Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_028998117.1 H537_RS0111925 thiamine pyrophosphate-binding protein
Query= curated2:Q7U5G1 (617 letters) >NCBI__GCF_000430725.1:WP_028998117.1 Length = 577 Score = 256 bits (653), Expect = 2e-72 Identities = 193/570 (33%), Positives = 271/570 (47%), Gaps = 45/570 (7%) Query: 11 GGLDANAPQTISGAAALMDALRRHGVDTIFGYPGGAILPIYDALHIAESEGWVKHILVRH 70 GG + T G L++AL GVDT+FG PG + L D +H E ++ I RH Sbjct: 3 GGREEAVQNTRPGGHLLVEALIAQGVDTVFGVPGESFLAALDGMH--ERRDAIRFIACRH 60 Query: 71 EQAGTHAADAYARATGKVGVCFGTSGPGATNLVTGIATAQMDSVPMVVITGQVPRPAIGT 130 E A+A + TG+ GVCF T GPGATN G+ TA DS P++++ GQV R Sbjct: 61 EGGAAFMAEAQGKLTGRPGVCFVTRGPGATNAAIGVHTAFQDSTPLLLLVGQVARHQRDR 120 Query: 131 DAFQETD---IFGI-TLPIVKHSWVVRDPADLGSIVAQAFLIAASGRPGPVLIDIPKDV- 185 +AFQE D +FG TL + K V D L VA+AF +A GRPGPV++ +P+DV Sbjct: 121 EAFQELDFRQVFGPGTLGMAKWVAEVDDAERLPEYVARAFHVAMQGRPGPVVLALPEDVL 180 Query: 186 -GQEQFNYVP-VEPGSVIPGGFHQPEPPLDAAVAAALDLIEQAQRPLLYVGGGAISACAH 243 G +P VEP P A+ L+ QA+RPL+ GG SA + Sbjct: 181 SGPAAAPVLPRVEPAQAWPA---------PGALRQLRTLLLQAERPLVIAGGSGWSAESA 231 Query: 244 DSLRMLAERYQLPVTTTLMGKGAFDENDALSVGMLGMHGTAYANFAVTECDLLIAVGARF 303 +L+ AE + LPV + FD G +G+ V + DLLIAVG R Sbjct: 232 QALQRFAENWNLPVGCGFRFQDTFDNRHPNYAGDVGIGINPRLAQRVRDADLLIAVGVRL 291 Query: 304 DDRVTG---KLDTFAPRARVVHFEIDPAEIGKNRKADVAVLGDLGLSLARMVEISLQRTA 360 + TG ++ P+ ++VH E+G+ AD+ L SLA + TA Sbjct: 292 GEMTTGGYTLIEPPRPKQKLVHLHAGAEELGRVYAADLL----LQCSLAAAGKALETLTA 347 Query: 361 EPRT--AAWLERINTWKDRYPLTIPPAEGAIYPQEVLLAVRDLAP-DAIVTTDVGQHQMW 417 P+ A W D +PP + +V+LA+ LAP D++ T G + W Sbjct: 348 PPQLPWAGWTASARA--DFEANRVPPPVAPLDMAQVVLAIERLAPADSLYTNGAGNYSGW 405 Query: 418 AAQHLR------NGPRGWISSAGLGTMGFGMPAAMGAQVAMPDRQVVCIAGDASILMNIQ 471 ++LR +G +A G MG+G+PAA+ A + P R + +AGD LM Q Sbjct: 406 LHRYLRYRGLQHHGRTQLAPTA--GAMGYGVPAAVAAALLYPQRTAINLAGDGDFLMTGQ 463 Query: 472 ELGTLAAYGL-----PVKVVIVNNHWQGMVRQWQESFYDERYSASDMLNGMPDFIALARS 526 EL T AYG + ++V+N G +R QE Y R S SD+ N PDF ALARS Sbjct: 464 ELATAVAYGANRGAGRLVSIVVDNGTYGTIRMHQERHYPGRVSGSDLFN--PDFAALARS 521 Query: 527 FGVDGVKITDRELLHRDLAAALQSPTPTMI 556 +G ++ E AL P ++ Sbjct: 522 YGWRAARVDTTEAFEPAFQEALSEGPPMLL 551 Lambda K H 0.320 0.136 0.414 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: 1049 Number of extensions: 63 Number of successful extensions: 9 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: 617 Length of database: 577 Length adjustment: 37 Effective length of query: 580 Effective length of database: 540 Effective search space: 313200 Effective search space used: 313200 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 (21.8 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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