RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 025823
(247 letters)
>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 = 330 bits (847), Expect = e-114
Identities = 124/248 (50%), Positives = 171/248 (68%), Gaps = 1/248 (0%)
Query: 1 MDGSHTRRGQPCWFRVPKVGMIAANDGVLLRNHISRILKNHFRDKPYYVDLLDLFNEVEF 60
MD S TRRGQ CW++ VG+ A ND LL + + R+LK + R +PYYV LL+LF + +
Sbjct: 120 MDQSLTRRGQLCWYKKEGVGLDAINDSFLLESSVYRVLKKYCRQRPYYVHLLELFLQTAY 179
Query: 61 QTASGQMIDLITTIEGEKDLSKYSLPLHRRIVQYKTAYYSFYLPVACALLMAG-ENLDKH 119
QT GQM+DLIT + DLS +S ++ IV+YKTA+YSFYLPVA A+ M G ++ ++H
Sbjct: 180 QTELGQMLDLITAPVSKVDLSHFSEERYKAIVKYKTAFYSFYLPVAAAMYMVGIDSKEEH 239
Query: 120 VEVKDILVQMGIYFQVQDDFLDCFGSPEVIGKVGTDIEDYKCSWLVVKALELCNEEQKKL 179
K IL++MG YFQ+QDD+LDCFG P + G VGTDI+D KCSWLVV+ L+ EQ++L
Sbjct: 240 ENAKAILLEMGEYFQIQDDYLDCFGDPALTGAVGTDIQDNKCSWLVVQCLQRVTPEQRQL 299
Query: 180 VHENYGKVDPACVAKVKELYKTLDLEGAFVEYEKESYEKLTKSIEAHPTKEVQAVLKSFL 239
+ +NYG+ +P VAKVKELY+ + + AF +YE+ SY +L + IE H + + +
Sbjct: 300 LEDNYGRKEPEKVAKVKELYEAVGMRAAFQQYEESSYRRLQELIEKHSNRLPKEIFLGLA 359
Query: 240 AKIYKRQK 247
KIYKRQK
Sbjct: 360 QKIYKRQK 367
>2qis_A Farnesyl pyrophosphate synthetase; trans-prenyltransferase,
structural genomics, structural GEN consortium, SGC,
transferase; HET: RIS; 1.80A {Homo sapiens} PDB: 4dem_F*
1yv5_A* 1yq7_A* 2opm_A* 2opn_A* 3cp6_A* 2rah_A* 2vf6_A*
1zw5_A* 3b7l_A* 3s4j_A* 3rye_A* 3n45_F* 2f89_F* 2f7m_F*
2f8z_F* 2f8c_F* 2f92_F* 2f9k_F* 3n1v_F* ...
Length = 374
Score = 325 bits (835), Expect = e-112
Identities = 118/248 (47%), Positives = 169/248 (68%), Gaps = 1/248 (0%)
Query: 1 MDGSHTRRGQPCWFRVPKVGMIAANDGVLLRNHISRILKNHFRDKPYYVDLLDLFNEVEF 60
MD S TRRGQ CW++ P VG+ A ND LL I R+LK + R++PYY++L++LF + +
Sbjct: 127 MDSSLTRRGQICWYQKPGVGLDAINDANLLEACIYRLLKLYCREQPYYLNLIELFLQSSY 186
Query: 61 QTASGQMIDLITTIEGEKDLSKYSLPLHRRIVQYKTAYYSFYLPVACALLMAGENLDK-H 119
QT GQ +DL+T +G DL +++ ++ IV+YK+A+YSFYLP+A A+ MAG + +K H
Sbjct: 187 QTEIGQTLDLLTAPQGNVDLVRFTEKRYKSIVKYKSAFYSFYLPIAAAMYMAGIDGEKEH 246
Query: 120 VEVKDILVQMGIYFQVQDDFLDCFGSPEVIGKVGTDIEDYKCSWLVVKALELCNEEQKKL 179
K IL++MG +FQ+QDD+LD FG P V GK+GTDI+D KCSWLVV+ L+ EQ ++
Sbjct: 247 ANAKKILLEMGEFFQIQDDYLDLFGDPSVTGKIGTDIQDNKCSWLVVQCLQRATPEQYQI 306
Query: 180 VHENYGKVDPACVAKVKELYKTLDLEGAFVEYEKESYEKLTKSIEAHPTKEVQAVLKSFL 239
+ ENYG+ + VA+VK LY+ LDL F++YE++SY + IE + AV
Sbjct: 307 LKENYGQKEAEKVARVKALYEELDLPAVFLQYEEDSYSHIMALIEQYAAPLPPAVFLGLA 366
Query: 240 AKIYKRQK 247
KIYKR+K
Sbjct: 367 RKIYKRRK 374
>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 = 317 bits (815), Expect = e-109
Identities = 103/262 (39%), Positives = 152/262 (58%), Gaps = 15/262 (5%)
Query: 1 MDGSHTRRGQPCWFRVPKVGM-IAANDGVLLRNHISRILKNHFRDKPYYVDLLDLFNEVE 59
MD S TRRG+PCW+R P V + A NDG+LL++ + + F D+P+ DLL FN V+
Sbjct: 129 MDNSVTRRGKPCWYRHPDVTVQCAINDGLLLKSWTHMMAMHFFADRPFLQDLLCRFNRVD 188
Query: 60 FQTASGQMIDLITTIEGEK-----------DLSKYSLPLHRRIVQYKTAYYSFYLPVACA 108
+ TA GQ+ D+ + + K D ++++L ++RIV+YKTAYY++ LP+
Sbjct: 189 YTTAVGQLYDVTSMFDSNKLDPDVSQPTTTDFAEFTLSNYKRIVKYKTAYYTYLLPLVMG 248
Query: 109 LLMAGENLDKHVE-VKDILVQMGIYFQVQDDFLDCFGSPEVIGKVGTDIEDYKCSWLVVK 167
L+++ + +++ + MG YFQVQDD +DCF PE +GKVGTDI+D KCSWL V
Sbjct: 249 LIVSEALPTVDMGVTEELAMLMGEYFQVQDDVMDCFTPPERLGKVGTDIQDAKCSWLAVT 308
Query: 168 ALELCNEEQKKLVHENYGKVDPACVAKVKELYKTLDLEGAFVEYEKESYEKLTKSIEAHP 227
L + Q NYG D VA V+ LY+ DL+G +V YE E++ + IE
Sbjct: 309 FLAKASSAQVAEFKANYGSGDSEKVATVRRLYEEADLQGDYVAYEAAVAEQVKELIEKLR 368
Query: 228 --TKEVQAVLKSFLAKIYKRQK 247
+ A +++ K YKRQK
Sbjct: 369 LCSPGFAASVETLWGKTYKRQK 390
>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 = 315 bits (810), Expect = e-108
Identities = 101/262 (38%), Positives = 145/262 (55%), Gaps = 15/262 (5%)
Query: 1 MDGSHTRRGQPCWFRVPKVG-MIAANDGVLLRNHISRILKNHFRDKPYYVDLLDLFNEVE 59
MDGS RRG+PCW+R P V A NDG++L++ + ++F D+P+ DLL LF +V+
Sbjct: 101 MDGSVMRRGKPCWYRFPGVTTQCAINDGIILKSWTQIMAWHYFADRPFLKDLLCLFQKVD 160
Query: 60 FQTASGQMIDLITTIEGEK-----------DLSKYSLPLHRRIVQYKTAYYSFYLPVACA 108
+ TA GQM D+ + + K D ++++ +++RIV+YKT +Y++ LP+
Sbjct: 161 YATAVGQMYDVTSMCDSNKLDPEVAQPMTTDFAEFTPAIYKRIVKYKTTFYTYLLPLVMG 220
Query: 109 LLMAGENLDKHVE-VKDILVQMGIYFQVQDDFLDCFGSPEVIGKVGTDIEDYKCSWLVVK 167
L ++ + V+ + +G YFQVQDD +DCF PE +GKVGTDIED KCSWL V
Sbjct: 221 LFVSEAAASVEMNLVERVAHLIGEYFQVQDDVMDCFTPPEQLGKVGTDIEDAKCSWLAVT 280
Query: 168 ALELCNEEQKKLVHENYGKVDPACVAKVKELYKTLDLEGAFVEYEKESYEKLTKSIEAHP 227
L N Q NYG DPA VA VK LY +L+ F YE E ++ IE
Sbjct: 281 FLGKANAAQVAEFKANYGDKDPAKVAVVKRLYSEANLQADFAAYEAEVVREVESLIEQLK 340
Query: 228 TKE--VQAVLKSFLAKIYKRQK 247
K + K +KR+K
Sbjct: 341 VKSPTFAESVAVVWEKTHKRKK 362
>2ihi_A Pyrophosphate synthase; PV092040, structural genomics, structural
genomics consortium, SGC, transferase; 2.00A {Plasmodium
vivax sai-1} PDB: 3mav_A 3cc9_A* 3ez3_A* 3ldw_A* 3mys_A*
3ph7_A* 3rbm_A*
Length = 395
Score = 294 bits (755), Expect = 1e-99
Identities = 85/267 (31%), Positives = 141/267 (52%), Gaps = 22/267 (8%)
Query: 1 MDGSHTRRGQPCWFRVPKVGM-IAANDGVLLRNHISRILKNHFRDKPYYVDLLDLFNEVE 59
MD RR + CW+ + V A ND +LL N I ++++ + R++ YVD++ F +
Sbjct: 128 MDKGEMRRNKYCWYLLKDVETKNAVNDVLLLYNSIYKLIEIYLRNESCYVDVIATFRDAT 187
Query: 60 FQTASGQMIDLITTIEGE-------------------KDLSKYSLPLHRRIVQYKTAYYS 100
+T GQ +D + D++ + +++ IV +KTAYYS
Sbjct: 188 LKTIIGQHLDTNIFSDKYSDAHREIDVNNINVPEQPVIDINMINFGVYKNIVIHKTAYYS 247
Query: 101 FYLPVACALLMAGENLDKHVE--VKDILVQMGIYFQVQDDFLDCFGSPEVIGKVGTDIED 158
F+LP+ C +L+AG +D + ++DI + MG YFQ+ DD+LD FG GKVG+DI++
Sbjct: 248 FFLPIVCGMLLAGIAVDNLIYKKIEDISMLMGEYFQIHDDYLDIFGDSTKTGKVGSDIQN 307
Query: 159 YKCSWLVVKALELCNEEQKKLVHENYGKVDPACVAKVKELYKTLDLEGAFVEYEKESYEK 218
K +W ++K ELC+E K + +NYGK + ACV + LY+ + + YEK K
Sbjct: 308 NKLTWPLIKTFELCSEPDKIKIVKNYGKNNLACVKVIDSLYEQYKIRKHYESYEKAQKAK 367
Query: 219 LTKSIEAHPTKEVQAVLKSFLAKIYKR 245
+ +I + ++ VLK L ++
Sbjct: 368 ILSAINELHHEGIEYVLKYLLEILFTG 394
>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 = 282 bits (724), Expect = 3e-95
Identities = 63/249 (25%), Positives = 113/249 (45%), Gaps = 16/249 (6%)
Query: 1 MDGSHTRRGQPCWFRVPKVGMIAANDGVLLRNHISRILK--NHFRDKPYYVDLLDLFNEV 58
MD RRG PCW+ V A ND L+ ++ + + + ++NE
Sbjct: 118 MDSGKFRRGAPCWYIVHGQSN-AINDIFFLKMLSLSLIFELSSVFGNDIVMKIQKIYNES 176
Query: 59 EFQTASGQMIDLITTIEGEKDLSKYSLPLHRRIVQYKTAYYSFYLPVACALLMAGENLDK 118
F T GQ +DL + D + +V+ KT+ Y+FY+PV L ++ +
Sbjct: 177 IFFTVLGQHLDLSYFDLSKADKISER---YFSMVEMKTSRYTFYMPVFFGLTLSEIQVSS 233
Query: 119 --HVEVKDILVQMGIYFQVQDDFLDCFGSPEVIGKVGTDIEDYKCSWLVVKALELCNEEQ 176
++ IL ++G ++QV +D D + DI +K +W + K+ E+ +EE
Sbjct: 234 AQLNLIEAILYKLGEFYQVHNDVSDYLFND----SNADDICRFKLTWPLQKSFEIADEEM 289
Query: 177 KKLVHENYGKVDPACVAKVKELYKTLDLEGAFVEYEKESYEKLTKSIEAHPTKEVQAVLK 236
K + ENYGK + VK+ Y L + ++EY++ + + L K ++ +Q V
Sbjct: 290 KLKISENYGKNS----SLVKDCYNLLKINEHYLEYQRNALDYLIKLVKDITDDSLQKVFI 345
Query: 237 SFLAKIYKR 245
+ +I +
Sbjct: 346 HLIHQISEL 354
>3lk5_A Geranylgeranyl pyrophosphate synthase; structural genomics, protein
structure initiative, geranylge pyrophosphate synthase;
1.90A {Corynebacterium glutamicum} PDB: 3qqv_A*
Length = 380
Score = 102 bits (256), Expect = 1e-25
Identities = 53/271 (19%), Positives = 100/271 (36%), Gaps = 32/271 (11%)
Query: 1 MDGSHTRRGQPC-WFRVPKVGMIAANDGVLLR--NHIS------------RILKNHFRDK 45
+D S TRRG P V +G +S +L++
Sbjct: 111 IDSSDTRRGAPTVHRAVEADHRANNFEGDPEHFGVSVSILAGDMALVWAEDMLQDSGLSA 170
Query: 46 PYYVDLLDLFNEVEFQTASGQMIDLITTIEGEKDLSKYSLPLHRRIVQYKTAYYSFYLPV 105
D + + + GQ++D+ + + + ++KTA Y+ P+
Sbjct: 171 EALARTRDAWRGMRTEVIGGQLLDIYLESHANESVELA-----DSVNRFKTAAYTIARPL 225
Query: 106 ACALLMAGENLDKHVEVKDILVQMGIYFQVQDDFLDCFGSPEVIGK-VGTDIEDYKCSWL 164
+AG + + +GI FQ++DD L FG P + GK G DI + K + L
Sbjct: 226 HLGASIAGGSPQLIDALLHYGHDIGIAFQLRDDLLGVFGDPAITGKPAGDDIREGKRTVL 285
Query: 165 VVKALELCNEEQKKLVHENYGKVDPAC----VAKVKELYKTLDLEGAFVEYEKESYEKLT 220
+ AL+ +++ + V +A + E + GA E E+ +
Sbjct: 286 LALALQRADKQSPEAATAIRAGVGKVTSPEDIAVITEHIRAT---GAEEEVEQRISQLTE 342
Query: 221 KSIEA----HPTKEVQAVLKSFLAKIYKRQK 247
+ EV+A L++ + +R++
Sbjct: 343 SGLAHLDDVDIPDEVRAQLRALAIRSTERRE 373
>1wmw_A Geranylgeranyl diphosphate synthetase; GGPP, prenyl diphosphate
synthase, structural genom riken structural
genomics/proteomics initiative; 1.55A {Thermus
thermophilus}
Length = 330
Score = 94.3 bits (235), Expect = 6e-23
Identities = 65/266 (24%), Positives = 104/266 (39%), Gaps = 38/266 (14%)
Query: 1 MDGSHTRRGQPC----WFRVPKVGMIAA-NDGVLLRNHISRILKNHFRDKPYYVDLLDLF 55
DGS RRG+P M A N G + + +L + ++L F
Sbjct: 82 EDGSEERRGRPALHRLH------PMPLALNAGDAMHAEMWGLLAEGLARGLFPPEVLLEF 135
Query: 56 NEVEFQTASGQMIDLITTIEGEKDLS--KYSLPLHRRIVQYKTAYYSFYLPVACALLMAG 113
+EV +TA GQ +DL+ T+ G DL Y R+V +K AYY+ P+ L+AG
Sbjct: 136 HEVVRRTAYGQHLDLLWTLGGTFDLRPEDY-----FRMVAHKAAYYTAVAPLRLGALLAG 190
Query: 114 ENLDKHVEVKDILVQ----MGIYFQVQDDFLDCFGSPEVIGK-VGTDIEDYKCSWLVVKA 168
+ + +G FQ+ DD L+ G GK D+ + K + ++++
Sbjct: 191 KTPP------AAYEEGGLRLGTAFQIVDDVLNLEGGEA-YGKERAGDLYEGKRTLILLRF 243
Query: 169 LELCNEEQKKLVHENYGK----VDPACVAKVKELYKTLD-LEGAF---VEYEKESYEKLT 220
LE E++ A V + E L A + E L
Sbjct: 244 LEEAPPEERARALALLALPREAKPEAEVGWLLERLLASRALAWAKAEAKRLQAEGLALLE 303
Query: 221 KSIEAHPTKEVQAVLKSFLAKIYKRQ 246
+ + P KE L+ LA + +R+
Sbjct: 304 AAFQDLPGKEALDHLRGLLAALVERR 329
>3nf2_A Putative polyprenyl synthetase; isoprenyl diphosphate synthase,
structural genomics, PSI, PR structure initiative,
nysgrc; 2.20A {Streptomyces coelicolor}
Length = 352
Score = 75.4 bits (186), Expect = 4e-16
Identities = 37/227 (16%), Positives = 59/227 (25%), Gaps = 54/227 (23%)
Query: 1 MDGSHTRRGQPCWFRVPKVGMIAAN------------DGVLLR--NHISRILKNHFRDKP 46
MDG RR + D + + +
Sbjct: 97 MDGDEQRRHRD-----------TVWKVHGPAQAILVGDALFALANEVLLEL------GTV 139
Query: 47 YYVDLLDLFNEVEFQTASGQMIDLITTIEGEKDLSKYSLPLHRRIVQYKTAYYSFYLPVA 106
+ GQ D+ + + + KT L +A
Sbjct: 140 EAGRATRRLTKASRSLIDGQAQDISYEHRDRVSVEEC-----LEMEGNKTGA----L-LA 189
Query: 107 CALLMAGENLDKHVEVKDIL----VQMGIYFQVQDDFLDCFGSPEVIGK-VGTDIEDYKC 161
CA + D L +G+ FQ DD L +G P+ GK +D+ K
Sbjct: 190 CASSIGAVLGGADERTADTLEKYGYHLGLAFQAVDDLLGIWGDPDATGKQTWSDLRQRKK 249
Query: 162 SWLVVKALELCNEEQKKLVHE--------NYGKVDPACVAKVKELYK 200
S VV AL ++L ++ A L +
Sbjct: 250 SLPVVAALAAGGAASERLGEILTADAKASDFANFSEEEFAARAALIE 296
>4dhd_A Polyprenyl synthetase; isoprenoid synthesis, isoprenoid diphosphate
synthase, trans; 1.65A {Pyrobaculum calidifontis}
Length = 358
Score = 73.5 bits (181), Expect = 2e-15
Identities = 49/223 (21%), Positives = 81/223 (36%), Gaps = 35/223 (15%)
Query: 1 MDGSHTRRGQPC----WFRVPKVGMIAA-NDGVLLRNHISRILKNHFRDKPYYVDLLDLF 55
+D RRG P + G AA G+ R I + D P
Sbjct: 88 IDRGDVRRGLPTVRKAF------GDNAAILVGIWYREAIEEAVL----DTPKPTLFAKEV 137
Query: 56 NEVEFQTASGQMIDLITTIEGEKDLSKYSLPLHR-------RIVQYKTAYYSFYLPVACA 108
EV G+ +D++ G D ++V KT +A A
Sbjct: 138 AEVIKAIDEGERLDILFEAAGRSDPYFVQARWREVTLDDYIKMVSLKTGAL-----IAAA 192
Query: 109 LLMAGENLDKHVEVKDILVQ----MGIYFQVQDDFLDCFGSPEVIGK-VGTDIEDYKCSW 163
++ + + G+ FQ+ DD LD +G P+ GK +G DI+++K
Sbjct: 193 AKWGVLSVSDDRGLAEAAWNFGMAAGVAFQIIDDVLDIYGDPKKFGKEIGKDIKEHKRGN 252
Query: 164 LVVK-ALELCNEEQKKLVHENYGK--VDPACVAKVKELYKTLD 203
VV AL E +++ + E + V+ A V + L ++
Sbjct: 253 AVVAVALSHLGEGERRRLLEILAREVVEEADVREAVALLDSVG 295
>1wy0_A Geranylgeranyl pyrophosphate synthetase; pyrococcus horikosh
structural genomics, riken structural
genomics/proteomics initiative, RSGI; 2.20A {Pyrococcus
horikoshii}
Length = 342
Score = 71.9 bits (177), Expect = 7e-15
Identities = 49/276 (17%), Positives = 93/276 (33%), Gaps = 53/276 (19%)
Query: 1 MDGSHTRRGQPCWFRVPKVGMIAANDGVLLRNHIS------------RILKNHFRDKPYY 48
MD TRRG+P + + +++ +
Sbjct: 89 MDMDETRRGKP-----------TVH--RIWGVNMAILAGDLLFSKAFEAVARAEIPPEKK 135
Query: 49 VDLLDLFNEVEFQTASGQMIDLITTIEGEKDLSKYSLPLHRRIVQYKTAYYSFYLPVACA 108
+L++ + + GQ DL + + +Y ++ KT +
Sbjct: 136 ARVLEVIVKASNELCEGQARDLEFEKKSTVTIEEY-----MEMISGKTG-----ALFEAS 185
Query: 109 LLMAGENLDKHVEVKDIL----VQMGIYFQVQDDFLDCFGSPEVIGK-VGTDIEDYKCSW 163
+ G + E L +GI FQ+ DD LD + +GK VG+DI K +
Sbjct: 186 AKVGGIIGTDNEEYIKALSSWGRNVGIAFQIWDDVLDLIADEKKLGKPVGSDIRKGKKTL 245
Query: 164 LVVKALELCNEEQKKLVHENYGKVDPAC-------------VAKVKELYKTLDLEGAFVE 210
+V E +E+ K+ + +GK V + +L K E
Sbjct: 246 IVAHFFENADEKDKQRFLKIFGKYAGDVKGRGIIEEDIKSDVMEAIDLLKKYGSIDYAAE 305
Query: 211 YEKESYEKLTKSIEAHPTKEVQAVLKSFLAKIYKRQ 246
K+ +K +++ P + + L+ I +R+
Sbjct: 306 IAKDMIKKANEALRILPKSKARMDLELLAKFIVERE 341
>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 = 61.6 bits (150), Expect = 2e-11
Identities = 46/264 (17%), Positives = 87/264 (32%), Gaps = 53/264 (20%)
Query: 1 MDGSHTRRGQPCWFRVPKVGMIAAND------GVLLRNHI-SR---ILKNHFRDKPYYVD 50
D + RRGQ ++ + N++ R ++ +P Y +
Sbjct: 83 EDNAPLRRGQT-----------TSHLIFGVPSTINTANYMYFRAMQLVSQLTTKEPLYHN 131
Query: 51 LLDLFNEVEFQTASGQMIDLITT-IEGEKDLS--KYSLPLHRRIVQYKTAYYSFYLPVAC 107
L+ +FNE GQ +D+ E + Y +V KT L
Sbjct: 132 LITIFNEELINLHRGQGLDIYWRDFLPEIIPTQEMY-----LNMVMNKTGG----LFRLT 182
Query: 108 ALLMA--GENLDKHVEVKDILVQMGIYFQVQDDFLDCFGSPEVIGK-VGTDIEDYKCSWL 164
LM + + + +GI +Q++DD+L+ K DI + K S+
Sbjct: 183 LRLMEALSPSSHHGHSLVPFINLLGIIYQIRDDYLNLKDFQMSSEKGFAEDITEGKLSFP 242
Query: 165 VVKALELC-----NEEQKKLVHENYGK-----VDPACVAKVKELYKTLDLEGAFVEYEKE 214
+V AL E+ +++ + + + ++ +L Y K
Sbjct: 243 IVHALNFTKTKGQTEQHNEILRILLLRTSDKDIKLKLIQILEFDTNSL-------AYTKN 295
Query: 215 SYEKLTKSIEAHPTKEVQAVLKSF 238
+L I+ + L S
Sbjct: 296 FINQLVNMIKNDNENKYLPDLASH 319
>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 = 59.6 bits (145), Expect = 9e-11
Identities = 46/258 (17%), Positives = 94/258 (36%), Gaps = 35/258 (13%)
Query: 1 MDGSHTRRGQPC----WFRVPKVGMIAANDGVLLRNHI-SRILKNHFRDKPYYVDLLDLF 55
D S RRG P + G+ + + N++ L+ D + LF
Sbjct: 68 EDNSKLRRGFPVAHSIY------GIPSV---INSANYVYFLGLEKVLTLDHP--DAVKLF 116
Query: 56 NEVEFQTASGQMIDLITTIEGEKDLSKYSLPLHRRIVQYKTAYYSFYLPVACALLMAGEN 115
+ GQ +D+ + + + ++ +V KT L LM +
Sbjct: 117 TRQLLELHQGQGLDI----YWRDNYTCPTEEEYKAMVLQKTGG----LFGLAVGLMQLFS 168
Query: 116 LDKHVEVKDILVQMGIYFQVQDDFLDCFGSPEVIGK-VGTDIEDYKCSWLVVKALELCNE 174
D ++K +L +G++FQ++DD+ + K D+ + K S+ + A+ E
Sbjct: 169 -DYKEDLKPLLNTLGLFFQIRDDYANLHSKEYSENKSFCEDLTEGKFSFPTIHAIWSRPE 227
Query: 175 EQKKLVHENYGKVDPACVAKVKELYKTLDLEGAFVEYEKESYEKLT----KSIEAHP-TK 229
+ + + + G+F EY + + ++L K I+A
Sbjct: 228 STQVQNILRQRTENIDIKKYCVHYLEDV---GSF-EYTRNTLKELEAKAYKQIDARGGNP 283
Query: 230 EVQAVLKSFLAKIYKRQK 247
E+ A++K + +
Sbjct: 284 ELVALVKHLSKMFKEENE 301
>3oyr_A Trans-isoprenyl diphosphate synthase; isoprenyl synthase, PSI,
protein structure initiative; HET: IPE; 2.00A
{Caulobacter crescentus}
Length = 345
Score = 51.9 bits (125), Expect = 4e-08
Identities = 33/154 (21%), Positives = 64/154 (41%), Gaps = 13/154 (8%)
Query: 50 DLLDLFNEVEFQTASGQMIDLITTIEGEKDLSKYSLPLHRRIVQYKTAYYSFYLPVACAL 109
L++ A G+++ L+ + + + Y I+Q KTA A
Sbjct: 151 KALEILARASRVIAEGEVLQLMRSHDLNLSQAVY-----LEIIQAKTAEL---FAAASEA 202
Query: 110 --LMAGENLDKHVEVKDILVQMGIYFQVQDDFLDCFGSPEVIGK-VGTDIEDYKCSWLVV 166
+ AG ++ K ++D + +G+ FQ+ DD LD G+ E +GK G D + K + ++
Sbjct: 203 GAVSAGVDVAKSEALRDYGLNLGLAFQLADDALDYGGATETLGKNAGDDFREGKATLPLL 262
Query: 167 KALELCNEEQKKLVHE--NYGKVDPACVAKVKEL 198
A+ + + + A + +EL
Sbjct: 263 LAIARSGPREAEFWERAIGRREQTEADFRRAREL 296
>2azj_A Geranylgeranyl pyrophosphate synthetase; hexpps,
trans-prenyltransferase; 2.40A {Sulfolobus solfataricus}
PDB: 2azk_A
Length = 289
Score = 51.5 bits (124), Expect = 5e-08
Identities = 38/196 (19%), Positives = 66/196 (33%), Gaps = 43/196 (21%)
Query: 1 MDGSHTRRGQPCWFRVPKVGMIAANDGVLLRNHIS-----RILKNHFR--DKPYYVDLLD 53
+D TRRG AA V+ N ++ R Y D L+
Sbjct: 92 VDLDATRRGDK-----------AAW--VVYGNRKVIFITNYLIPTALRIIQTSYGDDALN 138
Query: 54 LFNEVEFQTASGQMIDLITTIEGEKDLSKYSLPLHRRIVQYKTAYYSFYLPVACALL--M 111
E+ T+ G + D+ D Y R ++ KT L +L
Sbjct: 139 TSIELWKDTSVGALRDMYD----NSD---Y-----IRTIELKTGS----LFKLSTVLSAY 182
Query: 112 AGENLDKHVEVKDILVQMGIYFQVQDDFLDCFGS----PEVIGK-VGTDIEDYKCSWLVV 166
A ++ + ++ D+ +GI +QV DDF+D + K + + K V
Sbjct: 183 ASKHYNTKQQMLDVGKYLGIIYQVIDDFVDYKTKKVEEIDGSAKQLFKYYREGKLEEYVR 242
Query: 167 KALELCNEEQKKLVHE 182
++ +L+
Sbjct: 243 SVYLEYKQKYDELISN 258
>3mzv_A Decaprenyl diphosphate synthase; transferase, structural genomics,
PSI-2, protein structure initiative; 1.90A {Rhodobacter
capsulatus}
Length = 341
Score = 51.5 bits (124), Expect = 7e-08
Identities = 34/154 (22%), Positives = 59/154 (38%), Gaps = 13/154 (8%)
Query: 50 DLLDLFNEVEFQTASGQMIDLITTIEGEKDLSKYSLPLHRRIVQYKTAYYSFYLPVACAL 109
++++ A G+++ L Y R+++ KTA A +
Sbjct: 139 RVMEILANASAVIAEGEVLQLTAAQNLATTEDIY-----LRVIRGKTAAL---FSAATEV 190
Query: 110 --LMAGENLDKHVEVKDILVQMGIYFQVQDDFLDCFGSPEVIGK-VGTDIEDYKCSWLVV 166
++ G D+ + D +GI FQ+ DD LD G IGK G D + K + V+
Sbjct: 191 GGIIGGAPEDQVQALFDYGDALGIAFQIVDDLLDYGGKSAEIGKNTGDDFRERKLTMPVI 250
Query: 167 KALELCNEEQKKLVHE--NYGKVDPACVAKVKEL 198
KA+ L +E ++ G + L
Sbjct: 251 KAVALADEAERAFWKRVIEKGDQQDGDLEHAMAL 284
>3tc1_A Octaprenyl pyrophosphate synthase; all alpha-helices fold,
transferase; 2.00A {Helicobacter pylori}
Length = 315
Score = 51.1 bits (123), Expect = 8e-08
Identities = 32/152 (21%), Positives = 55/152 (36%), Gaps = 36/152 (23%)
Query: 63 ASGQMIDLITTIEGEKDLSKYSLPLHRRIVQYKTAYYSFYLPVACALLMA---------- 112
+ G++ D+ D KY RI++ KTA+ A MA
Sbjct: 135 SRGEIEDVFVGECFNSDKQKY-----WRILEDKTAH----FIEASLKSMAILLNKDAKIY 185
Query: 113 ---GENLDKHVEVKDILVQMGIYFQVQDDFLDCFGSPEVIGK-VGTDIEDYKCSWLVVKA 168
G N G+ FQ+ DD LD + +GK +D ++ K + +
Sbjct: 186 ADFGLNF-------------GMAFQIIDDLLDITQDAKTLGKPNFSDFKEGKTTLPYLLL 232
Query: 169 LELCNEEQKKLVHENYGKVDPACVAKVKELYK 200
E N+ + L+ + + + KE +K
Sbjct: 233 YEKLNQHDQGLLISYFKQDSHEIIEWTKEKFK 264
>3lom_A Geranyltranstransferase; geranyltransferase, structural genomics,
PSI, protein structure initiative, nysgrc; 2.30A
{Legionella pneumophila subsp}
Length = 313
Score = 50.3 bits (121), Expect = 1e-07
Identities = 29/125 (23%), Positives = 54/125 (43%), Gaps = 18/125 (14%)
Query: 65 GQMIDLITTIEGEKDLSKYSLPLHRRIVQYKTAYYSFYLPVACALL--MAGENLDKHVEV 122
GQ +DL + +++ L R I KT L +AC + A + + ++
Sbjct: 163 GQSLDLSE--LAKSSVTEEQL---REIHLLKTGK----LILACFEMVLAAQHEVSE--QI 211
Query: 123 KDILVQ----MGIYFQVQDDFLDCFGSPEVIGK-VGTDIEDYKCSWLVVKALELCNEEQK 177
K L +G+ FQ+QDD+LD + +++GK +D + K ++ + + EE
Sbjct: 212 KSALRTYGKHIGLVFQMQDDYLDLYAPTQILGKGRSSDQANQKTTFATLFNKQQLEEEIA 271
Query: 178 KLVHE 182
Sbjct: 272 VHYQI 276
>3uca_A Geranyltranstransferase; isoprenoid synthesis, isoprenoid
diphosphate synthase; 2.00A {Clostridium perfringens}
Length = 324
Score = 50.0 bits (120), Expect = 2e-07
Identities = 29/122 (23%), Positives = 59/122 (48%), Gaps = 13/122 (10%)
Query: 65 GQMIDLITTIEGEKDLSKYSLPLHRRIVQYKTAY---YSFYLPVACALLMAGENLDKHVE 121
GQ++D+I E ++++S L + KT S + ++A + +
Sbjct: 185 GQIVDIIN--EDKEEISLKEL---DYMHLKKTGELIKAS----IMSGAVLAEASEGDIKK 235
Query: 122 VKDILVQMGIYFQVQDDFLDCFGSPEVIGK-VGTDIEDYKCSWLVVKALELCNEEQKKLV 180
++ ++G+ FQ++DD LD G+ + +GK V D E K +++ + LE C ++ +
Sbjct: 236 LEGFGYKLGLAFQIKDDILDVVGNAKDLGKNVHKDQESNKNNYITIFGLEECKKKCVNIT 295
Query: 181 HE 182
E
Sbjct: 296 EE 297
>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 = 49.9 bits (120), Expect = 2e-07
Identities = 28/139 (20%), Positives = 52/139 (37%), Gaps = 12/139 (8%)
Query: 63 ASGQMIDLITTIEGEKDLSKYSLPLHRRIVQYKTAYYSFYLPVACAL--LMAGENLDKHV 120
G++ + + L Y + KTA ++C +AG
Sbjct: 156 LQGELHQMDLNYREDITLDAY-----LNEIAGKTAEL---FALSCYQGAQLAGAPQSVID 207
Query: 121 EVKDILVQMGIYFQVQDDFLDCFGSPEVIGK-VGTDIEDYKCSWLVVKALELCNEEQKKL 179
+DI + +G +Q+ DD LD G P+ K V D+ S ++ +L + KL
Sbjct: 208 RTRDIGIAIGCAYQMLDDILDYAGDPKRTQKPVLEDLRSGVYSLPLLLSLSHAPRDFHKL 267
Query: 180 VHENYGKVDPACVAKVKEL 198
+ + + + V+ L
Sbjct: 268 LKKK-QAMTLEDIKHVQAL 285
>3aqb_B Component B of hexaprenyl diphosphate synthase; prenyltransferase,
transferase; 2.40A {Micrococcus luteus} PDB: 3aqc_B*
Length = 325
Score = 49.5 bits (119), Expect = 2e-07
Identities = 29/179 (16%), Positives = 63/179 (35%), Gaps = 11/179 (6%)
Query: 50 DLLDLFNEVEFQTASGQMIDLITTIEGEKDLSKYSLPLHRRIVQYKTAYYSFYLPVACAL 109
+F++ + G+ + + Y R + KTA + +C L
Sbjct: 130 KFHQIFSKTILEVCFGEFDQMADRFNYPVSFTAY-----LRRINRKTAIL---IEASCHL 181
Query: 110 --LMAGENLDKHVEVKDILVQMGIYFQVQDDFLDCFGSPEVIGK-VGTDIEDYKCSWLVV 166
L + + +K +G+ +Q+ DD LD +GK VG+DI + ++ ++
Sbjct: 182 GALSSQLDEQSTYHIKQFGHCIGMSYQIIDDILDYTSDEATLGKPVGSDIRNGHITYPLM 241
Query: 167 KALELCNEEQKKLVHENYGKVDPACVAKVKELYKTLDLEGAFVEYEKESYEKLTKSIEA 225
A+ E+ + + +V + + + E S + K+
Sbjct: 242 AAIANLKEQDDDKLEAVVKHLTSTSDDEVYQYIVSQVKQYGIEPAELLSRKYGDKAKYH 300
>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 = 48.7 bits (117), Expect = 4e-07
Identities = 26/103 (25%), Positives = 41/103 (39%), Gaps = 21/103 (20%)
Query: 65 GQMIDLITTIEGEKDLSKYSLPLHRRIVQYKTAY---YSFYLPVACALLMAG---ENLDK 118
GQ +D+ E +L R+ KT ++ ++AG L
Sbjct: 152 GQALDI----AAETAAVPLTLDEIIRLQAGKTGALISFA----AQAGAILAGADRGPLTA 203
Query: 119 HVEVKDILVQMGIYFQVQDDFLDCFGSPEVIGK-VGTDIEDYK 160
+ +G+ FQ+ DD LD G+ E GK +G D E +K
Sbjct: 204 YAT------ALGLAFQIADDILDVEGNEEAAGKRLGKDAEAHK 240
>2h8o_A Geranyltranstransferase; geranyltransferase,agrobacterium
tumefaciens, structural GEN PSI-2, protein structure
initiative; 1.60A {Agrobacterium tumefaciens}
Length = 335
Score = 48.0 bits (115), Expect = 8e-07
Identities = 25/99 (25%), Positives = 39/99 (39%), Gaps = 12/99 (12%)
Query: 65 GQMIDLITTIEGE-KDLSKYSLPLHRRIVQYKT-AYYSFYLPVACALLMAGENLDKHVEV 122
GQ +DL E K + + + KT A F ++AG N + +
Sbjct: 197 GQALDL----AAEKKAPDEDGI---ITLQAMKTGALLRF--ACEAGAIIAGSNQAERQRL 247
Query: 123 KDILVQMGIYFQVQDDFLDCFGSPEVIGK-VGTDIEDYK 160
+ ++G+ FQ+ DD LD +GK G D K
Sbjct: 248 RLFGEKIGLSFQLADDLLDLTADAATMGKATGKDAARGK 286
>3p8l_A Geranyltranstransferase; isoprenyl synthase, structural genomics,
PSI, protein struct initiative, nysgrc; 2.00A
{Enterococcus faecalis}
Length = 302
Score = 48.0 bits (115), Expect = 9e-07
Identities = 25/101 (24%), Positives = 42/101 (41%), Gaps = 16/101 (15%)
Query: 65 GQMIDLITTIEGE-KDLSKYSLPLHRRIVQYKTAY---YSFYLPVACALLMAGENLDKHV 120
GQM D+ EGE L+ L + + KT ++ + ++A + +
Sbjct: 161 GQMGDI----EGEKVSLTLEEL---AAVHEKKTGALIEFA----LIAGGVLANQTEEVIG 209
Query: 121 EVKDILVQMGIYFQVQDDFLDCFGSPEVIGK-VGTDIEDYK 160
+ G+ FQ++DD LD + +GK VG D K
Sbjct: 210 LLTQFAHHYGLAFQIRDDLLDATSTEADLGKKVGRDEALNK 250
>1rtr_A Geranyltranstransferase; 2.50A {Staphylococcus aureus} SCOP:
a.128.1.1
Length = 301
Score = 47.6 bits (114), Expect = 9e-07
Identities = 28/123 (22%), Positives = 57/123 (46%), Gaps = 16/123 (13%)
Query: 65 GQMIDLITTIEGE-KDLSKYSLPLHRRIVQYKTAY---YSFYLPVACALLMAGENLDKHV 120
GQM+D+ + E + + +L I + KT ++ V A +A +
Sbjct: 153 GQMLDM----QSEGQPIDLETL---EMIHKTKTGALLTFA----VMSAADIANVDDTTKE 201
Query: 121 EVKDILVQMGIYFQVQDDFLDCFGSPEVIGK-VGTDIEDYKCSWLVVKALELCNEEQKKL 179
++ +G+ FQ++DD LDC+G +GK VG+D+E+ K +++ + + ++
Sbjct: 202 HLESYSYHLGMMFQIKDDLLDCYGDEAKLGKKVGSDLENNKSTYVSLLGKDGAEDKLTYH 261
Query: 180 VHE 182
Sbjct: 262 RDA 264
>3p8r_A Geranyltranstransferase; isoprenyl synthase, structural genomics,
PSI, protein struct initiative, nysgrc; 2.50A {Vibrio
cholerae}
Length = 302
Score = 47.6 bits (114), Expect = 1e-06
Identities = 34/128 (26%), Positives = 52/128 (40%), Gaps = 25/128 (19%)
Query: 65 GQMIDLITTIEGE-KDLSKYSLPLHRRIVQYKTA---YYSFYLPVACALLMAGENLDKHV 120
GQ +DL E + +S L I + KT + + L AGE +
Sbjct: 163 GQALDL----AAENRLISLEEL---ETIHRNKTGALMRCA----IRLGALAAGEKGRAML 211
Query: 121 EV-----KDILVQMGIYFQVQDDFLDCFGSPEVIGK-VGTDIEDYKCSWLVVKALELCNE 174
+ + G+ FQVQDD LD E +GK G+D E K ++ + LE +
Sbjct: 212 PHLDRYAEAV----GLAFQVQDDILDIISDTETLGKPQGSDQELNKSTYPALLGLEGAQQ 267
Query: 175 EQKKLVHE 182
+ L+ E
Sbjct: 268 KAHTLLQE 275
>3npk_A Geranyltranstransferase; isoprene biosynthesis, SGX, structural
genomics protein structure initiative; 1.50A
{Campylobacter jejuni}
Length = 291
Score = 47.2 bits (113), Expect = 1e-06
Identities = 31/123 (25%), Positives = 55/123 (44%), Gaps = 18/123 (14%)
Query: 65 GQMIDLITTIEGE-KDLSKYSLPLHRRIVQYKTAY---YSFYLPVACALLMAGENLDKHV 120
GQ ID E K LS L + +KTA + + + N ++
Sbjct: 150 GQAIDC----FFEDKRLSLNEL---EFLHTHKTARLIAAA----LKMGCEICELNNEESN 198
Query: 121 EVKDILVQMGIYFQVQDDFLDCFGSPEVIGK-VGTDIEDYKCSWLVVKALELCNEEQKKL 179
++ + +++G+ FQ+ DD +D S E GK DI K S++ + LE + ++ L
Sbjct: 199 QIYKLGLKLGLIFQINDDIIDVTTSQEQSGKPTNNDIH--KNSFVNLLGLEQAIKTKENL 256
Query: 180 VHE 182
++E
Sbjct: 257 LNE 259
>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 = 47.2 bits (113), Expect = 1e-06
Identities = 36/127 (28%), Positives = 57/127 (44%), Gaps = 23/127 (18%)
Query: 65 GQMIDLITTIEGEKDLSKYSLPLHRRIVQYKTA---YYSFYLPVACALLMAGENLDKHVE 121
GQ +DL EG K + +L RI ++KT + V L AG+ + +
Sbjct: 157 GQALDLDA--EG-KHVPLDAL---ERIHRHKTGALIRAA----VRLGALSAGDKGRRALP 206
Query: 122 V-----KDILVQMGIYFQVQDDFLDCFGSPEVIGK-VGTDIEDYKCSWLVVKALELCNEE 175
V + I G+ FQVQDD LD G +GK G D + K ++ + LE ++
Sbjct: 207 VLDKYAESI----GLAFQVQDDILDVVGDTATLGKRQGADQQLGKSTYPALLGLEQARKK 262
Query: 176 QKKLVHE 182
+ L+ +
Sbjct: 263 ARDLIDD 269
>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 = 46.4 bits (111), Expect = 2e-06
Identities = 33/127 (25%), Positives = 50/127 (39%), Gaps = 23/127 (18%)
Query: 65 GQMIDLITTIEGEKDLSKYSLPLHRRIVQYKTA---YYSFYLPVACALLMAGENLDKHVE 121
GQ IDL + G L + +L + ++KT S V L +G ++
Sbjct: 157 GQAIDLGS--VG-LKLDQQAL---EYMHRHKTGALIEAS----VILGALASGRAEKGELK 206
Query: 122 V-----KDILVQMGIYFQVQDDFLDCFGSPEVIGK-VGTDIEDYKCSWLVVKALELCNEE 175
+ I G+ FQVQDD LD +GK G DI K ++ + L E
Sbjct: 207 ALQTYAQAI----GLAFQVQDDILDVESDTATLGKRQGADIARDKPTYPALLGLAAAKEY 262
Query: 176 QKKLVHE 182
+L +
Sbjct: 263 ALELRDQ 269
>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 = 47.2 bits (111), Expect = 3e-06
Identities = 32/226 (14%), Positives = 73/226 (32%), Gaps = 41/226 (18%)
Query: 32 NHISRILKNHFRDKPYYVDLLDLFNEVEFQTASGQMID--------LITTIEGEKDLSKY 83
+ I L+ + KPY LL L V+ + + + L+TT K ++ +
Sbjct: 228 HSIQAELRRLLKSKPYENCLLVL-LNVQ----NAKAWNAFNLSCKILLTT--RFKQVTDF 280
Query: 84 SLPLHRRIVQYKTAYYSFYLPVACALLMAGENLDKHVEVKDILVQMGIYFQVQDDFLDCF 143
+ + +LL + LD +D+ ++
Sbjct: 281 LSAATTTHISLDHHSMTLTPDEVKSLL--LKYLD--CRPQDLPREV------------LT 324
Query: 144 GSPEVIGKVGTDIEDYKCSWLVVKALELCNEEQKKLVHENYGKVDPACVAKVKELYKTLD 203
+P + + I D +W K + ++ ++ + ++P A+ ++++ L
Sbjct: 325 TNPRRLSIIAESIRDGLATWDNWKHVN--CDKLTTIIESSLNVLEP---AEYRKMFDRL- 378
Query: 204 LEGAFVEYEKESYEKLTKSIEAHPTKEVQAVLKSFLAK--IYKRQK 247
F L+ +V V+ + K+ K
Sbjct: 379 --SVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPK 422
Score = 40.2 bits (93), Expect = 4e-04
Identities = 43/291 (14%), Positives = 74/291 (25%), Gaps = 132/291 (45%)
Query: 19 VGMIAANDGVLLRNHISRI--LKNHFRDK------------------PYYVDL------- 51
+ +IA +R+ ++ K+ DK + L
Sbjct: 330 LSIIAE----SIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSA 385
Query: 52 ------LDLF-NEVEFQTASGQMIDLITT--IEGEKDLSKYSLP---------------L 87
L L +V + L +E + S S+P L
Sbjct: 386 HIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYAL 445
Query: 88 HRRIV-QYKTA---------------YYSFYLPVACALLMAGENLDKHVEVKDILVQMGI 131
HR IV Y Y+ ++ L E+ ++ + +
Sbjct: 446 HRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHH---LKNIEHPERMTLFRMV------ 496
Query: 132 YFQVQDDFLDCFGSPEVIGKVGTDIEDYKCSWLVVKALELCNEEQKKLVHENYGKVDPAC 191
FLD F +L ++K+ H+ A
Sbjct: 497 -------FLD-F------------------RFL-----------EQKIRHD-----STAW 514
Query: 192 VAKVKELYKTLDLEGAFVEYEKESYEKLTKSIEAHPTKEVQAVLKSFLAKI 242
A L L + Y+ + + V A+L FL KI
Sbjct: 515 NASGSILNTLQQL---------KFYKPYICDNDPKYERLVNAILD-FLPKI 555
>3ts7_A Geranyltranstransferase; isoprenoid synthesis, farnesyl diphosphate
synthase; 1.94A {Methylococcus capsulatus}
Length = 324
Score = 46.5 bits (111), Expect = 3e-06
Identities = 29/124 (23%), Positives = 46/124 (37%), Gaps = 17/124 (13%)
Query: 65 GQMIDLITTIEGE-KDLSKYSLPLHRRIVQYKTAYYSFYLPVAC----ALLMAGENLDKH 119
GQ IDL K L L + KT L A L G ++
Sbjct: 163 GQAIDL----ASVGKKLDLPGL---ENMHIRKTGA----LIRASVRLACLARPGLPAEQF 211
Query: 120 VEVKDILVQMGIYFQVQDDFLDCFGSPEVIGK-VGTDIEDYKCSWLVVKALELCNEEQKK 178
+ +G+ FQ+QDD LD + +GK G D + K ++ + L E+ ++
Sbjct: 212 DRLDHYAKCIGLAFQIQDDILDEESDTQTLGKTRGKDRDHNKPNYPALLGLSGAKEKAEE 271
Query: 179 LVHE 182
+
Sbjct: 272 MHEA 275
>4f62_A Geranyltranstransferase; enzyme function initiative, structural
genomics; 2.10A {Marinomonas SP}
Length = 317
Score = 46.5 bits (111), Expect = 3e-06
Identities = 33/128 (25%), Positives = 51/128 (39%), Gaps = 25/128 (19%)
Query: 65 GQMIDLITTIEGE-KDLSKYSLPLHRRIVQYKTA---YYSFYLPVACALLMAGENLDKHV 120
GQMIDL E K++S L ++ +KT S V L G+ + +
Sbjct: 156 GQMIDL----SSENKNISLAEL---EQMHVHKTGALIKAS----VRMGALSTGQVKPEQL 204
Query: 121 EV-----KDILVQMGIYFQVQDDFLDCFGSPEVIGK-VGTDIEDYKCSWLVVKALELCNE 174
I G+ FQVQDD +D E +GK +D E K ++ + L+
Sbjct: 205 AKLDAYAHAI----GLAFQVQDDIIDLTSDTETLGKTQFSDAEANKATYPKLLGLDGAKA 260
Query: 175 EQKKLVHE 182
+L +
Sbjct: 261 LVVRLHEQ 268
>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 = 45.7 bits (109), Expect = 5e-06
Identities = 24/100 (24%), Positives = 38/100 (38%), Gaps = 14/100 (14%)
Query: 65 GQMIDLITTIEGEKDLSKYSLPLHRRIVQYKTA---YYSFYLPVACALLMAGENLDKHVE 121
GQ D+ + E L R + + KT +Y+ V L++ +
Sbjct: 160 GQAKDI----QSEH--VNLPLSQLRVLHKEKTGALLHYA----VQAGLILGQAPEAQWPA 209
Query: 122 VKDILVQMGIYFQVQDDFLDCFGSPEVIGK-VGTDIEDYK 160
G+ FQ+ DD LD SP +GK D ++ K
Sbjct: 210 YLQFADAFGLAFQIYDDILDVVSSPAEMGKATQKDADEAK 249
>4fp4_A Polyprenyl synthetase; isoprenoid synthesis, isoprenoid diphosphate
synthase, trans; HET: GER UNL; 2.00A {Pyrobaculum
calidifontis}
Length = 285
Score = 45.1 bits (107), Expect = 6e-06
Identities = 28/159 (17%), Positives = 60/159 (37%), Gaps = 22/159 (13%)
Query: 63 ASGQMIDLITTIEGEKDLSKYSLPLHRRIVQYKTAYYSFYLPVACALLMAGENLDKHVE- 121
+ GQ +DL EGE+D + ++KTA + L++ G + +E
Sbjct: 146 SVGQALDL----EGERD----------KAAEFKTAPL-IEAALVMPLVILGR--RELIET 188
Query: 122 VKDILVQMGIYFQVQDDFLDCFGSPEVIGKVGTDIEDYKCSWLVVKALELCNEEQKKLVH 181
K + ++GI +Q DD+ D + +I + + + + ++L+
Sbjct: 189 AKKLGTKLGILYQYSDDYSDENVERPETKSIANEIG--RYLLKIKEHVGDAIAPFERLIK 246
Query: 182 ENYGKVDPACVAKVKELYKTLDLEGA--FVEYEKESYEK 218
GK + + + + L + + +EK
Sbjct: 247 YLIGKALEGTLTVSRTIAENLYFQSHHHHHHWSHPQFEK 285
>3rmg_A Octaprenyl-diphosphate synthase; structural genomics, protein
structure initiative, isoprene biosynthesis,
transferase; 2.30A {Bacteroides thetaiotaomicron}
Length = 334
Score = 45.3 bits (108), Expect = 7e-06
Identities = 23/116 (19%), Positives = 45/116 (38%), Gaps = 9/116 (7%)
Query: 90 RIVQYKTAYYSFYLPVACAL--LMAGENLDKHVEVKDILVQMGIYFQVQDDFLDCFGSPE 147
+++ KTA L ++ + + +GI FQ++DD D + +
Sbjct: 168 DVIRKKTAAL---FAACAEAAALSVQVGEEEVAFARLLGEYIGICFQIKDDIFD-YFDSK 223
Query: 148 VIGK-VGTDIEDYKCSWLVVKALELCNEEQKKLVHE--NYGKVDPACVAKVKELYK 200
IGK G D+ + K + + AL + + + G P + ++ E K
Sbjct: 224 KIGKPTGNDMLEGKLTLPALYALNTTKDAWAEQIAFKVKEGTATPDEIVRLIEFTK 279
>3llw_A Geranyltranstransferase (ISPA); structural genomics, PSI, protein
structure initiative, nysgrc; 2.30A {Helicobacter
pylori} PDB: 3q1o_A*
Length = 311
Score = 45.0 bits (107), Expect = 8e-06
Identities = 33/127 (25%), Positives = 49/127 (38%), Gaps = 25/127 (19%)
Query: 65 GQMIDLITTIEGE-KDLSKYSLPLHRRIVQYKTAY---YSFYLPVACALLMAGENLDKHV 120
GQ +D E L+ L + ++KTA S + L+ +G +
Sbjct: 164 GQALDC----YFENTPLNLEQL---TFLHEHKTAKLISAS----LIMGLVASGIKDE--- 209
Query: 121 EVKDILVQ----MGIYFQVQDDFLDCFGSPEVIGK-VGTDIEDYKCSWLVVKALELCNEE 175
E+ L MG+ FQV DD +D E GK D K S++ + LE N
Sbjct: 210 ELFKWLQAFGLKMGLCFQVLDDIIDVTQDEEESGKTTHLDSA--KNSFVNLLGLERANNY 267
Query: 176 QKKLVHE 182
+ L E
Sbjct: 268 AQTLKTE 274
>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 = 44.9 bits (107), Expect = 8e-06
Identities = 30/151 (19%), Positives = 62/151 (41%), Gaps = 15/151 (9%)
Query: 90 RIVQYKTAYYSFYLPVACAL--LMAGENLDKHVEVKDILVQMGIYFQVQDDFLDCFGSPE 147
RIV+ K+ +A L L+ GE + + ++ V +G +Q+ DD +D F E
Sbjct: 161 RIVEGKSG---ALFGLALQLPALLEGELGED---LYNLGVTIGTIYQMFDDIMD-FAGME 213
Query: 148 VIGK-VGTDIEDYKCSWLVVKALELCNEEQKKLVHENYGKVDPACVAKVKELYKTLDLEG 206
IGK D+++ S+ +V A+E E ++ + ++ + + + + L + +
Sbjct: 214 KIGKDGFLDLKNGVASFPLVTAMEKFPEARQMFENRDWSGLM-SFMREKGILKECEETLK 272
Query: 207 AFVEYEKESYEKLTKSIEAHPTKEVQAVLKS 237
V+ L + + S
Sbjct: 273 VLVKNVIIENSWL----RDFVDGIFKIKISS 299
>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 = 44.6 bits (106), Expect = 1e-05
Identities = 44/212 (20%), Positives = 74/212 (34%), Gaps = 40/212 (18%)
Query: 1 MDGSHTRRGQPCWFRVPKVGMIAANDGVLLRNHIS---------RILKNHFRDKPYYVDL 51
MD + RRG P +AN N ++ + V
Sbjct: 118 MDEASMRRGVP-----------SAN--ARWDNSVAILAGDILLAHASGLMSQLGTDTVAH 164
Query: 52 L-DLFNEVEFQTASGQMIDLITTIEGEKDLSKYSLPLHRRIVQYKTAYYSFYLPVACAL- 109
+ F E+ +GQM + + + D ++ +++ KT + A L
Sbjct: 165 FAETFGEL----VTGQMRETVGP--RDTDPIEHYT----NVIREKTG--VL-IASAGYLG 211
Query: 110 -LMAGENLDKHVEVKDILVQMGIYFQVQDDFLDCFGSPEVIGK-VGTDIEDYKCSWLVVK 167
+ AG + +K+ +G+ FQ+ DD +D F GK GTD+ + + V+
Sbjct: 212 AMHAGAAPEHIDALKNFGAAVGMIFQIVDDIIDIFSETHESGKTPGTDLREGVFTLPVLY 271
Query: 168 ALELCNEEQKKLVHE-NYGKVDPACVAKVKEL 198
AL +L D V V EL
Sbjct: 272 ALREDTPVGAELRDILTGPLEDDETVNHVLEL 303
>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 = 40.4 bits (95), Expect = 3e-04
Identities = 29/156 (18%), Positives = 63/156 (40%), Gaps = 22/156 (14%)
Query: 50 DLLDLFNEVEFQTASGQMIDLITTIEGEKDLSKYSLPLHRRIVQYKTAYYSFYLPVACAL 109
+++ L +G+ +++ ++ E + Y + YKTA S + +C
Sbjct: 153 EVVALLATAVEHLVTGETMEITSSTEQRYSMDYY-----MQKTYYKTA--SL-ISNSCKA 204
Query: 110 --LMAGENLDKHVEVKDILVQ----MGIYFQVQDDFLDCFGSPEVIGK-VGTDIEDYKCS 162
++ G+ EV + + +G+ FQ+ DD LD G+ +GK +DI +
Sbjct: 205 VAVLTGQT----AEVAVLAFEYGRNLGLAFQLIDDILDFTGTSASLGKGSLSDIRHGVIT 260
Query: 163 WLVVKALELCNEEQKKLVHENYGKVDPACVAKVKEL 198
++ A+E + ++ + + V E
Sbjct: 261 APILFAMEEFPQLREVVDQVEKDPRN---VDIALEY 293
>3ipi_A Geranyltranstransferase; isoprene biosynthesis, helical bundle,
protein structure initiative II (PSI II), structural
genomics, nysgxrc; 1.90A {Methanosarcina mazei}
Length = 295
Score = 38.4 bits (90), Expect = 0.001
Identities = 17/114 (14%), Positives = 33/114 (28%), Gaps = 15/114 (13%)
Query: 90 RIVQYKTAYYSFYLPVACALL---MAGENLDKHVEVKDILVQMGIYFQVQDDFLDCFGSP 146
+ + KTA L A + G + +G +Q+ DD L+
Sbjct: 161 KCIYKKTAS----LFAISASIGAYTGGAEEELAERFSHFGNALGTAYQIVDDILEFLEVV 216
Query: 147 EVIGKVGTDIEDYKCSWLVVKALELCNEEQKKLVHE---NYGKVDPACVAKVKE 197
E G + + + + EE K + + + +E
Sbjct: 217 E-----GKESKFTSETLPHIYMKSTSKEEALKKSIDCVKLHVAAAKETLETFRE 265
>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 = 36.0 bits (84), Expect = 0.006
Identities = 22/85 (25%), Positives = 37/85 (43%), Gaps = 12/85 (14%)
Query: 65 GQMIDLITTIEGE-KDLSKYSLPLHRRIVQYKTAY---YSFYLPVACALLMAGENLDKHV 120
GQ++D+ E DL+ L + I +KTA S ++ G + ++
Sbjct: 165 GQVVDI----SSEGLDLNNVGLEHLKFIHLHKTAALLEAS----AVLGGIIGGGSDEEIE 216
Query: 121 EVKDILVQMGIYFQVQDDFLDCFGS 145
++ +G+ FQV DD LD S
Sbjct: 217 RLRKFARCIGLLFQVVDDILDVTKS 241
>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 = 35.9 bits (82), Expect = 0.006
Identities = 37/184 (20%), Positives = 68/184 (36%), Gaps = 19/184 (10%)
Query: 1 MDGSHTRRGQP-CWFRVPKVGMIAANDGVLLRNHISRILKNHFRDKPYYVDLLDLFNEVE 59
+D + RRG P C + + A DG+ L + + F+E
Sbjct: 91 IDNADFRRGXPSCHRTYGEDIALLAGDGLF-------FLAFSQISXIGNSXIFEEFSETA 143
Query: 60 FQTASGQMIDLITTIEGEKDLSKYSLPLHRRIVQYKTAYYSFYLPVACALLMAGENLDKH 119
+ G+ +D+ E E+ + S + R+ + T F + ++ G +
Sbjct: 144 YXLLLGEAMDV----EFERRXMEVSQEMVERMYAFXTGAL-FAFCFSAPFILXGXDHTXM 198
Query: 120 VEVKDILVQMGIYFQVQDDFLDCFGSPEVIGK-VGTDIEDYKCSWLVVKALELCNEEQKK 178
+ + G+ FQ+ DD D GS E +GK +G D E + + ++ E
Sbjct: 199 XLLGEXF---GVAFQIYDDLXDILGSFEKVGKDLGKDTE--XVTLVXXVGIQXAREMADX 253
Query: 179 LVHE 182
E
Sbjct: 254 YYEE 257
>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 = 34.5 bits (78), Expect = 0.013
Identities = 7/30 (23%), Positives = 17/30 (56%), Gaps = 5/30 (16%)
Query: 212 EKESYEKLTKSI-----EAHPTKEVQAVLK 236
EK++ +KL S+ ++ P ++A ++
Sbjct: 18 EKQALKKLQASLKLYADDSAPALAIKATME 47
Score = 28.0 bits (61), Expect = 2.1
Identities = 11/37 (29%), Positives = 17/37 (45%), Gaps = 10/37 (27%)
Query: 194 KVKELYKTLDLEGAFVEYEKESYEKLTKSIEAHPTKE 230
+K+L +L L Y +S L +I+A T E
Sbjct: 21 ALKKLQASLKL------YADDSAPAL--AIKA--TME 47
>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 = 34.6 bits (79), Expect = 0.031
Identities = 25/129 (19%), Positives = 45/129 (34%), Gaps = 33/129 (25%)
Query: 125 ILVQMGIYF---QVQDDFLDCFGSPEVIGKVGTDIEDYKCSWLVVKALELCNEEQKKLVH 181
+LV +F Q+Q+ F PE D E + LV K L +
Sbjct: 20 LLVPTASFFIASQLQEQFNKIL--PEPTEGFAADDEPTTPAELVGKFLGYVSSL------ 71
Query: 182 ENYGKVDPACVAKVKELYKTLDLEGAFVEYEKESY----------EKLTKSIEAHPTKEV 231
V+P+ V + ++ L E+E Y KL + + K
Sbjct: 72 -----VEPSKVGQFDQV-----LNLCLTEFE-NCYLEGNDIHALAAKLLQENDTTLVK-T 119
Query: 232 QAVLKSFLA 240
+ ++K+++
Sbjct: 120 KELIKNYIT 128
Score = 29.6 bits (66), Expect = 1.2
Identities = 23/183 (12%), Positives = 54/183 (29%), Gaps = 47/183 (25%)
Query: 31 RNHISRILKNHFRDKPYYVDLLDLFNEVEFQTASGQMIDLITTIEGEKDLSKYSLPLHRR 90
+S +++ + + L++ +E ++ D + +I S PL
Sbjct: 192 AETLSELIRTTLDAEKVFTQGLNILEWLE-NPSNTPDKDYLLSIP-------ISCPL--- 240
Query: 91 IVQYKTAYYSFY------------------------LPVACALLMAG------ENLDKHV 120
I + A+Y L A A+ ++ K +
Sbjct: 241 IGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAI 300
Query: 121 EVKDILVQMGIYFQVQDDFLDCFGSPEVIGKVGTDIEDYKCSWLVVKALELCNEEQKKLV 180
+L +G + + + + P ++ + E L + L + Q +
Sbjct: 301 T---VLFFIG--VRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQE-QVQDYVN 354
Query: 181 HEN 183
N
Sbjct: 355 KTN 357
>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 = 33.8 bits (78), Expect = 0.031
Identities = 13/101 (12%), Positives = 33/101 (32%), Gaps = 16/101 (15%)
Query: 65 GQMIDLITTIEGEKDLSKYSLPLHRRIVQYKTA---YYSFYLPVACALLMAGENLDKHVE 121
GQ +L + + + + K AC ++ G + DK +
Sbjct: 156 GQYHEL----GLNQLNDLELI---EYVCKKKEGTLHACG----AACGAILGGCDEDKIEK 204
Query: 122 VKDILVQMGIYFQVQDDFLDCF-GSPEVIGK-VGTDIEDYK 160
++ + +G + F G + + + ++E +
Sbjct: 205 LRRFGLYVGTVQGLLGKNRSGFEGRIKELKELAVKELESFG 245
>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 = 33.0 bits (76), Expect = 0.069
Identities = 16/109 (14%), Positives = 32/109 (29%), Gaps = 26/109 (23%)
Query: 65 GQMIDLITTIEGEKDLSKYSLPLHRRIVQYKTAY---YSFYLPVACALLMAG------EN 115
G + E SL + + K AC ++ G +
Sbjct: 154 GLHREE----EIVD--GNTSLDFIEYVCKKKYGEMHACG----AACGAILGGAAEEEIQK 203
Query: 116 LDK---HVEVKDILVQMGIYFQVQDDFLDC---FGSPEVIGK-VGTDIE 157
L + +++M Q+ D+ + + E +G G + E
Sbjct: 204 LRNFGLYQGTLRGMMEMKNSHQLIDENIIGKLKELALEELGGFHGKNAE 252
>3rws_A MTN13 protein; zeatin, cytokinin, hormone, lucerne, nodulin, NODU
plant protein; HET: ZEA; 1.85A {Medicago truncatula}
Length = 168
Score = 31.2 bits (70), Expect = 0.17
Identities = 17/78 (21%), Positives = 35/78 (44%), Gaps = 6/78 (7%)
Query: 155 DIEDYKCSWLVVKALELCNEEQKKLVHENY--GKVDPACVAKVKELYKTLDLEGA----F 208
D E+ ++ V + + L ++ +K+V E + C+ K Y T + +
Sbjct: 79 DRENCAYTYSVYEGIALSDQPLEKIVFEFKLVPTPEEGCIVKSTTKYYTKGDDIELSKDY 138
Query: 209 VEYEKESYEKLTKSIEAH 226
+E E +E TK++E+
Sbjct: 139 LEAGIERFEGFTKAVESF 156
>1d1n_A Initiation factor 2; beta-barrel, gene regulation; NMR
{Geobacillus stearothermophilus} SCOP: b.43.3.1
Length = 99
Score = 28.6 bits (65), Expect = 0.58
Identities = 11/30 (36%), Positives = 17/30 (56%), Gaps = 3/30 (10%)
Query: 14 FRVPKVGMIA---ANDGVLLRNHISRILKN 40
F+V KVG IA DG + R+ R+++
Sbjct: 15 FKVSKVGTIAGCYVTDGKITRDSKVRLIRQ 44
>1zo1_I IF2, translation initiation factor 2; E. coli, ribosome, initiation
of protein synthesis, cryo-eletron microscopy,
translation/RNA complex; 13.80A {Escherichia coli}
Length = 501
Score = 29.8 bits (68), Expect = 0.86
Identities = 11/30 (36%), Positives = 19/30 (63%), Gaps = 3/30 (10%)
Query: 14 FRVPKVGMIAA---NDGVLLRNHISRILKN 40
F+ PK G IA +GV+ R++ R+L++
Sbjct: 417 FKSPKFGAIAGCMVTEGVVKRHNPIRVLRD 446
>1e09_A PRU AV 1; allergen, major cherry allergen, pathogenesis-related
protein, heteronuclear structure; NMR {Prunus avium}
SCOP: d.129.3.1 PDB: 1h2o_A 2lpx_A
Length = 159
Score = 29.2 bits (65), Expect = 0.86
Identities = 16/76 (21%), Positives = 29/76 (38%), Gaps = 4/76 (5%)
Query: 155 DIEDYKCSWLVVKALELCNEEQKKLVHENY-GKVDPACVAKVKELYKTL---DLEGAFVE 210
D E+Y S+ +++ L + +K + K Y T +++ V+
Sbjct: 75 DKENYSYSYTLIEGDALGDTLEKISYETKLVASPSGGSIIKSTSHYHTKGNVEIKEEHVK 134
Query: 211 YEKESYEKLTKSIEAH 226
KE L K IE +
Sbjct: 135 AGKEKASNLFKLIETY 150
>1icx_A Protein LLR18A, LLPR10.1A; 7-stranded beta sheet, C-terminal helix,
allergen; 1.95A {Lupinus luteus} SCOP: d.129.3.1 PDB:
1ifv_A
Length = 155
Score = 28.8 bits (64), Expect = 0.89
Identities = 12/75 (16%), Positives = 24/75 (32%), Gaps = 3/75 (4%)
Query: 155 DIEDYKCSWLVVKALELCNEEQKKLVHENY-GKVDPACVAKVKELYKTLD--LEGAFVEY 211
D + ++ ++ L +K D + K+ + T L +
Sbjct: 74 DEANLTYNYSIIGGEGLDESLEKISYESKILPGPDGGSIGKINVKFHTKGDVLSETVRDQ 133
Query: 212 EKESYEKLTKSIEAH 226
K L K+IE +
Sbjct: 134 AKFKGLGLFKAIEGY 148
>4a8u_A Major pollen allergen BET V 1-J; PR-10 protein; 1.16A {Betula
pendula} PDB: 4a8v_A* 4a87_A* 4a81_A* 4a80_A* 4a83_A*
4a86_A* 4a85_A* 4a88_A 4a8g_A* 1b6f_A 1btv_A 1bv1_A
1fsk_A 4a84_A* 1llt_A 1fm4_A* 3k78_A 1qmr_A
Length = 159
Score = 28.8 bits (64), Expect = 1.0
Identities = 13/76 (17%), Positives = 33/76 (43%), Gaps = 4/76 (5%)
Query: 155 DIEDYKCSWLVVKALELCNEEQKKLVHENY-GKVDPACVAKVKELYKTLD---LEGAFVE 210
D ++K S+ V++ + + +K + + K+ Y T ++ ++
Sbjct: 75 DHTNFKYSYSVIEGGPVGDTLEKISNEIKIVATPNGGSILKINNKYHTKGDHEVKAEQIK 134
Query: 211 YEKESYEKLTKSIEAH 226
KE E L +++E++
Sbjct: 135 ASKEMGETLLRAVESY 150
>3ie5_A Phenolic oxidative coupling protein HYP-1; hypericin, ST JOHN'S
WORT, depression, allergy, PR-10 protein, cytokinin,
plant hormones; HET: PGE PG4 PE8 1PE; 1.69A {Hypericum
perforatum}
Length = 165
Score = 28.1 bits (62), Expect = 1.7
Identities = 10/75 (13%), Positives = 26/75 (34%), Gaps = 3/75 (4%)
Query: 155 DIEDYKCSWLVVKALELCNEEQKKLVHENYGKVDPACVAKVKELYKTLD---LEGAFVEY 211
D ++ C + + + L + +K + V K+ Y + V+
Sbjct: 82 DAANFYCKYTLFEGDVLRDNIEKVVYEVKLEAVGGGSKGKITVTYHPKPGCTVNEEEVKI 141
Query: 212 EKESYEKLTKSIEAH 226
++ + K +E +
Sbjct: 142 GEKKAYEFYKQVEEY 156
>2qim_A PR10.2B; trans-zeatin, cytokinin, plant hormones, plant protein,
PR-1 protein, pathogenesis-related protein, allergen;
HET: ZEA; 1.35A {Lupinus luteus} PDB: 3e85_A* 1xdf_A*
2k7h_A
Length = 158
Score = 28.1 bits (62), Expect = 1.8
Identities = 7/44 (15%), Positives = 15/44 (34%), Gaps = 3/44 (6%)
Query: 186 KVDPACVAKVKELYKTLD---LEGAFVEYEKESYEKLTKSIEAH 226
+ + KV +T + K + K+IE++
Sbjct: 107 GANGGSIGKVTIKIETKGDAQPNEEEGKAAKARGDAFFKAIESY 150
>1tw0_A Pathogenesis-related class 10 protein SPE-16; seven antiparallel
beta-sheet, plant protein; 2.20A {Pachyrhizus erosus}
SCOP: d.129.3.1 PDB: 1txc_A*
Length = 157
Score = 28.0 bits (62), Expect = 1.9
Identities = 12/76 (15%), Positives = 22/76 (28%), Gaps = 4/76 (5%)
Query: 155 DIEDYKCSWLVVKALELCNEEQKKLVHENY-GKVDPACVAKVKELYKTLD---LEGAFVE 210
D + + +V L +K ++KV + T L A +
Sbjct: 74 DEANLGYDYSIVGGTGLPESLEKLSFETKVVAGSGGGSISKVTLKFHTKGDAPLSDAVRD 133
Query: 211 YEKESYEKLTKSIEAH 226
K+IE +
Sbjct: 134 DALAKGAGFFKAIEGY 149
>2i9y_A Major latex protein-like protein 28 or MLP-like protein 28;
AT1G70830, BET V1-like, structural genomics, protein
structure initiative; NMR {Arabidopsis thaliana}
Length = 166
Score = 28.0 bits (62), Expect = 1.9
Identities = 8/39 (20%), Positives = 16/39 (41%)
Query: 188 DPACVAKVKELYKTLDLEGAFVEYEKESYEKLTKSIEAH 226
P + Y+ + E A E + +++K I+ H
Sbjct: 123 GPGSIVHWHLEYEKISEEVAHPETLLQFCVEVSKEIDEH 161
>2po3_A 4-dehydrase; external aldimine, PLP, aminotransferase, TDP-sugar;
HET: T4K; 2.10A {Streptomyces venezuelae}
Length = 424
Score = 27.6 bits (62), Expect = 4.1
Identities = 8/33 (24%), Positives = 10/33 (30%), Gaps = 2/33 (6%)
Query: 20 GMIAANDGVLLRNHISRILKNHFRDKPYYVDLL 52
G + +D L R L N D P
Sbjct: 208 GAVVTDDADLAAR--IRALHNFGFDLPGGSPAG 238
>1smk_A Malate dehydrogenase, glyoxysomal; tricarboxylic cycle, glyoxysome,
NAD, glyoxylate bypass, oxidoreductase; HET: CIT; 2.50A
{Citrullus lanatus} PDB: 1sev_A
Length = 326
Score = 27.6 bits (62), Expect = 4.5
Identities = 16/120 (13%), Positives = 36/120 (30%), Gaps = 38/120 (31%)
Query: 91 IVQYK----TAYYSFYLPVACALLMAGENLDKHVEVKDILVQMGI----YFQVQDDFLDC 142
+V+ K +A S A+ A + ++ + G+ + Q L
Sbjct: 221 VVEAKAGAGSATLS---MAYAAVKFA-DAC-----LRGLRGDAGVIECAFVSSQVTELPF 271
Query: 143 FGSPEVIGKVGTDIEDYKCSWLVVKALELC--NEEQKKLVHENYGKVDPACVAKVKELYK 200
F S +G+ G + + L NE ++ + ++ +
Sbjct: 272 FASKVRLGRNG-----------IEEVYSLGPLNEYERIGLE--------KAKKELAGSIE 312
>1mld_A Malate dehydrogenase; oxidoreductase(NAD(A)-CHOH(D)); HET: CIT;
1.83A {Sus scrofa} SCOP: c.2.1.5 d.162.1.1 PDB: 2dfd_A*
Length = 314
Score = 27.2 bits (61), Expect = 4.9
Identities = 17/117 (14%), Positives = 39/117 (33%), Gaps = 32/117 (27%)
Query: 91 IVQYKT----AYYS-FYLPVACALLMAGENLDKHVEVKDILVQMGIYFQVQDDFLDCFGS 145
+V+ K A S Y + K + ++ + + Q+ F +
Sbjct: 213 VVKAKAGAGSATLSMAYAGARFVFSLVDAMNGK----EGVVE--CSFVKSQETDCPYFST 266
Query: 146 PEVIGKVGTDIEDYKCSWLVVKALELC--NEEQKKLVHENYGKVDPACVAKVKELYK 200
P ++GK G + K L + + ++K++ + ++K K
Sbjct: 267 PLLLGKKG-----------IEKNLGIGKISPFEEKMIA--------EAIPELKASIK 304
>2vjg_A Major allergen DAU C 1; major carrot allergen, pathogenesis-related
protein, plant defense; HET: P4C PG4 PGE; 2.70A {Daucus
carota} PDB: 2wql_A* 2bk0_A
Length = 154
Score = 26.5 bits (58), Expect = 5.2
Identities = 12/76 (15%), Positives = 24/76 (31%), Gaps = 4/76 (5%)
Query: 155 DIEDYKCSWLVVKALELCNEEQKKLVHENY-GKVDPACVAKVKELYKTLD---LEGAFVE 210
+ E V+ L + H D + K ++ T + ++
Sbjct: 75 NKEALSYDSTVIDGDILLGFIESIETHMVVVPTADGGSITKTTAIFHTKGDAVVPEENIK 134
Query: 211 YEKESYEKLTKSIEAH 226
+ L K+IEA+
Sbjct: 135 FADAQNTALFKAIEAY 150
>1y7t_A Malate dehydrogenase; NAD-dependent-MDH-NADPH complex,
oxidoreductase; HET: NDP; 1.65A {Thermus thermophilus}
SCOP: c.2.1.5 d.162.1.1 PDB: 1iz9_A* 2cvq_A* 1bmd_A*
1bdm_A* 1wze_A* 1wzi_A*
Length = 327
Score = 26.9 bits (60), Expect = 7.0
Identities = 9/39 (23%), Positives = 15/39 (38%), Gaps = 8/39 (20%)
Query: 141 DCFGSPEVIGKVGTDIEDYKCSWLVVKALELCNEEQKKL 179
S V K G + VV+ LE+ +K++
Sbjct: 277 GIVYSFPVTAKDGA--------YRVVEGLEINEFARKRM 307
>3hhp_A Malate dehydrogenase; MDH, citric acid cycle, TCA cycle, NAD,
oxidoreductase, tricarboxylic acid cycle; 1.45A
{Escherichia coli k-12} PDB: 2pwz_A 2cmd_A* 1emd_A*
1ib6_A* 1ie3_A* 4e0b_A*
Length = 312
Score = 26.4 bits (59), Expect = 8.4
Identities = 17/112 (15%), Positives = 31/112 (27%), Gaps = 26/112 (23%)
Query: 91 IVQYKT----AYYSFYLPVACALLMAGENLDKHVEVKDILVQMGIYFQVQDDFLDCFGSP 146
+V+ K A S A + + ++ + Q F P
Sbjct: 213 VVEAKAGGGSATLS---MGQAAARFGLSLVRALQGEQGVVECAYVEGDGQYA--RFFSQP 267
Query: 147 EVIGKVGTDIEDYKCSWLVVKALELCNEEQKKLVHENYGKVDPACVAKVKEL 198
++GK G +E+ L EQ L + +K+
Sbjct: 268 LLLGKNG--VEE------RKSIGTLSAFEQNAL---------EGMLDTLKKD 302
>3ju7_A Putative PLP-dependent aminotransferase; NP_978343.1, struct
genomics, joint center for structural genomics, JCSG;
HET: LLP PGE; 2.19A {Bacillus cereus atcc 10987}
Length = 377
Score = 26.3 bits (59), Expect = 9.7
Identities = 4/33 (12%), Positives = 13/33 (39%), Gaps = 2/33 (6%)
Query: 20 GMIAANDGVLLRNHISRILKNHFRDKPYYVDLL 52
G+I + + ++ + + N D ++
Sbjct: 199 GLIYSKNEEDIQR--IKRMGNFGFDTNRECTMM 229
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
0.321 0.138 0.409
Gapped
Lambda K H
0.267 0.0744 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,840,447
Number of extensions: 230165
Number of successful extensions: 600
Number of sequences better than 10.0: 1
Number of HSP's gapped: 570
Number of HSP's successfully gapped: 80
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 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (25.3 bits)