Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_058929161.1 AU252_RS01175 acetolactate synthase catalytic subunit
Query= curated2:O08353 (599 letters) >NCBI__GCF_001484605.1:WP_058929161.1 Length = 571 Score = 260 bits (665), Expect = 1e-73 Identities = 181/566 (31%), Positives = 292/566 (51%), Gaps = 33/566 (5%) Query: 4 AEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARASGK 63 A+ + AL V+ +FG L A + + R E AA +DG++R SG+ Sbjct: 5 ADVIAAALSRHGVKAIFGQSNPTALLL--AAEKIGIRQIFYRTENAAGVMSDGFSRISGQ 62 Query: 64 VGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMPIVK 123 +GV +GP AT V +A A S PM+ L +VP+ + +AFQE+D LF + K Sbjct: 63 IGVVAAQNGPAATLFVAPMAEALKASIPMLVLVQEVPSSVRDRNAFQELDHEALFAGVSK 122 Query: 124 HNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKL---I 180 +I + + A IA +GRPGPV + LPKDV L+ +PSK + + Sbjct: 123 WTRRIDDPSRAEDYVDLAMTIANSGRPGPVVLLLPKDVLGLK------SVPSKFRRTQNL 176 Query: 181 GYNPTTIGHPR--QIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTL 238 G P P + +A +LIA+A+ P+I+AGGGV +S A EEL +L E +PV TT Sbjct: 177 GQFPLDRPRPAADAVARAAELIANAQSPLIIAGGGVHVSDAVEELAQLQERAYLPVATTN 236 Query: 239 MGKGCISENHPLALG----MVGMHGTKPANY---CLSESDVLISIGCRFSDRITGDIKSF 291 MGKG + E PL+LG + G +G PA++ +S +DV++ IG R ++ T + Sbjct: 237 MGKGAVDETAPLSLGVAANITGKNG--PAHFHLPLISNADVVVLIGTRTNENGTDNWTLT 294 Query: 292 ATNAKIIHIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQ 351 + +A IHID+D EIG+N + ++GDA+ ++++ LD + +K + Sbjct: 295 SPDATYIHIDVDGLEIGRNYE-SIRLLGDARAAIEDLTAALDKL--DLTKREAALAGLVA 351 Query: 352 WIENVNSLKKSSI-PVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMA 410 IE+ K++I ++ D P+ P++I+ EL A+++ + I+ D + +W+ Sbjct: 352 TIEDGRRQHKAAIAELLASDSSPVAPERILAELDALLEPTD-----IVVADASYSSIWVT 406 Query: 411 HYFKTQTP-RSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIA 469 Y ++ P + FL GL +G+G P +GAK+A P S+V+ I GDGGF EL T Sbjct: 407 SYLTSRRPGQRFLVPRGLAGLGWGLPLGMGAKLASPASRVVAIVGDGGFAHVWSELETAV 466 Query: 470 EYNIPVVICIFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPN 529 NIPVV+ + +N LG +N F+ + ++ F D +A S G ++ Sbjct: 467 RENIPVVVIVLNNALLGYQRHAENFFFDQTTTAIAFAPV-DHAAMARSTGAAGVLVDKAE 525 Query: 530 EINEALKEAINCDEPYLLDFAIDPSS 555 ++ AL +A+ ++D DP + Sbjct: 526 DLRAALADALASSNTTVIDVITDPDA 551 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: 695 Number of extensions: 30 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: 571 Length adjustment: 37 Effective length of query: 562 Effective length of database: 534 Effective search space: 300108 Effective search space used: 300108 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