Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_058931183.1 AU252_RS13570 glyoxylate carboligase
Query= curated2:O08353 (599 letters) >NCBI__GCF_001484605.1:WP_058931183.1 Length = 592 Score = 333 bits (855), Expect = 9e-96 Identities = 188/556 (33%), Positives = 314/556 (56%), Gaps = 39/556 (7%) Query: 1 MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLI-HLLTRHEQAAAHAADGYAR 59 M +A + L E FG PG A+ PFY A+ + + H L RH + A+H ADGY+R Sbjct: 4 MRTVDAAVAILVKEGAIEAFGLPGAAINPFYSAMRKNGGVRHTLARHVEGASHMADGYSR 63 Query: 60 AS-GKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLF 118 A G +G+CIGTSGP T+++TG+ A +DS PM+ +TGQ P + + FQ +D + Sbjct: 64 AKDGNIGICIGTSGPAGTDMITGLYAAWADSIPMLCITGQAPVAKLHKEDFQAVDIQTIA 123 Query: 119 MPIVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQ--ELELDIDKHPIPSK 176 P+ K I + Q+P F+ AF++ ++GRPGPV +DLP DVQ E+E DID Sbjct: 124 APVTKMAMTIMEPGQVPGAFQKAFQLMRSGRPGPVLLDLPFDVQMAEIEFDID------- 176 Query: 177 VKLIGYNPTTIGHP----RQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNI 232 Y P + P +Q++KA+ ++ +A+RP+I+AGGG++ +GA+ +L++L ELLN+ Sbjct: 177 ----AYEPIVVQKPTASRKQLEKALDMLTAAERPLIVAGGGIINAGASAQLVELAELLNV 232 Query: 233 PVCTTLMGKGCISENHPLALGMVGMHGT-KPANYCLSESDVLISIGCRFSDRITGDIKSF 291 PV TLMG G I ++H L GMVG+ + + N + SD +I IG R+++R TG + ++ Sbjct: 233 PVIPTLMGWGTIPDDHVLMAGMVGLQTSHRYGNETMLASDFVIGIGNRWANRHTGGLDTY 292 Query: 292 ATNAKIIHIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQ 351 K +HIDI+P +IG+ + D+ I DA L +I+ + ++ + + + Sbjct: 293 TAGRKFVHIDIEPTQIGRVFSPDLGIASDAGAALDGLIE-----LARERQAAKSLPDYAG 347 Query: 352 WIENVNSLKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAH 411 W+ + K + ++++PIKPQ++ +E+ + K+T + +G +Q+ A Sbjct: 348 WVAECTARKGALQRKTHFENVPIKPQRVYEEM-----NKAFGKDTTYVSTIGLSQIAGAQ 402 Query: 412 YFKTQTPRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEY 471 PR ++++G G +G+ P+A+G KPD V+ ++GD F +EL A++ Sbjct: 403 LLHVFGPRQWINAGQAGPLGWTAPAALGVVRGKPDETVVALSGDYDFQFMIEELAVGAQF 462 Query: 472 NIPVVICIFDNRTLGMVYQWQNLFYGKRQCSVNF---------GGAPDFIKLAESYGIKA 522 N+P + + +N LG++ Q Q F ++ S+ F G D +K+AE G KA Sbjct: 463 NLPYIHVVVNNSYLGLIRQSQRGFEMEQNVSLAFENINSPETNGYGVDHVKVAEGLGCKA 522 Query: 523 RRIESPNEINEALKEA 538 R+E+P+++ A +A Sbjct: 523 IRVENPSDLPAAFDKA 538 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: 813 Number of extensions: 39 Number of successful extensions: 7 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: 592 Length adjustment: 37 Effective length of query: 562 Effective length of database: 555 Effective search space: 311910 Effective search space used: 311910 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