RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 026945
(230 letters)
>1vhn_A Putative flavin oxidoreducatase; structural genomics, unknown
function; HET: FMN; 1.59A {Thermotoga maritima} SCOP:
c.1.4.1
Length = 318
Score = 107 bits (269), Expect = 4e-28
Identities = 43/214 (20%), Positives = 87/214 (40%), Gaps = 23/214 (10%)
Query: 1 MDNLPLVKSLVEKLALNLNVPVSCKIRVFPNLQDTIKYAKMLEDAGCSLLAVHGRTRDEK 60
+ +L + +V +L +++ S K R+ + + ++L + G + +H RT
Sbjct: 108 LKDLRHFRYIVRELRKSVSGKFSVKTRLGWEKNEVEEIYRILVEEGVDEVFIHTRTV--V 165
Query: 61 DGKKFRADWNAIKAVKNALRIPVLANGNVRHMEDVQKCLEETGCEGVLSAESLLENPALF 120
RA+W A+ ++ RIP +G++ ED ++ LEE+GC+G+L A + P +F
Sbjct: 166 QSFTGRAEWKALSVLEK--RIPTFVSGDIFTPEDAKRALEESGCDGLLVARGAIGRPWIF 223
Query: 121 ----AGFRTAEWIVGSEEISKDGNLDQADLLVEYLKLCEKYPVPWRMIRSHVHKLLGEW- 175
R+ ++ S E +LL++ E+ V +R +
Sbjct: 224 KQIKDFLRSGKYSEPSREEILRTFERHLELLIKT--KGERKAV--VEMRKFLA-----GY 274
Query: 176 FRIQPG---VREDLNAQNRLTFEFLYNLVDRLRE 206
+ G RE + + L + +
Sbjct: 275 TKDLKGARRFREKVMKIE--EVQILKEMFYNFIK 306
>1y0e_A Putative N-acetylmannosamine-6-phosphate 2-epimer; mannac-6-P
epimerase, NANE, structural genomics, protein STR
initiative, PSI; 1.95A {Staphylococcus aureus subsp}
SCOP: c.1.2.5
Length = 223
Score = 44.9 bits (106), Expect = 5e-06
Identities = 16/76 (21%), Positives = 32/76 (42%), Gaps = 3/76 (3%)
Query: 34 DTIKYAKMLEDAGCSLLAV--HGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRH 91
T++ AK G + HG T + ++ D+ +K V ++ V+A GNV
Sbjct: 127 ATVEEAKNAARLGFDYIGTTLHGYTSYTQGQLLYQNDFQFLKDVLQSVDAKVIAEGNVIT 186
Query: 92 MEDVQKCLEETGCEGV 107
+ ++ + + G
Sbjct: 187 PDMYKRVM-DLGVHCS 201
>1vzw_A Phosphoribosyl isomerase A; histidine biosynthesis, tryptophan
biosynthesis; 1.8A {Streptomyces coelicolor} SCOP:
c.1.2.1 PDB: 2vep_A 2x30_A
Length = 244
Score = 44.5 bits (106), Expect = 8e-06
Identities = 23/85 (27%), Positives = 36/85 (42%), Gaps = 5/85 (5%)
Query: 34 DTIKYAKMLEDAGCSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRHME 93
D + L GC+ V T KDG + +K V A PV+A+G V ++
Sbjct: 147 DLYETLDRLNKEGCARYVV---TDIAKDGTLQGPNLELLKNVCAATDRPVVASGGVSSLD 203
Query: 94 DVQKC--LEETGCEGVLSAESLLEN 116
D++ L G EG + ++L
Sbjct: 204 DLRAIAGLVPAGVEGAIVGKALYAK 228
Score = 29.4 bits (67), Expect = 0.73
Identities = 23/103 (22%), Positives = 31/103 (30%), Gaps = 18/103 (17%)
Query: 69 WNAIKAVKNALRIPVLANGNVRHMEDVQKCLEETGCEGVLSAESLLENPALFAGFRTAEW 128
I V A+ I V +G +R + + L TGC V + LE P A+
Sbjct: 64 RALIAEVAQAMDIKVELSGGIRDDDTLAAAL-ATGCTRVNLGTAALETPEWV-----AKV 117
Query: 129 --------IVG----SEEISKDGNLDQADLLVEYLKLCEKYPV 159
VG + G L E L K
Sbjct: 118 IAEHGDKIAVGLDVRGTTLRGRGWTRDGGDLYETLDRLNKEGC 160
>2y88_A Phosphoribosyl isomerase A; aromatic amino acid biosynthesis,
TIM-barrel, His biosynthesis, tryptophan biosynthesis;
HET: 2ER; 1.33A {Mycobacterium tuberculosis} PDB: 2y89_A
2y85_A*
Length = 244
Score = 44.1 bits (105), Expect = 1e-05
Identities = 22/85 (25%), Positives = 37/85 (43%), Gaps = 5/85 (5%)
Query: 34 DTIKYAKMLEDAGCSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRHME 93
D + L+ GCS V T KDG + + + V + PV+A+G V ++
Sbjct: 150 DLWDVLERLDSEGCSRFVV---TDITKDGTLGGPNLDLLAGVADRTDAPVIASGGVSSLD 206
Query: 94 DVQKC--LEETGCEGVLSAESLLEN 116
D++ L G EG + ++L
Sbjct: 207 DLRAIATLTHRGVEGAIVGKALYAR 231
Score = 28.3 bits (64), Expect = 2.0
Identities = 16/53 (30%), Positives = 22/53 (41%), Gaps = 1/53 (1%)
Query: 69 WNAIKAVKNALRIPVLANGNVRHMEDVQKCLEETGCEGVLSAESLLENPALFA 121
+ V L + V +G +R E + L TGC V + LENP A
Sbjct: 63 HELLAEVVGKLDVQVELSGGIRDDESLAAAL-ATGCARVNVGTAALENPQWCA 114
>1qo2_A Molecule: N-((5-phosphoribosyl)-formimino)-5-aminoimidazol-
4-carboxamid ribonucleotid...; isomerase, histidine
biosynthesis; 1.85A {Thermotoga maritima} SCOP: c.1.2.1
PDB: 2cff_A 2w79_A
Length = 241
Score = 39.9 bits (94), Expect = 3e-04
Identities = 19/89 (21%), Positives = 33/89 (37%), Gaps = 8/89 (8%)
Query: 33 QDTIKYAKMLEDAGCSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRHM 92
D + K L++ G + T EKDG D++ K + + VLA G +
Sbjct: 144 IDPVSLLKRLKEYGLEEIVH---TEIEKDGTLQEHDFSLTKKIAIEAEVKVLAAGGISSE 200
Query: 93 EDVQK-----CLEETGCEGVLSAESLLEN 116
++ +GV+ + LE
Sbjct: 201 NSLKTAQKVHTETNGLLKGVIVGRAFLEG 229
>1ps9_A 2,4-dienoyl-COA reductase; iron-sulfur, TIM barrel, flavodoxin,
flavin, electron transfer, hydride transfer,
oxidoreductase; HET: FAD FMN NAP MDE; 2.20A {Escherichia
coli} SCOP: c.1.4.1 c.3.1.1 c.4.1.1
Length = 671
Score = 40.0 bits (94), Expect = 4e-04
Identities = 12/93 (12%), Positives = 33/93 (35%), Gaps = 5/93 (5%)
Query: 32 LQDTIKYAKMLEDAGCSLLAVHGRTRDEKD---GKKFRADWNA--IKAVKNALRIPVLAN 86
+T++ A+ +E AG +++ + + + + +K + +P++
Sbjct: 227 FAETVELAQAIEAAGATIINTGIGWHEARIPTIATPVPRGAFSWVTRKLKGHVSLPLVTT 286
Query: 87 GNVRHMEDVQKCLEETGCEGVLSAESLLENPAL 119
+ + L + V A L + L
Sbjct: 287 NRINDPQVADDILSRGDADMVSMARPFLADAEL 319
>2zbt_A Pyridoxal biosynthesis lyase PDXS; pyridoxine biosynthesis,
structural genomics, NPPSFA; 1.65A {Thermus
thermophilus} PDB: 2iss_A*
Length = 297
Score = 39.3 bits (91), Expect = 5e-04
Identities = 23/82 (28%), Positives = 39/82 (47%), Gaps = 4/82 (4%)
Query: 35 TIKYAKMLEDAG-CSLLAVHGRTRD-EKDGKKFR-ADWNAIKAVKNALRIPVLANGNVRH 91
T + A + E+AG +++A+ D G R +D IK + A+ IPV+A + H
Sbjct: 30 TPEQAVIAEEAGAVAVMALERVPADIRAQGGVARMSDPKIIKEIMAAVSIPVMAKVRIGH 89
Query: 92 MEDVQKCLEETGCEGVLSAESL 113
+ LE G + + +E L
Sbjct: 90 FVEAM-ILEAIGVDFIDESEVL 110
>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 = 39.6 bits (92), Expect = 6e-04
Identities = 49/265 (18%), Positives = 86/265 (32%), Gaps = 99/265 (37%)
Query: 29 FPNLQDTIK-YAKMLEDAGCSLLAVHGRT-----RDEKDGKK-FRADWNAIKAVKNA--- 78
F L+D + Y ++ D L+ T R D +K F N ++ ++N
Sbjct: 170 FEELRDLYQTYHVLVGD----LIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNT 225
Query: 79 ------LRIPV---------LANGNV------RHMEDVQKCLE-ETGC-EGVLSA----- 110
L IP+ LA+ V +++ L+ TG +G+++A
Sbjct: 226 PDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAE 285
Query: 111 ----ESLLEN-----PALFAGFRTAEWIVGSE--EISKDGNLDQADLLVEYLKLCEKYPV 159
ES + LF +I G E + +L +L + L+ E P
Sbjct: 286 TDSWESFFVSVRKAITVLF-------FI-GVRCYEAYPNTSLP-PSILEDSLENNEGVPS 336
Query: 160 PWRMI------RSHVHKLLGEWFRIQPGVREDLNAQNRL---------TF------EFLY 198
P M+ + V + + L A ++ + LY
Sbjct: 337 P--MLSISNLTQEQVQDYVNK-------TNSHLPAGKQVEISLVNGAKNLVVSGPPQSLY 387
Query: 199 NLVDRLRELGV-------RIPLYKK 216
L LR+ RIP ++
Sbjct: 388 GLNLTLRKAKAPSGLDQSRIPFSER 412
Score = 37.3 bits (86), Expect = 0.004
Identities = 44/240 (18%), Positives = 68/240 (28%), Gaps = 109/240 (45%)
Query: 8 KSLVEKLALNLNVPVSCKIRVFPNL-QDTIKYAKMLEDAGCSLLAV----H----GRTRD 58
+SL LNL + K + L Q I +++ L V H D
Sbjct: 384 QSLY---GLNLTL---RKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASD 437
Query: 59 --EKDGKKFRADWNAIKAVKNALRIPVLA--NGNVRHMEDVQKCLEETGCEGVLSAESLL 114
KD K +NA ++IPV +G D++ + S+
Sbjct: 438 LINKDLVKNNVSFNA-----KDIQIPVYDTFDG-----SDLRVL-----------SGSIS 476
Query: 115 ENPALFAGFRTAEWIVGSEEISKDGNLDQADLLVEYLKLCEKYPVPW----RMIRSHVHK 170
E R + I+ + PV W + +H+
Sbjct: 477 E--------RIVDCII-------------------------RLPVKWETTTQFKATHI-- 501
Query: 171 L-LGEWFRIQPGVREDLNAQNRLTFEFLYNLVDRLRE-LGVRIPLYKKDADDAEILADDL 228
L G PG L L R ++ GVR+ I+A L
Sbjct: 502 LDFG------PGGASGLG-----------VLTHRNKDGTGVRV-----------IVAGTL 533
Score = 35.8 bits (82), Expect = 0.010
Identities = 26/133 (19%), Positives = 42/133 (31%), Gaps = 39/133 (29%)
Query: 21 PVSCKIRVF--PNLQDTIKYAKMLEDA--------GCSL-LAVHGRTRDEKDGKKFRADW 69
PV+ F L + +D + + V+ D DG R
Sbjct: 422 PVAS---PFHSHLLVPAS--DLINKDLVKNNVSFNAKDIQIPVY----DTFDGSDLRVLS 472
Query: 70 NAI--KAVKNALRIPV----LANGNVRHMED------------VQKCLEETGCEGVLSAE 111
+I + V +R+PV H+ D + + TG V+ A
Sbjct: 473 GSISERIVDCIIRLPVKWETTTQFKATHILDFGPGGASGLGVLTHRNKDGTGVR-VIVAG 531
Query: 112 SLLENPALFAGFR 124
+L NP GF+
Sbjct: 532 TLDINPDDDYGFK 544
>3gr7_A NADPH dehydrogenase; flavin, FMN, beta-alpha-barrel,
oxidoreductase, flavoprotein; HET: FMN; 2.30A
{Geobacillus kaustophilus} PDB: 3gr8_A*
Length = 340
Score = 38.7 bits (91), Expect = 8e-04
Identities = 18/92 (19%), Positives = 36/92 (39%), Gaps = 5/92 (5%)
Query: 31 NLQDTIKYAKMLEDAGCSLLAVH--GRTRDEKD-GKKFRADWNAIKAVKNALRIPVLANG 87
+D + YAK +++ G L+ V + ++ + A + ++ IP A G
Sbjct: 227 TAKDYVPYAKRMKEQGVDLVDVSSGAIVPARMNVYPGYQVPF-A-ELIRREADIPTGAVG 284
Query: 88 NVRHMEDVQKCLEETGCEGVLSAESLLENPAL 119
+ ++ L+ + V LL NP
Sbjct: 285 LITSGWQAEEILQNGRADLVFLGRELLRNPYW 316
>1z41_A YQJM, probable NADH-dependent flavin oxidoreductase YQJ; FMN,
beta-alpha-barrel; HET: FMN; 1.30A {Bacillus subtilis}
SCOP: c.1.4.1 PDB: 1z42_A* 1z44_A* 1z48_A*
Length = 338
Score = 38.7 bits (91), Expect = 0.001
Identities = 13/92 (14%), Positives = 36/92 (39%), Gaps = 5/92 (5%)
Query: 31 NLQDTIKYAKMLEDAGCSLLAVH--GRTRDEKD-GKKFRADWNAIKAVKNALRIPVLANG 87
++ D I +AK +++ G L+ + + ++ + A + ++ + A G
Sbjct: 227 DIADHIGFAKWMKEQGVDLIDCSSGALVHADINVFPGYQVSF-A-EKIREQADMATGAVG 284
Query: 88 NVRHMEDVQKCLEETGCEGVLSAESLLENPAL 119
+ ++ L+ + + LL +P
Sbjct: 285 MITDGSMAEEILQNGRADLIFIGRELLRDPFF 316
>3q58_A N-acetylmannosamine-6-phosphate 2-epimerase; TIM beta/alpha barrel,
ribulose-phosphate binding barrel, carbohydrate
metabolic process; HET: BTB; 1.80A {Salmonella enterica
subsp}
Length = 229
Score = 38.1 bits (88), Expect = 0.001
Identities = 10/75 (13%), Positives = 17/75 (22%), Gaps = 3/75 (4%)
Query: 34 DTIKYAKMLEDAGCSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRHME 93
T+ G + D + + +A V+A G
Sbjct: 137 STVNEGISCHQKGIEFIGTTLSGYTG-PITPVEPDLAMVTQLSHA-GCRVIAEGRYNTPA 194
Query: 94 DVQKCLEETGCEGVL 108
+ E G V
Sbjct: 195 LAANAI-EHGAWAVT 208
>1jvn_A Glutamine, bifunctional histidine biosynthesis protein hishf;
substrate channeling, amidotransferase, TIM-barrel AS A
SUBS tunnel; HET: 143; 2.10A {Saccharomyces cerevisiae}
SCOP: c.1.2.1 c.23.16.1 PDB: 1ox4_B* 1ox5_A* 1ox6_A
1ox4_A
Length = 555
Score = 38.6 bits (90), Expect = 0.001
Identities = 21/79 (26%), Positives = 34/79 (43%), Gaps = 7/79 (8%)
Query: 34 DTIKYAKMLED--AGCSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRH 91
+ + E AG LL +KDG D I+ VK+A++IPV+A+
Sbjct: 453 GVWELTRACEALGAGEILL-----NCIDKDGSNSGYDLELIEHVKDAVKIPVIASSGAGV 507
Query: 92 MEDVQKCLEETGCEGVLSA 110
E ++ +T + L A
Sbjct: 508 PEHFEEAFLKTRADACLGA 526
>3o07_A Pyridoxine biosynthesis protein SNZ1; (beta/alpha)8-barrel,
pyridoxal 5-phosphate synthase, PLP G3 SNO1,
biosynthetic protein; HET: 1GP; 1.80A {Saccharomyces
cerevisiae} PDB: 3o06_A 3o05_A* 3fem_A
Length = 291
Score = 38.2 bits (88), Expect = 0.001
Identities = 27/92 (29%), Positives = 46/92 (50%), Gaps = 6/92 (6%)
Query: 35 TIKYAKMLEDAG-CSLLAVHGRTRD-EKDGKKFR-ADWNAIKAVKNALRIPVLANGNVRH 91
T + AK+ E +G C+++A+ D K GK R +D IK + N++ IPV+A + H
Sbjct: 20 TPEQAKIAEKSGACAVMALESIPADMRKSGKVCRMSDPKMIKDIMNSVSIPVMAKVRIGH 79
Query: 92 MEDVQKCLEETGCEGVLSAESLLENPALFAGF 123
+ Q +E + + ES + PA +
Sbjct: 80 FVEAQ-IIEALEVDYI--DESEVLTPADWTHH 108
>3igs_A N-acetylmannosamine-6-phosphate 2-epimerase 2; energy metabolism,
sugars, csgid, carbohydrate metabolism, isomerase; HET:
MSE 16G; 1.50A {Salmonella enterica subsp}
Length = 232
Score = 37.8 bits (87), Expect = 0.001
Identities = 10/75 (13%), Positives = 21/75 (28%), Gaps = 3/75 (4%)
Query: 34 DTIKYAKMLEDAGCSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRHME 93
++ + G ++ D +KA+ +A V+A G
Sbjct: 137 SSVDDGLACQRLGADIIGTTMSGYTT-PDTPEEPDLPLVKALHDA-GCRVIAEGRYNSPA 194
Query: 94 DVQKCLEETGCEGVL 108
+ + G V
Sbjct: 195 LAAEAI-RYGAWAVT 208
>3hgj_A Chromate reductase; TIM barrel, oxidoreductase; HET: FMN; 2.00A
{Thermus scotoductus} PDB: 3hf3_A*
Length = 349
Score = 37.9 bits (89), Expect = 0.001
Identities = 22/93 (23%), Positives = 40/93 (43%), Gaps = 6/93 (6%)
Query: 31 NLQDTIKYAKMLEDAGCSLLAVH--GRTRDEK--DGKKFRADWNAIKAVKNALRIPVLAN 86
+L+DT+ +A+ L++ G LL G + F+ + A AV+ + + A
Sbjct: 237 SLEDTLAFARRLKELGVDLLDCSSGGVVLRVRIPLAPGFQVPF-A-DAVRKRVGLRTGAV 294
Query: 87 GNVRHMEDVQKCLEETGCEGVLSAESLLENPAL 119
G + E + L+ + VL LL +P
Sbjct: 295 GLITTPEQAETLLQAGSADLVLLGRVLLRDPYF 327
>3l5l_A Xenobiotic reductase A; TIM barrel, oxidoreductase; HET: BU3 FMN;
1.03A {Pseudomonas putida} PDB: 3l5m_A* 3n19_B* 3n16_A*
3l68_A* 3l67_A* 3l65_A* 3l66_A* 3n14_A* 2h8z_A* 2h90_A*
2h8x_A*
Length = 363
Score = 37.9 bits (89), Expect = 0.002
Identities = 18/93 (19%), Positives = 36/93 (38%), Gaps = 6/93 (6%)
Query: 31 NLQDTIKYAKMLEDAGCSLLAVH--GRTRDEK--DGKKFRADWNAIKAVKNALRIPVLAN 86
L+++I+ A+ + G LL+V D G F A + V+ ++PV +
Sbjct: 244 TLEESIELARRFKAGGLDLLSVSVGFTIPDTNIPWGPAFMGPI-A-ERVRREAKLPVTSA 301
Query: 87 GNVRHMEDVQKCLEETGCEGVLSAESLLENPAL 119
+ + L+ + V + L +P
Sbjct: 302 WGFGTPQLAEAALQANQLDLVSVGRAHLADPHW 334
>3tdn_A FLR symmetric alpha-beta TIM barrel; symmetric superfold, de novo
protein; 1.40A {Synthetic construct} PDB: 3og3_A 3tdm_A
Length = 247
Score = 37.5 bits (88), Expect = 0.002
Identities = 23/88 (26%), Positives = 38/88 (43%), Gaps = 8/88 (9%)
Query: 34 DTIKYAKMLED--AGCSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRH 91
+ +E AG LL T ++DG K D I+ V+ +P++A+G
Sbjct: 157 LLRDWVVEVEKRGAGEILL-----TSIDRDGTKSGYDTEMIRFVRPLTTLPIIASGGAGK 211
Query: 92 MEDVQKCLEETGCEGVLSAESLLENPAL 119
ME + G + V + +ENP+L
Sbjct: 212 MEHFLEAFLR-GADKVSINTAAVENPSL 238
>2nv1_A Pyridoxal biosynthesis lyase PDXS; (beta/alpha)8-barrel, synthase;
2.08A {Bacillus subtilis} PDB: 2nv2_A* 1znn_A
Length = 305
Score = 35.9 bits (82), Expect = 0.007
Identities = 26/92 (28%), Positives = 44/92 (47%), Gaps = 6/92 (6%)
Query: 35 TIKYAKMLEDAG-CSLLAVHGRTRD-EKDGKKFR-ADWNAIKAVKNALRIPVLANGNVRH 91
+ AK+ E+AG +++A+ D G R AD ++ V NA+ IPV+A + H
Sbjct: 30 NAEQAKIAEEAGAVAVMALERVPADIRAAGGVARMADPTIVEEVMNAVSIPVMAKARIGH 89
Query: 92 MEDVQKCLEETGCEGVLSAESLLENPALFAGF 123
+ + + LE G + + ES + PA
Sbjct: 90 IVEAR-VLEAMGVDYI--DESEVLTPADEEFH 118
>1yxy_A Putative N-acetylmannosamine-6-phosphate 2-epimer; structural
genomics, epimerase, PSI, structure initiative; 1.60A
{Streptococcus pyogenes} SCOP: c.1.2.5
Length = 234
Score = 34.5 bits (79), Expect = 0.015
Identities = 17/76 (22%), Positives = 28/76 (36%), Gaps = 6/76 (7%)
Query: 34 DTIKYAKMLEDAGCSLLAV--HGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGNVRH 91
T + AG + G T + D I+A+ A I V+A G +
Sbjct: 141 STFDEGLVAHQAGIDFVGTTLSGYTPYSRQEAG--PDVALIEALCKA-GIAVIAEGKIHS 197
Query: 92 MEDVQKCLEETGCEGV 107
E+ +K + G G+
Sbjct: 198 PEEAKKIN-DLGVAGI 212
>3kru_A NADH:flavin oxidoreductase/NADH oxidase; homotetramer, dimer of
dimers, TIM barrel, thermophilic, OLD enzyme; HET: FMN;
1.60A {Thermoanaerobacter pseudethanolicus AT} PDB:
3krz_A*
Length = 343
Score = 33.7 bits (78), Expect = 0.036
Identities = 18/90 (20%), Positives = 34/90 (37%), Gaps = 6/90 (6%)
Query: 31 NLQDTIKYAKMLEDAGCSLLAV-HGRTRDEK--DGKKFRADWNAIKAVKNALRIPVLANG 87
N+ ++Y M++ L+ V G + ++ + A + +K I A G
Sbjct: 228 NIDMMVEYINMIK-DKVDLIDVSSGGLLNVDINLYPGYQVKY-A-ETIKKRCNIKTSAVG 284
Query: 88 NVRHMEDVQKCLEETGCEGVLSAESLLENP 117
+ E ++ L + V LL NP
Sbjct: 285 LITTQELAEEILSNERADLVALGRELLRNP 314
>3cwo_X Beta/alpha-barrel protein based on 1THF and 1TMY; XRAY, CHEY, HISF,
half barrel, de novo protein; 3.10A {Thermotoga
maritima} PDB: 2lle_A
Length = 237
Score = 33.3 bits (77), Expect = 0.048
Identities = 19/82 (23%), Positives = 33/82 (40%), Gaps = 14/82 (17%)
Query: 34 DTIKYAKMLED--AGCSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLAN---GN 88
+ +E AG LL T ++DG K D I+ V+ +P++A+ G
Sbjct: 131 LLRDWVVEVEKRGAGEILL-----TSIDRDGTKSGYDTEMIRFVRPLTTLPIIASGGAGK 185
Query: 89 VRHMEDVQKCLEETGCEGVLSA 110
+ H + G + L+A
Sbjct: 186 MEHFLEAFL----AGADAALAA 203
>3l5a_A NADH/flavin oxidoreductase/NADH oxidase; OLD yellow enzyme family,
OYE-like FMN-binding domain, TIM B oxidoreductase; HET:
PGE; 1.65A {Staphylococcus aureus}
Length = 419
Score = 33.4 bits (77), Expect = 0.049
Identities = 12/78 (15%), Positives = 25/78 (32%), Gaps = 7/78 (8%)
Query: 31 NLQDTIKYAKMLEDA-GCSLLAV----HGRTRDEKDGKKFRADWNAIKAVKNAL--RIPV 83
+ + + + D LA+ ++ + V L RIP+
Sbjct: 262 TIDEFNQLIDWVMDVSNIQYLAIASWGRHIYQNTSRTPGDHFGRPVNQIVYEHLAGRIPL 321
Query: 84 LANGNVRHMEDVQKCLEE 101
+A+G + E L+
Sbjct: 322 IASGGINSPESALDALQH 339
>1h5y_A HISF; histidine biosynthesis, TIM-barrel; 2.0A {Pyrobaculum
aerophilum} SCOP: c.1.2.1
Length = 253
Score = 32.8 bits (76), Expect = 0.053
Identities = 27/82 (32%), Positives = 42/82 (51%), Gaps = 14/82 (17%)
Query: 34 DTIKYAKMLED--AGCSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANG---N 88
D +K+AK +E+ AG LL T ++DG D I+ V +++RIPV+A+G
Sbjct: 155 DAVKWAKEVEELGAGEILL-----TSIDRDGTGLGYDVELIRRVADSVRIPVIASGGAGR 209
Query: 89 VRHMEDVQKCLEETGCEGVLSA 110
V H + G + VL+A
Sbjct: 210 VEHFYEAAA----AGADAVLAA 227
>3vkj_A Isopentenyl-diphosphate delta-isomerase; type 2 isopentenyl
diphosphate isomerase; HET: FNR; 1.70A {Sulfolobus
shibatae} PDB: 2zrv_A* 2zrw_A* 2zrx_A* 2zry_A* 2zrz_A*
3b03_A* 3b04_A* 3b05_A* 3b06_A* 2zru_A*
Length = 368
Score = 33.3 bits (76), Expect = 0.055
Identities = 24/127 (18%), Positives = 46/127 (36%), Gaps = 26/127 (20%)
Query: 11 VEKLALNLNVPVSCKIRVFPNLQDTIKYAKMLEDAGCSLLAV--HGRT--------RDEK 60
+ ++ L+VP+ K +++ AK+L G G T RD +
Sbjct: 179 LRDISKELSVPIIVKESGNGI---SMETAKLLYSYGIKNFDTSGQGGTNWIAIEMIRDIR 235
Query: 61 DGKKFR------ADW-----NAIKAVKNALR-IPVLANGNVRHMEDVQKCLEETGCEGVL 108
G DW +I V+ ++ ++ +G +R D K + G +
Sbjct: 236 RGNWKAESAKNFLDWGVPTAASIMEVRYSVPDSFLVGSGGIRSGLDAAKAI-ALGADIAG 294
Query: 109 SAESLLE 115
A +L+
Sbjct: 295 MALPVLK 301
>2hjp_A Phosphonopyruvate hydrolase; phosporus-Ca cleavage, PEP
mutase/isocitrate lyase superfamily; HET: XYS PPR; 1.90A
{Variovorax SP} PDB: 2dua_A* 2hrw_A
Length = 290
Score = 33.0 bits (76), Expect = 0.059
Identities = 9/55 (16%), Positives = 22/55 (40%), Gaps = 8/55 (14%)
Query: 32 LQDTIKYAKMLEDAGCSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLAN 86
Q+ ++ + E+AG + +H R + + F W ++P++
Sbjct: 165 QQEAVRRGQAYEEAGADAILIHSRQKTPDEILAFVKSWPG--------KVPLVLV 211
>1thf_D HISF protein; thermophIle, TIM-barrel, histidine biosynthesis,
lyase, phosphate-binding sites; 1.45A {Thermotoga
maritima} SCOP: c.1.2.1 PDB: 2wjz_A 2a0n_A* 1gpw_A
1vh7_A 2rkx_A 3iio_A 3iip_A* 3iiv_A
Length = 253
Score = 32.8 bits (76), Expect = 0.068
Identities = 19/82 (23%), Positives = 33/82 (40%), Gaps = 14/82 (17%)
Query: 34 DTIKYAKMLED--AGCSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANG---N 88
+ +E AG LL T ++DG K D I+ V+ +P++A+G
Sbjct: 152 LLRDWVVEVEKRGAGEILL-----TSIDRDGTKSGYDTEMIRFVRPLTTLPIIASGGAGK 206
Query: 89 VRHMEDVQKCLEETGCEGVLSA 110
+ H + G + L+A
Sbjct: 207 MEHFLEAFL----AGADAALAA 224
>1ka9_F Imidazole glycerol phosphtate synthase; riken structural
genomics/proteomics initiative, RSGI, structural
genomics, transferase; 2.30A {Thermus thermophilus}
SCOP: c.1.2.1
Length = 252
Score = 32.4 bits (75), Expect = 0.072
Identities = 21/82 (25%), Positives = 36/82 (43%), Gaps = 14/82 (17%)
Query: 34 DTIKYAKMLED--AGCSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANG---N 88
+++A + AG LL T ++DG K D + V A+ +PV+A+G
Sbjct: 153 HAVEWAVKGVELGAGEILL-----TSMDRDGTKEGYDLRLTRMVAEAVGVPVIASGGAGR 207
Query: 89 VRHMEDVQKCLEETGCEGVLSA 110
+ H + + G E L+A
Sbjct: 208 MEHFLEAFQ----AGAEAALAA 225
>3jva_A Dipeptide epimerase; enolase superfamily, isomerase; 1.70A
{Enterococcus faecalis V583} PDB: 3jw7_A* 3jzu_A*
3k1g_A* 3kum_A*
Length = 354
Score = 32.6 bits (75), Expect = 0.075
Identities = 15/96 (15%), Positives = 35/96 (36%), Gaps = 22/96 (22%)
Query: 20 VPVSCKIRVFPN----LQDTIKYAKMLEDAGCSL----LAVHGRTRDEKDGKKFRADWNA 71
V K+R+ N +D +K + L D L + R D
Sbjct: 180 VGFDIKLRLDANQAWTPKDAVKAIQALADYQIELVEQPVK--------------RRDLEG 225
Query: 72 IKAVKNALRIPVLANGNVRHMEDVQKCLEETGCEGV 107
+K V + + ++A+ + +D + +++ + +
Sbjct: 226 LKYVTSQVNTTIMADESCFDAQDALELVKKGTVDVI 261
>1p0k_A Isopentenyl-diphosphate delta-isomerase; terpene biosynthesis,
dimethylallyl diphosphate, flavoprotein; 1.90A {Bacillus
subtilis} SCOP: c.1.4.1 PDB: 1p0n_A*
Length = 349
Score = 32.8 bits (75), Expect = 0.078
Identities = 20/105 (19%), Positives = 45/105 (42%), Gaps = 20/105 (19%)
Query: 11 VEKLALNLNVPVSCKIRVFPNLQDTIKYAKMLEDAGCSLLAV--HGRT--------RDEK 60
+E++ ++VPV K F + + A L +AG + + + +G T R ++
Sbjct: 170 IEQICSRVSVPVIVKEVGFGMSKAS---AGKLYEAGAAAVDIGGYGGTNFSKIENLRRQR 226
Query: 61 DGKKFRADW-----NAIKAVKNAL-RIPVLANGNVRHMEDVQKCL 99
F W ++ +++ ++A+G ++ DV K +
Sbjct: 227 QISFFN-SWGISTAASLAEIRSEFPASTMIASGGLQDALDVAKAI 270
>1i1q_B Anthranilate synthase component II; tryptophan biosynthesis, lyase;
HET: TRP; 1.90A {Salmonella typhimurium} SCOP: c.23.16.1
PDB: 1i7q_B 1i7s_B*
Length = 192
Score = 32.0 bits (74), Expect = 0.082
Identities = 13/35 (37%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 196 FLYNLVDRLRELGVRIPLYKKDADDAEILADDLAS 230
F +NL D+LR G + +Y+ A+ L D LA+
Sbjct: 12 FTWNLADQLRTNGHNVVIYRNHI-PAQTLIDRLAT 45
>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 = 31.8 bits (71), Expect = 0.089
Identities = 8/38 (21%), Positives = 15/38 (39%), Gaps = 16/38 (42%)
Query: 59 EKDGKKFRADWNAIKAVKNALRI------PVLA-NGNV 89
EK A+K ++ +L++ P LA +
Sbjct: 18 EK---------QALKKLQASLKLYADDSAPALAIKATM 46
Score = 28.4 bits (62), Expect = 1.2
Identities = 10/23 (43%), Positives = 13/23 (56%), Gaps = 4/23 (17%)
Query: 204 LRELGVRIPLYKKDADD-AEILA 225
L++L + LY ADD A LA
Sbjct: 22 LKKLQASLKLY---ADDSAPALA 41
>2w6r_A Imidazole glycerol phosphate synthase subunit HISF; lyase, fusion
protein, cobalamin, precorrin, novel fold, VIT; 2.10A
{Thermotoga maritima}
Length = 266
Score = 32.2 bits (74), Expect = 0.092
Identities = 19/82 (23%), Positives = 33/82 (40%), Gaps = 14/82 (17%)
Query: 34 DTIKYAKMLED--AGCSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLAN---GN 88
+ +E AG LL T ++DG K D I+ V+ +P++A+ G
Sbjct: 157 LLRDWVVEVEKRGAGEILL-----TSIDRDGTKSGYDTEMIRFVRPLTTLPIIASGGAGK 211
Query: 89 VRHMEDVQKCLEETGCEGVLSA 110
+ H + G + L+A
Sbjct: 212 MEHFLEAFL----AGADAALAA 229
>3q45_A Mandelate racemase/muconate lactonizing enzyme FA possible
chloromuconate cycloisomerase...; (beta/alpha)8-barrel;
3.00A {Cytophaga hutchinsonii} PDB: 3q4d_A
Length = 368
Score = 31.5 bits (72), Expect = 0.20
Identities = 15/96 (15%), Positives = 37/96 (38%), Gaps = 22/96 (22%)
Query: 20 VPVSCKIRVFPN----LQDTIKYAKMLEDAGCSL----LAVHGRTRDEKDGKKFRADWNA 71
S +R+ N ++ I+ +LE ++ R + A
Sbjct: 181 AGDSITLRIDANQGWSVETAIETLTLLEPYNIQHCEEPVS--------------RNLYTA 226
Query: 72 IKAVKNALRIPVLANGNVRHMEDVQKCLEETGCEGV 107
+ ++ A RIP++A+ + + D ++ ++ C+
Sbjct: 227 LPKIRQACRIPIMADESCCNSFDAERLIQIQACDSF 262
>3k30_A Histamine dehydrogenase; 6-S-cysteinyl-FMN, ADP binding site,
oxidoreductase; HET: FMN ADP; 2.70A {Pimelobacter
simplex}
Length = 690
Score = 31.5 bits (72), Expect = 0.23
Identities = 9/77 (11%), Positives = 25/77 (32%), Gaps = 11/77 (14%)
Query: 32 LQDTIKYAKMLEDAGCSLLAVHGR-------TRDEKDGKKFRADWNAIKAVKNALRIPVL 84
+D + L + G +R +G + ++ + +K PV+
Sbjct: 243 REDIEGVLRELGELPDLWDFAMGSWEGDSVTSRFAPEG--RQEEF--VAGLKKLTTKPVV 298
Query: 85 ANGNVRHMEDVQKCLEE 101
G + + + ++
Sbjct: 299 GVGRFTSPDAMVRQIKA 315
>1vcf_A Isopentenyl-diphosphate delta-isomerase; TIM barrel, structural
genomics, riken structural genomics/P initiative, RSGI;
HET: FMN; 2.60A {Thermus thermophilus} SCOP: c.1.4.1
PDB: 1vcg_A* 3dh7_A*
Length = 332
Score = 31.1 bits (70), Expect = 0.26
Identities = 21/94 (22%), Positives = 32/94 (34%), Gaps = 18/94 (19%)
Query: 39 AKMLEDAGCSLLAV--HG---------RTRDEKDGKKFRADWN-----AIKAVKNAL-RI 81
A L D + + V G R + + AI V+ L +
Sbjct: 198 ALALRDLPLAAVDVAGAGGTSWARVEEWVRFGEVRHPELCEIGIPTARAILEVREVLPHL 257
Query: 82 PVLANGNVRHMEDVQKCLEETGCEGVLSAESLLE 115
P++A+G V D K L G + + A LL
Sbjct: 258 PLVASGGVYTGTDGAKAL-ALGADLLAVARPLLR 290
>3sr7_A Isopentenyl-diphosphate delta-isomerase; isopentenyl pyrophosphate
isomerase, TIM-barrel; 2.04A {Streptococcus mutans}
Length = 365
Score = 30.9 bits (70), Expect = 0.32
Identities = 21/109 (19%), Positives = 38/109 (34%), Gaps = 21/109 (19%)
Query: 7 VKSLVEKLALNLNVPVSCKIRVFPNLQDTIKYAKMLEDAGCS--LLAVHGRT-------- 56
K + A L +P K F +K + D G ++ G T
Sbjct: 194 WKKHLSDYAKKLQLPFILKEVGFG---MDVKTIQTAIDLGVKTVDISGRGGTSFAYIENR 250
Query: 57 RDEKDGKKFRADW-----NAIKAVKNAL-RIPVLANGNVRHMEDVQKCL 99
R + + W + + + ++ +LA+G +RH D+ K L
Sbjct: 251 RGGN--RSYLNQWGQTTAQVLLNAQPLMDKVEILASGGIRHPLDIIKAL 297
>1s2w_A Phosphoenolpyruvate phosphomutase; phosphonopyruvate, phosphonate
biosynthesis pathway, isomera; 1.69A {Mytilus edulis}
SCOP: c.1.12.7 PDB: 1m1b_A 1s2t_A 1s2v_A 1pym_A 1s2u_A
Length = 295
Score = 30.3 bits (69), Expect = 0.42
Identities = 13/55 (23%), Positives = 23/55 (41%), Gaps = 8/55 (14%)
Query: 32 LQDTIKYAKMLEDAGCSLLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLAN 86
L + +K A+ +AG + +H + D D + F WN + PV+
Sbjct: 169 LDEALKRAEAYRNAGADAILMHSKKADPSDIEAFMKAWNN--------QGPVVIV 215
>2zad_A Muconate cycloisomerase; muconate lactonizing enzyme (MLE), TM0006,
struct genomics, NPPSFA; HET: 1PE; 1.60A {Thermotoga
maritima} PDB: 3deq_A 3der_A* 3des_A* 3dfy_A
Length = 345
Score = 30.3 bits (69), Expect = 0.51
Identities = 17/92 (18%), Positives = 33/92 (35%), Gaps = 20/92 (21%)
Query: 24 CKIRVFPN----LQDTIKYAKMLEDAGCSLLAV----HGRTRDEKDGKKFRADWNAIKAV 75
K V N ++ +++A+ + G + R D +K V
Sbjct: 183 AKYIVDANMGYTQKEAVEFARAVYQKGIDIAVYEQPVR------------REDIEGLKFV 230
Query: 76 KNALRIPVLANGNVRHMEDVQKCLEETGCEGV 107
+ PV A+ + R DV + ++E + V
Sbjct: 231 RFHSPFPVAADESARTKFDVMRLVKEEAVDYV 262
>3no5_A Uncharacterized protein; PFAM DUF849 domain containing protein,
structural genomics, center for structural genomics,
JCSG; HET: MSE; 1.90A {Ralstonia eutropha}
Length = 275
Score = 30.0 bits (67), Expect = 0.59
Identities = 17/100 (17%), Positives = 35/100 (35%), Gaps = 11/100 (11%)
Query: 17 NLNVPVSCKIRVFPNLQDTIKYAKMLEDAGCSLLAVHGRTRDEK---DGKKFRADWNAIK 73
N VP++ + + ++ + +AG +L+ +H R DE + +F I+
Sbjct: 22 NPAVPIT--------VSEQVESTQAAFEAGATLVHLHVRNDDETPTSNPDRFALVLEGIR 73
Query: 74 AVKNALRIPVLANGNVRHMEDVQKCLEETGCEGVLSAESL 113
+ V G + L L+ S+
Sbjct: 74 KHAPGMITQVSTGGRSGAGNERGAMLSLRPDMASLATGSV 113
>3kts_A Glycerol uptake operon antiterminator regulatory; structural
genomics, PSI-2, protein structur initiative; HET: UNL;
2.75A {Listeria monocytogenes str}
Length = 192
Score = 29.3 bits (66), Expect = 0.69
Identities = 8/29 (27%), Positives = 15/29 (51%)
Query: 72 IKAVKNALRIPVLANGNVRHMEDVQKCLE 100
++ + L IPV+A G + E V + +
Sbjct: 142 VQKMTQKLHIPVIAGGLIETSEQVNQVIA 170
>3b0p_A TRNA-dihydrouridine synthase; TIM barrel, oxidoreductase; HET: FMN;
1.70A {Thermus thermophilus} PDB: 3b0u_X* 3b0v_C*
Length = 350
Score = 29.5 bits (67), Expect = 0.89
Identities = 13/62 (20%), Positives = 31/62 (50%), Gaps = 10/62 (16%)
Query: 1 MDNLPLVKSLVEKLALNLNVPVSCKIRV-------FPNLQDTIKYAKMLEDAGCSLLAVH 53
+ +L V+ +++ + + VPV+ K+R+ + L ++ + + +AG + VH
Sbjct: 108 LLDLARVREILKAMGEAVRVPVTVKMRLGLEGKETYRGLAQSV---EAMAEAGVKVFVVH 164
Query: 54 GR 55
R
Sbjct: 165 AR 166
>3u9i_A Mandelate racemase/muconate lactonizing enzyme, C domain protein;
structural genomics, PSI-biology; 2.90A {Roseiflexus SP}
Length = 393
Score = 29.2 bits (66), Expect = 1.2
Identities = 13/94 (13%), Positives = 28/94 (29%), Gaps = 24/94 (25%)
Query: 24 CKIRVFPN----LQDTIKYAKMLEDAGCSL------LAVHGRTRDEKDGKKFRADWNAIK 73
++ + N D ++ ML G +A D ++
Sbjct: 218 ARLILDGNCGYTAPDALRLLDMLGVHGIVPALFEQPVAKD--------------DEEGLR 263
Query: 74 AVKNALRIPVLANGNVRHMEDVQKCLEETGCEGV 107
+ R+PV A+ +V D + + +
Sbjct: 264 RLTATRRVPVAADESVASATDAARLARNAAVDVL 297
>3ro6_B Putative chloromuconate cycloisomerase; TIM barrel; 2.20A
{Methylococcus capsulatus} PDB: 3rit_A
Length = 356
Score = 28.8 bits (65), Expect = 1.3
Identities = 11/98 (11%), Positives = 31/98 (31%), Gaps = 22/98 (22%)
Query: 20 VPVSCKIRVFPN----LQDTIKYAKMLEDAGCSL----LAVHGRTRDEKDGKKFRADWNA 71
+ +RV PN ++ +++++ G +
Sbjct: 181 LAGRAVVRVDPNQSYDRDGLLRLDRLVQELGIEFIEQPFPAG--------------RTDW 226
Query: 72 IKAVKNALRIPVLANGNVRHMEDVQKCLEETGCEGVLS 109
++A+ A+R + A+ ++ D G+ +
Sbjct: 227 LRALPKAIRRRIAADESLLGPADAFALAAPPAACGIFN 264
>1tkk_A Similar to chloromuconate cycloisomerase; epimerase, enolase super
family,; 2.10A {Bacillus subtilis} SCOP: c.1.11.2
d.54.1.1 PDB: 1jpm_A
Length = 366
Score = 28.8 bits (65), Expect = 1.6
Identities = 14/81 (17%), Positives = 31/81 (38%), Gaps = 16/81 (19%)
Query: 31 NLQDTIKYAKMLEDAGCSLLA----VHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLAN 86
++ + + +EDAG + VH + D +K V +A P++A+
Sbjct: 197 RPKEAVTAIRKMEDAGLGIELVEQPVH------------KDDLAGLKKVTDATDTPIMAD 244
Query: 87 GNVRHMEDVQKCLEETGCEGV 107
+V + L+ + +
Sbjct: 245 ESVFTPRQAFEVLQTRSADLI 265
>1dp7_P MHC class II transcription factor HRFX1; winged helix, protein- DNA
conovel mode of DNA recognition, transcription/DNA
complex; HET: DNA BRU; 1.50A {Synthetic} SCOP: a.4.5.20
Length = 76
Score = 26.8 bits (59), Expect = 2.0
Identities = 7/33 (21%), Positives = 18/33 (54%)
Query: 125 TAEWIVGSEEISKDGNLDQADLLVEYLKLCEKY 157
T +W++ + E ++ +L ++ L YL ++
Sbjct: 1 TVQWLLDNYETAEGVSLPRSTLYNHYLLHSQEQ 33
>2agk_A 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino) methylideneamino]
imidazole-4-carboxamide...; TIM alpha/beta barrel; HET:
CIT; 1.30A {Saccharomyces cerevisiae}
Length = 260
Score = 27.9 bits (62), Expect = 2.7
Identities = 7/79 (8%), Positives = 25/79 (31%), Gaps = 10/79 (12%)
Query: 34 DTIKYAKMLEDAGCSLLAVHGRTRD-EKDGKKFRADWNAIKAVKNALR----IPVLANGN 88
+ + +H + +G D + + + + ++ G
Sbjct: 158 ELNADTFRELRKYTNEFLIH----AADVEGLCGGIDELLVSKLFEWTKDYDDLKIVYAGG 213
Query: 89 VRHMEDVQKCLEETGCEGV 107
+ ++D++ ++E V
Sbjct: 214 AKSVDDLKL-VDELSHGKV 231
>3ik4_A Mandelate racemase/muconate lactonizing protein; structural
genomics, enolase, epimerase, PSI-2, protein STRU
initiative; 2.10A {Herpetosiphon aurantiacus atcc 23779}
Length = 365
Score = 28.0 bits (63), Expect = 2.9
Identities = 12/92 (13%), Positives = 25/92 (27%), Gaps = 20/92 (21%)
Query: 24 CKIRVFPN----LQDTIKYAKMLEDAGCSLLAV----HGRTRDEKDGKKFRADWNAIKAV 75
+ V N ++ + + + ++ R DW + V
Sbjct: 188 APLIVDGNCGYDVERALAFCAACKAESIPMVLFEQPLP------------REDWAGMAQV 235
Query: 76 KNALRIPVLANGNVRHMEDVQKCLEETGCEGV 107
V A+ + R DV + E +
Sbjct: 236 TAQSGFAVAADESARSAHDVLRIAREGTASVI 267
>1zlp_A PSR132, petal death protein; TIM-barrel, helix
swapping,2-ethyl-3-methylmalate lyase, 2-P methylmalate
lyase, lyase/PEP mutase superfamily; 2.70A {Dianthus
caryophyllus}
Length = 318
Score = 27.7 bits (62), Expect = 3.0
Identities = 12/56 (21%), Positives = 21/56 (37%), Gaps = 13/56 (23%)
Query: 32 LQDTIKYAKMLEDAGCSLLAVHG-RTRDEKDGKKFRADWNAIKAVKNALRIPVLAN 86
L++ I+ A + ++AG V DE +K V + +AN
Sbjct: 188 LEEGIRRANLYKEAGADATFVEAPANVDE------------LKEVSAKTKGLRIAN 231
>3r0u_A Enzyme of enolase superfamily; structural genomics, putative
epimerase, PSI-biolog YORK structural genomics research
consortium; HET: MSE TAR; 1.90A {Francisella
philomiragia subsp} PDB: 3px5_A* 3r0k_A* 3r10_A 3r11_A
3r1z_A*
Length = 379
Score = 27.7 bits (62), Expect = 3.2
Identities = 10/42 (23%), Positives = 21/42 (50%)
Query: 66 RADWNAIKAVKNALRIPVLANGNVRHMEDVQKCLEETGCEGV 107
D A+ + IPV+A+ +V +D ++ ++E C +
Sbjct: 225 YYDIKAMAEITKFSNIPVVADESVFDAKDAERVIDEQACNMI 266
>3ih1_A Methylisocitrate lyase; alpha-beta structure, TIM-barrel, center
for structural GENO infectious diseases, csgid; 2.00A
{Bacillus anthracis str} PDB: 3kz2_A
Length = 305
Score = 27.7 bits (62), Expect = 3.6
Identities = 10/56 (17%), Positives = 20/56 (35%), Gaps = 13/56 (23%)
Query: 32 LQDTIKYAKMLEDAGCSLLAVHG-RTRDEKDGKKFRADWNAIKAVKNALRIPVLAN 86
L + I+ A AG + ++ +E + + + P+LAN
Sbjct: 174 LDEAIERANAYVKAGADAIFPEALQSEEE------------FRLFNSKVNAPLLAN 217
>3qld_A Mandelate racemase/muconate lactonizing protein; structural
genomics, PSI-2, isomerase; HET: MSE; 1.85A
{Alicyclobacillus acidocaldarius LAA1}
Length = 388
Score = 27.7 bits (62), Expect = 3.7
Identities = 8/42 (19%), Positives = 19/42 (45%)
Query: 66 RADWNAIKAVKNALRIPVLANGNVRHMEDVQKCLEETGCEGV 107
DW + ++ +LR PV + +VR + +++ +
Sbjct: 226 EDDWFDLAKLQASLRTPVCLDESVRSVRELKLTARLGAARVL 267
>1xg4_A Probable methylisocitrate lyase; 2-methylisocitrate lyase/inhibitor
complex, isocitrate lyase superfamily; HET: ICT; 1.60A
{Escherichia coli} PDB: 1xg3_A* 1mum_A 1oqf_A 1ujq_A
1o5q_A
Length = 295
Score = 27.3 bits (61), Expect = 3.9
Identities = 11/56 (19%), Positives = 21/56 (37%), Gaps = 13/56 (23%)
Query: 32 LQDTIKYAKMLEDAGCSLLAVHG-RTRDEKDGKKFRADWNAIKAVKNALRIPVLAN 86
L I+ A+ +AG +L + +A+++P+LAN
Sbjct: 166 LDAAIERAQAYVEAGAEMLFPEAITELAM------------YRQFADAVQVPILAN 209
>3i5p_A Nucleoporin NUP170; helical stack, membrane, mRNA transport,
nuclear pore complex, nucleus, phosphoprotein, protein
transport; 3.20A {Saccharomyces cerevisiae}
Length = 525
Score = 27.4 bits (60), Expect = 4.1
Identities = 8/52 (15%), Positives = 17/52 (32%), Gaps = 3/52 (5%)
Query: 126 AEWIVGSEEISKDGNLDQADLLVEYLKLCEKYPVPWRMIRSHVHKLLGEWFR 177
+ IV I + + +L E + + L+ EW++
Sbjct: 432 SGSIV---SIFITAGVSFNKMYYILKELIETSDSDNSVFNKEMTWLIHEWYK 480
>2ps2_A Putative mandelate racemase/muconate lactonizing enzyme; structural
genomics, NYSGXRC, target 9440A, enolase superfamily,
PSI-2; 1.80A {Aspergillus oryzae RIB40}
Length = 371
Score = 27.2 bits (61), Expect = 4.5
Identities = 10/79 (12%), Positives = 27/79 (34%), Gaps = 16/79 (20%)
Query: 31 NLQDTIKYAKMLEDAGCSLL--AVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGN 88
+++ ++ ++L L A W +++ IP++ +
Sbjct: 202 SVETALRLLRLLPHGLDFALEAPC--------------ATWRECISLRRKTDIPIIYDEL 247
Query: 89 VRHMEDVQKCLEETGCEGV 107
+ + K L + EG+
Sbjct: 248 ATNEMSIVKILADDAAEGI 266
>3s5s_A Mandelate racemase/muconate lactonizing enzyme FA protein;
PSI-biology, structural genomics, NEW YORK structural
genomi research consortium; 2.40A {Sorangium cellulosum}
Length = 389
Score = 27.3 bits (61), Expect = 4.7
Identities = 14/92 (15%), Positives = 26/92 (28%), Gaps = 20/92 (21%)
Query: 24 CKIRVFPN----LQDTIKYAKMLEDAGCSLLAV----HGRTRDEKDGKKFRADWNAIKAV 75
+ + N + + G + + R DW+ +K V
Sbjct: 189 ASLILDGNGGLTAGEALALVAHARRLGADVALLEQPVP------------RDDWDGMKEV 236
Query: 76 KNALRIPVLANGNVRHMEDVQKCLEETGCEGV 107
+ V A+ + EDV + E V
Sbjct: 237 TRRAGVDVAADESAASAEDVLRVAAERAATVV 268
>3eoo_A Methylisocitrate lyase; seattle structural genomics center for
infectious disease, ssgcid; 2.90A {Burkholderia
pseudomallei 1655}
Length = 298
Score = 27.3 bits (61), Expect = 4.9
Identities = 12/56 (21%), Positives = 24/56 (42%), Gaps = 13/56 (23%)
Query: 32 LQDTIKYAKMLEDAGCSLLAVHG-RTRDEKDGKKFRADWNAIKAVKNALRIPVLAN 86
+ I+ A +AG ++ +T D+ + K A+++P+LAN
Sbjct: 170 IDAAIERAIAYVEAGADMIFPEAMKTLDD------------YRRFKEAVKVPILAN 213
>1wuf_A Hypothetical protein LIN2664; structural genomics, unknown
function, nysgxrc target T2186, superfamily, protein
structure initiative, PSI; 2.90A {Listeria innocua}
SCOP: c.1.11.2 d.54.1.1
Length = 393
Score = 27.3 bits (61), Expect = 5.1
Identities = 7/42 (16%), Positives = 19/42 (45%)
Query: 66 RADWNAIKAVKNALRIPVLANGNVRHMEDVQKCLEETGCEGV 107
D+ ++ L+ + + N+R ++DV++ C +
Sbjct: 238 TKDFVDHAWLQKQLKTRICLDENIRSVKDVEQAHSIGSCRAI 279
>4e8g_A Enolase, mandelate racemase/muconate lactonizing enzyme, N domain
protein; putative racemase, nysgrc, structural genomics,
PSI-biology; 2.00A {Paracoccus denitrificans}
Length = 391
Score = 26.9 bits (60), Expect = 5.4
Identities = 5/41 (12%), Positives = 16/41 (39%)
Query: 67 ADWNAIKAVKNALRIPVLANGNVRHMEDVQKCLEETGCEGV 107
I A++ ++ + + + + V + + C+G
Sbjct: 245 NTLEEIAAIRGRVQHGIYLDESGEDLSTVIRAAGQGLCDGF 285
>1vkf_A Glycerol uptake operon antiterminator-related Pro; struc genomics,
joint center for structural genomics, JCSG, prote
structure initiative; HET: CIT; 1.65A {Thermotoga
maritima} SCOP: c.1.29.1
Length = 188
Score = 26.5 bits (59), Expect = 5.4
Identities = 8/30 (26%), Positives = 14/30 (46%)
Query: 71 AIKAVKNALRIPVLANGNVRHMEDVQKCLE 100
A K + V+A G V E+ ++ L+
Sbjct: 140 APKVARKIPGRTVIAAGLVETEEEAREILK 169
>3mwc_A Mandelate racemase/muconate lactonizing protein; enolase,
structural genomics, protein structure initiative,
nysgrc; 1.80A {Kosmotoga olearia}
Length = 400
Score = 27.0 bits (60), Expect = 5.5
Identities = 2/42 (4%), Positives = 11/42 (26%)
Query: 66 RADWNAIKAVKNALRIPVLANGNVRHMEDVQKCLEETGCEGV 107
+K + + P+ + ++ + +
Sbjct: 241 YEALLDLKELGERIETPICLDESLISSRVAEFVAKLGISNIW 282
>2pmq_A Mandelate racemase/muconate lactonizing enzyme; structural
genomics, isomerase, PSI-2; HET: MSE; 1.72A {Roseovarius
SP}
Length = 377
Score = 26.9 bits (60), Expect = 5.7
Identities = 3/41 (7%), Positives = 14/41 (34%)
Query: 67 ADWNAIKAVKNALRIPVLANGNVRHMEDVQKCLEETGCEGV 107
+ ++A++ + + + + V + +G
Sbjct: 224 NSFEDLEAIRPLCHHALYMDEDGTSLNTVITAAATSLVDGF 264
>3fv9_G Mandelate racemase/muconate lactonizing enzyme; structural
genomics, mandelate racemase/muconatelactonizing
hydrolase, PSI-2; 1.90A {Roseovarius nubinhibens ism}
PDB: 2pce_A
Length = 386
Score = 26.9 bits (60), Expect = 5.7
Identities = 9/41 (21%), Positives = 21/41 (51%)
Query: 67 ADWNAIKAVKNALRIPVLANGNVRHMEDVQKCLEETGCEGV 107
A W K+++ +P+L + ++ D+ + + C+GV
Sbjct: 230 ASWAETKSLRARCALPLLLDELIQTETDLIAAIRDDLCDGV 270
>3eez_A Putative mandelate racemase/muconate lactonizing enzyme; structural
genomics, unknown function, PSI-2, protein structure
initiative; 2.80A {Silicibacter pomeroyi}
Length = 378
Score = 26.5 bits (59), Expect = 7.1
Identities = 6/41 (14%), Positives = 15/41 (36%)
Query: 67 ADWNAIKAVKNALRIPVLANGNVRHMEDVQKCLEETGCEGV 107
+ I A++ PV + + ++D + + E
Sbjct: 224 ETLDDIAAIRPLHSAPVSVDECLVTLQDAARVARDGLAEVF 264
>2o8r_A Polyphosphate kinase; structural genomics, protein structure
initiative, PSI, nysgrc, NEW YORK structural genomics
research consortium; HET: MSE; 2.70A {Porphyromonas
gingivalis} SCOP: a.7.15.1 d.322.1.2 d.136.1.4 d.136.1.4
Length = 705
Score = 26.7 bits (60), Expect = 8.2
Identities = 5/41 (12%), Positives = 16/41 (39%), Gaps = 10/41 (24%)
Query: 36 IKYAKMLEDAGCSL------LAVHGR----TRDEKDGKKFR 66
++ ++ + +G + L VH + G++ +
Sbjct: 416 LRLSERMRRSGIRIVYSMPGLKVHAKTALILYHTPAGERPQ 456
>3ihg_A RDME; flavoenzyme, anthracycline, polyketide biosynthesis,
merohedral twinning, enzyme mechanism, hydroxylase,
flavoprotein; HET: FAD VAK; 2.49A {Streptomyces
purpurascens}
Length = 535
Score = 26.6 bits (59), Expect = 8.5
Identities = 12/81 (14%), Positives = 23/81 (28%), Gaps = 10/81 (12%)
Query: 141 LDQADLLVEYLKLCEKYPVPWRMIRSHVHKLLGEWFRIQPGVREDLNAQNR-LTFEFLYN 199
L + E ++ + + + GE R +D+ A T
Sbjct: 57 LRIGGVADEVVRADDIRGTQGDFVIRLAESVRGEILRTVSESFDDMVAATEPCTPAGWAM 116
Query: 200 ---------LVDRLRELGVRI 211
L+ + R+ G I
Sbjct: 117 LSQDKLEPILLAQARKHGGAI 137
>2zc8_A N-acylamino acid racemase; octamer, TIM beta/alpha-barrel,
metal-binding, metal binding; 1.95A {Thermus
thermophilus}
Length = 369
Score = 26.5 bits (59), Expect = 8.5
Identities = 6/42 (14%), Positives = 14/42 (33%)
Query: 66 RADWNAIKAVKNALRIPVLANGNVRHMEDVQKCLEETGCEGV 107
D ++ L P+ + ++ E +K +E
Sbjct: 218 YDDLLDHAKLQRELSTPICLDESLTGAEKARKAIELGAGRVF 259
>1wv2_A Thiazole moeity, thiazole biosynthesis protein THIG; structural
genomics, protein structure initiative, PSI; 2.90A
{Pseudomonas aeruginosa} SCOP: c.1.31.1
Length = 265
Score = 26.4 bits (59), Expect = 9.0
Identities = 25/106 (23%), Positives = 42/106 (39%), Gaps = 15/106 (14%)
Query: 28 VFPNLQDTIKYAKMLEDAGCS----LLAVHGRTRDEKDGKKFRADWNAIKAVKNALRIPV 83
V D A+ L + GC L + G G +N ++ + ++PV
Sbjct: 138 VMVYTSDDPIIARQLAEIGCIAVMPLAGLIG------SGLGICNPYN-LRIILEEAKVPV 190
Query: 84 LANGNVRHMEDVQKCLEETGCEGVL--SAESLLENPALFAG-FRTA 126
L + V D + E GCE VL +A + ++P + A + A
Sbjct: 191 LVDAGVGTASDAAIAM-ELGCEAVLMNTAIAHAKDPVMMAEAMKHA 235
>2p8b_A Mandelate racemase/muconate lactonizing enzyme family protein;
enolase superfamily, prediction of function; HET: NSK;
1.70A {Bacillus cereus atcc 14579} PDB: 2p88_A* 2p8c_A*
Length = 369
Score = 26.4 bits (59), Expect = 9.2
Identities = 8/79 (10%), Positives = 30/79 (37%), Gaps = 14/79 (17%)
Query: 31 NLQDTIKYAKMLEDAGCSLL--AVHGRTRDEKDGKKFRADWNAIKAVKNALRIPVLANGN 88
N +T+ + L + V D +A+ +++ +P++ +
Sbjct: 198 NSANTLTALRSLGHLNIDWIEQPVI------------ADDIDAMAHIRSKTDLPLMIDEG 245
Query: 89 VRHMEDVQKCLEETGCEGV 107
++ ++++ ++ + V
Sbjct: 246 LKSSREMRQIIKLEAADKV 264
>1qdl_B Protein (anthranilate synthase (TRPG-SUBUNIT)); tryptophan
biosynthesis, glutamine amidotransferase, allosteric
interaction, lyase; 2.50A {Sulfolobus solfataricus}
SCOP: c.23.16.1
Length = 195
Score = 25.9 bits (58), Expect = 9.6
Identities = 8/31 (25%), Positives = 13/31 (41%), Gaps = 1/31 (3%)
Query: 196 FLYNLVDRLRELGVRIPLYKKDA-DDAEILA 225
F+YN+ + ELG + + D I
Sbjct: 13 FVYNIAQIVGELGSYPIVIRNDEISIKGIER 43
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.320 0.138 0.411
Gapped
Lambda K H
0.267 0.0733 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,651,988
Number of extensions: 219431
Number of successful extensions: 915
Number of sequences better than 10.0: 1
Number of HSP's gapped: 900
Number of HSP's successfully gapped: 95
Length of query: 230
Length of database: 6,701,793
Length adjustment: 90
Effective length of query: 140
Effective length of database: 4,188,903
Effective search space: 586446420
Effective search space used: 586446420
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (25.3 bits)