Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_078428364.1 BK574_RS08995 hypothetical protein
Query= curated2:O08353 (599 letters) >NCBI__GCF_002019605.1:WP_078428364.1 Length = 589 Score = 233 bits (593), Expect = 2e-65 Identities = 173/563 (30%), Positives = 271/563 (48%), Gaps = 38/563 (6%) Query: 5 EAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIH-LLTRHEQAAAHAADGYARASGK 63 +A+ + LE +++ +FG PGG + YD L+ S + +L RHEQ A+ A+ Y R +GK Sbjct: 24 QAITQVLEEMEIDYVFGMPGGYMGTLYDGLYDSKSVKPILIRHEQVASIMAEIYGRLTGK 83 Query: 64 VGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVP--------TKLIGNDAFQEIDAL 115 GV TN G A SPM+ LT + +G + D Sbjct: 84 PGVFTAQGAWSITNGAMGALEALQGCSPMIILTDMTDNYPYSHQGSYQVGTGEYGGYDVK 143 Query: 116 GLFMPIVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPS 175 + I K+ Q + + + + +G GP + + ++ + P Sbjct: 144 KVMDGITKYVTVAYGPEQAVQSLQLVAKQSLSGNQGPTALIFHSNAINGKVTPEGSPKIY 203 Query: 176 KVKLIGYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVC 235 P + I A + I +A++PII+AG GV + A EL L EL PV Sbjct: 204 HTSKYLVKPNHFETEKNIAIACERIMNAEKPIIIAGNGVHNAKAYYELQLLAELTGAPVT 263 Query: 236 TTLMGKGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNA 295 TT GK I+E HP A+G++G G AN LS++DVL+ +G + + T + N Sbjct: 264 TTAQGKSTIAETHPNAVGVMGNWGQDVANEHLSKADVLLVVGSKLAPTDTCNATPELINP 323 Query: 296 K---IIHIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQW 352 II IDI+P VD P++GDAK IL ++I + N K+ +E I++ Sbjct: 324 SRQTIIQIDIEPKNASWTFPVDQPLIGDAKNILSQMITYVKS--NFLEKQQVVQERIAK- 380 Query: 353 IENVNSLKKSSIPVMDYDD-----IPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQM 407 IE + K I M+ ++ PI PQ++VKE+ +VID+ NTI+T D G+N++ Sbjct: 381 IE----ISKKEIGYMECEEQYSNATPILPQRVVKEIESVIDE-----NTIVTLDAGENRV 431 Query: 408 WMAHYFKTQTPRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGT 467 + HY KT+ P S +S G MG+ P+A+ K+ P KV+ I GDGGF M L T Sbjct: 432 YNIHYLKTKAPGSLISPASAGGMGYSIPAALATKLVYPARKVLSICGDGGFPMTMNGLMT 491 Query: 468 IAEYNIPVVICIFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPD--FIKLAESYGIKARRI 525 EY++P+V+ I +N LG V Q + V PD F ++A S+G +I Sbjct: 492 SLEYDLPIVVVILNNSALGWVKNAQ-------EDRVIASTYPDYNFSEIARSFGCNGVKI 544 Query: 526 ESPNEINEALKEAINCDEPYLLD 548 + ++ A+++A + ++D Sbjct: 545 DKAEDLAPAIEKAFESGKTTVID 567 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: 752 Number of extensions: 40 Number of successful extensions: 6 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: 589 Length adjustment: 37 Effective length of query: 562 Effective length of database: 552 Effective search space: 310224 Effective search space used: 310224 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