RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 029266
(196 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 = 229 bits (586), Expect = 2e-75
Identities = 136/223 (60%), Positives = 166/223 (74%), Gaps = 27/223 (12%)
Query: 1 MGNKLAILAGDLLISRALVALASLKHTEVI---------------------------MEC 33
MGNK+++LAGD L+SRA ALA+LK+TEV+ M+
Sbjct: 126 MGNKMSVLAGDFLLSRACGALAALKNTEVVALLATAVEHLVTGETMEITSSTEQRYSMDY 185
Query: 34 YMQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSAS 93
YMQKTY KTA+L+SNSCKAVA L+GQ EVA LAFEYG+NLGLA+QLIDDILDFTGTSAS
Sbjct: 186 YMQKTYYKTASLISNSCKAVAVLTGQTAEVAVLAFEYGRNLGLAFQLIDDILDFTGTSAS 245
Query: 94 LGKASLTDLRNGIITAPILFAMEEFPQLRAFINSSSDNPANVDVILEYLGKSHGIQRTTE 153
LGK SL+D+R+G+ITAPILFAMEEFPQLR ++ +P NVD+ LEYLGKS GIQR E
Sbjct: 246 LGKGSLSDIRHGVITAPILFAMEEFPQLREVVDQVEKDPRNVDIALEYLGKSKGIQRARE 305
Query: 154 LALKHASLAAAAIDSLPETHDVDATNARTALVHITQKIITRNK 196
LA++HA+LAAAAI SLPET + D +R AL+ +T ++ITRNK
Sbjct: 306 LAMEHANLAAAAIGSLPETDNEDVKRSRRALIDLTHRVITRNK 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 = 161 bits (409), Expect = 4e-49
Identities = 48/224 (21%), Positives = 90/224 (40%), Gaps = 36/224 (16%)
Query: 2 GNKLAILAGDLLISRALVALA----------------------------SLKHTEVIMEC 33
G + AI AGD + + + ++ ++
Sbjct: 116 GQRNAIYAGDFMFTVYFDQVLKSTTDRSLIQNHIDAMHRILQGELHQMDLNYREDITLDA 175
Query: 34 YMQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSAS 93
Y+ + KTA L + SC A L+G + V + G +G AYQ++DDILD+ G
Sbjct: 176 YLNEIAGKTAELFALSCYQGAQLAGAPQSVIDRTRDIGIAIGCAYQMLDDILDYAGDPKR 235
Query: 94 LGKASLTDLRNGIITAPILFAMEEFP--QLRAFINSSSDNPANVDVILEYLGKSHGIQRT 151
K L DLR+G+ + P+L ++ P + + ++ + + + G+
Sbjct: 236 TQKPVLEDLRSGVYSLPLLLSLSHAPRDFHKLLKKKQAMTLEDIKHVQALVAQYDGVGAA 295
Query: 152 TELALKHASLAAAAIDSLPETHDVDATNARTALVHITQKIITRN 195
+LA + A I LP +A+ +L +T+ ++ R+
Sbjct: 296 KQLAQDYTDRALTLIQQLPV------GSAQQSLEQLTRLLLRRD 333
>3aqb_B Component B of hexaprenyl diphosphate synthase; prenyltransferase,
transferase; 2.40A {Micrococcus luteus} PDB: 3aqc_B*
Length = 325
Score = 155 bits (394), Expect = 7e-47
Identities = 57/227 (25%), Positives = 102/227 (44%), Gaps = 39/227 (17%)
Query: 2 GNKLAILAGDLLISRALVALASLKHTEVI---------------------------MECY 34
AI G L++RAL +A++ +++ Y
Sbjct: 104 DKDTAIRTGHFLLARALQNIATINNSKFHQIFSKTILEVCFGEFDQMADRFNYPVSFTAY 163
Query: 35 MQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASL 94
+++ KTA L+ SC A S E+ ++G +G++YQ+IDDILD+T A+L
Sbjct: 164 LRRINRKTAILIEASCHLGALSSQLDEQSTYHIKQFGHCIGMSYQIIDDILDYTSDEATL 223
Query: 95 GKASLTDLRNGIITAPILFAM-----EEFPQLRAFI-NSSSDNPANVDVILEYLGKSHGI 148
GK +D+RNG IT P++ A+ ++ +L A + + +S + V + K +GI
Sbjct: 224 GKPVGSDIRNGHITYPLMAAIANLKEQDDDKLEAVVKHLTSTSDDEVYQYIVSQVKQYGI 283
Query: 149 QRTTELALKHASLAAAAIDSLPETHDVDATNARTALVHITQKIITRN 195
+ L+ K+ A + L + +N + L I +K++ R
Sbjct: 284 EPAELLSRKYGDKAKYHLSQLQD------SNIKDYLEEIHEKMLKRV 324
>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 = 150 bits (382), Expect = 8e-45
Identities = 54/222 (24%), Positives = 96/222 (43%), Gaps = 35/222 (15%)
Query: 2 GNKLAILAGDLLISRALVALASLKHTEV-------------------------IMECYMQ 36
N +AILAGD+L++ A ++ L V +E Y
Sbjct: 135 DNSVAILAGDILLAHASGLMSQLGTDTVAHFAETFGELVTGQMRETVGPRDTDPIEHYTN 194
Query: 37 KTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASLGK 96
KT L++++ A +G E +G +G+ +Q++DDI+D + GK
Sbjct: 195 VIREKTGVLIASAGYLGAMHAGAAPEHIDALKNFGAAVGMIFQIVDDIIDIFSETHESGK 254
Query: 97 ASLTDLRNGIITAPILFAM----EEFPQLRAFINSSSDNPANVDVILEYLGKSHGIQRTT 152
TDLR G+ T P+L+A+ +LR + ++ V+ +LE L +S G Q
Sbjct: 255 TPGTDLREGVFTLPVLYALREDTPVGAELRDILTGPLEDDETVNHVLELLSQSGGRQAAL 314
Query: 153 ELALKHASLAAAAIDSLPETHDVDATNARTALVHITQKIITR 194
+ ++ +A A +D LP+ + + AL ++ + R
Sbjct: 315 DEVYRYMDIANAELDRLPD------STVKEALRNLATFTVKR 350
>3oyr_A Trans-isoprenyl diphosphate synthase; isoprenyl synthase, PSI,
protein structure initiative; HET: IPE; 2.00A
{Caulobacter crescentus}
Length = 345
Score = 150 bits (381), Expect = 9e-45
Identities = 56/225 (24%), Positives = 87/225 (38%), Gaps = 38/225 (16%)
Query: 2 GNKLAILAGDLLISRALVALASLKHTEVI---------------------------MECY 34
G ++L GD L +RA + + + Y
Sbjct: 125 GGAQSVLVGDFLFARAFELMVETNSMKALEILARASRVIAEGEVLQLMRSHDLNLSQAVY 184
Query: 35 MQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASL 94
++ KTA L + + +A A +G + +YG NLGLA+QL DD LD+ G + +L
Sbjct: 185 LEIIQAKTAELFAAASEAGAVSAGVDVAKSEALRDYGLNLGLAFQLADDALDYGGATETL 244
Query: 95 GKASLTDLRNGIITAPILFAM-----EEFPQLRAFINSSSDNPANVDVILEYLGKSHGIQ 149
GK + D R G T P+L A+ E I A+ E + S +
Sbjct: 245 GKNAGDDFREGKATLPLLLAIARSGPREAEFWERAIGRREQTEADFRRARELIIGSGALD 304
Query: 150 RTTELALKHASLAAAAIDSLPETHDVDATNARTALVHITQKIITR 194
T +LA +A A AA+ P + R AL + ++R
Sbjct: 305 ATLDLAADYADKAKAALAMFPA------NDWREALEELADFAVSR 343
>3rmg_A Octaprenyl-diphosphate synthase; structural genomics, protein
structure initiative, isoprene biosynthesis,
transferase; 2.30A {Bacteroides thetaiotaomicron}
Length = 334
Score = 147 bits (374), Expect = 7e-44
Identities = 52/227 (22%), Positives = 91/227 (40%), Gaps = 39/227 (17%)
Query: 2 GNKLAILAGDLLISRALVALASLKHTEVI---------------------------MECY 34
NK+++LAGD L++ +LV + E+I E Y
Sbjct: 107 NNKVSVLAGDYLLATSLVHAEQTNNYEIIRLVSSLGQKLAEGELLQLSNVSNHSFSEEVY 166
Query: 35 MQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASL 94
KTAAL + +A A EE A G+ +G+ +Q+ DDI D+ S +
Sbjct: 167 FDVIRKKTAALFAACAEAAALSVQVGEEEVAFARLLGEYIGICFQIKDDIFDYFD-SKKI 225
Query: 95 GKASLTDLRNGIITAPILFAM-----EEFPQLRAFINSSSDNPANVDVILEYLGKSHGIQ 149
GK + D+ G +T P L+A+ Q+ + + P + ++E+ + GI+
Sbjct: 226 GKPTGNDMLEGKLTLPALYALNTTKDAWAEQIAFKVKEGTATPDEIVRLIEFTKDNGGIE 285
Query: 150 RTTELALKHASLAAAAIDSLPETHDVDATNARTALVHITQKIITRNK 196
++ A + +LP+ +N AL ++ R K
Sbjct: 286 YACRTIEQYKKKAFDLLAALPD------SNICLALRTYLDYVVAREK 326
>3mzv_A Decaprenyl diphosphate synthase; transferase, structural genomics,
PSI-2, protein structure initiative; 1.90A {Rhodobacter
capsulatus}
Length = 341
Score = 147 bits (372), Expect = 2e-43
Identities = 50/227 (22%), Positives = 92/227 (40%), Gaps = 38/227 (16%)
Query: 2 GNKLAILAGDLLISRALVALASLKHTEVI---------------------------MECY 34
NK ++L GD L +R+ + + V+ + Y
Sbjct: 113 DNKSSVLVGDYLFARSFQLMTDTGNMRVMEILANASAVIAEGEVLQLTAAQNLATTEDIY 172
Query: 35 MQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASL 94
++ KTAAL S + + + G E+ F+YG LG+A+Q++DD+LD+ G SA +
Sbjct: 173 LRVIRGKTAALFSAATEVGGIIGGAPEDQVQALFDYGDALGIAFQIVDDLLDYGGKSAEI 232
Query: 95 GKASLTDLRNGIITAPILFAM-----EEFPQLRAFINSSSDNPANVDVILEYLGKSHGIQ 149
GK + D R +T P++ A+ E + I +++ + + K ++
Sbjct: 233 GKNTGDDFRERKLTMPVIKAVALADEAERAFWKRVIEKGDQQDGDLEHAMALMTKHGTLE 292
Query: 150 RTTELALKHASLAAAAIDSLPETHDVDATNARTALVHITQKIITRNK 196
T A+ A A+ LP+ R L + ++ R +
Sbjct: 293 ATRLAAIGWTDTARKALAKLPD------HPLRQMLDDLADYVVERVR 333
>3tc1_A Octaprenyl pyrophosphate synthase; all alpha-helices fold,
transferase; 2.00A {Helicobacter pylori}
Length = 315
Score = 137 bits (347), Expect = 5e-40
Identities = 49/223 (21%), Positives = 90/223 (40%), Gaps = 42/223 (18%)
Query: 2 GNKLAILAGDLLISRALVALASL--------------------------KHTEVIMECYM 35
GN A++ GD+ S+A L+ + + + Y
Sbjct: 97 GNFNAVMLGDVFYSKAFFELSKMGELIAQALSNAVLRLSRGEIEDVFVGECFNSDKQKYW 156
Query: 36 QKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASLG 95
+ +KTA + S K++A L + ++ ++G N G+A+Q+IDD+LD T + +LG
Sbjct: 157 RILEDKTAHFIEASLKSMAILLNKDAKIY---ADFGLNFGMAFQIIDDLLDITQDAKTLG 213
Query: 96 KASLTDLRNGIITAPILFAMEEF-PQLRAFINS--SSDNPANVDVILEYLGKSHGIQRTT 152
K + +D + G T P L E+ + + S D+ ++ E + I+ T
Sbjct: 214 KPNFSDFKEGKTTLPYLLLYEKLNQHDQGLLISYFKQDSHEIIEWTKEKFKQYGIIEETL 273
Query: 153 ELALKHASLAAAAIDSLPETHDVDATNARTALVHITQKIITRN 195
+ A ++ A AI L + Q +I+R
Sbjct: 274 KTAQVYSKKALEAIKGEN----------NLILEKLAQDVISRT 306
>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 = 132 bits (334), Expect = 3e-38
Identities = 43/208 (20%), Positives = 82/208 (39%), Gaps = 35/208 (16%)
Query: 2 GNKLAILAGDLLISRALVALASLKHTEVI--------------------------MECYM 35
G+K A+ AGDL++ A + + + ++ E Y+
Sbjct: 101 GDKAAVAAGDLVLVSAFHTVEEIGNNKLRRAFLNVIGKMSEAELIEQLSRYKPITKEEYL 160
Query: 36 QKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASLG 95
+ K+ AL + + A L G+ E + G +G YQ+ DDI+DF G +G
Sbjct: 161 RIVEGKSGALFGLALQLPALLEGELGEDL---YNLGVTIGTIYQMFDDIMDFAGM-EKIG 216
Query: 96 KASLTDLRNGIITAPILFAMEEFPQLRAFINSSSDNPANVDVILEYLGKSHGIQRTTELA 155
K DL+NG+ + P++ AME+FP+ R + + ++ ++ + ++ E
Sbjct: 217 KDGFLDLKNGVASFPLVTAMEKFPEARQMFEN-----RDWSGLMSFMREKGILKECEETL 271
Query: 156 LKHASLAAAAIDSLPETHDVDATNARTA 183
L + D ++
Sbjct: 272 KVLVKNVIIENSWLRDFVDGIFKIKISS 299
>1wy0_A Geranylgeranyl pyrophosphate synthetase; pyrococcus horikosh
structural genomics, riken structural
genomics/proteomics initiative, RSGI; 2.20A {Pyrococcus
horikoshii}
Length = 342
Score = 125 bits (316), Expect = 3e-35
Identities = 58/242 (23%), Positives = 90/242 (37%), Gaps = 54/242 (22%)
Query: 2 GNKLAILAGDLLISRALVALASL--------------------------------KHTEV 29
G +AILAGDLL S+A A+A K + V
Sbjct: 106 GVNMAILAGDLLFSKAFEAVARAEIPPEKKARVLEVIVKASNELCEGQARDLEFEKKSTV 165
Query: 30 IMECYMQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTG 89
+E YM+ KT AL S K + EE +G+N+G+A+Q+ DD+LD
Sbjct: 166 TIEEYMEMISGKTGALFEASAKVGGIIGTDNEEYIKALSSWGRNVGIAFQIWDDVLDLIA 225
Query: 90 TSASLGKASLTDLRNGIITAPILFAME-----EFPQLRAFINSSSDNP-----------A 133
LGK +D+R G T + E + + + + +
Sbjct: 226 DEKKLGKPVGSDIRKGKKTLIVAHFFENADEKDKQRFLKIFGKYAGDVKGRGIIEEDIKS 285
Query: 134 NVDVILEYLGKSHGIQRTTELALKHASLAAAAIDSLPETHDVDATNARTALVHITQKIIT 193
+V ++ L K I E+A A A+ LP+ + AR L + + I+
Sbjct: 286 DVMEAIDLLKKYGSIDYAAEIAKDMIKKANEALRILPK------SKARMDLELLAKFIVE 339
Query: 194 RN 195
R
Sbjct: 340 RE 341
>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 = 123 bits (312), Expect = 5e-35
Identities = 38/227 (16%), Positives = 71/227 (31%), Gaps = 42/227 (18%)
Query: 2 GNKLAILAGDLLISRALVALASLKHTEVI----------------------------MEC 33
G I + + + L + +L H + + E
Sbjct: 85 GIPSVINSANYVYFLGLEKVLTLDHPDAVKLFTRQLLELHQGQGLDIYWRDNYTCPTEEE 144
Query: 34 YMQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSAS 93
Y KT L + + S +E++ LGL +Q+ DD + S
Sbjct: 145 YKAMVLQKTGGLFGLAVGLMQLFSDYKEDLK----PLLNTLGLFFQIRDDYANLHSKEYS 200
Query: 94 LGKASLTDLRNGIITAPILFAMEEFP---QLRAFINSSSDNPANVDVILEYLGKSHGIQR 150
K+ DL G + P + A+ P Q++ + ++N + YL +
Sbjct: 201 ENKSFCEDLTEGKFSFPTIHAIWSRPESTQVQNILRQRTENIDIKKYCVHYLEDVGSFEY 260
Query: 151 TTELALKHASLAAAAIDSLPETHDVDATNARTALVH-ITQKIITRNK 196
T + + A ID+ ALV +++ N+
Sbjct: 261 TRNTLKELEAKAYKQIDARGGNP------ELVALVKHLSKMFKEENE 301
>4dhd_A Polyprenyl synthetase; isoprenoid synthesis, isoprenoid diphosphate
synthase, trans; 1.65A {Pyrobaculum calidifontis}
Length = 358
Score = 123 bits (311), Expect = 2e-34
Identities = 39/240 (16%), Positives = 70/240 (29%), Gaps = 55/240 (22%)
Query: 2 GNKLAILAGDLLISRALVALASLKHTEVIMEC---------------------------- 33
G+ AIL G A+ + +
Sbjct: 105 GDNAAILVGIWYREAIEEAVLDTPKPTLFAKEVAEVIKAIDEGERLDILFEAAGRSDPYF 164
Query: 34 ------------YMQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLI 81
Y++ KT AL++ + K +A A+ +G G+A+Q+I
Sbjct: 165 VQARWREVTLDDYIKMVSLKTGALIAAAAKWGVLSVSDDRGLAEAAWNFGMAAGVAFQII 224
Query: 82 DDILDFTGTSASLGKASLTDLRNGIITAPILFAM------EEFPQLRAFINSSSDNPANV 135
DD+LD G GK D++ ++ E +L + A+V
Sbjct: 225 DDVLDIYGDPKKFGKEIGKDIKEHKRGNAVVAVALSHLGEGERRRLLEILAREVVEEADV 284
Query: 136 DVILEYLGKSHGIQRTTELALKHASLAAAAIDSLPETHDVDATNARTALVHITQKIITRN 195
+ L + LA ++ A + +P L + I+ R
Sbjct: 285 REAVALLDSVGAREEALRLAARYREEAERHLAKIPN---------NGTLKELLDFIVARE 335
>3nf2_A Putative polyprenyl synthetase; isoprenyl diphosphate synthase,
structural genomics, PSI, PR structure initiative,
nysgrc; 2.20A {Streptomyces coelicolor}
Length = 352
Score = 123 bits (310), Expect = 3e-34
Identities = 47/236 (19%), Positives = 89/236 (37%), Gaps = 46/236 (19%)
Query: 2 GNKLAILAGDLLISRA---LVALASLKHTEVI---------------------------M 31
G AIL GD L + A L+ L +++ +
Sbjct: 114 GPAQAILVGDALFALANEVLLELGTVEAGRATRRLTKASRSLIDGQAQDISYEHRDRVSV 173
Query: 32 ECYMQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTS 91
E ++ NKT AL++ + A L G E A +YG +LGLA+Q +DD+L G
Sbjct: 174 EECLEMEGNKTGALLACASSIGAVLGGADERTADTLEKYGYHLGLAFQAVDDLLGIWGDP 233
Query: 92 ASLGKASLTDLRNGIITAPILFAMEE-FPQLRAFI----------NSSSDNPANVDVILE 140
+ GK + +DLR + P++ A+ + ++ +
Sbjct: 234 DATGKQTWSDLRQRKKSLPVVAALAAGGAASERLGEILTADAKASDFANFSEEEFAARAA 293
Query: 141 YLGKSHGIQRTTELALKHASLAAAAIDSLPETHDVDATNARTALVHITQKIITRNK 196
+ ++ G + T + A + ++A A+D++ R + ++ R +
Sbjct: 294 LIEEAGGREWTADEARRQHTIAIEALDAVDMPDR-----VRDRFTALADFVVVRKR 344
>3ipi_A Geranyltranstransferase; isoprene biosynthesis, helical bundle,
protein structure initiative II (PSI II), structural
genomics, nysgxrc; 1.90A {Methanosarcina mazei}
Length = 295
Score = 116 bits (294), Expect = 2e-32
Identities = 43/218 (19%), Positives = 72/218 (33%), Gaps = 62/218 (28%)
Query: 2 GNKLAILAGDLLISRALVALASL-------------------------KHTEVIMECYMQ 36
G A+L GD LI++++ ++ + Y +
Sbjct: 102 GPSGALLCGDYLIAKSIAFISPYGEKVIQDFGKAGMDMAEGEVLDLKLEDESFGENDYFK 161
Query: 37 KTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASLGK 96
Y KTA+L + S AY G EE+A +G LG AYQ++DDIL+F
Sbjct: 162 CIYKKTASLFAISASIGAYTGGAEEELAERFSHFGNALGTAYQIVDDILEFL------EV 215
Query: 97 ASLTDLRNGIITAPILFAMEEFPQLRAFINSSSDNPANVDVILEYLGKSHGIQRTTELAL 156
+ + T P ++ K ++++ +
Sbjct: 216 VEGKESKFTSETLPHIYMKST-------------------------SKEEALKKSIDCVK 250
Query: 157 KHASLAAAAIDSLPETHDVDATNARTALVHITQKIITR 194
H + A +++ E AR L IT I
Sbjct: 251 LHVAAAKETLETFRE------CPARDKLFQITDYITVD 282
>3lk5_A Geranylgeranyl pyrophosphate synthase; structural genomics, protein
structure initiative, geranylge pyrophosphate synthase;
1.90A {Corynebacterium glutamicum} PDB: 3qqv_A*
Length = 380
Score = 107 bits (268), Expect = 5e-28
Identities = 49/236 (20%), Positives = 86/236 (36%), Gaps = 47/236 (19%)
Query: 2 GNKLAILAGDLLISRALVALASLKH----------------TEVI--------------- 30
G ++ILAGD+ + A L TEVI
Sbjct: 144 GVSVSILAGDMALVWAEDMLQDSGLSAEALARTRDAWRGMRTEVIGGQLLDIYLESHANE 203
Query: 31 -MECYMQKTYNKTAA-LVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFT 88
+E KTAA ++ A ++G ++ YG ++G+A+QL DD+L
Sbjct: 204 SVELADSVNRFKTAAYTIARPLHLGASIAGGSPQLIDALLHYGHDIGIAFQLRDDLLGVF 263
Query: 89 GTSASLGKASLTDLRNGIITAPILFAM--------EEFPQLRAFINSSSDNPANVDVILE 140
G A GK + D+R G T + A+ E +RA + + P ++ VI E
Sbjct: 264 GDPAITGKPAGDDIREGKRTVLLALALQRADKQSPEAATAIRAGVGKVTS-PEDIAVITE 322
Query: 141 YLGKSHGIQRTTELALKHASLAAAAIDSLPETHDVDATNARTALVHITQKIITRNK 196
++ + + + + A +D + + R L + + R +
Sbjct: 323 HIRATGAEEEVEQRISQLTESGLAHLDDVDIPDE-----VRAQLRALAIRSTERRE 373
>2azj_A Geranylgeranyl pyrophosphate synthetase; hexpps,
trans-prenyltransferase; 2.40A {Sulfolobus solfataricus}
PDB: 2azk_A
Length = 289
Score = 103 bits (260), Expect = 2e-27
Identities = 33/176 (18%), Positives = 59/176 (33%), Gaps = 29/176 (16%)
Query: 2 GNKLAILAGDLLISRALVALASLKHTEVI--------------------MECYMQKTYNK 41
GN+ I + LI AL + + + + Y++ K
Sbjct: 109 GNRKVIFITNYLIPTALRIIQTSYGDDALNTSIELWKDTSVGALRDMYDNSDYIRTIELK 168
Query: 42 TAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSA----SLGKA 97
T +L S AY S + + GK LG+ YQ+IDD +D+ K
Sbjct: 169 TGSLFKLSTVLSAYASKHYNTKQQML-DVGKYLGIIYQVIDDFVDYKTKKVEEIDGSAKQ 227
Query: 98 SLTDLRNGIITAPILFAMEEF-PQLRAFINS---SSDNPANVDVILEYLGKSHGIQ 149
R G + + E+ + I++ S + + + E+L +
Sbjct: 228 LFKYYREGKLEEYVRSVYLEYKQKYDELISNIPFQSKYLSEIRSLPEFLANGLLKE 283
>1wmw_A Geranylgeranyl diphosphate synthetase; GGPP, prenyl diphosphate
synthase, structural genom riken structural
genomics/proteomics initiative; 1.55A {Thermus
thermophilus}
Length = 330
Score = 100 bits (252), Expect = 6e-26
Identities = 48/235 (20%), Positives = 80/235 (34%), Gaps = 47/235 (20%)
Query: 2 GNKLAILAGDLLISRALVALASLKH----------------------------------T 27
LA+ AGD + + LA
Sbjct: 99 PMPLALNAGDAMHAEMWGLLAEGLARGLFPPEVLLEFHEVVRRTAYGQHLDLLWTLGGTF 158
Query: 28 EVIMECYMQKTYNKTAAL-VSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILD 86
++ E Y + +K A + A L+G+ A E G LG A+Q++DD+L+
Sbjct: 159 DLRPEDYFRMVAHKAAYYTAVAPLRLGALLAGKTPPAA--YEEGGLRLGTAFQIVDDVLN 216
Query: 87 FTGTSASLGKASLTDLRNGIITAPILFAME-----EFPQLRAFINSSSDN--PANVDVIL 139
G A GK DL G T +L +E E + A + + A V +L
Sbjct: 217 LEGGEA-YGKERAGDLYEGKRTLILLRFLEEAPPEERARALALLALPREAKPEAEVGWLL 275
Query: 140 EYLGKSHGIQRTTELALKHASLAAAAIDSLPETHDVDATNARTALVHITQKIITR 194
E L S + A + + A +++ + D+ A L + ++ R
Sbjct: 276 ERLLASRALAWAKAEAKRLQAEGLALLEAAFQ--DLPGKEALDHLRGLLAALVER 328
>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 = 99.4 bits (248), Expect = 2e-25
Identities = 36/238 (15%), Positives = 71/238 (29%), Gaps = 46/238 (19%)
Query: 2 GNKLAILAGDLLISRALVALASLKH----------------------------------- 26
G I + + RA+ ++ L
Sbjct: 100 GVPSTINTANYMYFRAMQLVSQLTTKEPLYHNLITIFNEELINLHRGQGLDIYWRDFLPE 159
Query: 27 TEVIMECYMQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILD 86
E Y+ NKT L + + + LS +L + LG+ YQ+ DD L+
Sbjct: 160 IIPTQEMYLNMVMNKTGGLFRLTLRLMEALSPSSHHGHSLV-PFINLLGIIYQIRDDYLN 218
Query: 87 FTGTSASLGKASLTDLRNGIITAPILFAME------EFPQLRAFINSSSDNPANVDV--- 137
S K D+ G ++ PI+ A+ + Q + ++ D+
Sbjct: 219 LKDFQMSSEKGFAEDITEGKLSFPIVHALNFTKTKGQTEQHNEILRILLLRTSDKDIKLK 278
Query: 138 ILEYLGKSHG-IQRTTELALKHASLAAAAIDSLPETHDVDATNARTALVHITQKIITR 194
+++ L + T + ++ ++ ++ T L II
Sbjct: 279 LIQILEFDTNSLAYTKNFINQLVNMIKNDNENKYLPDLASHSDTATNLHDELLYIIDH 336
>4fp4_A Polyprenyl synthetase; isoprenoid synthesis, isoprenoid diphosphate
synthase, trans; HET: GER UNL; 2.00A {Pyrobaculum
calidifontis}
Length = 285
Score = 97.8 bits (244), Expect = 4e-25
Identities = 30/186 (16%), Positives = 58/186 (31%), Gaps = 34/186 (18%)
Query: 2 GNKLAILAGDLLISRALVALASL---------KHTEVI--------MECYMQKTYNKTAA 44
G+ AI+A D LI+ ++ +L + + + KTA
Sbjct: 108 GDGRAIVASDWLIAESIKMAVNLGADVVTYLADVAQRLSVGQALDLEGERDKAAEFKTAP 167
Query: 45 LVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASLGKASLTDLRN 104
L+ + + G+RE + T + G LG+ YQ DD D K+ ++
Sbjct: 168 LIEAALVMPLVILGRRELIETAK-KLGTKLGILYQYSDDYSDENVERPE-TKSIANEI-- 223
Query: 105 GIITAPILFAM-----EEFPQLRAFINSSSDNPANVDVILEYLGKSHGIQRTTELALKHA 159
G I + ++ I + + V + + + H
Sbjct: 224 GRYLLKIKEHVGDAIAPFERLIKYLIGKALEGTLTVSRTIA--------ENLYFQSHHHH 275
Query: 160 SLAAAA 165
+
Sbjct: 276 HHWSHP 281
>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 = 95.2 bits (237), Expect = 1e-23
Identities = 31/171 (18%), Positives = 53/171 (30%), Gaps = 12/171 (7%)
Query: 31 MECYMQKTYNKTAAL--VSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFT 88
E Y KTA A+ + +E A +G +Q+ DD LD
Sbjct: 204 EERYKAIVKYKTAFYSFYLPVAAAMYMVGIDSKEEHENAKAILLEMGEYFQIQDDYLDCF 263
Query: 89 GTSASLGKASLTDLRNGIITAPILFAMEEF-PQLRAFI--NSSSDNPANVDVILEYLGKS 145
G A G TD+++ + ++ ++ P+ R + N P V + E
Sbjct: 264 GDPALTGAVG-TDIQDNKCSWLVVQCLQRVTPEQRQLLEDNYGRKEPEKVAKVKELYEAV 322
Query: 146 HGIQRTTELALKHASLAAAAIDSLPETHDVDATNARTALVHITQKIITRNK 196
+ I+ + + + QKI R K
Sbjct: 323 GMRAAFQQYEESSYRRLQELIEKHSN------RLPKEIFLGLAQKIYKRQK 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 = 88.7 bits (220), Expect = 3e-21
Identities = 28/171 (16%), Positives = 53/171 (30%), Gaps = 12/171 (7%)
Query: 31 MECYMQKTYNKTAALVSNSCKAVAYLSGQ--REEVATLAFEYGKNLGLAYQLIDDILDFT 88
+ Y K+A A A E+ A + +G +Q+ DD LD
Sbjct: 211 EKRYKSIVKYKSAFYSFYLPIAAAMYMAGIDGEKEHANAKKILLEMGEFFQIQDDYLDLF 270
Query: 89 GTSASLGKASLTDLRNGIITAPILFAMEEF-PQLRAFI--NSSSDNPANVDVILEYLGKS 145
G + GK TD+++ + ++ ++ P+ + N V + +
Sbjct: 271 GDPSVTGKIG-TDIQDNKCSWLVVQCLQRATPEQYQILKENYGQKEAEKVARVKALYEEL 329
Query: 146 HGIQRTTELALKHASLAAAAIDSLPETHDVDATNARTALVHITQKIITRNK 196
+ S A I+ + + +KI R K
Sbjct: 330 DLPAVFLQYEEDSYSHIMALIEQYAAPL------PPAVFLGLARKIYKRRK 374
>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 = 82.9 bits (205), Expect = 3e-19
Identities = 27/197 (13%), Positives = 59/197 (29%), Gaps = 10/197 (5%)
Query: 5 LAILAGDLLISRALVALASLKHTEVIMECYMQKTYNKTAAL-VSNSCKAVAYLSGQ-REE 62
+ + + + + E Y + KT ++S
Sbjct: 171 VTSMCDSNKLDPEVAQPMTTDFAEFTPAIYKRIVKYKTTFYTYLLPLVMGLFVSEAAASV 230
Query: 63 VATLAFEYGKNLGLAYQLIDDILDFTGTSASLGKASLTDLRNGIITAPILFAMEEF-PQL 121
L +G +Q+ DD++D LGK TD+ + + + + +
Sbjct: 231 EMNLVERVAHLIGEYFQVQDDVMDCFTPPEQLGKVG-TDIEDAKCSWLAVTFLGKANAAQ 289
Query: 122 RAFI--NSSSDNPANVDVILEYLGKSHGIQRTTELALKHASLAAAAIDSLPETHDVDATN 179
A N +PA V V+ +++ + + I+ L +
Sbjct: 290 VAEFKANYGDKDPAKVAVVKRLYSEANLQADFAAYEAEVVREVESLIEQLKV----KSPT 345
Query: 180 ARTALVHITQKIITRNK 196
++ + +K R K
Sbjct: 346 FAESVAVVWEKTHKRKK 362
>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 = 83.1 bits (205), Expect = 4e-19
Identities = 30/151 (19%), Positives = 50/151 (33%), Gaps = 7/151 (4%)
Query: 27 TEVIMECYMQKTYNKTAALVSNSCKAVAYLSGQR---EEVATLAFEYGKNLGLAYQLIDD 83
+ Y +KTA L + + +G +Q+ DD
Sbjct: 228 NMINFGVYKNIVIHKTAYYSFFLPIVCGMLLAGIAVDNLIYKKIEDISMLMGEYFQIHDD 287
Query: 84 ILDFTGTSASLGKASLTDLRNGIITAPILFAMEEF-PQLRAFI--NSSSDNPANVDVILE 140
LD G S GK +D++N +T P++ E + I N +N A V VI
Sbjct: 288 YLDIFGDSTKTGKVG-SDIQNNKLTWPLIKTFELCSEPDKIKIVKNYGKNNLACVKVIDS 346
Query: 141 YLGKSHGIQRTTELALKHASLAAAAIDSLPE 171
+ + + +AI+ L
Sbjct: 347 LYEQYKIRKHYESYEKAQKAKILSAINELHH 377
>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 = 79.2 bits (195), Expect = 8e-18
Identities = 27/176 (15%), Positives = 51/176 (28%), Gaps = 10/176 (5%)
Query: 26 HTEVIMECYMQKTYNKTAAL-VSNSCKAVAYLSGQR-EEVATLAFEYGKNLGLAYQLIDD 83
E + Y + KTA +S + E +G +Q+ DD
Sbjct: 220 FAEFTLSNYKRIVKYKTAYYTYLLPLVMGLIVSEALPTVDMGVTEELAMLMGEYFQVQDD 279
Query: 84 ILDFTGTSASLGKASLTDLRNGIITAPILFAMEEF-PQLRAFI--NSSSDNPANVDVILE 140
++D LGK TD+++ + + + + A N S + V +
Sbjct: 280 VMDCFTPPERLGKVG-TDIQDAKCSWLAVTFLAKASSAQVAEFKANYGSGDSEKVATVRR 338
Query: 141 YLGKSHGIQRTTELALKHASLAAAAIDSLPETHDVDATNARTALVHITQKIITRNK 196
++ A I+ L ++ + K R K
Sbjct: 339 LYEEADLQGDYVAYEAAVAEQVKELIEKLRLCSP----GFAASVETLWGKTYKRQK 390
>3uca_A Geranyltranstransferase; isoprenoid synthesis, isoprenoid
diphosphate synthase; 2.00A {Clostridium perfringens}
Length = 324
Score = 75.4 bits (186), Expect = 1e-16
Identities = 37/149 (24%), Positives = 56/149 (37%), Gaps = 39/149 (26%)
Query: 6 AILAGDLLISRA--LVALASLKHTEVIMEC------------------------------ 33
A+LAGD L++ A ++ SL+ + ++
Sbjct: 140 AVLAGDALLNEAMKILVDYSLEEGKSALKATKIIADAAGSDGMIGGQIVDIINEDKEEIS 199
Query: 34 -----YMQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFT 88
YM KT L+ S + A L+ E +G LGLA+Q+ DDILD
Sbjct: 200 LKELDYMHL--KKTGELIKASIMSGAVLAEASEGDIKKLEGFGYKLGLAFQIKDDILDVV 257
Query: 89 GTSASLGKASLTDLRNGIITAPILFAMEE 117
G + LGK D + +F +EE
Sbjct: 258 GNAKDLGKNVHKDQESNKNNYITIFGLEE 286
>1rtr_A Geranyltranstransferase; 2.50A {Staphylococcus aureus} SCOP:
a.128.1.1
Length = 301
Score = 74.2 bits (183), Expect = 3e-16
Identities = 35/148 (23%), Positives = 57/148 (38%), Gaps = 38/148 (25%)
Query: 6 AILAGDLLISRA--LVALASLKHTEVIMEC------------------------------ 33
AILAGD L+++A L++ EV ++
Sbjct: 108 AILAGDALLTKAFELISSDDRLTDEVKIKVLQRLSIASGHVGMVGGQMLDMQSEGQPIDL 167
Query: 34 ----YMQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTG 89
+ K KT AL++ + + A ++ + Y +LG+ +Q+ DD+LD G
Sbjct: 168 ETLEMIHK--TKTGALLTFAVMSAADIANVDDTTKEHLESYSYHLGMMFQIKDDLLDCYG 225
Query: 90 TSASLGKASLTDLRNGIITAPILFAMEE 117
A LGK +DL N T L +
Sbjct: 226 DEAKLGKKVGSDLENNKSTYVSLLGKDG 253
>3p8l_A Geranyltranstransferase; isoprenyl synthase, structural genomics,
PSI, protein struct initiative, nysgrc; 2.00A
{Enterococcus faecalis}
Length = 302
Score = 73.0 bits (180), Expect = 6e-16
Identities = 42/147 (28%), Positives = 62/147 (42%), Gaps = 37/147 (25%)
Query: 6 AILAGDLLISRA--LVALASLKHTEVI----------------------MEC-------- 33
AILAGD L++ A L++L+ L +E + +E
Sbjct: 117 AILAGDGLLTGAFQLLSLSQLGLSEKVLLMQQLAKAAGNQGMVSGQMGDIEGEKVSLTLE 176
Query: 34 ---YMQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGT 90
+ + KT AL+ + A L+ Q EEV L ++ + GLA+Q+ DD+LD T T
Sbjct: 177 ELAAVHE--KKTGALIEFALIAGGVLANQTEEVIGLLTQFAHHYGLAFQIRDDLLDATST 234
Query: 91 SASLGKASLTDLRNGIITAPILFAMEE 117
A LGK D T P L +
Sbjct: 235 EADLGKKVGRDEALNKSTYPALLGIAG 261
>2h8o_A Geranyltranstransferase; geranyltransferase,agrobacterium
tumefaciens, structural GEN PSI-2, protein structure
initiative; 1.60A {Agrobacterium tumefaciens}
Length = 335
Score = 73.1 bits (180), Expect = 8e-16
Identities = 27/84 (32%), Positives = 44/84 (52%), Gaps = 2/84 (2%)
Query: 34 YMQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSAS 93
+Q KT AL+ +C+A A ++G + +G+ +GL++QL DD+LD T +A+
Sbjct: 216 TLQA--MKTGALLRFACEAGAIIAGSNQAERQRLRLFGEKIGLSFQLADDLLDLTADAAT 273
Query: 94 LGKASLTDLRNGIITAPILFAMEE 117
+GKA+ D G T L
Sbjct: 274 MGKATGKDAARGKGTLVALRGEAW 297
>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 = 71.1 bits (175), Expect = 3e-15
Identities = 24/84 (28%), Positives = 36/84 (42%), Gaps = 2/84 (2%)
Query: 34 YMQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSAS 93
+ K KT AL+ + +A L E ++ GLA+Q+ DDILD + A
Sbjct: 179 VLHK--EKTGALLHYAVQAGLILGQAPEAQWPAYLQFADAFGLAFQIYDDILDVVSSPAE 236
Query: 94 LGKASLTDLRNGIITAPILFAMEE 117
+GKA+ D T P +
Sbjct: 237 MGKATQKDADEAKNTYPGKLGLIG 260
>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 = 71.1 bits (175), Expect = 4e-15
Identities = 30/86 (34%), Positives = 44/86 (51%), Gaps = 5/86 (5%)
Query: 34 YMQKTYNKTAALVSNSCKAVAYLSGQ--REEVATLAFEYGKNLGLAYQLIDDILDFTGTS 91
YM + +KT AL+ S A SG+ + E+ L Y + +GLA+Q+ DDILD +
Sbjct: 176 YMHR--HKTGALIEASVILGALASGRAEKGELKALQ-TYAQAIGLAFQVQDDILDVESDT 232
Query: 92 ASLGKASLTDLRNGIITAPILFAMEE 117
A+LGK D+ T P L +
Sbjct: 233 ATLGKRQGADIARDKPTYPALLGLAA 258
>4f62_A Geranyltranstransferase; enzyme function initiative, structural
genomics; 2.10A {Marinomonas SP}
Length = 317
Score = 70.7 bits (174), Expect = 4e-15
Identities = 29/86 (33%), Positives = 44/86 (51%), Gaps = 5/86 (5%)
Query: 34 YMQKTYNKTAALVSNSCKAVAYLSGQ--REEVATLAFEYGKNLGLAYQLIDDILDFTGTS 91
M +KT AL+ S + A +GQ E++A L Y +GLA+Q+ DDI+D T +
Sbjct: 175 QMHV--HKTGALIKASVRMGALSTGQVKPEQLAKLD-AYAHAIGLAFQVQDDIIDLTSDT 231
Query: 92 ASLGKASLTDLRNGIITAPILFAMEE 117
+LGK +D T P L ++
Sbjct: 232 ETLGKTQFSDAEANKATYPKLLGLDG 257
>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 = 70.3 bits (173), Expect = 6e-15
Identities = 40/152 (26%), Positives = 61/152 (40%), Gaps = 43/152 (28%)
Query: 6 AILAGDLLISRALVALASLKHTEVIMEC-------------------------------- 33
AILAGD L + A L+ EV
Sbjct: 110 AILAGDALQTLAFSILSDADMPEVSDRDRISMISELASASGIAGMCGGQALDLDAEGKHV 169
Query: 34 ------YMQKTYNKTAALVSNSCKAVAYLSGQ--REEVATLAFEYGKNLGLAYQLIDDIL 85
+ + +KT AL+ + + A +G R + L +Y +++GLA+Q+ DDIL
Sbjct: 170 PLDALERIHR--HKTGALIRAAVRLGALSAGDKGRRALPVLD-KYAESIGLAFQVQDDIL 226
Query: 86 DFTGTSASLGKASLTDLRNGIITAPILFAMEE 117
D G +A+LGK D + G T P L +E+
Sbjct: 227 DVVGDTATLGKRQGADQQLGKSTYPALLGLEQ 258
>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 = 71.0 bits (174), Expect = 6e-15
Identities = 33/234 (14%), Positives = 55/234 (23%), Gaps = 51/234 (21%)
Query: 2 GNKLAILAGDLLISRALVALASLKH----------------------------------- 26
G AI L +L + L
Sbjct: 135 GQSNAINDIFFLKMLSLSLIFELSSVFGNDIVMKIQKIYNESIFFTVLGQHLDLSYFDLS 194
Query: 27 -TEVIMECYMQKTYNKTAAL-VSNSCKAVAYLSGQR--EEVATLAFEYGKNLGLAYQLID 82
+ I E Y KT+ LS + L LG YQ+ +
Sbjct: 195 KADKISERYFSMVEMKTSRYTFYMPVFFGLTLSEIQVSSAQLNLIEAILYKLGEFYQVHN 254
Query: 83 DILDFTGTSASLGKASLTDLRNGIITAPILFAMEEFP--QLRAFINSSSDNPANVDVILE 140
D+ D+ ++ D+ +T P+ + E + N + V
Sbjct: 255 DVSDYLF-----NDSNADDICRFKLTWPLQKSFEIADEEMKLKISENYGKNSSLVKDCYN 309
Query: 141 YLGKSHGIQRTTELALKHASLAAAAIDSLPETHDVDATNARTALVHITQKIITR 194
L + AL + I D + I++ I
Sbjct: 310 LLKINEHYLEYQRNALDYLIKLVKDITD-----DSLQKVFIHLIHQISELITNS 358
>3lom_A Geranyltranstransferase; geranyltransferase, structural genomics,
PSI, protein structure initiative, nysgrc; 2.30A
{Legionella pneumophila subsp}
Length = 313
Score = 70.3 bits (173), Expect = 7e-15
Identities = 24/85 (28%), Positives = 36/85 (42%), Gaps = 3/85 (3%)
Query: 34 YMQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFE-YGKNLGLAYQLIDDILDFTGTSA 92
+ KT L+ + V + E A YGK++GL +Q+ DD LD +
Sbjct: 183 EIHL--LKTGKLILACFEMVLAAQHEVSEQIKSALRTYGKHIGLVFQMQDDYLDLYAPTQ 240
Query: 93 SLGKASLTDLRNGIITAPILFAMEE 117
LGK +D N T LF ++
Sbjct: 241 ILGKGRSSDQANQKTTFATLFNKQQ 265
>3ts7_A Geranyltranstransferase; isoprenoid synthesis, farnesyl diphosphate
synthase; 1.94A {Methylococcus capsulatus}
Length = 324
Score = 70.3 bits (173), Expect = 7e-15
Identities = 25/86 (29%), Positives = 35/86 (40%), Gaps = 5/86 (5%)
Query: 34 YMQKTYNKTAALVSNSCKAVAYLSGQ--REEVATLAFEYGKNLGLAYQLIDDILDFTGTS 91
M KT AL+ S + E+ L Y K +GLA+Q+ DDILD +
Sbjct: 182 NMHI--RKTGALIRASVRLACLARPGLPAEQFDRLD-HYAKCIGLAFQIQDDILDEESDT 238
Query: 92 ASLGKASLTDLRNGIITAPILFAMEE 117
+LGK D + P L +
Sbjct: 239 QTLGKTRGKDRDHNKPNYPALLGLSG 264
>3p8r_A Geranyltranstransferase; isoprenyl synthase, structural genomics,
PSI, protein struct initiative, nysgrc; 2.50A {Vibrio
cholerae}
Length = 302
Score = 69.9 bits (172), Expect = 9e-15
Identities = 25/85 (29%), Positives = 42/85 (49%), Gaps = 3/85 (3%)
Query: 34 YMQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFE-YGKNLGLAYQLIDDILDFTGTSA 92
+ + NKT AL+ + + A +G++ + Y + +GLA+Q+ DDILD +
Sbjct: 182 TIHR--NKTGALMRCAIRLGALAAGEKGRAMLPHLDRYAEAVGLAFQVQDDILDIISDTE 239
Query: 93 SLGKASLTDLRNGIITAPILFAMEE 117
+LGK +D T P L +E
Sbjct: 240 TLGKPQGSDQELNKSTYPALLGLEG 264
>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 = 69.5 bits (171), Expect = 1e-14
Identities = 28/84 (33%), Positives = 37/84 (44%), Gaps = 5/84 (5%)
Query: 34 YMQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSAS 93
+Q KT AL+S + +A A L+G T Y LGLA+Q+ DDILD G +
Sbjct: 173 RLQA--GKTGALISFAAQAGAILAGADRGPLT---AYATALGLAFQIADDILDVEGNEEA 227
Query: 94 LGKASLTDLRNGIITAPILFAMEE 117
GK D T L +
Sbjct: 228 AGKRLGKDAEAHKATFVSLLGLAG 251
>3npk_A Geranyltranstransferase; isoprene biosynthesis, SGX, structural
genomics protein structure initiative; 1.50A
{Campylobacter jejuni}
Length = 291
Score = 67.6 bits (166), Expect = 6e-14
Identities = 19/63 (30%), Positives = 33/63 (52%)
Query: 40 NKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASLGKASL 99
+KTA L++ + K + E + ++ G LGL +Q+ DDI+D T + GK +
Sbjct: 173 HKTARLIAAALKMGCEICELNNEESNQIYKLGLKLGLIFQINDDIIDVTTSQEQSGKPTN 232
Query: 100 TDL 102
D+
Sbjct: 233 NDI 235
>3llw_A Geranyltranstransferase (ISPA); structural genomics, PSI, protein
structure initiative, nysgrc; 2.30A {Helicobacter
pylori} PDB: 3q1o_A*
Length = 311
Score = 65.0 bits (159), Expect = 5e-13
Identities = 24/85 (28%), Positives = 41/85 (48%), Gaps = 5/85 (5%)
Query: 34 YMQKTYNKTAALVSNSCKAVAYLSGQR-EEVATLAFEYGKNLGLAYQLIDDILDFTGTSA 92
++ + +KTA L+S S SG + EE+ +G +GL +Q++DDI+D T
Sbjct: 183 FLHE--HKTAKLISASLIMGLVASGIKDEELFKWLQAFGLKMGLCFQVLDDIIDVTQDEE 240
Query: 93 SLGKASLTDLRNGIITAPILFAMEE 117
GK + D + + L +E
Sbjct: 241 ESGKTTHLD--SAKNSFVNLLGLER 263
>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 = 57.7 bits (140), Expect = 1e-10
Identities = 21/138 (15%), Positives = 36/138 (26%), Gaps = 41/138 (29%)
Query: 6 AILAGDLLISRALVALASLKHTEVI----------------------------MEC---- 33
+L GD +I L +A +
Sbjct: 108 ELLTGDGIIPFGLELMARSMDPTRNNPDRILRAIIELTRVMGSEGIVEGQYHELGLNQLN 167
Query: 34 ------YMQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILD- 86
Y+ K K L + A L G E+ +G +G L+
Sbjct: 168 DLELIEYVCK--KKEGTLHACGAACGAILGGCDEDKIEKLRRFGLYVGTVQGLLGKNRSG 225
Query: 87 FTGTSASLGKASLTDLRN 104
F G L + ++ +L +
Sbjct: 226 FEGRIKELKELAVKELES 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 = 57.6 bits (140), Expect = 2e-10
Identities = 18/58 (31%), Positives = 32/58 (55%), Gaps = 2/58 (3%)
Query: 34 YMQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTS 91
++ +KTAAL+ S + G +E ++ + +GL +Q++DDILD T +S
Sbjct: 187 FIHL--HKTAALLEASAVLGGIIGGGSDEEIERLRKFARCIGLLFQVVDDILDVTKSS 242
>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 = 46.7 bits (110), Expect = 1e-06
Identities = 24/98 (24%), Positives = 38/98 (38%), Gaps = 3/98 (3%)
Query: 4 KLAILAGDLLISRALVALASLKHTEVIMECYMQKTYNKTAALVSNSCKAVAYLSGQREEV 63
+ + A LL+ A+ + EV E + T AL + A L G
Sbjct: 138 EFSETAYXLLLGEAMDVEFERRXMEVSQEMVERMYAFXTGALFAFCFSAPFILXGXDHTX 197
Query: 64 ATLAFEYGKNLGLAYQLIDDILDFTGTSASLGKASLTD 101
G+ G+A+Q+ DD+ D G+ +GK D
Sbjct: 198 MX---LLGEXFGVAFQIYDDLXDILGSFEKVGKDLGKD 232
>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 = 46.5 bits (111), Expect = 1e-06
Identities = 20/98 (20%), Positives = 33/98 (33%), Gaps = 16/98 (16%)
Query: 34 YMQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGL---------AYQLIDDI 84
Y+ K K + + A L G EE +G G ++QLID+
Sbjct: 173 YVCK--KKYGEMHACGAACGAILGGAAEEEIQKLRNFGLYQGTLRGMMEMKNSHQLIDEN 230
Query: 85 LD---FTGTSASLGKA--SLTDLRNGIITAPILFAMEE 117
+ LG +L + ++ P L+A
Sbjct: 231 IIGKLKELALEELGGFHGKNAELMSSLVAEPSLYAAHH 268
>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 = 40.0 bits (93), Expect = 3e-04
Identities = 37/175 (21%), Positives = 58/175 (33%), Gaps = 53/175 (30%)
Query: 31 MECYMQKTYNKT-AALVSNSCKAVA-YLSGQ-----REEVATLAFEYGKNLGLAYQLIDD 83
+ + + TY + +V N+ + + G+ RE + + FE + L + I
Sbjct: 1649 ADNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIFK 1708
Query: 84 ILDFTGTSASL----GKASLTDLRNGIITAPILFAMEEFPQLRAFINSSSDNPANVDVIL 139
++ TS + G S T T P L ME +A
Sbjct: 1709 EINEHSTSYTFRSEKGLLSATQ-----FTQPALTLME-----KA--------------AF 1744
Query: 140 EYLGKSHG-IQRTTELALKH-----ASLAAAAIDSLP-ETHDVDATNARTALVHI 187
E L KS G I A H A+LA+ A D + E +V
Sbjct: 1745 EDL-KSKGLIPADATFA-GHSLGEYAALASLA-DVMSIE----SL--VE--VVFY 1788
>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 = 28.8 bits (63), Expect = 0.73
Identities = 12/28 (42%), Positives = 12/28 (42%), Gaps = 6/28 (21%)
Query: 155 ALK--HASLAAAAIDSLPETHDVDATNA 180
ALK ASL A DS P A A
Sbjct: 21 ALKKLQASLKLYADDSAPAL----AIKA 44
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 29.1 bits (64), Expect = 1.1
Identities = 22/205 (10%), Positives = 51/205 (24%), Gaps = 62/205 (30%)
Query: 4 KLAILAGDLLISRALVALASLKHTEVIMECYMQKTYNKTAALVSNSCKAVAYLSGQREEV 63
+L++ I L++L + + + K +
Sbjct: 377 RLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKY---------------------- 414
Query: 64 ATLAFEYGKNLGLAYQLIDDILDFTGTSASLGKASLTDLRNGIITAPILFAMEEFPQLRA 123
+L + K + L+ + L I+ + + +
Sbjct: 415 -SLVEKQPKE--STISIPSIYLELKVKL-----ENEYALHRSIV--------DHYNIPKT 458
Query: 124 FINSSSDNPANVDVILEYLGKSH--GIQRTTELA---------------LKHASLAAAAI 166
F + P ++G H I+ + ++H S A A
Sbjct: 459 FDSDDLIPPYLDQYFYSHIGH-HLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNAS 517
Query: 167 DSLPET-HDVDATNARTALVHITQK 190
S+ T + + +I
Sbjct: 518 GSILNTLQQL-----KFYKPYICDN 537
>3bl5_A Queuosine biosynthesis protein QUEC; PREQ1 biosynthesis, RNA
modification, tRNA, hydrolase; 2.95A {Bacillus subtilis}
Length = 219
Score = 26.1 bits (58), Expect = 7.8
Identities = 18/78 (23%), Positives = 25/78 (32%), Gaps = 32/78 (41%)
Query: 51 KAVAYLSG-------------QREEVATLAFEYG--------------KNLGLAYQLIDD 83
KA+ SG + EEV T+ F Y + LG+ L+D
Sbjct: 5 KAIVVFSGGQDSTTCLLWALKEFEEVETVTFHYNQRHSQEVEVAKSIAEKLGVKNHLLDM 64
Query: 84 ILDFTGTSASLGKASLTD 101
L L +LT
Sbjct: 65 SL-----LNQLAPNALTR 77
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.317 0.131 0.354
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: 2,856,314
Number of extensions: 173557
Number of successful extensions: 531
Number of sequences better than 10.0: 1
Number of HSP's gapped: 477
Number of HSP's successfully gapped: 66
Length of query: 196
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 107
Effective length of database: 4,216,824
Effective search space: 451200168
Effective search space used: 451200168
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.0 bits)