RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy9101
(255 letters)
>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 = 183 bits (465), Expect = 3e-56
Identities = 81/158 (51%), Positives = 105/158 (66%), Gaps = 8/158 (5%)
Query: 100 LALVVAYKMLAQPSELTPENLHLAQILGWCVEIVSLKTSMGQSLDLSTAN----DLSKFT 155
L Y++L P L+L ++ S +T +GQ+LDL TA DL +FT
Sbjct: 155 LLEACIYRLLKLYCREQPYYLNLIELFLQ----SSYQTEIGQTLDLLTAPQGNVDLVRFT 210
Query: 156 MDRYEAIVKYKTAFYSFQLPVALAMHMAGMQDVEVHRQARTLLLEMGHFFQVQDDYLDCF 215
RY++IVKYK+AFYSF LP+A AM+MAG+ + H A+ +LLEMG FFQ+QDDYLD F
Sbjct: 211 EKRYKSIVKYKSAFYSFYLPIAAAMYMAGIDGEKEHANAKKILLEMGEFFQIQDDYLDLF 270
Query: 216 GTPDVTGKIGTDIEDGKCSWLAVVALQRATPAQRKLME 253
G P VTGKIGTDI+D KCSWL V LQRATP Q ++++
Sbjct: 271 GDPSVTGKIGTDIQDNKCSWLVVQCLQRATPEQYQILK 308
Score = 85.6 bits (212), Expect = 1e-19
Identities = 34/108 (31%), Positives = 51/108 (47%), Gaps = 22/108 (20%)
Query: 27 LSKDESRDFMAIFPDLVRDLT-DAGRHSDIPDVTKWYAKVLQYNKAISNNVYLGTYFIVQ 85
+ E +DF+ F +VR LT D H +I D +VL+YN
Sbjct: 30 VYAQEKQDFVQHFSQIVRVLTEDEMGHPEIGDAIARLKEVLEYN---------------- 73
Query: 86 VLQYNVPSGKKNRGLALVVAYKMLAQPSELTPENLHLAQILGWCVEIV 133
GK NRGL +VVA++ L +P + ++L A +GWCVE++
Sbjct: 74 -----AIGGKYNRGLTVVVAFRELVEPRKQDADSLQRAWTVGWCVELL 116
>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 = 182 bits (464), Expect = 5e-56
Identities = 81/153 (52%), Positives = 104/153 (67%), Gaps = 8/153 (5%)
Query: 105 AYKMLAQPSELTPENLHLAQILGWCVEIVSLKTSMGQSLDLSTAN----DLSKFTMDRYE 160
Y++L + P +HL ++ + +T +GQ LDL TA DLS F+ +RY+
Sbjct: 153 VYRVLKKYCRQRPYYVHLLELFLQ----TAYQTELGQMLDLITAPVSKVDLSHFSEERYK 208
Query: 161 AIVKYKTAFYSFQLPVALAMHMAGMQDVEVHRQARTLLLEMGHFFQVQDDYLDCFGTPDV 220
AIVKYKTAFYSF LPVA AM+M G+ E H A+ +LLEMG +FQ+QDDYLDCFG P +
Sbjct: 209 AIVKYKTAFYSFYLPVAAAMYMVGIDSKEEHENAKAILLEMGEYFQIQDDYLDCFGDPAL 268
Query: 221 TGKIGTDIEDGKCSWLAVVALQRATPAQRKLME 253
TG +GTDI+D KCSWL V LQR TP QR+L+E
Sbjct: 269 TGAVGTDIQDNKCSWLVVQCLQRVTPEQRQLLE 301
Score = 92.1 bits (229), Expect = 6e-22
Identities = 39/116 (33%), Positives = 56/116 (48%), Gaps = 22/116 (18%)
Query: 18 PPLAATNTVLSKDESRDFMAIFPDLVRDLT-DAGRHSDIPDVTKWYAKVLQYNKAISNNV 76
P L + V+ + E +F+ FP +VRDLT D H ++ D +VLQYN
Sbjct: 14 PALRNLSPVVVEREREEFVGFFPQIVRDLTEDGIGHPEVGDAVARLKEVLQYN------- 66
Query: 77 YLGTYFIVQVLQYNVPSGKKNRGLALVVAYKMLAQPSELTPENLHLAQILGWCVEI 132
P GK NRGL +V AY+ L+ P + E+L A +GWC+E+
Sbjct: 67 --------------APGGKCNRGLTVVAAYRELSGPGQKDAESLRCALAVGWCIEL 108
>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 = 172 bits (437), Expect = 4e-52
Identities = 50/138 (36%), Positives = 73/138 (52%), Gaps = 15/138 (10%)
Query: 133 VSLKTSMGQSLDLSTAN---------------DLSKFTMDRYEAIVKYKTAFYSFQLPVA 177
V T++GQ D+++ D ++FT Y+ IVKYKT FY++ LP+
Sbjct: 159 VDYATAVGQMYDVTSMCDSNKLDPEVAQPMTTDFAEFTPAIYKRIVKYKTTFYTYLLPLV 218
Query: 178 LAMHMAGMQDVEVHRQARTLLLEMGHFFQVQDDYLDCFGTPDVTGKIGTDIEDGKCSWLA 237
+ + ++ + +G +FQVQDD +DCF P+ GK+GTDIED KCSWLA
Sbjct: 219 MGLFVSEAAASVEMNLVERVAHLIGEYFQVQDDVMDCFTPPEQLGKVGTDIEDAKCSWLA 278
Query: 238 VVALQRATPAQRKLMEVN 255
V L +A AQ + N
Sbjct: 279 VTFLGKANAAQVAEFKAN 296
Score = 62.9 bits (153), Expect = 1e-11
Identities = 15/108 (13%), Positives = 33/108 (30%), Gaps = 27/108 (25%)
Query: 31 ESRDFMAIFPDLVRDLTD--AGRHSDIPDVTKWYAKVLQYNKAISNNVYLGTYFIVQVLQ 88
F++++ ++ L D ++ P+ ++ ++
Sbjct: 3 SMERFLSVYDEVQAFLLDQLQSKYEIDPNRARYLRIMMDTT------------------- 43
Query: 89 YNVPSGKKNRGLALVVAYKML----AQPSELTPENLHLAQILGWCVEI 132
GK RG+ +V + LH A + GW +E
Sbjct: 44 --CLGGKYFRGMTVVNVAEGFLAVTQHDEATKERILHDACVGGWMIEF 89
>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 = 172 bits (438), Expect = 6e-52
Identities = 55/171 (32%), Positives = 82/171 (47%), Gaps = 19/171 (11%)
Query: 100 LALVVAYKMLAQPSELTPENLHLAQILGWCVEIVSLKTSMGQSLDLSTAN---------- 149
L + M P L V T++GQ D+++
Sbjct: 158 LLKSWTHMMAMHFFADRPFLQDLLCRFNR----VDYTTAVGQLYDVTSMFDSNKLDPDVS 213
Query: 150 -----DLSKFTMDRYEAIVKYKTAFYSFQLPVALAMHMAGMQDVEVHRQARTLLLEMGHF 204
D ++FT+ Y+ IVKYKTA+Y++ LP+ + + ++ L + MG +
Sbjct: 214 QPTTTDFAEFTLSNYKRIVKYKTAYYTYLLPLVMGLIVSEALPTVDMGVTEELAMLMGEY 273
Query: 205 FQVQDDYLDCFGTPDVTGKIGTDIEDGKCSWLAVVALQRATPAQRKLMEVN 255
FQVQDD +DCF P+ GK+GTDI+D KCSWLAV L +A+ AQ + N
Sbjct: 274 FQVQDDVMDCFTPPERLGKVGTDIQDAKCSWLAVTFLAKASSAQVAEFKAN 324
Score = 79.5 bits (196), Expect = 2e-17
Identities = 20/138 (14%), Positives = 41/138 (29%), Gaps = 33/138 (23%)
Query: 7 LSQKSKILSHDPPLAATNTVLSKDESRDFMAIFPDLVRDLTD--AGRHSDIPDVTKWYAK 64
+ H L + ++ + FM ++ ++ L + + P+ ++ K
Sbjct: 1 MGSSHHHHHHSSGLVPRGSHMASMPMQMFMQVYDEIQMFLLEELELKFDMDPNRVRYLRK 60
Query: 65 VLQYNKAISNNVYLGTYFIVQVLQYNVPSGKKNRGLALVVAYKMLA----------QPSE 114
++ GK NRGL ++ + L
Sbjct: 61 ---------------------MMDTTCLGGKYNRGLTVIDVAESLLSLSPNNNGEEDDGA 99
Query: 115 LTPENLHLAQILGWCVEI 132
LH A + GW +E
Sbjct: 100 RRKRVLHDACVCGWMIEF 117
>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 = 167 bits (425), Expect = 3e-50
Identities = 31/158 (19%), Positives = 66/158 (41%), Gaps = 12/158 (7%)
Query: 100 LALVVAYKMLAQPSELTPEN--LHLAQILGWCVEIVSLKTSMGQSLDLSTAN-DLSKFTM 156
+++ ++ + S + + + + +I T +GQ LDLS + +
Sbjct: 145 FLKMLSLSLIFELSSVFGNDIVMKIQKIYNE----SIFFTVLGQHLDLSYFDLSKADKIS 200
Query: 157 DRYEAIVKYKTAFYSFQLPVALAMHMAGMQ-DVEVHRQARTLLLEMGHFFQVQDDYLDCF 215
+RY ++V+ KT+ Y+F +PV + ++ +Q +L ++G F+QV +D D
Sbjct: 201 ERYFSMVEMKTSRYTFYMPVFFGLTLSEIQVSSAQLNLIEAILYKLGEFYQVHNDVSDYL 260
Query: 216 GTPDVTGKIGTDIEDGKCSWLAVVALQRATPAQRKLME 253
DI K +W + + A + +
Sbjct: 261 FND----SNADDICRFKLTWPLQKSFEIADEEMKLKIS 294
Score = 70.6 bits (173), Expect = 3e-14
Identities = 22/122 (18%), Positives = 44/122 (36%), Gaps = 19/122 (15%)
Query: 11 SKILSHDPPLAATNTVLSKDESRDFMAIFPDLVRDLTDAGRHSDIPDVTKWYAKVLQYNK 70
S H + + DF+ + + + + + D + V++Y
Sbjct: 4 SHHHHHHSSGRENLYFQGEYDYTDFINYYDKFKVIVYNVLKKLPLND--EIRKPVIEY-- 59
Query: 71 AISNNVYLGTYFIVQVLQYNVPSGKKNRGLALVVAYKMLAQPSELTPENLHLAQILGWCV 130
+ + YNV GK RG LV+ + + S + ++++ +LGW V
Sbjct: 60 ------------YLNCIDYNVKKGKHIRGKILVLISSLSSAYSNIKRDSIY---LLGWVV 104
Query: 131 EI 132
E
Sbjct: 105 EA 106
>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 = 159 bits (403), Expect = 7e-47
Identities = 46/180 (25%), Positives = 80/180 (44%), Gaps = 28/180 (15%)
Query: 100 LALVVAYKMLAQPSELTPENLHLAQILGWCVEIVSLKTSMGQSLDLSTAN---------- 149
L YK++ + + +LKT +GQ LD + +
Sbjct: 157 LLYNSIYKLIEIYLRNESCYVDVIATFRD----ATLKTIIGQHLDTNIFSDKYSDAHREI 212
Query: 150 -------------DLSKFTMDRYEAIVKYKTAFYSFQLPVALAMHMAGM-QDVEVHRQAR 195
D++ Y+ IV +KTA+YSF LP+ M +AG+ D ++++
Sbjct: 213 DVNNINVPEQPVIDINMINFGVYKNIVIHKTAYYSFFLPIVCGMLLAGIAVDNLIYKKIE 272
Query: 196 TLLLEMGHFFQVQDDYLDCFGTPDVTGKIGTDIEDGKCSWLAVVALQRATPAQRKLMEVN 255
+ + MG +FQ+ DDYLD FG TGK+G+DI++ K +W + + + + + N
Sbjct: 273 DISMLMGEYFQIHDDYLDIFGDSTKTGKVGSDIQNNKLTWPLIKTFELCSEPDKIKIVKN 332
Score = 68.8 bits (168), Expect = 1e-13
Identities = 21/120 (17%), Positives = 44/120 (36%), Gaps = 27/120 (22%)
Query: 19 PLAATNTVLSKDESRDFMAIFP----DLVRDLTDAGRHSDIPD-VTKWYAKVLQYNKAIS 73
+ TN+ + F ++ + L + +I + ++K+Y + YN
Sbjct: 20 GMKETNSEEADSGLAFFRNMYDKYRDAFLSHLNEYSLEEEIKEHISKYYKLLFDYN---- 75
Query: 74 NNVYLGTYFIVQVLQYNVPSGKKNRGLALVVAYKMLAQPSELTPENLHLAQILGWCVEIV 133
GK NRG+ +++ Y+ + ++ A L WC+EI+
Sbjct: 76 -----------------CLGGKNNRGILVILIYEYVK-NRDINSSEWEKAACLAWCIEIL 117
>3lk5_A Geranylgeranyl pyrophosphate synthase; structural genomics, protein
structure initiative, geranylge pyrophosphate synthase;
1.90A {Corynebacterium glutamicum} PDB: 3qqv_A*
Length = 380
Score = 100 bits (250), Expect = 8e-25
Identities = 42/156 (26%), Positives = 70/156 (44%), Gaps = 9/156 (5%)
Query: 100 LALVVAYKMLAQPSELTPENLHLAQILGW-CVEIVSLKTSMGQSLDLSTANDLSKFTMDR 158
+ALV A ML E++ GQ LD+ + + +++
Sbjct: 154 MALVWAEDMLQDSGLSAEALARTRDAWRGMRTEVI-----GGQLLDIYLESHAN-ESVEL 207
Query: 159 YEAIVKYKTAFYSFQLPVALAMHMAGMQDVEVHRQARTLLLEMGHFFQVQDDYLDCFGTP 218
+++ ++KTA Y+ P+ L +AG ++ ++G FQ++DD L FG P
Sbjct: 208 ADSVNRFKTAAYTIARPLHLGASIAGG-SPQLIDALLHYGHDIGIAFQLRDDLLGVFGDP 266
Query: 219 DVTGK-IGTDIEDGKCSWLAVVALQRATPAQRKLME 253
+TGK G DI +GK + L +ALQRA +
Sbjct: 267 AITGKPAGDDIREGKRTVLLALALQRADKQSPEAAT 302
>1wmw_A Geranylgeranyl diphosphate synthetase; GGPP, prenyl diphosphate
synthase, structural genom riken structural
genomics/proteomics initiative; 1.55A {Thermus
thermophilus}
Length = 330
Score = 84.7 bits (210), Expect = 2e-19
Identities = 35/156 (22%), Positives = 59/156 (37%), Gaps = 10/156 (6%)
Query: 100 LALVVAYKMLAQPSELTPENLHLAQILGWCVEIVSLKTSMGQSLDLS-TANDLSKFTMDR 158
+ +LA+ + V + GQ LDL T +
Sbjct: 109 AMHAEMWGLLAEGLARGLFPPEVLLEFHEVVRRTAY----GQHLDLLWTLGGTFDLRPED 164
Query: 159 YEAIVKYKTAFYSFQLPVALAMHMAGMQDVEVHRQARTLLLEMGHFFQVQDDYLDCFGTP 218
Y +V +K A+Y+ P+ L +AG + + L +G FQ+ DD L+ G
Sbjct: 165 YFRMVAHKAAYYTAVAPLRLGALLAGKTPPAAYEEGG---LRLGTAFQIVDDVLNLEGGE 221
Query: 219 DVTGK-IGTDIEDGKCSWLAVVALQRATPAQRKLME 253
GK D+ +GK + + + L+ A P +R
Sbjct: 222 -AYGKERAGDLYEGKRTLILLRFLEEAPPEERARAL 256
>3nf2_A Putative polyprenyl synthetase; isoprenyl diphosphate synthase,
structural genomics, PSI, PR structure initiative,
nysgrc; 2.20A {Streptomyces coelicolor}
Length = 352
Score = 84.3 bits (209), Expect = 4e-19
Identities = 36/159 (22%), Positives = 56/159 (35%), Gaps = 22/159 (13%)
Query: 102 LVVAYKMLAQPSELTPENLHLAQILGWCVEIVSLKTSMGQSLDLSTANDLSKFTMDRYEA 161
+A ++L + T E + L + GQ+ D+S + +++
Sbjct: 126 FALANEVLLELG--TVEAGRATRRLTKASRSLI----DGQAQDISYEHRDR-VSVEECLE 178
Query: 162 IVKYKTAFYSFQLPVAL---AMHMAGM---QDVEVHRQARTLLLEMGHFFQVQDDYLDCF 215
+ KT AL A + + D +G FQ DD L +
Sbjct: 179 MEGNKTG--------ALLACASSIGAVLGGADERTADTLEKYGYHLGLAFQAVDDLLGIW 230
Query: 216 GTPDVTGK-IGTDIEDGKCSWLAVVALQRATPAQRKLME 253
G PD TGK +D+ K S V AL A +L E
Sbjct: 231 GDPDATGKQTWSDLRQRKKSLPVVAALAAGGAASERLGE 269
>1wy0_A Geranylgeranyl pyrophosphate synthetase; pyrococcus horikosh
structural genomics, riken structural
genomics/proteomics initiative, RSGI; 2.20A {Pyrococcus
horikoshii}
Length = 342
Score = 81.2 bits (201), Expect = 4e-18
Identities = 28/156 (17%), Positives = 59/156 (37%), Gaps = 14/156 (8%)
Query: 102 LVVAYKMLAQPSELTPENLHLAQILGWCVEIVSLKTSMGQSLDLSTANDLSKFTMDRYEA 161
A++ +A+ + + +++ + GQ+ DL + T++ Y
Sbjct: 118 FSKAFEAVARAEIPPEKKARVLEVIVKASNELCE----GQARDLEFEKKST-VTIEEYME 172
Query: 162 IVKYKTAFYSFQLPVALAMHMAGM---QDVEVHRQARTLLLEMGHFFQVQDDYLDCFGTP 218
++ KT L + + G+ + E + + +G FQ+ DD LD
Sbjct: 173 MISGKTG----AL-FEASAKVGGIIGTDNEEYIKALSSWGRNVGIAFQIWDDVLDLIADE 227
Query: 219 DVTGK-IGTDIEDGKCSWLAVVALQRATPAQRKLME 253
GK +G+DI GK + + + A ++
Sbjct: 228 KKLGKPVGSDIRKGKKTLIVAHFFENADEKDKQRFL 263
>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 = 69.6 bits (171), Expect = 3e-14
Identities = 30/116 (25%), Positives = 51/116 (43%), Gaps = 8/116 (6%)
Query: 140 GQSLDLSTANDLSKFTMDRYEAIVKYKTAFYSFQLPVALAMHMAGMQDVEVHRQARTLLL 199
GQ LD+ ++ + T + Y+A+V KT F L V L + ++ TL
Sbjct: 126 GQGLDIYWRDNYTCPTEEEYKAMVLQKTGGL-FGLAVGLMQLFSD-YKEDLKPLLNTL-- 181
Query: 200 EMGHFFQVQDDYLDCFGTPDVTGK-IGTDIEDGKCSWLAVVALQRATPAQRKLMEV 254
G FFQ++DDY + K D+ +GK S+ + A+ P ++ +
Sbjct: 182 --GLFFQIRDDYANLHSKEYSENKSFCEDLTEGKFSFPTIHAIWSR-PESTQVQNI 234
>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 = 68.2 bits (167), Expect = 2e-13
Identities = 33/152 (21%), Positives = 59/152 (38%), Gaps = 10/152 (6%)
Query: 102 LVVAYKMLAQPSELTPENLHLAQILGWCVEIVSLKTSMGQSLDLSTANDLSKF--TMDRY 159
A ++++Q + P +L I + GQ LD+ + L + T + Y
Sbjct: 112 YFRAMQLVSQLTTKEPLYHNLITIF----NEELINLHRGQGLDIYWRDFLPEIIPTQEMY 167
Query: 160 EAIVKYKTAFYSFQLPVALAMHMAGMQDVEVHRQARTLLLEMGHFFQVQDDYLDCFGTPD 219
+V KT F+L + L ++ + +G +Q++DDYL+
Sbjct: 168 LNMVMNKTGGL-FRLTLRLMEALSPSSHHG--HSLVPFINLLGIIYQIRDDYLNLKDFQM 224
Query: 220 VTGK-IGTDIEDGKCSWLAVVALQRATPAQRK 250
+ K DI +GK S+ V AL +
Sbjct: 225 SSEKGFAEDITEGKLSFPIVHALNFTKTKGQT 256
>4dhd_A Polyprenyl synthetase; isoprenoid synthesis, isoprenoid diphosphate
synthase, trans; 1.65A {Pyrobaculum calidifontis}
Length = 358
Score = 68.1 bits (167), Expect = 2e-13
Identities = 38/169 (22%), Positives = 58/169 (34%), Gaps = 31/169 (18%)
Query: 102 LVVAYKMLAQPSELTPENLHLAQILGW-CVEIVSLKTSMGQSLDLSTANDLSKF------ 154
+ + TP+ A+ + I G+ LD+
Sbjct: 117 REAIEEAVLD----TPKPTLFAKEVAEVIKAIDE-----GERLDILFEAAGRSDPYFVQA 167
Query: 155 -----TMDRYEAIVKYKTAFYSFQLPVALAMHMAGM---QDVEVHRQARTLLLEMGHFFQ 206
T+D Y +V KT +A A + D + A + G FQ
Sbjct: 168 RWREVTLDDYIKMVSLKTGAL-----IAAAAKWGVLSVSDDRGLAEAAWNFGMAAGVAFQ 222
Query: 207 VQDDYLDCFGTPDVTGK-IGTDIEDGKCSWLAV-VALQRATPAQRKLME 253
+ DD LD +G P GK IG DI++ K V VAL +R+ +
Sbjct: 223 IIDDVLDIYGDPKKFGKEIGKDIKEHKRGNAVVAVALSHLGEGERRRLL 271
>3mzv_A Decaprenyl diphosphate synthase; transferase, structural genomics,
PSI-2, protein structure initiative; 1.90A {Rhodobacter
capsulatus}
Length = 341
Score = 59.6 bits (145), Expect = 1e-10
Identities = 31/120 (25%), Positives = 51/120 (42%), Gaps = 14/120 (11%)
Query: 140 GQSLDLSTANDLSKFTMDRYEAIVKYKTA--FYSFQLPVALAMHMAGM---QDVEVHRQA 194
G+ L L+ A +L+ T D Y +++ KTA F + A + G+ + +
Sbjct: 154 GEVLQLTAAQNLA-TTEDIYLRVIRGKTAALF-------SAATEVGGIIGGAPEDQVQAL 205
Query: 195 RTLLLEMGHFFQVQDDYLDCFGTPDVTGK-IGTDIEDGKCSWLAVVALQRATPAQRKLME 253
+G FQ+ DD LD G GK G D + K + + A+ A A+R +
Sbjct: 206 FDYGDALGIAFQIVDDLLDYGGKSAEIGKNTGDDFRERKLTMPVIKAVALADEAERAFWK 265
>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 = 59.6 bits (145), Expect = 1e-10
Identities = 29/122 (23%), Positives = 49/122 (40%), Gaps = 10/122 (8%)
Query: 138 SMGQSLDLSTANDLSKFTMDRYEAIVKYKTAFYSFQLPVALAMHMAGM---QDVEVHRQA 194
G+ + T+D Y + KTA +L AL+ + V +
Sbjct: 156 LQGELHQMDLNYREDI-TLDAYLNEIAGKTA----EL-FALSCYQGAQLAGAPQSVIDRT 209
Query: 195 RTLLLEMGHFFQVQDDYLDCFGTPDVTGK-IGTDIEDGKCSWLAVVALQRATPAQRKLME 253
R + + +G +Q+ DD LD G P T K + D+ G S +++L A KL++
Sbjct: 210 RDIGIAIGCAYQMLDDILDYAGDPKRTQKPVLEDLRSGVYSLPLLLSLSHAPRDFHKLLK 269
Query: 254 VN 255
Sbjct: 270 KK 271
>3oyr_A Trans-isoprenyl diphosphate synthase; isoprenyl synthase, PSI,
protein structure initiative; HET: IPE; 2.00A
{Caulobacter crescentus}
Length = 345
Score = 59.6 bits (145), Expect = 1e-10
Identities = 35/120 (29%), Positives = 54/120 (45%), Gaps = 14/120 (11%)
Query: 140 GQSLDLSTANDLSKFTMDRYEAIVKYKTA--FYSFQLPVALAMHMAGM---QDVEVHRQA 194
G+ L L ++DL+ + Y I++ KTA F A A + DV
Sbjct: 166 GEVLQLMRSHDLN-LSQAVYLEIIQAKTAELF-------AAASEAGAVSAGVDVAKSEAL 217
Query: 195 RTLLLEMGHFFQVQDDYLDCFGTPDVTGK-IGTDIEDGKCSWLAVVALQRATPAQRKLME 253
R L +G FQ+ DD LD G + GK G D +GK + ++A+ R+ P + + E
Sbjct: 218 RDYGLNLGLAFQLADDALDYGGATETLGKNAGDDFREGKATLPLLLAIARSGPREAEFWE 277
>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 = 57.7 bits (140), Expect = 6e-10
Identities = 29/121 (23%), Positives = 51/121 (42%), Gaps = 11/121 (9%)
Query: 138 SMGQSLDLSTANDLSKFTMDRYEAIVKYKTAFYSFQLPVALAMHMAGM---QDVEVHRQA 194
GQ + D ++ Y +++ KT L +A A ++ M E
Sbjct: 173 VTGQMRETVGPRDTD--PIEHYTNVIREKTG----VL-IASAGYLGAMHAGAAPEHIDAL 225
Query: 195 RTLLLEMGHFFQVQDDYLDCFGTPDVTGK-IGTDIEDGKCSWLAVVALQRATPAQRKLME 253
+ +G FQ+ DD +D F +GK GTD+ +G + + AL+ TP +L +
Sbjct: 226 KNFGAAVGMIFQIVDDIIDIFSETHESGKTPGTDLREGVFTLPVLYALREDTPVGAELRD 285
Query: 254 V 254
+
Sbjct: 286 I 286
>3aqb_B Component B of hexaprenyl diphosphate synthase; prenyltransferase,
transferase; 2.40A {Micrococcus luteus} PDB: 3aqc_B*
Length = 325
Score = 57.3 bits (139), Expect = 8e-10
Identities = 22/120 (18%), Positives = 45/120 (37%), Gaps = 10/120 (8%)
Query: 138 SMGQSLDLSTANDLSKFTMDRYEAIVKYKTAFYSFQLPVALAMHMAGM---QDVEVHRQA 194
G+ ++ + + Y + KTA L + + H+ + D +
Sbjct: 143 CFGEFDQMADRFNYP-VSFTAYLRRINRKTA----IL-IEASCHLGALSSQLDEQSTYHI 196
Query: 195 RTLLLEMGHFFQVQDDYLDCFGTPDVTGK-IGTDIEDGKCSWLAVVALQRATPAQRKLME 253
+ +G +Q+ DD LD GK +G+DI +G ++ + A+ +E
Sbjct: 197 KQFGHCIGMSYQIIDDILDYTSDEATLGKPVGSDIRNGHITYPLMAAIANLKEQDDDKLE 256
>3tc1_A Octaprenyl pyrophosphate synthase; all alpha-helices fold,
transferase; 2.00A {Helicobacter pylori}
Length = 315
Score = 54.5 bits (132), Expect = 6e-09
Identities = 21/121 (17%), Positives = 45/121 (37%), Gaps = 19/121 (15%)
Query: 140 GQSLDLSTANDLSKFTMDRYEAIVKYKTA--FYSFQLPVALAMHMAGM---QDVEVHRQ- 193
G+ D+ + +Y I++ KTA ++ + +D +++
Sbjct: 137 GEIEDVFVGECFN-SDKQKYWRILEDKTAHFI-------EASLKSMAILLNKDAKIYADF 188
Query: 194 ARTLLLEMGHFFQVQDDYLDCFGTPDVTGK-IGTDIEDGKCSWLAVVALQRATPAQRKLM 252
G FQ+ DD LD GK +D ++GK + ++ ++ + L+
Sbjct: 189 GLNF----GMAFQIIDDLLDITQDAKTLGKPNFSDFKEGKTTLPYLLLYEKLNQHDQGLL 244
Query: 253 E 253
Sbjct: 245 I 245
>2azj_A Geranylgeranyl pyrophosphate synthetase; hexpps,
trans-prenyltransferase; 2.40A {Sulfolobus solfataricus}
PDB: 2azk_A
Length = 289
Score = 53.1 bits (128), Expect = 2e-08
Identities = 22/130 (16%), Positives = 43/130 (33%), Gaps = 24/130 (18%)
Query: 133 VSLKTSMGQSLDLSTANDLSKFTMDRYEAIVKYKTA--FYSFQLPVALAMHMAGM--QDV 188
+ TS+G D+ +D Y ++ KT F L+ ++ +
Sbjct: 143 LWKDTSVGALRDMYDNSD--------YIRTIELKTGSLF-------KLSTVLSAYASKHY 187
Query: 189 EVHRQARTLLLEMGHFFQVQDDYLDCFGT----PDVTGK-IGTDIEDGKCSWLAVVALQR 243
+Q + +G +QV DD++D D + K + +GK
Sbjct: 188 NTKQQMLDVGKYLGIIYQVIDDFVDYKTKKVEEIDGSAKQLFKYYREGKLEEYVRSVYLE 247
Query: 244 ATPAQRKLME 253
+L+
Sbjct: 248 YKQKYDELIS 257
>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 = 53.0 bits (128), Expect = 2e-08
Identities = 27/122 (22%), Positives = 54/122 (44%), Gaps = 13/122 (10%)
Query: 133 VSLKTSMGQSLDLSTANDLSKFTMDRYEAIVKYKTA--FYSFQLPVALAMHMAGMQDVEV 190
V K S + ++ + T + Y IV+ K+ F LA+ + + + E+
Sbjct: 135 VIGKMSEAELIEQLSRYK--PITKEEYLRIVEGKSGALF-------GLALQLPALLEGEL 185
Query: 191 HRQARTLLLEMGHFFQVQDDYLDCFGTPDVTGK-IGTDIEDGKCSWLAVVALQRATPAQR 249
L + +G +Q+ DD +D G + GK D+++G S+ V A+++ A++
Sbjct: 186 GEDLYNLGVTIGTIYQMFDDIMDFAGM-EKIGKDGFLDLKNGVASFPLVTAMEKFPEARQ 244
Query: 250 KL 251
Sbjct: 245 MF 246
>3rmg_A Octaprenyl-diphosphate synthase; structural genomics, protein
structure initiative, isoprene biosynthesis,
transferase; 2.30A {Bacteroides thetaiotaomicron}
Length = 334
Score = 52.6 bits (127), Expect = 3e-08
Identities = 33/120 (27%), Positives = 52/120 (43%), Gaps = 15/120 (12%)
Query: 140 GQSLDLSTANDLSKFTMDRYEAIVKYKTA--FYSFQLPVALAMHMAGM---QDVEVHRQA 194
G+ L LS ++ S F+ + Y +++ KTA F A A + E A
Sbjct: 148 GELLQLSNVSNHS-FSEEVYFDVIRKKTAALF-------AACAEAAALSVQVGEEEVAFA 199
Query: 195 RTLLLEMGHFFQVQDDYLDCFGTPDVTGK-IGTDIEDGKCSWLAVVALQRATPAQRKLME 253
R L +G FQ++DD D + GK G D+ +GK + A+ AL A + +
Sbjct: 200 RLLGEYIGICFQIKDDIFD-YFDSKKIGKPTGNDMLEGKLTLPALYALNTTKDAWAEQIA 258
>3m0g_A Farnesyl diphosphate synthase; structural genomics, protein
structure initiative, NYSGXRC, biosynthesis,
transferase, PSI-2; 1.90A {Rhodobacter capsulatus} PDB:
3lvs_A
Length = 297
Score = 50.7 bits (122), Expect = 9e-08
Identities = 36/144 (25%), Positives = 57/144 (39%), Gaps = 13/144 (9%)
Query: 105 AYKMLAQPSELTPEN-LHLAQILGWCVEIVSLKTSM--GQSLDLSTANDLSKFTMDRYEA 161
A+++ P + EN + L L S M GQ+LD++ T+D
Sbjct: 118 AFELCTDPVLGSAENRVALVAALAQA----SGAEGMVYGQALDIAAETAAVPLTLDEIIR 173
Query: 162 IVKYKTAFYSFQLPVALAMHMAGMQDVEVHRQARTLLLEMGHFFQVQDDYLDCFGTPDVT 221
+ KT +AG + A L G FQ+ DD LD G +
Sbjct: 174 LQAGKTG-ALISFAAQAGAILAGADRGPLTAYATAL----GLAFQIADDILDVEGNEEAA 228
Query: 222 GK-IGTDIEDGKCSWLAVVALQRA 244
GK +G D E K ++++++ L A
Sbjct: 229 GKRLGKDAEAHKATFVSLLGLAGA 252
>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 = 51.2 bits (122), Expect = 1e-07
Identities = 39/245 (15%), Positives = 72/245 (29%), Gaps = 77/245 (31%)
Query: 30 DESRDFMAIFPDLVRDLTD-AGRH-----SDIPDVTKWYAKVLQYNKAISN------NVY 77
+E RD + LV DL + D K + + L + + N Y
Sbjct: 171 EELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDY 230
Query: 78 LGTYFI----VQVLQYNVPSGKKNRGLALVVAYKMLAQPSELTPENL--HLAQILGWCVE 131
L + I + V+Q LA Y + A+ TP L +L G
Sbjct: 231 LLSIPISCPLIGVIQ-----------LA---HYVVTAKLLGFTPGELRSYLKGATGHSQG 276
Query: 132 IVSLKTSMGQSLDLSTANDLSKFTMDRYEAIVKY-KTAFYSFQLPVALAMHMAGMQDVEV 190
+V+ ++ ++ + F + ++ K F+ G V
Sbjct: 277 LVT-------AVAIAETDSWESF----FVSVRKAITVLFFI------------G---VRC 310
Query: 191 HRQARTLLLEMGHFFQVQDDYLDCFGTPDVTGKIGTDIEDGKCSWLAVVALQRATPAQRK 250
+ L ++D + G P L++ L + Q
Sbjct: 311 YEAYPNTSLPPS---ILEDSLENNEGVP--------------SPMLSISNLTQEQ-VQDY 352
Query: 251 LMEVN 255
+ + N
Sbjct: 353 VNKTN 357
Score = 30.0 bits (67), Expect = 0.84
Identities = 17/81 (20%), Positives = 33/81 (40%), Gaps = 24/81 (29%)
Query: 70 KAISNNVYLGTYFIVQVLQYNVP------SGKKNRGLALVVAYKMLAQPSELTPENLHLA 123
+ + V T ++V+++ YNV +G AL +L + L
Sbjct: 1827 QYVVERVGKRTGWLVEIVNYNVENQQYVAAGDLR---ALDTVTNVL--------NFIKLQ 1875
Query: 124 QILGWCVEIVSLKTSMGQSLD 144
+I +I+ L+ S+ SL+
Sbjct: 1876 KI-----DIIELQKSL--SLE 1889
>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 = 49.3 bits (118), Expect = 3e-07
Identities = 34/152 (22%), Positives = 65/152 (42%), Gaps = 17/152 (11%)
Query: 108 MLAQPSEL--TPENLHLAQILGWCVEIVSLKTSMGQSLDLSTANDLSKFTMDRYEAIVKY 165
+L++ +N + +L VE + G++++++++ + +MD Y Y
Sbjct: 138 LLSRACGALAALKNTEVVALLATAVEHLVT----GETMEITSSTEQRY-SMDYYMQKTYY 192
Query: 166 KTAFYSFQLPVALAMHMAGM---QDVEVHRQARTLLLEMGHFFQVQDDYLDCFGTPDVTG 222
KTA L ++ + + Q EV A +G FQ+ DD LD GT G
Sbjct: 193 KTA----SL-ISNSCKAVAVLTGQTAEVAVLAFEYGRNLGLAFQLIDDILDFTGTSASLG 247
Query: 223 K-IGTDIEDGKCSWLAVVALQRATPAQRKLME 253
K +DI G + ++ P R++++
Sbjct: 248 KGSLSDIRHGVIT-APILFAMEEFPQLREVVD 278
>3lom_A Geranyltranstransferase; geranyltransferase, structural genomics,
PSI, protein structure initiative, nysgrc; 2.30A
{Legionella pneumophila subsp}
Length = 313
Score = 49.2 bits (118), Expect = 4e-07
Identities = 32/113 (28%), Positives = 45/113 (39%), Gaps = 17/113 (15%)
Query: 140 GQSLDLSTANDLSKFTMDRYEAIVKYKTAFYSFQLPVAL---AMHMAGMQDVEVHRQART 196
GQSLDLS S T ++ I KT L M EV Q ++
Sbjct: 163 GQSLDLS-ELAKSSVTEEQLREIHLLKTG--------KLILACFEMVLAAQHEVSEQIKS 213
Query: 197 LLLEMGHF----FQVQDDYLDCFGTPDVTGK-IGTDIEDGKCSWLAVVALQRA 244
L G FQ+QDDYLD + + GK +D + K ++ + Q+
Sbjct: 214 ALRTYGKHIGLVFQMQDDYLDLYAPTQILGKGRSSDQANQKTTFATLFNKQQL 266
>3ipi_A Geranyltranstransferase; isoprene biosynthesis, helical bundle,
protein structure initiative II (PSI II), structural
genomics, nysgxrc; 1.90A {Methanosarcina mazei}
Length = 295
Score = 48.4 bits (116), Expect = 6e-07
Identities = 19/116 (16%), Positives = 39/116 (33%), Gaps = 19/116 (16%)
Query: 140 GQSLDLSTANDLSKFTMDRYEAIVKYKTA--FYSFQLPVALAMHMAGM---QDVEVHRQA 194
G+ LDL ++ F + Y + KTA F A++ + + E+ +
Sbjct: 142 GEVLDLKLEDE--SFGENDYFKCIYKKTASLF-------AISASIGAYTGGAEEELAERF 192
Query: 195 RTLLLEMGHFFQVQDDYLDCFGTPDVTGKIGTDIEDGKCSWLAVVALQRATPAQRK 250
+G +Q+ DD L+ G + + + + + K
Sbjct: 193 SHFGNALGTAYQIVDDILEFLEVV-----EGKESKFTSETLPHIYMKSTSKEEALK 243
>4fp4_A Polyprenyl synthetase; isoprenoid synthesis, isoprenoid diphosphate
synthase, trans; HET: GER UNL; 2.00A {Pyrobaculum
calidifontis}
Length = 285
Score = 48.1 bits (115), Expect = 8e-07
Identities = 27/118 (22%), Positives = 46/118 (38%), Gaps = 19/118 (16%)
Query: 138 SMGQSLDLSTANDLSKFTMDRYEAIVKYKTAFYSFQLPVALAMHMAGM--QDVEVHRQAR 195
S+GQ+LDL + ++KTA L + A+ M + E+ A+
Sbjct: 146 SVGQALDL----------EGERDKAAEFKTA----PL-IEAALVMPLVILGRRELIETAK 190
Query: 196 TLLLEMGHFFQVQDDYLDCFGTPDVTGKIGTDIEDGKCSWLAVVALQRATPAQRKLME 253
L ++G +Q DDY D T I +I G+ + A +L++
Sbjct: 191 KLGTKLGILYQYSDDYSDENVERPETKSIANEI--GRYLLKIKEHVGDAIAPFERLIK 246
>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 = 48.0 bits (115), Expect = 8e-07
Identities = 34/113 (30%), Positives = 52/113 (46%), Gaps = 18/113 (15%)
Query: 140 GQSLDLSTANDLSKFTMDRYEAIVKYKTAFYSFQLPVAL---AMHMAGMQDVEVHRQART 196
GQ+LDL +D E I ++KT AL A+ + + + R+A
Sbjct: 157 GQALDLDAEG--KHVPLDALERIHRHKTG--------ALIRAAVRLGALSAGDKGRRALP 206
Query: 197 LLLEMGHF----FQVQDDYLDCFGTPDVTGK-IGTDIEDGKCSWLAVVALQRA 244
+L + FQVQDD LD G GK G D + GK ++ A++ L++A
Sbjct: 207 VLDKYAESIGLAFQVQDDILDVVGDTATLGKRQGADQQLGKSTYPALLGLEQA 259
>4f62_A Geranyltranstransferase; enzyme function initiative, structural
genomics; 2.10A {Marinomonas SP}
Length = 317
Score = 48.0 bits (115), Expect = 9e-07
Identities = 39/151 (25%), Positives = 64/151 (42%), Gaps = 25/151 (16%)
Query: 105 AYKMLAQPSELTPEN-LHLAQILGWCVEIVSLKTSM--GQSLDLSTANDLSKFTMDRYEA 161
A+++L+ P+ PE + L Q L S + M GQ +DLS+ N ++ E
Sbjct: 122 AFELLSNPTSAQPELAIKLIQELVVA----SGRNGMITGQMIDLSSEN--KNISLAELEQ 175
Query: 162 IVKYKTAFYSFQLPVAL---AMHMAGMQDVEVHRQARTLLLEMGHF----FQVQDDYLDC 214
+ +KT AL ++ M + +V + L H FQVQDD +D
Sbjct: 176 MHVHKTG--------ALIKASVRMGALSTGQVKPEQLAKLDAYAHAIGLAFQVQDDIIDL 227
Query: 215 FGTPDVTGK-IGTDIEDGKCSWLAVVALQRA 244
+ GK +D E K ++ ++ L A
Sbjct: 228 TSDTETLGKTQFSDAEANKATYPKLLGLDGA 258
>3p8r_A Geranyltranstransferase; isoprenyl synthase, structural genomics,
PSI, protein struct initiative, nysgrc; 2.50A {Vibrio
cholerae}
Length = 302
Score = 48.0 bits (115), Expect = 1e-06
Identities = 33/113 (29%), Positives = 49/113 (43%), Gaps = 18/113 (15%)
Query: 140 GQSLDLSTANDLSKFTMDRYEAIVKYKTAFYSFQLPVAL---AMHMAGMQDVEVHRQART 196
GQ+LDL+ N +++ E I + KT AL A+ + + E R
Sbjct: 163 GQALDLAAEN--RLISLEELETIHRNKTG--------ALMRCAIRLGALAAGEKGRAMLP 212
Query: 197 LLLEMGHF----FQVQDDYLDCFGTPDVTGK-IGTDIEDGKCSWLAVVALQRA 244
L FQVQDD LD + GK G+D E K ++ A++ L+ A
Sbjct: 213 HLDRYAEAVGLAFQVQDDILDIISDTETLGKPQGSDQELNKSTYPALLGLEGA 265
>3ts7_A Geranyltranstransferase; isoprenoid synthesis, farnesyl diphosphate
synthase; 1.94A {Methylococcus capsulatus}
Length = 324
Score = 47.2 bits (113), Expect = 2e-06
Identities = 27/113 (23%), Positives = 45/113 (39%), Gaps = 18/113 (15%)
Query: 140 GQSLDLSTANDLSKFTMDRYEAIVKYKTAFYSFQLPVAL---AMHMAGMQDVEVHRQART 196
GQ++DL++ K + E + KT AL ++ +A + + +
Sbjct: 163 GQAIDLASVG--KKLDLPGLENMHIRKTG--------ALIRASVRLACLARPGLPAEQFD 212
Query: 197 LLLEMGHF----FQVQDDYLDCFGTPDVTGK-IGTDIEDGKCSWLAVVALQRA 244
L FQ+QDD LD GK G D + K ++ A++ L A
Sbjct: 213 RLDHYAKCIGLAFQIQDDILDEESDTQTLGKTRGKDRDHNKPNYPALLGLSGA 265
>3uca_A Geranyltranstransferase; isoprenoid synthesis, isoprenoid
diphosphate synthase; 2.00A {Clostridium perfringens}
Length = 324
Score = 47.3 bits (113), Expect = 2e-06
Identities = 28/150 (18%), Positives = 55/150 (36%), Gaps = 23/150 (15%)
Query: 105 AYKMLAQPSELTPEN-LHLAQILGWCVEIVSLKTSM--GQSLDLSTANDLSKFTMDRYEA 161
A K+L S ++ L +I+ M GQ +D+ D + ++ +
Sbjct: 151 AMKILVDYSLEEGKSALKATKIIADAAGS----DGMIGGQIVDII-NEDKEEISLKELDY 205
Query: 162 IVKYKTAFYSFQLPVAL---AMHMAGM---QDVEVHRQARTLLLEMGHFFQVQDDYLDCF 215
+ KT L ++ + ++ ++G FQ++DD LD
Sbjct: 206 MHLKKTG--------ELIKASIMSGAVLAEASEGDIKKLEGFGYKLGLAFQIKDDILDVV 257
Query: 216 GTPDVTGK-IGTDIEDGKCSWLAVVALQRA 244
G GK + D E K +++ + L+
Sbjct: 258 GNAKDLGKNVHKDQESNKNNYITIFGLEEC 287
>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 = 46.8 bits (110), Expect = 3e-06
Identities = 32/195 (16%), Positives = 62/195 (31%), Gaps = 69/195 (35%)
Query: 26 VLSKDESRDF---MAIFPDLVRDLTDAGRHSDIPDVTKWYAKVLQ--YNKAISNNVYLGT 80
VL E R +++FP + IP +L + I ++V +
Sbjct: 365 VLEPAEYRKMFDRLSVFPP----------SAHIP------TILLSLIWFDVIKSDVMV-- 406
Query: 81 YFIVQVLQYNVPSGKKNRGLA------LVVAYKMLAQPSELTPEN---LHLAQILGWCVE 131
+V L L ++ + ++ EN LH I+
Sbjct: 407 --VVNKLH--------KYSLVEKQPKESTISIPSIYLELKVKLENEYALH-RSIVD---- 451
Query: 132 IVSLKTSMGQSLDLSTANDLSKFTMDRYEAIVKYKTAFYSFQLPVALAMHMAGMQDVEVH 191
++ ++ D +DL +D+Y FYS + H+ ++ E
Sbjct: 452 ----HYNIPKTFDS---DDLIPPYLDQY---------FYSH-----IGHHLKNIEHPERM 490
Query: 192 RQARTLLLEMGHFFQ 206
R + L+ F +
Sbjct: 491 TLFRMVFLDF-RFLE 504
Score = 41.8 bits (97), Expect = 2e-04
Identities = 36/218 (16%), Positives = 65/218 (29%), Gaps = 72/218 (33%)
Query: 33 RDFMAIF-PDLVRDLTDAGRHSDIPDVTKWYAKVLQYNKAI-SNNVYLGTYFIVQVL-QY 89
+D +++F V + D D+ D+ K + + I S + GT + L
Sbjct: 19 KDILSVFEDAFVDNF-DC---KDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSK 74
Query: 90 NVPSGKKNRGLALVVAYKMLAQPSELTPENLHLAQILGWCVEIV--SLKTSMGQSLDLST 147
+K L + YK L P E S+ T M
Sbjct: 75 QEEMVQKFVEEVLRINYKFLMSP---------------IKTEQRQPSMMTRMYIEQRDRL 119
Query: 148 AND---LSKFTMDRYEAIVKYKTAFYSFQLPVALAMHMAGMQDVEVHRQARTLLLEMGHF 204
ND +K+ + R + +K + A + P ++V +
Sbjct: 120 YNDNQVFAKYNVSRLQPYLKLRQALLELR-P---------AKNVLID------------- 156
Query: 205 FQVQDDYLDCFGTPDVTGKIGTDIEDGKCSWLAVVALQ 242
G +G+ GK +W+A+
Sbjct: 157 -----------------GVLGS----GK-TWVALDVCL 172
Score = 33.3 bits (75), Expect = 0.080
Identities = 36/253 (14%), Positives = 72/253 (28%), Gaps = 62/253 (24%)
Query: 19 PLAATNTVLSKDE-SRDFMAIFPDLVRDLTDAGRH-SDIPDVT--------KWY--AKVL 66
L N V +K SR L A +V K + V
Sbjct: 118 RLYNDNQVFAKYNVSR------LQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVC 171
Query: 67 QYNK---AISNNVY---LGTYF----IVQVLQYNVPSGKKNRGLALVVAYKMLAQPSELT 116
K + ++ L ++++LQ + + + S
Sbjct: 172 LSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQ--------KLLYQIDPNWTSRSDHSSNI 223
Query: 117 PENLHLAQILGWCVEIVSLKTSMGQSL----DLSTANDLSKFTMD-------RYEAIVKY 165
+H Q ++ K L ++ A + F + R++ + +
Sbjct: 224 KLRIHSIQ--AELRRLLKSK-PYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDF 280
Query: 166 KTAFYSFQLPVALAMHMAGMQDVEVHRQARTLLLEMGHFFQVQDDYL---DCFGTPDVTG 222
+A + ++L H + + ++LLL+ + + L P
Sbjct: 281 LSAATTTH--ISLDHHSMTL----TPDEVKSLLLK---YLDCRPQDLPREVLTTNPRRLS 331
Query: 223 KIGTDIEDGKCSW 235
I I DG +W
Sbjct: 332 IIAESIRDGLATW 344
>1rtr_A Geranyltranstransferase; 2.50A {Staphylococcus aureus} SCOP:
a.128.1.1
Length = 301
Score = 46.0 bits (110), Expect = 4e-06
Identities = 38/150 (25%), Positives = 65/150 (43%), Gaps = 24/150 (16%)
Query: 105 AYKMLAQPSELTPEN-LHLAQILGWCVEIVSLKTSM--GQSLDLSTANDLSKFTMDRYEA 161
A+++++ LT E + + Q L S M GQ LD+ + ++ E
Sbjct: 119 AFELISSDDRLTDEVKIKVLQRLSIA----SGHVGMVGGQMLDMQSEG--QPIDLETLEM 172
Query: 162 IVKYKTAFYSFQLPVAL---AMHMAGM---QDVEVHRQARTLLLEMGHFFQVQDDYLDCF 215
I K KT AL A+ A D + +G FQ++DD LDC+
Sbjct: 173 IHKTKTG--------ALLTFAVMSAADIANVDDTTKEHLESYSYHLGMMFQIKDDLLDCY 224
Query: 216 GTPDVTGK-IGTDIEDGKCSWLAVVALQRA 244
G GK +G+D+E+ K ++++++ A
Sbjct: 225 GDEAKLGKKVGSDLENNKSTYVSLLGKDGA 254
>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 = 45.3 bits (108), Expect = 7e-06
Identities = 28/113 (24%), Positives = 43/113 (38%), Gaps = 18/113 (15%)
Query: 140 GQSLDLSTANDLSKFTMDRYEAIVKYKTAFYSFQLPVAL---AMHMAGMQDVEVHRQART 196
GQ++DL + K E + ++KT AL ++ + + +
Sbjct: 157 GQAIDLGSVG--LKLDQQALEYMHRHKTG--------ALIEASVILGALASGRAEKGELK 206
Query: 197 LLLEMGHF----FQVQDDYLDCFGTPDVTGK-IGTDIEDGKCSWLAVVALQRA 244
L FQVQDD LD GK G DI K ++ A++ L A
Sbjct: 207 ALQTYAQAIGLAFQVQDDILDVESDTATLGKRQGADIARDKPTYPALLGLAAA 259
>2h8o_A Geranyltranstransferase; geranyltransferase,agrobacterium
tumefaciens, structural GEN PSI-2, protein structure
initiative; 1.60A {Agrobacterium tumefaciens}
Length = 335
Score = 45.0 bits (107), Expect = 1e-05
Identities = 28/106 (26%), Positives = 39/106 (36%), Gaps = 5/106 (4%)
Query: 140 GQSLDLSTANDLSKFTMDRYEAIVKYKTAFYSFQLPVALAMHMAGMQDVEVHRQARTLLL 199
GQ+LDL+ D + KT + +AG E R R
Sbjct: 197 GQALDLAAEK--KAPDEDGIITLQAMKTG-ALLRFACEAGAIIAGSNQAERQR-LRLFGE 252
Query: 200 EMGHFFQVQDDYLDCFGTPDVTGK-IGTDIEDGKCSWLAVVALQRA 244
++G FQ+ DD LD GK G D GK + +A+ A
Sbjct: 253 KIGLSFQLADDLLDLTADAATMGKATGKDAARGKGTLVALRGEAWA 298
>3llw_A Geranyltranstransferase (ISPA); structural genomics, PSI, protein
structure initiative, nysgrc; 2.30A {Helicobacter
pylori} PDB: 3q1o_A*
Length = 311
Score = 44.6 bits (106), Expect = 1e-05
Identities = 28/106 (26%), Positives = 54/106 (50%), Gaps = 6/106 (5%)
Query: 140 GQSLDLSTANDLSKFTMDRYEAIVKYKTAFYSFQLPVALAMHMAGMQDVEVHRQARTLLL 199
GQ+LD N + +++ + ++KTA + + + +G++D E+ + + L
Sbjct: 164 GQALDCYFEN--TPLNLEQLTFLHEHKTAKL-ISASLIMGLVASGIKDEELFKWLQAFGL 220
Query: 200 EMGHFFQVQDDYLDCFGTPDVTGK-IGTDIEDGKCSWLAVVALQRA 244
+MG FQV DD +D + +GK D K S++ ++ L+RA
Sbjct: 221 KMGLCFQVLDDIIDVTQDEEESGKTTHLDS--AKNSFVNLLGLERA 264
>3p8l_A Geranyltranstransferase; isoprenyl synthase, structural genomics,
PSI, protein struct initiative, nysgrc; 2.00A
{Enterococcus faecalis}
Length = 302
Score = 43.4 bits (103), Expect = 3e-05
Identities = 29/112 (25%), Positives = 44/112 (39%), Gaps = 17/112 (15%)
Query: 140 GQSLDLSTANDLSKFTMDRYEAIVKYKTAFYSFQLPVAL---AMHMAGM---QDVEVHRQ 193
GQ D+ T++ A+ + KT AL A+ G+ Q EV
Sbjct: 161 GQMGDIEGEK--VSLTLEELAAVHEKKTG--------ALIEFALIAGGVLANQTEEVIGL 210
Query: 194 ARTLLLEMGHFFQVQDDYLDCFGTPDVTGK-IGTDIEDGKCSWLAVVALQRA 244
G FQ++DD LD T GK +G D K ++ A++ + A
Sbjct: 211 LTQFAHHYGLAFQIRDDLLDATSTEADLGKKVGRDEALNKSTYPALLGIAGA 262
>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 = 42.6 bits (101), Expect = 6e-05
Identities = 23/112 (20%), Positives = 39/112 (34%), Gaps = 17/112 (15%)
Query: 140 GQSLDLSTANDLSKFTMDRYEAIVKYKTAFYSFQLPVAL---AMHMAGM---QDVEVHRQ 193
GQ+ D+ + + + + + K KT AL A+ +
Sbjct: 160 GQAKDIQSEH--VNLPLSQLRVLHKEKTG--------ALLHYAVQAGLILGQAPEAQWPA 209
Query: 194 ARTLLLEMGHFFQVQDDYLDCFGTPDVTGK-IGTDIEDGKCSWLAVVALQRA 244
G FQ+ DD LD +P GK D ++ K ++ + L A
Sbjct: 210 YLQFADAFGLAFQIYDDILDVVSSPAEMGKATQKDADEAKNTYPGKLGLIGA 261
>3npk_A Geranyltranstransferase; isoprene biosynthesis, SGX, structural
genomics protein structure initiative; 1.50A
{Campylobacter jejuni}
Length = 291
Score = 39.5 bits (93), Expect = 5e-04
Identities = 28/112 (25%), Positives = 52/112 (46%), Gaps = 19/112 (16%)
Query: 140 GQSLDLSTANDLSKFTMDRYEAIVKYKTAFYSFQLPVAL---AMHMAGM---QDVEVHRQ 193
GQ++D + + +++ E + +KTA L A+ M + E Q
Sbjct: 150 GQAIDCFFED--KRLSLNELEFLHTHKTA--------RLIAAALKMGCEICELNNEESNQ 199
Query: 194 ARTLLLEMGHFFQVQDDYLDCFGTPDVTGK-IGTDIEDGKCSWLAVVALQRA 244
L L++G FQ+ DD +D + + +GK DI K S++ ++ L++A
Sbjct: 200 IYKLGLKLGLIFQINDDIIDVTTSQEQSGKPTNNDIH--KNSFVNLLGLEQA 249
>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 = 36.7 bits (84), Expect = 0.004
Identities = 18/91 (19%), Positives = 34/91 (37%), Gaps = 6/91 (6%)
Query: 140 GQSLDLSTANDLSKFTMDRYEAIVKYKTAFYSFQLPVALAMHMAGMQDVEVHRQARTLLL 199
G+++D+ + + + E + + T F + + G +
Sbjct: 149 GEAMDVEFERRXMEVSQEMVERMYAFXTGAL-FAFCFSAPFILXGXDHTXMXLLGEXF-- 205
Query: 200 EMGHFFQVQDDYLDCFGTPDVTGK-IGTDIE 229
G FQ+ DD D G+ + GK +G D E
Sbjct: 206 --GVAFQIYDDLXDILGSFEKVGKDLGKDTE 234
>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 = 33.3 bits (77), Expect = 0.050
Identities = 27/112 (24%), Positives = 46/112 (41%), Gaps = 28/112 (25%)
Query: 140 GQSLDL-STANDLSKFTMDRYEAIVKYKTAFYSFQLPVAL---AMHMAGM---QDVEVHR 192
GQ +D+ S DL+ ++ + I +KTA AL + + G+ E
Sbjct: 165 GQVVDISSEGLDLNNVGLEHLKFIHLHKTA--------ALLEASAVLGGIIGGGSDEEIE 216
Query: 193 QARTLLLEMGHFFQVQDDYLDCFGTPDVTGKIGTDIEDGKCSWLAVVALQRA 244
+ R +G FQV DD L DVT K ++ ++ L+++
Sbjct: 217 RLRKFARCIGLLFQVVDDIL------DVTK-------SSKLTYPKLMGLEKS 255
>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 = 28.0 bits (63), Expect = 2.9
Identities = 16/119 (13%), Positives = 36/119 (30%), Gaps = 17/119 (14%)
Query: 140 GQSLDLSTANDLSKFTMDRYEAIVKYKTAFYSFQLPVALAMHMAGMQDVEVHRQAR---- 195
G + + ++D E + K K A + G + E+ +
Sbjct: 154 GLHREEEIVD--GNTSLDFIEYVCKKKYG-EMHACGAACGAILGGAAEEEIQKLRNFGLY 210
Query: 196 ----TLLLEMGHFFQVQDDYLDC---FGTPDVTGK-IGTDIED--GKCSWLAVVALQRA 244
++EM + Q+ D+ + + G G + E + ++ A
Sbjct: 211 QGTLRGMMEMKNSHQLIDENIIGKLKELALEELGGFHGKNAELMSSLVAEPSLYAAHHH 269
>3aay_A Putative thiosulfate sulfurtransferase; sulfurtranserase,
structural genomics, PSI, structure initiative; 1.90A
{Mycobacterium tuberculosis} PDB: 3aax_A 3hwi_A
Length = 277
Score = 27.2 bits (61), Expect = 4.6
Identities = 13/45 (28%), Positives = 21/45 (46%), Gaps = 7/45 (15%)
Query: 37 AIFPDLVRDLTDAGRHSDIPDVTKWYAKVLQYNKAISNN----VY 77
AI D DL D + D D ++ +K+L + I+N +Y
Sbjct: 42 AIKLDWRTDLQDPVKR-DFVDAQQF-SKLLS-ERGIANEDTVILY 83
>3u22_A Putative HMUY_LIKE heme binding protein; transport, structural
genomics, joint center for structural JCSG, protein
structure initiative; HET: UNL; 2.12A {Bacteroides
vulgatus}
Length = 202
Score = 26.7 bits (58), Expect = 6.8
Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 5/30 (16%)
Query: 72 ISNNVYL-----GTYFIVQVLQYNVPSGKK 96
+SN VY+ GTY V++ Y SG K
Sbjct: 160 LSNKVYMVKLKDGTYAAVRLTNYMNASGVK 189
>3u52_C Phenol hydroxylase component PHL; 4-helix bundle, dioxygen,
hydrocarbons, oxidore; HET: MPO EPE; 1.95A {Pseudomonas
stutzeri} PDB: 2inn_C* 2inp_C
Length = 333
Score = 26.5 bits (58), Expect = 9.0
Identities = 17/94 (18%), Positives = 31/94 (32%), Gaps = 10/94 (10%)
Query: 165 YKTAFYSFQLPVALAMHMAGMQDVEVHRQARTLLLEMGHFFQVQDD-----YLDCFGTPD 219
+ +P+ A M + ++ A + H + D YL
Sbjct: 115 TQKQLLRLLVPLRHVELGANMNNAKIAGDATATTVSQMHIYTGMDRLGIGQYLSRIAL-M 173
Query: 220 VTGKIGTDIEDGKCSWLAVVALQRATPAQRKLME 253
+ G G +++ K W+ Q RKL+E
Sbjct: 174 IDGSTGAALDESKAYWMDDEMWQ----PMRKLVE 203
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.320 0.133 0.387
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: 3,764,256
Number of extensions: 218324
Number of successful extensions: 416
Number of sequences better than 10.0: 1
Number of HSP's gapped: 362
Number of HSP's successfully gapped: 60
Length of query: 255
Length of database: 6,701,793
Length adjustment: 91
Effective length of query: 164
Effective length of database: 4,160,982
Effective search space: 682401048
Effective search space used: 682401048
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: 56 (25.4 bits)