Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_010443520.1 G7G_RS0121375 thiamine pyrophosphate-binding protein
Query= curated2:O08353 (599 letters) >NCBI__GCF_000192475.1:WP_010443520.1 Length = 593 Score = 296 bits (758), Expect = 2e-84 Identities = 185/570 (32%), Positives = 292/570 (51%), Gaps = 44/570 (7%) Query: 4 AEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARASGK 63 AE ++ LE +V+ +FG G + AL S + + RHEQ A+HAAD YAR + K Sbjct: 12 AEHIVDFLERREVKHVFGLCGHTNIAVLAALAESPIDFVTVRHEQIASHAADAYARVTDK 71 Query: 64 VGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALG------L 117 V + PG TN TGVA A D PMV + G +PT G QE++ + Sbjct: 72 ASVVLSHLSPGLTNCATGVANAALDCIPMVVIAGDIPTHYYGKHPHQEVNLHADAAQWEI 131 Query: 118 FMPIVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPS-K 176 + P VK +++ + + EI AF +A++G+PGPV +++P +DI IPS Sbjct: 132 YRPFVKRAWRVDRADLMAEILEKAFHLAESGQPGPVLVNVP-------MDIFSEVIPSDS 184 Query: 177 VKLIGYNPTTIGHP----RQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNI 232 I N + P ++ ++ +A A+ P+ GGG+LL+ A+EEL + VE + + Sbjct: 185 FDRIRDNTRALKKPSIDDESAREIVEALAKAENPVAYVGGGILLAQASEELREFVEHMGL 244 Query: 233 PVCTTLMGKGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSF- 291 PV +LMGKG + ++HPL LGM G GT+ N +D + ++G RF + D S+ Sbjct: 245 PVAHSLMGKGALRDDHPLVLGMTGFWGTELVNQSCLNADYIFAVGTRFKE---ADCSSWY 301 Query: 292 ------ATNAKIIHIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENND 345 +K+IHIDI+P EIG+N ++ +V DAK L+ L+ + + + Sbjct: 302 PGYTFNIPGSKVIHIDIEPQEIGRNYPTEIGVVADAKAALRV----LNRVAREMYPDGFK 357 Query: 346 KENISQWIENVNS-LKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQ 404 + + Q I + + K ++ + P+ P++I+ + + + + IITTDVG Sbjct: 358 RPALEQKIADFRTDFKARNLEMAISSAFPMMPERILADTRKALPE-----DAIITTDVGW 412 Query: 405 NQMWMAHYFKTQTPRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQE 464 N+ + F TP S L+ GG TMGFG P AIGAK+A PD V+ + GDGGF N Sbjct: 413 NKNGVGQQFDILTPGSILTPGGFATMGFGPPGAIGAKLAAPDRVVLSLVGDGGFGQNPSM 472 Query: 465 LGTIAEYNIPVVICIFDNRTLGMVYQWQNLFYGKRQCSVNFGGA------PDFIKLAESY 518 L T E ++ ++ + +N G + Q YG + G A P + +A +Y Sbjct: 473 LATAVELDLGIIWLVMNNNAFGTIAGLQKAHYGLTYGTTFPGSAEAPANGPGYADIARAY 532 Query: 519 GIKARRIESPNEINEALKEAINCDEPYLLD 548 G + R+ + +E+ AL+ AI +P +LD Sbjct: 533 GAEGHRLSAADELLPALEAAIASGKPTVLD 562 Lambda K H 0.319 0.137 0.405 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 860 Number of extensions: 40 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 599 Length of database: 593 Length adjustment: 37 Effective length of query: 562 Effective length of database: 556 Effective search space: 312472 Effective search space used: 312472 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 (21.7 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory