Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_012975773.1 AZL_RS17220 glyoxylate carboligase
Query= curated2:O08353 (599 letters) >NCBI__GCF_000010725.1:WP_012975773.1 Length = 589 Score = 345 bits (886), Expect = 2e-99 Identities = 186/554 (33%), Positives = 317/554 (57%), Gaps = 35/554 (6%) Query: 1 MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLI-HLLTRHEQAAAHAADGYAR 59 M AEA ++ LE E +++ FG PG A+ PFY A+ + H+L RH + A+H A+GY R Sbjct: 4 MTAAEAAVRVLEREGIDVCFGVPGAAINPFYAAMQRRGTMRHVLARHVEGASHMAEGYTR 63 Query: 60 A-SGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLF 118 A +G +GVCIGTSGP T+++TG+ +A +DS P++ +TGQ P + + FQ I+ + Sbjct: 64 AEAGNIGVCIGTSGPAGTDMITGLYSAIADSIPILCITGQAPRARLHKEDFQAINVPDIA 123 Query: 119 MPIVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVK 178 P+ K + + Q+P +F+ AF + ++GRPGPV IDLP DVQ E++ D Sbjct: 124 KPVTKWALTVLEPAQVPYVFQQAFHLMRSGRPGPVLIDLPIDVQMAEIEFDDET------ 177 Query: 179 LIGYNPTTIGHP----RQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPV 234 Y P + P Q++KA+ + A+A+RP+++AGGG++ + A+++L++ ELL +PV Sbjct: 178 ---YEPLPVYKPAATRAQVEKALAMFAAAERPLVVAGGGIINADASDKLVEFAELLGVPV 234 Query: 235 CTTLMGKGCISENHPLALGMVGMH-GTKPANYCLSESDVLISIGCRFSDRITGDIKSFAT 293 TLMG G I ++HPL GMVG+ + N + +SD ++ IG R+++R TG ++ + Sbjct: 235 IPTLMGWGTIPDDHPLMAGMVGLQTAHRYGNATMLKSDFVLGIGNRWANRHTGSVEVYTK 294 Query: 294 NAKIIHIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWI 353 K +H+DI+P +IG+ D+ IV DA L I+ + ++ K +++ W+ Sbjct: 295 GRKFVHVDIEPTQIGRVFMPDLGIVSDAGAALDLFIE-----VAREWKAEGRFKDLGGWV 349 Query: 354 ENVNSLKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYF 413 ++ K+S D+D +P+KPQ++ +E+ + ++T T +G +Q+ A + Sbjct: 350 KDCQGRKRSMHRRSDFDQVPMKPQRVYQEMNSA-----FGQDTTYVTTIGLSQIAGAQFL 404 Query: 414 KTQTPRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNI 473 PR +++ G G +G+ P+A+G +VA P +++ ++GD F +EL A++ + Sbjct: 405 HVYKPRHWINCGQAGPLGWTLPAALGVRVADPKRRIVALSGDYDFQFMIEELAVGAQHKL 464 Query: 474 PVVICIFDNRTLGMVYQWQNLFYGKRQCSVNFG--GAP-------DFIKLAESYGIKARR 524 P + + +N LG++ Q Q F Q ++F AP D + +AE G KA R Sbjct: 465 PYIHVLVNNAYLGLIRQAQRAFQMDFQVQLSFENINAPEIGVYGVDHVAVAEGLGCKAIR 524 Query: 525 IESPNEINEALKEA 538 + P+ I EA +A Sbjct: 525 VTEPDRIQEAFTQA 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: 803 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: 589 Length adjustment: 37 Effective length of query: 562 Effective length of database: 552 Effective search space: 310224 Effective search space used: 310224 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 Apr 10 2024. The underlying query database was built on Apr 09 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