Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_084076292.1 BUB04_RS07600 thiamine pyrophosphate-binding protein
Query= curated2:Q7U5G1 (617 letters) >NCBI__GCF_900129305.1:WP_084076292.1 Length = 537 Score = 191 bits (484), Expect = 9e-53 Identities = 153/515 (29%), Positives = 235/515 (45%), Gaps = 50/515 (9%) Query: 30 ALRRHGVDTIFGYPGGAILPIYDALHIAESEGWVKHILVRHEQAGTHAADAYARATGKVG 89 +L+R GV+ FG PGG +P +A+ E EG ++ +LV +E + AD AR +G+V Sbjct: 11 SLKRAGVEVCFGIPGGPWIPYMEAM---EREG-LEFVLVANEASAGFMADVTARLSGRVA 66 Query: 90 VCFGTSGPGATNLVTGIATAQMDSVPMVVITGQVPRPAIGTDAFQETDIFGITLPIVKHS 149 C GT GPGA NL TG+ A +D P++ T ++ + D + P+ K + Sbjct: 67 ACHGTFGPGAVNLATGVGCALLDRSPLLAFTSEMGDAMLARVTQMNIDHQRLFSPLTKKT 126 Query: 150 WVVRDPADLGSIVAQAFLIAASGRPGPVLIDIPKDVG------QEQFNYVPVEPGSVIPG 203 W +R P D+ + V A IA S PGPV + +P D+ + + VEP ++ Sbjct: 127 WRLR-PRDVAAQVRDAVGIARSEVPGPVHLGLPADLADVDAAEENLSERIAVEPPAL--- 182 Query: 204 GFHQPEPPLDAAVAAALDLIEQAQRPLLYVGGGAISACAHDSLRMLAERYQLPVTTTLMG 263 PE L AA L QA+RPLL VG A+ L + +PV T M Sbjct: 183 ----PESGLLEEAAAVLG---QARRPLLAVGLTALRLGMAKDLLNFLSAHPMPVVLTAMA 235 Query: 264 KGAFDENDALSVGMLGMHGTAYANFAVTECDLLIAVGARFDDRVTGKLDTFAPRARVVHF 323 KG E G+L + + DL++ VG D V +++ P +VH Sbjct: 236 KGLVREEHGCYAGVLFHAASDELASFIARADLVVGVGY---DPVEFNYESWLPDVPLVHA 292 Query: 324 EIDPAEIGKNRKADVAVLGDLGLSLARMVEISLQRTAEPRTAAWLE-RINTWKDRYPLTI 382 + ++ + V V+GD +L + + P AW E + +DR + Sbjct: 293 DTRSCDVPAGVRVAVDVVGDPRETLRFLAD------RPPGPLAWEEGELQDLRDRLHKRL 346 Query: 383 PPAEGAIYPQEVLLAVRDLAP-DAIVTTDVGQH-----QMWAAQHLRNGPRGWISSAGLG 436 PA P L +R + P D I+T DVG H Q+W P ++ + G Sbjct: 347 QPAGAGFGPVAALRTLRQVLPRDGILTCDVGAHTHLLGQLWETP----APGLFVMTNGWS 402 Query: 437 TMGFGMPAAMGAQVAMPDRQVVCIAGDASILMNIQELGTLAAYGLPVKVVIVNNHWQGMV 496 +MGFG+PAA+ A+ +PDR VVC+ GD LM E+ T GL V +V++ + ++ Sbjct: 403 SMGFGIPAALAAKRCLPDRPVVCVTGDGGFLMMAGEIVTARRLGLSVVIVVLADGSLSLI 462 Query: 497 R---QWQES------FYDERYSASDMLNGMPDFIA 522 R W+++ +D +D G P F A Sbjct: 463 RVKEAWRKTPPVGVGLHDGPLLGTDTFLGAPVFRA 497 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: 932 Number of extensions: 43 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: 617 Length of database: 537 Length adjustment: 36 Effective length of query: 581 Effective length of database: 501 Effective search space: 291081 Effective search space used: 291081 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 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