDLPAMDDDDLRRGKPTCHKAYDEATAILAGDGLQALAFHVLAQDPSIAV 139
Query: 194 IMEC--------------------------------------YMQKTYNKTAALVSNSCK 215
E M KT AL+ S +
Sbjct: 140 PAENRIAMIETLAKASGPAGMVGGQAIDLASVGKKLDLPGLENMHI--RKTGALIRASVR 197
Query: 216 AVAYLSGQ--REEVATLAFEYGKNLGLAYQLIDDILDFTGTSASLGKASLTDLRNGIITA 273
E+ L Y K +GLA+Q+ DDILD + +LGK D +
Sbjct: 198 LACLARPGLPAEQFDRLD-HYAKCIGLAFQIQDDILDEESDTQTLGKTRGKDRDHNKPNY 256
Query: 274 PILFAMEE 281
P L +
Sbjct: 257 PALLGLSG 264
>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 = 99 bits (250), Expect = 3e-24
Identities = 67/267 (25%), Positives = 101/267 (37%), Gaps = 83/267 (31%)
Query: 136 EMIHVASLIHDDV--LDDADTRRGIGSLSSVMGNKLAILAGDLLISRALVALASLKHTEV 193
E IH SLIHDD+ +DD D RRG+ + G AILAGD L + A L+ EV
Sbjct: 74 ECIHAYSLIHDDLPAMDDDDLRRGLPTCHVKFGEANAILAGDALQTLAFSILSDADMPEV 133
Query: 194 IMEC--------------------------------------YMQKTYNKTAALVSNSCK 215
+ + +KT AL+ + +
Sbjct: 134 SDRDRISMISELASASGIAGMCGGQALDLDAEGKHVPLDALERIHR--HKTGALIRAAVR 191
Query: 216 AVAYLSGQ--REEVATLAFEYGKNLGLAYQLIDDILDFTGTSASLGKASLTDLRNGIITA 273
A +G R + L +Y +++GLA+Q+ DDILD G +A+LGK D + G T
Sbjct: 192 LGALSAGDKGRRALPVLD-KYAESIGLAFQVQDDILDVVGDTATLGKRQGADQQLGKST- 249
Query: 274 PILFAMEEFPQLRAFINSSSDNPANVDVILEYLGKSHGIQRTTELALKHASLAAAAIDSL 333
+P L G+++ + A A ++ L
Sbjct: 250 --------YPAL------------------------LGLEQARKKARDLIDDARQSLKQL 277
Query: 334 PETHDVDATNARTALVHITQKIITRNK 360
E + + +AL + II RNK
Sbjct: 278 AE----QSLDT-SALEALADYIIQRNK 299
>3llw_A Geranyltranstransferase (ISPA); structural genomics, PSI, protein
structure initiative, nysgrc; 2.30A {Helicobacter
pylori} PDB: 3q1o_A*
Length = 311
Score = 98.9 bits (247), Expect = 8e-24
Identities = 53/231 (22%), Positives = 88/231 (38%), Gaps = 53/231 (22%)
Query: 89 GKKLCPTVILLMATALNVCTPELSPNVLGNTLILDLRRRQQCIAEITEMIHVASLIHDDV 148
GK+ P L +A + + N IA E +H SLIHDD+
Sbjct: 48 GKRFRP--KLFLAVLCALVGQKDYSNQQTEYFK---------IALSIECLHTYSLIHDDL 96
Query: 149 --LDDADTRRGIGSLSSVMGNKLAILAGDLLISRALVALASLK-HTEVIMEC-------- 197
+D+A RR +L + A+L GD L + + L++ + +I+E
Sbjct: 97 PCMDNAALRRNHPTLHAKYDETTAVLIGDALNTYSFELLSNALLESHIIVELIKILSANG 156
Query: 198 --------------------------YMQKTYNKTAALVSNSCKAVAYLSGQR-EEVATL 230
++ + +KTA L+S S SG + EE+
Sbjct: 157 GIKGMILGQALDCYFENTPLNLEQLTFLHE--HKTAKLISASLIMGLVASGIKDEELFKW 214
Query: 231 AFEYGKNLGLAYQLIDDILDFTGTSASLGKASLTDLRNGIITAPILFAMEE 281
+G +GL +Q++DDI+D T GK + D + + L +E
Sbjct: 215 LQAFGLKMGLCFQVLDDIIDVTQDEEESGKTTHLD--SAKNSFVNLLGLER 263
>3p8r_A Geranyltranstransferase; isoprenyl synthase, structural genomics,
PSI, protein struct initiative, nysgrc; 2.50A {Vibrio
cholerae}
Length = 302
Score = 98.4 bits (246), Expect = 9e-24
Identities = 50/188 (26%), Positives = 72/188 (38%), Gaps = 45/188 (23%)
Query: 136 EMIHVASLIHDDV--LDDADTRRGIGSLSSVMGNKLAILAGDLLISRALVALASLKHTEV 193
E IH SLIHDD+ +DD + RRG + AIL GD L + A LA +
Sbjct: 80 ECIHAYSLIHDDLPAMDDDELRRGKPTCHIQFDEATAILTGDALQTLAFTILAEGDLSAA 139
Query: 194 IMEC--------------------------------------YMQKTYNKTAALVSNSCK 215
+ + NKT AL+ + +
Sbjct: 140 GETQRVAMLQALAEASGAQGMCLGQALDLAAENRLISLEELETIHR--NKTGALMRCAIR 197
Query: 216 AVAYLSGQ--REEVATLAFEYGKNLGLAYQLIDDILDFTGTSASLGKASLTDLRNGIITA 273
A +G+ R + L Y + +GLA+Q+ DDILD + +LGK +D T
Sbjct: 198 LGALAAGEKGRAMLPHLD-RYAEAVGLAFQVQDDILDIISDTETLGKPQGSDQELNKSTY 256
Query: 274 PILFAMEE 281
P L +E
Sbjct: 257 PALLGLEG 264
>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 = 98.5 bits (246), Expect = 1e-23
Identities = 46/183 (25%), Positives = 70/183 (38%), Gaps = 39/183 (21%)
Query: 136 EMIHVASLIHDDV--LDDADTRRGIGSLSSVMGNKLAILAGDLLISRA--LVALASLKHT 191
E++H SLIHDD+ +D+ RRG + G +A LAGD L++ A + L T
Sbjct: 80 ELLHTYSLIHDDLPAMDNDALRRGEPTNHVKFGAGMATLAGDGLLTLAFQWLTATDLPAT 139
Query: 192 EVI----------------------MEC-----------YMQKTYNKTAALVSNSCKAVA 218
++ + K KT AL+ + +A
Sbjct: 140 MQAALVQALATAAGPSGMVAGQAKDIQSEHVNLPLSQLRVLHK--EKTGALLHYAVQAGL 197
Query: 219 YLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASLGKASLTDLRNGIITAPILFA 278
L E ++ GLA+Q+ DDILD + A +GKA+ D T P
Sbjct: 198 ILGQAPEAQWPAYLQFADAFGLAFQIYDDILDVVSSPAEMGKATQKDADEAKNTYPGKLG 257
Query: 279 MEE 281
+
Sbjct: 258 LIG 260
>3npk_A Geranyltranstransferase; isoprene biosynthesis, SGX, structural
genomics protein structure initiative; 1.50A
{Campylobacter jejuni}
Length = 291
Score = 97.3 bits (243), Expect = 2e-23
Identities = 53/215 (24%), Positives = 81/215 (37%), Gaps = 55/215 (25%)
Query: 89 GKKLCPTVILLMATALNVCTPELSPNVLGNTLILDLRRRQQCIAEITEMIHVASLIHDDV 148
GK LL++ L+ +A E IH SLIHDD+
Sbjct: 39 GKHFRA--QLLLSVV----------QSNKPELLNQALD----VALALEFIHTYSLIHDDL 82
Query: 149 --LDDADTRRGIGSLSSVMGNKLAILAGDLLISRA--LVALASLKHTEVI---------- 194
+D+AD RRGI +L AIL GD L + A +++ A LK I
Sbjct: 83 PAMDNADFRRGIPTLHKSYDETTAILVGDALNTEAFLVLSHAHLKDEIKIKLIKTLAFNA 142
Query: 195 ------------MEC-----------YMQKTYNKTAALVSNSCKAVAYLSGQREEVATLA 231
++ +KTA L++ + K + E +
Sbjct: 143 GLNGMVIGQAIDCFFEDKRLSLNELEFLHT--HKTARLIAAALKMGCEICELNNEESNQI 200
Query: 232 FEYGKNLGLAYQLIDDILDFTGTSASLGKASLTDL 266
++ G LGL +Q+ DDI+D T + GK + D+
Sbjct: 201 YKLGLKLGLIFQINDDIIDVTTSQEQSGKPTNNDI 235
>3lom_A Geranyltranstransferase; geranyltransferase, structural genomics,
PSI, protein structure initiative, nysgrc; 2.30A
{Legionella pneumophila subsp}
Length = 313
Score = 96.9 bits (242), Expect = 4e-23
Identities = 49/188 (26%), Positives = 71/188 (37%), Gaps = 44/188 (23%)
Query: 136 EMIHVASLIHDDV--LDDADTRRGIGSLSSVMGNKLAILAGDLLISRA------------ 181
E+ H SLIHDD+ +D+ D RRG S AIL GD + + A
Sbjct: 80 ELTHCYSLIHDDLPAMDNDDLRRGKPSCHKAFDEATAILVGDGMQALAIEVLLMRLSPLL 139
Query: 182 --------------------LVA-----LASLKHTEVIMEC--YMQKTYNKTAALVSNSC 214
+V+ L+ L + V E + KT L+
Sbjct: 140 PAAQVVAITQVLVNASGISGMVSGQSLDLSELAKSSVTEEQLREIHL--LKTGKLILACF 197
Query: 215 KAVAYLSGQREEVATLAFE-YGKNLGLAYQLIDDILDFTGTSASLGKASLTDLRNGIITA 273
+ V + E A YGK++GL +Q+ DD LD + LGK +D N T
Sbjct: 198 EMVLAAQHEVSEQIKSALRTYGKHIGLVFQMQDDYLDLYAPTQILGKGRSSDQANQKTTF 257
Query: 274 PILFAMEE 281
LF ++
Sbjct: 258 ATLFNKQQ 265
>3qkc_B Geranyl diphosphate synthase small subunit; structural genomics,
protein structure initiative, NEW YORK structural
genomix research consortium; 2.20A {Antirrhinum majus}
Length = 273
Score = 89.7 bits (223), Expect = 9e-21
Identities = 27/172 (15%), Positives = 49/172 (28%), Gaps = 42/172 (24%)
Query: 136 EMIHVASLIHDDVLDDADTRRGIGSLSSVMGNKLAILAGDLLISRALVALASLKHTEVI- 194
++HVA+ H++ L D + + +L GD +I L +A
Sbjct: 75 HLMHVAAYTHEN-LPLTDGPMSKSEIQHKFDPNIELLTGDGIIPFGLELMARSMDPTRNN 133
Query: 195 ---------------------------MEC----------YMQKTYNKTAALVSNSCKAV 217
+ Y+ K K L +
Sbjct: 134 PDRILRAIIELTRVMGSEGIVEGQYHELGLNQLNDLELIEYVCK--KKEGTLHACGAACG 191
Query: 218 AYLSGQREEVATLAFEYGKNLGLAYQLIDDILD-FTGTSASLGKASLTDLRN 268
A L G E+ +G +G L+ F G L + ++ +L +
Sbjct: 192 AILGGCDEDKIEKLRRFGLYVGTVQGLLGKNRSGFEGRIKELKELAVKELES 243
>2j1p_A Geranylgeranyl pyrophosphate synthetase; transferase, isoprene
biosynthesis, multifunctional enzyme, carotenoid
biosynthesis; HET: GRG; 1.8A {Sinapis alba} PDB: 2j1o_A
3kra_A 3krc_A* 3krf_A* 3kro_A* 3krp_A* 3oab_A* 3oac_A*
Length = 293
Score = 89.6 bits (223), Expect = 1e-20
Identities = 48/163 (29%), Positives = 70/163 (42%), Gaps = 45/163 (27%)
Query: 136 EMIHVASLIHDDV--LDDADTRRGIGSLSSVMGNKLAILAGDLLISRALVALASLKHTEV 193
EMIH SLIHDD+ +D+ D RRG + V G +A+LAGD L+S A LAS +EV
Sbjct: 82 EMIHTMSLIHDDLPCMDNDDLRRGKPTNHKVYGEDVAVLAGDALLSFAFEHLASATSSEV 141
Query: 194 IMEC-----------------------------------------YMQKTYNKTAALVSN 212
++ +KTAAL+
Sbjct: 142 SPARVVRAVGELAKAIGTEGLVAGQVVDISSEGLDLNNVGLEHLKFIHL--HKTAALLEA 199
Query: 213 SCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTS 255
S + G +E ++ + +GL +Q++DDILD T +S
Sbjct: 200 SAVLGGIIGGGSDEEIERLRKFARCIGLLFQVVDDILDVTKSS 242
>2ihi_A Pyrophosphate synthase; PV092040, structural genomics, structural
genomics consortium, SGC, transferase; 2.00A {Plasmodium
vivax sai-1} PDB: 3mav_A 3cc9_A* 3ez3_A* 3ldw_A* 3mys_A*
3ph7_A* 3rbm_A*
Length = 395
Score = 85.8 bits (212), Expect = 8e-19
Identities = 30/151 (19%), Positives = 50/151 (33%), Gaps = 7/151 (4%)
Query: 191 TEVIMECYMQKTYNKTAALVSNSCKAVAYLSGQR---EEVATLAFEYGKNLGLAYQLIDD 247
+ Y +KTA L + + +G +Q+ DD
Sbjct: 228 NMINFGVYKNIVIHKTAYYSFFLPIVCGMLLAGIAVDNLIYKKIEDISMLMGEYFQIHDD 287
Query: 248 ILDFTGTSASLGKASLTDLRNGIITAPILFAMEEF-PQLRAFI--NSSSDNPANVDVILE 304
LD G S GK +D++N +T P++ E + I N +N A V VI
Sbjct: 288 YLDIFGDSTKTGKVG-SDIQNNKLTWPLIKTFELCSEPDKIKIVKNYGKNNLACVKVIDS 346
Query: 305 YLGKSHGIQRTTELALKHASLAAAAIDSLPE 335
+ + + +AI+ L
Sbjct: 347 LYEQYKIRKHYESYEKAQKAKILSAINELHH 377
>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* 3oab_B* 3oac_B*
Length = 274
Score = 78.5 bits (194), Expect = 8e-17
Identities = 32/201 (15%), Positives = 57/201 (28%), Gaps = 57/201 (28%)
Query: 136 EMIHVASLIHDDV-LDDADTRRGIGSLSSVMGNKLAILAGDLLISRALVALASLKHTEVI 194
++H A+ +H+ + L D ++ G + +L GD ++ LA
Sbjct: 70 HLVHAAAYVHEHLPLTDGSRPVSKPAIQHKYGPNVELLTGDGIVPFGFELLAGSVDPART 129
Query: 195 -----------------------------MEC-----------YMQKTYNKTAALVSNSC 214
E Y+ K K + +
Sbjct: 130 DDPDRILRVIIEISRAGGPEGMISGLHREEEIVDGNTSLDFIEYVCK--KKYGEMHACGA 187
Query: 215 KAVAYLSGQREEVATLAFEYGKNLGL---------AYQLIDDILD---FTGTSASLGKA- 261
A L G EE +G G ++QLID+ + LG
Sbjct: 188 ACGAILGGAAEEEIQKLRNFGLYQGTLRGMMEMKNSHQLIDENIIGKLKELALEELGGFH 247
Query: 262 -SLTDLRNGIITAPILFAMEE 281
+L + ++ P L+A
Sbjct: 248 GKNAELMSSLVAEPSLYAAHH 268
>2ftz_A Geranyltranstransferase; TM0161, structural GE joint center for
structural genomics, JCSG, protein structu initiative,
PSI; HET: MLY; 1.90A {Thermotoga maritima}
Length = 284
Score = 72.2 bits (176), Expect = 1e-14
Identities = 46/180 (25%), Positives = 69/180 (38%), Gaps = 35/180 (19%)
Query: 131 IAEITEMIHVASLIHDDV--LDDADTRRGIGSLSSVMGNKLAILAGDLLISRALVALASL 188
+A E+ H ASLIHDD+ +D+AD RRG S G +A+LAGD L A ++ +
Sbjct: 71 VAVAVELFHTASLIHDDLPPIDNADFRRGXPSCHRTYGEDIALLAGDGLFFLAFSQISXI 130
Query: 189 ----------------------------KHTEVIMECYMQKTYNKTAALVSNSCKAVAYL 220
+ EV E + T AL + A L
Sbjct: 131 GNSXIFEEFSETAYXLLLGEAMDVEFERRXMEVSQEMVERMYAFXTGALFAFCFSAPFIL 190
Query: 221 SGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASLGKASLTDLRNGIITAPILFAME 280
G G+ G+A+Q+ DD+ D G+ +GK D +T ++
Sbjct: 191 XGXDHTXMX---LLGEXFGVAFQIYDDLXDILGSFEKVGKDLGKD--TEXVTLVXXVGIQ 245
>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 = 50.6 bits (120), Expect = 5e-07
Identities = 48/369 (13%), Positives = 101/369 (27%), Gaps = 109/369 (29%)
Query: 29 RRYGHQPTFRNS-----N-ENKKHLDPFS-----LVGDELSLISMRLRSMVVAEVPELAS 77
RR + N N +N K + F+ L+ ++ L + +
Sbjct: 235 RRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHH 294
Query: 78 AAGYFFKEGVEGKKLCPTVILLMATALNVCTPELSPNVL-GNTLILDL------------ 124
+ E L+ L+ +L VL N L +
Sbjct: 295 SMTLTPDEVKS----------LLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATW 344
Query: 125 -RRRQQCIAEITEMIHVASLIHDDVLDDADTRRGIGSLSSVMGNKLAILAGDLLISRALV 183
+ ++T +I +SL +VL+ A+ R+ M ++L++ I L+
Sbjct: 345 DNWKHVNCDKLTTIIE-SSL---NVLEPAEYRK--------MFDRLSVFPPSAHIPTILL 392
Query: 184 ALASLKHTEVIMECYMQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQ 243
+L + + + K + +L + K
Sbjct: 393 SLIWFDVIKSDVMVVVNKLHKY-----------------------SLVEKQPKE--STIS 427
Query: 244 LIDDILDFTGTSASLGKASLTDLRNGIITAPILFAMEEFPQLRAFINSSSDNPANVDVIL 303
+ L+ + L I+ + + + F + P
Sbjct: 428 IPSIYLELKVKL-----ENEYALHRSIV--------DHYNIPKTFDSDDLIPPYLDQYFY 474
Query: 304 EYLGKSH--GIQRTTELA---------------LKHASLAAAAIDSLPET-HDVDATNAR 345
++G H I+ + ++H S A A S+ T + +
Sbjct: 475 SHIGH-HLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQL-----K 528
Query: 346 TALVHITQK 354
+I
Sbjct: 529 FYKPYICDN 537
>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 = 39.6 bits (92), Expect = 0.002
Identities = 37/175 (21%), Positives = 58/175 (33%), Gaps = 53/175 (30%)
Query: 195 MECYMQKTYNKT-AALVSNSCKAVA-YLSGQ-----REEVATLAFEYGKNLGLAYQLIDD 247
+ + + TY + +V N+ + + G+ RE + + FE + L + I
Sbjct: 1649 ADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFK 1708
Query: 248 ILDFTGTSASL----GKASLTDLRNGIITAPILFAMEEFPQLRAFINSSSDNPANVDVIL 303
++ TS + G S T T P L ME +A
Sbjct: 1709 EINEHSTSYTFRSEKGLLSATQ-----FTQPALTLME-----KA--------------AF 1744
Query: 304 EYLGKSHG-IQRTTELALKH-----ASLAAAAIDSLP-ETHDVDATNARTALVHI 351
E L KS G I A H A+LA+ A D + E +V
Sbjct: 1745 EDL-KSKGLIPADATFA-GHSLGEYAALASLA-DVMSIE----SL--VE--VVFY 1788
>1hss_A 0.19 alpha-amylase inhibitor; cereal inhibitor, animal amylase;
2.06A {Triticum aestivum} SCOP: a.52.1.2
Length = 124
Score = 30.5 bits (68), Expect = 0.31
Identities = 21/113 (18%), Positives = 38/113 (33%), Gaps = 29/113 (25%)
Query: 15 PRNSLPSCRWILSHRRYGHQPTFRNSNENKKHLDPFSLVGD---ELSLISMR-----LRS 66
+LP+CR +L + G Q P +++ D +L+ IS L S
Sbjct: 13 QVPALPACRPLLRLQCNGSQV-------------PEAVLRDCCQQLAHISEWCRCGALYS 59
Query: 67 MVVAEVPELASAAGYFFKEGVEGKKLCPT-VILLMATAL----NVCTPELSPN 114
M+ + E + G C V+ L A ++ + +
Sbjct: 60 MLDSMYKEHGAQEGQAGTGAFPR---CRREVVKLTAASITAVCRLPIVVDASG 109
>1b1u_A Protein (alpha-amylase/trypsin inhibitor RATI); bifunctional,
hydrolase inhibitor; 2.20A {Eleusine coracana} SCOP:
a.52.1.2 PDB: 1bip_A 1tmq_B
Length = 122
Score = 29.0 bits (64), Expect = 1.0
Identities = 17/74 (22%), Positives = 23/74 (31%), Gaps = 18/74 (24%)
Query: 15 PRNSLPSCRWILSHRRYGHQPTFRNSNENKKHLDPFSLVGD---ELSLISMR-----LRS 66
P N L SCRW +S R G P L + +L I +R
Sbjct: 13 PHNPLDSCRWYVSTRTCGVGPR----------LATQEMKARCCRQLEAIPAYCRCEAVRI 62
Query: 67 MVVAEVPELASAAG 80
++ V G
Sbjct: 63 LMDGVVTPSGQHEG 76
>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 = 1.5
Identities = 12/28 (42%), Positives = 12/28 (42%), Gaps = 6/28 (21%)
Query: 319 ALK--HASLAAAAIDSLPETHDVDATNA 344
ALK ASL A DS P A A
Sbjct: 21 ALKKLQASLKLYADDSAPAL----AIKA 44
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
0.320 0.133 0.375
Gapped
Lambda K H
0.267 0.0696 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,358,225
Number of extensions: 332989
Number of successful extensions: 782
Number of sequences better than 10.0: 1
Number of HSP's gapped: 692
Number of HSP's successfully gapped: 79
Length of query: 360
Length of database: 6,701,793
Length adjustment: 95
Effective length of query: 265
Effective length of database: 4,049,298
Effective search space: 1073063970
Effective search space used: 1073063970
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 (21.8 bits)
S2: 58 (26.2 bits)