Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_041550322.1 SARO_RS11970 acetolactate synthase large subunit
Query= curated2:O08353 (599 letters) >NCBI__GCF_000013325.1:WP_041550322.1 Length = 551 Score = 261 bits (666), Expect = 7e-74 Identities = 171/554 (30%), Positives = 269/554 (48%), Gaps = 30/554 (5%) Query: 4 AEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHL-LTRHEQAAAHAADGYARASG 62 ++ I+ LE E E +FG PG L F D+L S I L LTRHEQ A A Y R +G Sbjct: 8 SDLFIECLEEEGCEYIFGVPGEENLDFLDSLSRSKKIRLVLTRHEQGAGFMAATYGRHTG 67 Query: 63 KVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMPIV 122 K GVCI T GPGATN VT A A PM+ +TGQ P K FQ +D + + PI Sbjct: 68 KTGVCIATLGPGATNFVTAAAYATLGGMPMLMITGQKPIKKSKQGRFQILDVVSMMGPIT 127 Query: 123 KHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKH--PIPSKVKLI 180 K Q+ + IP R A+ +A+ +PG HI+LP+D+ D+H +P K L+ Sbjct: 128 KFTHQMASSDNIPSRVREAYRLAEEEKPGATHIELPEDI------ADEHTTSVPLKRSLV 181 Query: 181 GYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLMG 240 P + + +A+ + +AK P+++ G G + LL+ VE IP TT +G Sbjct: 182 -RRPN--ADAKSVAQAVHALQNAKAPVLVIGAGANRKMTGKMLLEFVEKTGIPFLTTQLG 238 Query: 241 KGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNAKIIHI 300 KG I E HP LG + + + ++D++I++G ++ ++ T +IH+ Sbjct: 239 KGVIDERHPKFLGCAALSSGDFVHRAVEDADIIINVGHDVIEKPPFFMREGGT--PVIHV 296 Query: 301 DIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIENVNSLK 360 AE+ + ++GD + I Q+ K++ N N + + Sbjct: 297 STKTAEVDPVYFPSIEVIGD----IANAIWQM-----KEAITPNPAWNFDHMLAYRAAEV 347 Query: 361 KSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQTPRS 420 + P+ P+ P +V+++ + + + II D G ++W A + P + Sbjct: 348 AHTAPLAADMRFPVFPPHLVQQVRDCMPE-----DGIICLDNGVYKIWFARGYTAYKPNT 402 Query: 421 FLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVVICIF 480 L L TMG G PSA+ + + PD KV+ I GDGGFMMN QE+ T + + + I Sbjct: 403 VLLDNALATMGAGLPSAMMSAMLYPDRKVMAICGDGGFMMNSQEMETAVRLGLNLTVLIL 462 Query: 481 DNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEINEALKEAIN 540 ++ GM+ +W+ G + + PDF+K A+SYG K R+ES + + L + Sbjct: 463 NDSAYGMI-RWKQANMGFEDFGLTYNN-PDFVKYADSYGAKGYRVESAEHLEKLLAHCRD 520 Query: 541 CDEPYLLDFAIDPS 554 +L+D +D S Sbjct: 521 TPGVHLIDCPVDYS 534 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: 746 Number of extensions: 28 Number of successful extensions: 5 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: 551 Length adjustment: 36 Effective length of query: 563 Effective length of database: 515 Effective search space: 289945 Effective search space used: 289945 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