RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 020845
(320 letters)
>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 = 232 bits (593), Expect = 2e-75
Identities = 134/276 (48%), Positives = 181/276 (65%), Gaps = 20/276 (7%)
Query: 34 MAMSTPNKNKSYWTSVHEDIGAHLRQAVVVKEPVEVYEPMRHFVFAAPVNMAPALCVAAC 93
M+++ ++Y ++ DI ++L++A+ ++ P V+EPM H FAAP A ALCVAAC
Sbjct: 1 MSLTRT---QTYRATIESDIESYLKKAIPIRAPESVFEPMHHLTFAAPRTSASALCVAAC 57
Query: 94 ELVGGHREQAIVAAAALHVMHAASFIHENLPLSDRTSLIPKSKPTMYHAFKPNTELLVAD 153
ELVGG R A+ AAAA+H+MH A++ HENLPL+D P SK + H F PN ELL D
Sbjct: 58 ELVGGDRSDAMAAAAAVHLMHVAAYTHENLPLTDG----PMSKSEIQHKFDPNIELLTGD 113
Query: 154 AMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQCDDDDRKL 213
++PFGLEL+A S +P NN RILR ++E+TR MGS+G+VEGQY+EL
Sbjct: 114 GIIPFGLELMARSMDPTRNNPDRILRAIIELTRVMGSEGIVEGQYHELGL---------- 163
Query: 214 NGITDVEMTYETYKKKEGRLHACGAACGAILGGGSEKEIELLRRYGFYVGMIQGIVSRRL 273
N + D+E+ KKKEG LHACGAACGAILGG E +IE LRR+G YVG +QG++ +
Sbjct: 164 NQLNDLELIEYVCKKKEGTLHACGAACGAILGGCDEDKIEKLRRFGLYVGTVQGLLGKNR 223
Query: 274 GPTE-EIEELKKLAFKLREVNSFNDENAEVIFSLVD 308
E I+ELK+LA K E+ SF E E+I + +
Sbjct: 224 SGFEGRIKELKELAVK--ELESFGGEKIELIRGVFE 257
>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 = 207 bits (528), Expect = 1e-65
Identities = 101/232 (43%), Positives = 152/232 (65%), Gaps = 12/232 (5%)
Query: 43 KSYWTSVHEDIGAHLRQAVVVKEPVEVYEPMRHFVFAAPVNMAPALCVAACELVGGHREQ 102
+ YW ++ DI +L++++ ++ P V+ PM H FAAP A LC+AACELVGG R Q
Sbjct: 2 QPYWAAIEADIERYLKKSITIRPPETVFGPMHHLTFAAPATAASTLCLAACELVGGDRSQ 61
Query: 103 AIVAAAALHVMHAASFIHENLPLSDRTSLIPKSKPTMYHAFKPNTELLVADAMLPFGLEL 162
A+ AAAA+H++HAA+++HE+LPL+D + P SKP + H + PN ELL D ++PFG EL
Sbjct: 62 AMAAAAAIHLVHAAAYVHEHLPLTDGS--RPVSKPAIQHKYGPNVELLTGDGIVPFGFEL 119
Query: 163 LASSDNPA-GNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQCDDDDRKLNGITDVEM 221
LA S +PA ++ RILRV++E++RA G +G++ G + E + + + +
Sbjct: 120 LAGSVDPARTDDPDRILRVIIEISRAGGPEGMISGLHREEEIVDGNTSLDFIEYV----- 174
Query: 222 TYETYKKKEGRLHACGAACGAILGGGSEKEIELLRRYGFYVGMIQGIVSRRL 273
KKK G +HACGAACGAILGG +E+EI+ LR +G Y G ++G++ +
Sbjct: 175 ----CKKKYGEMHACGAACGAILGGAAEEEIQKLRNFGLYQGTLRGMMEMKN 222
>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 = 129 bits (327), Expect = 1e-35
Identities = 74/240 (30%), Positives = 123/240 (51%), Gaps = 18/240 (7%)
Query: 30 MMVTMAMSTPNKNKSYWTSVHEDIGAHLRQAVVVKEPVEVYEPMRHFVFAAPVNMAPALC 89
MM SY + + L AV ++EP++++E MR+ + A + P LC
Sbjct: 1 MMRGSHHHHHTDPISYIIRKADSVNKALDSAVPLREPLKIHEAMRYSLLAGGKRVRPVLC 60
Query: 90 VAACELVGGHREQAIVAAAALHVMHAASFIHENLPLSD-----RTSLIPKSKPTMYHAFK 144
+AACELVGG A+ AA A+ ++H S IH++LP D R KPT + +
Sbjct: 61 IAACELVGGEESLAMPAACAVEMIHTMSLIHDDLPCMDNDDLRR------GKPTNHKVYG 114
Query: 145 PNTELLVADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCS 204
+ +L DA+L F E LAS+ + + R++R + E+ +A+G++G+V GQ ++
Sbjct: 115 EDVAVLAGDALLSFAFEHLASATSS-EVSPARVVRAVGELAKAIGTEGLVAGQVVDISSE 173
Query: 205 QCDDDDRKLNGITDVEMTYETYKKKEGRLHACGAACGAILGGGSEKEIELLRRYGFYVGM 264
D ++ L + + + K L A G I+GGGS++EIE LR++ +G+
Sbjct: 174 GLDLNNVGLEHLKFI------HLHKTAALLEASAVLGGIIGGGSDEEIERLRKFARCIGL 227
>3ts7_A Geranyltranstransferase; isoprenoid synthesis, farnesyl diphosphate
synthase; 1.94A {Methylococcus capsulatus}
Length = 324
Score = 120 bits (304), Expect = 4e-32
Identities = 49/234 (20%), Positives = 89/234 (38%), Gaps = 14/234 (5%)
Query: 34 MAMSTPNKNKSYWTSVHEDIGAHLRQAVVVKE--PVEVYEPMRHFVFAAPVNMAPALCVA 91
M M+ + S E + L + + P +++ MR+ V M P L A
Sbjct: 1 MVMNPERSLSDFMRSSQERVERALDARLPAADRMPERLHQAMRYSVLGGGKRMRPLLTYA 60
Query: 92 ACELVGGHREQAIVAAAALHVMHAASFIHENLPLSDRTSLIPKSKPTMYHAFKPNTELLV 151
+ +G + A A+ +H S IH++LP D L + KPT + A+ T +L
Sbjct: 61 TGQTIGVAADLLDGPACAVEFIHVYSLIHDDLPAMDDDDL-RRGKPTCHKAYDEATAILA 119
Query: 152 ADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQCDDDDR 211
D + +LA + + + ++ + +A G G+V GQ +L D
Sbjct: 120 GDGLQALAFHVLAQDPSI-AVPAENRIAMIETLAKASGPAGMVGGQAIDLASVGKKLDLP 178
Query: 212 KLNGITDVEMTYETYKKKEGRLHACGAACGAILGGG-SEKEIELLRRYGFYVGM 264
L + + +K G L + G ++ + L Y +G+
Sbjct: 179 GLENM---------HIRKTGALIRASVRLACLARPGLPAEQFDRLDHYAKCIGL 223
>2h8o_A Geranyltranstransferase; geranyltransferase,agrobacterium
tumefaciens, structural GEN PSI-2, protein structure
initiative; 1.60A {Agrobacterium tumefaciens}
Length = 335
Score = 120 bits (304), Expect = 4e-32
Identities = 63/268 (23%), Positives = 109/268 (40%), Gaps = 25/268 (9%)
Query: 10 LPAHVAPRRNHSRPSLSY-----RPMMVTMAMSTPNKN-KSYWTSVHEDIGAHLRQAV-- 61
+P+ R ++ RP M N ++ A L +
Sbjct: 1 MPSSRRVRSRCCAFGITKRFACIRPACQRARMDAQMTNFETRLRENAAKTEALLGHLLSG 60
Query: 62 -----VVKEPVEVYEPMRHFVFAAPVNMAPALCVAACELVGGHREQAIVAAAALHVMHAA 116
+ P + E MRH V + P L + + L+GG E + AAL +H
Sbjct: 61 EARADEITRPQNLLEAMRHGVLNGGKRLRPFLVIESVALLGGDAEAGLHVGAALECLHCY 120
Query: 117 SFIHENLPLSDRTSLIPKSKPTMYHAFKPNTELLVADAMLPFGLELLASSDNPAGNNSGR 176
S +H++LP D L + +PT++ F T +L D++L +++AS DNP + R
Sbjct: 121 SLVHDDLPAMDDDDL-RRGQPTVHRKFDEATAILAGDSLLTLAFDIIASDDNPL--AAER 177
Query: 177 ILRVMVEMTRAMGSQGVVEGQYNELQCSQCDDDDRKLNGITDVEMTYETYKKKEGRLHAC 236
+++ + RA G G+ GQ +L + D+ + + K G L
Sbjct: 178 KAALVISLARAAGIGGMAGGQALDLAAEKKAPDEDGIITL---------QAMKTGALLRF 228
Query: 237 GAACGAILGGGSEKEIELLRRYGFYVGM 264
GAI+ G ++ E + LR +G +G+
Sbjct: 229 ACEAGAIIAGSNQAERQRLRLFGEKIGL 256
>3lom_A Geranyltranstransferase; geranyltransferase, structural genomics,
PSI, protein structure initiative, nysgrc; 2.30A
{Legionella pneumophila subsp}
Length = 313
Score = 117 bits (295), Expect = 8e-31
Identities = 53/234 (22%), Positives = 97/234 (41%), Gaps = 13/234 (5%)
Query: 34 MAMSTPNKNKSYWTSVHEDIGAHLRQAV--VVKEPVEVYEPMRHFVFAAPVNMAPALCVA 91
M++++ NK + +L Q + ++ ++ + + +F+ + P L
Sbjct: 1 MSLNSTQMNKQVIDKYTQRHELYLEQLLNEIIIPAPQIRSALHYALFSGGKRIRPILVYL 60
Query: 92 ACELVGGHREQAIVAAAALHVMHAASFIHENLPLSDRTSLIPKSKPTMYHAFKPNTELLV 151
A +L+ + + AAAL + H S IH++LP D L + KP+ + AF T +LV
Sbjct: 61 AGDLIDVDQGVLDIIAAALELTHCYSLIHDDLPAMDNDDL-RRGKPSCHKAFDEATAILV 119
Query: 152 ADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQCDDDDR 211
D M +E+L +P + +++ + + A G G+V GQ +L
Sbjct: 120 GDGMQALAIEVLLMRLSP-LLPAAQVVAITQVLVNASGISGMVSGQSLDLSELAKSS--- 175
Query: 212 KLNGITDVEMTYETYKKKEGRLHACGAACGAILGGG-SEKEIELLRRYGFYVGM 264
E E + K G+L SE+ LR YG ++G+
Sbjct: 176 -----VTEEQLREIHLLKTGKLILACFEMVLAAQHEVSEQIKSALRTYGKHIGL 224
>3p8r_A Geranyltranstransferase; isoprenyl synthase, structural genomics,
PSI, protein struct initiative, nysgrc; 2.50A {Vibrio
cholerae}
Length = 302
Score = 116 bits (292), Expect = 2e-30
Identities = 55/234 (23%), Positives = 94/234 (40%), Gaps = 14/234 (5%)
Query: 34 MAMSTPNKNKSYWTSVHEDIGAHLRQAV--VVKEPVEVYEPMRHFVFAAPVNMAPALCVA 91
MA + + +S + L Q + + + + + E MR+ + P L
Sbjct: 1 MAHHHHHHSLEALSSYQQRNNQQLDQWLNRIPFQTLPLIEAMRYGLLLGGKRARPYLVYI 60
Query: 92 ACELVGGHREQAIVAAAALHVMHAASFIHENLPLSDRTSLIPKSKPTMYHAFKPNTELLV 151
+++G A+A+ +HA S IH++LP D L + KPT + F T +L
Sbjct: 61 TGQMLGCELSDLDTPASAVECIHAYSLIHDDLPAMDDDEL-RRGKPTCHIQFDEATAILT 119
Query: 152 ADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQCDDDDR 211
DA+ +LA D A + + + ++ + A G+QG+ GQ +L
Sbjct: 120 GDALQTLAFTILAEGDLSAAGET-QRVAMLQALAEASGAQGMCLGQALDLAAENRLISLE 178
Query: 212 KLNGITDVEMTYETYKKKEGRLHACGAACGAILGGG-SEKEIELLRRYGFYVGM 264
+L I ++ K G L C GA+ G + L RY VG+
Sbjct: 179 ELETI---------HRNKTGALMRCAIRLGALAAGEKGRAMLPHLDRYAEAVGL 223
>3uca_A Geranyltranstransferase; isoprenoid synthesis, isoprenoid
diphosphate synthase; 2.00A {Clostridium perfringens}
Length = 324
Score = 116 bits (292), Expect = 2e-30
Identities = 46/224 (20%), Positives = 93/224 (41%), Gaps = 14/224 (6%)
Query: 43 KSYWTSVHEDIGAHLRQAVVVKE--PVEVYEPMRHFVFAAPVNMAPALCVAACELVGGHR 100
S+ E++ L+ +Y+ M + + + P L + + +
Sbjct: 34 AMNINSLKEEVDQSLKAYFNKDREYNKVLYDSMAYSINVGGKRIRPILMLLSYYIYKSDY 93
Query: 101 EQAIVAAAALHVMHAASFIHENLPLSDRTSLIPKSKPTMYHAFKPNTELLVADAMLPFGL 160
++ + A A+ ++H S IH++LP D L + KPT + F +L DA+L +
Sbjct: 94 KKILTPAMAIEMIHTYSLIHDDLPCMDNDDL-RRGKPTNHKVFGEAIAVLAGDALLNEAM 152
Query: 161 ELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQCDDDDRKLNGITDVE 220
++L + + L+ + A GS G++ GQ ++ ++ ++
Sbjct: 153 KILV---DYSLEEGKSALKATKIIADAAGSDGMIGGQIVDIINEDKEE--------ISLK 201
Query: 221 MTYETYKKKEGRLHACGAACGAILGGGSEKEIELLRRYGFYVGM 264
+ KK G L GA+L SE +I+ L +G+ +G+
Sbjct: 202 ELDYMHLKKTGELIKASIMSGAVLAEASEGDIKKLEGFGYKLGL 245
>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 = 114 bits (289), Expect = 4e-30
Identities = 59/225 (26%), Positives = 96/225 (42%), Gaps = 14/225 (6%)
Query: 43 KSYWTSVHEDIGAHLRQAVVVK--EPVEVYEPMRHFVFAAPVNMAPALCVAACELVGGHR 100
+Y S + A + E +YE MR+ V + P L AACE +GG
Sbjct: 4 TAYQASSQARVDAAMHTLFTAPSPELARLYEAMRYSVMNGGKRVRPLLAYAACEALGGKP 63
Query: 101 EQAIVAAAALHVMHAASFIHENLPLSDRTSLIPKSKPTMYHAFKPNTELLVADAMLPFGL 160
EQA AA A+ ++HA S +H++LP D L + +PT + AF +L D +
Sbjct: 64 EQANGAACAVELIHAYSLVHDDLPAMDDDDL-RRGQPTTHKAFDEACAILAGDGLQSLAF 122
Query: 161 ELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQCDDDDRKLNGITDVE 220
L ++ LR++ + +A G G+V GQ +L D + L +
Sbjct: 123 SALLDPALS-DASAEIRLRMVTTLAQAAGPAGMVGGQAIDLGSVGLKLDQQALEYM---- 177
Query: 221 MTYETYKKKEGRLHACGAACGAILGGG-SEKEIELLRRYGFYVGM 264
++ K G L GA+ G + E++ L+ Y +G+
Sbjct: 178 -----HRHKTGALIEASVILGALASGRAEKGELKALQTYAQAIGL 217
>4f62_A Geranyltranstransferase; enzyme function initiative, structural
genomics; 2.10A {Marinomonas SP}
Length = 317
Score = 114 bits (288), Expect = 6e-30
Identities = 59/237 (24%), Positives = 100/237 (42%), Gaps = 23/237 (9%)
Query: 30 MMVTMAMSTPNKNKSYWTSVHEDIGAHLRQAVVVKEPVE-VYEPMRHFVFAAPVNMAPAL 88
M++ + K + T + +L Q + P ++ MR+ +F + P L
Sbjct: 1 MVMNL--------KQFSTYTQSRVDQYLEQQLSDYAPANQLHNAMRYSLFNGGKRIRPML 52
Query: 89 CVAACELVGGHREQAIVAAAALHVMHAASFIHENLPLSDRTSLIPKSKPTMYHAFKPNTE 148
A+ +LVG +AAAL +HA S IH++LP D L + KPT + F T
Sbjct: 53 TYASAQLVGDISSLTDASAAALESIHAYSLIHDDLPAMDNDEL-RRGKPTCHIQFDEATA 111
Query: 149 LLVADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQCDD 208
+L DA+ F ELL+ NP ++++ E+ A G G++ GQ +L +
Sbjct: 112 ILAGDALQTFAFELLS---NPTSAQPELAIKLIQELVVASGRNGMITGQMIDLSSENKNI 168
Query: 209 DDRKLNGITDVEMTYETYKKKEGRLHACGAACGAILGGG-SEKEIELLRRYGFYVGM 264
+L + + K G L GA+ G +++ L Y +G+
Sbjct: 169 SLAELEQM---------HVHKTGALIKASVRMGALSTGQVKPEQLAKLDAYAHAIGL 216
>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 = 114 bits (287), Expect = 8e-30
Identities = 47/225 (20%), Positives = 84/225 (37%), Gaps = 14/225 (6%)
Query: 43 KSYWTSVHEDIGAHLRQAV--VVKEPVEVYEPMRHFVFAAPVNMAPALCVAACELVGGHR 100
+ + L + + + + V E M++ + P L A + G
Sbjct: 4 PQQLEACVKQANQALSRFIAPLPFQNTPVVETMQYGALLGGKRLRPFLVYATGHMFGVST 63
Query: 101 EQAIVAAAALHVMHAASFIHENLPLSDRTSLIPKSKPTMYHAFKPNTELLVADAMLPFGL 160
AAA+ +HA S IH++LP D L + PT + F +L DA+
Sbjct: 64 NTLDAPAAAVECIHAYSLIHDDLPAMDDDDL-RRGLPTCHVKFGEANAILAGDALQTLAF 122
Query: 161 ELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQCDDDDRKLNGITDVE 220
+L+ +D P + + ++ E+ A G G+ GQ +L L I
Sbjct: 123 SILSDADMP-EVSDRDRISMISELASASGIAGMCGGQALDLDAEGKHVPLDALERI---- 177
Query: 221 MTYETYKKKEGRLHACGAACGAILGGG-SEKEIELLRRYGFYVGM 264
++ K G L GA+ G + + +L +Y +G+
Sbjct: 178 -----HRHKTGALIRAAVRLGALSAGDKGRRALPVLDKYAESIGL 217
>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 = 111 bits (281), Expect = 7e-29
Identities = 54/232 (23%), Positives = 93/232 (40%), Gaps = 18/232 (7%)
Query: 36 MSTPNKN-KSYWTSVHEDIGAHLRQAV-VVKEPVEVYEPMRHFVFAAPVNMAPALCVAAC 93
MS N ++ + A L+QA+ + ++ M + V A + P L VA
Sbjct: 1 MSLINARLIAFEDQWVPALNAPLKQAILADSQDAQLAAAMTYSVLAGGKRLRPLLTVATM 60
Query: 94 ELVGG--HREQAIVAAAALHVMHAASFIHENLPLSDRTSLIPKSKPTMYHAFKPNTELLV 151
+ +G E+ AL ++H S IH++LP D +L + +PT + F L
Sbjct: 61 QSLGVTFVPERHWRPVMALELLHTYSLIHDDLPAMDNDAL-RRGEPTNHVKFGAGMATLA 119
Query: 152 ADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQCDDDDR 211
D +L + L ++D PA ++ + A G G+V GQ ++Q +
Sbjct: 120 GDGLLTLAFQWLTATDLPAT----MQAALVQALATAAGPSGMVAGQAKDIQSEHVNLPLS 175
Query: 212 KLNGITDVEMTYETYKKKEGRLHACGAACGAILGGGSEKEIELLRRYGFYVG 263
+L + +K+K G L G ILG E + ++ G
Sbjct: 176 QLRVL---------HKEKTGALLHYAVQAGLILGQAPEAQWPAYLQFADAFG 218
>3p8l_A Geranyltranstransferase; isoprenyl synthase, structural genomics,
PSI, protein struct initiative, nysgrc; 2.00A
{Enterococcus faecalis}
Length = 302
Score = 111 bits (279), Expect = 1e-28
Identities = 51/234 (21%), Positives = 96/234 (41%), Gaps = 17/234 (7%)
Query: 34 MAMSTPNKN-KSYWTSVHEDIGAHLRQAV-VVKEPVEVYEPMRHFVFAAPVNMAPALCVA 91
MA + + ++ + + + E + E M + + A + P L +
Sbjct: 1 MAHHHHHHSLTNFSQQHLPLVEKVMVDFIAEYTENERLKEAMLYSIHAGGKRLRPLLVLT 60
Query: 92 ACELVGGHREQAIV-AAAALHVMHAASFIHENLPLSDRTSLIPKSKPTMYHAFKPNTELL 150
E AA+L ++H S IH++LP D L + KPT + F T +L
Sbjct: 61 TVAAFQKEMETQDYQVAASLEMIHTYSLIHDDLPAMDDDDL-RRGKPTNHKVFGEATAIL 119
Query: 151 VADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQCDDDD 210
D +L +LL+ S + +M ++ +A G+QG+V GQ +++ +
Sbjct: 120 AGDGLLTGAFQLLSLSQLGLS----EKVLLMQQLAKAAGNQGMVSGQMGDIEGEKVSLTL 175
Query: 211 RKLNGITDVEMTYETYKKKEGRLHACGAACGAILGGGSEKEIELLRRYGFYVGM 264
+L + ++KK G L G +L +E+ I LL ++ + G+
Sbjct: 176 EELAAV---------HEKKTGALIEFALIAGGVLANQTEEVIGLLTQFAHHYGL 220
>1rtr_A Geranyltranstransferase; 2.50A {Staphylococcus aureus} SCOP:
a.128.1.1
Length = 301
Score = 110 bits (278), Expect = 1e-28
Identities = 50/234 (21%), Positives = 93/234 (39%), Gaps = 22/234 (9%)
Query: 31 MVTMAMSTPNKNKSYWTSVHEDIGAHLRQAVVVKEPVEVYEPMRHFVFAAPVNMAPALCV 90
M + M V+ ++ + ++V ++ E M + + A + P L +
Sbjct: 1 MTNLPM------NKLIDEVNNELSVAINKSV---MDTQLEESMLYSLNAGGKRIRPVLLL 51
Query: 91 AACELVGGHREQAIVAAAALHVMHAASFIHENLPLSDRTSLIPKSKPTMYHAFKPNTELL 150
+ + E + +A AL ++H S IH++LP D + K T + + T +L
Sbjct: 52 LTLDSLNTEYELGMKSAIALEMIHTYSLIHDDLPAMDNDDY-RRGKLTNHKVYGEWTAIL 110
Query: 151 VADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQCDDDD 210
DA+L EL++ + ++V+ ++ A G G+V GQ ++Q D
Sbjct: 111 AGDALLTKAFELIS---SDDRLTDEVKIKVLQRLSIASGHVGMVGGQMLDMQSEGQPIDL 167
Query: 211 RKLNGITDVEMTYETYKKKEGRLHACGAACGAILGGGSEKEIELLRRYGFYVGM 264
L I +K K G L A + + E L Y +++GM
Sbjct: 168 ETLEMI---------HKTKTGALLTFAVMSAADIANVDDTTKEHLESYSYHLGM 212
>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 = 109 bits (274), Expect = 6e-28
Identities = 44/226 (19%), Positives = 87/226 (38%), Gaps = 23/226 (10%)
Query: 43 KSYWTSVHEDIGAHLRQAVVVKEPVEVYEPMRHFVFAAPVN----MAPALCVAACELVGG 98
V + + + A+ ++ + M + + L + + + G
Sbjct: 4 SERLKEVQDAVETAMAAAIGRLPAGDLRDAMAY-----AAQGGKRLRAFLAIESAAIHGI 58
Query: 99 HREQAIVAAAALHVMHAASFIHENLPLSDRTSLIPKSKPTMYHAFKPNTELLVADAMLPF 158
QA+ AA A+ +HA S +H+++P D L + PT++ + T +L DA+
Sbjct: 59 SMAQAMPAALAVEALHAYSLVHDDMPCMDNDDL-RRGLPTVHKKWDDATAVLAGDALQTL 117
Query: 159 GLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQCDDDDRKLNGITD 218
EL +P ++ + ++ + +A G++G+V GQ ++
Sbjct: 118 AFELCT---DPVLGSAENRVALVAALAQASGAEGMVYGQALDIAAETAAVP-------LT 167
Query: 219 VEMTYETYKKKEGRLHACGAACGAILGGGSEKEIELLRRYGFYVGM 264
++ K G L + A GAIL G L Y +G+
Sbjct: 168 LDEIIRLQAGKTGALISFAAQAGAILAGADR---GPLTAYATALGL 210
>4dhd_A Polyprenyl synthetase; isoprenoid synthesis, isoprenoid diphosphate
synthase, trans; 1.65A {Pyrobaculum calidifontis}
Length = 358
Score = 110 bits (276), Expect = 8e-28
Identities = 45/218 (20%), Positives = 82/218 (37%), Gaps = 17/218 (7%)
Query: 51 EDIGAHLRQAVVVKEPVEVYEPMRHFVFAAPVNMAPALCVAACELVGGHREQAIVAAAAL 110
++ L + + + + E + + V + P L +AA E V G A+ AAA +
Sbjct: 15 AEVEKALVRYLSIGLAEDFREAVLYQVKTGGKRLRPLLTLAAAEAVSGQWRPALPAAAIV 74
Query: 111 HVMHAASFIHENLPLSDRTSLIPKSKPTMYHAFKPNTELLVADAMLPFGLELLASSDNPA 170
++H S I++++ DR + + PT+ AF N +LV E + + P
Sbjct: 75 ELIHNYSLIYDDI--IDR-GDVRRGLPTVRKAFGDNAAILVGIWYREAIEEAVLDTPKPT 131
Query: 171 GNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQCDDDDRKLNGITDVEMTYETY---- 226
+ + E+ +A+ EG+ ++ D E+T + Y
Sbjct: 132 -----LFAKEVAEVIKAI-----DEGERLDILFEAAGRSDPYFVQARWREVTLDDYIKMV 181
Query: 227 KKKEGRLHACGAACGAILGGGSEKEIELLRRYGFYVGM 264
K G L A A G + E +G G+
Sbjct: 182 SLKTGALIAAAAKWGVLSVSDDRGLAEAAWNFGMAAGV 219
>3llw_A Geranyltranstransferase (ISPA); structural genomics, PSI, protein
structure initiative, nysgrc; 2.30A {Helicobacter
pylori} PDB: 3q1o_A*
Length = 311
Score = 106 bits (266), Expect = 9e-27
Identities = 45/240 (18%), Positives = 104/240 (43%), Gaps = 25/240 (10%)
Query: 34 MAMSTPNKNKSYWTSVHEDIGAHLRQAVVVKE--PVEVYEPMRHFVFAAPVNMAPALCVA 91
M++S+PN S++ + E + L+ + E + + V P L +A
Sbjct: 1 MSLSSPNL--SFYYNECERFESFLKNHHLHLESFHPYLEKAFFEMVLNGGKRFRPKLFLA 58
Query: 92 ACELVGG------HREQAIVAAAALHVMHAASFIHENLPLSDRTSLIPKSKPTMYHAFKP 145
+ G + + A ++ +H S IH++LP D +L ++ PT++ +
Sbjct: 59 VLCALVGQKDYSNQQTEYFKIALSIECLHTYSLIHDDLPCMDNAAL-RRNHPTLHAKYDE 117
Query: 146 NTELLVADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQ 205
T +L+ DA+ + ELL+++ + I+ ++ ++ G +G++ GQ +
Sbjct: 118 TTAVLIGDALNTYSFELLSNALLES----HIIVELIKILSANGGIKGMILGQALDCYFEN 173
Query: 206 CDDDDRKLNGITDVEMTYETYKKKEGRLHACGAACGAILGGGSEKEI-ELLRRYGFYVGM 264
+ +L + ++ K +L + G + G ++E+ + L+ +G +G+
Sbjct: 174 TPLNLEQLTFL---------HEHKTAKLISASLIMGLVASGIKDEELFKWLQAFGLKMGL 224
>3npk_A Geranyltranstransferase; isoprene biosynthesis, SGX, structural
genomics protein structure initiative; 1.50A
{Campylobacter jejuni}
Length = 291
Score = 104 bits (262), Expect = 2e-26
Identities = 41/222 (18%), Positives = 82/222 (36%), Gaps = 17/222 (7%)
Query: 46 WTSVHEDIGAHLRQAVVVKE--PVEVYEPMRHFVFAAPVNMAPALCVAACELVGGHR-EQ 102
++ E HL + + E E + + A + L ++ + Q
Sbjct: 2 SLNLKELFIHHLEKNLPKVESFHPFFNEALALMLKAGGKHFRAQLLLSVVQSNKPELLNQ 61
Query: 103 AIVAAAALHVMHAASFIHENLPLSDRTSLIPKSKPTMYHAFKPNTELLVADAMLPFGLEL 162
A+ A AL +H S IH++LP D + PT++ ++ T +LV DA+ +
Sbjct: 62 ALDVALALEFIHTYSLIHDDLPAMDNADF-RRGIPTLHKSYDETTAILVGDALNTEAFLV 120
Query: 163 LASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQCDDDDRKLNGITDVEMT 222
L+ + ++++ + G G+V GQ + +L +
Sbjct: 121 LSHAHLKDE----IKIKLIKTLAFNAGLNGMVIGQAIDCFFEDKRLSLNELEFL------ 170
Query: 223 YETYKKKEGRLHACGAACGAILGGGSEKEIELLRRYGFYVGM 264
+ K RL A G + + +E + + G +G+
Sbjct: 171 ---HTHKTARLIAAALKMGCEICELNNEESNQIYKLGLKLGL 209
>1wy0_A Geranylgeranyl pyrophosphate synthetase; pyrococcus horikosh
structural genomics, riken structural
genomics/proteomics initiative, RSGI; 2.20A {Pyrococcus
horikoshii}
Length = 342
Score = 103 bits (260), Expect = 1e-25
Identities = 54/223 (24%), Positives = 92/223 (41%), Gaps = 35/223 (15%)
Query: 51 EDIGAHLRQAVVVKEPVEVYEPMRHFVFAAPVNMAPALCVAACELVGGHREQAIVAAAAL 110
+ I + + + K+P +YE RH+ A + P + + + E VGG +AI A A+
Sbjct: 16 KLIDEKIFELIPEKDPRVLYEAARHYPLAGGKRVRPFVVLTSTEAVGGDPLRAIYPAVAI 75
Query: 111 HVMHAASFIHENLPLSDRTSLIPKS-----KPTMYHAFKPNTELLVADAMLPFGLELLAS 165
++H S +H+ D ++ KPT++ + N +L D + E +A
Sbjct: 76 ELIHNYSLVHD-----D---IMDMDETRRGKPTVHRIWGVNMAILAGDLLFSKAFEAVAR 127
Query: 166 SDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQCDDDDRKLNGITDVEMTYET 225
++ P RV+ + +A S + EGQ L +T E
Sbjct: 128 AEIPPEKK----ARVLEVIVKA--SNELCEGQA--RD----------LEFEKKSTVTIEE 169
Query: 226 Y----KKKEGRLHACGAACGAILGGGSEKEIELLRRYGFYVGM 264
Y K G L A G I+G +E+ I+ L +G VG+
Sbjct: 170 YMEMISGKTGALFEASAKVGGIIGTDNEEYIKALSSWGRNVGI 212
>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 = 101 bits (252), Expect = 3e-25
Identities = 41/260 (15%), Positives = 83/260 (31%), Gaps = 22/260 (8%)
Query: 36 MSTPNKNKSYWTSVHEDIGAHLRQAVVVKEPVEVYEPMRHFVFAAPVNMAPALCVAACEL 95
M + + + E + +R+ + + E M + + P L + E
Sbjct: 1 MGSDKIHHHHHHMKXEXVEERIREILRPGWDLLTEEAMLYSATVGGXRIRPLLVLTLGED 60
Query: 96 VGGHREQAIVAAAALHVMHAASFIHENLPLSDRTSLIPKSKPTMYHAFKPNTELLVADAM 155
+G E + A A+ + H AS IH++LP D + P+ + + + LL D +
Sbjct: 61 LGVEEEXLLDVAVAVELFHTASLIHDDLPPIDNADF-RRGXPSCHRTYGEDIALLAGDGL 119
Query: 156 LPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQCDDDDRKLNG 215
++ + + + ++ G+ +++ + +
Sbjct: 120 FFLAFSQISXIG-----------NSXIFEEFSETAYXLLLGEAMDVEFERRXME------ 162
Query: 216 ITDVEMTYETYKKKEGRLHACGAACGAILGGGSEKEIELLRRYGFYVGMIQGIVSRRLGP 275
EM Y G L A + IL G + G G+ I
Sbjct: 163 -VSQEMVERMYAFXTGALFAFCFSAPFILXGXDH---TXMXLLGEXFGVAFQIYDDLXDI 218
Query: 276 TEEIEELKKLAFKLREVNSF 295
E++ K K E +
Sbjct: 219 LGSFEKVGKDLGKDTEXVTL 238
>3nf2_A Putative polyprenyl synthetase; isoprenyl diphosphate synthase,
structural genomics, PSI, PR structure initiative,
nysgrc; 2.20A {Streptomyces coelicolor}
Length = 352
Score = 97.8 bits (244), Expect = 2e-23
Identities = 48/196 (24%), Positives = 83/196 (42%), Gaps = 19/196 (9%)
Query: 69 VYEPMRHFVFAAPVNMAPALCVAACELVGGHREQAIVAAAALHVMHAASFIHENLPLSDR 128
+ + PAL V + E+ G E + A A+ ++H S +H++ L D
Sbjct: 42 IDAQGNPADGDGGKAVRPALAVLSAEVTGAAPEVGVPGAVAVELVHNFSLLHDD--LMDG 99
Query: 129 TSLIPKSKPTMYHAFKPNTELLVADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAM 188
+ + T++ P +LV DA+ E+L +GR R + + +R
Sbjct: 100 -DEQRRHRDTVWKVHGPAQAILVGDALFALANEVLLELGTVE---AGRATRRLTKASR-- 153
Query: 189 GSQGVVEGQYNELQCSQCDDDDRKLNGITDVEMTYETYKKKEGRLHACGAACGAILGGGS 248
+++GQ S D VE E K G L AC ++ GA+LGG
Sbjct: 154 ---SLIDGQA--QDISYEHRDR------VSVEECLEMEGNKTGALLACASSIGAVLGGAD 202
Query: 249 EKEIELLRRYGFYVGM 264
E+ + L +YG+++G+
Sbjct: 203 ERTADTLEKYGYHLGL 218
>1wmw_A Geranylgeranyl diphosphate synthetase; GGPP, prenyl diphosphate
synthase, structural genom riken structural
genomics/proteomics initiative; 1.55A {Thermus
thermophilus}
Length = 330
Score = 89.3 bits (222), Expect = 1e-20
Identities = 37/222 (16%), Positives = 66/222 (29%), Gaps = 29/222 (13%)
Query: 49 VHEDIGAHLRQAVVVKEPVEVYEPMRHFVFAAPVNMAPALCVAACELVGGHREQAIVAAA 108
+ + + L + +P+ + ++ + + L V + G E + AA
Sbjct: 8 IRQALQERLLARLDHPDPL-YRDLLQDYPRRGGKMLRGLLTVYSALAHGAPLEAGLEAAT 66
Query: 109 ALHVMHAASFIHENLPLSDRTSLIPKS-----KPTMYHAFKPNTELLVADAMLPFGLELL 163
AL + +H+ D + S +P ++ L DAM LL
Sbjct: 67 ALELFQNWVLVHD-----D---IEDGSEERRGRPALHRLHPMPLALNAGDAMHAEMWGLL 118
Query: 164 ASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQCDDDDRKLNGITDVEMTY 223
A +L E+ R GQ+ +L + D E +
Sbjct: 119 AEGLARGLFPP-EVLLEFHEVVRR-----TAYGQHLDLLWTLGGTFD------LRPEDYF 166
Query: 224 ETYKKKEGRLHACGA-ACGAILGGGSEKEIELLRRYGFYVGM 264
K A GA+L G + G +G
Sbjct: 167 RMVAHKAAYYTAVAPLRLGALLAGKTPPAA--YEEGGLRLGT 206
>3ipi_A Geranyltranstransferase; isoprene biosynthesis, helical bundle,
protein structure initiative II (PSI II), structural
genomics, nysgxrc; 1.90A {Methanosarcina mazei}
Length = 295
Score = 82.7 bits (205), Expect = 3e-18
Identities = 41/223 (18%), Positives = 85/223 (38%), Gaps = 42/223 (18%)
Query: 51 EDIGAHLRQAVVVKEPVEVYEPMRHFVFAAPVNMAPALCVAACELVGGHREQAIVAAAAL 110
+ A +++++ + E + + + H + + P + + E+ G +++ AA A+
Sbjct: 12 RYVEAGIKESITLIEDPGLKKMVEHVCHSGGKRIRPIILLLVSEICSGSYSRSLNAALAV 71
Query: 111 HVMHAASFIH-----ENLPLSDRTSLIPKSKPTMYHAFKPNTELLVADAMLPFGLELLAS 165
+MH+AS IH + L+ ++ P+ F P+ LL D ++ + ++
Sbjct: 72 EMMHSASLIHDDLLDQ--------GLVRRNLPSAPEKFGPSGALLCGDYLIAKSIAFISP 123
Query: 166 SDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQCDDDDRKLNGITDVEMTYET 225
++++ + M EG+ +L+ D
Sbjct: 124 YGE-------KVIQDFGKAGMDM-----AEGEVLDLKLE-------------DESFGEND 158
Query: 226 Y----KKKEGRLHACGAACGAILGGGSEKEIELLRRYGFYVGM 264
Y KK L A A+ GA GG E+ E +G +G
Sbjct: 159 YFKCIYKKTASLFAISASIGAYTGGAEEELAERFSHFGNALGT 201
>3lk5_A Geranylgeranyl pyrophosphate synthase; structural genomics, protein
structure initiative, geranylge pyrophosphate synthase;
1.90A {Corynebacterium glutamicum} PDB: 3qqv_A*
Length = 380
Score = 82.1 bits (203), Expect = 1e-17
Identities = 46/261 (17%), Positives = 81/261 (31%), Gaps = 43/261 (16%)
Query: 33 TMAMSTPNKNKSYWTSVHEDIGAHLRQAV---------VVKEPVEVYEPMRHFVFAAPVN 83
+++S+ + + E + L Q + + + +R FV
Sbjct: 5 DVSLSSFDAHDLDLDKFPEVVRDRLTQFLDAQELTIADIGAPVTDAVAHLRSFVLNGGKR 64
Query: 84 MAPALCVAACELVGGHR------EQAIVAAAALHVMHAASFIH-------------ENLP 124
+ P A GH+ E + AAA+L + A + IH +
Sbjct: 65 IRPLYAWAGFLAAQGHKNSSEKLESVLDAAASLEFIQACALIHDDIIDSSDTRRGAPTVH 124
Query: 125 LSDRTSLIPKSKPTMYHAFKPNTELLVADAMLPFGLELLASSDNPAGNNSGRILRVMVEM 184
+ + F + +L D L + ++L S A + R M
Sbjct: 125 RAVEADHRANNFEGDPEHFGVSVSILAGDMALVWAEDMLQDSGLSAEALA-RTRDAWRGM 183
Query: 185 TRAMGSQGVVEGQYNELQCSQCDDDDRKLNGITDVEMTYETYKKKEGR-LHACGAACGAI 243
V+ GQ L + VE+ + K A GA
Sbjct: 184 RTE-----VIGGQL--LDIYLESHAN------ESVELADSVNRFKTAAYTIARPLHLGAS 230
Query: 244 LGGGSEKEIELLRRYGFYVGM 264
+ GGS + I+ L YG +G+
Sbjct: 231 IAGGSPQLIDALLHYGHDIGI 251
>4fp4_A Polyprenyl synthetase; isoprenoid synthesis, isoprenoid diphosphate
synthase, trans; HET: GER UNL; 2.00A {Pyrobaculum
calidifontis}
Length = 285
Score = 78.2 bits (193), Expect = 7e-17
Identities = 30/217 (13%), Positives = 78/217 (35%), Gaps = 36/217 (16%)
Query: 51 EDIGAHLRQAVVVKEPVEVYEPMRHFVFAAPVNMAPALCVAACELVGGH---REQAIVAA 107
E + A L + EP+ + + +RH++ + P L + + + + AA
Sbjct: 15 ERVKARLNKVGEELEPISLRKAVRHYIETPGKLLRPLLLLTFTYSIDRRSIMDPRILEAA 74
Query: 108 AALHVMHAASFIHENLPLSDRTSLIPKSKPTMYHAFKPNTELLVADAMLPFGLELLASSD 167
A + ++H S + ++ + D+ + T + ++ +D ++ +++ +
Sbjct: 75 AIVELLHVVSLLQDD--VMDQ-HDQRRGIKTPRAMYGDGRAIVASDWLIAESIKMAVNLG 131
Query: 168 NPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQCSQCDDDDRKLNGITDVEMTYETYK 227
++ + A +Q + GQ +L+ + + +
Sbjct: 132 A-------DVVTYL-----ADVAQRLSVGQALDLEGER-----------------DKAAE 162
Query: 228 KKEGRLHACGAACGAILGGGSEKEIELLRRYGFYVGM 264
K L ++ G E IE ++ G +G+
Sbjct: 163 FKTAPLIEAALVMPLVILGRRE-LIETAKKLGTKLGI 198
>3oyr_A Trans-isoprenyl diphosphate synthase; isoprenyl synthase, PSI,
protein structure initiative; HET: IPE; 2.00A
{Caulobacter crescentus}
Length = 345
Score = 78.5 bits (194), Expect = 1e-16
Identities = 46/253 (18%), Positives = 89/253 (35%), Gaps = 47/253 (18%)
Query: 27 YRPMMVTMAMSTPNKNKSY---WTSVHEDIGA---HLRQAVVVKEPVEVYEPMRHFVFAA 80
+ + A + P K+ S D+ + + + + H + A
Sbjct: 6 HHHSLDAAAATLPRKSGSVDRLVRLAEADMAGVNRLITDRMQSDVAI-IPALAEHLIAAG 64
Query: 81 PVNMAPALCVAACELVGGHREQAIVAAAALHVMHAASFIH-----ENLPLSDRTSLIPKS 135
+ P + VAA L G + AAA+ +H A+ +H S + +
Sbjct: 65 GKRLRPLMTVAAARLAGADNDHFQKLAAAVEFIHTATLLHDDVVDG--------SQLRRG 116
Query: 136 KPTMYHAFKPNTELLVADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVE 195
K + + +LV D + EL+ +++ + L ++ +R + E
Sbjct: 117 KVAAHLIWGGAQSVLVGDFLFARAFELMVETNSM------KALEILARASRVI-----AE 165
Query: 196 GQYNELQCSQCDDDDRKLNGITDVEMTYETY----KKKEGRLHACGAACGAILGGGSEKE 251
G+ +L S D+ ++ Y + K L A + GA+ G +
Sbjct: 166 GEVLQLMRSH------------DLNLSQAVYLEIIQAKTAELFAAASEAGAVSAGVDVAK 213
Query: 252 IELLRRYGFYVGM 264
E LR YG +G+
Sbjct: 214 SEALRDYGLNLGL 226
>3mzv_A Decaprenyl diphosphate synthase; transferase, structural genomics,
PSI-2, protein structure initiative; 1.90A {Rhodobacter
capsulatus}
Length = 341
Score = 73.4 bits (181), Expect = 5e-15
Identities = 39/188 (20%), Positives = 74/188 (39%), Gaps = 40/188 (21%)
Query: 86 PALCVAACELVGGHREQAIVAAAALHVMHAASFIH-----ENLPLSDRTSLIPKSKPTMY 140
P L +AA LVG + AA + +H A+ +H E S + +PT
Sbjct: 58 PMLTLAAARLVGYGGPFHVHLAATVEFIHTATLLHDDVVDE--------SRQRRGRPTAN 109
Query: 141 HAFKPNTELLVADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNE 200
+ + +LV D + +L+ + N R++ ++ + + EG+ +
Sbjct: 110 LLWDNKSSVLVGDYLFARSFQLMTDTGNM------RVMEILANASAVI-----AEGEVLQ 158
Query: 201 LQCSQCDDDDRKLNGITDVEMTYETY----KKKEGRLHACGAACGAILGGGSEKEIELLR 256
L +Q ++ T + Y + K L + G I+GG E +++ L
Sbjct: 159 LTAAQ------------NLATTEDIYLRVIRGKTAALFSAATEVGGIIGGAPEDQVQALF 206
Query: 257 RYGFYVGM 264
YG +G+
Sbjct: 207 DYGDALGI 214
>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 = 73.8 bits (181), Expect = 6e-15
Identities = 37/286 (12%), Positives = 86/286 (30%), Gaps = 41/286 (14%)
Query: 12 AHVAPRRNHSRPSLSYRPMMVTMAMSTPNKNKSY---WTSVHEDIGAHLRQAVVVKE--- 65
+H + R +L ++ M T + + + + + +HL + + +E
Sbjct: 3 SHHHHHHSSGRENLYFQGMKETNSEEADSGLAFFRNMYDKYRDAFLSHLNEYSLEEEIKE 62
Query: 66 -PVEVYEPMRHFVFAAPVNMAPALCVAACELVGGHR------EQAIVAAAALHVMHAASF 118
+ Y+ + + N L + E V E+A A + ++ AA
Sbjct: 63 HISKYYKLLFDYNCLGGKNNRGILVILIYEYVKNRDINSSEWEKAACLAWCIEILQAAFL 122
Query: 119 IHENLPLSDRTSLIPKSKPTMYHAFKPNTELLVADAMLPFGLEL-LASSDNPAGNNSGRI 177
+ ++ + D+ + ++K Y T+ V D +L + L + +
Sbjct: 123 VADD--IMDK-GEMRRNKYCWYLLKDVETKNAVNDVLLLYNSIYKLIEIYLRNESCYVDV 179
Query: 178 LRVMVEMTRAMGSQGVVEGQYNELQCSQCDDDDRKLNGITDV------------EMTYET 225
+ + T + GQ+ + D + + +
Sbjct: 180 IATFRDATLK-----TIIGQHLDTNIFSDKYSDAHREIDVNNINVPEQPVIDINMINFGV 234
Query: 226 Y----KKKEGRLH-ACGAACGAILGGGS--EKEIELLRRYGFYVGM 264
Y K CG +L G + + + +G
Sbjct: 235 YKNIVIHKTAYYSFFLPIVCGMLLAGIAVDNLIYKKIEDISMLMGE 280
>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 = 73.2 bits (180), Expect = 8e-15
Identities = 34/270 (12%), Positives = 81/270 (30%), Gaps = 44/270 (16%)
Query: 18 RNHSRPSLSYRPMMVTMAMSTPNKNK----SYWTSVHEDIGAHLRQAVVVKEPVEVYEPM 73
+ + +P + ++ + + ++ + D+ V + V + +
Sbjct: 3 KFTGVNAKFQQPALRNLSPVVVEREREEFVGFFPQIVRDLTEDGIGHPEVGDAVARLKEV 62
Query: 74 RHFVFAAPVNMA------PALCVAACELVGGHREQ-------AIVAAAALHVMHAASFIH 120
+ N VAA + G ++ A+ + + AAS +
Sbjct: 63 LQY------NAPGGKCNRGLTVVAAYRELSGPGQKDAESLRCALAVGWCIELFQAASLVA 116
Query: 121 ENLPLSDRTSLIPKSKPTMYHAFKPNTELLVADAMLPFGLELLASSDNPAGNNSGRILRV 180
+++ D+ SL + + Y + + +L + + +L +
Sbjct: 117 DDI--MDQ-SLTRRGQLCWYKKEGVGLDAINDSFLLESSVYRVLKKYCRQRPYYVHLLEL 173
Query: 181 MVEMTRAMGSQGVVEGQYNELQCSQCDDDDRKLNGITDVEMTYETY----KKKEGRLH-- 234
++ GQ +L + D + E Y K K
Sbjct: 174 FLQTAYQ-----TELGQMLDLITAPVSKVD-------LSHFSEERYKAIVKYKTAFYSFY 221
Query: 235 ACGAACGAILGGGSEKEIELLRRYGFYVGM 264
AA ++G S++E E + +G
Sbjct: 222 LPVAAAMYMVGIDSKEEHENAKAILLEMGE 251
>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 = 72.9 bits (179), Expect = 1e-14
Identities = 32/259 (12%), Positives = 69/259 (26%), Gaps = 45/259 (17%)
Query: 36 MSTPNKNKSYWTSVHEDIGAHLRQAV-VVKEPVEVYEPMRHFVFAAPVNMA------PAL 88
M++ + S + V + L+ + M
Sbjct: 1 MASMERFLSVYDEVQAFLLDQLQSKYEIDPNRARYLRIMMDT------TCLGGKYFRGMT 54
Query: 89 CVAACELVGGHREQ-----------AIVAAAALHVMHAASFIHENLPLSDRTSLIPKSKP 137
V E + A V + + A + +++ D S++ + KP
Sbjct: 55 VVNVAEGFLAVTQHDEATKERILHDACVGGWMIEFLQAHYLVEDDIM--DG-SVMRRGKP 111
Query: 138 TMYHAFKPNTELLVADAMLP--FGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVE 195
Y T+ + D ++ + + +L + ++ A
Sbjct: 112 CWYRFPGVTTQCAINDGIILKSWTQIMAWHYFADR-PFLKDLLCLFQKVDYA-----TAV 165
Query: 196 GQY----NELQCSQCDDDDRKLNGITDVEMTYETY----KKKEGRLH-ACGAACGAILGG 246
GQ + ++ D + + E T Y K K G +
Sbjct: 166 GQMYDVTSMCDSNKLDPEVAQPMTTDFAEFTPAIYKRIVKYKTTFYTYLLPLVMGLFVSE 225
Query: 247 GS-EKEIELLRRYGFYVGM 264
+ E+ L+ R +G
Sbjct: 226 AAASVEMNLVERVAHLIGE 244
>3aqb_B Component B of hexaprenyl diphosphate synthase; prenyltransferase,
transferase; 2.40A {Micrococcus luteus} PDB: 3aqc_B*
Length = 325
Score = 71.1 bits (175), Expect = 3e-14
Identities = 27/188 (14%), Positives = 69/188 (36%), Gaps = 40/188 (21%)
Query: 86 PALCVAACELVGGHREQAIVAAAALHVMHAASFIH-----ENLPLSDRTSLIPKSKPTMY 140
P + + L ++ I A +L ++H AS +H S + + +++
Sbjct: 49 PMFVLLSGFLNDTQKDDLIRTAVSLELVHMASLVHDDYIDN--------SDMRRGNTSVH 100
Query: 141 HAFKPNTELLVADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNE 200
AF +T + +L L+ +A+ +N + ++ + + G++++
Sbjct: 101 IAFDKDTAIRTGHFLLARALQNIATINNS------KFHQIFSKTILEV-----CFGEFDQ 149
Query: 201 LQCSQCDDDDRKLNGITDVEMTYETY----KKKEGRLHACGAACGAILGGGSEKEIELLR 256
+ + +++ Y +K L GA+ E+ ++
Sbjct: 150 MADRF------------NYPVSFTAYLRRINRKTAILIEASCHLGALSSQLDEQSTYHIK 197
Query: 257 RYGFYVGM 264
++G +GM
Sbjct: 198 QFGHCIGM 205
>3rmg_A Octaprenyl-diphosphate synthase; structural genomics, protein
structure initiative, isoprene biosynthesis,
transferase; 2.30A {Bacteroides thetaiotaomicron}
Length = 334
Score = 68.8 bits (169), Expect = 2e-13
Identities = 39/188 (20%), Positives = 73/188 (38%), Gaps = 40/188 (21%)
Query: 86 PALCVAACELVGGHREQAIVAAAALHVMHAASFIH-----ENLPLSDRTSLIPKSKPTMY 140
P L + L G + AA +L ++H AS +H E S + + ++
Sbjct: 52 PILVLLVARLYGAVTPATLHAAVSLELLHTASLVHDDVVDE--------STERRGQLSVN 103
Query: 141 HAFKPNTELLVADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNE 200
F +L D +L L ++N I+R++ + + + ++G +
Sbjct: 104 AIFNNKVSVLAGDYLLATSLVHAEQTNNY------EIIRLVSSLGQKL-AEGEL------ 150
Query: 201 LQCSQCDDDDRKLNGITDVEMTYETY----KKKEGRLHACGAACGAILGGGSEKEIELLR 256
LQ L+ +++ + E Y +KK L A A A+ E+E+ R
Sbjct: 151 LQ----------LSNVSNHSFSEEVYFDVIRKKTAALFAACAEAAALSVQVGEEEVAFAR 200
Query: 257 RYGFYVGM 264
G Y+G+
Sbjct: 201 LLGEYIGI 208
>2azj_A Geranylgeranyl pyrophosphate synthetase; hexpps,
trans-prenyltransferase; 2.40A {Sulfolobus solfataricus}
PDB: 2azk_A
Length = 289
Score = 68.5 bits (168), Expect = 2e-13
Identities = 23/189 (12%), Positives = 52/189 (27%), Gaps = 48/189 (25%)
Query: 86 PALCVAACELVGGHREQAIVAAAALHVMHAASFIH-----ENLPLSDRTSLIPKSKPTMY 140
L + +GG + + A A+ ++H+AS + +
Sbjct: 54 GTLNMFFTVALGGDIKDSYGGALAIEILHSASLALCDIVDL--------DATRRGDKAAW 105
Query: 141 HAFKPNTELLVADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNE 200
+ + + + ++P L ++ +S L +E+ + G +
Sbjct: 106 VVYGNRKVIFITNYLIPTALRIIQTSYGD------DALNTSIELWKDT-----SVGALRD 154
Query: 201 LQCSQCDDDDRKLNGITDVEMTYETY----KKKEGRLHACGAACGAILGGGSEKEIELLR 256
+ Y + K G L A + +
Sbjct: 155 M-------------------YDNSDYIRTIELKTGSLFKLSTVLSAYA-SKHYNTKQQML 194
Query: 257 RYGFYVGMI 265
G Y+G+I
Sbjct: 195 DVGKYLGII 203
>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 = 68.3 bits (167), Expect = 4e-13
Identities = 31/268 (11%), Positives = 75/268 (27%), Gaps = 27/268 (10%)
Query: 12 AHVAPRRNHSRPSLSYRPMMVTMAMSTPNKNKS-----YWTSVHEDIGAHLRQAVVVKEP 66
+H + R +L ++ M S + +++ + + + +
Sbjct: 3 SHHHHHHSSGRENLYFQGHMNGDQNSDVYAQEKQDFVQHFSQIVRVLTEDEMGHPEIGDA 62
Query: 67 VEVYEPMRHFVFAAPVNMAPALCVAACELVGGHREQ-------AIVAAAALHVMHAASFI 119
+ + + + V A + R+Q A + ++ A +
Sbjct: 63 IARLKEVLEYNAIGGKYNRGLTVVVAFRELVEPRKQDADSLQRAWTVGWCVELLQAFFLV 122
Query: 120 HENLPLSDRTSLIPKSKPTMYHAFKPNTE-LLVADAMLPFGLELLASSDNPAGNNSGRIL 178
++ + D SL + + Y + + A+ + LL ++
Sbjct: 123 ADD--IMDS-SLTRRGQICWYQKPGVGLDAINDANLLEACIYRLLKLYCREQ-PYYLNLI 178
Query: 179 RVMVEMTRAMGSQGVVEGQYNELQCSQCDDDDRKLNGITDVEMTYETYKKKEGRLHACGA 238
+ ++ + GQ L + L T + K K
Sbjct: 179 ELFLQSSYQ-----TEIGQT--LDLLTAPQGNVDLVRFT-EKRYKSIVKYKSAFYSFYLP 230
Query: 239 ACGAILGGG--SEKEIELLRRYGFYVGM 264
A+ G EKE ++ +G
Sbjct: 231 IAAAMYMAGIDGEKEHANAKKILLEMGE 258
>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 = 67.8 bits (166), Expect = 5e-13
Identities = 28/206 (13%), Positives = 71/206 (34%), Gaps = 23/206 (11%)
Query: 64 KEPVEVYEPMRHFVFAAPVNMAPALCVAACELVGGHREQAIVAAAALHVMHAASFIHENL 123
+ + +P H + N L V ++ ++Q + + + ++H +S + ++
Sbjct: 23 QNESLISKPYNHILLKPGKNFRLNLIVQINRVMNLPKDQLAIVSQIVELLHNSSLLIDD- 81
Query: 124 PLSDRTSLIPKSKPTMYHAFKPNTELLVADAMLPFGLELLASSDNPAGNNSGRILRVMVE 183
+ D + + + + T + F + + A+ M ++L++ ++ + E
Sbjct: 82 -IEDN-APLRRGQTTSHLIFGVPSTINTANYMYFRAMQLVSQLTTKE-PLYHNLITIFNE 138
Query: 184 MTRAMGSQGVVEGQYNELQCSQCDDDDRKLNGITDVEMTYETYKK----KEGRLHACGAA 239
+ GQ ++ + + ++ T E Y K G L
Sbjct: 139 ELINLH-----RGQGLDIYWR---------DFLPEIIPTQEMYLNMVMNKTGGLFRLTLR 184
Query: 240 CGAILGGGSEKEIELLRRYGFYVGMI 265
L S L + +G+I
Sbjct: 185 LMEALSPSSH-HGHSLVPFINLLGII 209
>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 = 65.7 bits (161), Expect = 2e-12
Identities = 27/205 (13%), Positives = 63/205 (30%), Gaps = 31/205 (15%)
Query: 64 KEPVEVYEPMRHFVFAAPVNMAPALCVAACELVGGHREQAIVAAAALHVMHAASFIH--- 120
+ EP ++ + + L A + ++ + ++H AS +
Sbjct: 8 TVQRILLEPYKYLLQLPGKQVRTKLSQAFNHWLKVPEDKLQIIIEVTEMLHNASLLIDDI 67
Query: 121 ENLPLSDRTSLIPKSKPTMYHAFKPNTELLVADAMLPFGLELLASSDNPAGNNSGRILRV 180
E D S + + P + + + + A+ + GLE + + D+P +++
Sbjct: 68 E-----DN-SKLRRGFPVAHSIYGIPSVINSANYVYFLGLEKVLTLDHP------DAVKL 115
Query: 181 MVEMTRAMGSQGVVEGQYNELQCSQCDDDDRKLNGITDVEMTYETYKKKEGRLHACGAAC 240
+ +GQ ++ D+ E +K G L
Sbjct: 116 FTRQLLELH-----QGQGLDIYW--RDNYT-----CPTEEEYKAMVLQKTGGLFGLAVGL 163
Query: 241 GAILGGGSEKEIELLRRYGFYVGMI 265
+ E L+ +G+
Sbjct: 164 MQLFSDYKED----LKPLLNTLGLF 184
>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 = 65.2 bits (159), Expect = 5e-12
Identities = 35/272 (12%), Positives = 73/272 (26%), Gaps = 47/272 (17%)
Query: 19 NHSRPSLSYRPMMVTMAMSTPNKNKSYWTSVHEDIGAHLRQAVVVKEPVEVYEPMRHFVF 78
+H S R + +Y+ + L++ + E + + +++
Sbjct: 5 HHHHHHSSGRENLYFQGEYDYTDFINYYDKFKVIVYNVLKKLPLNDEIRK--PVIEYYLN 62
Query: 79 AAPVNMA------PALCVAACELVGG----HREQAIVAAAALHVMHAASFIH---ENLPL 125
N+ + V L R+ + + + A I
Sbjct: 63 CIDYNVKKGKHIRGKILVLISSLSSAYSNIKRDSIYLLGWVVEAIQALILIADDIM---- 118
Query: 126 SDRTSLIPKSKPTMYHAFKPNTELLVADAMLPFGLELLASSDNPAGNNS-GRILRVMVEM 184
D + P Y + + + L L+ + GN+ +I ++ E
Sbjct: 119 -DS-GKFRRGAPCWYIVHGQSNAINDIFFLKMLSLSLIFELSSVFGNDIVMKIQKIYNES 176
Query: 185 TRAMGSQGVVEGQYNELQCSQCDDDDRKLNGITDVEMTYETY----KKKEGRLH-ACGAA 239
V GQ+ +L D E Y + K R
Sbjct: 177 IFF-----TVLGQHLDLSYFDLSKAD----------KISERYFSMVEMKTSRYTFYMPVF 221
Query: 240 CGAILGG--GSEKEIELLRRYGFYVGM---IQ 266
G L S ++ L+ + +G +
Sbjct: 222 FGLTLSEIQVSSAQLNLIEAILYKLGEFYQVH 253
>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 = 64.6 bits (158), Expect = 7e-12
Identities = 44/253 (17%), Positives = 79/253 (31%), Gaps = 43/253 (16%)
Query: 23 PSLSYRPMMVTMAMSTPNKNKSYWTSVHEDIGA---HLRQAVVVKEPVEVYEPMRHFVFA 79
L + T A + +++ + L + E + + + H A
Sbjct: 14 HGLGKEGVSTTGASQVEFGDPELTARINDAMVQVEELLHTELSSGEDF-LVDIVMHLTRA 72
Query: 80 APVNMAPALCVAACELVGGH-REQAIVAAAALHVMHAASFIHENLPLSDR---TSLIPKS 135
P + A E E I AA + + H A+ H D + + +
Sbjct: 73 GGKRFRPMFALLASEFGEKPLSENVIKAAVVVEITHLATLYH------DDVMDEASMRRG 126
Query: 136 KPTMYHAFKPNTELLVADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVE 195
P+ + + +L D +L L++ + E + V
Sbjct: 127 VPSANARWDNSVAILAGDILLAHASGLMSQLGTDT-------VAHFAETFGEL-----VT 174
Query: 196 GQYNELQCSQCDDDDRKLNGITDVEMTYETY----KKKEGRLHACGAACGAILGGGSEKE 251
GQ + D D E Y ++K G L A GA+ G + +
Sbjct: 175 GQM--RETVGPRDTD-----------PIEHYTNVIREKTGVLIASAGYLGAMHAGAAPEH 221
Query: 252 IELLRRYGFYVGM 264
I+ L+ +G VGM
Sbjct: 222 IDALKNFGAAVGM 234
>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 = 64.1 bits (156), Expect = 9e-12
Identities = 32/285 (11%), Positives = 60/285 (21%), Gaps = 57/285 (20%)
Query: 19 NHSRPSLSYRPMMVTMAMSTPNKNKSYWTSVHEDIGAHLRQAV-VVKEPVEVYEPMRHFV 77
+H S P MA + + + L + V M
Sbjct: 6 HHHHHSSGLVPRGSHMASMPMQMFMQVYDEIQMFLLEELELKFDMDPNRVRYLRKMMDT- 64
Query: 78 FAAPVNMA------PALCVAACELVGGHR-----------------EQAIVAAAALHVMH 114
+ E + A V + +
Sbjct: 65 -----TCLGGKYNRGLTVIDVAESLLSLSPNNNGEEDDGARRKRVLHDACVCGWMIEFLQ 119
Query: 115 AASFIHENLPLSDR---TSLIPKSKPTMYHAFKPNTELLVADAMLP--FGLELLASSDNP 169
A + D S+ + KP Y + + D +L + +
Sbjct: 120 AHYLVE------DDIMDNSVTRRGKPCWYRHPDVTVQCAINDGLLLKSWTHMMAMHFFAD 173
Query: 170 AGNNSGRILRVMVEMTRAMGSQGVVEGQY----NELQCSQCDDDDRKLNGITDVEMTYET 225
+L + GQ + ++ D D + E T
Sbjct: 174 R-PFLQDLLCRFNRVDYT-----TAVGQLYDVTSMFDSNKLDPDVSQPTTTDFAEFTLSN 227
Query: 226 Y----KKKEGRLHACGA-ACGAILGGG-SEKEIELLRRYGFYVGM 264
Y K K G I+ ++ + +G
Sbjct: 228 YKRIVKYKTAYYTYLLPLVMGLIVSEALPTVDMGVTEELAMLMGE 272
>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 = 62.6 bits (153), Expect = 3e-11
Identities = 29/189 (15%), Positives = 59/189 (31%), Gaps = 40/189 (21%)
Query: 86 PALCVAACELVGGH-REQAIVAAAALHVMHAASFIHENLPLSDRTSLIPKS-----KPTM 139
P Q AAA+ ++H + IH+ D +I S T+
Sbjct: 60 PGYFYLFSTFGNAATPAQLQAGAAAIEILHVGTLIHD-----D---VIDDSPTRRGVRTI 111
Query: 140 YHAFKPNTELLVADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYN 199
+ + D M + + S +++ ++ + ++G+ +
Sbjct: 112 QMTYGQRNAIYAGDFMFTVYFDQVLKS-----TTDRSLIQNHIDAMHRI-----LQGELH 161
Query: 200 ELQCSQCDDDDRKLNGITDVEMTYETY----KKKEGRLHACGAACGAILGGGSEKEIELL 255
++ + ++T + Y K L A GA L G + I+
Sbjct: 162 QMDLNY------------REDITLDAYLNEIAGKTAELFALSCYQGAQLAGAPQSVIDRT 209
Query: 256 RRYGFYVGM 264
R G +G
Sbjct: 210 RDIGIAIGC 218
>3tc1_A Octaprenyl pyrophosphate synthase; all alpha-helices fold,
transferase; 2.00A {Helicobacter pylori}
Length = 315
Score = 59.6 bits (145), Expect = 3e-10
Identities = 21/188 (11%), Positives = 52/188 (27%), Gaps = 44/188 (23%)
Query: 86 PALCVAACELVGGHREQAIVAAAALHVMHAASFIH-----ENLPLSDRTSLIPKSKPTMY 140
L + + ++A+ + ++ AS +H + + + + P++
Sbjct: 42 LMLALLNEKTDAILLDKALNLCTIVEMIQTASLLHDDVIDK--------ATMRRKLPSIN 93
Query: 141 HAFKPNTELLVADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNE 200
F +++ D L+ I + + + S+G +
Sbjct: 94 ALFGNFNAVMLGDVFYSKAFFELSKMGE-------LIAQALSNAVLRL-SRGEI------ 139
Query: 201 LQCSQCDDDDRKLNGITDVEMTYETY----KKKEGRLHACGAACGAILGGGSEKEIELLR 256
+ + Y + K AIL K+ ++
Sbjct: 140 ED----------VFVGECFNSDKQKYWRILEDKTAHFIEASLKSMAILLN---KDAKIYA 186
Query: 257 RYGFYVGM 264
+G GM
Sbjct: 187 DFGLNFGM 194
>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 = 56.9 bits (138), Expect = 2e-09
Identities = 33/187 (17%), Positives = 61/187 (32%), Gaps = 41/187 (21%)
Query: 86 PALCVAACELVGGHR-EQAIVAAAALHVMHAASFIHENLPLSDR---TSLIPKSKPTMYH 141
L + + + G E AI + AAL ++H AS +H D + + K T+
Sbjct: 45 VRLSILSFKNRGVEIGEDAISSLAALELVHLASLLH------DDVIDGARFRRGKETINF 98
Query: 142 AFKPNTELLVADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNEL 201
+ + D +L + N ++ R + + M S+ + +
Sbjct: 99 MYGDKAAVAAGDLVLVSAFHTVEEIGNN------KLRRAFLNVIGKM-SEAEL------I 145
Query: 202 QCSQCDDDDRKLNGITDVEMTYETY----KKKEGRLHACGAACGAILGGGSEKEIELLRR 257
+ +T E Y + K G L A+L G ++ L
Sbjct: 146 EQLSRYKP-----------ITKEEYLRIVEGKSGALFGLALQLPALLEGELGED---LYN 191
Query: 258 YGFYVGM 264
G +G
Sbjct: 192 LGVTIGT 198
>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 = 51.6 bits (124), Expect = 1e-07
Identities = 32/246 (13%), Positives = 70/246 (28%), Gaps = 68/246 (27%)
Query: 51 EDIGAHLRQAVVVKEPVEVYEPMRHFVFAAPV--NMAPALCVAACELVGGHREQAIVA-- 106
+ LR+ V+ + P + +F + + + +A++
Sbjct: 19 SLLSNKLREMVLAEVPK-LASAAEYFFKRGVQGKQFRSTILLLMATALDVRVPEALIGES 77
Query: 107 ---------------AAALHVMHAASFIHENLPLSD---------RTSLIPKSKPTMYHA 142
A ++H AS +H D R ++
Sbjct: 78 TDIVTSELRVRQRGIAEITEMIHVASLLH------DDVLDDADTRR------GVGSLNVV 125
Query: 143 FKPNTELLVADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQ 202
+L D +L LA+ N ++ ++ + V G+ ++
Sbjct: 126 MGNKMSVLAGDFLLSRACGALAALKNT------EVVALLATAVEHL-----VTGET--ME 172
Query: 203 CSQCDDDDRKLNGITDVEMTYETY----KKKEGRLHACGAACGAILGGGSEKEIELLRRY 258
+ T+ + + Y K L + A+L G + + L Y
Sbjct: 173 ----------ITSSTEQRYSMDYYMQKTYYKTASLISNSCKAVAVLTGQTAEVAVLAFEY 222
Query: 259 GFYVGM 264
G +G+
Sbjct: 223 GRNLGL 228
>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 = 38.9 bits (90), Expect = 0.002
Identities = 54/368 (14%), Positives = 111/368 (30%), Gaps = 112/368 (30%)
Query: 26 SYRPM----MVTMAM------STPNKNKSYWTSVHEDIGAHLRQAVVVKEPVEVYEPMRH 75
+Y + + A T + +T +I L P P +
Sbjct: 179 TYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGL-NILEWLE------NPSNT--PDKD 229
Query: 76 FVFAAPVNMAPALCV-------AACELVG--------------GHREQAIVAAAAL---- 110
++ + P++ P + V +L+G GH Q +V A A+
Sbjct: 230 YLLSIPISC-PLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGH-SQGLVTAVAIAETD 287
Query: 111 ----------HVMHAASFI----HENLPLSDRTSLIPKSKPTMYHAFKPNTE------LL 150
+ FI +E P TSL P++ N E L
Sbjct: 288 SWESFFVSVRKAITVLFFIGVRCYEAYP---NTSL----PPSILEDSLENNEGVPSPMLS 340
Query: 151 VADAMLPFGLELLASSDNPAGNNSGRILRVMVEMTRAMGSQGVVEGQYNELQ--CSQCDD 208
+++ ++ + N ++ +V + + VV G L
Sbjct: 341 ISNLTQEQ-VQDYVNKTNSHLPAGKQVEISLVNGAKNL----VVSGPPQSLYGLNLTL-- 393
Query: 209 DDRKLNGITDVEMTYETYKKKEGRLHACGAACGA-----ILGGGSEKEIELLRRYGFYVG 263
RK + ++ + + +++ + + +L S+ + L +
Sbjct: 394 --RKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNV--- 448
Query: 264 MIQGIVSRRLG-P---TEEIEELKKLAFKLREVNSFNDENAEVIFSL-VD------DNIT 312
++ + P T + +L+ L+ S ++ + I L V T
Sbjct: 449 ---SFNAKDIQIPVYDTFDGSDLRVLS------GSISERIVDCIIRLPVKWETTTQFKAT 499
Query: 313 HVLGFNLG 320
H+L F G
Sbjct: 500 HILDFGPG 507
Score = 37.3 bits (86), Expect = 0.007
Identities = 38/223 (17%), Positives = 74/223 (33%), Gaps = 60/223 (26%)
Query: 20 HS-RP-SLSYRPMMVTMAMSTPNKNKSYWTSVHEDIGAHLRQA----VVVKEPVEVYEPM 73
+S RP +LS+ + + P + + + E L + EP E +
Sbjct: 4 YSTRPLTLSHGSLEHVL--LVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELV 61
Query: 74 RHFV-FAAPVNMAPALCVAACELVG---GHREQAIVAAAALHVMHAASFIHEN-LPLSDR 128
F+ + + + + P+ +++ E + +H + AA + EN L
Sbjct: 62 GKFLGYVSSL-VEPSKVGQFDQVLNLCLTEFENCYLEGNDIHAL-AAKLLQENDTTLVKT 119
Query: 129 TSLIPKSKPTMYHAF----KPNTELLVADAMLPFGLELLASSDNPAGNNSGRILRVMVEM 184
LI K+ A +P + +++ L A + A +++
Sbjct: 120 KELI-KNY---ITARIMAKRPFDK--KSNSAL-----FRAVGEGNA--------QLVA-- 158
Query: 185 TRAMGSQGVVEGQYNELQCSQCDDDDRKLNGITDVEMTYETYK 227
G QG + + EL R L Y+TY
Sbjct: 159 --IFGGQGNTDDYFEEL---------RDL---------YQTYH 181
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 37.3 bits (86), Expect = 0.003
Identities = 15/76 (19%), Positives = 23/76 (30%), Gaps = 25/76 (32%)
Query: 184 MTRAMGSQGVVEGQY-----NELQCSQCDDDDRKLNGITDVEMTYETYKKKEGRLHACGA 238
MTR S G+ L C +C K+ + + + + C
Sbjct: 2 MTRE--SIDKRAGRRGPNLNIVLTCPECKVYPPKI--VER-------FSEGD---VVCA- 46
Query: 239 ACGAILGG-----GSE 249
CG +L SE
Sbjct: 47 LCGLVLSDKLVDTRSE 62
>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 = 38.7 bits (89), Expect = 0.003
Identities = 46/293 (15%), Positives = 82/293 (27%), Gaps = 94/293 (32%)
Query: 2 AKAL--SVLNLPAHVAPRRNHSRPSLSYRPMMVTM--AMSTPNKNKS-YWTSVHEDIGAH 56
K L +LP N P +++ W V+ D
Sbjct: 308 LKYLDCRPQDLP-REVLTTN---------PRRLSIIAESIRDGLATWDNWKHVNCD---- 353
Query: 57 LRQAVVVKEPVEVYEP--MRH-----FVFAAPVNMAPA--LCVAACELVGGHREQAIVAA 107
+ +++ + V EP R VF ++ P L + +++ + +V
Sbjct: 354 -KLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHI-PTILLSLIWFDVI--KSDVMVV-- 407
Query: 108 AALHVMHAAS-----------FIH-----ENLPLSDRTSL---------IPKSKPT---- 138
++ +H S I + L + +L IPK+ +
Sbjct: 408 --VNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLI 465
Query: 139 ------------MYHAFKP-NTELLVADAMLPFGLELLAS---SDNPAGNNSGRILRVMV 182
+H + E + M+ L D+ A N SG IL +
Sbjct: 466 PPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQ 525
Query: 183 EMTRAMGSQGVVEGQYNELQCSQCDDDDRKLNGITDVEMTYET--YKKKEGRL 233
++ Y C +R +N I D E K L
Sbjct: 526 QLKF-----------YKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDL 567
>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 = 34.2 bits (77), Expect = 0.025
Identities = 9/38 (23%), Positives = 17/38 (44%), Gaps = 15/38 (39%)
Query: 58 RQAVVVKE---PVEVYEPMRHFVFAAPVNMAPALCVAA 92
+QA+ K+ +++Y + APAL + A
Sbjct: 19 KQAL--KKLQASLKLYAD----------DSAPALAIKA 44
Score = 29.1 bits (64), Expect = 1.1
Identities = 9/25 (36%), Positives = 14/25 (56%), Gaps = 7/25 (28%)
Query: 278 EIEELKKL--AFKLREVNSFNDENA 300
E + LKKL + KL + D++A
Sbjct: 18 EKQALKKLQASLKL-----YADDSA 37
>3r2v_A PB2 C-terminal subunit; structural genomics, seattle structural
genomics center for infectious disease, ssgcid,
polymerase BASI H3N2, H1N1; 1.30A {Influenza a virus}
PDB: 2vy6_A 3cw4_A 3l56_A 3kc6_A 3khw_A 2gmo_A 2jdq_D
Length = 216
Score = 30.9 bits (69), Expect = 0.43
Identities = 23/66 (34%), Positives = 25/66 (37%), Gaps = 9/66 (13%)
Query: 225 TYKKKEGRLHACGAACGA----ILGGGSEKEIELLRRYGFYVGMIQGIVSRRLGPTEEIE 280
Y K RL G G S E +LR GF +I G RR GP I
Sbjct: 120 NYNKTTKRLTILGKDAGTLIEDPDESTSGVESAVLR--GF---LIIGKEDRRYGPALSIN 174
Query: 281 ELKKLA 286
EL LA
Sbjct: 175 ELSNLA 180
>2nra_C PI protein; protein-DNA complex, DNA replication, replication-DNA
comple; 3.10A {Escherichia coli} SCOP: a.4.5.10 a.4.5.10
Length = 276
Score = 28.6 bits (63), Expect = 2.9
Identities = 6/22 (27%), Positives = 11/22 (50%)
Query: 211 RKLNGITDVEMTYETYKKKEGR 232
++ T++ T +KEGR
Sbjct: 233 AEIKKKTEISFVGFTVHEKEGR 254
>3b42_A GSU0935, methyl-accepting chemotaxis protein, putative; PAS domain,
C-type heme containing sensor, unknown function,
signaling protein; HET: HEM; 1.90A {Geobacter
sulfurreducens}
Length = 135
Score = 27.6 bits (61), Expect = 3.4
Identities = 8/27 (29%), Positives = 10/27 (37%)
Query: 198 YNELQCSQCDDDDRKLNGITDVEMTYE 224
NE +C C D G V + E
Sbjct: 101 PNEQRCQSCHDAGAAYLGGLLVTTSIE 127
>1vhy_A Hypothetical protein HI0303; PSI, protein structure initiative, NEW
YORK SGX research CEN structural genomics, nysgxrc; HET:
MSE; 1.90A {Haemophilus influenzae} SCOP: b.122.1.2
c.116.1.5 PDB: 1nxz_A
Length = 257
Score = 27.2 bits (61), Expect = 7.1
Identities = 9/32 (28%), Positives = 11/32 (34%), Gaps = 8/32 (25%)
Query: 245 GGGSEKEIELLRRYGFYVGMIQGIVSRRLGPT 276
GG S +EI + GF LG
Sbjct: 200 GGLSAQEIAQTEQQGF--------TEILLGKR 223
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
0.319 0.134 0.390
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: 4,997,728
Number of extensions: 313214
Number of successful extensions: 1018
Number of sequences better than 10.0: 1
Number of HSP's gapped: 907
Number of HSP's successfully gapped: 67
Length of query: 320
Length of database: 6,701,793
Length adjustment: 94
Effective length of query: 226
Effective length of database: 4,077,219
Effective search space: 921451494
Effective search space used: 921451494
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: 57 (25.8 bits)