Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_013836184.1 THICY_RS08405 acetolactate synthase large subunit
Query= curated2:O08353 (599 letters) >NCBI__GCF_000214825.1:WP_013836184.1 Length = 547 Score = 314 bits (805), Expect = 5e-90 Identities = 193/555 (34%), Positives = 299/555 (53%), Gaps = 27/555 (4%) Query: 1 MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARA 60 MN A+ +K LE E+VE +FG PG L DAL S++ + TRHEQ AA AD Y R Sbjct: 1 MNAAQLFVKCLENEQVEFIFGIPGEENLDLVDALLDSEIRFITTRHEQGAAFMADVYGRL 60 Query: 61 SGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMP 120 +GK GVC+ T GPGATNLVTGVA A+ D++P+VA+ GQ T + ++ Q +D + +F P Sbjct: 61 TGKAGVCLSTLGPGATNLVTGVADANMDNAPLVAIAGQAATTRMHKESHQVVDLVSMFKP 120 Query: 121 IVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLI 180 I K+ QI + +PE+ R AF+IAQT +PG ID P+++ E+ P+P K Sbjct: 121 ITKYATQILEPDTVPEVVRKAFKIAQTEKPGASFIDFPENIAEMA--TLSQPLPVK---- 174 Query: 181 GYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLMG 240 ++ T + IK+A+ I SA+ P+IL G G + + A+ ++ L + NIP T M Sbjct: 175 -HSRPTTASEKLIKEAVLAIQSAESPLILVGNGAIRANASAQVYALAKQRNIPTVNTFMA 233 Query: 241 KGCIS-ENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNAKIIH 299 KG + + A+G G+ N S++D++I IG + + + +IIH Sbjct: 234 KGVVPFFKNATAMGTAGLQKGDYENGGFSKADLVICIGFDMVE-YHPHLWNPRHQHRIIH 292 Query: 300 IDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIENVNSL 359 ID PAE+ + ++ ++GD + + QL ++N + D + +N Sbjct: 293 IDPLPAEVDASYLPEIELIGD----IASNLLQLSAMLNTRANFPLDHPLRDATMAEMNRC 348 Query: 360 KKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQTPR 419 K S D P+ PQKI+ +L + N I DVG ++MW+A F+ + P Sbjct: 349 KVS-------QDFPLLPQKIIWDLRTA-----MKSNDIAICDVGAHKMWIARMFRAEKPN 396 Query: 420 SFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVVICI 479 + + S G MG P AI AK+A P+ V+ +TGD GFMMN QE+ T P+VI I Sbjct: 397 TCIISNGFAGMGIAVPGAIAAKLAMPNRAVVAVTGDAGFMMNSQEIETALRCETPIVILI 456 Query: 480 FDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEINEALKEAI 539 +++ G++ Q YG R ++F PDF++ A+S+G K RI +E+ L++A+ Sbjct: 457 WNDSQYGLIEWKQTRKYG-RAAYIDFKN-PDFVQYAQSFGAKGYRINQADELLPTLEQAL 514 Query: 540 NCDEPYLLDFAIDPS 554 + ++D +D S Sbjct: 515 KDNTVSVIDCPVDYS 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: 708 Number of extensions: 30 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: 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