Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_028488024.1 Q394_RS0103325 acetolactate synthase
Query= curated2:O08353 (599 letters) >NCBI__GCF_000621325.1:WP_028488024.1 Length = 557 Score = 259 bits (661), Expect = 3e-73 Identities = 172/554 (31%), Positives = 295/554 (53%), Gaps = 46/554 (8%) Query: 4 AEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARASGK 63 +E ++K L V+ LFG PG +LP YD L+ S + +L +HEQ AA A GYAR SG+ Sbjct: 6 SELLVKFLHRLGVDTLFGMPGAHILPVYDDLYGSGIQTVLVKHEQGAAFMAGGYARVSGR 65 Query: 64 VGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQE-------IDALG 116 +G CI T+GPGA+NL+TG+A A++D P++ +TG+ PT + G QE ID Sbjct: 66 IGACITTAGPGASNLITGIANAYADKLPVLVITGEAPTYIFGRGGLQESSGEGGSIDQTA 125 Query: 117 LFMPIVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDI-------D 169 LF + +++ I++T + + A + PGPV + +P +VQ+ +D D Sbjct: 126 LFSGVTRYHKLIERTDYLVNVLNQAARQLVSDVPGPVVLSIPVNVQKELVDASILDKLPD 185 Query: 170 KHPIPSKVKLIGYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSG-ANEELLKLVE 228 HP+P K+K+ P+ +++ +I SAKRP++LAG G + S A++ L + + Sbjct: 186 LHPLP-KLKIA---------PQTLEQCGDMIRSAKRPVVLAGYGCIQSATAHDALCEFSQ 235 Query: 229 LLNIPVCTTLMGKGCISENHPLALGMVGMHGTKPA-NYCLSESDVLISIGCRFSDRITGD 287 LNIPV ++L GKG I E L+LG +G+ + A +Y + E+D++I +G F++R + Sbjct: 236 RLNIPVASSLKGKGAIDERSALSLGSLGVTSSGHAMHYFMHEADLIILLGAGFNERTSYV 295 Query: 288 IKSFATNAK-IIHIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDK 346 + N K II +D + ++ K D+ I D L+ IN + + Sbjct: 296 WNAALLNGKKIIQVDRNVTQLEKVFKADLAIQSDLGDFLQS--------INGWCAQQVIE 347 Query: 347 ENISQWIENVNSLKKSSIPVMDYDDIPIKPQK--IVKELMAVIDDLNINKNTIITTDVGQ 404 I ++ + K+ M+ D I ++ +VK A+++ N ++ D Sbjct: 348 PKICP---DLAAFKRGIDQQMEADGTVIFGEQFDLVKTFFALLEQ-QFNDGIVLVDD--- 400 Query: 405 NQMWMAHYFKTQTPRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQE 464 N ++ ++++ F+ + G+ ++G P+AIG++ D + GDGGF M C E Sbjct: 401 NIIFAQNFYRVTPQDHFVPNTGVSSLGHAIPAAIGSRFTV-DKPTFAVIGDGGFQMCCME 459 Query: 465 LGTIAEYNIPVVICIFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARR 524 + T Y+IP+ I +F+N+TLG++ + Q+ Y +R +F PD+ LA+S+GI + Sbjct: 460 IMTAVNYHIPLNIVLFNNQTLGLIRKNQHQQYEQRFLDCDFKN-PDYALLAQSFGINHFK 518 Query: 525 IESPNEINEALKEA 538 IE+ + + +A Sbjct: 519 IETDADCEQVFAQA 532 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: 747 Number of extensions: 53 Number of successful extensions: 7 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: 557 Length adjustment: 36 Effective length of query: 563 Effective length of database: 521 Effective search space: 293323 Effective search space used: 293323 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