BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 020845
(320 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3QKC|B Chain B, Crystal Structure Of Geranyl Diphosphate Synthase Small
Subunit From Antirrhinum Majus
pdb|3QKC|A Chain A, Crystal Structure Of Geranyl Diphosphate Synthase Small
Subunit From Antirrhinum Majus
Length = 273
Score = 194 bits (493), Expect = 6e-50, Method: Compositional matrix adjust.
Identities = 110/265 (41%), Positives = 146/265 (55%), Gaps = 17/265 (6%)
Query: 40 NKNKSYWTSVHEDIGAHLRQAXXXXXXXXXXXXMRHFVFAAPVNMAPALCVAACELVGGH 99
+ ++Y ++ DI ++L++A M H FAAP A ALCVAACELVGG
Sbjct: 4 TRTQTYRATIESDIESYLKKAIPIRAPESVFEPMHHLTFAAPRTSASALCVAACELVGGD 63
Query: 100 REQXXXXXXXXXXXXXXSFIHENLPLSDRTSLIPKSKPTMYHAFKPNTELLVADAMLPFG 159
R ++ HENLPL+D P SK + H F PN ELL D ++PFG
Sbjct: 64 RSDAMAAAAAVHLMHVAAYTHENLPLTDG----PMSKSEIQHKFDPNIELLTGDGIIPFG 119
Query: 160 LELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQCDDDDRKLNGITDV 219
LEL+A S +P NN RILR ++E+TR MGS+G+VEGQY+EL LN + D+
Sbjct: 120 LELMARSMDPTRNNPDRILRAIIELTRVMGSEGIVEGQYHEL----------GLNQLNDL 169
Query: 220 EMTYETYKKKEGRLHXXXXXXXXXXXXXSEKEIELLRRYGFYVGMIQGIVSR-RLGPTEE 278
E+ KKKEG LH E +IE LRR+G YVG +QG++ + R G
Sbjct: 170 ELIEYVCKKKEGTLHACGAACGAILGGCDEDKIEKLRRFGLYVGTVQGLLGKNRSGFEGR 229
Query: 279 IEELKKLAFKLREVNSFNDENAEVI 303
I+ELK+LA K E+ SF E E+I
Sbjct: 230 IKELKELAVK--ELESFGGEKIELI 252
>pdb|3KRA|B Chain B, Mint Heterotetrameric Geranyl Pyrophosphate Synthase In
Complex With Magnesium
pdb|3KRA|C Chain C, Mint Heterotetrameric Geranyl Pyrophosphate Synthase In
Complex With Magnesium
pdb|3KRC|B Chain B, Mint Heterotetrameric Geranyl Pyrophosphate Synthase In
Complex With Ipp
pdb|3KRC|C Chain C, Mint Heterotetrameric Geranyl Pyrophosphate Synthase In
Complex With Ipp
pdb|3KRF|B Chain B, Mint Heterotetrameric Geranyl Pyrophosphate Synthase In
Complex With Magnesium, Ipp, And Dmaspp (I)
pdb|3KRF|C Chain C, Mint Heterotetrameric Geranyl Pyrophosphate Synthase In
Complex With Magnesium, Ipp, And Dmaspp (I)
pdb|3KRO|B Chain B, Mint Heterotetrameric Geranyl Pyrophosphate Synthase In
Complex With Magnesium, Ipp, And Dmaspp (Ii)
pdb|3KRO|C Chain C, Mint Heterotetrameric Geranyl Pyrophosphate Synthase In
Complex With Magnesium, Ipp, And Dmaspp (Ii)
pdb|3KRP|B Chain B, Mint Heterotetrameric Geranyl Pyrophosphate Synthase In
Complex With Magnesium And Gpp
pdb|3KRP|C Chain C, Mint Heterotetrameric Geranyl Pyrophosphate Synthase In
Complex With Magnesium And Gpp
Length = 274
Score = 162 bits (411), Expect = 2e-40, Method: Compositional matrix adjust.
Identities = 95/270 (35%), Positives = 146/270 (54%), Gaps = 18/270 (6%)
Query: 43 KSYWTSVHEDIGAHLRQAXXXXXXXXXXXXMRHFVFAAPVNMAPALCVAACELVGGHREQ 102
+ YW ++ DI +L+++ M H FAAP A LC+AACELVGG R Q
Sbjct: 2 QPYWAAIEADIERYLKKSITIRPPETVFGPMHHLTFAAPATAASTLCLAACELVGGDRSQ 61
Query: 103 XXXXXXXXXXXXXXSFIHENLPLSDRTSLIPKSKPTMYHAFKPNTELLVADAMLPFGLEL 162
+++HE+LPL+D + P SKP + H + PN ELL D ++PFG EL
Sbjct: 62 AMAAAAAIHLVHAAAYVHEHLPLTDGSR--PVSKPAIQHKYGPNVELLTGDGIVPFGFEL 119
Query: 163 LASSDNPA-GNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQCDDDDRKLNGITDVEM 221
LA S +PA ++ RILRV++E++RA G +G++ G + E + ++G T ++
Sbjct: 120 LAGSVDPARTDDPDRILRVIIEISRAGGPEGMISGLHRE---------EEIVDGNTSLDF 170
Query: 222 TYETYKKKEGRLHXXXXXXXXXXXXXSEKEIELLRRYGFYVGMIQGIV----SRRLGPTE 277
KKK G +H +E+EI+ LR +G Y G ++G++ S +L
Sbjct: 171 IEYVCKKKYGEMHACGAACGAILGGAAEEEIQKLRNFGLYQGTLRGMMEMKNSHQLIDEN 230
Query: 278 EIEELKKLAFKLREVNSFNDENAEVIFSLV 307
I +LK+LA L E+ F+ +NAE++ SLV
Sbjct: 231 IIGKLKELA--LEELGGFHGKNAELMSSLV 258
>pdb|3OAB|B Chain B, Mint Deletion Mutant Of Heterotetrameric Geranyl
Pyrophosphate Synthase In Complex With Ligands
pdb|3OAB|C Chain C, Mint Deletion Mutant Of Heterotetrameric Geranyl
Pyrophosphate Synthase In Complex With Ligands
pdb|3OAC|B Chain B, Mint Deletion Mutant Of Heterotetrameric Geranyl
Pyrophosphate Synthase In Complex With Ligands
pdb|3OAC|C Chain C, Mint Deletion Mutant Of Heterotetrameric Geranyl
Pyrophosphate Synthase In Complex With Ligands
Length = 264
Score = 149 bits (376), Expect = 2e-36, Method: Compositional matrix adjust.
Identities = 90/272 (33%), Positives = 140/272 (51%), Gaps = 28/272 (10%)
Query: 43 KSYWTSVHEDIGAHLRQAXXXXXXXXXXXXMRHFVFAAPVNMAPALCVAACELVGGHREQ 102
+ YW ++ DI +L+++ M H FAAP A LC+AACELVGG R Q
Sbjct: 2 QPYWAAIEADIERYLKKSITIRPPETVFGPMHHLTFAAPATAASTLCLAACELVGGDRSQ 61
Query: 103 XXXXXXXXXXXXXXSFIHENLPLSDRTSLIPKSKPTMYHAFKPNTELLVADAMLPFGLEL 162
+++HE+LP P + H + PN ELL D ++PFG EL
Sbjct: 62 AMAAAAAIHLVHAAAYVHEHLP------------PAIQHKYGPNVELLTGDGIVPFGFEL 109
Query: 163 LASSDNPA-GNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQCDDDDRKLNGITDVEM 221
LA S +PA ++ RILRV++E++RA G +G++ G + E + ++G T ++
Sbjct: 110 LAGSVDPARTDDPDRILRVIIEISRAGGPEGMISGLHRE---------EEIVDGNTSLDF 160
Query: 222 TYETYKKKEGRLHXXXXXXXXXXXXXSEKEIELLRRYGFYVGMIQGIV----SRRLGPTE 277
KKK G +H +E+EI+ LR +G Y G ++G++ S +L
Sbjct: 161 IEYVCKKKYGEMHACGAACGAILGGAAEEEIQKLRNFGLYQGTLRGMMEMKNSHQLIDEN 220
Query: 278 EIEELKKLAFKLREVNSFNDENAEVIFSLVDD 309
I +LK+LA L E+ F+ +NAE++ SLV +
Sbjct: 221 IIGKLKELA--LEELGGFHGKNAELMSSLVAE 250
>pdb|3KRA|A Chain A, Mint Heterotetrameric Geranyl Pyrophosphate Synthase In
Complex With Magnesium
pdb|3KRA|D Chain D, Mint Heterotetrameric Geranyl Pyrophosphate Synthase In
Complex With Magnesium
pdb|3KRC|A Chain A, Mint Heterotetrameric Geranyl Pyrophosphate Synthase In
Complex With Ipp
pdb|3KRC|D Chain D, Mint Heterotetrameric Geranyl Pyrophosphate Synthase In
Complex With Ipp
pdb|3KRF|A Chain A, Mint Heterotetrameric Geranyl Pyrophosphate Synthase In
Complex With Magnesium, Ipp, And Dmaspp (I)
pdb|3KRF|D Chain D, Mint Heterotetrameric Geranyl Pyrophosphate Synthase In
Complex With Magnesium, Ipp, And Dmaspp (I)
pdb|3KRO|A Chain A, Mint Heterotetrameric Geranyl Pyrophosphate Synthase In
Complex With Magnesium, Ipp, And Dmaspp (Ii)
pdb|3KRO|D Chain D, Mint Heterotetrameric Geranyl Pyrophosphate Synthase In
Complex With Magnesium, Ipp, And Dmaspp (Ii)
pdb|3KRP|A Chain A, Mint Heterotetrameric Geranyl Pyrophosphate Synthase In
Complex With Magnesium And Gpp
pdb|3KRP|D Chain D, Mint Heterotetrameric Geranyl Pyrophosphate Synthase In
Complex With Magnesium And Gpp
pdb|3OAB|A Chain A, Mint Deletion Mutant Of Heterotetrameric Geranyl
Pyrophosphate Synthase In Complex With Ligands
pdb|3OAB|D Chain D, Mint Deletion Mutant Of Heterotetrameric Geranyl
Pyrophosphate Synthase In Complex With Ligands
pdb|3OAC|A Chain A, Mint Deletion Mutant Of Heterotetrameric Geranyl
Pyrophosphate Synthase In Complex With Ligands
pdb|3OAC|D Chain D, Mint Deletion Mutant Of Heterotetrameric Geranyl
Pyrophosphate Synthase In Complex With Ligands
Length = 295
Score = 85.9 bits (211), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 63/218 (28%), Positives = 103/218 (47%), Gaps = 15/218 (6%)
Query: 73 MRHFVFAAPVNMAPALCVAACELVGGHREQXXXXXXXXXXXXXXSFIHENLPLSDRTSLI 132
MR+ + A + P LC+AACELVGG S +H++LP D L
Sbjct: 35 MRYSLLAGGKRVRPMLCIAACELVGGDESTAMPAACAVEMIHTMSLMHDDLPCMDNDDL- 93
Query: 133 PKSKPTMYHAFKPNTELLVADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQG 192
+ KPT + AF + +L DA+L F E +A++ G RI+RV+ E+ ++GS+G
Sbjct: 94 RRGKPTNHMAFGESVAVLAGDALLSFAFEHVAAATK--GAPPERIVRVLGELAVSIGSEG 151
Query: 193 VVEGQYNELQCSQCDDDDRKLNGITDVEMTYETY--KKKEGRLHXXXXXXXXXXXXXSEK 250
+V GQ ++ CS+ G+ +V + + + K L E+
Sbjct: 152 LVAGQVVDV-CSE---------GMAEVGLDHLEFIHHHKTAALLQGSVVLGAILGGGKEE 201
Query: 251 EIELLRRYGFYVGMIQGIVSRRLGPTEEIEELKKLAFK 288
E+ LR++ +G++ +V L T+ +EL K A K
Sbjct: 202 EVAKLRKFANCIGLLFQVVDDILDVTKSSKELGKTAGK 239
>pdb|2J1P|A Chain A, Geranylgeranyl Diphosphate Synthase From Sinapis Alba In
Complex With Ggpp
pdb|2J1P|B Chain B, Geranylgeranyl Diphosphate Synthase From Sinapis Alba In
Complex With Ggpp
Length = 293
Score = 82.8 bits (203), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 59/204 (28%), Positives = 98/204 (48%), Gaps = 8/204 (3%)
Query: 74 RHFVFAAPVNMAPALCVAACELVGGHREQXXXXXXXXXXXXXXSFIHENLPLSDRTSLIP 133
R+ + A + P LC+AACELVGG S IH++LP D L
Sbjct: 45 RYSLLAGGKRVRPVLCIAACELVGGEESLAXPAACAVEXIHTXSLIHDDLPCXDNDDL-R 103
Query: 134 KSKPTMYHAFKPNTELLVADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGV 193
+ KPT + + + +L DA+L F E LAS+ + + R++R + E+ +A+G++G+
Sbjct: 104 RGKPTNHKVYGEDVAVLAGDALLSFAFEHLASA-TSSEVSPARVVRAVGELAKAIGTEGL 162
Query: 194 VEGQYNELQCSQCDDDDRKLNGITDVEMTYETYKKKEGRLHXXXXXXXXXXXXXSEKEIE 253
V GQ ++ D LN + + + + K L S++EIE
Sbjct: 163 VAGQVVDISSEGLD-----LNNVGLEHLKF-IHLHKTAALLEASAVLGGIIGGGSDEEIE 216
Query: 254 LLRRYGFYVGMIQGIVSRRLGPTE 277
LR++ +G++ +V L T+
Sbjct: 217 RLRKFARCIGLLFQVVDDILDVTK 240
>pdb|2J1O|A Chain A, Geranylgeranyl Diphosphate Synthase From Sinapis Alba
Length = 268
Score = 59.7 bits (143), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 49/206 (23%), Positives = 86/206 (41%), Gaps = 37/206 (17%)
Query: 73 MRHFVFAAPVNMAPALCVAACELVGGHREQXXXXXXXXXXXXXXSFIHENLPLSDRTSLI 132
MR+ + A + P LC+AACELVGG S IH+++
Sbjct: 44 MRYSLLAGGKRVRPVLCIAACELVGGEESLAMPAACAVEMIHTMSLIHDDV--------- 94
Query: 133 PKSKPTMYHAFKPNTELLVADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQG 192
+ + +L DA+L F E LAS+ + + R++R + E+ +A+G++G
Sbjct: 95 ----------YGEDVAVLAGDALLSFAFEHLASA-TSSEVSPARVVRAVGELAKAIGTEG 143
Query: 193 VVEGQYNELQCSQCDDDDRKLNGITDVEMTYETYK--KKEGRLHXXXXXXXXXXXXXSEK 250
+V GQ + I++V + + + K L S++
Sbjct: 144 LVAGQVVD---------------ISNVGLEHLKFIHLHKTAALLEASAVLGGIIGGGSDE 188
Query: 251 EIELLRRYGFYVGMIQGIVSRRLGPT 276
EIE LR++ +G++ +V L T
Sbjct: 189 EIERLRKFARCIGLLFQVVDDILDVT 214
>pdb|4F62|A Chain A, Crystal Structure Of A Putative Farnesyl-Diphosphate
Synthase From Marinomonas Sp. Med121 (Target Efi-501980)
pdb|4F62|B Chain B, Crystal Structure Of A Putative Farnesyl-Diphosphate
Synthase From Marinomonas Sp. Med121 (Target Efi-501980)
Length = 317
Score = 55.8 bits (133), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 37/129 (28%), Positives = 57/129 (44%), Gaps = 4/129 (3%)
Query: 73 MRHFVFAAPVNMAPALCVAACELVGGHREQXXXXXXXXXXXXXXSFIHENLPLSDRTSLI 132
MR+ +F + P L A+ +LVG S IH++LP D L
Sbjct: 37 MRYSLFNGGKRIRPMLTYASAQLVGDISSLTDASAAALESIHAYSLIHDDLPAMDNDEL- 95
Query: 133 PKSKPTMYHAFKPNTELLVADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQG 192
+ KPT + F T +L DA+ F ELL+ NP ++++ E+ A G G
Sbjct: 96 RRGKPTCHIQFDEATAILAGDALQTFAFELLS---NPTSAQPELAIKLIQELVVASGRNG 152
Query: 193 VVEGQYNEL 201
++ GQ +L
Sbjct: 153 MITGQMIDL 161
>pdb|3P8R|A Chain A, Crystal Structure Of Polyprenyl Synthase From Vibrio
Cholerae
Length = 302
Score = 44.7 bits (104), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 42/85 (49%), Gaps = 2/85 (2%)
Query: 117 SFIHENLPLSDRTSLIPKSKPTMYHAFKPNTELLVADAMLPFGLELLASSDNPAGNNSGR 176
S IH++LP D L + KPT + F T +L DA+ +LA D A + R
Sbjct: 86 SLIHDDLPAMDDDEL-RRGKPTCHIQFDEATAILTGDALQTLAFTILAEGDLSAAGETQR 144
Query: 177 ILRVMVEMTRAMGSQGVVEGQYNEL 201
+ ++ + A G+QG+ GQ +L
Sbjct: 145 V-AMLQALAEASGAQGMCLGQALDL 168
>pdb|3UCA|A Chain A, Crystal Structure Of Isoprenoid Synthase (Target
Efi-501974) From Clostridium Perfringens
pdb|3UCA|B Chain B, Crystal Structure Of Isoprenoid Synthase (Target
Efi-501974) From Clostridium Perfringens
Length = 324
Score = 44.3 bits (103), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 45/180 (25%), Positives = 80/180 (44%), Gaps = 12/180 (6%)
Query: 117 SFIHENLPLSDRTSLIPKSKPTMYHAFKPNTELLVADAMLPFGLELLASSDNPAGNNSGR 176
S IH++LP D L + KPT + F +L DA+L +++L G ++ +
Sbjct: 110 SLIHDDLPCMDNDDL-RRGKPTNHKVFGEAIAVLAGDALLNEAMKILVDYSLEEGKSALK 168
Query: 177 ILRVMVEMTRAMGSQGVVEGQYNELQCSQCDDDDRKLNGITDVEMTYETYKKKEGRLHXX 236
+++ + A GS G++ GQ ++ ++D + I+ E+ Y + KK G L
Sbjct: 169 ATKIIAD---AAGSDGMIGGQIVDI----INEDKEE---ISLKELDY-MHLKKTGELIKA 217
Query: 237 XXXXXXXXXXXSEKEIELLRRYGFYVGMIQGIVSRRLGPTEEIEELKKLAFKLREVNSFN 296
SE +I+ L +G+ +G+ I L ++L K K +E N N
Sbjct: 218 SIMSGAVLAEASEGDIKKLEGFGYKLGLAFQIKDDILDVVGNAKDLGKNVHKDQESNKNN 277
>pdb|3LOM|A Chain A, Crystal Structure Of Geranyltransferase From Legionella
Pneumophila
pdb|3LOM|B Chain B, Crystal Structure Of Geranyltransferase From Legionella
Pneumophila
Length = 313
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 38/150 (25%), Positives = 67/150 (44%), Gaps = 11/150 (7%)
Query: 117 SFIHENLPLSDRTSLIPKSKPTMYHAFKPNTELLVADAMLPFGLELLASSDNPAGNNSGR 176
S IH++LP D L + KP+ + AF T +LV D M +E+L +P + +
Sbjct: 86 SLIHDDLPAMDNDDL-RRGKPSCHKAFDEATAILVGDGMQALAIEVLLMRLSPL-LPAAQ 143
Query: 177 ILRVMVEMTRAMGSQGVVEGQYNELQCSQCDDDDRKLNGITDVEMTYETYKKKEGRLHXX 236
++ + + A G G+V GQ D + + +T+ E E + K G+L
Sbjct: 144 VVAITQVLVNASGISGMVSGQ-------SLDLSELAKSSVTE-EQLREIHLLKTGKLILA 195
Query: 237 XXXXXXXXXXXSEKEIE-LLRRYGFYVGMI 265
++I+ LR YG ++G++
Sbjct: 196 CFEMVLAAQHEVSEQIKSALRTYGKHIGLV 225
>pdb|2H8O|A Chain A, The 1.6a Crystal Structure Of The Geranyltransferase From
Agrobacterium Tumefaciens
Length = 335
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 28/97 (28%), Positives = 45/97 (46%), Gaps = 1/97 (1%)
Query: 73 MRHFVFAAPVNMAPALCVAACELVGGHREQXXXXXXXXXXXXXXSFIHENLPLSDRTSLI 132
MRH V + P L + + L+GG E S +H++LP D L
Sbjct: 77 MRHGVLNGGKRLRPFLVIESVALLGGDAEAGLHVGAALECLHCYSLVHDDLPAMDDDDL- 135
Query: 133 PKSKPTMYHAFKPNTELLVADAMLPFGLELLASSDNP 169
+ +PT++ F T +L D++L +++AS DNP
Sbjct: 136 RRGQPTVHRKFDEATAILAGDSLLTLAFDIIASDDNP 172
>pdb|1RTR|A Chain A, Crystal Structure Of S. Aureus Farnesyl Pyrophosphate
Synthase
pdb|1RTR|B Chain B, Crystal Structure Of S. Aureus Farnesyl Pyrophosphate
Synthase
Length = 301
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 36/149 (24%), Positives = 60/149 (40%), Gaps = 13/149 (8%)
Query: 117 SFIHENLPLSDRTSLIPKSKPTMYHAFKPNTELLVADAMLPFGLELLASSDNPAGNNSGR 176
S IH++LP D + K T + + T +L DA+L EL++S D
Sbjct: 78 SLIHDDLPAMDNDDY-RRGKLTNHKVYGEWTAILAGDALLTKAFELISSDDRLTDEVK-- 134
Query: 177 ILRVMVEMTRAMGSQGVVEGQYNELQCSQCDDDDRKLNGITDVEMTYETYKKKEGRLHXX 236
++V+ ++ A G G+V GQ ++Q D+E +K K G L
Sbjct: 135 -IKVLQRLSIASGHVGMVGGQMLDMQSE---------GQPIDLETLEMIHKTKTGALLTF 184
Query: 237 XXXXXXXXXXXSEKEIELLRRYGFYVGMI 265
+ E L Y +++GM+
Sbjct: 185 AVMSAADIANVDDTTKEHLESYSYHLGMM 213
>pdb|3Q1O|A Chain A, Crystal Structure Of Geranyltransferase From Helicobacter
Pylori Complexed With Magnesium And Isoprenyl
Diphosphate
pdb|3Q1O|B Chain B, Crystal Structure Of Geranyltransferase From Helicobacter
Pylori Complexed With Magnesium And Isoprenyl
Diphosphate
pdb|3Q1O|C Chain C, Crystal Structure Of Geranyltransferase From Helicobacter
Pylori Complexed With Magnesium And Isoprenyl
Diphosphate
pdb|3Q1O|D Chain D, Crystal Structure Of Geranyltransferase From Helicobacter
Pylori Complexed With Magnesium And Isoprenyl
Diphosphate
Length = 310
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 39/180 (21%), Positives = 80/180 (44%), Gaps = 15/180 (8%)
Query: 117 SFIHENLPLSDRTSLIPKSKPTMYHAFKPNTELLVADAMLPFGLELLASSDNPAGNNSGR 176
S IH++LP D +L ++ PT++ + T +L+ DA+ + ELL+ N+
Sbjct: 97 SLIHDDLPCMDNAAL-RRNHPTLHAKYDETTAVLIGDALNTYSFELLS--------NALL 147
Query: 177 ILRVMVEMTRAMGSQGVVEGQYNELQCSQCDDDDRKLNGITDVEMTYETYKKKEGRLHXX 236
++VE+ + + + G ++G Q C ++ LN +E ++ K +L
Sbjct: 148 ESHIIVELIKILSANGGIKGMILG-QALDCYFENTPLN----LEQLTFLHEHKTAKLISA 202
Query: 237 XXXXXXXXXXXSEKEI-ELLRRYGFYVGMIQGIVSRRLGPTEEIEELKKLAFKLREVNSF 295
++E+ + L+ +G +G+ ++ + T++ EE K NSF
Sbjct: 203 SLIMGLVASGIKDEELFKWLQAFGLKMGLCFQVLDDIIDVTQDEEESGKTTHLDSAKNSF 262
>pdb|3LLW|A Chain A, Crystal Structure Of Geranyltransferase From Helicobacter
Pylori 26695
pdb|3LLW|B Chain B, Crystal Structure Of Geranyltransferase From Helicobacter
Pylori 26695
pdb|3LLW|C Chain C, Crystal Structure Of Geranyltransferase From Helicobacter
Pylori 26695
pdb|3LLW|D Chain D, Crystal Structure Of Geranyltransferase From Helicobacter
Pylori 26695
Length = 311
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 39/180 (21%), Positives = 80/180 (44%), Gaps = 15/180 (8%)
Query: 117 SFIHENLPLSDRTSLIPKSKPTMYHAFKPNTELLVADAMLPFGLELLASSDNPAGNNSGR 176
S IH++LP D +L ++ PT++ + T +L+ DA+ + ELL+ N+
Sbjct: 90 SLIHDDLPCMDNAAL-RRNHPTLHAKYDETTAVLIGDALNTYSFELLS--------NALL 140
Query: 177 ILRVMVEMTRAMGSQGVVEGQYNELQCSQCDDDDRKLNGITDVEMTYETYKKKEGRLHXX 236
++VE+ + + + G ++G Q C ++ LN +E ++ K +L
Sbjct: 141 ESHIIVELIKILSANGGIKGMILG-QALDCYFENTPLN----LEQLTFLHEHKTAKLISA 195
Query: 237 XXXXXXXXXXXSEKEI-ELLRRYGFYVGMIQGIVSRRLGPTEEIEELKKLAFKLREVNSF 295
++E+ + L+ +G +G+ ++ + T++ EE K NSF
Sbjct: 196 SLIMGLVASGIKDEELFKWLQAFGLKMGLCFQVLDDIIDVTQDEEESGKTTHLDSAKNSF 255
>pdb|3P8L|A Chain A, Crystal Structure Of Polyprenyl Synthase From Enterococcus
Faecalis V583
pdb|3P8L|B Chain B, Crystal Structure Of Polyprenyl Synthase From Enterococcus
Faecalis V583
Length = 302
Score = 31.2 bits (69), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 30/133 (22%), Positives = 59/133 (44%), Gaps = 13/133 (9%)
Query: 132 IPKSKPTMYHAFKPNTELLVADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQ 191
+ + KPT + F T +L D +L +LL+ S ++L +M ++ +A G+Q
Sbjct: 101 LRRGKPTNHKVFGEATAILAGDGLLTGAFQLLSLSQLGLSE---KVL-LMQQLAKAAGNQ 156
Query: 192 GVVEGQYNELQCSQCDDDDRKLNGITDVEMTYETYKKKEGRLHXXXXXXXXXXXXXSEKE 251
G+V GQ +++ + +L + ++KK G L +E+
Sbjct: 157 GMVSGQMGDIEGEKVSLTLEELAAV---------HEKKTGALIEFALIAGGVLANQTEEV 207
Query: 252 IELLRRYGFYVGM 264
I LL ++ + G+
Sbjct: 208 IGLLTQFAHHYGL 220
>pdb|1RQJ|A Chain A, Active Conformation Of Farnesyl Pyrophosphate Synthase
Bound To Isopentyl Pyrophosphate And Risedronate
pdb|1RQJ|B Chain B, Active Conformation Of Farnesyl Pyrophosphate Synthase
Bound To Isopentyl Pyrophosphate And Risedronate
Length = 299
Score = 30.4 bits (67), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 1/65 (1%)
Query: 137 PTMYHAFKPNTELLVADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEG 196
PT + F +L DA+ +L+ +D P ++ RI ++ E+ A G G+ G
Sbjct: 99 PTCHVKFGEANAILAGDALQTLAFSILSDADMPEVSDRDRI-SMISELASASGIAGMCGG 157
Query: 197 QYNEL 201
Q +L
Sbjct: 158 QALDL 162
>pdb|1RQI|A Chain A, Active Conformation Of Farnesyl Pyrophosphate Synthase
Bound To Isopentyl Pyrophosphate And Dimethylallyl S-
Thiolodiphosphate
pdb|1RQI|B Chain B, Active Conformation Of Farnesyl Pyrophosphate Synthase
Bound To Isopentyl Pyrophosphate And Dimethylallyl S-
Thiolodiphosphate
Length = 300
Score = 30.0 bits (66), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 1/65 (1%)
Query: 137 PTMYHAFKPNTELLVADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEG 196
PT + F +L DA+ +L+ +D P ++ RI ++ E+ A G G+ G
Sbjct: 100 PTCHVKFGEANAILAGDALQTLAFSILSDADMPEVSDRDRI-SMISELASASGIAGMCGG 158
Query: 197 QYNEL 201
Q +L
Sbjct: 159 QALDL 163
>pdb|3LJI|A Chain A, Crystal Structure Of Putative Geranyltranstransferase From
Pseudomonas Fluorescens Pf-5
pdb|3LSN|A Chain A, Crystal Structure Of Putative Geranyltranstransferase From
Pseudomonas Fluorescens Pf-5 Complexed With Magnesium
Length = 304
Score = 29.6 bits (65), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 29/104 (27%), Positives = 46/104 (44%), Gaps = 8/104 (7%)
Query: 86 PALCVAACELVGGHREQXXXXXXXXXXXXXXSFIHENLPLSDRTSLIPKSKPTMYHAFKP 145
P L AACE +GG EQ S +H++L + + + +PT + AF
Sbjct: 49 PLLAYAACEALGGKPEQANGAACAVELIHAYSLVHDDL-PAXDDDDLRRGQPTTHKAFDE 107
Query: 146 NTELLVADAMLPFGLELLASSD--NPAGNNSGRILRVMVEMTRA 187
+L D GL+ LA S +PA +++ +R+ T A
Sbjct: 108 ACAILAGD-----GLQSLAFSALLDPALSDASAEIRLRXVTTLA 146
>pdb|3P41|A Chain A, Crystal Structure Of Polyprenyl Synthetase From
Pseudomonas Fluorescens Pf-5 Complexed With Magnesium
And Isoprenyl Pyrophosphate
Length = 303
Score = 29.6 bits (65), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 29/104 (27%), Positives = 46/104 (44%), Gaps = 8/104 (7%)
Query: 86 PALCVAACELVGGHREQXXXXXXXXXXXXXXSFIHENLPLSDRTSLIPKSKPTMYHAFKP 145
P L AACE +GG EQ S +H++L + + + +PT + AF
Sbjct: 56 PLLAYAACEALGGKPEQANGAACAVELIHAYSLVHDDL-PAXDDDDLRRGQPTTHKAFDE 114
Query: 146 NTELLVADAMLPFGLELLASSD--NPAGNNSGRILRVMVEMTRA 187
+L D GL+ LA S +PA +++ +R+ T A
Sbjct: 115 AXAILAGD-----GLQSLAFSALLDPALSDASAEIRLRXVTTLA 153
>pdb|3LVS|A Chain A, Crystal Structure Of Farnesyl Diphosphate Synthase From
Rhodobacter Capsulatus Sb1003
pdb|3LVS|B Chain B, Crystal Structure Of Farnesyl Diphosphate Synthase From
Rhodobacter Capsulatus Sb1003
Length = 298
Score = 29.6 bits (65), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 39/81 (48%), Gaps = 4/81 (4%)
Query: 117 SFIHENLPLSDRTSLIPKSKPTMYHAFKPNTELLVADAMLPFGLELLASSDNPAGNNSGR 176
S +H+++P D L + PT++ + T +L DA+ EL +D G+ R
Sbjct: 78 SLVHDDMPCMDNDDL-RRGLPTVHKKWDDATAVLAGDALQTLAFEL--CTDPVLGSAENR 134
Query: 177 ILRVMVEMTRAMGSQGVVEGQ 197
+ V + G++G+V GQ
Sbjct: 135 VALVAALAQAS-GAEGMVYGQ 154
>pdb|3NPK|A Chain A, The Crystal Structure Of Geranyltranstransferase From
Campylobacter Jejuni
pdb|3NPK|B Chain B, The Crystal Structure Of Geranyltranstransferase From
Campylobacter Jejuni
Length = 291
Score = 29.6 bits (65), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 117 SFIHENLPLSDRTSLIPKSKPTMYHAFKPNTELLVADAM 155
S IH++LP D + PT++ ++ T +LV DA+
Sbjct: 76 SLIHDDLPAXDNADF-RRGIPTLHKSYDETTAILVGDAL 113
>pdb|2FOR|A Chain A, Crystal Structure Of The Shigella Flexneri Farnesyl
Pyrophosphate Synthase Complex With An Isopentenyl
Pyrophosphate
pdb|2FOR|B Chain B, Crystal Structure Of The Shigella Flexneri Farnesyl
Pyrophosphate Synthase Complex With An Isopentenyl
Pyrophosphate
Length = 323
Score = 27.7 bits (60), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 31/65 (47%), Gaps = 1/65 (1%)
Query: 137 PTMYHAFKPNTELLVADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEG 196
PT + F +L DA+ +L+ ++ P ++ RI ++ E+ A G G+ G
Sbjct: 123 PTCHVKFGEANAILAGDALQTLAFSILSDANMPEVSDRDRI-SMISELASASGIAGMCGG 181
Query: 197 QYNEL 201
Q +L
Sbjct: 182 QALDL 186
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.318 0.133 0.387
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,071,016
Number of Sequences: 62578
Number of extensions: 280687
Number of successful extensions: 522
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 495
Number of HSP's gapped (non-prelim): 25
length of query: 320
length of database: 14,973,337
effective HSP length: 99
effective length of query: 221
effective length of database: 8,778,115
effective search space: 1939963415
effective search space used: 1939963415
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)