Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_011951079.1 SWIT_RS01140 acetolactate synthase large subunit
Query= curated2:O08353 (599 letters) >NCBI__GCF_000016765.1:WP_011951079.1 Length = 550 Score = 265 bits (677), Expect = 4e-75 Identities = 172/557 (30%), Positives = 270/557 (48%), Gaps = 36/557 (6%) Query: 4 AEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHL-LTRHEQAAAHAADGYARASG 62 ++ I+ LE E E +FG PG L D+L S I L LTRHEQ A A Y R +G Sbjct: 6 SDLFIQCLEEEGCEYIFGVPGEENLDMLDSLSRSTKIKLILTRHEQGAGFMAATYGRHTG 65 Query: 63 KVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMPIV 122 K GVC+ T GPGATN VT A A P++ +TGQ P K FQ ++ + + PI Sbjct: 66 KTGVCMATLGPGATNFVTAAAYAQLGGMPILMVTGQKPIKKSKQGRFQILEVVEMMKPIT 125 Query: 123 KHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLIGY 182 K Q+ IP R A+ +A+ +PG HI+ P+DV + D P+ + + Sbjct: 126 KFTHQLASADNIPSRIREAYRLAEEEKPGATHIEFPEDVADEH--TDSKPLK---RSLAR 180 Query: 183 NPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLMGKG 242 P + ++ A+K+I AK PI++ G G LL+ +E IP TT +GKG Sbjct: 181 RPE--AEDKAVRAAVKMIEDAKSPILVIGAGGNRKQTGRMLLQFIEKTGIPFVTTQLGKG 238 Query: 243 CISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNAKIIHIDI 302 I E HP LG + + + +D++I++G ++ +++ T +IH+ Sbjct: 239 VIDECHPKFLGCAALSAGDFVHRSIEHADLIINVGHDVIEKPPFFMRNGGT--PVIHVSS 296 Query: 303 DPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQW-IENVNSLKK 361 AE+ V ++GD I N K D +W + + +K Sbjct: 297 KTAEVDPVYFPQVEVIGD--------------IANAIWKMQKDIVPSGRWNFDFMMKARK 342 Query: 362 SSI----PVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQT 417 + + + D + PI P +V+E+ + + II D G ++W A + + Sbjct: 343 AEVAHTETLEDDERFPIFPPHLVREIRRAMP-----ADGIICLDNGVYKIWFARNYPARQ 397 Query: 418 PRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVVI 477 + L L TMG G PSA+ + + PD KV+ I GDGGFMMN QE+ T + + + Sbjct: 398 QNTVLLDNALATMGAGLPSAMASAMVYPDRKVMAICGDGGFMMNSQEMETAVRLGLNITV 457 Query: 478 CIFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEINEALKE 537 I ++ + GM+ +W+ G + + +G PDF+K AESYG K R+ES + + +KE Sbjct: 458 LILNDSSYGMI-RWKQANMGFKDWGLTYGN-PDFVKYAESYGAKGHRVESAAHLTKLIKE 515 Query: 538 AINCDEPYLLDFAIDPS 554 ++ +L+D +D S Sbjct: 516 CLDTPGVHLIDCPVDYS 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: 739 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: 550 Length adjustment: 36 Effective length of query: 563 Effective length of database: 514 Effective search space: 289382 Effective search space used: 289382 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