Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_068166335.1 HTA01S_RS00630 thiamine pyrophosphate-binding protein
Query= curated2:Q7U5G1 (617 letters) >NCBI__GCF_001592305.1:WP_068166335.1 Length = 569 Score = 236 bits (601), Expect = 3e-66 Identities = 177/554 (31%), Positives = 261/554 (47%), Gaps = 42/554 (7%) Query: 27 LMDALRRHGVDTIFGYPGGAILPIYDALHIAESEGWVKHILVRHEQAGTHAADAYARATG 86 L++ L GV FG PG + L + D H ++ ++ R E A+A + TG Sbjct: 10 LVECLIAQGVTHAFGVPGESYLAVLDGFHAHADR--IRFVINRQEGGAAFMAEAQGKLTG 67 Query: 87 KVGVCFGTSGPGATNLVTGIATAQMDSVPMVVITGQVPRPAIGTDAFQETD---IFG-IT 142 + GVCF T GPGATN G+ TA DS PMV+ G V A +AFQE D FG T Sbjct: 68 RPGVCFVTRGPGATNASIGLHTAFQDSTPMVLFVGDVASDARDREAFQEVDYLSFFGPST 127 Query: 143 LPIVKHSWVVRDPADLGSIVAQAFLIAASGRPGPVLIDIPKDVGQEQFNYVP---VEPGS 199 + K + D + VA+AF A +GRPGPV++ +P+D+ + + P VEP Sbjct: 128 KGMAKRVERIDDARRIPEYVARAFATAMNGRPGPVVLVLPEDMLTQPVDAKPLPRVEPVQ 187 Query: 200 VIPGGFHQPEPPLDAAVAAALDLIEQAQRPLLYVGGGAISACAHDSLRMLAERYQLPVTT 259 + P A+ +L+ QA+RPL+ GGG ++ A +L+ AE +QLPV Sbjct: 188 ----AWSDP-----GALRGLRELLLQAERPLVIAGGGGWTSQAAAALQRFAENWQLPVAN 238 Query: 260 TLMGKGAFDENDALSVGMLGMHGTAYANFAVTECDLLIAVGARFDDRVTG---KLDTFAP 316 + FD + G +G+ V E DLLIA+G R + TG ++ P Sbjct: 239 AFRFQDCFDNHHPNYAGDVGLGINPALAKRVRESDLLIAIGPRLGEATTGGYALIEAPVP 298 Query: 317 RARVVHFEIDPAEIGKNRKADVAVLGDLGLSLARMVEISLQRTAEPRTAAWLERINTWKD 376 + ++VH E+ + +A +A+ + + AR +E+ P AW + Sbjct: 299 KQKLVHIHASAEELNRVYQATLAINATMN-AAARSLEV----LTAPPGVAWGQWTQACHA 353 Query: 377 RYPLTIPPAEGAI-------YPQEVLLAVRDLAPDAIVTTDVGQHQMWAAQHLR-----N 424 Y I PA G I P + + L DA++T G W + R Sbjct: 354 DYLANIDPANGGIVLPGSIDMPALIATLQQHLPADAVLTNGAGNFASWLHRFYRYHGLVK 413 Query: 425 GPRGWISSAGLGTMGFGMPAAMGAQVAMPDRQVVCIAGDASILMNIQELGTLAAYGLPVK 484 G + ++ G MG+G+PA +GA + + R IAGD LMN QEL T +G Sbjct: 414 GHKTQLAPTN-GAMGYGVPAGIGAAI-LTGRTAFTIAGDGDFLMNGQELATAVQHGAKSI 471 Query: 485 VVIVNNHWQGMVRQWQESFYDERYSASDMLNGMPDFIALARSFGVDGVKITDRELLHRDL 544 V+++NN G +R QE Y S SD+ N PDF ALAR++G +IT L Sbjct: 472 VLLLNNGTYGTIRMHQEREYPAHVSGSDLRN--PDFCALARAYGYAAERITHTAEFEPAL 529 Query: 545 AAALQSPTPTMIDV 558 AL +P+ T+I+V Sbjct: 530 LRALVAPSGTVIEV 543 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: 948 Number of extensions: 56 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: 617 Length of database: 569 Length adjustment: 37 Effective length of query: 580 Effective length of database: 532 Effective search space: 308560 Effective search space used: 308560 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