RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy3877
(145 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 = 182 bits (463), Expect = 2e-58
Identities = 82/137 (59%), Positives = 99/137 (72%)
Query: 2 MAIRLMQLFSDTKSDFTTLAGILGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPI 61
+A+ LMQLFSD K D L LGL+FQ+RDDY NL SKEYSENKSFCEDLTEGKFSFP
Sbjct: 159 LAVGLMQLFSDYKEDLKPLLNTLGLFFQIRDDYANLHSKEYSENKSFCEDLTEGKFSFPT 218
Query: 62 IHAIQSRPDDRQVIQILRQRTRDVEVKKYCISLLDRFGSFEHTREVLKELDVSARTEVAR 121
IHAI SRP+ QV ILRQRT ++++KKYC+ L+ GSFE+TR LKEL+ A ++
Sbjct: 219 IHAIWSRPESTQVQNILRQRTENIDIKKYCVHYLEDVGSFEYTRNTLKELEAKAYKQIDA 278
Query: 122 LGGNPLLEAILDELLTW 138
GGNP L A++ L
Sbjct: 279 RGGNPELVALVKHLSKM 295
>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 = 144 bits (364), Expect = 4e-43
Identities = 39/131 (29%), Positives = 64/131 (48%), Gaps = 10/131 (7%)
Query: 1 MMAIRLMQLFSDTKS---DFTTLAGILGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKF 57
+ +RLM+ S + +LG+ +Q+RDDY NL + S K F ED+TEGK
Sbjct: 180 RLTLRLMEALSPSSHHGHSLVPFINLLGIIYQIRDDYLNLKDFQMSSEKGFAEDITEGKL 239
Query: 58 SFPIIHAIQ------SRPDDRQVIQILRQRTRDVEVKKYCISLL-DRFGSFEHTREVLKE 110
SFPI+HA+ ++++IL RT D ++K I +L S +T+ + +
Sbjct: 240 SFPIVHALNFTKTKGQTEQHNEILRILLLRTSDKDIKLKLIQILEFDTNSLAYTKNFINQ 299
Query: 111 LDVSARTEVAR 121
L + +
Sbjct: 300 LVNMIKNDNEN 310
>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 = 109 bits (273), Expect = 2e-29
Identities = 22/136 (16%), Positives = 56/136 (41%), Gaps = 8/136 (5%)
Query: 1 MMAIRLMQLFSDTKSDFTTLAGILGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFP 60
+ + +Q+ S + + LG ++QV +D + Y N S +D+ K ++P
Sbjct: 223 GLTLSEIQVSSAQLNLIEAILYKLGEFYQVHNDVSD-----YLFNDSNADDICRFKLTWP 277
Query: 61 IIHAIQSRPDDRQVIQILRQRTRDVEVKKYCISLLD-RFGSFEHTREVLKELDVSARTEV 119
+ + + ++ ++I ++ + K C +LL E+ R L L + ++
Sbjct: 278 LQKSFEIADEE-MKLKISENYGKNSSLVKDCYNLLKINEHYLEYQRNALDYLIKLVK-DI 335
Query: 120 ARLGGNPLLEAILDEL 135
+ ++ ++
Sbjct: 336 TDDSLQKVFIHLIHQI 351
>4dhd_A Polyprenyl synthetase; isoprenoid synthesis, isoprenoid diphosphate
synthase, trans; 1.65A {Pyrobaculum calidifontis}
Length = 358
Score = 58.5 bits (142), Expect = 4e-11
Identities = 24/113 (21%), Positives = 49/113 (43%), Gaps = 3/113 (2%)
Query: 24 LGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQSR---PDDRQVIQILRQ 80
G+ FQ+ DD ++ K +D+ E K ++ S + R++++IL +
Sbjct: 217 AGVAFQIIDDVLDIYGDPKKFGKEIGKDIKEHKRGNAVVAVALSHLGEGERRRLLEILAR 276
Query: 81 RTRDVEVKKYCISLLDRFGSFEHTREVLKELDVSARTEVARLGGNPLLEAILD 133
+ + ++LLD G+ E + A +A++ N L+ +LD
Sbjct: 277 EVVEEADVREAVALLDSVGAREEALRLAARYREEAERHLAKIPNNGTLKELLD 329
>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 = 56.1 bits (136), Expect = 2e-10
Identities = 19/110 (17%), Positives = 46/110 (41%), Gaps = 1/110 (0%)
Query: 24 LGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQSRPDDRQVIQILRQRTR 83
+G +Q+ DD + K EDL G +S P++ ++ P D + +Q
Sbjct: 216 IGCAYQMLDDILDYAGDPKRTQKPVLEDLRSGVYSLPLLLSLSHAPRDFHKLLKKKQAMT 275
Query: 84 DVEVKKYCISLLDRFGSFEHTREVLKELDVSARTEVARLGGNPLLEAILD 133
++K +L+ ++ +++ ++ A T + +L +++
Sbjct: 276 LEDIKH-VQALVAQYDGVGAAKQLAQDYTDRALTLIQQLPVGSAQQSLEQ 324
>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 = 54.2 bits (131), Expect = 1e-09
Identities = 28/111 (25%), Positives = 55/111 (49%), Gaps = 1/111 (0%)
Query: 24 LGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQ-SRPDDRQVIQILRQRT 82
+G+ FQ+ DD ++ S+ + K+ DL EG F+ P+++A++ P ++ IL
Sbjct: 232 VGMIFQIVDDIIDIFSETHESGKTPGTDLREGVFTLPVLYALREDTPVGAELRDILTGPL 291
Query: 83 RDVEVKKYCISLLDRFGSFEHTREVLKELDVSARTEVARLGGNPLLEAILD 133
D E + + LL + G + + + A E+ RL + + EA+ +
Sbjct: 292 EDDETVNHVLELLSQSGGRQAALDEVYRYMDIANAELDRLPDSTVKEALRN 342
>3nf2_A Putative polyprenyl synthetase; isoprenyl diphosphate synthase,
structural genomics, PSI, PR structure initiative,
nysgrc; 2.20A {Streptomyces coelicolor}
Length = 352
Score = 54.3 bits (131), Expect = 1e-09
Identities = 22/120 (18%), Positives = 42/120 (35%), Gaps = 8/120 (6%)
Query: 24 LGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQ-SRPDDRQVIQILRQRT 82
LGL FQ DD + + K DL + K S P++ A+ ++ +IL
Sbjct: 216 LGLAFQAVDDLLGIWGDPDATGKQTWSDLRQRKKSLPVVAALAAGGAASERLGEILTADA 275
Query: 83 RDVEVKKYC-------ISLLDRFGSFEHTREVLKELDVSARTEVARLGGNPLLEAILDEL 135
+ + + +L++ G E T + + A + + + L
Sbjct: 276 KASDFANFSEEEFAARAALIEEAGGREWTADEARRQHTIAIEALDAVDMPDRVRDRFTAL 335
>3mzv_A Decaprenyl diphosphate synthase; transferase, structural genomics,
PSI-2, protein structure initiative; 1.90A {Rhodobacter
capsulatus}
Length = 341
Score = 54.2 bits (131), Expect = 1e-09
Identities = 28/114 (24%), Positives = 55/114 (48%), Gaps = 3/114 (2%)
Query: 24 LGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQ--SRPDDRQVIQILRQR 81
LG+ FQ+ DD + K K+ +D E K + P+I A+ + +++ +
Sbjct: 212 LGIAFQIVDDLLDYGGKSAEIGKNTGDDFRERKLTMPVIKAVALADEAERAFWKRVIEKG 271
Query: 82 TRDVEVKKYCISLLDRFGSFEHTREVLKELDVSARTEVARLGGNPLLEAILDEL 135
+ ++ ++L+ + G+ E TR +AR +A+L +PL + LD+L
Sbjct: 272 DQQDGDLEHAMALMTKHGTLEATRLAAIGWTDTARKALAKLPDHPLRQM-LDDL 324
>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 = 53.4 bits (128), Expect = 2e-09
Identities = 17/115 (14%), Positives = 37/115 (32%), Gaps = 4/115 (3%)
Query: 24 LGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQ-SRPDDRQVIQILRQRT 82
+G YFQV+DD + + K D+ + K S+ + + + +
Sbjct: 270 MGEYFQVQDDVMDCFTPPERLGKV-GTDIQDAKCSWLAVTFLAKASSAQVAEFKANYGSG 328
Query: 83 RDVEVKKYCISLLDRFGSFEHTREVLKELDVSARTEVARL-GGNPLLEAILDELL 136
+V L + + + + +L +P A ++ L
Sbjct: 329 DSEKVAT-VRRLYEEADLQGDYVAYEAAVAEQVKELIEKLRLCSPGFAASVETLW 382
>3oyr_A Trans-isoprenyl diphosphate synthase; isoprenyl synthase, PSI,
protein structure initiative; HET: IPE; 2.00A
{Caulobacter crescentus}
Length = 345
Score = 52.7 bits (127), Expect = 4e-09
Identities = 26/112 (23%), Positives = 51/112 (45%), Gaps = 2/112 (1%)
Query: 24 LGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQ-SRPDDRQVI-QILRQR 81
LGL FQ+ DD + + K+ +D EGK + P++ AI S P + + + + +R
Sbjct: 224 LGLAFQLADDALDYGGATETLGKNAGDDFREGKATLPLLLAIARSGPREAEFWERAIGRR 283
Query: 82 TRDVEVKKYCISLLDRFGSFEHTREVLKELDVSARTEVARLGGNPLLEAILD 133
+ + L+ G+ + T ++ + A+ +A N EA+ +
Sbjct: 284 EQTEADFRRARELIIGSGALDATLDLAADYADKAKAALAMFPANDWREALEE 335
>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 = 52.0 bits (125), Expect = 7e-09
Identities = 25/99 (25%), Positives = 43/99 (43%), Gaps = 3/99 (3%)
Query: 24 LGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQSRPDDRQVIQILRQRTR 83
LGL FQ+ DD + S K D+ G + PI+ A++ P R+V+ + + R
Sbjct: 226 LGLAFQLIDDILDFTGTSASLGKGSLSDIRHGVITAPILFAMEEFPQLREVVDQVEKDPR 285
Query: 84 DVEVKKYCISLLDRFGSFEHTREVLKELDVSARTEVARL 122
+V+ + L + + RE+ E A + L
Sbjct: 286 NVD---IALEYLGKSKGIQRARELAMEHANLAAAAIGSL 321
>3lk5_A Geranylgeranyl pyrophosphate synthase; structural genomics, protein
structure initiative, geranylge pyrophosphate synthase;
1.90A {Corynebacterium glutamicum} PDB: 3qqv_A*
Length = 380
Score = 51.7 bits (124), Expect = 9e-09
Identities = 22/116 (18%), Positives = 43/116 (37%), Gaps = 4/116 (3%)
Query: 24 LGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQ-SRPDDRQVIQILRQ-- 80
+G+ FQ+RDD + K +D+ EGK + + A+Q + + +R
Sbjct: 249 IGIAFQLRDDLLGVFGDPAITGKPAGDDIREGKRTVLLALALQRADKQSPEAATAIRAGV 308
Query: 81 -RTRDVEVKKYCISLLDRFGSFEHTREVLKELDVSARTEVARLGGNPLLEAILDEL 135
+ E + G+ E + + +L S + + + A L L
Sbjct: 309 GKVTSPEDIAVITEHIRATGAEEEVEQRISQLTESGLAHLDDVDIPDEVRAQLRAL 364
>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 = 51.3 bits (123), Expect = 1e-08
Identities = 23/114 (20%), Positives = 46/114 (40%), Gaps = 4/114 (3%)
Query: 24 LGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQ-SRPDDRQVIQILRQRT 82
+G YFQ++DDY + D+ + K S+ ++ +Q P+ RQ+++ R
Sbjct: 249 MGEYFQIQDDYLDCFGDPALTGA-VGTDIQDNKCSWLVVQCLQRVTPEQRQLLEDNYGRK 307
Query: 83 RDVEVKKYCISLLDRFGSFEHTREVLKELDVSARTEVARLGGNPLLEAILDELL 136
+V K L + G ++ + + + + N L + I L
Sbjct: 308 EPEKVAK-VKELYEAVGMRAAFQQYEESSYRRLQELIEKH-SNRLPKEIFLGLA 359
>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 = 51.1 bits (122), Expect = 1e-08
Identities = 24/114 (21%), Positives = 46/114 (40%), Gaps = 4/114 (3%)
Query: 24 LGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQ-SRPDDRQVIQILRQRT 82
+G YFQ+ DDY ++ K D+ K ++P+I + D+ I +
Sbjct: 278 MGEYFQIHDDYLDIFGDSTKTGK-VGSDIQNNKLTWPLIKTFELCSEPDKIKIVKNYGK- 335
Query: 83 RDVEVKKYCISLLDRFGSFEHTREVLKELDVSARTEVARLGGNPLLEAILDELL 136
++ K SL +++ +H K + + L + +E +L LL
Sbjct: 336 NNLACVKVIDSLYEQYKIRKHYESYEKAQKAKILSAINEL-HHEGIEYVLKYLL 388
>3rmg_A Octaprenyl-diphosphate synthase; structural genomics, protein
structure initiative, isoprene biosynthesis,
transferase; 2.30A {Bacteroides thetaiotaomicron}
Length = 334
Score = 49.9 bits (120), Expect = 3e-08
Identities = 21/112 (18%), Positives = 45/112 (40%), Gaps = 3/112 (2%)
Query: 24 LGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQ--SRPDDRQVIQILRQR 81
+G+ FQ++DD + + K D+ EGK + P ++A+ Q+ +++
Sbjct: 206 IGICFQIKDDIFDYFDSK-KIGKPTGNDMLEGKLTLPALYALNTTKDAWAEQIAFKVKEG 264
Query: 82 TRDVEVKKYCISLLDRFGSFEHTREVLKELDVSARTEVARLGGNPLLEAILD 133
T + I G E+ +++ A +A L + + A+
Sbjct: 265 TATPDEIVRLIEFTKDNGGIEYACRTIEQYKKKAFDLLAALPDSNICLALRT 316
>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 = 49.8 bits (119), Expect = 3e-08
Identities = 16/115 (13%), Positives = 35/115 (30%), Gaps = 4/115 (3%)
Query: 24 LGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQ-SRPDDRQVIQILRQRT 82
+G YFQV+DD + + K D+ + K S+ + + + +
Sbjct: 242 IGEYFQVQDDVMDCFTPPEQLGKV-GTDIEDAKCSWLAVTFLGKANAAQVAEFKANYGDK 300
Query: 83 RDVEVKKYCISLLDRFGSFEHTREVLKELDVSARTEVARL-GGNPLLEAILDELL 136
+V L E+ + + +L +P + +
Sbjct: 301 DPAKVAV-VKRLYSEANLQADFAAYEAEVVREVESLIEQLKVKSPTFAESVAVVW 354
>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 = 49.6 bits (119), Expect = 4e-08
Identities = 26/103 (25%), Positives = 41/103 (39%), Gaps = 9/103 (8%)
Query: 24 LGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQSRPDDRQVIQILRQRTR 83
+G +Q+ DD + E K DL G SFP++ A++ P+ RQ+ R
Sbjct: 196 IGTIYQMFDDIMDFAGME-KIGKDGFLDLKNGVASFPLVTAMEKFPEARQMF-----ENR 249
Query: 84 DVEVKKYCISLLDRFGSFEHTREVLKELDVSARTEVARLGGNP 126
D +S + G + E LK L + E + L
Sbjct: 250 DWS---GLMSFMREKGILKECEETLKVLVKNVIIENSWLRDFV 289
>1wmw_A Geranylgeranyl diphosphate synthetase; GGPP, prenyl diphosphate
synthase, structural genom riken structural
genomics/proteomics initiative; 1.55A {Thermus
thermophilus}
Length = 330
Score = 49.6 bits (119), Expect = 4e-08
Identities = 27/118 (22%), Positives = 44/118 (37%), Gaps = 7/118 (5%)
Query: 24 LGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQ-SRPDDRQVIQILRQRT 82
LG FQ+ DD NL E + K DL EGK + ++ ++ + P++R L
Sbjct: 204 LGTAFQIVDDVLNLEGGE-AYGKERAGDLYEGKRTLILLRFLEEAPPEERARALALLALP 262
Query: 83 R----DVEVKKYCISLLDRFGSFEHTREVLKELDVSARTEVARLGGNPLLEAILDELL 136
R + EV + L + + K L + + + LD L
Sbjct: 263 REAKPEAEVGW-LLERLLASRALAWAKAEAKRLQAEGLALLEAAFQDLPGKEALDHLR 319
>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 = 49.4 bits (118), Expect = 5e-08
Identities = 20/114 (17%), Positives = 47/114 (41%), Gaps = 4/114 (3%)
Query: 24 LGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQ-SRPDDRQVIQILRQRT 82
+G +FQ++DDY +L K D+ + K S+ ++ +Q + P+ Q+++ +
Sbjct: 256 MGEFFQIQDDYLDLFGDPSVTGKIG-TDIQDNKCSWLVVQCLQRATPEQYQILKENYGQK 314
Query: 83 RDVEVKKYCISLLDRFGSFEHTREVLKELDVSARTEVARLGGNPLLEAILDELL 136
+V + +L + + ++ + + PL A+ L
Sbjct: 315 EAEKVAR-VKALYEELDLPAVFLQYEEDSYSHIMALIEQY-AAPLPPAVFLGLA 366
>3aqb_B Component B of hexaprenyl diphosphate synthase; prenyltransferase,
transferase; 2.40A {Micrococcus luteus} PDB: 3aqc_B*
Length = 325
Score = 49.2 bits (118), Expect = 5e-08
Identities = 23/114 (20%), Positives = 53/114 (46%), Gaps = 5/114 (4%)
Query: 24 LGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQ--SRPDDRQVIQILRQ- 80
+G+ +Q+ DD + S E + K D+ G ++P++ AI DD ++ +++
Sbjct: 203 IGMSYQIIDDILDYTSDEATLGKPVGSDIRNGHITYPLMAAIANLKEQDDDKLEAVVKHL 262
Query: 81 -RTRDVEVKKYCISLLDRFGSFEHTREVLKELDVSARTEVARLGGNPLLEAILD 133
T D EV +Y I + E + ++ A+ +++L + + + + +
Sbjct: 263 TSTSDDEVYQY-IVSQVKQYGIEPAELLSRKYGDKAKYHLSQLQDSNIKDYLEE 315
>3tc1_A Octaprenyl pyrophosphate synthase; all alpha-helices fold,
transferase; 2.00A {Helicobacter pylori}
Length = 315
Score = 49.1 bits (118), Expect = 5e-08
Identities = 17/89 (19%), Positives = 37/89 (41%), Gaps = 4/89 (4%)
Query: 24 LGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQ-SRPDDRQVI-QILRQR 81
G+ FQ+ DD ++ + K D EGK + P + + D+ ++ +Q
Sbjct: 192 FGMAFQIIDDLLDITQDAKTLGKPNFSDFKEGKTTLPYLLLYEKLNQHDQGLLISYFKQD 251
Query: 82 TRDVEVKKYCISLLDRFGSFEHTREVLKE 110
+ E+ ++ ++G E T + +
Sbjct: 252 SH--EIIEWTKEKFKQYGIIEETLKTAQV 278
>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 = 47.9 bits (113), Expect = 2e-07
Identities = 30/166 (18%), Positives = 52/166 (31%), Gaps = 45/166 (27%)
Query: 10 FSDTKSDFTTLAGILGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQSRP 69
+ S T L + L +Q+ ++ + + K + ++S+P
Sbjct: 189 LKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNI-KLRIHSIQAELRRL-----LKSKP 242
Query: 70 --------DD---RQVI-------QILRQRTRDVEV-------KKYCISLLDRFGSFEH- 103
+ + +IL TR +V ISL +
Sbjct: 243 YENCLLVLLNVQNAKAWNAFNLSCKILLT-TRFKQVTDFLSAATTTHISLDHHSMTLTPD 301
Query: 104 -TREVL-KELDVSA---RTEVARLGGNPLLEAILDELL-----TWD 139
+ +L K LD EV L NP +I+ E + TWD
Sbjct: 302 EVKSLLLKYLDCRPQDLPREV--LTTNPRRLSIIAESIRDGLATWD 345
Score = 39.8 bits (92), Expect = 1e-04
Identities = 20/94 (21%), Positives = 39/94 (41%), Gaps = 10/94 (10%)
Query: 37 LCSKEYSENKSFCEDLTEGKFSFPIIHAIQSRPDDRQVIQIL----RQRT-RDVEV-KKY 90
L SK+ + F E++ + F ++ I++ ++ + R R D +V KY
Sbjct: 71 LLSKQEEMVQKFVEEVLRINYKF-LMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKY 129
Query: 91 CISLLDRFGSFEHTREVLKELDVSARTEVARLGG 124
+S R + R+ L EL + + + G
Sbjct: 130 NVS---RLQPYLKLRQALLELRPAKNVLIDGVLG 160
>1wy0_A Geranylgeranyl pyrophosphate synthetase; pyrococcus horikosh
structural genomics, riken structural
genomics/proteomics initiative, RSGI; 2.20A {Pyrococcus
horikoshii}
Length = 342
Score = 47.3 bits (113), Expect = 2e-07
Identities = 28/130 (21%), Positives = 56/130 (43%), Gaps = 16/130 (12%)
Query: 24 LGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQ-SRPDDRQVI-QILRQR 81
+G+ FQ+ DD +L + E K D+ +GK + + H + + D+Q +I +
Sbjct: 210 VGIAFQIWDDVLDLIADEKKLGKPVGSDIRKGKKTLIVAHFFENADEKDKQRFLKIFGKY 269
Query: 82 TRDVEVKKYC-----------ISLLDRFGSFEHTREVLKELDVSARTEVARLGGNP---L 127
DV+ + I LL ++GS ++ E+ K++ A + L +
Sbjct: 270 AGDVKGRGIIEEDIKSDVMEAIDLLKKYGSIDYAAEIAKDMIKKANEALRILPKSKARMD 329
Query: 128 LEAILDELLT 137
LE + ++
Sbjct: 330 LELLAKFIVE 339
>2azj_A Geranylgeranyl pyrophosphate synthetase; hexpps,
trans-prenyltransferase; 2.40A {Sulfolobus solfataricus}
PDB: 2azk_A
Length = 289
Score = 46.2 bits (110), Expect = 7e-07
Identities = 14/84 (16%), Positives = 31/84 (36%), Gaps = 5/84 (5%)
Query: 24 LGLYFQVRDDYCNLCSKEYSENKSF----CEDLTEGKFSFPIIHAIQ-SRPDDRQVIQIL 78
LG+ +QV DD+ + +K+ E + EGK + + ++I +
Sbjct: 200 LGIIYQVIDDFVDYKTKKVEEIDGSAKQLFKYYREGKLEEYVRSVYLEYKQKYDELISNI 259
Query: 79 RQRTRDVEVKKYCISLLDRFGSFE 102
+++ + + L E
Sbjct: 260 PFQSKYLSEIRSLPEFLANGLLKE 283
>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 = 3e-04
Identities = 12/89 (13%), Positives = 27/89 (30%), Gaps = 18/89 (20%)
Query: 24 LGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQSRPDD--RQVIQILRQR 81
LG +Q+ DD E K + + P I+ + ++ ++ I ++
Sbjct: 199 LGTAYQIVDDILEFLEVV--EGK----ESKFTSETLPHIYMKSTSKEEALKKSIDCVKLH 252
Query: 82 T----------RDVEVKKYCISLLDRFGS 100
R+ + + D
Sbjct: 253 VAAAKETLETFRECPARDKLFQITDYITV 281
>4fp4_A Polyprenyl synthetase; isoprenoid synthesis, isoprenoid diphosphate
synthase, trans; HET: GER UNL; 2.00A {Pyrobaculum
calidifontis}
Length = 285
Score = 33.1 bits (76), Expect = 0.018
Identities = 13/62 (20%), Positives = 28/62 (45%), Gaps = 4/62 (6%)
Query: 24 LGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQ-SRPDDRQVIQILRQRT 82
LG+ +Q DDY + + E KS ++ G++ I + + ++I+ L +
Sbjct: 196 LGILYQYSDDYSDENVER-PETKSIANEI--GRYLLKIKEHVGDAIAPFERLIKYLIGKA 252
Query: 83 RD 84
+
Sbjct: 253 LE 254
>1q7e_A Hypothetical protein YFDW; structural genomics, intertwined dimer,
PSI, protein structu initiative; HET: MSE; 1.60A
{Escherichia coli} SCOP: c.123.1.1 PDB: 1pqy_A* 1q6y_A*
1pt7_A 1pt5_A 1pt8_A*
Length = 428
Score = 31.0 bits (71), Expect = 0.10
Identities = 10/21 (47%), Positives = 13/21 (61%), Gaps = 1/21 (4%)
Query: 102 EHTREVLKELDVSARTEVARL 122
EHT VL+EL S E+A +
Sbjct: 393 EHTAAVLQELGYSD-DEIAAM 412
>3ubm_A COAT2, formyl-COA:oxalate COA-transferase; HET: COA; 1.99A
{Acetobacter aceti}
Length = 456
Score = 30.7 bits (70), Expect = 0.12
Identities = 11/21 (52%), Positives = 13/21 (61%), Gaps = 1/21 (4%)
Query: 102 EHTREVLKELDVSARTEVARL 122
+HT EVL EL SA E+ L
Sbjct: 429 QHTDEVLAELGYSA-EEIKSL 448
>2vjq_A Formyl-coenzyme A transferase; class III COA transferase; HET: EPE;
1.8A {Oxalobacter formigenes} PDB: 2vjp_A 2vjm_A*
2vjl_A* 2vjk_A* 1p5h_A 1p5r_A* 2vjn_A* 1t4c_A* 2vjo_A*
2vjm_B* 1vgr_A* 1t3z_A* 1t4c_B* 1vgq_A*
Length = 428
Score = 30.3 bits (69), Expect = 0.17
Identities = 10/21 (47%), Positives = 13/21 (61%), Gaps = 1/21 (4%)
Query: 102 EHTREVLKELDVSARTEVARL 122
EHT EVLKEL + ++ L
Sbjct: 403 EHTDEVLKELGLDD-AKIKEL 422
>2rkk_A Vacuolar protein sorting-associated protein VTA1; MIT motif,
cytoplasm, endosome, lipid transport, membrane, protein
transport; 2.90A {Saccharomyces cerevisiae}
Length = 168
Score = 30.1 bits (67), Expect = 0.18
Identities = 10/54 (18%), Positives = 20/54 (37%), Gaps = 3/54 (5%)
Query: 76 QILRQRTRDVEVKKYCISLLDRFGSFEHTREVLKELDVSARTEVARLGGNPLLE 129
IL + R E+ LLD E ++ + + ++ + N L+
Sbjct: 35 LILSEEDRSQEMTALATELLDT---IEAFKKEIGGESEAEDSDKSLHVMNTLIH 85
>1xk7_A Crotonobetainyl-COA:carnitine COA-transferase; CAIB,
montreal-kingston bacterial structural genomics
initiative, BSGI, structural genomics; 1.60A
{Escherichia coli} SCOP: c.123.1.1 PDB: 1xk6_A 1xvt_A*
1xvu_A* 1xvv_A* 1xa3_A* 1xa4_A*
Length = 408
Score = 29.5 bits (67), Expect = 0.34
Identities = 5/21 (23%), Positives = 9/21 (42%), Gaps = 1/21 (4%)
Query: 102 EHTREVLKELDVSARTEVARL 122
T +LK + S ++ L
Sbjct: 379 MDTAAILKNIGYSE-NDIQEL 398
>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 = 27.3 bits (60), Expect = 2.3
Identities = 28/160 (17%), Positives = 42/160 (26%), Gaps = 58/160 (36%)
Query: 9 LFSDTKSDFTTLAGILG------LYFQ-VRDDY------------------CNLCSKEYS 43
LF L I G YF+ +RD Y L
Sbjct: 145 LFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLD 204
Query: 44 ENKSF------------------CEDLTEGKFSFPIIHAIQ------------SRPDD-R 72
K F + L S P+I IQ P + R
Sbjct: 205 AEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELR 264
Query: 73 QVIQILRQRTRDVEVKKYCISLLDRFGSF-EHTREVLKEL 111
++ ++ + V I+ D + SF R+ + L
Sbjct: 265 SYLKGATGHSQGL-VTAVAIAETDSWESFFVSVRKAITVL 303
>4ed9_A CAIB/BAIF family protein; ssgcid, NIH, niaid, SBRI, UW, emerald
biostructures, structu genomics; HET: NHE; 1.95A
{Brucella suis}
Length = 385
Score = 26.3 bits (59), Expect = 3.8
Identities = 5/11 (45%), Positives = 6/11 (54%)
Query: 102 EHTREVLKELD 112
EH + ELD
Sbjct: 373 EHGAAIRAELD 383
>2cy7_A Cysteine protease APG4B; papain-like fold, autophagy, hydrolase;
1.90A {Homo sapiens} SCOP: d.3.1.22 PDB: 2d1i_A 2zzp_A
2z0d_A 2z0e_A
Length = 396
Score = 26.4 bits (57), Expect = 3.9
Identities = 7/48 (14%), Positives = 20/48 (41%), Gaps = 8/48 (16%)
Query: 24 LGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQSRPDD 71
+G + + DD+ + C + + L+ + P+ ++ +P
Sbjct: 322 VGFFCKTEDDFNDWCQQ--------VKKLSLLGGALPMFELVEQQPSH 361
>3lou_A Formyltetrahydrofolate deformylase; structural genomics, JOI for
structural genomics, JCSG, protein structure initiative
hydrolase; HET: MSE; 1.90A {Burkholderia mallei}
Length = 292
Score = 26.4 bits (59), Expect = 4.1
Identities = 14/37 (37%), Positives = 17/37 (45%), Gaps = 4/37 (10%)
Query: 50 EDLTEGKFSFPIIHAIQSRPDDRQVIQILRQRTRDVE 86
+DL EG PII + R D + L RDVE
Sbjct: 233 DDLDEG----PIIEQVVERVDHSYRPEQLLAVGRDVE 265
>3maj_A DNA processing chain A; MCSG, PSI-2, structural genomics, protein
structure initiati midwest center for structural
genomics; HET: DNA; 2.05A {Rhodopseudomonas palustris}
Length = 382
Score = 26.1 bits (58), Expect = 4.6
Identities = 15/62 (24%), Positives = 21/62 (33%), Gaps = 12/62 (19%)
Query: 94 LLDRFGSFEHTREVLKELDVSARTEVARLGGNPLLEAILDEL----------LTWDTPDS 143
L++ FGS E L EL + R AR G P + E+ +
Sbjct: 42 LINHFGSARAALERLPEL--ARRGGAARAGRIPSEDEARREIEAGRRIGVELVAPGETGY 99
Query: 144 PK 145
P
Sbjct: 100 PT 101
>4dgw_A PRE-mRNA-splicing factor PRP9; zinc finger; 3.11A {Saccharomyces
cerevisiae}
Length = 402
Score = 26.0 bits (56), Expect = 5.3
Identities = 10/41 (24%), Positives = 17/41 (41%)
Query: 8 QLFSDTKSDFTTLAGILGLYFQVRDDYCNLCSKEYSENKSF 48
+ + KSDF L + + YC CS+ + + F
Sbjct: 268 AVENLIKSDFEHSYCRGSLRSEAKGIYCPFCSRWFKTSSVF 308
>2p82_A Cysteine protease ATG4A; autophagy, hydrolase, protein transport,
thiol Pro transport, UBL conjugation pathway, structural
genomics; 2.10A {Homo sapiens} SCOP: d.3.1.22
Length = 355
Score = 26.0 bits (56), Expect = 5.5
Identities = 10/48 (20%), Positives = 16/48 (33%), Gaps = 9/48 (18%)
Query: 24 LGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQSRPDD 71
LG + + D+ N CS E K + + +Q P
Sbjct: 316 LGFFCKEEKDFDNWCSLVQKEI---------LKENLRMFELVQKHPSH 354
>1rws_A Hypothetical protein PF1061; residual dipolar couplings, structural
genomics, unknown FUN; NMR {Pyrococcus furiosus} SCOP:
d.15.3.2 PDB: 1sf0_A
Length = 77
Score = 24.6 bits (53), Expect = 6.0
Identities = 11/64 (17%), Positives = 29/64 (45%), Gaps = 14/64 (21%)
Query: 73 QVIQILRQRTRDVEVKKYCISLLDRFGSFEHTREVLKELDVSARTEVARLGGNPLLEAIL 132
+V I R +++E ++ R++L+ + + + +A++ G +LE
Sbjct: 13 KVKVIGRNIEKEIEWREGM-----------KVRDILRAVGFNTESAIAKVNGKVVLE--- 58
Query: 133 DELL 136
D+ +
Sbjct: 59 DDEV 62
>3rdw_A Putative arsenate reductase; structural genomics, center for
structural genomics of infec diseases, csgid,
oxidoreductase; 2.20A {Yersinia pestis}
Length = 121
Score = 25.3 bits (56), Expect = 6.3
Identities = 13/63 (20%), Positives = 29/63 (46%), Gaps = 4/63 (6%)
Query: 72 RQVIQILRQRTRDVEVKKYCISLLDRFGSFEHTREVLKELDVSARTEVARLGGNPLLEAI 131
R+ + ++ Q+ +V Y L+ S + +E+L++L S ++ R +
Sbjct: 19 RETLALVEQQGITPQVVLY----LETPPSVDKLKELLQQLGFSDARQLMRTKEDLYKTLN 74
Query: 132 LDE 134
LD+
Sbjct: 75 LDD 77
>1wot_A Putative minimal nucleotidyltransferase; alpha and beta, structural
genomics, riken structural genomics/proteomics
initiative, RSGI; NMR {Thermus thermophilus} SCOP:
d.218.1.5
Length = 98
Score = 25.0 bits (55), Expect = 6.4
Identities = 5/31 (16%), Positives = 13/31 (41%), Gaps = 1/31 (3%)
Query: 71 DRQVIQILRQRTRDVEVKKYCISLLDRFGSF 101
D + ++ R+ + ++ + FGS
Sbjct: 5 DLETLRARREAVLSL-CARHGAVRVRVFGSV 34
>1s3c_A Arsenate reductase; ARSC, arsenite, oxidoreductase; 1.25A
{Escherichia coli} PDB: 1sd9_A 1i9d_A 1j9b_A 1sd8_A
1jzw_A* 1sk1_A* 1sjz_A* 1sk0_A* 1sk2_A 1s3d_A
Length = 141
Score = 25.1 bits (55), Expect = 7.1
Identities = 11/63 (17%), Positives = 27/63 (42%), Gaps = 5/63 (7%)
Query: 72 RQVIQILRQRTRDVEVKKYCISLLDRFGSFEHTREVLKELDVSARTEVARLGGNPLLEAI 131
R ++++R + + Y L+ S + +++ ++ +S R + R P +
Sbjct: 16 RNTLEMIRNSGTEPTIILY----LENPPSRDELVKLIADMGISVR-ALLRKNVEPYEQLG 70
Query: 132 LDE 134
L E
Sbjct: 71 LAE 73
>1ygy_A PGDH, D-3-phosphoglycerate dehydrogenase; oxidoreductase, serine
biosy structural genomics, PSI, protein structure
initiative; HET: TAR; 2.30A {Mycobacterium tuberculosis}
SCOP: c.2.1.4 c.23.12.1 d.58.18.1 d.81.2.2 PDB: 3dc2_A*
3ddn_A*
Length = 529
Score = 25.4 bits (56), Expect = 8.0
Identities = 16/85 (18%), Positives = 27/85 (31%), Gaps = 14/85 (16%)
Query: 72 RQVIQILRQR-----------TRDVEVKKYCISLLDRFGSF--EHTREVLKELDVSARTE 118
V L + EV + + L+ + G + E+ L V R E
Sbjct: 298 ESVRLALAGEFVPDAVNVGGGVVNEEVAPW-LDLVRKLGVLAGVLSDELPVSLSVQVRGE 356
Query: 119 VARLGGNPLLEAILDELLTWDTPDS 143
+A L + L L + D+
Sbjct: 357 LAAEEVEVLRLSALRGLFSAVIEDA 381
>3dkq_A PKHD-type hydroxylase SBAL_3634; putative oxygenase, structural
genomics, JOI for structural genomics, JCSG; 2.26A
{Shewanella baltica OS155}
Length = 243
Score = 25.3 bits (55), Expect = 8.7
Identities = 7/27 (25%), Positives = 13/27 (48%)
Query: 105 REVLKELDVSARTEVARLGGNPLLEAI 131
R +L +LD S ++ A+ L +
Sbjct: 203 RRLLFQLDQSIQSLTAQTAAEQELFNL 229
>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli}
SCOP: c.37.1.20
Length = 195
Score = 25.0 bits (55), Expect = 9.0
Identities = 16/48 (33%), Positives = 25/48 (52%), Gaps = 10/48 (20%)
Query: 41 EYSENKSFCEDLTE----GKFSFPIIHAIQSRPDD-RQVIQILRQRTR 83
K + DLTE GK P+I R ++ R+ IQ+L++RT+
Sbjct: 1 HMQALKKYTIDLTERAEQGKLD-PVI----GRDEEIRRTIQVLQRRTK 43
>3f0i_A Arsenate reductase; structural genomics, IDP01300, vibrio CH center
for structural genomics of infectious diseases, CSGI
oxidoreductase; HET: MSE; 1.88A {Vibrio cholerae}
Length = 119
Score = 24.5 bits (54), Expect = 9.3
Identities = 12/63 (19%), Positives = 26/63 (41%), Gaps = 4/63 (6%)
Query: 72 RQVIQILRQRTRDVEVKKYCISLLDRFGSFEHTREVLKELDVSARTEVARLGGNPLLEAI 131
R+ + +L + +V KY L+ S E + + ++L ++ + R E
Sbjct: 18 RETLALLENQGIAPQVIKY----LETSPSVEELKRLYQQLGLNEVRAMMRCKEELYKELN 73
Query: 132 LDE 134
L +
Sbjct: 74 LGD 76
>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural
genomics, structural genomics consortium, SGC, unknown
function; 1.70A {Plasmodium falciparum}
Length = 187
Score = 25.0 bits (55), Expect = 9.4
Identities = 16/48 (33%), Positives = 24/48 (50%), Gaps = 10/48 (20%)
Query: 42 YSENKSFCEDLTE----GKFSFPIIHAIQSRPDD-RQVIQILRQRTRD 84
Y + + DLT GK P+I R + R+ IQIL +RT++
Sbjct: 2 YQALEKYSRDLTALARAGKLD-PVI----GRDTEIRRAIQILSRRTKN 44
>3n0v_A Formyltetrahydrofolate deformylase; formyl transferase, ACT domain,
structural genomics, joint C structural genomics, JCSG;
HET: MSE; 2.25A {Pseudomonas putida}
Length = 286
Score = 25.2 bits (56), Expect = 9.8
Identities = 12/37 (32%), Positives = 15/37 (40%), Gaps = 4/37 (10%)
Query: 50 EDLTEGKFSFPIIHAIQSRPDDRQVIQILRQRTRDVE 86
DL EG PII D + L + RD+E
Sbjct: 228 NDLDEG----PIIAQGVEVVDHSHYPEDLIAKGRDIE 260
>3o1l_A Formyltetrahydrofolate deformylase; structural genomics, joint
center for structural genomics, J protein structure
initiative; HET: MSE; 2.20A {Pseudomonas syringae PV}
Length = 302
Score = 25.3 bits (56), Expect = 10.0
Identities = 13/37 (35%), Positives = 17/37 (45%), Gaps = 4/37 (10%)
Query: 50 EDLTEGKFSFPIIHAIQSRPDDRQVIQILRQRTRDVE 86
E+L G PII R R I+ + + RDVE
Sbjct: 243 EELDAG----PIIEQDVVRVSHRDSIENMVRFGRDVE 275
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
0.322 0.138 0.405
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: 2,230,031
Number of extensions: 124500
Number of successful extensions: 400
Number of sequences better than 10.0: 1
Number of HSP's gapped: 375
Number of HSP's successfully gapped: 70
Length of query: 145
Length of database: 6,701,793
Length adjustment: 85
Effective length of query: 60
Effective length of database: 4,328,508
Effective search space: 259710480
Effective search space used: 259710480
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 (21.9 bits)
S2: 52 (23.9 bits)