Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate BPHYT_RS08835 BPHYT_RS08835 glyoxylate carboligase
Query= curated2:O08353 (599 letters) >FitnessBrowser__BFirm:BPHYT_RS08835 Length = 591 Score = 327 bits (837), Expect = 1e-93 Identities = 181/553 (32%), Positives = 310/553 (56%), Gaps = 33/553 (5%) Query: 1 MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHS-DLIHLLTRHEQAAAHAADGYAR 59 M +A + LE E ++ FG PG A+ PFY A+ + ++ H+L RH + A+H A+GY R Sbjct: 4 MRAVDAAVLVLEKEGIDTAFGVPGAAINPFYSAMRKAGNISHVLARHVEGASHMAEGYTR 63 Query: 60 AS-GKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLF 118 A G +GVCIGTSGP T+++TG+ +A +DS P++A+TGQ P + + FQ +D + Sbjct: 64 AQPGNIGVCIGTSGPAGTDMITGLYSAQADSIPILAITGQAPRARLYKEDFQAVDIESIA 123 Query: 119 MPIVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQ--ELELDIDKH-PIPS 175 P+ K +++ +P +F+ AF + ++GRPGPV +DLP DVQ E+E DID + P+P Sbjct: 124 KPVTKWAVTVREPALVPRVFQQAFHLMRSGRPGPVLVDLPIDVQLAEIEFDIDTYEPLPV 183 Query: 176 KVKLIGYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVC 235 Y P +QI+ A+ L+ ++ +P+I++GGGVL + A + L+ E + +PV Sbjct: 184 ------YKPKAT--RKQIEAALTLLNNSDKPLIVSGGGVLNAAAEDLLVTFAETIGVPVI 235 Query: 236 TTLMGKGCISENHPLALGMVGMHGT-KPANYCLSESDVLISIGCRFSDRITGDIKSFATN 294 TLM G I ++HPL GMVG+ + + N + SD ++ IG R+++R TG ++ + Sbjct: 236 PTLMSWGAIPDDHPLMAGMVGLQTSHRYGNATMLASDFVLGIGNRWANRHTGSVEVYTKG 295 Query: 295 AKIIHIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIE 354 K +H+DI+P +IG+ D+ IV DAK L+ ++ + K+ K ++ S W+ Sbjct: 296 RKFVHVDIEPTQIGRVFGPDLGIVSDAKAALELFVE-----VAKEWKAAGKLKDRSAWVA 350 Query: 355 NVNSLKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFK 414 + K++ +D++P+KPQ++ +E+ V ++T + +G +Q+ A + Sbjct: 351 DCQERKRTMHRKTHFDNVPMKPQRVYEEMNQV-----FGRDTCYVSTIGLSQIAGAQFLH 405 Query: 415 TQTPRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIP 474 R++++ G G +G+ P+A+G + A P ++ ++GD F +EL A++ +P Sbjct: 406 VYKARNWINCGQAGPLGWTIPAALGVRAADPQRPIVALSGDYDFQFMIEELAAGAQFKLP 465 Query: 475 VVICIFDNRTLGMVYQWQNLFYGKRQCSVNF---------GGAPDFIKLAESYGIKARRI 525 V + +N LG++ Q Q F + F G D + +AE G KA R+ Sbjct: 466 YVHVVVNNSYLGLIRQAQRAFDMDFCVQLGFENINAPEMNGYGVDHVAVAEGLGCKAIRV 525 Query: 526 ESPNEINEALKEA 538 P E+ AL +A Sbjct: 526 FKPEELKPALLKA 538 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: 780 Number of extensions: 40 Number of successful extensions: 7 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: 591 Length adjustment: 37 Effective length of query: 562 Effective length of database: 554 Effective search space: 311348 Effective search space used: 311348 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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