Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_074201909.1 BUQ81_RS08105 acetolactate synthase large subunit
Query= curated2:O08353 (599 letters) >NCBI__GCF_900141795.1:WP_074201909.1 Length = 548 Score = 319 bits (818), Expect = 2e-91 Identities = 194/558 (34%), Positives = 308/558 (55%), Gaps = 35/558 (6%) Query: 2 NGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARAS 61 N A+ +++ LEAE+V +FG PG L DAL S + + TRHEQ AA AD Y R + Sbjct: 3 NAAQLLVQCLEAEEVRFIFGIPGEENLDLIDALADSPIQFITTRHEQGAAFMADVYGRLT 62 Query: 62 GKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMPI 121 GK GVCI T GPGATNLVTGVA A+ D +P+VAL GQ T + ++ Q +D + LF PI Sbjct: 63 GKAGVCISTLGPGATNLVTGVADANMDRAPIVALAGQAATTRMHKESHQVLDLVSLFNPI 122 Query: 122 VKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLIG 181 K+ QI + +PE+ R AF++AQ+ +PG ID P+++ ++ + P+P + + + Sbjct: 123 SKYAAQILEPETVPEVVRKAFKVAQSEKPGATFIDFPENI--AKMPVPNTPLPVRRERLP 180 Query: 182 YNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLMGK 241 P + +KKA +LI +A+ P+ILAG GV+ + A+ EL E L IPV T M K Sbjct: 181 MAPES-----HLKKAAELIDAAENPLILAGNGVIRTHAHLELQAFAEALQIPVVNTFMAK 235 Query: 242 GCIS-ENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNA----K 296 G + +PLALG G+ N ++D++I++G D + + + N + Sbjct: 236 GVVPFFKNPLALGTAGLQAGDYENCGFRDADLVITVG---FDMV--EYHPYLWNPHHSHR 290 Query: 297 IIHIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIENV 356 IIHID AE+ ++ D+ +VG+ + + +++L ++ ++ IE + Sbjct: 291 IIHIDTTAAEVDQDYLPDIELVGN----IAKNLRRLTHLGIAPKHSRIGRQLRHSLIEEM 346 Query: 357 NSLKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQ 416 N S+ P+KPQKI+ +L V+ + I DVG ++MWMA F+ + Sbjct: 347 NRCSHSTA-------WPLKPQKIIWDLRTVLP-----REGITVVDVGAHKMWMARMFRAE 394 Query: 417 TPRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVV 476 P + + S G +MG P AI A + P+ V+ ++GD GFMMN QEL T + +V Sbjct: 395 QPNTCIISNGFASMGIALPGAIAAALTYPERPVVAVSGDAGFMMNVQELETAVRLGVNMV 454 Query: 477 ICIFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEINEALK 536 + I+++ G++ +W+ R V+FG PDF++LA+S+G + RI+ + ALK Sbjct: 455 VLIWNDGGYGLI-EWKQQRQFGRSAYVSFGN-PDFVQLAQSFGAQGTRIDRAEALQPALK 512 Query: 537 EAINCDEPYLLDFAIDPS 554 A+ +++D +D S Sbjct: 513 SALEAGGLHVIDCPVDYS 530 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: 730 Number of extensions: 32 Number of successful extensions: 8 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