Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_005808155.1 DHAF_RS01020 sulfoacetaldehyde acetyltransferase
Query= curated2:O08353 (599 letters) >NCBI__GCF_000021925.1:WP_005808155.1 Length = 578 Score = 279 bits (714), Expect = 2e-79 Identities = 172/573 (30%), Positives = 293/573 (51%), Gaps = 29/573 (5%) Query: 1 MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARA 60 M +EA+ + L AE ++ + G G A + D + + + RHEQ+A H D + R Sbjct: 6 MTPSEAICETLVAEGIDHVTGIVGSAFMDLLDLFPTAGIRFIPVRHEQSAGHMEDAFCRV 65 Query: 61 SGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMP 120 +G+ GV IG +GPG TN+VT VA A+S +PMV + T +G D FQE D + +F Sbjct: 66 TGRAGVIIGQNGPGITNMVTSVAAANSAHTPMVVICPSAGTPTVGWDGFQEADTVKIFEA 125 Query: 121 IVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKD-----VQELELDIDKHPIPS 175 I K ++ + + R+AF IA R GPV D+P+D + E L+ ++ + Sbjct: 126 ITKETIRVPHPSRAADCLRTAFRIAYAER-GPVLYDIPRDYFYGEISEQILEPHQYRVDQ 184 Query: 176 KVKLIGYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVC 235 + G + KA +L+ SA+RP+I++G GV+ + + + + K+ E+L PV Sbjct: 185 R---------GCGDLASLDKAAELLISAQRPVIISGRGVVDTQSKDIVAKIAEILTAPVA 235 Query: 236 TTLMGKGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCR---FSDRITGDIKSFA 292 T + +HPL +G +G G+K A ++E+DV+++IG R F DI F Sbjct: 236 CTYLHNDAFPYDHPLWVGPIGYMGSKAAMNLVAEADVILAIGTRLSVFGTTPQYDIDYFP 295 Query: 293 TNAKIIHIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQW 352 +AKII +DI+P I + V+V ++ DA+ +E++K+L+ + ++ + ++Q Sbjct: 296 ESAKIIQVDINPRNIARTHPVEVGLIADAREAAREILKRLE---ERIAEPKVSQSRLTQI 352 Query: 353 IENVNSLKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHY 412 N+ ++ + D PI P++ + E+ + + N I+ TD+G Y Sbjct: 353 KAQQNAWEEEIVQSAMVDGYPINPRRALYEIQKALPE-----NAIVATDIGNVSSTANSY 407 Query: 413 FKTQTPRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYN 472 K + +++ G GF +P+A+GA++A+PDS V+ I GDG + M+ E+ T E+N Sbjct: 408 LKFKGAGKHIAALTFGNTGFAYPAALGAQLAEPDSPVVAIIGDGAWGMSLHEVSTAVEHN 467 Query: 473 IPVVICIFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEIN 532 +PVV +F N + Q FY R V+ F +A + G + R+ E+ Sbjct: 468 LPVVAIVFRNGAWCAEKKNQIDFYNNRFVGVDIPTPESFAPVAIAMGAEGIRVSKAEEVG 527 Query: 533 EALKEAINCDEPYLLDFAIDPSSALSMVPPGAK 565 ALK A++ +P +L+ D + PP K Sbjct: 528 PALKRALDSRKPTVLEIVCD---GTQLAPPFRK 557 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: 755 Number of extensions: 29 Number of successful extensions: 5 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: 578 Length adjustment: 37 Effective length of query: 562 Effective length of database: 541 Effective search space: 304042 Effective search space used: 304042 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