RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3879
(247 letters)
>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 = 213 bits (544), Expect = 7e-69
Identities = 93/145 (64%), Positives = 118/145 (81%)
Query: 9 EQDEKLLQPYTYISQVPGKQIRTKLAYAFNNWLNIPEEKLLAIGDIIQMLHNSSLLIDDI 68
LL+PY Y+ Q+PGKQ+RTKL+ AFN+WL +PE+KL I ++ +MLHN+SLLIDDI
Sbjct: 8 TVQRILLEPYKYLLQLPGKQVRTKLSQAFNHWLKVPEDKLQIIIEVTEMLHNASLLIDDI 67
Query: 69 EDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGHPEATAVYTEQLLELHRGQ 128
EDNS LRRG PVAHSIYGI S IN+ANYV + LEKV +L HP+A ++T QLLELH+GQ
Sbjct: 68 EDNSKLRRGFPVAHSIYGIPSVINSANYVYFLGLEKVLTLDHPDAVKLFTRQLLELHQGQ 127
Query: 129 GMEIYWRDNYTCPSEEEYRTMTIRK 153
G++IYWRDNYTCP+EEEY+ M ++K
Sbjct: 128 GLDIYWRDNYTCPTEEEYKAMVLQK 152
Score = 136 bits (345), Expect = 4e-39
Identities = 61/85 (71%), Positives = 72/85 (84%)
Query: 158 IDDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGHPEATAVYTEQLLEL 217
IDDIEDNS LRRG PVAHSIYGI S IN+ANYV + LEKV +L HP+A ++T QLLEL
Sbjct: 64 IDDIEDNSKLRRGFPVAHSIYGIPSVINSANYVYFLGLEKVLTLDHPDAVKLFTRQLLEL 123
Query: 218 HRGQGMEIYWRDNYTCPSEEEYRTM 242
H+GQG++IYWRDNYTCP+EEEY+ M
Sbjct: 124 HQGQGLDIYWRDNYTCPTEEEYKAM 148
>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 = 199 bits (509), Expect = 3e-63
Identities = 63/153 (41%), Positives = 93/153 (60%), Gaps = 7/153 (4%)
Query: 8 PEQDEKLLQPYTYISQVPGKQIRTKLAYAFNNWLNIPEEKLLAIGDIIQMLHNSSLLIDD 67
+ + + +PY +I PGK R L N +N+P+++L + I+++LHNSSLLIDD
Sbjct: 22 SQNESLISKPYNHILLKPGKNFRLNLIVQINRVMNLPKDQLAIVSQIVELLHNSSLLIDD 81
Query: 68 IEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGHPE-----ATAVYTEQLL 122
IEDN+ LRRG +H I+G+ STIN ANY+ A++ V L E ++ E+L+
Sbjct: 82 IEDNAPLRRGQTTSHLIFGVPSTINTANYMYFRAMQLVSQLTTKEPLYHNLITIFNEELI 141
Query: 123 ELHRGQGMEIYWRDNY--TCPSEEEYRTMTIRK 153
LHRGQG++IYWRD P++E Y M + K
Sbjct: 142 NLHRGQGLDIYWRDFLPEIIPTQEMYLNMVMNK 174
Score = 125 bits (316), Expect = 1e-34
Identities = 42/92 (45%), Positives = 57/92 (61%), Gaps = 7/92 (7%)
Query: 158 IDDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGHPE-----ATAVYTE 212
IDDIEDN+ LRRG +H I+G+ STIN ANY+ A++ V L E ++ E
Sbjct: 79 IDDIEDNAPLRRGQTTSHLIFGVPSTINTANYMYFRAMQLVSQLTTKEPLYHNLITIFNE 138
Query: 213 QLLELHRGQGMEIYWRDNY--TCPSEEEYRTM 242
+L+ LHRGQG++IYWRD P++E Y M
Sbjct: 139 ELINLHRGQGLDIYWRDFLPEIIPTQEMYLNM 170
>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 = 146 bits (370), Expect = 3e-42
Identities = 35/165 (21%), Positives = 67/165 (40%), Gaps = 18/165 (10%)
Query: 7 DPEQDEKLLQPYTYISQV------PGKQIRTKL----AYAFNNWLNIPEEKLLAIGDIIQ 56
P DE Y GK IR K+ + + + NI + + +G +++
Sbjct: 46 LPLNDEIRKPVIEYYLNCIDYNVKKGKHIRGKILVLISSLSSAYSNIKRDSIYLLGWVVE 105
Query: 57 MLHNSSLLIDDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGHP----- 111
+ L+ DDI D+ RRG P + ++G ++ IN ++ ++L + L
Sbjct: 106 AIQALILIADDIMDSGKFRRGAPCWYIVHGQSNAINDIFFLKMLSLSLIFELSSVFGNDI 165
Query: 112 --EATAVYTEQLLELHRGQGMEIYWRD-NYTCPSEEEYRTMTIRK 153
+ +Y E + GQ +++ + D + E Y +M K
Sbjct: 166 VMKIQKIYNESIFFTVLGQHLDLSYFDLSKADKISERYFSMVEMK 210
Score = 99.1 bits (247), Expect = 2e-24
Identities = 21/93 (22%), Positives = 41/93 (44%), Gaps = 8/93 (8%)
Query: 158 IDDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGHP-------EATAVY 210
DDI D+ RRG P + ++G ++ IN ++ ++L + L + +Y
Sbjct: 114 ADDIMDSGKFRRGAPCWYIVHGQSNAINDIFFLKMLSLSLIFELSSVFGNDIVMKIQKIY 173
Query: 211 TEQLLELHRGQGMEIYWRD-NYTCPSEEEYRTM 242
E + GQ +++ + D + E Y +M
Sbjct: 174 NESIFFTVLGQHLDLSYFDLSKADKISERYFSM 206
>1wmw_A Geranylgeranyl diphosphate synthetase; GGPP, prenyl diphosphate
synthase, structural genom riken structural
genomics/proteomics initiative; 1.55A {Thermus
thermophilus}
Length = 330
Score = 79.7 bits (197), Expect = 1e-17
Identities = 35/152 (23%), Positives = 54/152 (35%), Gaps = 6/152 (3%)
Query: 8 PEQDEKLLQPYTYISQVPGKQIRTKLAYAFNNWLNIPEEKLLAIGDIIQMLHNSSLLIDD 67
D + GK +R L P E L +++ N L+ DD
Sbjct: 21 DHPDPLYRDLLQDYPRRGGKMLRGLLTVYSALAHGAPLEAGLEAATALELFQNWVLVHDD 80
Query: 68 IEDNSILRRGIPVAHSIYGIASTINAANYVVAIALE-----KVQSLGHPEATAVYTEQLL 122
IED S RRG P H ++ + +NA + + A + L PE + E +
Sbjct: 81 IEDGSEERRGRPALHRLHPMPLALNAGDAMHAEMWGLLAEGLARGLFPPEVLLEFHEVVR 140
Query: 123 ELHRGQGMEIYW-RDNYTCPSEEEYRTMTIRK 153
GQ +++ W E+Y M K
Sbjct: 141 RTAYGQHLDLLWTLGGTFDLRPEDYFRMVAHK 172
Score = 58.9 bits (143), Expect = 2e-10
Identities = 24/90 (26%), Positives = 37/90 (41%), Gaps = 6/90 (6%)
Query: 159 DDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALE-----KVQSLGHPEATAVYTEQ 213
DDIED S RRG P H ++ + +NA + + A + L PE + E
Sbjct: 79 DDIEDGSEERRGRPALHRLHPMPLALNAGDAMHAEMWGLLAEGLARGLFPPEVLLEFHEV 138
Query: 214 LLELHRGQGMEIYW-RDNYTCPSEEEYRTM 242
+ GQ +++ W E+Y M
Sbjct: 139 VRRTAYGQHLDLLWTLGGTFDLRPEDYFRM 168
>4dhd_A Polyprenyl synthetase; isoprenoid synthesis, isoprenoid diphosphate
synthase, trans; 1.65A {Pyrobaculum calidifontis}
Length = 358
Score = 70.5 bits (173), Expect = 2e-14
Identities = 34/164 (20%), Positives = 59/164 (35%), Gaps = 12/164 (7%)
Query: 2 LSKSGDPEQDEKLLQPYTYISQVPGKQIRTKLAYAFNNWLNIPEEKLLAIGDIIQMLHNS 61
L + E + Y + GK++R L A ++ L I++++HN
Sbjct: 21 LVRYLSIGLAEDFREAVLYQVKTGGKRLRPLLTLAAAEAVSGQWRPALPAAAIVELIHNY 80
Query: 62 SLLIDDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGHP--------EA 113
SL+ DDI D +RRG+P +G + I + E V P E
Sbjct: 81 SLIYDDIIDRGDVRRGLPTVRKAFGDNAAILVGIWYREAIEEAVLDTPKPTLFAKEVAEV 140
Query: 114 TAVYTE----QLLELHRGQGMEIYWRDNYTCPSEEEYRTMTIRK 153
E +L G+ + + + + ++Y M K
Sbjct: 141 IKAIDEGERLDILFEAAGRSDPYFVQARWREVTLDDYIKMVSLK 184
Score = 50.4 bits (121), Expect = 1e-07
Identities = 19/96 (19%), Positives = 32/96 (33%), Gaps = 12/96 (12%)
Query: 159 DDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGHP--------EATAVY 210
DDI D +RRG+P +G + I + E V P E
Sbjct: 85 DDIIDRGDVRRGLPTVRKAFGDNAAILVGIWYREAIEEAVLDTPKPTLFAKEVAEVIKAI 144
Query: 211 TE----QLLELHRGQGMEIYWRDNYTCPSEEEYRTM 242
E +L G+ + + + + ++Y M
Sbjct: 145 DEGERLDILFEAAGRSDPYFVQARWREVTLDDYIKM 180
>3nf2_A Putative polyprenyl synthetase; isoprenyl diphosphate synthase,
structural genomics, PSI, PR structure initiative,
nysgrc; 2.20A {Streptomyces coelicolor}
Length = 352
Score = 70.1 bits (172), Expect = 3e-14
Identities = 34/141 (24%), Positives = 53/141 (37%), Gaps = 4/141 (2%)
Query: 16 QPYTYISQVPGKQIRTKLAYAFNNWLNIPEEKLLAIGDIIQMLHNSSLLIDDIEDNSILR 75
GK +R LA E + ++++HN SLL DD+ D R
Sbjct: 44 AQGNPADGDGGKAVRPALAVLSAEVTGAAPEVGVPGAVAVELVHNFSLLHDDLMDGDEQR 103
Query: 76 RGIPVAHSIYGIASTINAANYVVAIA---LEKVQSLGHPEATAVYTEQLLELHRGQGMEI 132
R ++G A I + + A+A L ++ ++ AT T+ L GQ +I
Sbjct: 104 RHRDTVWKVHGPAQAILVGDALFALANEVLLELGTVEAGRATRRLTKASRSLIDGQAQDI 163
Query: 133 YWRDNYTCPSEEEYRTMTIRK 153
+ S EE M K
Sbjct: 164 SYEHRDR-VSVEECLEMEGNK 183
Score = 51.2 bits (123), Expect = 9e-08
Identities = 22/87 (25%), Positives = 35/87 (40%), Gaps = 4/87 (4%)
Query: 159 DDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIA---LEKVQSLGHPEATAVYTEQLL 215
DD+ D RR ++G A I + + A+A L ++ ++ AT T+
Sbjct: 94 DDLMDGDEQRRHRDTVWKVHGPAQAILVGDALFALANEVLLELGTVEAGRATRRLTKASR 153
Query: 216 ELHRGQGMEIYWRDNYTCPSEEEYRTM 242
L GQ +I + S EE M
Sbjct: 154 SLIDGQAQDISYEHRDR-VSVEECLEM 179
>2azj_A Geranylgeranyl pyrophosphate synthetase; hexpps,
trans-prenyltransferase; 2.40A {Sulfolobus solfataricus}
PDB: 2azk_A
Length = 289
Score = 64.6 bits (158), Expect = 2e-12
Identities = 31/113 (27%), Positives = 48/113 (42%)
Query: 26 GKQIRTKLAYAFNNWLNIPEEKLLAIGDIIQMLHNSSLLIDDIEDNSILRRGIPVAHSIY 85
GK+ R L F L + I++LH++SL + DI D RRG A +Y
Sbjct: 49 GKRFRGTLNMFFTVALGGDIKDSYGGALAIEILHSASLALCDIVDLDATRRGDKAAWVVY 108
Query: 86 GIASTINAANYVVAIALEKVQSLGHPEATAVYTEQLLELHRGQGMEIYWRDNY 138
G I NY++ AL +Q+ +A E + G ++Y +Y
Sbjct: 109 GNRKVIFITNYLIPTALRIIQTSYGDDALNTSIELWKDTSVGALRDMYDNSDY 161
Score = 44.6 bits (106), Expect = 9e-06
Identities = 20/73 (27%), Positives = 30/73 (41%)
Query: 159 DDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGHPEATAVYTEQLLELH 218
DI D RRG A +YG I NY++ AL +Q+ +A E +
Sbjct: 89 CDIVDLDATRRGDKAAWVVYGNRKVIFITNYLIPTALRIIQTSYGDDALNTSIELWKDTS 148
Query: 219 RGQGMEIYWRDNY 231
G ++Y +Y
Sbjct: 149 VGALRDMYDNSDY 161
>1wy0_A Geranylgeranyl pyrophosphate synthetase; pyrococcus horikosh
structural genomics, riken structural
genomics/proteomics initiative, RSGI; 2.20A {Pyrococcus
horikoshii}
Length = 342
Score = 64.6 bits (158), Expect = 2e-12
Identities = 35/157 (22%), Positives = 62/157 (39%), Gaps = 6/157 (3%)
Query: 2 LSKSGDPEQDEKLLQPYTYISQVPGKQIRTKLAYAFNNWLNIPEEKLLAIGDIIQMLHNS 61
+ + + L + + GK++R + + + + I+++HN
Sbjct: 22 IFELIPEKDPRVLYEAARHYPLAGGKRVRPFVVLTSTEAVGGDPLRAIYPAVAIELIHNY 81
Query: 62 SLLIDDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALE-----KVQSLGHPEATAV 116
SL+ DDI D RRG P H I+G+ I A + + + A E ++ V
Sbjct: 82 SLVHDDIMDMDETRRGKPTVHRIWGVNMAILAGDLLFSKAFEAVARAEIPPEKKARVLEV 141
Query: 117 YTEQLLELHRGQGMEIYWRDNYTCPSEEEYRTMTIRK 153
+ EL GQ ++ + T + EEY M K
Sbjct: 142 IVKASNELCEGQARDLEFEKKST-VTIEEYMEMISGK 177
Score = 45.0 bits (107), Expect = 1e-05
Identities = 25/89 (28%), Positives = 37/89 (41%), Gaps = 6/89 (6%)
Query: 159 DDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALE-----KVQSLGHPEATAVYTEQ 213
DDI D RRG P H I+G+ I A + + + A E ++ V +
Sbjct: 86 DDIMDMDETRRGKPTVHRIWGVNMAILAGDLLFSKAFEAVARAEIPPEKKARVLEVIVKA 145
Query: 214 LLELHRGQGMEIYWRDNYTCPSEEEYRTM 242
EL GQ ++ + T + EEY M
Sbjct: 146 SNELCEGQARDLEFEKKST-VTIEEYMEM 173
>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 = 64.2 bits (156), Expect = 4e-12
Identities = 24/172 (13%), Positives = 53/172 (30%), Gaps = 13/172 (7%)
Query: 8 PEQDEKLLQPYTYISQVPGKQIRTKL------AYAFNNWLNIPEEKLLAIGDIIQMLHNS 61
E K + + + GK R L + + EK + I++L +
Sbjct: 61 KEHISKYYKLLFDYNCLGGKNNRGILVILIYEYVKNRDINSSEWEKAACLAWCIEILQAA 120
Query: 62 SLLIDDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGHPEATAVYTEQL 121
L+ DDI D +RR + + + + + ++ + + Y + +
Sbjct: 121 FLVADDIMDKGEMRRNKYCWYLLKDVETKNAVNDVLLLYNSIYKLIEIYLRNESCYVDVI 180
Query: 122 LELHR-------GQGMEIYWRDNYTCPSEEEYRTMTIRKFDMRIDDIEDNSI 166
GQ ++ + + E I + + DI +
Sbjct: 181 ATFRDATLKTIIGQHLDTNIFSDKYSDAHREIDVNNINVPEQPVIDINMINF 232
Score = 40.3 bits (94), Expect = 3e-04
Identities = 6/28 (21%), Positives = 11/28 (39%)
Query: 159 DDIEDNSILRRGIPVAHSIYGIASTINA 186
DDI D +RR + + + +
Sbjct: 125 DDIMDKGEMRRNKYCWYLLKDVETKNAV 152
>4fp4_A Polyprenyl synthetase; isoprenoid synthesis, isoprenoid diphosphate
synthase, trans; HET: GER UNL; 2.00A {Pyrobaculum
calidifontis}
Length = 285
Score = 62.0 bits (151), Expect = 1e-11
Identities = 36/155 (23%), Positives = 68/155 (43%), Gaps = 14/155 (9%)
Query: 2 LSKSGDPEQDEKLLQPYTYISQVPGKQIR---TKLAYAFNNWLNIPEEKLLAIGDIIQML 58
L+K G+ + L + + + PGK +R + +I + ++L I+++L
Sbjct: 21 LNKVGEELEPISLRKAVRHYIETPGKLLRPLLLLTFTYSIDRRSIMDPRILEAAAIVELL 80
Query: 59 HNSSLLIDDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGHPEATAVYT 118
H SLL DD+ D RRGI ++YG I A+++++A +++ +LG +
Sbjct: 81 HVVSLLQDDVMDQHDQRRGIKTPRAMYGDGRAIVASDWLIAESIKMAVNLG-ADVVTYLA 139
Query: 119 EQLLELHRGQGMEIYWRDNYTCPSEEEYRTMTIRK 153
+ L GQ +++ E E K
Sbjct: 140 DVAQRLSVGQALDL----------EGERDKAAEFK 164
Score = 40.8 bits (96), Expect = 2e-04
Identities = 17/67 (25%), Positives = 34/67 (50%), Gaps = 1/67 (1%)
Query: 159 DDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGHPEATAVYTEQLLELH 218
DD+ D RRGI ++YG I A+++++A +++ +LG + + L
Sbjct: 88 DDVMDQHDQRRGIKTPRAMYGDGRAIVASDWLIAESIKMAVNLG-ADVVTYLADVAQRLS 146
Query: 219 RGQGMEI 225
GQ +++
Sbjct: 147 VGQALDL 153
>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 = 62.5 bits (152), Expect = 1e-11
Identities = 31/163 (19%), Positives = 61/163 (37%), Gaps = 18/163 (11%)
Query: 8 PEQDEKLLQPYTYISQVPGKQIRTKLAYAFNNWLNIPE-------EKLLAIGDIIQMLHN 60
+ +L + Y + GK R L P ++ +G +++L
Sbjct: 60 GDAIARLKEVLEYNAI-GGKYNRGLTVVVAFRELVEPRKQDADSLQRAWTVGWCVELLQA 118
Query: 61 SSLLIDDIEDNSILRRGIPVAHSIYGIAST-INAANYVVAIALE--KVQSLGHP---EAT 114
L+ DDI D+S+ RRG + G+ IN AN + A K+ P
Sbjct: 119 FFLVADDIMDSSLTRRGQICWYQKPGVGLDAINDANLLEACIYRLLKLYCREQPYYLNLI 178
Query: 115 AVYTEQLLELHRGQGMEIYW----RDNYTCPSEEEYRTMTIRK 153
++ + + GQ +++ + +E+ Y+++ K
Sbjct: 179 ELFLQSSYQTEIGQTLDLLTAPQGNVDLVRFTEKRYKSIVKYK 221
Score = 45.6 bits (108), Expect = 7e-06
Identities = 20/94 (21%), Positives = 39/94 (41%), Gaps = 10/94 (10%)
Query: 159 DDIEDNSILRRGIPVAHSIYGIAST-INAANYVVAIALE--KVQSLGHP---EATAVYTE 212
DDI D+S+ RRG + G+ IN AN + A K+ P ++ +
Sbjct: 124 DDIMDSSLTRRGQICWYQKPGVGLDAINDANLLEACIYRLLKLYCREQPYYLNLIELFLQ 183
Query: 213 QLLELHRGQGMEIYW----RDNYTCPSEEEYRTM 242
+ GQ +++ + +E+ Y+++
Sbjct: 184 SSYQTEIGQTLDLLTAPQGNVDLVRFTEKRYKSI 217
>3lk5_A Geranylgeranyl pyrophosphate synthase; structural genomics, protein
structure initiative, geranylge pyrophosphate synthase;
1.90A {Corynebacterium glutamicum} PDB: 3qqv_A*
Length = 380
Score = 62.1 bits (151), Expect = 2e-11
Identities = 33/167 (19%), Positives = 60/167 (35%), Gaps = 28/167 (16%)
Query: 14 LLQPYTYISQVPGKQIRTKLAYA------FNNWLNIPEEKLLAIGDIIQMLHNSSLLIDD 67
+ GK+IR A+A + + E +L ++ + +L+ DD
Sbjct: 50 AVAHLRSFVLNGGKRIRPLYAWAGFLAAQGHKNSSEKLESVLDAAASLEFIQACALIHDD 109
Query: 68 IEDNSILRRGIPVAHSI----------------YGIASTINAANYVVAIALEKVQSLGHP 111
I D+S RRG P H +G++ +I A + + A + +Q G
Sbjct: 110 IIDSSDTRRGAPTVHRAVEADHRANNFEGDPEHFGVSVSILAGDMALVWAEDMLQDSGLS 169
Query: 112 -----EATAVYTEQLLELHRGQGMEIYWRDNYTCPSEEEYRTMTIRK 153
+ E+ GQ ++IY + S E ++ K
Sbjct: 170 AEALARTRDAWRGMRTEVIGGQLLDIYLESHAN-ESVELADSVNRFK 215
Score = 43.6 bits (103), Expect = 2e-05
Identities = 23/105 (21%), Positives = 39/105 (37%), Gaps = 22/105 (20%)
Query: 159 DDIEDNSILRRGIPVAHSI----------------YGIASTINAANYVVAIALEKVQSLG 202
DDI D+S RRG P H +G++ +I A + + A + +Q G
Sbjct: 108 DDIIDSSDTRRGAPTVHRAVEADHRANNFEGDPEHFGVSVSILAGDMALVWAEDMLQDSG 167
Query: 203 HP-----EATAVYTEQLLELHRGQGMEIYWRDNYTCPSEEEYRTM 242
+ E+ GQ ++IY + S E ++
Sbjct: 168 LSAEALARTRDAWRGMRTEVIGGQLLDIYLESHAN-ESVELADSV 211
>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 = 59.8 bits (145), Expect = 1e-10
Identities = 33/163 (20%), Positives = 64/163 (39%), Gaps = 18/163 (11%)
Query: 8 PEQDEKLLQPYTYISQVPGKQIR---TKLAY-AFNNWLNIPEEKL---LAIGDIIQMLHN 60
+ +L + Y + GK R AY + E L LA+G I++
Sbjct: 53 GDAVARLKEVLQYNAP-GGKCNRGLTVVAAYRELSGPGQKDAESLRCALAVGWCIELFQA 111
Query: 61 SSLLIDDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALE---KVQSLGHP---EAT 114
+SL+ DDI D S+ RRG + G+ ++++ ++ K P
Sbjct: 112 ASLVADDIMDQSLTRRGQLCWYKKEGVGLDAINDSFLLESSVYRVLKKYCRQRPYYVHLL 171
Query: 115 AVYTEQLLELHRGQGMEIYW----RDNYTCPSEEEYRTMTIRK 153
++ + + GQ +++ + + + SEE Y+ + K
Sbjct: 172 ELFLQTAYQTELGQMLDLITAPVSKVDLSHFSEERYKAIVKYK 214
Score = 41.7 bits (98), Expect = 1e-04
Identities = 17/94 (18%), Positives = 38/94 (40%), Gaps = 10/94 (10%)
Query: 159 DDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALE---KVQSLGHP---EATAVYTE 212
DDI D S+ RRG + G+ ++++ ++ K P ++ +
Sbjct: 117 DDIMDQSLTRRGQLCWYKKEGVGLDAINDSFLLESSVYRVLKKYCRQRPYYVHLLELFLQ 176
Query: 213 QLLELHRGQGMEIYW----RDNYTCPSEEEYRTM 242
+ GQ +++ + + + SEE Y+ +
Sbjct: 177 TAYQTELGQMLDLITAPVSKVDLSHFSEERYKAI 210
>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 = 58.7 bits (141), Expect = 2e-10
Identities = 37/150 (24%), Positives = 66/150 (44%), Gaps = 2/150 (1%)
Query: 2 LSKSGDPEQDEKLLQPYTYISQVPGKQIRTKLAYAFNNWLNIPEEKLLAIGDIIQMLHNS 61
+ + P D + Y + V G +IR L L + EE LL + +++ H +
Sbjct: 22 IREILRPGWDLLTEEAMLYSATVGGXRIRPLLVLTLGEDLGVEEEXLLDVAVAVELFHTA 81
Query: 62 SLLIDDIE--DNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGHPEATAVYTE 119
SL+ DD+ DN+ RRG P H YG + A + + +A ++ +G+ ++E
Sbjct: 82 SLIHDDLPPIDNADFRRGXPSCHRTYGEDIALLAGDGLFFLAFSQISXIGNSXIFEEFSE 141
Query: 120 QLLELHRGQGMEIYWRDNYTCPSEEEYRTM 149
L G+ M++ + S+E M
Sbjct: 142 TAYXLLLGEAMDVEFERRXMEVSQEMVERM 171
Score = 36.3 bits (83), Expect = 0.005
Identities = 19/80 (23%), Positives = 35/80 (43%)
Query: 163 DNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGHPEATAVYTEQLLELHRGQG 222
DN+ RRG P H YG + A + + +A ++ +G+ ++E L G+
Sbjct: 92 DNADFRRGXPSCHRTYGEDIALLAGDGLFFLAFSQISXIGNSXIFEEFSETAYXLLLGEA 151
Query: 223 MEIYWRDNYTCPSEEEYRTM 242
M++ + S+E M
Sbjct: 152 MDVEFERRXMEVSQEMVERM 171
>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 = 58.9 bits (143), Expect = 2e-10
Identities = 35/153 (22%), Positives = 64/153 (41%), Gaps = 18/153 (11%)
Query: 18 YTYISQVPGKQIRTKLAYAFNNWLNIPEEKLLAIGD-----------------IIQMLHN 60
Y + V GKQ R+ + L++ + L I +M+H
Sbjct: 42 YFFKRGVQGKQFRSTILLLMATALDVRVPEALIGESTDIVTSELRVRQRGIAEITEMIHV 101
Query: 61 SSLLIDDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGHPEATAVYTEQ 120
+SLL DD+ D++ RRG+ + + G ++ A +++++ A + +L + E A+
Sbjct: 102 ASLLHDDVLDDADTRRGVGSLNVVMGNKMSVLAGDFLLSRACGALAALKNTEVVALLATA 161
Query: 121 LLELHRGQGMEIYWRDNYTCPSEEEYRTMTIRK 153
+ L G+ MEI S + Y T K
Sbjct: 162 VEHLVTGETMEITSSTEQRY-SMDYYMQKTYYK 193
Score = 43.1 bits (102), Expect = 4e-05
Identities = 19/81 (23%), Positives = 39/81 (48%), Gaps = 1/81 (1%)
Query: 159 DDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGHPEATAVYTEQLLELH 218
DD+ D++ RRG+ + + G ++ A +++++ A + +L + E A+ + L
Sbjct: 107 DDVLDDADTRRGVGSLNVVMGNKMSVLAGDFLLSRACGALAALKNTEVVALLATAVEHLV 166
Query: 219 RGQGMEIYWRDNYTCPSEEEY 239
G+ MEI S + Y
Sbjct: 167 TGETMEITSSTEQRY-SMDYY 186
>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 = 58.7 bits (142), Expect = 2e-10
Identities = 19/144 (13%), Positives = 38/144 (26%), Gaps = 7/144 (4%)
Query: 24 VPGKQIRTKLAYAFNNWLNIPEEKLLAIGDIIQMLHNSSLLIDDIEDNSILRRGIPVAHS 83
+ G +I+ L L+ DDI DNS+ RRG P +
Sbjct: 84 LLSLSPNNNGEEDDGARRKRVLHDACVCGWMIEFLQAHYLVEDDIMDNSVTRRGKPCWYR 143
Query: 84 IYGI--ASTINAANYVVAIALEKVQSLGHP-----EATAVYTEQLLELHRGQGMEIYWRD 136
+ IN + + + + GQ ++
Sbjct: 144 HPDVTVQCAINDGLLLKSWTHMMAMHFFADRPFLQDLLCRFNRVDYTTAVGQLYDVTSMF 203
Query: 137 NYTCPSEEEYRTMTIRKFDMRIDD 160
+ + + T + + +
Sbjct: 204 DSNKLDPDVSQPTTTDFAEFTLSN 227
Score = 43.3 bits (102), Expect = 4e-05
Identities = 14/76 (18%), Positives = 23/76 (30%), Gaps = 7/76 (9%)
Query: 159 DDIEDNSILRRGIPVAHSIYGI--ASTINAANYVVAIALEKVQSLGHP-----EATAVYT 211
DDI DNS+ RRG P + + IN + + + +
Sbjct: 126 DDIMDNSVTRRGKPCWYRHPDVTVQCAINDGLLLKSWTHMMAMHFFADRPFLQDLLCRFN 185
Query: 212 EQLLELHRGQGMEIYW 227
GQ ++
Sbjct: 186 RVDYTTAVGQLYDVTS 201
>3ipi_A Geranyltranstransferase; isoprene biosynthesis, helical bundle,
protein structure initiative II (PSI II), structural
genomics, nysgxrc; 1.90A {Methanosarcina mazei}
Length = 295
Score = 58.0 bits (141), Expect = 3e-10
Identities = 25/134 (18%), Positives = 63/134 (47%), Gaps = 3/134 (2%)
Query: 20 YISQVPGKQIRTKLAYAFNNWLNIPEEKLLAIGDIIQMLHNSSLLIDDIEDNSILRRGIP 79
++ GK+IR + + + + L ++M+H++SL+ DD+ D ++RR +P
Sbjct: 36 HVCHSGGKRIRPIILLLVSEICSGSYSRSLNAALAVEMMHSASLIHDDLLDQGLVRRNLP 95
Query: 80 VAHSIYGIASTINAANYVVAIALEKVQSLGHPEATAVYTEQLLELHRGQGMEIYWRDNYT 139
A +G + + +Y++A ++ + G + + + +++ G+ +++ D
Sbjct: 96 SAPEKFGPSGALLCGDYLIAKSIAFISPYG-EKVIQDFGKAGMDMAEGEVLDLKLEDESF 154
Query: 140 CPSEEEYRTMTIRK 153
E +Y +K
Sbjct: 155 --GENDYFKCIYKK 166
Score = 41.8 bits (99), Expect = 1e-04
Identities = 15/81 (18%), Positives = 39/81 (48%), Gaps = 3/81 (3%)
Query: 159 DDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGHPEATAVYTEQLLELH 218
DD+ D ++RR +P A +G + + +Y++A ++ + G + + + +++
Sbjct: 82 DDLLDQGLVRRNLPSAPEKFGPSGALLCGDYLIAKSIAFISPYG-EKVIQDFGKAGMDMA 140
Query: 219 RGQGMEIYWRDNYTCPSEEEY 239
G+ +++ D E +Y
Sbjct: 141 EGEVLDLKLEDESF--GENDY 159
>3oyr_A Trans-isoprenyl diphosphate synthase; isoprenyl synthase, PSI,
protein structure initiative; HET: IPE; 2.00A
{Caulobacter crescentus}
Length = 345
Score = 56.9 bits (138), Expect = 1e-09
Identities = 28/134 (20%), Positives = 58/134 (43%), Gaps = 1/134 (0%)
Query: 20 YISQVPGKQIRTKLAYAFNNWLNIPEEKLLAIGDIIQMLHNSSLLIDDIEDNSILRRGIP 79
++ GK++R + A + + ++ +H ++LL DD+ D S LRRG
Sbjct: 59 HLIAAGGKRLRPLMTVAAARLAGADNDHFQKLAAAVEFIHTATLLHDDVVDGSQLRRGKV 118
Query: 80 VAHSIYGIASTINAANYVVAIALEKVQSLGHPEATAVYTEQLLELHRGQGMEIYWRDNYT 139
AH I+G A ++ +++ A A E + +A + + G+ +++ +
Sbjct: 119 AAHLIWGGAQSVLVGDFLFARAFELMVETNSMKALEILARASRVIAEGEVLQLMRSHD-L 177
Query: 140 CPSEEEYRTMTIRK 153
S+ Y + K
Sbjct: 178 NLSQAVYLEIIQAK 191
Score = 36.5 bits (85), Expect = 0.005
Identities = 20/81 (24%), Positives = 37/81 (45%), Gaps = 1/81 (1%)
Query: 159 DDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGHPEATAVYTEQLLELH 218
DD+ D S LRRG AH I+G A ++ +++ A A E + +A + +
Sbjct: 105 DDVVDGSQLRRGKVAAHLIWGGAQSVLVGDFLFARAFELMVETNSMKALEILARASRVIA 164
Query: 219 RGQGMEIYWRDNYTCPSEEEY 239
G+ +++ + S+ Y
Sbjct: 165 EGEVLQLMRSHD-LNLSQAVY 184
>3aqb_B Component B of hexaprenyl diphosphate synthase; prenyltransferase,
transferase; 2.40A {Micrococcus luteus} PDB: 3aqc_B*
Length = 325
Score = 56.5 bits (137), Expect = 1e-09
Identities = 31/134 (23%), Positives = 66/134 (49%), Gaps = 1/134 (0%)
Query: 20 YISQVPGKQIRTKLAYAFNNWLNIPEEKLLAIGDIIQMLHNSSLLIDDIEDNSILRRGIP 79
+I GK++R + ++ L+ ++++H +SL+ DD DNS +RRG
Sbjct: 38 HILSSGGKRVRPMFVLLSGFLNDTQKDDLIRTAVSLELVHMASLVHDDYIDNSDMRRGNT 97
Query: 80 VAHSIYGIASTINAANYVVAIALEKVQSLGHPEATAVYTEQLLELHRGQGMEIYWRDNYT 139
H + + I ++++A AL+ + ++ + + ++++ +LE+ G+ ++ R NY
Sbjct: 98 SVHIAFDKDTAIRTGHFLLARALQNIATINNSKFHQIFSKTILEVCFGEFDQMADRFNYP 157
Query: 140 CPSEEEYRTMTIRK 153
S Y RK
Sbjct: 158 -VSFTAYLRRINRK 170
Score = 37.2 bits (87), Expect = 0.003
Identities = 21/81 (25%), Positives = 43/81 (53%), Gaps = 1/81 (1%)
Query: 159 DDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGHPEATAVYTEQLLELH 218
DD DNS +RRG H + + I ++++A AL+ + ++ + + ++++ +LE+
Sbjct: 84 DDYIDNSDMRRGNTSVHIAFDKDTAIRTGHFLLARALQNIATINNSKFHQIFSKTILEVC 143
Query: 219 RGQGMEIYWRDNYTCPSEEEY 239
G+ ++ R NY S Y
Sbjct: 144 FGEFDQMADRFNYP-VSFTAY 163
>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 = 55.6 bits (134), Expect = 3e-09
Identities = 27/186 (14%), Positives = 52/186 (27%), Gaps = 33/186 (17%)
Query: 1 MLSKSGDPEQDEKLLQPYTYISQVPGKQIRTKLAY-AFNNWLNIPEEKLLAIGDIIQ--- 56
+ SK + L+ + + GK R +L + + I+
Sbjct: 22 LQSKYEIDPNRARYLRIMMDTTCLGGKYFRGMTVVNVAEGFLAVTQHDEATKERILHDAC 81
Query: 57 -------MLHNSSLLIDDIEDNSILRRGIPVAHSIYGIAST--INAANYVVAIALEKVQS 107
L L+ DDI D S++RRG P + G+ + IN + +
Sbjct: 82 VGGWMIEFLQAHYLVEDDIMDGSVMRRGKPCWYRFPGVTTQCAINDGIILKSWTQIMAWH 141
Query: 108 LGHPEA-----------TAVYTE--QLLELH---RGQGMEIYWRDNYTCP----SEEEYR 147
T Q+ ++ ++ T + Y+
Sbjct: 142 YFADRPFLKDLLCLFQKVDYATAVGQMYDVTSMCDSNKLDPEVAQPMTTDFAEFTPAIYK 201
Query: 148 TMTIRK 153
+ K
Sbjct: 202 RIVKYK 207
Score = 39.8 bits (93), Expect = 5e-04
Identities = 14/76 (18%), Positives = 27/76 (35%), Gaps = 7/76 (9%)
Query: 159 DDIEDNSILRRGIPVAHSIYGIAST--INAANYVVAIALEKVQSLGHP-----EATAVYT 211
DDI D S++RRG P + G+ + IN + + + ++
Sbjct: 98 DDIMDGSVMRRGKPCWYRFPGVTTQCAINDGIILKSWTQIMAWHYFADRPFLKDLLCLFQ 157
Query: 212 EQLLELHRGQGMEIYW 227
+ GQ ++
Sbjct: 158 KVDYATAVGQMYDVTS 173
>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 = 55.0 bits (133), Expect = 4e-09
Identities = 27/128 (21%), Positives = 55/128 (42%), Gaps = 12/128 (9%)
Query: 20 YISQVPGKQIRTKLAYAFNNWLNIPE-EKLLAIGDIIQMLHNSSLLIDDIEDNSILRRGI 78
+ GK +R +L+ + E ++ ++++H +SLL DD+ D + RRG
Sbjct: 34 KDLPLYGKMLRVRLSILSFKNRGVEIGEDAISSLAALELVHLASLLHDDVIDGARFRRGK 93
Query: 79 PVAHSIYGIASTINAANYVVAIALEKVQSLGHPE-------ATAVYTE----QLLELHRG 127
+ +YG + + A + V+ A V+ +G+ + +E + L ++
Sbjct: 94 ETINFMYGDKAAVAAGDLVLVSAFHTVEEIGNNKLRRAFLNVIGKMSEAELIEQLSRYKP 153
Query: 128 QGMEIYWR 135
E Y R
Sbjct: 154 ITKEEYLR 161
Score = 39.5 bits (93), Expect = 5e-04
Identities = 18/81 (22%), Positives = 34/81 (41%), Gaps = 11/81 (13%)
Query: 159 DDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGHPE-------ATAVYT 211
DD+ D + RRG + +YG + + A + V+ A V+ +G+ + +
Sbjct: 81 DDVIDGARFRRGKETINFMYGDKAAVAAGDLVLVSAFHTVEEIGNNKLRRAFLNVIGKMS 140
Query: 212 E----QLLELHRGQGMEIYWR 228
E + L ++ E Y R
Sbjct: 141 EAELIEQLSRYKPITKEEYLR 161
>3mzv_A Decaprenyl diphosphate synthase; transferase, structural genomics,
PSI-2, protein structure initiative; 1.90A {Rhodobacter
capsulatus}
Length = 341
Score = 54.6 bits (132), Expect = 5e-09
Identities = 31/142 (21%), Positives = 64/142 (45%), Gaps = 17/142 (11%)
Query: 20 YISQVPGKQIRTKLAYAFNNWLNIPEEKLLAIGDIIQMLHNSSLLIDDIEDNSILRRGIP 79
++ + GK++R L A + + + ++ +H ++LL DD+ D S RRG P
Sbjct: 47 HLIEAGGKRLRPMLTLAAARLVGYGGPFHVHLAATVEFIHTATLLHDDVVDESRQRRGRP 106
Query: 80 VAHSIYGIASTINAANYVVAIALEKVQSLGHPE-------ATAVYTE-QLLELHRGQGME 131
A+ ++ S++ +Y+ A + + + G+ A+AV E ++L+L Q +
Sbjct: 107 TANLLWDNKSSVLVGDYLFARSFQLMTDTGNMRVMEILANASAVIAEGEVLQLTAAQNLA 166
Query: 132 IYWRDNYTCPSEEEYRTMTIRK 153
+E+ Y + K
Sbjct: 167 T---------TEDIYLRVIRGK 179
Score = 36.5 bits (85), Expect = 0.006
Identities = 22/89 (24%), Positives = 41/89 (46%), Gaps = 17/89 (19%)
Query: 159 DDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGHPE-------ATAVYT 211
DD+ D S RRG P A+ ++ S++ +Y+ A + + + G+ A+AV
Sbjct: 93 DDVVDESRQRRGRPTANLLWDNKSSVLVGDYLFARSFQLMTDTGNMRVMEILANASAVIA 152
Query: 212 E-QLLELHRGQGMEIYWRDNYTCPSEEEY 239
E ++L+L Q + +E+ Y
Sbjct: 153 EGEVLQLTAAQNLAT---------TEDIY 172
>3rmg_A Octaprenyl-diphosphate synthase; structural genomics, protein
structure initiative, isoprene biosynthesis,
transferase; 2.30A {Bacteroides thetaiotaomicron}
Length = 334
Score = 54.6 bits (132), Expect = 6e-09
Identities = 23/94 (24%), Positives = 43/94 (45%)
Query: 20 YISQVPGKQIRTKLAYAFNNWLNIPEEKLLAIGDIIQMLHNSSLLIDDIEDNSILRRGIP 79
+I + GK +R L L +++LH +SL+ DD+ D S RRG
Sbjct: 41 HIRKRNGKMMRPILVLLVARLYGAVTPATLHAAVSLELLHTASLVHDDVVDESTERRGQL 100
Query: 80 VAHSIYGIASTINAANYVVAIALEKVQSLGHPEA 113
++I+ ++ A +Y++A +L + + E
Sbjct: 101 SVNAIFNNKVSVLAGDYLLATSLVHAEQTNNYEI 134
Score = 34.5 bits (80), Expect = 0.022
Identities = 13/48 (27%), Positives = 25/48 (52%)
Query: 159 DDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGHPEA 206
DD+ D S RRG ++I+ ++ A +Y++A +L + + E
Sbjct: 87 DDVVDESTERRGQLSVNAIFNNKVSVLAGDYLLATSLVHAEQTNNYEI 134
>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 = 54.2 bits (131), Expect = 7e-09
Identities = 27/136 (19%), Positives = 59/136 (43%), Gaps = 3/136 (2%)
Query: 20 YISQVPGKQIRTKLAYAFNNWLN-IPEEKLLAIGDIIQMLHNSSLLIDDIEDNSILRRGI 78
+ + GK +R Y F+ + N +L A I++LH +L+ DD+ D+S RRG+
Sbjct: 49 ALLKSGGKLLRPGYFYLFSTFGNAATPAQLQAGAAAIEILHVGTLIHDDVIDDSPTRRGV 108
Query: 79 PVAHSIYGIASTINAANYVVAIALEK-VQSLGHPEATAVYTEQLLELHRGQGMEIYWRDN 137
YG + I A +++ + ++ ++S + + + + +G+ ++
Sbjct: 109 RTIQMTYGQRNAIYAGDFMFTVYFDQVLKSTTDRSLIQNHIDAMHRILQGELHQMDLNYR 168
Query: 138 YTCPSEEEYRTMTIRK 153
+ + Y K
Sbjct: 169 ED-ITLDAYLNEIAGK 183
Score = 36.5 bits (85), Expect = 0.006
Identities = 14/82 (17%), Positives = 36/82 (43%), Gaps = 2/82 (2%)
Query: 159 DDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEK-VQSLGHPEATAVYTEQLLEL 217
DD+ D+S RRG+ YG + I A +++ + ++ ++S + + + +
Sbjct: 96 DDVIDDSPTRRGVRTIQMTYGQRNAIYAGDFMFTVYFDQVLKSTTDRSLIQNHIDAMHRI 155
Query: 218 HRGQGMEIYWRDNYTCPSEEEY 239
+G+ ++ + + Y
Sbjct: 156 LQGELHQMDLNYRED-ITLDAY 176
>3tc1_A Octaprenyl pyrophosphate synthase; all alpha-helices fold,
transferase; 2.00A {Helicobacter pylori}
Length = 315
Score = 54.2 bits (131), Expect = 8e-09
Identities = 18/78 (23%), Positives = 40/78 (51%)
Query: 14 LLQPYTYISQVPGKQIRTKLAYAFNNWLNIPEEKLLAIGDIIQMLHNSSLLIDDIEDNSI 73
+ + ++ I + + LA I +K L + I++M+ +SLL DD+ D +
Sbjct: 25 IDELFSKIGPSKMLRSKLMLALLNEKTDAILLDKALNLCTIVEMIQTASLLHDDVIDKAT 84
Query: 74 LRRGIPVAHSIYGIASTI 91
+RR +P ++++G + +
Sbjct: 85 MRRKLPSINALFGNFNAV 102
Score = 32.2 bits (74), Expect = 0.12
Identities = 7/26 (26%), Positives = 17/26 (65%)
Query: 159 DDIEDNSILRRGIPVAHSIYGIASTI 184
DD+ D + +RR +P ++++G + +
Sbjct: 77 DDVIDKATMRRKLPSINALFGNFNAV 102
>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 = 47.7 bits (114), Expect = 1e-06
Identities = 25/121 (20%), Positives = 55/121 (45%), Gaps = 8/121 (6%)
Query: 20 YISQVPGKQIRTKLAYAFNNWLNIPE-EKLLAIGDIIQMLHNSSLLIDDIEDNSILRRGI 78
++++ GK+ R A + + P E ++ ++++ H ++L DD+ D + +RRG+
Sbjct: 68 HLTRAGGKRFRPMFALLASEFGEKPLSENVIKAAVVVEITHLATLYHDDVMDEASMRRGV 127
Query: 79 PVAHSIYGIASTINAANYVVAIALEKVQSLGHP------EATAVYTE-QLLELHRGQGME 131
P A++ + + I A + ++A A + LG E Q+ E + +
Sbjct: 128 PSANARWDNSVAILAGDILLAHASGLMSQLGTDTVAHFAETFGELVTGQMRETVGPRDTD 187
Query: 132 I 132
Sbjct: 188 P 188
Score = 33.8 bits (78), Expect = 0.036
Identities = 17/74 (22%), Positives = 32/74 (43%), Gaps = 7/74 (9%)
Query: 159 DDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGHP------EATAVYTE 212
DD+ D + +RRG+P A++ + + I A + ++A A + LG E
Sbjct: 115 DDVMDEASMRRGVPSANARWDNSVAILAGDILLAHASGLMSQLGTDTVAHFAETFGELVT 174
Query: 213 -QLLELHRGQGMEI 225
Q+ E + +
Sbjct: 175 GQMRETVGPRDTDP 188
>2h8o_A Geranyltranstransferase; geranyltransferase,agrobacterium
tumefaciens, structural GEN PSI-2, protein structure
initiative; 1.60A {Agrobacterium tumefaciens}
Length = 335
Score = 46.1 bits (110), Expect = 4e-06
Identities = 34/134 (25%), Positives = 61/134 (45%), Gaps = 5/134 (3%)
Query: 2 LSKSGDPEQDEKLLQPYTYISQVPGKQIRTKLAYAFNNWLNIPEEKLLAIGDIIQMLHNS 61
+++ + + + LL+ + GK++R L L E L +G ++ LH
Sbjct: 61 EARADEITRPQNLLEAMRHGVLNGGKRLRPFLVIESVALLGGDAEAGLHVGAALECLHCY 120
Query: 62 SLLIDDIE--DNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGHPEATAVYTE 119
SL+ DD+ D+ LRRG P H + A+ I A + ++ +A + + S +P A
Sbjct: 121 SLVHDDLPAMDDDDLRRGQPTVHRKFDEATAILAGDSLLTLAFDIIASDDNPLAAERKAA 180
Query: 120 QLLELHR---GQGM 130
++ L R GM
Sbjct: 181 LVISLARAAGIGGM 194
>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 = 45.3 bits (108), Expect = 6e-06
Identities = 21/68 (30%), Positives = 33/68 (48%), Gaps = 2/68 (2%)
Query: 26 GKQIRTKLAYAFNNWLNIPEEKLLAIGDIIQMLHNSSLLIDDIE--DNSILRRGIPVAHS 83
GK++R LA I + + ++ LH SL+ DD+ DN LRRG+P H
Sbjct: 41 GKRLRAFLAIESAAIHGISMAQAMPAALAVEALHAYSLVHDDMPCMDNDDLRRGLPTVHK 100
Query: 84 IYGIASTI 91
+ A+ +
Sbjct: 101 KWDDATAV 108
>3p8r_A Geranyltranstransferase; isoprenyl synthase, structural genomics,
PSI, protein struct initiative, nysgrc; 2.50A {Vibrio
cholerae}
Length = 302
Score = 45.3 bits (108), Expect = 7e-06
Identities = 23/81 (28%), Positives = 34/81 (41%), Gaps = 2/81 (2%)
Query: 8 PEQDEKLLQPYTYISQVPGKQIRTKLAYAFNNWLNIPEEKLLAIGDIIQMLHNSSLLIDD 67
P Q L++ Y + GK+ R L Y L L ++ +H SL+ DD
Sbjct: 32 PFQTLPLIEAMRYGLLLGGKRARPYLVYITGQMLGCELSDLDTPASAVECIHAYSLIHDD 91
Query: 68 IE--DNSILRRGIPVAHSIYG 86
+ D+ LRRG P H +
Sbjct: 92 LPAMDDDELRRGKPTCHIQFD 112
>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 = 45.3 bits (108), Expect = 7e-06
Identities = 24/81 (29%), Positives = 42/81 (51%), Gaps = 2/81 (2%)
Query: 8 PEQDEKLLQPYTYISQVPGKQIRTKLAYAFNNWLNIPEEKLLAIGDIIQMLHNSSLLIDD 67
P Q+ +++ Y + + GK++R L YA + + L A ++ +H SL+ DD
Sbjct: 26 PFQNTPVVETMQYGALLGGKRLRPFLVYATGHMFGVSTNTLDAPAAAVECIHAYSLIHDD 85
Query: 68 IE--DNSILRRGIPVAHSIYG 86
+ D+ LRRG+P H +G
Sbjct: 86 LPAMDDDDLRRGLPTCHVKFG 106
>4f62_A Geranyltranstransferase; enzyme function initiative, structural
genomics; 2.10A {Marinomonas SP}
Length = 317
Score = 44.5 bits (106), Expect = 1e-05
Identities = 23/68 (33%), Positives = 32/68 (47%), Gaps = 2/68 (2%)
Query: 26 GKQIRTKLAYAFNNWLNIPEEKLLAIGDIIQMLHNSSLLIDDIE--DNSILRRGIPVAHS 83
GK+IR L YA + A ++ +H SL+ DD+ DN LRRG P H
Sbjct: 45 GKRIRPMLTYASAQLVGDISSLTDASAAALESIHAYSLIHDDLPAMDNDELRRGKPTCHI 104
Query: 84 IYGIASTI 91
+ A+ I
Sbjct: 105 QFDEATAI 112
>3ts7_A Geranyltranstransferase; isoprenoid synthesis, farnesyl diphosphate
synthase; 1.94A {Methylococcus capsulatus}
Length = 324
Score = 44.5 bits (106), Expect = 1e-05
Identities = 26/86 (30%), Positives = 39/86 (45%), Gaps = 2/86 (2%)
Query: 8 PEQDEKLLQPYTYISQVPGKQIRTKLAYAFNNWLNIPEEKLLAIGDIIQMLHNSSLLIDD 67
E+L Q Y GK++R L YA + + + L ++ +H SL+ DD
Sbjct: 32 DRMPERLHQAMRYSVLGGGKRMRPLLTYATGQTIGVAADLLDGPACAVEFIHVYSLIHDD 91
Query: 68 IE--DNSILRRGIPVAHSIYGIASTI 91
+ D+ LRRG P H Y A+ I
Sbjct: 92 LPAMDDDDLRRGKPTCHKAYDEATAI 117
>3uca_A Geranyltranstransferase; isoprenoid synthesis, isoprenoid
diphosphate synthase; 2.00A {Clostridium perfringens}
Length = 324
Score = 44.2 bits (105), Expect = 1e-05
Identities = 29/87 (33%), Positives = 41/87 (47%), Gaps = 2/87 (2%)
Query: 7 DPEQDEKLLQPYTYISQVPGKQIRTKLAYAFNNWLNIPEEKLLAIGDIIQMLHNSSLLID 66
D E ++ L Y V GK+IR L +K+L I+M+H SL+ D
Sbjct: 55 DREYNKVLYDSMAYSINVGGKRIRPILMLLSYYIYKSDYKKILTPAMAIEMIHTYSLIHD 114
Query: 67 DIE--DNSILRRGIPVAHSIYGIASTI 91
D+ DN LRRG P H ++G A +
Sbjct: 115 DLPCMDNDDLRRGKPTNHKVFGEAIAV 141
>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 = 43.8 bits (104), Expect = 2e-05
Identities = 9/92 (9%), Positives = 29/92 (31%), Gaps = 5/92 (5%)
Query: 2 LSKSGDPEQDEKLLQPYTYISQVPGKQIRTKLAYAFNNWLNIPEEKLLAIGDIIQMLHNS 61
L K+ E + +P +++ + + L A + +A + ++H +
Sbjct: 21 LKKAIPIRAPESVFEPMHHLTFAAPRTSASALCVAACELVGGDRSDAMAAAAAVHLMHVA 80
Query: 62 SLLIDDI--EDNSILRRGIPVAHSIYGIASTI 91
+ +++ D + +
Sbjct: 81 AYTHENLPLTDG---PMSKSEIQHKFDPNIEL 109
>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 = 44.1 bits (105), Expect = 2e-05
Identities = 23/68 (33%), Positives = 34/68 (50%), Gaps = 2/68 (2%)
Query: 26 GKQIRTKLAYAFNNWLNIPEEKLLAIGDIIQMLHNSSLLIDDIE--DNSILRRGIPVAHS 83
GK++R LAYA L E+ ++++H SL+ DD+ D+ LRRG P H
Sbjct: 44 GKRVRPLLAYAACEALGGKPEQANGAACAVELIHAYSLVHDDLPAMDDDDLRRGQPTTHK 103
Query: 84 IYGIASTI 91
+ A I
Sbjct: 104 AFDEACAI 111
>3lom_A Geranyltranstransferase; geranyltransferase, structural genomics,
PSI, protein structure initiative, nysgrc; 2.30A
{Legionella pneumophila subsp}
Length = 313
Score = 43.8 bits (104), Expect = 2e-05
Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 2/63 (3%)
Query: 26 GKQIRTKLAYAFNNWLNIPEEKLLAIGDIIQMLHNSSLLIDDIE--DNSILRRGIPVAHS 83
GK+IR L Y + +++ + L I +++ H SL+ DD+ DN LRRG P H
Sbjct: 50 GKRIRPILVYLAGDLIDVDQGVLDIIAAALELTHCYSLIHDDLPAMDNDDLRRGKPSCHK 109
Query: 84 IYG 86
+
Sbjct: 110 AFD 112
>1rtr_A Geranyltranstransferase; 2.50A {Staphylococcus aureus} SCOP:
a.128.1.1
Length = 301
Score = 43.7 bits (104), Expect = 2e-05
Identities = 25/82 (30%), Positives = 36/82 (43%), Gaps = 2/82 (2%)
Query: 7 DPEQDEKLLQPYTYISQVPGKQIRTKLAYAFNNWLNIPEEKLLAIGDIIQMLHNSSLLID 66
D +L + Y GK+IR L + LN E + ++M+H SL+ D
Sbjct: 23 KSVMDTQLEESMLYSLNAGGKRIRPVLLLLTLDSLNTEYELGMKSAIALEMIHTYSLIHD 82
Query: 67 DIE--DNSILRRGIPVAHSIYG 86
D+ DN RRG H +YG
Sbjct: 83 DLPAMDNDDYRRGKLTNHKVYG 104
>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 = 42.5 bits (99), Expect = 8e-05
Identities = 38/299 (12%), Positives = 88/299 (29%), Gaps = 76/299 (25%)
Query: 2 LSKSGDPEQDEKLLQPYTYISQVPGKQIRTKLAYAFNNWLNIP------EEKLLAIGDII 55
L PE ++LQ Y QI ++ NI + +L + +
Sbjct: 189 LKNCNSPETVLEMLQKLLY-------QIDPNWTSRSDHSSNIKLRIHSIQAELRRL--LK 239
Query: 56 QMLHNSSLLI-DDIEDNSILR------------RGIPVAHSIYGIASTINAANY------ 96
+ + LL+ ++++ R V + +T + ++
Sbjct: 240 SKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLT 299
Query: 97 ------VVAIALE-KVQSL------GHPEATAVYTEQLLELHRGQGMEIYWRDNYTCPSE 143
++ L+ + Q L +P ++ E + G W+ + C
Sbjct: 300 PDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAE---SIRDGLATWDNWK-HVNCDKL 355
Query: 144 EEYRTMTIRKFD---MRIDDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQ- 199
++ + R + S+ + + + + V + + K+
Sbjct: 356 TTIIESSLNVLEPAEYR-KMFDRLSVFPPSAHIPTILLSLIWF-DVIKSDVMVVVNKLHK 413
Query: 200 -SL--GHPEATAVY-----------TEQLLELHRG-----QGMEIYWRDNYTCPSEEEY 239
SL P+ + + E LHR + + D+ P ++Y
Sbjct: 414 YSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQY 472
Score = 40.2 bits (93), Expect = 5e-04
Identities = 39/260 (15%), Positives = 77/260 (29%), Gaps = 87/260 (33%)
Query: 13 KLLQPYTYISQVPGKQIRTKLAYAFNNWLNIPEEKLLAI----------GDIIQMLHNSS 62
+L+P Y +++ +L+ F +IP LL++ ++ LH S
Sbjct: 364 NVLEPAEY------RKMFDRLS-VFPPSAHIPT-ILLSLIWFDVIKSDVMVVVNKLHKYS 415
Query: 63 LLIDDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGHPEATAVYTEQLL 122
L+ ++++I I SIY + + LE +L H Y +
Sbjct: 416 LVEKQPKESTI---SI---PSIY----------LELKVKLENEYAL-HRSIVDHY--NIP 456
Query: 123 ELHRGQGMEIYWRDNY----------TCPSEEEYRTMTIRKFDMR--------------- 157
+ + + D Y E + D R
Sbjct: 457 KTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNA 516
Query: 158 ----IDDIEDNSILRRGIPVAHSIY------------GIASTINAANY--VVAIALEKVQ 199
++ ++ + I Y I + + Y ++ IAL
Sbjct: 517 SGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDLLRIALM--- 573
Query: 200 SLGHPEATAVYTEQLLELHR 219
E A++ E ++ R
Sbjct: 574 ----AEDEAIFEEAHKQVQR 589
Score = 28.7 bits (63), Expect = 2.6
Identities = 35/250 (14%), Positives = 66/250 (26%), Gaps = 87/250 (34%)
Query: 7 DPEQDEKLLQPYTYISQVP----GKQIRTKLAYAFNNWLNIP-EEKLLAIGDIIQMLHNS 61
P ++ YI Q Q+ K N+ + L +
Sbjct: 104 QPSMMTRM-----YIEQRDRLYNDNQVFAKY--------NVSRLQPYLKL--------RQ 142
Query: 62 SLLIDDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQ----------SLGHP 111
+LL N ++ + G T A + KVQ +L +
Sbjct: 143 ALLELRPAKNVLI-------DGVLGSGKTWVALD---VCLSYKVQCKMDFKIFWLNLKNC 192
Query: 112 EATAVYTEQLLELHRGQGMEIYWRDNYTCPSEEEYRTMTIRKFDMRI------------- 158
+ E L +L ++ W S + R +I+ R+
Sbjct: 193 NSPETVLEMLQKLLYQ--IDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVL 250
Query: 159 DDIEDNSILR------------RGIPVAHSIYGIASTINAANYVVAIALEKVQ-SLGHPE 205
++++ R V + +A I+L+ +L E
Sbjct: 251 LNVQNAKAWNAFNLSCKILLTTRFKQVTDFL--------SAATTTHISLDHHSMTLTPDE 302
Query: 206 ATAVYTEQLL 215
+ LL
Sbjct: 303 -----VKSLL 307
>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 = 41.5 bits (98), Expect = 1e-04
Identities = 15/92 (16%), Positives = 31/92 (33%), Gaps = 3/92 (3%)
Query: 2 LSKSGDPEQDEKLLQPYTYISQVPGKQIRTKLAYAFNNWLNIPEEKLLAIGDIIQMLHNS 61
L KS E + P +++ + L A + + +A I ++H +
Sbjct: 16 LKKSITIRPPETVFGPMHHLTFAAPATAASTLCLAACELVGGDRSQAMAAAAAIHLVHAA 75
Query: 62 SLLIDDI--EDNSILRRGIPVAHSIYGIASTI 91
+ + + + D S P YG +
Sbjct: 76 AYVHEHLPLTDGS-RPVSKPAIQHKYGPNVEL 106
>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 = 41.0 bits (97), Expect = 2e-04
Identities = 22/68 (32%), Positives = 33/68 (48%), Gaps = 2/68 (2%)
Query: 26 GKQIRTKLAYAFNNWLNIPEEKLLAIGDIIQMLHNSSLLIDDIE--DNSILRRGIPVAHS 83
GK++R L A + E + ++M+H SL+ DD+ DN LRRG P H
Sbjct: 52 GKRVRPVLCIAACELVGGEESLAMPAACAVEMIHTMSLIHDDLPCMDNDDLRRGKPTNHK 111
Query: 84 IYGIASTI 91
+YG +
Sbjct: 112 VYGEDVAV 119
>3llw_A Geranyltranstransferase (ISPA); structural genomics, PSI, protein
structure initiative, nysgrc; 2.30A {Helicobacter
pylori} PDB: 3q1o_A*
Length = 311
Score = 40.3 bits (95), Expect = 3e-04
Identities = 22/69 (31%), Positives = 31/69 (44%), Gaps = 8/69 (11%)
Query: 26 GKQIRTKLAYA------FNNWLNIPEEKLLAIGDIIQMLHNSSLLIDDIE--DNSILRRG 77
GK+ R KL A + + + I I+ LH SL+ DD+ DN+ LRR
Sbjct: 48 GKRFRPKLFLAVLCALVGQKDYSNQQTEYFKIALSIECLHTYSLIHDDLPCMDNAALRRN 107
Query: 78 IPVAHSIYG 86
P H+ Y
Sbjct: 108 HPTLHAKYD 116
>3npk_A Geranyltranstransferase; isoprene biosynthesis, SGX, structural
genomics protein structure initiative; 1.50A
{Campylobacter jejuni}
Length = 291
Score = 39.9 bits (94), Expect = 4e-04
Identities = 19/64 (29%), Positives = 29/64 (45%), Gaps = 3/64 (4%)
Query: 26 GKQIRTKLAYAFNNWLNIP-EEKLLAIGDIIQMLHNSSLLIDDIE--DNSILRRGIPVAH 82
GK R +L + + L + ++ +H SL+ DD+ DN+ RRGIP H
Sbjct: 39 GKHFRAQLLLSVVQSNKPELLNQALDVALALEFIHTYSLIHDDLPAMDNADFRRGIPTLH 98
Query: 83 SIYG 86
Y
Sbjct: 99 KSYD 102
>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 = 39.5 bits (93), Expect = 5e-04
Identities = 27/83 (32%), Positives = 38/83 (45%), Gaps = 4/83 (4%)
Query: 8 PEQDEKLLQPYTYISQVPGKQIRTKLAYAFNNWLNIP--EEKLLAIGDIIQMLHNSSLLI 65
QD +L TY GK++R L A L + E+ +++LH SL+
Sbjct: 30 DSQDAQLAAAMTYSVLAGGKRLRPLLTVATMQSLGVTFVPERHWRPVMALELLHTYSLIH 89
Query: 66 DDIE--DNSILRRGIPVAHSIYG 86
DD+ DN LRRG P H +G
Sbjct: 90 DDLPAMDNDALRRGEPTNHVKFG 112
>3p8l_A Geranyltranstransferase; isoprenyl synthase, structural genomics,
PSI, protein struct initiative, nysgrc; 2.00A
{Enterococcus faecalis}
Length = 302
Score = 38.0 bits (89), Expect = 0.002
Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 3/64 (4%)
Query: 26 GKQIRTKLAYAFNNWLNIPEEKL-LAIGDIIQMLHNSSLLIDDIE--DNSILRRGIPVAH 82
GK++R L E + ++M+H SL+ DD+ D+ LRRG P H
Sbjct: 50 GKRLRPLLVLTTVAAFQKEMETQDYQVAASLEMIHTYSLIHDDLPAMDDDDLRRGKPTNH 109
Query: 83 SIYG 86
++G
Sbjct: 110 KVFG 113
>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 = 37.7 bits (87), Expect = 0.003
Identities = 31/199 (15%), Positives = 60/199 (30%), Gaps = 61/199 (30%)
Query: 74 LRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGHPEATAVYTEQ-----LLELH-RG 127
L + V + + IAS + + + L PE T + EL +
Sbjct: 16 LEHVLLVPTASFFIASQLQE---------QFNKIL--PEPTEGFAADDEPTTPAELVGKF 64
Query: 128 QGMEIYWRDNYTCPSEEEYRTMTIRKFD---MRIDDIEDNSILRRGIPVAHSIYGIASTI 184
G + ++ + + +F+ + +DI ++ +A + T
Sbjct: 65 LGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDI--HA-------LAAKLLQENDTT 115
Query: 185 NAA------NYVVAIALEKVQSLGHPEATAVYTEQLLELHR-----------GQG-MEIY 226
NY+ A + K + +A L GQG + Y
Sbjct: 116 LVKTKELIKNYITARIMAK-RPFDKKSNSA-----LFRAVGEGNAQLVAIFGGQGNTDDY 169
Query: 227 W---RDNYTCPSEEEYRTM 242
+ RD Y + Y +
Sbjct: 170 FEELRDLY-----QTYHVL 183
>3kb9_A EPI-isozizaene synthase; terpenoid cyclase, alpha-helical fold,
farnesyl diphosphate, metal-binding, lyase, magnesium;
HET: BTM; 1.60A {Streptomyces coelicolor} PDB: 3kbk_A
3lgk_A 3lg5_A*
Length = 382
Score = 30.9 bits (69), Expect = 0.33
Identities = 22/127 (17%), Positives = 37/127 (29%), Gaps = 17/127 (13%)
Query: 40 WLNIPEEKLLAIGDIIQMLHNSSLLIDDIEDNSI-------LRRGIPVAHSIYGIASTIN 92
+L P+E L AI D + DD D I RR + H+
Sbjct: 98 YLGAPDEVLQAIADYSAWF----FVWDDRHDRDIVHGRAGAWRRLRGLLHTALDSPGDHL 153
Query: 93 AANYVVAIAL----EKVQSLGHPEATAVYTEQLLELHRGQGMEIYWRDNYTCPSEEEYRT 148
+ ++ + A + + E + R P EEY
Sbjct: 154 HHEDTLVAGFADSVRRLYAFLPATWNARFARHFHTVIEAYDREFHNRTRGIVPGVEEY-- 211
Query: 149 MTIRKFD 155
+ +R+
Sbjct: 212 LELRRLT 218
Score = 30.5 bits (68), Expect = 0.47
Identities = 16/158 (10%), Positives = 38/158 (24%), Gaps = 16/158 (10%)
Query: 85 YGIASTINAANYVVAIALEKVQSLGHPEATAVYTEQLLELHRGQGMEIYWRDNYTCPSEE 144
+ Y + + + + A E L + W D+
Sbjct: 73 KRLMPADKVEEYADGLCYTDLMAGYYLGAPD---EVLQAIADYSAWFFVW-DDRHDRDIV 128
Query: 145 EYRTMTIRKFDMRIDDIEDNSILRRGIPVAHSIYGIASTINAANYVVAIALEKVQSLGHP 204
R R+ + D+ + ++ + + ++ +
Sbjct: 129 HGRAGAWRRLRGLLHTALDS--PGDHLHHEDTLVAGFADS----------VRRLYAFLPA 176
Query: 205 EATAVYTEQLLELHRGQGMEIYWRDNYTCPSEEEYRTM 242
A + + E + R P EEY +
Sbjct: 177 TWNARFARHFHTVIEAYDREFHNRTRGIVPGVEEYLEL 214
>3cvg_A Putative metal binding protein; PSI-II, NYSGXRC, periplasmic,
structural GENO protein structure initiative; 1.97A
{Coccidioides immitis}
Length = 294
Score = 29.4 bits (65), Expect = 0.86
Identities = 13/53 (24%), Positives = 20/53 (37%), Gaps = 2/53 (3%)
Query: 1 MLSKSGDPEQDEKLLQPYTYISQVPGKQIRTKLAYAFNNWLNIPEEKLLAIGD 53
++ K G + D+ LL P + K ++A F WL E I
Sbjct: 220 VIYKKGTNDADDPLLNPAHLLVGARAKN--AEMAKEFAKWLVSKEGGQKVIEG 270
>3v1v_A 2-MIB synthase, 2-methylisoborneol synthase; class I terpenoid
cyclase fold, DDXXXXD motif, NDXXSXXXE MOT
methylisoborneol biosynthesis; HET: GST; 1.80A
{Streptomyces coelicolor} PDB: 3v1x_A*
Length = 433
Score = 27.8 bits (61), Expect = 3.4
Identities = 17/123 (13%), Positives = 30/123 (24%), Gaps = 23/123 (18%)
Query: 46 EKLLAIGDIIQMLHNSSLLIDDIEDNSILRRGIPVAHSIYGIASTINAANYVVAI----- 100
+ L+ L + +DD + + + + I+ +
Sbjct: 174 DHLMLATR----LMVAENAVDDCYCEDHGGSPVGLGGRLLLAHTAIDHFHSTAEYTPTWQ 229
Query: 101 --------------ALEKVQSLGHPEATAVYTEQLLELHRGQGMEIYWRDNYTCPSEEEY 146
A+ P + Y + LH G E W P EY
Sbjct: 230 ASLAADAPRRAYDSAMGYFVRAATPSQSDRYRHDMARLHLGYLAEGAWAQTGHVPEVWEY 289
Query: 147 RTM 149
M
Sbjct: 290 LAM 292
Score = 27.8 bits (61), Expect = 3.5
Identities = 12/49 (24%), Positives = 15/49 (30%)
Query: 194 ALEKVQSLGHPEATAVYTEQLLELHRGQGMEIYWRDNYTCPSEEEYRTM 242
A+ P + Y + LH G E W P EY M
Sbjct: 244 AMGYFVRAATPSQSDRYRHDMARLHLGYLAEGAWAQTGHVPEVWEYLAM 292
>3qga_A UREA2, fusion of urease beta and gamma subunits; iron
metalloenzyme, alpha-beta barrel, hydrolase; HET: FME
KCX; 3.00A {Helicobacter mustelae} PDB: 3qgk_A*
Length = 225
Score = 27.0 bits (60), Expect = 6.1
Identities = 6/19 (31%), Positives = 10/19 (52%)
Query: 108 LGHPEATAVYTEQLLELHR 126
L PEA A + +++ R
Sbjct: 30 LNQPEAIAYISAHIMDEAR 48
Score = 27.0 bits (60), Expect = 6.1
Identities = 6/19 (31%), Positives = 10/19 (52%)
Query: 201 LGHPEATAVYTEQLLELHR 219
L PEA A + +++ R
Sbjct: 30 LNQPEAIAYISAHIMDEAR 48
>1e9y_A Urease subunit alpha; hydrolase, dodecamer; HET: KCX; 3.00A
{Helicobacter pylori} SCOP: b.85.3.1 d.8.1.1 PDB:
1e9z_A*
Length = 238
Score = 26.6 bits (59), Expect = 6.9
Identities = 6/19 (31%), Positives = 11/19 (57%)
Query: 108 LGHPEATAVYTEQLLELHR 126
L + EA A+ + ++E R
Sbjct: 30 LNYVEAVALISAHIMEEAR 48
Score = 26.6 bits (59), Expect = 6.9
Identities = 6/19 (31%), Positives = 11/19 (57%)
Query: 201 LGHPEATAVYTEQLLELHR 219
L + EA A+ + ++E R
Sbjct: 30 LNYVEAVALISAHIMEEAR 48
>3la4_A Urease; JACK bean, hydrolase, ME binding, nickel; HET: CME KCX;
2.05A {Canavalia ensiformis}
Length = 840
Score = 27.2 bits (60), Expect = 7.1
Identities = 7/19 (36%), Positives = 11/19 (57%)
Query: 108 LGHPEATAVYTEQLLELHR 126
L + EA A+ Q++E R
Sbjct: 30 LNYTEAVALIASQIMEYAR 48
Score = 27.2 bits (60), Expect = 7.1
Identities = 7/19 (36%), Positives = 11/19 (57%)
Query: 201 LGHPEATAVYTEQLLELHR 219
L + EA A+ Q++E R
Sbjct: 30 LNYTEAVALIASQIMEYAR 48
>1xzp_A Probable tRNA modification GTPase TRME; GTP-binding, THF-binding,
hydrolase; 2.30A {Thermotoga maritima} SCOP: a.24.25.1
c.37.1.8 d.250.1.2 PDB: 1xzq_A* 1xzp_B 1xzq_B*
Length = 482
Score = 26.7 bits (60), Expect = 8.9
Identities = 7/42 (16%), Positives = 17/42 (40%), Gaps = 4/42 (9%)
Query: 44 PEEKLLAIGDIIQMLHNSSLLIDDIEDNS----ILRRGIPVA 81
P+E G+++ L + + + +L RG+ +
Sbjct: 206 PDEIETNTGEVVTRLERIKEKLTEELKKADAGILLNRGLRMV 247
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 0.134 0.386
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: 3,978,897
Number of extensions: 242797
Number of successful extensions: 653
Number of sequences better than 10.0: 1
Number of HSP's gapped: 625
Number of HSP's successfully gapped: 102
Length of query: 247
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 156
Effective length of database: 4,160,982
Effective search space: 649113192
Effective search space used: 649113192
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 (21.6 bits)
S2: 56 (25.4 bits)