Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_005458823.1 SACCYDRAFT_RS19595 thiamine pyrophosphate-binding protein
Query= curated2:O08353 (599 letters) >NCBI__GCF_000244975.1:WP_005458823.1 Length = 547 Score = 242 bits (617), Expect = 3e-68 Identities = 168/556 (30%), Positives = 286/556 (51%), Gaps = 38/556 (6%) Query: 1 MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDL--IHLL-TRHEQAAAHAADGY 57 +NGA ++++ L V+ FG PG LP +DAL S+L I L+ RHEQAAAHAADGY Sbjct: 3 VNGARSLVRTLTELGVDAAFGLPGAHSLPIWDALADSELGGIRLVGVRHEQAAAHAADGY 62 Query: 58 ARASGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKL----IGNDAFQEID 113 +RA G +GV + T+GPGA N + V A + +SP++ + VP+ G + QEID Sbjct: 63 SRAVGSLGVALVTTGPGAVNTLRAVGEARASASPVLVIATDVPSTPRAAGTGRGSAQEID 122 Query: 114 ALG-LFMPIVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHP 172 LF P+ K F +++ +I + R A EIA + GPV++ +P D L + + P Sbjct: 123 CQERLFEPLTKAAFTVEQPTEIAAVVRRAAEIAMRPQSGPVYVGIPADF--LGEPVMEQP 180 Query: 173 IPSKVKLIGYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNI 232 P+ + G P ++ +++A + + A+RP+I GGG L SGA E + L E L Sbjct: 181 EPAGPVVPG--PPSVAS-EDVERAREALVEARRPLIWVGGGALRSGAGEAIGGLAERLAA 237 Query: 233 PVCTTLMGKGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFA 292 P+ TT +G + +HP L +H + E+DV++++G F +T + + Sbjct: 238 PIITTFAARGIVPPDHP-CLASNPVHAPE-VGALWDEADVVLAVGTDFDGTMTQNGR-MP 294 Query: 293 TNAKIIHIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQW 352 +I ++ID + KN D+ ++GDA+ EV+++L I+ + +++ Sbjct: 295 QPPGLIAVNIDAEDAAKNYPPDLLLLGDAR----EVVEELSLGISPKP----GLDELTRR 346 Query: 353 IENVNSLKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHY 412 ++ + + + K + E ++ + + + + +++ +D+ W+ + Sbjct: 347 LDEIEVRVRRRVR---------KEEPHAAEFLSALKE-TLPEGSVLVSDMCVAGYWIGGF 396 Query: 413 FKTQTPRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYN 472 + PR G GT+GFGFP+A+G A + +C+TGDGGF+ C EL T + Sbjct: 397 HRVSGPRQLALPTGWGTVGFGFPAALGVAAAGA-VRAVCVTGDGGFLPGCAELATAIQEK 455 Query: 473 IPVVICIFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIES-PNEI 531 +PV + I D+ GM+ ++ G V+ PDF+ LA+S+G+ A R++ Sbjct: 456 LPVTVVIVDDGGYGML-RYDQAHAGFEHHGVDL-VTPDFVGLAKSFGVYADRVDGFGRAF 513 Query: 532 NEALKEAINCDEPYLL 547 L+E DEP +L Sbjct: 514 RRLLREFTRSDEPNVL 529 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: 778 Number of extensions: 38 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 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