Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_015930309.1 MNOD_RS17755 acetolactate synthase
Query= curated2:O08353 (599 letters) >NCBI__GCF_000022085.1:WP_015930309.1 Length = 581 Score = 283 bits (723), Expect = 2e-80 Identities = 185/563 (32%), Positives = 299/563 (53%), Gaps = 26/563 (4%) Query: 1 MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARA 60 M GA+A+ AL+ V +FG + L + A H + + R E A A AD +AR Sbjct: 16 MTGADALAAALQRHGVREVFGQSIPSAL--FLAAPHYGIRQIGYRTENAGAAMADAFARI 73 Query: 61 SGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMP 120 SG+VGV +GP AT LV G+A A S P+VA+ V + +AFQE+D + LF Sbjct: 74 SGRVGVVAAQNGPAATLLVPGLAEALKASIPVVAIVQDVNRRFTDKNAFQELDHVALFSG 133 Query: 121 IVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLI 180 + K +I +I + AF A TGRPGP + +P D+ + +ID P + + Sbjct: 134 VAKWVRRIGDPSRIDDYVDMAFTAASTGRPGPAVLLVPLDILDERAEIDA-VAPRRAASL 192 Query: 181 GYNP--TTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTL 238 G P T+ P +I +A LIA+A+RP+++AGGGV SGA+ EL L + L +PV TT+ Sbjct: 193 GAYPLDRTVADPARIAEAASLIAAAQRPVVIAGGGVHSSGASAELAAL-QALGLPVGTTV 251 Query: 239 MGKGCISENHPLALGMVG-----MHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFAT 293 MGKG + E +PL+LG+VG + ++ +DV++ +G R + T + Sbjct: 252 MGKGAVDETNPLSLGVVGYFMAPRSRSSHLREVVTGADVVLLVGNRANQNGTDSWSLYPR 311 Query: 294 NAKIIHIDIDPAEIGKNVNVDVPIVGDAKL---ILKEVIKQLDYIINKDSKENNDKENIS 350 A+ +HID+D EIG+N + + GDAKL L E ++ ++D + + + Sbjct: 312 EARYVHIDVDGGEIGRNYEA-LRLAGDAKLTLAALTEALRATGLPGSQDRRAALEAQIAD 370 Query: 351 QWIENVNSLKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMA 410 + +++ ++D + +P++P++I+ E+ AV + TI+ D +W+A Sbjct: 371 ARARHAEDMRR----LVDMEAVPVRPERIMAEIDAV-----VTPETIMVADASYASIWIA 421 Query: 411 HYFKTQTP-RSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIA 469 ++ + P + FL+ G+ +G+G P A+GAK A+PD+ VIC+TGDGGF EL T Sbjct: 422 NFLTARKPGQRFLTPRGIAGLGWGLPFALGAKTARPDAPVICVTGDGGFGHVWSELETAR 481 Query: 470 EYNIPVVICIFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPN 529 +PVV+ + +N+ LG + +G +F A D +A + G RIE P Sbjct: 482 RMRLPVVLIVLNNQILGYQKHAELSLFGNFTDVCHF-EAVDHAAIARACGCTGVRIERPG 540 Query: 530 EINEALKEAINCDEPYLLDFAID 552 E++ AL++A+ D ++D D Sbjct: 541 ELSGALRDALAADSVTVIDVVTD 563 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: 802 Number of extensions: 35 Number of successful extensions: 8 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: 581 Length adjustment: 37 Effective length of query: 562 Effective length of database: 544 Effective search space: 305728 Effective search space used: 305728 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