Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_012854279.1 TCUR_RS19500 thiamine pyrophosphate-requiring protein
Query= curated2:O08353 (599 letters) >NCBI__GCF_000024385.1:WP_012854279.1 Length = 597 Score = 220 bits (561), Expect = 1e-61 Identities = 174/585 (29%), Positives = 271/585 (46%), Gaps = 43/585 (7%) Query: 7 MIKALEAEKVEILFGYPG----GALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARASG 62 ++K L VE +FGYPG G + F A + +RHE+ AA A GYA+ G Sbjct: 9 VLKRLRDWGVEHVFGYPGDGINGLIAAFGKAGDEPRFVQ--SRHEEMAAFQAVGYAKFGG 66 Query: 63 KVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMPIV 122 +VGVC+ TSGPGA +L+ G+ A D P+VA+ GQ +G + QE+D L LF + Sbjct: 67 RVGVCMATSGPGAIHLLNGLYDAKLDHVPVVAVVGQTDRAAMGGNYQQEVDLLSLFKDVA 126 Query: 123 KHNFQIQKTC-QIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKH---PIPSKVK 178 Q+ Q+P + A IA R P + +P D+QE +H +PS Sbjct: 127 SAYVQMATVPEQLPNLIDRALRIALAER-APTCVIIPADLQEETYRPPEHAFRQVPSSAP 185 Query: 179 LIGY-NPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTT 237 GY P T ++++A +++ + + IL G G GA E++++ EL V Sbjct: 186 --GYVRPLTRAPQPELERAAEILNAGSKVAILVGQGA--RGARREVMEVAELTGAGVAKA 241 Query: 238 LMGKGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNAKI 297 L+GK + ++ P G +G+ GT+P+ + + D L+ +G F T + F A+ Sbjct: 242 LLGKDVLPDDLPYVTGSIGLLGTRPSYELMRDCDTLLIVGSNFP--YTQYLPEFGA-ARA 298 Query: 298 IHIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIENVN 357 + ID+D IG +V +VGDA L+ +I L ++ S + N+++W E V Sbjct: 299 VQIDVDGRMIGMRYPTEVNLVGDAAETLRALIPLLRRKEDR-SWRRTVEHNVARWWEVVE 357 Query: 358 SLKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQT 417 + PI P ++ EL + + D N I+T D G W A + + Sbjct: 358 R-------QAHLEAEPINPMRLFWELSSRLPD-----NAIVTADSGSAANWYARDLRFRG 405 Query: 418 PRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMN-CQELGTIAEY----- 471 SG L TMG G P AIGAK A PD I + GDG MN EL T+ Y Sbjct: 406 QVRGSLSGTLSTMGPGVPYAIGAKFACPDRPAIALVGDGAMQMNGLAELITVQRYYQRWA 465 Query: 472 NIPVVICIFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPD--FIKLAESYGIKARRIESPN 529 + +V+ + N L V W+ G P+ + A S G++ ++ P Sbjct: 466 DPRLVVAVLHNNDLNQV-TWELRAMGGAPKFTESQSLPEVPYAAFARSLGLEGIEVDKPE 524 Query: 530 EINEALKEAINCDEPYLLDFAIDPSSALSMVPPGAKLTNIIDAVQ 574 I A + A++ P +LD +DP + +PP A+ + D + Sbjct: 525 AIGPAWERALSAGRPAVLDVRVDPD--IPPIPPHAEFEQLKDVAE 567 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: 804 Number of extensions: 49 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: 597 Length adjustment: 37 Effective length of query: 562 Effective length of database: 560 Effective search space: 314720 Effective search space used: 314720 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