Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_011952530.1 SWIT_RS08535 hypothetical protein
Query= curated2:O08353 (599 letters) >NCBI__GCF_000016765.1:WP_011952530.1 Length = 547 Score = 239 bits (611), Expect = 2e-67 Identities = 170/555 (30%), Positives = 278/555 (50%), Gaps = 43/555 (7%) Query: 1 MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHS-DLIHLL-TRHEQAAAHAADGYA 58 M GA+A++ + A + +FG PGG L F+DA+H + D + L TRHEQ AA+ A GYA Sbjct: 3 MTGAQALLGQILANGTDTIFGLPGGQLDHFFDAMHKAGDKLRLFGTRHEQGAAYMAFGYA 62 Query: 59 RASGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDA--FQEI-DAL 115 R++GK GV GPG N + +A++ ++P++ LTGQ+P+ IG E+ D L Sbjct: 63 RSTGKPGVYTVVPGPGVLNTTAALCSAYATNAPVLCLTGQIPSAGIGKGIGYLHELPDQL 122 Query: 116 GLFMPIVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPS 175 + K + P + A+ GRP PV +++P DV D+ P Sbjct: 123 ATMRTLTKWADRAMTPDAAPALVNEAYRQMGGGRPRPVSLEMPMDVMGASADVALLPKAE 182 Query: 176 KVKLIGYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVC 235 I P I +A KL+++A+ P+I+AGGG + +G E L +L +L PV Sbjct: 183 ----IDRGPAL--DDDAILRAAKLLSTARNPLIIAGGGAIAAG--EALQELAAMLQAPVV 234 Query: 236 TTLMGKGCISENHPLALGMVGMHGTKPANYCL-SESDVLISIGCRFSDRITGDIKSFATN 294 + G+G IS+ PL+ PA Y L ++DV+I +G R + + Sbjct: 235 SFRSGRGVISDRSPLSQMF-------PAGYELWKQADVVIGLGSRMEQQYL--YWKVPDH 285 Query: 295 AKIIHIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIE 354 K+I IDID EI + V I DA + ++ +L ++++ + ++ +++ + Sbjct: 286 MKVIRIDIDQEEIDRIAPPAVAIHADAADAVPALVAKLSGLLDRRASREDELRDLAARVR 345 Query: 355 NVNSLKKSSIPVMDYDDIPIKPQ-KIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYF 413 D +D ++PQ + + A + + + I T VG W A F Sbjct: 346 G------------DIED-RVQPQASYLAAIRAALPEDGYFVDEI--TQVGYTS-WYA--F 387 Query: 414 KTQTPRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNI 473 PR ++ G GT+G+G+ +A+G K A PD V+ I GDGGF+ E+ T A++ I Sbjct: 388 PVYEPRHLITCGYQGTLGYGYATALGVKAAHPDKAVVNIAGDGGFLFTANEMATAAQHGI 447 Query: 474 PVVICIFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEINE 533 +V +F+N V + Q ++G R + + PDF+K AES+GI+A R+ P + Sbjct: 448 ALVTVLFNNNKFQNVQRQQREWFGGRLIASDLKN-PDFVKFAESFGIRAERVYDPESLRR 506 Query: 534 ALKEAINCDEPYLLD 548 A+ A+ +EP L++ Sbjct: 507 AVSAALERNEPALIE 521 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: 703 Number of extensions: 33 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: 547 Length adjustment: 36 Effective length of query: 563 Effective length of database: 511 Effective search space: 287693 Effective search space used: 287693 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