BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= psy11141
(566 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3F0N|A Chain A, Mus Musculus Mevalonate Pyrophosphate Decarboxylase
pdb|3F0N|B Chain B, Mus Musculus Mevalonate Pyrophosphate Decarboxylase
Length = 414
Score = 295 bits (754), Expect = 7e-80, Method: Compositional matrix adjust.
Identities = 154/368 (41%), Positives = 225/368 (61%), Gaps = 42/368 (11%)
Query: 115 RMHAKTSVALSPDFTEDKLWLNGK-----------------KLAEQEKSSRE------MA 151
++ T+VA+S DFTED++WLNG+ +LA + +S+ +
Sbjct: 61 QLKTTTTVAISKDFTEDRIWLNGREEDVGQPRLQACLREIRRLARKRRSTEDGDTLPLSL 120
Query: 152 DWKMHICSENNFPTXXXXXXXXXXYSCLVFTLAYALGLNTSEVSHIARQGSGSACRSMFG 211
+K+H+ S NNFPT Y+CL +TLA G+ ++S +AR+GSGSACRS++G
Sbjct: 121 SYKVHVASVNNFPTAAGLASSAAGYACLAYTLAQVYGVE-GDLSEVARRGSGSACRSLYG 179
Query: 212 GFVRWKTLPEGQQSDGNGDIGRKQCELSNAEQIISESYWGSMRVIILVVNDQAKSTSSTD 271
GFV W+ G+Q+DG I R QI E +W +R++ILVV+ K T ST
Sbjct: 180 GFVEWQM---GEQADGKDSIAR---------QIAPEWHWPQLRILILVVSADKKQTGSTV 227
Query: 272 GMQRTTLTSTLYEHRVNTIVPSRCSGMEEALRARDFPRFAELTMKDSNQFHACCLDTYPP 331
GMQ + TSTL + R ++VP R M ++ +DF FA+LTMKDSNQFHA CLDT+PP
Sbjct: 228 GMQTSVETSTLLKFRAESVVPERMKEMTRCIQEQDFQGFAQLTMKDSNQFHATCLDTFPP 287
Query: 332 IVYMNDTSHSIVRFVHEFNTVVGETKVAYTFDAGPNACLYVLENTVPLLLSTLVQYFPPS 391
I Y+NDTS I++ VH FNT G+TKVAYTFDAGPNA ++ LE+TV ++ + FPP+
Sbjct: 288 ISYLNDTSRRIIQLVHRFNTHHGQTKVAYTFDAGPNAVIFTLEDTVAEFVAAVRHSFPPA 347
Query: 392 SGISAPYIRGLEYLNILPPVQLPS---FTPQPAGLLQYLISTKIGSGPKILDDIPNNHLL 448
+ +++GL+ +L +L + P P G +QY+I+T++G GP++LDD ++HLL
Sbjct: 348 AN-GDKFLKGLQVAPVLLSDELKAALVVEPSPGG-VQYIIATQVGPGPQVLDDT-HDHLL 404
Query: 449 NEAGAPKH 456
+ G P+
Sbjct: 405 GQDGLPQR 412
Score = 65.9 bits (159), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 34/81 (41%), Positives = 50/81 (61%), Gaps = 13/81 (16%)
Query: 457 LMFTLAYALGLNTSEVSHIARQGSGSACRSMFGGFVRWKTLPEGQQSEGNGDIGRKQFEL 516
L +TLA G+ ++S +AR+GSGSACRS++GGFV W+ G+Q++G I R
Sbjct: 148 LAYTLAQVYGVE-GDLSEVARRGSGSACRSLYGGFVEWQM---GEQADGKDSIAR----- 198
Query: 517 SNAEQIISESYWGSMRVIILV 537
QI E +W +R++ILV
Sbjct: 199 ----QIAPEWHWPQLRILILV 215
Score = 48.5 bits (114), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 21/52 (40%), Positives = 35/52 (67%), Gaps = 1/52 (1%)
Query: 33 EVAYTFDAGPNACLYVLENTVPLLLSTLVQYFPPSSGISAPYIRGLEYLNIL 84
+VAYTFDAGPNA ++ LE+TV ++ + FPP++ +++GL+ +L
Sbjct: 313 KVAYTFDAGPNAVIFTLEDTVAEFVAAVRHSFPPAAN-GDKFLKGLQVAPVL 363
>pdb|3D4J|A Chain A, Crystal Structure Of Human Mevalonate Diphosphate
Decarboxylase
pdb|3D4J|B Chain B, Crystal Structure Of Human Mevalonate Diphosphate
Decarboxylase
Length = 400
Score = 282 bits (722), Expect = 3e-76, Method: Compositional matrix adjust.
Identities = 154/368 (41%), Positives = 217/368 (58%), Gaps = 42/368 (11%)
Query: 114 QRMHAKTSVALSPDFTEDKLWLNGKK-----------------LAEQEKSSRE------M 150
++ T+ +S DFTED++WLNG++ LA + ++SR+
Sbjct: 46 DQLKTTTTAVISKDFTEDRIWLNGREEDVGQPRLQACLREIRCLARKRRNSRDGDPLPSS 105
Query: 151 ADWKMHICSENNFPTXXXXXXXXXXYSCLVFTLAYALGLNTSEVSHIARQGSGSACRSMF 210
K+H+ S NNFPT Y+CL +TLA G+ S++S +AR+GSGSACRS++
Sbjct: 106 LSCKVHVASVNNFPTAAGLASSAAGYACLAYTLARVYGVE-SDLSEVARRGSGSACRSLY 164
Query: 211 GGFVRWKTLPEGQQSDGNGDIGRKQCELSNAEQIISESYWGSMRVIILVVNDQAKSTSST 270
GGFV W+ G+Q+DG I R Q+ ES+W +RV+ILVV+ + K T ST
Sbjct: 165 GGFVEWQM---GEQADGKDSIAR---------QVAPESHWPELRVLILVVSAEKKLTGST 212
Query: 271 DGMQRTTLTSTLYEHRVNTIVPSRCSGMEEALRARDFPRFAELTMKDSNQFHACCLDTYP 330
GM+ + TS L R ++VP+R + M +R RDFP FA+LTMKDSNQFHA CLDT+P
Sbjct: 213 VGMRASVETSPLLRFRAESVVPARMAEMARCIRERDFPSFAQLTMKDSNQFHATCLDTFP 272
Query: 331 PIVYMNDTSHSIVRFVHEFNTVVGETKVAYTFDAGPNACLYVLENTVPLLLSTLVQYFPP 390
PI Y+N S I+ VH FN G+TKVAYTFDAGPNA ++ L++TV ++ + FPP
Sbjct: 273 PISYLNAISWRIIHLVHRFNAHHGDTKVAYTFDAGPNAVIFTLDDTVAEFVAAVWHGFPP 332
Query: 391 SSGISAPYIRGLEYLNILPPVQLP---SFTPQPAGLLQYLISTKIGSGPKILDDIPNNHL 447
S +++GL+ +L + P P G ++Y+I T++G GP+ILDD P HL
Sbjct: 333 GSNGDT-FLKGLQVRPAPLSAELQAALAMEPTPGG-VKYIIVTQVGPGPQILDD-PCAHL 389
Query: 448 LNEAGAPK 455
L G PK
Sbjct: 390 LGPDGLPK 397
Score = 70.5 bits (171), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 36/81 (44%), Positives = 52/81 (64%), Gaps = 13/81 (16%)
Query: 457 LMFTLAYALGLNTSEVSHIARQGSGSACRSMFGGFVRWKTLPEGQQSEGNGDIGRKQFEL 516
L +TLA G+ S++S +AR+GSGSACRS++GGFV W+ G+Q++G I R
Sbjct: 134 LAYTLARVYGVE-SDLSEVARRGSGSACRSLYGGFVEWQM---GEQADGKDSIAR----- 184
Query: 517 SNAEQIISESYWGSMRVIILV 537
Q+ ES+W +RV+ILV
Sbjct: 185 ----QVAPESHWPELRVLILV 201
Score = 44.7 bits (104), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/47 (42%), Positives = 32/47 (68%), Gaps = 1/47 (2%)
Query: 33 EVAYTFDAGPNACLYVLENTVPLLLSTLVQYFPPSSGISAPYIRGLE 79
+VAYTFDAGPNA ++ L++TV ++ + FPP S +++GL+
Sbjct: 299 KVAYTFDAGPNAVIFTLDDTVAEFVAAVWHGFPPGSNGDT-FLKGLQ 344
>pdb|1FI4|A Chain A, The X-Ray Crystal Structure Of Mevalonate 5-Diphosphate
Decarboxylase At 2.3 Angstrom Resolution
Length = 416
Score = 223 bits (569), Expect = 2e-58, Method: Compositional matrix adjust.
Identities = 147/426 (34%), Positives = 205/426 (48%), Gaps = 72/426 (16%)
Query: 41 GPNACLYVLENTVPLLLSTLVQYFPPSSGISAPYIRGLEYLNILPPVQVKLSNNDIITLK 100
G + +Y T P+ ++TL + + ++ P + V LS +D+ TL
Sbjct: 18 GSHXTVYTASVTAPVNIATLKYWGKRDTKLNLP---------TNSSISVTLSQDDLRTL- 67
Query: 101 SELNGIEPIEITFQRMHAKTSVALSPDFTEDKLWLNG---------------------KK 139
TS A +P+F D LWLNG K+
Sbjct: 68 -------------------TSAATAPEFERDTLWLNGEPHSIDNERTQNCLRDLRQLRKE 108
Query: 140 LAEQEKSSREMADWKMHICSENNFPTXXXXXXXXXXYSCLVFTLA--YALGLNTSEVSHI 197
++ S ++ WK+HI SENNFPT ++ LV +A Y L +TSE+S I
Sbjct: 109 XESKDASLPTLSQWKLHIVSENNFPTAAGLASSAAGFAALVSAIAKLYQLPQSTSEISRI 168
Query: 198 ARQGSGSACRSMFGGFVRWKTLPEGQQSDGNGDIGRKQCELSNAEQIISESYWGSMRVII 257
AR+GSGSACRS+FGG+V W+ G+ DG+ S A QI S W + +
Sbjct: 169 ARKGSGSACRSLFGGYVAWEX---GKAEDGHD---------SXAVQIADSSDWPQXKACV 216
Query: 258 LVVNDQAKSTSSTDGMQRTTLTSTLYEHRVNTIVPSRCSGMEEALRARDFPRFAELTMKD 317
LVV+D K SST G Q T TS L++ R+ +VP R +A+ +DF FA+ T D
Sbjct: 217 LVVSDIKKDVSSTQGXQLTVATSELFKERIEHVVPKRFEVXRKAIVEKDFATFAKETXXD 276
Query: 318 SNQFHACCLDTYPPIVYMNDTSHSIVRFVHEFNTVVGETKVAYTFDAGPNACLYVLENTV 377
SN FHA CLD++PPI Y NDTS I+ + H N GET VAYTFDAGPNA LY L
Sbjct: 277 SNSFHATCLDSFPPIFYXNDTSKRIISWCHTINQFYGETIVAYTFDAGPNAVLYYLAENE 336
Query: 378 PLLLSTLVQYFPPSSGISAPY-IRGLEYLNILPPVQLPSFTPQPAGL-----LQYLISTK 431
L + + + F G + LE N + +FT + L + +I T+
Sbjct: 337 SKLFAFIYKLFGSVPGWDKKFTTEQLEAFN--HQFESSNFTARELDLELQKDVARVILTQ 394
Query: 432 IGSGPK 437
+GSGP+
Sbjct: 395 VGSGPQ 400
Score = 58.5 bits (140), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 32/75 (42%), Positives = 43/75 (57%), Gaps = 12/75 (16%)
Query: 463 YALGLNTSEVSHIARQGSGSACRSMFGGFVRWKTLPEGQQSEGNGDIGRKQFELSNAEQI 522
Y L +TSE+S IAR+GSGSACRS+FGG+V W+ G+ +G+ S A QI
Sbjct: 156 YQLPQSTSEISRIARKGSGSACRSLFGGYVAWEX---GKAEDGHD---------SXAVQI 203
Query: 523 ISESYWGSMRVIILV 537
S W + +LV
Sbjct: 204 ADSSDWPQXKACVLV 218
Score = 35.0 bits (79), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 18/38 (47%), Positives = 23/38 (60%), Gaps = 2/38 (5%)
Query: 29 KYYIE--VAYTFDAGPNACLYVLENTVPLLLSTLVQYF 64
++Y E VAYTFDAGPNA LY L L + + + F
Sbjct: 310 QFYGETIVAYTFDAGPNAVLYYLAENESKLFAFIYKLF 347
>pdb|2HKE|A Chain A, Mevalonate Diphosphate Decarboxylase From Trypanosoma
Brucei
pdb|2HKE|B Chain B, Mevalonate Diphosphate Decarboxylase From Trypanosoma
Brucei
Length = 380
Score = 184 bits (466), Expect = 1e-46, Method: Compositional matrix adjust.
Identities = 115/348 (33%), Positives = 172/348 (49%), Gaps = 32/348 (9%)
Query: 109 IEITFQRMHAKTSVALSPDFTEDKLWLNGKK-------------LAEQEKSSREMADWKM 155
I ++ +KTSV L D D L LNG + L + E+ + K+
Sbjct: 39 ITLSASPFRSKTSVELRDDIETDTLRLNGTEVDVGKTPRVQSMLLHLRSTCPEELKNKKV 98
Query: 156 HICSENNFPTXXXXXXXXXXYSCLVFTLAYALGLNTSEVSHIARQGSGSACRSMFGGFVR 215
+I SENNFPT Y + L A +T+ VS +AR GSGSACRS FGGFV
Sbjct: 99 NIVSENNFPTAAGMASSASGYCAMSAALIRAFK-STTNVSMLARLGSGSACRSAFGGFVI 157
Query: 216 WKTLPEGQQSDGNGDIGRKQCELSNAEQIISESYWGSMRVIILVVNDQAKSTSSTDGMQR 275
W +G++ DG+ + A Q + E++W ++V+ V+ K SST GMQ+
Sbjct: 158 WN---KGEKPDGSDCV---------ATQFVDETHWPEIQVMCAVLKGAQKDVSSTKGMQQ 205
Query: 276 TTLTSTLYEHRVNTIVPSRCSGMEEALRARDFPRFAELTMKDSNQFHACCLDTYPPIVYM 335
+ TS L + R++ VP R A++ARDF FAE+ M +S+ C T P I Y
Sbjct: 206 SLKTSPLMKKRISETVPERMKIASRAIKARDFATFAEIAMLESDDLQEICATTEPKITYA 265
Query: 336 NDTSHSIVRFVHEFNTVVGETKVAYTFDAGPNACLYVLENTVPLLLSTLVQYFPPSSGIS 395
+ S++++R V +N G T +AYTFDAG N L+VL+ +P ++ L+++FP +
Sbjct: 266 TEDSYAMIRLVKAYNAKKGRTALAYTFDAGANCFLFVLKEDLPEAVAMLMEHFP--TPFE 323
Query: 396 APYIRGLEYLNILPPVQLPS----FTPQPAGLLQYLISTKIGSGPKIL 439
+ E L + V LP P + L+ + +G G K L
Sbjct: 324 KFFFGDRELLEKVKVVSLPDEYKKLIDHPKKPFEMLLQSPVGCGVKYL 371
Score = 52.8 bits (125), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 27/70 (38%), Positives = 42/70 (60%), Gaps = 12/70 (17%)
Query: 468 NTSEVSHIARQGSGSACRSMFGGFVRWKTLPEGQQSEGNGDIGRKQFELSNAEQIISESY 527
+T+ VS +AR GSGSACRS FGGFV W +G++ +G+ + A Q + E++
Sbjct: 132 STTNVSMLARLGSGSACRSAFGGFVIWN---KGEKPDGSDCV---------ATQFVDETH 179
Query: 528 WGSMRVIILV 537
W ++V+ V
Sbjct: 180 WPEIQVMCAV 189
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/39 (43%), Positives = 27/39 (69%)
Query: 27 SKKYYIEVAYTFDAGPNACLYVLENTVPLLLSTLVQYFP 65
+KK +AYTFDAG N L+VL+ +P ++ L+++FP
Sbjct: 281 AKKGRTALAYTFDAGANCFLFVLKEDLPEAVAMLMEHFP 319
>pdb|3QT5|A Chain A, Crystal Structure Of Staphylococcus Epidermidis Mevalonate
Diphosphate Decarboxylase
pdb|3QT5|B Chain B, Crystal Structure Of Staphylococcus Epidermidis Mevalonate
Diphosphate Decarboxylase
pdb|3QT6|A Chain A, Crystal Structure Of Staphylococcus Epidermidis Mevalonate
Diphosphate Decarboxylase Complexed With Inhibitor Dpgp
pdb|3QT6|B Chain B, Crystal Structure Of Staphylococcus Epidermidis Mevalonate
Diphosphate Decarboxylase Complexed With Inhibitor Dpgp
pdb|3QT7|A Chain A, Crystal Structure Of Staphylococcus Epidermidis Mevalonate
Diphosphate Decarboxylase Complexed With Inhibitor
6-Fmvapp
pdb|3QT7|B Chain B, Crystal Structure Of Staphylococcus Epidermidis Mevalonate
Diphosphate Decarboxylase Complexed With Inhibitor
6-Fmvapp
pdb|4DPT|A Chain A, Crystal Structure Of Staphylococcus Epidermidis Mevalonate
Diphosphate Decarboxylase Complexed With Inhibitor
6-Fmvapp And Atpgs
pdb|4DPT|B Chain B, Crystal Structure Of Staphylococcus Epidermidis Mevalonate
Diphosphate Decarboxylase Complexed With Inhibitor
6-Fmvapp And Atpgs
pdb|4DU7|A Chain A, Crystal Structure Of Staphylococcus Epidermidis Mevalonate
Diphosphate Decarboxylase Complexed With Substrate
Mevalonate Diphosphate
pdb|4DU7|B Chain B, Crystal Structure Of Staphylococcus Epidermidis Mevalonate
Diphosphate Decarboxylase Complexed With Substrate
Mevalonate Diphosphate
Length = 332
Score = 123 bits (309), Expect = 2e-28, Method: Compositional matrix adjust.
Identities = 92/303 (30%), Positives = 144/303 (47%), Gaps = 29/303 (9%)
Query: 109 IEITFQRMHAKTSVALSPDFTEDKLWLNGKKLAEQEKSS--------REMADWKMH--IC 158
+ +T R + +T V PDFTED L LNG ++ +EK R++A ++H I
Sbjct: 39 LSVTLDRFYTETKVTFDPDFTEDCLILNGNEVNAKEKEKIQNYMNIVRDLAGNRLHARIE 98
Query: 159 SENNFPTXXXXXXXXXXYSCLVFTLAYALGLNTSE--VSHIARQGSGSACRSMFGGFVRW 216
SEN PT Y+ L AL LN S+ +S +AR+GSGSA RS+FGGF W
Sbjct: 99 SENYVPTAAGLASSASAYAALAAACNEALSLNLSDTDLSRLARRGSGSASRSIFGGFAEW 158
Query: 217 KTLPEGQQSDGNGDIGRKQCELSNAEQIISESYWGSMRVIILVVNDQAKSTSSTDGMQRT 276
+ G+ D+ S A I S + + +I +V+N+Q+K SS GM T
Sbjct: 159 EK--------GHDDL------TSYAHGINSNGWEKDLSMIFVVINNQSKKVSSRSGMSLT 204
Query: 277 TLTSTLYEHRVNTIVPSRCSGMEEALRARDFPRFAELTMKDSNQFHACCLDTYPPIVYMN 336
TS Y++ ++ V + +EA++ +DF R E+ + + HA L PP Y+
Sbjct: 205 RDTSRFYQYWLDH-VDEDLNEAKEAVKNQDFQRLGEVIEANGLRMHATNLGAQPPFTYLV 263
Query: 337 DTSHSIVRFVHEFNTVVGETKVAYTFDAGPNACLYVLENTVPLLLSTLVQYFPPSSGISA 396
S+ + V + +T DAGPN + V + ++ ++ F S I++
Sbjct: 264 QESYDAMAIVEQCRK--ANLPCYFTMDAGPNVKVLVEKKNKQAVMEQFLKVFDESKIIAS 321
Query: 397 PYI 399
I
Sbjct: 322 DII 324
Score = 45.4 bits (106), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 18/34 (52%), Positives = 27/34 (79%)
Query: 462 AYALGLNTSEVSHIARQGSGSACRSMFGGFVRWK 495
A +L L+ +++S +AR+GSGSA RS+FGGF W+
Sbjct: 126 ALSLNLSDTDLSRLARRGSGSASRSIFGGFAEWE 159
>pdb|3QT8|A Chain A, Crystal Structure Of Mutant S192a Staphylococcus
Epidermidis Mevalonate Diphosphate Decarboxylase
Complexed With Inhibitor 6- Fmvapp
pdb|3QT8|B Chain B, Crystal Structure Of Mutant S192a Staphylococcus
Epidermidis Mevalonate Diphosphate Decarboxylase
Complexed With Inhibitor 6- Fmvapp
pdb|4DPU|A Chain A, Crystal Structure Of Staphylococcus Epidermidis S192a
Mevalonate Diphosphate Decarboxylase Complexed With
Inhibitor 6-Fmvapp And Atpgs
pdb|4DPU|B Chain B, Crystal Structure Of Staphylococcus Epidermidis S192a
Mevalonate Diphosphate Decarboxylase Complexed With
Inhibitor 6-Fmvapp And Atpgs
pdb|4DPX|A Chain A, Crystal Structure Of S192a Staphylococcus Epidermidis
Mevalonate Diphosphate Decarboxylase
pdb|4DPX|B Chain B, Crystal Structure Of S192a Staphylococcus Epidermidis
Mevalonate Diphosphate Decarboxylase
pdb|4DPY|A Chain A, Crystal Structure Of Staphylococcus Epidermidis S192a
Mevalonate Diphosphate Decarboxylase Complexed With
Inhibitor Dpgp
pdb|4DPY|B Chain B, Crystal Structure Of Staphylococcus Epidermidis S192a
Mevalonate Diphosphate Decarboxylase Complexed With
Inhibitor Dpgp
Length = 332
Score = 122 bits (307), Expect = 4e-28, Method: Compositional matrix adjust.
Identities = 91/303 (30%), Positives = 144/303 (47%), Gaps = 29/303 (9%)
Query: 109 IEITFQRMHAKTSVALSPDFTEDKLWLNGKKLAEQEKSS--------REMADWKMH--IC 158
+ +T R + +T V PDFTED L LNG ++ +EK R++A ++H I
Sbjct: 39 LSVTLDRFYTETKVTFDPDFTEDCLILNGNEVNAKEKEKIQNYMNIVRDLAGNRLHARIE 98
Query: 159 SENNFPTXXXXXXXXXXYSCLVFTLAYALGLNTSE--VSHIARQGSGSACRSMFGGFVRW 216
SEN PT Y+ L AL LN S+ +S +AR+GSGSA RS+FGGF W
Sbjct: 99 SENYVPTAAGLASSASAYAALAAACNEALSLNLSDTDLSRLARRGSGSASRSIFGGFAEW 158
Query: 217 KTLPEGQQSDGNGDIGRKQCELSNAEQIISESYWGSMRVIILVVNDQAKSTSSTDGMQRT 276
+ G+ D+ S A I S + + +I +V+N+Q+K S+ GM T
Sbjct: 159 EK--------GHDDL------TSYAHGINSNGWEKDLSMIFVVINNQSKKVSARSGMSLT 204
Query: 277 TLTSTLYEHRVNTIVPSRCSGMEEALRARDFPRFAELTMKDSNQFHACCLDTYPPIVYMN 336
TS Y++ ++ V + +EA++ +DF R E+ + + HA L PP Y+
Sbjct: 205 RDTSRFYQYWLDH-VDEDLNEAKEAVKNQDFQRLGEVIEANGLRMHATNLGAQPPFTYLV 263
Query: 337 DTSHSIVRFVHEFNTVVGETKVAYTFDAGPNACLYVLENTVPLLLSTLVQYFPPSSGISA 396
S+ + V + +T DAGPN + V + ++ ++ F S I++
Sbjct: 264 QESYDAMAIVEQCRK--ANLPCYFTMDAGPNVKVLVEKKNKQAVMEQFLKVFDESKIIAS 321
Query: 397 PYI 399
I
Sbjct: 322 DII 324
Score = 45.4 bits (106), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 18/34 (52%), Positives = 27/34 (79%)
Query: 462 AYALGLNTSEVSHIARQGSGSACRSMFGGFVRWK 495
A +L L+ +++S +AR+GSGSA RS+FGGF W+
Sbjct: 126 ALSLNLSDTDLSRLARRGSGSASRSIFGGFAEWE 159
>pdb|4DPW|A Chain A, Crystal Structure Of Staphylococcus Epidermidis D283a
Mevalonate Diphosphate Decarboxylase Complexed With
Mevalonate Diphosphate And Atpgs
pdb|4DPW|B Chain B, Crystal Structure Of Staphylococcus Epidermidis D283a
Mevalonate Diphosphate Decarboxylase Complexed With
Mevalonate Diphosphate And Atpgs
pdb|4DPW|C Chain C, Crystal Structure Of Staphylococcus Epidermidis D283a
Mevalonate Diphosphate Decarboxylase Complexed With
Mevalonate Diphosphate And Atpgs
pdb|4DPW|D Chain D, Crystal Structure Of Staphylococcus Epidermidis D283a
Mevalonate Diphosphate Decarboxylase Complexed With
Mevalonate Diphosphate And Atpgs
pdb|4DPW|E Chain E, Crystal Structure Of Staphylococcus Epidermidis D283a
Mevalonate Diphosphate Decarboxylase Complexed With
Mevalonate Diphosphate And Atpgs
pdb|4DPW|F Chain F, Crystal Structure Of Staphylococcus Epidermidis D283a
Mevalonate Diphosphate Decarboxylase Complexed With
Mevalonate Diphosphate And Atpgs
pdb|4DPW|G Chain G, Crystal Structure Of Staphylococcus Epidermidis D283a
Mevalonate Diphosphate Decarboxylase Complexed With
Mevalonate Diphosphate And Atpgs
pdb|4DPW|H Chain H, Crystal Structure Of Staphylococcus Epidermidis D283a
Mevalonate Diphosphate Decarboxylase Complexed With
Mevalonate Diphosphate And Atpgs
pdb|4DU8|A Chain A, Crystal Structure Of Staphylococcus Epidermidis D283a
Mevalonate Diphosphate Decarboxylase Complexed With
Inhibitor Dpgp
pdb|4DU8|B Chain B, Crystal Structure Of Staphylococcus Epidermidis D283a
Mevalonate Diphosphate Decarboxylase Complexed With
Inhibitor Dpgp
Length = 332
Score = 120 bits (301), Expect = 2e-27, Method: Compositional matrix adjust.
Identities = 93/310 (30%), Positives = 147/310 (47%), Gaps = 30/310 (9%)
Query: 109 IEITFQRMHAKTSVALSPDFTEDKLWLNGKKLAEQEKSS--------REMADWKMH--IC 158
+ +T R + +T V PDFTED L LNG ++ +EK R++A ++H I
Sbjct: 39 LSVTLDRFYTETKVTFDPDFTEDCLILNGNEVNAKEKEKIQNYMNIVRDLAGNRLHARIE 98
Query: 159 SENNFPTXXXXXXXXXXYSCLVFTLAYALGLNTSE--VSHIARQGSGSACRSMFGGFVRW 216
SEN PT Y+ L AL LN S+ +S +AR+GSGSA RS+FGGF W
Sbjct: 99 SENYVPTAAGLASSASAYAALAAACNEALSLNLSDTDLSRLARRGSGSASRSIFGGFAEW 158
Query: 217 KTLPEGQQSDGNGDIGRKQCELSNAEQIISESYWGSMRVIILVVNDQAKSTSSTDGMQRT 276
+ G+ D+ S A I S + + +I +V+N+Q+K SS GM T
Sbjct: 159 EK--------GHDDL------TSYAHGINSNGWEKDLSMIFVVINNQSKKVSSRSGMSLT 204
Query: 277 TLTSTLYEHRVNTIVPSRCSGMEEALRARDFPRFAELTMKDSNQFHACCLDTYPPIVYMN 336
TS Y++ ++ V + +EA++ +DF R E+ + + HA L PP Y+
Sbjct: 205 RDTSRFYQYWLDH-VDEDLNEAKEAVKNQDFQRLGEVIEANGLRMHATNLGAQPPFTYLV 263
Query: 337 DTSHSIVRFVHEFNTVVGETKVAYTFDAGPNACLYVLENTVPLLLSTLVQYFPPSSGISA 396
S+ + V + +T AGPN + V + ++ ++ F S I++
Sbjct: 264 QESYDAMAIVEQCRK--ANLPCYFTMAAGPNVKVLVEKKNKQAVMEQFLKVFDESKIIAS 321
Query: 397 PYI-RGLEYL 405
I G+E +
Sbjct: 322 DIISSGVEII 331
Score = 45.1 bits (105), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 18/34 (52%), Positives = 27/34 (79%)
Query: 462 AYALGLNTSEVSHIARQGSGSACRSMFGGFVRWK 495
A +L L+ +++S +AR+GSGSA RS+FGGF W+
Sbjct: 126 ALSLNLSDTDLSRLARRGSGSASRSIFGGFAEWE 159
>pdb|2HK2|A Chain A, Crystal Structure Of Mevalonate Diphosphate Decarboxylase
From Staphylococcus Aureus (Monoclinic Form)
pdb|2HK2|B Chain B, Crystal Structure Of Mevalonate Diphosphate Decarboxylase
From Staphylococcus Aureus (Monoclinic Form)
pdb|2HK3|A Chain A, Crystal Structure Of Mevalonate Diphosphate Decarboxylase
From Staphylococcus Aureus (Orthorhombic Form)
pdb|2HK3|B Chain B, Crystal Structure Of Mevalonate Diphosphate Decarboxylase
From Staphylococcus Aureus (Orthorhombic Form)
Length = 331
Score = 112 bits (280), Expect = 5e-25, Method: Compositional matrix adjust.
Identities = 88/310 (28%), Positives = 144/310 (46%), Gaps = 30/310 (9%)
Query: 109 IEITFQRMHAKTSVALSPDFTEDKLWLNGKKLA--EQEKSSREMA--------DWKMHIC 158
I +T ++ + +T V + T+D+ WLNG+K++ E EK S+ M DW I
Sbjct: 38 ISVTLEKFYTETKVTFNDQLTQDQFWLNGEKVSGKELEKISKYMDIVRNRAGIDWYAEIE 97
Query: 159 SENNFPTXXXXXXXXXXYSCLVFTLAYALGLNTSE--VSHIARQGSGSACRSMFGGFVRW 216
S+N PT Y+ L AL + S+ +S +AR GSGSA RS++GGF W
Sbjct: 98 SDNFVPTAAGLASSASAYAALAAACNQALDMQLSDKDLSRLARIGSGSASRSIYGGFAEW 157
Query: 217 KTLPEGQQSDGNGDIGRKQCELSNAEQIISESYWGSMRVIILVVNDQAKSTSSTDGMQRT 276
+ G D E S A + S + + +I +V+N +K S GM T
Sbjct: 158 EK--------GYSD------ETSYAVPLESNHFEDDLAMIFVVINQHSKKVPSRYGMSLT 203
Query: 277 TLTSTLYEHRVNTIVPSRCSGMEEALRARDFPRFAELTMKDSNQFHACCLDTYPPIVYMN 336
TS Y++ ++ I + + A++ +DF R E+ ++ + HA L + PP Y+
Sbjct: 204 RNTSRFYQYWLDHI-DEDLAEAKAAIQDKDFKRLGEVIEENGLRMHATNLGSTPPFTYLV 262
Query: 337 DTSHSIVRFVHEFNTVVGETKVAYTFDAGPNACLYVLENTVPLLLSTLVQYFPPSSGISA 396
S+ ++ VHE +T DAGPN + V + ++ L+ F + I +
Sbjct: 263 QESYDVMALVHECRE--AGYPCYFTMDAGPNVKILVEKKNKQQIIDKLLTQFDNNQIIDS 320
Query: 397 PYI-RGLEYL 405
I G+E +
Sbjct: 321 DIIATGIEII 330
Score = 40.0 bits (92), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 16/34 (47%), Positives = 24/34 (70%)
Query: 462 AYALGLNTSEVSHIARQGSGSACRSMFGGFVRWK 495
A + L+ ++S +AR GSGSA RS++GGF W+
Sbjct: 125 ALDMQLSDKDLSRLARIGSGSASRSIYGGFAEWE 158
>pdb|2GS8|A Chain A, Structure Of Mevalonate Pyrophosphate Decarboxylase From
Streptococcus Pyogenes
Length = 317
Score = 37.7 bits (86), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 36/130 (27%), Positives = 52/130 (40%), Gaps = 5/130 (3%)
Query: 256 IILVVNDQAKSTSSTDGMQRTTLTSTLYEHRVNTIVPSRCSGMEEALRARDFPRFAELTM 315
I LV+N K SS +G + TST ++ V + L+ +F + +LT
Sbjct: 175 IXLVLNAAKKPISSREGXKLCRDTSTTFDQWVEQSAIDYQHXLT-YLKTNNFEKVGQLTE 233
Query: 316 KDSNQFHACCLDTYPPIVYMNDTSHSIVRFVHEFNTVVGETKVAY-TFDAGPNACLYVLE 374
++ HA PP Y+ S+ V E E Y T DAGPN + LE
Sbjct: 234 ANALAXHATTKTANPPFSYLTKESYQAXEAVKELR---QEGFACYFTXDAGPNVKVLCLE 290
Query: 375 NTVPLLLSTL 384
+ L L
Sbjct: 291 KDLAQLAERL 300
>pdb|3LTO|A Chain A, Crystal Structure Of A Mevalonate Diphosphate
Decarboxylase From Legionella Pneumophila
pdb|3LTO|B Chain B, Crystal Structure Of A Mevalonate Diphosphate
Decarboxylase From Legionella Pneumophila
Length = 323
Score = 37.4 bits (85), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 51/221 (23%), Positives = 78/221 (35%), Gaps = 32/221 (14%)
Query: 157 ICSENNFPTXXXXXXXXXXYSCLVFTLAYALGLNT-------SEVSHIARQGSGSACRSM 209
I S NNFP ++ L + AL T E + ++R GSGS+CRS
Sbjct: 95 IQSSNNFPHSSGLASSASSFAALTKCASIALSELTQKPLPSIDEQAQLSRLGSGSSCRSF 154
Query: 210 FGGFVRWKTLPEGQQSDGNGDIGRKQCELSNAEQIISESYWGSMRVIILVVNDQAKSTSS 269
+ + W GD I Y + +I V++ Q K S
Sbjct: 155 YAPWALW-----------TGD----------KVSAIDLPYKDLLHQVI-VISSQEKEIPS 192
Query: 270 TDGMQRTTLTSTLYEHRVNTIVPSRCSGMEEALRARDFPRFAELTMKDSNQFHACCLDTY 329
+ TS YE R + + A +D+ ++ + H
Sbjct: 193 RVA-HKLVKTSPFYETRSER-AEANLKLLLNAFENKDWTSIYQICWHEFLDXHQLFKTCE 250
Query: 330 PPIVYMNDTSHSIVRFVHEFNTVVGETKVAYTFDAGPNACL 370
P Y+ D + I+ + +F G+ V T DAGPN L
Sbjct: 251 KPFSYITDNTLHILSVIEKFWNEKGDGPVV-TXDAGPNVHL 290
>pdb|4GG6|F Chain F, Protein Complex
pdb|4GG6|H Chain H, Protein Complex
pdb|4GG8|F Chain F, Immune Receptor
pdb|4GG8|B Chain B, Immune Receptor
Length = 245
Score = 31.6 bits (70), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 25/102 (24%), Positives = 40/102 (39%), Gaps = 23/102 (22%)
Query: 43 NACLYVLENTVPLLLSTLVQYFPPSSGISAPYIRGLEYLNILPPVQVKLSNNDIITLKSE 102
++ LY ++V + T QYF P + ++ + N+ PP E
Sbjct: 85 DSALYFCASSVAVSAGTYEQYFGPGTRLTVTE----DLKNVFPP---------------E 125
Query: 103 LNGIEPIEITFQRMHAKTSVALS----PDFTEDKLWLNGKKL 140
+ EP E T V L+ PD E W+NGK++
Sbjct: 126 VAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEV 167
>pdb|2AXJ|A Chain A, Crystal Structures Of T Cell Receptor Beta Chains Related
To Rheumatoid Arthritis
pdb|2AXJ|B Chain B, Crystal Structures Of T Cell Receptor Beta Chains Related
To Rheumatoid Arthritis
Length = 242
Score = 30.8 bits (68), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 31/119 (26%), Positives = 47/119 (39%), Gaps = 9/119 (7%)
Query: 30 YYIEVAYTFDAGPNACLYVL----ENTVPLLLSTLVQYFPPSSGISAPYIRGLEYLNILP 85
YY ++ F G A Y + + + PL + T Q P + + A RG E L
Sbjct: 47 YYSQIVNDFQKGDIAEGYSVSREKKESFPLTV-TSAQKNPTAFYLCASRDRGTEKLFFGS 105
Query: 86 PVQVKLSNNDIITLKSELNGIEPIEITFQRMHAKTSVALS----PDFTEDKLWLNGKKL 140
Q+ + + E+ EP E T V L+ PD E W+NGK++
Sbjct: 106 GTQLSVLEDLNKVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEV 164
>pdb|2C1G|A Chain A, Structure Of Streptococcus Pneumoniae Peptidoglycan
Deacetylase (Sppgda)
Length = 431
Score = 30.0 bits (66), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 25/61 (40%), Positives = 28/61 (45%), Gaps = 15/61 (24%)
Query: 3 SYLSEKIKIPKLSWFYWDKKLNKESKKYYIEVAYTFDAGPNACLYVLENTVPLLLSTLVQ 62
SYL EK L Y+DKK K VA TFD GPN T P +L TL +
Sbjct: 216 SYLLEKD--AALYQSYFDKKHQKV-------VALTFDDGPNPA------TTPQVLETLAK 260
Query: 63 Y 63
Y
Sbjct: 261 Y 261
>pdb|3SB2|A Chain A, Crystal Structure Of The Rna Chaperone Hfq From
Herbaspirillum Seropedicae Smr1
pdb|3SB2|B Chain B, Crystal Structure Of The Rna Chaperone Hfq From
Herbaspirillum Seropedicae Smr1
pdb|3SB2|C Chain C, Crystal Structure Of The Rna Chaperone Hfq From
Herbaspirillum Seropedicae Smr1
pdb|3SB2|D Chain D, Crystal Structure Of The Rna Chaperone Hfq From
Herbaspirillum Seropedicae Smr1
pdb|3SB2|E Chain E, Crystal Structure Of The Rna Chaperone Hfq From
Herbaspirillum Seropedicae Smr1
pdb|3SB2|F Chain F, Crystal Structure Of The Rna Chaperone Hfq From
Herbaspirillum Seropedicae Smr1
Length = 79
Score = 29.6 bits (65), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 18/71 (25%), Positives = 36/71 (50%), Gaps = 10/71 (14%)
Query: 238 LSNAEQIISESYWGSMR-----VIILVVND-----QAKSTSSTDGMQRTTLTSTLYEHRV 287
+SN Q++ + + ++R V I +VN +S + R T+T +Y+H +
Sbjct: 1 MSNKGQLLQDPFLNALRKEHVPVSIYLVNGIKLQGHVESFDQYVVLLRNTVTQMVYKHAI 60
Query: 288 NTIVPSRCSGM 298
+T+VP+R +
Sbjct: 61 STVVPARAVNL 71
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.318 0.134 0.404
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,792,756
Number of Sequences: 62578
Number of extensions: 694254
Number of successful extensions: 1442
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1377
Number of HSP's gapped (non-prelim): 34
length of query: 566
length of database: 14,973,337
effective HSP length: 104
effective length of query: 462
effective length of database: 8,465,225
effective search space: 3910933950
effective search space used: 3910933950
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)