Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_028485570.1 B076_RS0100430 acetolactate synthase large subunit
Query= curated2:O08353 (599 letters) >NCBI__GCF_000483485.1:WP_028485570.1 Length = 548 Score = 312 bits (799), Expect = 3e-89 Identities = 197/577 (34%), Positives = 310/577 (53%), Gaps = 31/577 (5%) Query: 1 MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARA 60 M A+ ++ LE E VE +FG PG L DAL S + + TRHEQ AA AD Y R Sbjct: 1 MKAAKLFVQCLENEGVEFIFGIPGEENLDIMDALLDSKIQFITTRHEQGAAFMADVYGRL 60 Query: 61 SGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMP 120 +G+ GVC+ T GPGATNLVTGVA A+ D++P+VA+ GQ T + ++ Q +D + +F P Sbjct: 61 TGRAGVCLSTLGPGATNLVTGVADANMDNAPLVAIAGQAATTRMHKESHQVVDLVSMFKP 120 Query: 121 IVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLI 180 I K+ Q+ + IPE+ R AF++A+ +PG IDLP+++ E+D D+ P+P+ Sbjct: 121 ITKYATQVLEPETIPEVVRKAFKLAEAEKPGATFIDLPENI--TEMDTDETPLPTSA--- 175 Query: 181 GYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLMG 240 N T+ ++ A +LI +A+ P+IL G G + + A +L VE +IPV T M Sbjct: 176 --NRLTLADHELLEAAAELIQNAEYPLILVGNGAVRAEAGHDLQMFVEKHSIPVVNTFMA 233 Query: 241 KGCIS-ENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNAKIIH 299 KG I + +A+G G+ N ++DV+I +G + + + N KIIH Sbjct: 234 KGIIPFFKNGMAMGSAGLQKGDYENGGFEKADVVICVGFDMVE-YHPHLWNPKRNHKIIH 292 Query: 300 IDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKEN-NDKENISQWIENVNS 358 ID +E+ + + ++G+ + + L +I K + + D I+ +N Sbjct: 293 IDTKKSEVDHSYIPQIELIGN----IGRNLSALGELIPKPQRNSLIDFPLRDAMIKEMNR 348 Query: 359 LKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQTP 418 S+ D P+ PQKI+ +L + K I DVG ++MWMA F+ P Sbjct: 349 CSTST-------DWPMLPQKIIWDLRTA-----MKKADIAICDVGAHKMWMARMFRCDLP 396 Query: 419 RSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVVIC 478 + + S G MG P AI AK+A PD V+ +TGD GFMMN QE+ T N PVVI Sbjct: 397 NTCIISNGFAGMGIAVPGAIAAKLAYPDKAVVAVTGDAGFMMNSQEIETALRCNAPVVIL 456 Query: 479 IFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEINEALKEA 538 I+++ G++ +W+ R ++F PDF+ A+S+G + RIES +++ ALK+A Sbjct: 457 IWNDSQYGLI-EWKQQRRFGRSAYIDFKN-PDFVAYAKSFGAEGVRIESADQLLPALKKA 514 Query: 539 INCDEPYLLDFAIDPSSALSMVPPGAKLTNIIDAVQE 575 +N + ++D +D S + A L N++ +++ Sbjct: 515 LNANTVTVIDCPVDYSQNDRLT---ALLGNVLSEIED 548 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: 719 Number of extensions: 29 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: 548 Length adjustment: 36 Effective length of query: 563 Effective length of database: 512 Effective search space: 288256 Effective search space used: 288256 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