RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy9378
(522 letters)
>2oo0_A ODC, ornithine decarboxylase; beta-alpha barrel, sheet, lyase; HET:
PLP; 1.90A {Homo sapiens}
Length = 471
Score = 390 bits (1005), Expect = e-132
Identities = 154/314 (49%), Positives = 195/314 (62%), Gaps = 33/314 (10%)
Query: 209 KEDAFYVLDVGEIVRKHEDWKLKLPRVDPYYAVKCNDSQMVLEVLAALGTGFDCAS---- 264
+DAFYV D+G+I++KH W LPRV P+YAVKCNDS+ +++ LAA GTGFDCAS
Sbjct: 46 DKDAFYVADLGDILKKHLRWLKALPRVTPFYAVKCNDSKAIVKTLAATGTGFDCASKTEI 105
Query: 265 -------------------KPISHIRYAAEYGIDTMTFDNEIELQKVKQFHPTAQLVIRI 305
K +S I+YAA G+ MTFD+E+EL KV + HP A+LV+RI
Sbjct: 106 QLVQSLGVPPERIIYANPCKQVSQIKYAANNGVQMMTFDSEVELMKVARAHPKAKLVLRI 165
Query: 306 RCDAEVAQCQLGMKFGCDPISEAPRLLRLAKSLDLDVVGVSFHVGSGCGDPPVFGRAIYS 365
D A C+L +KFG + LL AK L++DVVGVSFHVGSGC DP F +AI
Sbjct: 166 ATDDSKAVCRLSVKFGATL-RTSRLLLERAKELNIDVVGVSFHVGSGCTDPETFVQAISD 224
Query: 366 ARQIFDLGNSLGFSMRVLDLGGGYPGYTGY--SMNRIAEIINVALDEYFPVEEGVSIIAE 423
AR +FD+G +GFSM +LD+GGG+PG I +IN ALD+YFP + GV IIAE
Sbjct: 225 ARCVFDMGAEVGFSMYLLDIGGGFPGSEDVKLKFEEITGVINPALDKYFPSDSGVRIIAE 284
Query: 424 PGRYYVASAFTLATLIHSKRDILGANSSV-------PTHTMYYINDGVYGSFNCIIYDHA 476
PGRYYVASAFTLA I +K+ +L + MYY+NDGVYGSFNCI+YDHA
Sbjct: 285 PGRYYVASAFTLAVNIIAKKIVLKEQTGSDDEDESSEQTFMYYVNDGVYGSFNCILYDHA 344
Query: 477 VCTPIPFNVMDDSQ 490
P+ +
Sbjct: 345 HVKPLLQKRPKPDE 358
Score = 108 bits (271), Expect = 2e-25
Identities = 34/74 (45%), Positives = 49/74 (66%)
Query: 4 RETLVPSSVWGPTCDGLDKVNDDILLPEMPVGSWLIYRDMGAYTLPVASTFNGFPIPKVH 63
E SS+WGPTCDGLD++ + LPEM VG W+++ +MGAYT+ ASTFNGF P ++
Sbjct: 357 DEKYYSSSIWGPTCDGLDRIVERCDLPEMHVGDWMLFENMGAYTVAAASTFNGFQRPTIY 416
Query: 64 AVIEEHIWLMLKDR 77
V+ W +++
Sbjct: 417 YVMSGPAWQLMQQF 430
>7odc_A Protein (ornithine decarboxylase); pyridoxal-5'-phosphate, PLP,
group IV decarboxylase, polyami parasitical,
chemotherapy target, putrescine; HET: PLP; 1.60A {Mus
musculus} SCOP: b.49.2.3 c.1.6.1 PDB: 2on3_A 1d7k_A*
Length = 424
Score = 388 bits (999), Expect = e-131
Identities = 152/314 (48%), Positives = 194/314 (61%), Gaps = 33/314 (10%)
Query: 209 KEDAFYVLDVGEIVRKHEDWKLKLPRVDPYYAVKCNDSQMVLEVLAALGTGFDCAS---- 264
+DAFYV D+G+I++KH W LPRV P+YAVKCNDS+ ++ LAA+GTGFDCAS
Sbjct: 36 DKDAFYVADLGDILKKHLRWLKALPRVTPFYAVKCNDSRAIVSTLAAIGTGFDCASKTEI 95
Query: 265 -------------------KPISHIRYAAEYGIDTMTFDNEIELQKVKQFHPTAQLVIRI 305
K +S I+YAA G+ MTFD+EIEL KV + HP A+LV+RI
Sbjct: 96 QLVQGLGVPAERVIYANPCKQVSQIKYAASNGVQMMTFDSEIELMKVARAHPKAKLVLRI 155
Query: 306 RCDAEVAQCQLGMKFGCDPISEAPRLLRLAKSLDLDVVGVSFHVGSGCGDPPVFGRAIYS 365
D A C+L +KFG + LL AK L++DV+GVSFHVGSGC DP F +A+
Sbjct: 156 ATDDSKAVCRLSVKFGATL-KTSRLLLERAKELNIDVIGVSFHVGSGCTDPDTFVQAVSD 214
Query: 366 ARQIFDLGNSLGFSMRVLDLGGGYPGY--TGYSMNRIAEIINVALDEYFPVEEGVSIIAE 423
AR +FD+ +GFSM +LD+GGG+PG T I +IN ALD+YFP + GV IIAE
Sbjct: 215 ARCVFDMATEVGFSMHLLDIGGGFPGSEDTKLKFEEITSVINPALDKYFPSDSGVRIIAE 274
Query: 424 PGRYYVASAFTLATLIHSKRDILGA-------NSSVPTHTMYYINDGVYGSFNCIIYDHA 476
PGRYYVASAFTLA I +K+ + + S MYY+NDGVYGSFNCI+YDHA
Sbjct: 275 PGRYYVASAFTLAVNIIAKKTVWKEQPGSDDEDESNEQTFMYYVNDGVYGSFNCILYDHA 334
Query: 477 VCTPIPFNVMDDSQ 490
+ +
Sbjct: 335 HVKALLQKRPKPDE 348
Score = 108 bits (273), Expect = 8e-26
Identities = 35/73 (47%), Positives = 50/73 (68%)
Query: 5 ETLVPSSVWGPTCDGLDKVNDDILLPEMPVGSWLIYRDMGAYTLPVASTFNGFPIPKVHA 64
E SS+WGPTCDGLD++ + LPEM VG W+++ +MGAYT+ ASTFNGF P ++
Sbjct: 348 EKYYSSSIWGPTCDGLDRIVERCNLPEMHVGDWMLFENMGAYTVAAASTFNGFQRPNIYY 407
Query: 65 VIEEHIWLMLKDR 77
V+ +W ++K
Sbjct: 408 VMSRPMWQLMKQI 420
>1f3t_A ODC, ornithine decarboxylase; beta-alpha-barrel, modified greek KEY
beta-sheet, lyase; HET: PLP; 2.00A {Trypanosoma brucei}
SCOP: b.49.2.3 c.1.6.1 PDB: 1qu4_A* 1szr_C* 2tod_A*
1njj_A*
Length = 425
Score = 388 bits (999), Expect = e-131
Identities = 152/313 (48%), Positives = 196/313 (62%), Gaps = 33/313 (10%)
Query: 210 EDAFYVLDVGEIVRKHEDWKLKLPRVDPYYAVKCNDSQMVLEVLAALGTGFDCAS----- 264
D F+V D+G+IVRKHE WK LPRV P+YAVKCND VL LAALGTGFDCAS
Sbjct: 37 GDPFFVADLGDIVRKHETWKKCLPRVTPFYAVKCNDDWRVLGTLAALGTGFDCASNTEIQ 96
Query: 265 ------------------KPISHIRYAAEYGIDTMTFDNEIELQKVKQFHPTAQLVIRIR 306
K ISHIRYA + G+D MTFD EL+KV + HP A++V+RI
Sbjct: 97 RVRGIGVPPEKIIYANPCKQISHIRYARDSGVDVMTFDCVDELEKVAKTHPKAKMVLRIS 156
Query: 307 CDAEVAQCQLGMKFGCDPISEAPRLLRLAKSLDLDVVGVSFHVGSGCGDPPVFGRAIYSA 366
D +A+C+L +KFG + +L AK L++DV GVSFHVGSG D F +AI +
Sbjct: 157 TDDSLARCRLSVKFGAKV-EDCRFILEQAKKLNIDVTGVSFHVGSGSTDASTFAQAISDS 215
Query: 367 RQIFDLGNSLGFSMRVLDLGGGYPGY--TGYSMNRIAEIINVALDEYFPVEEGVSIIAEP 424
R +FD+G LGF+M +LD+GGG+PG IA +IN AL+++FP + ++I+AEP
Sbjct: 216 RFVFDMGTELGFNMHILDIGGGFPGTRDAPLKFEEIAGVINNALEKHFPPDLKLTIVAEP 275
Query: 425 GRYYVASAFTLATLIHSKRDILGANSSV-------PTHTMYYINDGVYGSFNCIIYDHAV 477
GRYYVASAFTLA + +K+ G + V MYY+NDGVYGSFNCI+YDHAV
Sbjct: 276 GRYYVASAFTLAVNVIAKKVTPGVQTDVGAHAESNAQSFMYYVNDGVYGSFNCILYDHAV 335
Query: 478 CTPIPFNVMDDSQ 490
P+P ++
Sbjct: 336 VRPLPQREPIPNE 348
Score = 104 bits (261), Expect = 3e-24
Identities = 36/73 (49%), Positives = 50/73 (68%)
Query: 5 ETLVPSSVWGPTCDGLDKVNDDILLPEMPVGSWLIYRDMGAYTLPVASTFNGFPIPKVHA 64
E L PSSVWGPTCDGLD++ + LPEM VG WL++ DMGAYT+ S+FNGF P ++
Sbjct: 348 EKLYPSSVWGPTCDGLDQIVERYYLPEMQVGEWLLFEDMGAYTVVGTSSFNGFQSPTIYY 407
Query: 65 VIEEHIWLMLKDR 77
V+ ++++
Sbjct: 408 VVSGLPDHVVREL 420
>2nva_A Arginine decarboxylase, A207R protein; PLP, TIM barrel, eukaryotic
ODC- like, lyase; HET: PL2; 1.80A {Paramecium bursaria
chlorella virus 1} PDB: 2nv9_A*
Length = 372
Score = 383 bits (987), Expect = e-130
Identities = 103/307 (33%), Positives = 161/307 (52%), Gaps = 34/307 (11%)
Query: 209 KEDAFYVLDVGEIVRKHEDWKLKLPRVDPYYAVKCNDSQMVLEVLAALGTGFDCAS---- 264
+ +FYV + + W + PRV P+YAVKCN+ +++L+ + FDCAS
Sbjct: 15 QTKSFYVSSPKIVEDLIDQWTILFPRVTPHYAVKCNNDEVLLKTMCDKNVNFDCASSSEI 74
Query: 265 -------------------KPISHIRYAAEYGIDTMTFDNEIELQKVKQFHPTAQLVIRI 305
K I + +A + G+D TFD+ EL K+ +HP ++++RI
Sbjct: 75 KKVIQIGVSPSRIIFAHTMKTIDDLIFAKDQGVDIATFDSSFELDKIHTYHPNCKMILRI 134
Query: 306 RCDAEVAQCQLGMKFGCDPISEAPRLLRLAKSLDLDVVGVSFHVGSGCGDPPVFGRAIYS 365
RCD A QLG KFG + E LL AK LD++V+G+SFHVGSG +P + RAI S
Sbjct: 135 RCDDPNATVQLGNKFGANE-DEIRHLLEYAKQLDIEVIGISFHVGSGSRNPEAYYRAIKS 193
Query: 366 ARQIFDLGNSLGFSMRVLDLGGGYPG--YTGYSMNRIAEIINVALDEYFPVEEGVSIIAE 423
+++ F+ S+G +LD+GGG G +++ IN A+ ++FP E+ V+I+AE
Sbjct: 194 SKEAFNEAISVGHKPYILDIGGGLHADIDEGELSTYMSDYINDAIKDFFP-EDTVTIVAE 252
Query: 424 PGRYYVASAFTLATLIHSKRDILGANSSVPTHTMYYINDGVYGSFNCIIYDHAVCTPIPF 483
PGR++ LAT + KR Y+ N+ YG F+ +I++ +V TP
Sbjct: 253 PGRFFAEHYSVLATQVIGKRV-------RDGLYEYFFNESTYGGFSNVIFEKSVPTPQLL 305
Query: 484 NVMDDSQ 490
+ D +
Sbjct: 306 RDVPDDE 312
Score = 95.7 bits (239), Expect = 1e-21
Identities = 25/61 (40%), Positives = 40/61 (65%)
Query: 5 ETLVPSSVWGPTCDGLDKVNDDILLPEMPVGSWLIYRDMGAYTLPVASTFNGFPIPKVHA 64
E VPS ++G TCDG+D +N ++ LPE+ +G W+ + GAYT + ++FNGF V+
Sbjct: 312 EEYVPSVLYGCTCDGVDVINHNVALPELHIGDWVYFPSWGAYTNVLTTSFNGFGEYDVYY 371
Query: 65 V 65
+
Sbjct: 372 I 372
>3btn_A Antizyme inhibitor 1; TIM-like A/B barrel domain and A sheet
domain, structural genomics, israel structural
proteomics center, ISPC; 2.05A {Mus musculus}
Length = 448
Score = 382 bits (983), Expect = e-129
Identities = 117/318 (36%), Positives = 175/318 (55%), Gaps = 33/318 (10%)
Query: 204 DNVGMKEDAFYVLDVGEIVRKHEDWKLKLPRVDPYYAVKCNDSQMVLEVLAALGTGFDCA 263
++ ++AF+V D+G+IV+KH W+ + ++ P+Y VKCN + VLE+LAALGTGF C+
Sbjct: 31 EHTLTGKNAFFVGDLGKIVKKHSQWQTVVAQIKPFYTVKCNSTPAVLEILAALGTGFACS 90
Query: 264 S-----------------------KPISHIRYAAEYGIDTMTFDNEIELQKVKQFHPTAQ 300
S K +S I+YAA+ G++ MT DNEIEL+K+ + HP A+
Sbjct: 91 SKNEMALVQELGVSPENIIFTSPCKQVSQIKYAAKVGVNIMTCDNEIELKKIARNHPNAK 150
Query: 301 LVIRIRCDAEVAQCQLGMKFGCDPISEAPRLLRLAKSLDLDVVGVSFHVGSGCGDPPVFG 360
+++ I + + MKFG LL AK LD+ ++GV FHV S C + V+
Sbjct: 151 VLLHIATEDNIGGEDGNMKFGTTL-KNCRHLLECAKELDVQIIGVKFHVSSACKEYQVYV 209
Query: 361 RAIYSARQIFDLGNSLGFSMRVLDLGGGYPGYTGYSMNRIAEIINVALDEYFPVEEGVSI 420
A+ AR +FD+ GF+M +LD+GGG+ G T + + +I+ LD YFP G+ I
Sbjct: 210 HALSDARCVFDMAGEFGFTMNMLDIGGGFTG-TEIQLEEVNHVISPLLDIYFPEGSGIQI 268
Query: 421 IAEPGRYYVASAFTLATLIHSKRDILGAN--------SSVPTHTMYYINDGVYGSFNCII 472
I+EPG YYV+SAFTLA I +K+ + S +YY+NDGVYGSF +
Sbjct: 269 ISEPGSYYVSSAFTLAVNIIAKKVVENDKFSSGVEKNGSDEPAFVYYMNDGVYGSFASKL 328
Query: 473 YDHAVCTPIPFNVMDDSQ 490
+ P + +
Sbjct: 329 SEDLNTIPEVHKKYKEDE 346
Score = 108 bits (272), Expect = 1e-25
Identities = 30/81 (37%), Positives = 46/81 (56%)
Query: 5 ETLVPSSVWGPTCDGLDKVNDDILLPEMPVGSWLIYRDMGAYTLPVASTFNGFPIPKVHA 64
E L SS+WGP+CD LD++ + LLPE+ VG WLI+ +MGA + S FN F P ++
Sbjct: 346 EPLFTSSLWGPSCDELDQIVESCLLPELNVGDWLIFDNMGADSFHEPSAFNDFQRPAIYF 405
Query: 65 VIEEHIWLMLKDRLPLTQDHF 85
++ W ++D +
Sbjct: 406 MMSFSDWYEMQDAGITSDAMM 426
>2plj_A Lysine/ornithine decarboxylase; type IV decarboxylase, beta/alpha
barrel, beta barrel, lyase; HET: P3T; 1.70A {Vibrio
vulnificus} PDB: 2plk_A*
Length = 419
Score = 355 bits (912), Expect = e-118
Identities = 85/296 (28%), Positives = 135/296 (45%), Gaps = 38/296 (12%)
Query: 209 KEDAFYVLDVGEIVRKHEDWKLKLPRVDPYYAVKCNDSQMVLEVLAALGTGFDCAS---- 264
+LD I +++ K LP V +YA+K +V+ L A G FD A+
Sbjct: 53 FGAPLLLLDCDVIRQQYRALKNALPNVTLHYALKPLPHPVVVRTLLAEGASFDLATTGEV 112
Query: 265 -------------------KPISHIRYAAEYGIDTMTFDNEIELQKVKQFHPTAQLVIRI 305
K + IR A YG + DN EL+K K + +L++R+
Sbjct: 113 ELVASEGVPADLTIHTHPIKRDADIRDALAYGCNVFVVDNLNELEKFKAYRDDVELLVRL 172
Query: 306 RCDAEVAQCQLGMKFGCDPISEAPRLLRLAKSLDLDVVGVSFHVGSGCGDPPVFGRAIYS 365
A L KFGC P +A ++ AK ++ + G+SFHVGS +P + AI++
Sbjct: 173 SFRNSEAFADLSKKFGCSP-EQALVIIETAKEWNIRIKGLSFHVGSQTTNPNKYVEAIHT 231
Query: 366 ARQIFDLGNSLGF-SMRVLDLGGGYPG-YTG--YSMNRIAEIINVALDEYFPVEEGVSII 421
R + + G ++ LD+GGG+P YT +++ IN AL E V ++
Sbjct: 232 CRHVMEQVVERGLPALSTLDIGGGFPVNYTQQVMPIDQFCAPINEALSLLP---ETVHVL 288
Query: 422 AEPGRYYVASAFTLATLIHSKRDILGANSSVPTHTMYYINDGVYGSFNCIIYDHAV 477
AEPGR+ A A T + + + YY++DG+YGSF+ +++D A
Sbjct: 289 AEPGRFICAPAVTSVASVMGQAE-------REGQIWYYLDDGIYGSFSGLMFDDAR 337
Score = 95.0 bits (237), Expect = 3e-21
Identities = 27/68 (39%), Positives = 39/68 (57%)
Query: 5 ETLVPSSVWGPTCDGLDKVNDDILLPEMPVGSWLIYRDMGAYTLPVASTFNGFPIPKVHA 64
L+PS + GPTCD +D + ++ILLP++ G +I R MGAYT A+ FN F + A
Sbjct: 347 GELIPSVLSGPTCDSVDVIAENILLPKLNNGDLVIGRTMGAYTSATATDFNFFKRAQTIA 406
Query: 65 VIEEHIWL 72
+ E
Sbjct: 407 LNEFVASS 414
>1knw_A Diaminopimelate decarboxylase; pyridoxal-phosphate,
decarboxylation, lysin barrel, lyase; HET: PLP MES;
2.10A {Escherichia coli} SCOP: b.49.2.3 c.1.6.1 PDB:
1ko0_A*
Length = 425
Score = 99 bits (250), Expect = 7e-23
Identities = 48/271 (17%), Positives = 90/271 (33%), Gaps = 49/271 (18%)
Query: 213 FYVLDVGEIVRKHEDWKLKLPRVDPYYAVKCNDSQMVLEVLAALGTGFDCAS-------- 264
+V D I R+ K + V +A K + +L ++ G D S
Sbjct: 28 VWVYDAQIIRRQIAALK-QFDVV--RFAQKACSNIHILRLMREQGVKVDSVSLGEIERAL 84
Query: 265 -------------------KPISHIRYAAEYGIDTMTFDNEIELQKVKQFHPTAQLVIRI 305
+ + +E I + + L ++ Q P ++ +R+
Sbjct: 85 AAGYNPQTHPDDIVFTADVIDQATLERVSELQI-PVNAGSVDMLDQLGQVSPGHRVWLRV 143
Query: 306 RCDAEV---AQCQLGM---KFGCDPISEAPRLLRLAKSLDLDVVGVSFHVGSGCGDPPVF 359
+ G K G ++ P L + + L +VG+ H+GSG +
Sbjct: 144 NPGFGHGHSQKTNTGGENSKHGI-WYTDLPAALDVIQRHHLQLVGIHMHIGSGVDYAHLE 202
Query: 360 GRAIYSARQIFDLGNSLGFSMRVLDLGGGY-----PGYTGYSMNRIAEIINVALDEY-FP 413
RQ+ + G L + + GGG G + N A ++
Sbjct: 203 QVCGAMVRQVIEFGQDL----QAISAGGGLSVPYQQGEEAVDTEHYYGLWNAAREQIARH 258
Query: 414 VEEGVSIIAEPGRYYVASA-FTLATLIHSKR 443
+ V + EPGR+ VA + + + K+
Sbjct: 259 LGHPVKLEIEPGRFLVAQSGVLITQVRSVKQ 289
>2j66_A BTRK, decarboxylase; butirosin, AHBA biosynthesis, lyase; HET: PLP;
1.65A {Bacillus circulans}
Length = 428
Score = 98.8 bits (247), Expect = 2e-22
Identities = 51/276 (18%), Positives = 104/276 (37%), Gaps = 49/276 (17%)
Query: 213 FYVLDVGEIVRKHEDWKLKL-PRVDPYYAVKCNDSQMVLEVLAALGTGFDCAS------- 264
FY+ D I + + + P + Y ++K N++ + ++ G G + AS
Sbjct: 19 FYLYDGDFIEAHYRQLRSRTNPAIQFYLSLKANNNIHLAKLFRQWGLGVEVASAGELALA 78
Query: 265 ----------------KPISHIRYAAEYGIDTMTFDNEIELQKV----KQFHPTAQLVIR 304
K S + A + GI + ++ EL + ++ + TA++ IR
Sbjct: 79 RHAGFSAENIIFSGPGKKRSELEIAVQSGIYCIIAESVEELFYIEELAEKENKTARVAIR 138
Query: 305 I--RCDAEVAQCQLGM---KFGCDPISEAPRLLRLAKSLD-LDVVGVSFHVGSGCGDPPV 358
I ++G +FG D S ++ +SL +G+ + G+ +
Sbjct: 139 INPDKSFGSTAIKMGGVPRQFGMD-ESMLDAVMDAVRSLQFTKFIGIHVYTGTQNLNTDS 197
Query: 359 FGRAIYSARQIFDLGNSL----GFSMRVLDLGGG-----YPGYTGYSMNRIAEIINVALD 409
+ + DLG ++ G ++LGGG + + +I ++ +
Sbjct: 198 IIES---MKYTVDLGRNIYERYGIVCECINLGGGFGVPYFSHEKALDIGKITRTVSDYVQ 254
Query: 410 EYFPVE-EGVSIIAEPGRYYVASA-FTLATLIHSKR 443
E + I E GRY +A A + +++ K
Sbjct: 255 EARDTRFPQTTFIIESGRYLLAQAAVYVTEVLYRKA 290
Score = 31.4 bits (72), Expect = 0.75
Identities = 15/48 (31%), Positives = 22/48 (45%), Gaps = 1/48 (2%)
Query: 14 GPTCDGLDKVNDDILLPEMPVGSWLIYRDMGAYTLPVAST-FNGFPIP 60
GP C D + D+ +P + G + + GAY L + F G P P
Sbjct: 343 GPLCTPEDCLGKDVHVPALYPGDLVCVLNSGAYGLSFSPVHFLGHPTP 390
>2qgh_A Diaminopimelate decarboxylase; lyase; HET: PLP LYS; 2.30A
{Helicobacter pylori} PDB: 3c5q_A*
Length = 425
Score = 95.7 bits (239), Expect = 2e-21
Identities = 69/265 (26%), Positives = 103/265 (38%), Gaps = 46/265 (17%)
Query: 213 FYVLDVGEIVRKHEDWKLKLPRVDP--YYAVKCNDSQMVLEVLAALGTGFDCAS------ 264
FY+ D +I + ++K YA+K N + +L +LA L +G DC S
Sbjct: 35 FYLYDFDKIKQAFLNYKEAFKGRKSLICYALKANSNLSILSLLAHLESGADCVSIGEIQR 94
Query: 265 -----------------KPISHIRYAAEYGIDTMTFDNEIELQKV----KQFHPTAQLVI 303
K I A + I + ++ +EL+ + + A++ I
Sbjct: 95 ALKAGIKPYRIVFSGVGKSAFEIEQALKLNILFLNVESFMELKTIETIAQSLGIKARISI 154
Query: 304 RI--RCDAEV-AQCQLGM---KFGCDPISEAPRLLRLAKSLD-LDVVGVSFHVGSGCGDP 356
RI DA+ G+ KFG EA + AK L+ V V FH+GS D
Sbjct: 155 RINPNIDAKTHPYISTGLKENKFGV-GEKEALEMFLWAKKSAFLEPVSVHFHIGSQLLDL 213
Query: 357 PVFGRAIYSARQIFDLGNSLGFSMRVLDLGGG----YPGYTGYSMNRIAEIINVALDEYF 412
A +I +LG +R D+GGG Y + A+ I AL
Sbjct: 214 EPIIEASQKVAKIAKSLIALGIDLRFFDVGGGIGVSYENEETIKLYDYAQGILNALQGL- 272
Query: 413 PVEEGVSIIAEPGRYYVASAFTLAT 437
++II EPGR VA + L T
Sbjct: 273 ----DLTIICEPGRSIVAESGELIT 293
Score = 29.0 bits (66), Expect = 4.3
Identities = 16/47 (34%), Positives = 22/47 (46%)
Query: 14 GPTCDGLDKVNDDILLPEMPVGSWLIYRDMGAYTLPVASTFNGFPIP 60
GP C+ D D LPE+ G + +GAY +AS +N P
Sbjct: 346 GPVCESSDTFLKDAHLPELEPGDKIAIEKVGAYGSSMASQYNSRPKL 392
>2p3e_A Diaminopimelate decarboxylase; southeast collaboratory for struct
genomics, riken spring-8 center; 1.99A {Aquifex
aeolicus}
Length = 420
Score = 94.5 bits (236), Expect = 4e-21
Identities = 62/271 (22%), Positives = 104/271 (38%), Gaps = 46/271 (16%)
Query: 213 FYVLDVGEIVRKHEDWKLKLPRVDPYYAVKCNDSQMVLEVLAALGTGFDCAS-------- 264
YV I + E ++ P YAVK N + ++++L LG G D S
Sbjct: 36 LYVYSSNFIKERFEAYRKAFPDALICYAVKANFNPHLVKLLGELGAGADIVSGGELYLAK 95
Query: 265 ---------------KPISHIRYAAEYGIDTMTFDNEIELQKV----KQFHPTAQLVIRI 305
K + A + I ++ EL + + A++ IR+
Sbjct: 96 KAGIPPERIVYAGVGKTEKELTDAVDSEILMFNVESRQELDVLNEIAGKLGKKARIAIRV 155
Query: 306 R--CDAEV-AQCQLGM---KFGCDPISEAPRLLRLAKSLD-LDVVGVSFHVGSGCGDPPV 358
D + GM KFG D I EA + A L+ L++VG+ H+GS D
Sbjct: 156 NPDVDPKTHPYIATGMQKSKFGVD-IREAQKEYEYASKLENLEIVGIHCHIGSQILDISP 214
Query: 359 FGRAIYSARQIFDLGNSLGFSMRVLDLGGG-----YPGYTGYSMNRIAEIINVALDEYFP 413
+ A+ +++ GF ++ LD+GGG P + +A+++ L+
Sbjct: 215 YREAVEKVVSLYESLTQKGFDIKYLDIGGGLGIKYKPEDKEPAPQDLADLLKDLLENV-- 272
Query: 414 VEEGVSIIAEPGRYYVASA-FTLATLIHSKR 443
II EPGR + +A + + K
Sbjct: 273 ---KAKIILEPGRSIMGNAGILITQVQFLKD 300
Score = 28.6 bits (65), Expect = 4.8
Identities = 14/47 (29%), Positives = 22/47 (46%)
Query: 14 GPTCDGLDKVNDDILLPEMPVGSWLIYRDMGAYTLPVASTFNGFPIP 60
GP C+ D + D + E+ G +L GAY ++S +N P
Sbjct: 345 GPICETGDFLALDREIEEVQRGEYLAVLSAGAYGFAMSSHYNMRPRA 391
>3n2b_A Diaminopimelate decarboxylase; LYSA, lyase, structural genom center
for structural genomics of infectious diseases, CSGI;
1.80A {Vibrio cholerae}
Length = 441
Score = 93.4 bits (233), Expect = 1e-20
Identities = 70/262 (26%), Positives = 102/262 (38%), Gaps = 39/262 (14%)
Query: 213 FYVLDVGEIVRKHEDWKLKLPRVDP--YYAVKCNDSQMVLEVLAALGTGFDCAS------ 264
YV + R + + YAVK N + VL LA LG+GFD S
Sbjct: 54 LYVYSRATLERHWHAFDKSVGDYPHLICYAVKANSNLGVLNTLARLGSGFDIVSVGELER 113
Query: 265 -----------------KPISHIRYAAEYGIDTMTFDNEIELQKV----KQFHPTAQLVI 303
K + ++ A + I ++E ELQ++ + A + +
Sbjct: 114 VLAAGGDPSKVVFSGVGKTEAEMKRALQLKIKCFNVESEPELQRLNKVAGELGVKAPISL 173
Query: 304 RI--RCDAEV-AQCQLGM---KFGCDPISEAPRLLRLAKSLD-LDVVGVSFHVGSGCGDP 356
RI DA+ G+ KFG A ++ RLA SL LDV G+ H+GS
Sbjct: 174 RINPDVDAKTHPYISTGLRDNKFGI-TFDRAAQVYRLAHSLPNLDVHGIDCHIGSQLTAL 232
Query: 357 PVFGRAIYSARQIFDLGNSLGFSMRVLDLGGGYP-GYTGYSMNRIAEIINVALDEYFPVE 415
F A + D + G +R LD+GGG Y + +E AL +
Sbjct: 233 APFIDATDRLLALIDSLKAEGIHIRHLDVGGGLGVVYRDELPPQPSEYAK-ALLDRLERH 291
Query: 416 EGVSIIAEPGRYYVASAFTLAT 437
+ +I EPGR A+A L T
Sbjct: 292 RDLELIFEPGRAIAANAGVLVT 313
>3mt1_A Putative carboxynorspermidine decarboxylase prote; PSI2, MCSG,
structural genomics; 2.50A {Sinorhizobium meliloti}
Length = 365
Score = 91.9 bits (229), Expect = 2e-20
Identities = 39/255 (15%), Positives = 82/255 (32%), Gaps = 46/255 (18%)
Query: 213 FYVLDVGEIVRKHEDWK--LKLPRVDPYYAVKCNDSQMVLEVLAALGTGFDCAS------ 264
+Y++D ++ R E + A+KC + V +++ G +S
Sbjct: 6 YYLIDKAKLTRNMERIAHVREKSGAKALLALKCFATWSVFDLMRDYMDGTTSSSLFEVRL 65
Query: 265 -----KPISHI----------RYAAEYGIDTMTFDNEIELQKVKQFHPTAQLVIRI--RC 307
+H + D + F++ +L++ +R+ +
Sbjct: 66 GRERFGKETHAYSVAYGDNEIDEVVSHA-DKIIFNSISQLERFADKAAGIARGLRLNPQV 124
Query: 308 DAE----VAQCQLGMKFGCDPISEAPRLLRLAKSLDLDVVGVSFHVGSGCGDPPVFGRAI 363
+ + + G + + R++ + G H D +F R +
Sbjct: 125 SSSSFDLADPARPFSRLGEWDVPKVERVMD-------RINGFMIHNNCENKDFGLFDRML 177
Query: 364 YSARQIFDLGNSLGFSMRVLDLGGGYPG-YTGYSMNRIAEIINVALDEYFPVEEGVSIIA 422
+ F +L + + LGGG Y ++ + + D Y GV I
Sbjct: 178 GEIEERFG---ALIARVDWVSLGGGIHFTGDDYPVDAFSARLRAFSDRY-----GVQIYL 229
Query: 423 EPGRYYVASAFTLAT 437
EPG + + TL
Sbjct: 230 EPGEASITKSTTLEV 244
Score = 49.1 bits (118), Expect = 2e-06
Identities = 15/83 (18%), Positives = 33/83 (39%), Gaps = 6/83 (7%)
Query: 1 YPYRETLVPSS------VWGPTCDGLDKVNDDILLPEMPVGSWLIYRDMGAYTLPVASTF 54
Y ++P+ + G +C D + E+ VG + ++D YT+ + F
Sbjct: 273 YRETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWF 332
Query: 55 NGFPIPKVHAVIEEHIWLMLKDR 77
NG +P + + +++
Sbjct: 333 NGVKMPAIAIRELDGSVRTVREF 355
>3vab_A Diaminopimelate decarboxylase 1; structural genomics, seattle
structural genomics center for infectious disease,
ssgcid; HET: LLP; 2.10A {Brucella melitensis BV}
Length = 443
Score = 91.8 bits (229), Expect = 4e-20
Identities = 71/267 (26%), Positives = 102/267 (38%), Gaps = 48/267 (17%)
Query: 213 FYVLDVGEIVRKHEDWKLKLPRVDP--YYAVKCNDSQMVLEVLAALGTGFDCAS------ 264
FYV I R + +D YA+K N +Q VL LA LG G D S
Sbjct: 51 FYVYSRATIERHFRVFHDAFADMDTLVTYALKANSNQAVLTALAKLGAGADTVSQGEIRR 110
Query: 265 -----------------KPISHIRYAAEYGIDTMTFDNEIELQKV----KQFHPTAQLVI 303
K + +A E GI ++E EL+ + A + +
Sbjct: 111 ALAAGIPANRIVFSGVGKTPREMDFALEAGIYCFNVESEPELEILSARAVAAGKVAPVSL 170
Query: 304 RI--RCDAEV-AQCQLGM---KFGCDPISEAPRLLRLAKSLD-LDVVGVSFHVGSGCGDP 356
RI DA+ A+ G KFG P +A A SL L+VVG+ H+GS D
Sbjct: 171 RINPDVDAKTHAKISTGKSENKFGI-PRDKARAAYARAASLPGLNVVGIDMHIGSQIIDL 229
Query: 357 PVFGRAIYSARQIFDLGNSLGFSMRVLDLGGG------YPGYTGYSMNRIAEIINVALDE 410
F A ++ + G ++R +D+GGG P A+I+ +
Sbjct: 230 EPFDNAFALMAELVKELQADGHNIRHVDVGGGLGIPYRTPNTPPPPPVAYAQIVAKHIKP 289
Query: 411 YFPVEEGVSIIAEPGRYYVASAFTLAT 437
G+ + EPGR V +A L T
Sbjct: 290 L-----GLKTVFEPGRLIVGNAGLLVT 311
Score = 29.4 bits (67), Expect = 3.1
Identities = 12/47 (25%), Positives = 21/47 (44%)
Query: 14 GPTCDGLDKVNDDILLPEMPVGSWLIYRDMGAYTLPVASTFNGFPIP 60
GP C+ D + D + + G + GAY ++ST+N +
Sbjct: 365 GPVCETGDYLGLDREVAKPAPGDLIAICTTGAYGAVLSSTYNSRLLI 411
>2o0t_A Diaminopimelate decarboxylase; PLP binding enzyme, lysine
biosynthesis, STRU genomics, TB structural genomics
consortium, TBSGC; HET: LLP; 2.33A {Mycobacterium
tuberculosis} PDB: 1hkv_A* 1hkw_A
Length = 467
Score = 91.5 bits (228), Expect = 6e-20
Identities = 55/307 (17%), Positives = 100/307 (32%), Gaps = 67/307 (21%)
Query: 213 FYVLDVGEIVRKHEDWKLKL-PRVDPYYAVKCNDSQMVLEVLAALGTGFDCAS------- 264
+V+D + + + + +YA K V ++ G D +
Sbjct: 44 LFVIDEDDFRSRCRETAAAFGSGANVHYAAKAFLCSEVARWISEEGLCLDVCTGGELAVA 103
Query: 265 ----------------KPISHIRYAAEYGIDTMTFDNEIELQKV----KQFHPTAQLVIR 304
K +S + A + G+ + D+ E++++ + +++R
Sbjct: 104 LHASFPPERITLHGNNKSVSELTAAVKAGVGHIVVDSMTEIERLDAIAGEAGIVQDVLVR 163
Query: 305 IRCDAE------VAQCQLGMKFGCDPIS-EAPRLLRLAKSLD-LDVVGVSFHVGSGCGDP 356
+ E ++ KFG S A +R + D L +VG+ H+GS D
Sbjct: 164 LTVGVEAHTHEFISTAHEDQKFGLSVASGAAMAAVRRVFATDHLRLVGLHSHIGSQIFDV 223
Query: 357 PVFGRAIYSARQIFDL--------GNSLGFSMRVLDLGGGY----------PGYTGYSMN 398
F A A ++ L G + +DLGGG P
Sbjct: 224 DGFELA---AHRVIGLLRDVVGEFGPEKTAQIATVDLGGGLGISYLPSDDPPPIAEL-AA 279
Query: 399 RIAEIINVALDEY-FPVEEGVSIIAEPGRYYVASA-FTLATLIHSKRDILGANSSVPTHT 456
++ I++ P + ++ EPGR TL + K + S H
Sbjct: 280 KLGTIVSDESTAVGLPTPK---LVVEPGRAIAGPGTITLYEVGTVKD----VDVSATAHR 332
Query: 457 MYYINDG 463
Y DG
Sbjct: 333 RYVSVDG 339
Score = 29.1 bits (66), Expect = 4.4
Identities = 19/75 (25%), Positives = 33/75 (44%), Gaps = 1/75 (1%)
Query: 2 PYRETLVPSSVWGPTCDGLDKVNDDILLP-EMPVGSWLIYRDMGAYTLPVASTFNGFPIP 60
VP+ + G C+ D + D +P ++ G + GAY ++S +N P
Sbjct: 362 VSDAPPVPARLVGKHCESGDIIVRDTWVPDDIRPGDLVAVAATGAYCYSLSSRYNMVGRP 421
Query: 61 KVHAVIEEHIWLMLK 75
V AV + L+L+
Sbjct: 422 AVVAVHAGNARLVLR 436
>1twi_A Diaminopimelate decarboxylase; antibiotic resistance, lysine
biosynthesis, structural genomics, NYSGXRC, PSI; HET:
LYS PLP; 2.00A {Methanocaldococcus jannaschii} SCOP:
b.49.2.3 c.1.6.1 PDB: 1tuf_A*
Length = 434
Score = 90.3 bits (225), Expect = 1e-19
Identities = 65/285 (22%), Positives = 100/285 (35%), Gaps = 59/285 (20%)
Query: 213 FYVLDVGEIVRKHEDWKLKLPRVDPY--------YAVKCNDSQMVLEVLAALGTGFDCAS 264
YV+ +I + + R + YA K N + + +LA LG G D S
Sbjct: 32 LYVMSEEQIKINYNRYIEAFKRWEEETGKEFIVAYAYKANANLAITRLLAKLGCGADVVS 91
Query: 265 -----------------------KPISHIRYAAEYGIDTMTFDNEIELQKV----KQFHP 297
K I E I D+ EL + K+
Sbjct: 92 GGELYIAKLSNVPSKKIVFNGNCKTKEEIIMGIEANIRAFNVDSISELILINETAKELGE 151
Query: 298 TAQLVIRIRCDAEV---AQCQLGM---KFGCDPIS-EAPRLLRLAKSLD-LDVVGVSFHV 349
TA + RI + + G+ KFG D S A + +++A ++ ++VVGV H+
Sbjct: 152 TANVAFRINPNVNPKTHPKISTGLKKNKFGLDVESGIAMKAIKMALEMEYVNVVGVHCHI 211
Query: 350 GSGCGDPPVFGRAIYSARQIFDLGNSLGFSMRVLDLGGGY----------PGYTGYSMNR 399
GS D F G + ++LGGG P
Sbjct: 212 GSQLTDISPFIEETRKVMDFVVELKEEGIEIEDVNLGGGLGIPYYKDKQIPTQKDL---- 267
Query: 400 IAEIINVALDEYFPVEEGVSIIAEPGRYYVASA-FTLATLIHSKR 443
A+ I + +Y E ++I EPGR VA+A + L + H K
Sbjct: 268 -ADAIINTMLKYKDKVEMPNLILEPGRSLVATAGYLLGKVHHIKE 311
Score = 28.6 bits (65), Expect = 5.5
Identities = 15/49 (30%), Positives = 25/49 (51%)
Query: 14 GPTCDGLDKVNDDILLPEMPVGSWLIYRDMGAYTLPVASTFNGFPIPKV 62
G C+ D D L ++ VG L D+GAY + +A+ +N P++
Sbjct: 355 GGLCESSDVFGRDRELDKVEVGDVLAIFDVGAYGISMANNYNARGRPRM 403
>2yxx_A Diaminopimelate decarboxylase; TM1517, TIM beta/alpha barrel fold,
lyase, structural genomi NPPSFA; HET: PLP; 1.70A
{Thermotoga maritima}
Length = 386
Score = 89.1 bits (222), Expect = 2e-19
Identities = 48/265 (18%), Positives = 104/265 (39%), Gaps = 46/265 (17%)
Query: 213 FYVLDVGEIVRKHEDWKLKLPRVDP--YYAVKCNDSQMVLEVLAALGTGFDCAS------ 264
YV + ++ K V+ +AVK N++ ++L++L G G D +
Sbjct: 15 TYVYFEETLRKRSRLVKEVFEGVNLLPTFAVKANNNPVLLKILREEGFGMDVVTKGELLA 74
Query: 265 -----------------KPISHIRYAAEYGIDTMTFDNEIELQKVKQFHP-TAQLVIRI- 305
K + + + + D+ E++ ++ +P + IR+
Sbjct: 75 AKLAGVPSHTVVWNGNGKSRDQMEHFLREDVRIVNVDSFEEMEIWRELNPEGVEYFIRVN 134
Query: 306 -RCDAEV-AQCQLGM---KFGCDPISEAPRLLRLAKSLDLDVVGVSFHVGSGCGDPPVFG 360
DA+ G+ KFG + + + +S +++ G+ H+GS F
Sbjct: 135 PEVDAKTHPHISTGLKKHKFGIP-LEDLDSFMERFRS--MNIRGLHVHIGSQITRVEPFV 191
Query: 361 RAIYSARQIFDLGNSLGFSMRVLDLGGGYP-GYTGYSMNRIAEIINVALDEYFPVEEGVS 419
A ++ S + +++GGG+ Y+G ++ ++ + + ++
Sbjct: 192 EA---FSKVVRA--SERYGFEEINIGGGWGINYSGEELD-LSSYREKVVPD---LKRFKR 242
Query: 420 IIAEPGRYYVASA-FTLATLIHSKR 443
+I E GRY VA + + L ++ KR
Sbjct: 243 VIVEIGRYIVAPSGYLLLRVVLVKR 267
Score = 30.1 bits (69), Expect = 1.8
Identities = 14/47 (29%), Positives = 23/47 (48%)
Query: 14 GPTCDGLDKVNDDILLPEMPVGSWLIYRDMGAYTLPVASTFNGFPIP 60
GP C+ D + D LPE+ G + + GAY +++ +N P
Sbjct: 311 GPLCESGDVIAYDRELPEVEPGDIIAVENAGAYGYTMSNNYNSTTRP 357
>3n29_A Carboxynorspermidine decarboxylase; lyase; HET: PLP; 1.90A
{Campylobacter jejuni subsp}
Length = 418
Score = 88.6 bits (220), Expect = 4e-19
Identities = 39/284 (13%), Positives = 81/284 (28%), Gaps = 54/284 (19%)
Query: 213 FYVLDVGEIVRKHEDWK--LKLPRVDPYYAVKCNDSQMVLEVLAALGTGFDCAS------ 264
Y+L+ ++ + E + A+K ++++ G C+
Sbjct: 46 AYILEEDKLRKNCELLASVGEKSGAKVLLALKGFAFSGAMKIVGEYLKGCTCSGLWEAKF 105
Query: 265 -----KPISH----------IRYAAEYGIDTMTFDNEIELQKVKQFHPTAQLVIRI--RC 307
H I A + F++ + K + L +R
Sbjct: 106 AKEYMDKEIHTYSPAFKEDEIGEIASLS-HHIVFNSLAQFHKFQSKTQKNSLGLRCNVEF 164
Query: 308 DA-EVAQCQLGM---KFGCDPISEAPRLLRLAKSLDLDVVGVSFHVGSGCGDPPVFGRAI 363
+ G + + A + G+ FH +
Sbjct: 165 SLAPKELYNPCGRYSRLGI-RAKDFENVDLNA------IEGLHFHALCEESADA-LEAVL 216
Query: 364 YSARQIFDLGNSLGFSMRVLDLGGGYP-GYTGYSMNRIAEIINVALDEYFPVEEGVSIIA 422
+ F M+ ++ GGG+ GY + ++ + D+Y GV +
Sbjct: 217 KVFEEKFG---KWIGQMKWVNFGGGHHITKKGYDVEKLIALCKNFSDKY-----GVQVYL 268
Query: 423 EPGRYYVASAFTLAT----LIHSKRDILGANSSVPTH---TMYY 459
EPG L +I +++ I ++S H T+
Sbjct: 269 EPGEAVGWQTGNLVASVVDIIENEKQIAILDTSSEAHMPDTIIM 312
Score = 45.8 bits (109), Expect = 2e-05
Identities = 14/62 (22%), Positives = 31/62 (50%)
Query: 14 GPTCDGLDKVNDDILLPEMPVGSWLIYRDMGAYTLPVASTFNGFPIPKVHAVIEEHIWLM 73
G TC D + + ++ +G +++ D YT+ +TFNG +P + + ++ M
Sbjct: 346 GNTCLAGDVMGEYAFDKKLKIGDKIVFLDQIHYTIVKNTTFNGIRLPNLMLLDHKNELQM 405
Query: 74 LK 75
++
Sbjct: 406 IR 407
>3nzq_A ADC, biosynthetic arginine decarboxylase; alpha-beta protein,
structural genomics, PSI-biology, protei structure
initiative; 3.10A {Escherichia coli}
Length = 666
Score = 84.6 bits (209), Expect = 2e-17
Identities = 46/253 (18%), Positives = 86/253 (33%), Gaps = 56/253 (22%)
Query: 239 YAVKCNDSQMVLEVLAALGT--GFDCASKP-----------------------ISHIRYA 273
Y +K N + V+E L G G + SK +IR A
Sbjct: 124 YPIKVNQHRRVIESLIHSGEPLGLEAGSKAELMAVLAHAGMTRSVIVCNGYKDREYIRLA 183
Query: 274 AEYGID----TMTFDNEIELQKV----KQFHPTAQLVIRIRCDAEVA--QCQLGM---KF 320
+ + E+ V ++ + +L +R R ++ + G KF
Sbjct: 184 LIGEKMGHKVYLVIEKMSEIAIVLDEAERLNVVPRLGVRARLASQGSGKWQSSGGEKSKF 243
Query: 321 GCDPISEAPRLLRLAKSLDL--DVVGVSFHVGSGCGDPPVFGRAIYSARQIFDLGNSLGF 378
G ++ +L+ + + + FH+GS + + + + + + LG
Sbjct: 244 GL-AATQVLQLVETLREAGRLDSLQLLHFHLGSQMANIRDIATGVRESARFYVELHKLGV 302
Query: 379 SMRVLDLGGG-----------YPGYTGYSMNRIAEIINVALDEYFPVEEGVS---IIAEP 424
+++ D+GGG Y +N A I A+ + E G+ +I E
Sbjct: 303 NIQCFDVGGGLGVDYEGTRSQSDCSVNYGLNEYANNIIWAIGDAC-EENGLPHPTVITES 361
Query: 425 GRYYVASAFTLAT 437
GR A L +
Sbjct: 362 GRAVTAHHTVLVS 374
>3n2o_A ADC, biosynthetic arginine decarboxylase; lyase; HET: PLP; 2.30A
{Vibrio vulnificus}
Length = 648
Score = 80.3 bits (198), Expect = 4e-16
Identities = 55/309 (17%), Positives = 100/309 (32%), Gaps = 72/309 (23%)
Query: 239 YAVKCNDSQMVLEVLAALG-------TGFDCASKP----------------IS------- 268
Y +K N + V++ + A G + SKP +
Sbjct: 102 YPIKVNQQREVVDEILASQAQLETKQLGLEAGSKPELLAVLAMAQHASSVIVCNGYKDRE 161
Query: 269 HIRYAAEYGID----TMTFDNEIELQKV----KQFHPTAQLVIRIRCDAEVA--QCQLGM 318
+IR A + + EL V K T +L IRIR ++ A G
Sbjct: 162 YIRLALIGEKLGHKVFIVLEKMSELDLVLREAKSLGVTPRLGIRIRLASQGAGKWQASGG 221
Query: 319 ---KFGCDPISEAPRLLRLAKSLDL--DVVGVSFHVGSGCGDPPVFGRAIYSARQIFDLG 373
KFG S+ ++ K + + V FH+GS + + + + +
Sbjct: 222 EKSKFGL-SASQVLNVISRLKKENQLDTLQLVHFHLGSQMANIRDVRNGVNESARFYCEL 280
Query: 374 NSLGFSMRVLDLGGG-----------YPGYTGYSMNRIAEIINVALDEYFPVEEGVS--- 419
+LG ++ D+GGG Y + A I + + +
Sbjct: 281 RTLGANITYFDVGGGLAIDYDGTRSQSSNSMNYGLVEYARNIVNTVGDVC-KDYKQPMPV 339
Query: 420 IIAEPGRYYVASAFTLAT-LIHSKR------DILGANSSVPTHTMY----YINDGVYGSF 468
II+E GR A L + +I ++ + + + M+ +++G
Sbjct: 340 IISESGRSLTAHHAVLISNVIGTETYKPETVTEPEEDFPLLLNNMWRSWLNLHNGTDARA 399
Query: 469 NCIIYDHAV 477
IY+
Sbjct: 400 LIEIYNDTQ 408
>3nzp_A Arginine decarboxylase; alpha-beta protein, structural genomics,
PSI-biology, protei structure initiative; HET: PLP;
3.00A {Campylobacter jejuni subsp}
Length = 619
Score = 70.6 bits (173), Expect = 4e-13
Identities = 48/253 (18%), Positives = 85/253 (33%), Gaps = 55/253 (21%)
Query: 239 YAVKCNDSQMVLEVLAALGT----GFDCASKP----------------------ISHIRY 272
Y +K N ++ L LG G + SK I
Sbjct: 83 YPLKVNQYPGFVKNLVKLGKDYNYGLEAGSKAELLLAMAYNNEGAPITVNGFKDRELINI 142
Query: 273 AAEYGID----TMTFDNEIELQKV-----KQFHPTAQLVIRIRCDAEVA--QCQLGM--- 318
T+T + EL+ + ++F P + +R+R + + G
Sbjct: 143 GFIAAEMGHNITLTIEGLNELEAIIDIAKERFKPKPNIGLRVRLHSAGVGIWAKSGGINS 202
Query: 319 KFGCDPISEAPRLLRLAKSLDL--DVVGVSFHVGSGCGDPPVFGRAIYSARQIFDLGNSL 376
KFG +E + L K L + FH+GS + +A+ A I+ +
Sbjct: 203 KFGLT-STELIEAVNLLKENKLLEQFTMIHFHLGSQITEIHPLKKALNEAGNIYTELRKM 261
Query: 377 GF-SMRVLDLGGG----YPGYTG-----YSMNRIAEIINVALDEYFPVEEG--VSIIAEP 424
G +++ ++LGGG Y + Y++ A + L ++ I E
Sbjct: 262 GAKNLKAINLGGGLAVEYSQFKNEKSRNYTLREYANDVVFILKNIAEQKKDLEPDIFIES 321
Query: 425 GRYYVASAFTLAT 437
GR+ A+ L
Sbjct: 322 GRFVAANHAVLIA 334
>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 = 57.9 bits (139), Expect = 6e-09
Identities = 61/439 (13%), Positives = 120/439 (27%), Gaps = 121/439 (27%)
Query: 75 KDRLPLTQDHFIKENQPVRNDSWDELPHM---DDYEDIIPFSYFAYLNCYPNVNMKLQNP 131
KD L + +D F+ D D + ++ + II ++
Sbjct: 19 KDILSVFEDAFVDNFDC--KDVQDMPKSILSKEEIDHII----------------MSKDA 60
Query: 132 EDQIYVL-----DRGNDAVHVMKSIILSGVPVYNYP---DNIRVLPEFQPTISVWKRIPK 183
L + + V +L NY I+ QP++
Sbjct: 61 VSGTLRLFWTLLSKQEEMVQKFVEEVLR----INYKFLMSPIKTEQR-QPSM------MT 109
Query: 184 SLMVYPRTDDMTQVPVYNYPDNVGMKE------DAFYVLDVGEIVRKH------------ 225
+ + R V+ NV + A L + V
Sbjct: 110 RMYIEQRDRLYNDNQVFA-KYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVAL 168
Query: 226 ---EDWKLKLPRVDPYYAV---KCNDSQMVLEVLAALGTGFDCASKPISHIRYAAEYGID 279
+K++ + + CN + VLE+L L D S + I
Sbjct: 169 DVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIH 228
Query: 280 TMTFDNEIELQKVKQFHPTAQLVIRIRCDAEVAQCQLGMKFGCDPISEAPRLL---RLAK 336
++ L K K + LV+ +A+ C ++L R +
Sbjct: 229 SIQ-AELRRLLKSKP-YENCLLVLLNVQNAKAWN---AFNLSC-------KILLTTRFKQ 276
Query: 337 SLDLDVVGVSFHVGSGCGDPPVFGRAIYSARQIF---------DL------GNSLGFSM- 380
D + H+ D + + DL N S+
Sbjct: 277 VTDFLSAATTTHI---SLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSII 333
Query: 381 --RVLDLGGGYPGYTGYSMNRIAEIINVALDEYFPVEEGVSIIAEPGRYYVASAFTLATL 438
+ D + + + +++ II +L+ P AE + + L+
Sbjct: 334 AESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEP--------AEYRKMFDR----LS-- 379
Query: 439 IHSKRDILGANSSVPTHTM 457
+ ++ +PT +
Sbjct: 380 ------VFPPSAHIPTILL 392
Score = 35.6 bits (81), Expect = 0.040
Identities = 46/297 (15%), Positives = 81/297 (27%), Gaps = 124/297 (41%)
Query: 2 PYRETL-VPSSVWGPT--------CDGL----DKVNDDIL---------LPEMPVG---- 35
PY L V +V C L K D L L +
Sbjct: 242 PYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPD 301
Query: 36 -------SWLIYRDMGAYTLP-VASTFNGFPIPKVHAVIEEHIWLMLKDRLPLTQDHFIK 87
+L D LP T N P+ ++I ++D L
Sbjct: 302 EVKSLLLKYL---DCRPQDLPREVLTTN----PRRLSII----AESIRDGL--------- 341
Query: 88 ENQPVRNDSWDELPHM--DDYEDIIPFSYFAYLNCYPNVNMKLQNPED--QIYVLDRGND 143
+WD H+ D II S + P + +++
Sbjct: 342 -------ATWDNWKHVNCDKLTTIIESSL------------NVLEPAEYRKMFD------ 376
Query: 144 AVHVMKSIILSGVPVYNYPDNIRVLPEFQPTISV-WKRIP------------KSLMVYPR 190
S+ +P + + P +S+ W + K +V +
Sbjct: 377 ----RLSV---------FPPSAHI-PT--ILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQ 420
Query: 191 TDDMTQVPVYNYPD---NVGMKEDAFY-----VLDVGEIVRKHEDWKLKLPRVDPYY 239
+ T + P + +K + Y ++D I + + L P +D Y+
Sbjct: 421 PKEST----ISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYF 473
Score = 32.9 bits (74), Expect = 0.28
Identities = 13/74 (17%), Positives = 24/74 (32%), Gaps = 15/74 (20%)
Query: 71 WLMLKDRLPLTQD-----HFIKENQPVRNDSWDELPHMDDYEDIIPFSYFAYLNCYPN-- 123
W L Q +I +N P + L ++ D +P L C
Sbjct: 514 WNASGSILNTLQQLKFYKPYICDNDPKY----ERL--VNAILDFLP-KIEENLICSKYTD 566
Query: 124 -VNMKLQNPEDQIY 136
+ + L ++ I+
Sbjct: 567 LLRIALMAEDEAIF 580
>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 = 54.3 bits (130), Expect = 8e-08
Identities = 87/579 (15%), Positives = 174/579 (30%), Gaps = 194/579 (33%)
Query: 43 MGAYTL-PV----ASTFNGFPIP-KVHAVIEEHIWLMLKDR----LPLTQDHFIKENQPV 92
M AY+ P+ S + +P + + L+++ LP + F +++P
Sbjct: 1 MDAYSTRPLTLSHGSLEHVLLVPTASFFIASQ-----LQEQFNKILPEPTEGFAADDEPT 55
Query: 93 RNDSWDEL-----PHMDDYEDIIPFSYFAYLNCYPNVNMKLQNPEDQIYVLDRGNDAVHV 147
+ EL ++ + F + +N+ L E+ L GND +H
Sbjct: 56 ---TPAELVGKFLGYVSSLVEPSKVGQFDQV-----LNLCLTEFENCY--L-EGND-IH- 102
Query: 148 MKSIILSGVPVYNYPDNIRVLPEFQPTISVWKRIPKSLMVYPRTDDMTQVPVYNYPDNV- 206
++ +L E T+ K + K+ Y M + P ++
Sbjct: 103 --ALAAK------------LLQENDTTLVKTKELIKN---YITARIMAKRPFDKKSNSAL 145
Query: 207 ------------------GMKEDAF---------YVLDVGEIVRKHEDWKLKLPR----V 235
G +D F Y + VG++++ + +L R
Sbjct: 146 FRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDA 205
Query: 236 DPYYAVKCNDSQMVLEVLAALGTGFDC---ASKPIS----HIRYAAEYGIDTMTFDNEIE 288
+ + N +LE L D S PIS + A Y +
Sbjct: 206 EKVFTQGLN----ILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVV---------- 251
Query: 289 LQKVKQFHPTAQLVIRIR----CDAEV--AQCQLGMKFGCDPISEA---PRLLRLAKSLD 339
K+ F P +L ++ + A I+E +
Sbjct: 252 TAKLLGFTP-GELRSYLKGATGHSQGLVTAVA----------IAETDSWESFFVSVRK-- 298
Query: 340 LDVVGVSFHVGSGCGDPPVFGRAIYSARQIFDLGNSLGFSMRVLDLGGGYPGY----TGY 395
+ V F +G C + + + D L+ G P +
Sbjct: 299 --AITVLFFIGVRCYE--AYPNTSLPPSILED----------SLENNEGVPSPMLSISNL 344
Query: 396 SMNRIAEIINVALDEYFPVEEGVSI--IAEPGRYYVA-SAFTLATLI------------- 439
+ ++ + +N + + P + V I + V+ +L L
Sbjct: 345 TQEQVQDYVN-KTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLD 403
Query: 440 -----HSKRDILGANS----SVPTHTMYYINDGVYGSFNCIIYDHAVCTPIPFNVMDDSQ 490
S+R + +N + P H+ + + + I D V + FN D
Sbjct: 404 QSRIPFSERKLKFSNRFLPVASPFHSHLLV-----PASDLINKD-LVKNNVSFNAKD--- 454
Query: 491 VSLRSPLF-------LQE------SFLLSCLSLFFCVLW 516
++ P++ L+ ++ C+ + V W
Sbjct: 455 --IQIPVYDTFDGSDLRVLSGSISERIVDCI-IRLPVKW 490
Score = 39.6 bits (92), Expect = 0.003
Identities = 45/319 (14%), Positives = 86/319 (26%), Gaps = 127/319 (39%)
Query: 206 VGMKEDAFYVLDVGEIVRKHEDWKLKLPRVDPYYAVKCNDSQMVLEVLAALGTGFDCASK 265
GM D Y + + + W R D ++ + GF
Sbjct: 1629 QGMGMD-LY--KTSKAAQ--DVWN----RADNHF----------KDTY-----GFS---- 1660
Query: 266 PISHIRYAAEYGIDTMTFDNEIELQKVKQFHPTAQLVIRIRCDAEVAQCQLGMKFGCDPI 325
I I +N + L H + RIR + + I
Sbjct: 1661 -ILDI-----------VINNPVNLT----IHFGGEKGKRIR--------ENYSAMIFETI 1696
Query: 326 SEA-PRLLRLAKSLDLDVVGVSFHVGSGCGD-----------PPVF--GRAIYS---ARQ 368
+ + ++ K ++ +F + P + +A + ++
Sbjct: 1697 VDGKLKTEKIFKEINEHSTSYTFR-----SEKGLLSATQFTQPALTLMEKAAFEDLKSKG 1751
Query: 369 IFDL-----GNSLGFSMRVLDLGGGYPGYTGYSMNRIAEIINVALDEYFPVEEGVSIIAE 423
+ G+SLG Y+ A +L + +E V ++
Sbjct: 1752 LIPADATFAGHSLG----------------EYA----A---LASLADVMSIESLVEVVFY 1788
Query: 424 PGRYYVASAFTLATLIHSKRDILGANSSVPTHTMYYINDGVYGSFNCIIYDHAVCTPIP- 482
G + A RD LG ++ + M IN G + V +
Sbjct: 1789 RGM-TMQVA--------VPRDELGRSN----YGMIAINPGRVAASFSQEALQYVVERVGK 1835
Query: 483 ----------FNVMDDSQV 491
+NV ++ Q
Sbjct: 1836 RTGWLVEIVNYNV-ENQQY 1853
>3qc0_A Sugar isomerase; TIM barrel, structural genomics, joint center for
structural genomics, JCSG, protein structure initiative,
PSI-biology,; HET: UNL PG4; 1.45A {Sinorhizobium
meliloti} PDB: 3ju2_A
Length = 275
Score = 32.8 bits (75), Expect = 0.19
Identities = 25/116 (21%), Positives = 41/116 (35%), Gaps = 7/116 (6%)
Query: 327 EAPRLLRLAKSLDLDVVGVSFHVGSGCGDPPVFGRAIYSARQIFDLGNSLGFSMRVLDLG 386
R+ ++ L + G+ D +AI R+ D LG + ++ +
Sbjct: 46 GLGEAGRIVRANGLKLTGLCRGGFFPAPDASGREKAIDDNRRAVDEAAELG-ADCLVLVA 104
Query: 387 GGYPGYTG---YSMNRIAEIINVALDEYFPVEEGVSIIAEP-GRYYVASAFTLATL 438
GG PG + + + E I L GV + EP Y A + TL
Sbjct: 105 GGLPGGSKNIDAARRMVVEGIAAVLPHA--RAAGVPLAIEPLHPMYAADRACVNTL 158
>3u0h_A Xylose isomerase domain protein; structural genomics, PSI-biology,
midwest center for structu genomics, MCSG, TIM barrel;
2.30A {Alicyclobacillus acidocaldarius subsp}
Length = 281
Score = 31.3 bits (71), Expect = 0.67
Identities = 14/97 (14%), Positives = 28/97 (28%), Gaps = 3/97 (3%)
Query: 328 APRLLRLAKSLDLDVVGVSFHVGSGCGDPPVFGRAIYSARQIFDLGNSLGFSMRVLDLGG 387
+ + + L + + + PVF R + L LG L
Sbjct: 49 DAAVEAMFQRRGLVLANLGLPLNLY-DSEPVFLRELSLLPDRARLCARLGARSVTAFLWP 107
Query: 388 GYPGYTGYSMNRIAEIINVALDEYFPVEEGVSIIAEP 424
++++A I E + G+ + E
Sbjct: 108 SMDEEPVRYISQLARRIRQVAVEL--LPLGMRVGLEY 142
>1i60_A IOLI protein; beta barrel, structural genomics, PSI, protein
structure initiative, midwest center for structural
genomics, MCSG; 1.60A {Bacillus subtilis} SCOP: c.1.15.4
PDB: 1i6n_A
Length = 278
Score = 29.7 bits (67), Expect = 1.9
Identities = 13/118 (11%), Positives = 33/118 (27%), Gaps = 8/118 (6%)
Query: 327 EAPRLLRLAKSLDLDVVGVSFHVGSGCGDPPVFGRAIYSARQIFDLGNSLGFSMRVLDLG 386
L ++ + + ++ V D I + + + +LG V+ +
Sbjct: 47 SLDDLAEYFQTHHIKPLALNALVFFNNRDEKGHNEIITEFKGMMETCKTLG-VKYVVAVP 105
Query: 387 GGYPGYTGYS--MNRIAEIINVALDEYFPVEEGVSIIAEP---GRYYVASAFTLATLI 439
+++ L + GV I E + V + ++
Sbjct: 106 LVTEQKIVKEEIKKSSVDVLT-ELSDIA-EPYGVKIALEFVGHPQCTVNTFEQAYEIV 161
>2h8o_A Geranyltranstransferase; geranyltransferase,agrobacterium
tumefaciens, structural GEN PSI-2, protein structure
initiative; 1.60A {Agrobacterium tumefaciens}
Length = 335
Score = 28.8 bits (65), Expect = 4.0
Identities = 5/30 (16%), Positives = 6/30 (20%)
Query: 397 MNRIAEIINVALDEYFPVEEGVSIIAEPGR 426
+ A L E I P
Sbjct: 43 LRENAAKTEALLGHLLSGEARADEITRPQN 72
>4f62_A Geranyltranstransferase; enzyme function initiative, structural
genomics; 2.10A {Marinomonas SP}
Length = 317
Score = 28.0 bits (63), Expect = 7.1
Identities = 3/31 (9%), Positives = 9/31 (29%)
Query: 397 MNRIAEIINVALDEYFPVEEGVSIIAEPGRY 427
++ L++ + + RY
Sbjct: 9 STYTQSRVDQYLEQQLSDYAPANQLHNAMRY 39
>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 = 27.6 bits (60), Expect = 7.5
Identities = 7/23 (30%), Positives = 11/23 (47%), Gaps = 3/23 (13%)
Query: 222 VRKHEDWKLKL--PRVDPYYAVK 242
++K + LKL P A+K
Sbjct: 22 LKKLQA-SLKLYADDSAPALAIK 43
>1a7j_A Phosphoribulokinase; transferase, calvin cycle; 2.50A {Rhodobacter
sphaeroides} SCOP: c.37.1.6
Length = 290
Score = 27.7 bits (61), Expect = 8.2
Identities = 15/126 (11%), Positives = 41/126 (32%), Gaps = 3/126 (2%)
Query: 211 DAFYVLDVGEIVRKHEDWKLKLPRVDPYYAVKCNDSQMVLEVLAALGTGFDCASKPISHI 270
DAF+ + ++ + + +++ + N+ + + V G ++ H
Sbjct: 42 DAFHRFNRADMKAELDRRYAAGDATFSHFSYEANELKELERVFREYGETGQGRTRTYVHD 101
Query: 271 RY-AAEYGIDTMTFDNEIELQKVKQFHP-TAQLVIRIRCDAEVAQCQLGMKFGCDPISEA 328
AA G+ F + + + + +A +K G P+
Sbjct: 102 DAEAARTGVAPGNFTDWRDFDSDSHLLFYEGLHGAVVNSEVNIAG-LADLKIGVVPVINL 160
Query: 329 PRLLRL 334
+ ++
Sbjct: 161 EWIQKI 166
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
0.323 0.141 0.445
Gapped
Lambda K H
0.267 0.0739 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 8,571,847
Number of extensions: 545479
Number of successful extensions: 1281
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1211
Number of HSP's successfully gapped: 59
Length of query: 522
Length of database: 6,701,793
Length adjustment: 98
Effective length of query: 424
Effective length of database: 3,965,535
Effective search space: 1681386840
Effective search space used: 1681386840
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 59 (26.5 bits)