Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_012976370.1 AZL_RS20450 thiamine pyrophosphate-binding protein
Query= curated2:O08353 (599 letters) >NCBI__GCF_000010725.1:WP_012976370.1 Length = 584 Score = 279 bits (713), Expect = 3e-79 Identities = 175/575 (30%), Positives = 308/575 (53%), Gaps = 27/575 (4%) Query: 1 MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSD--LIHLLTRHEQAAAHAADGYA 58 M GA+ +++ L A V+++FG PG +PFY+AL + + H++ R E++A + AD Y Sbjct: 1 MRGADILVEMLIAYGVDVVFGVPGDTNVPFYEALQEREGRIRHVMARDERSAGYMADAYG 60 Query: 59 RASGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLF 118 R + K V SG GA + VA +++ S P++ LT +P G E+D LF Sbjct: 61 RFTSKPAVFECPSGAGAMYSLPPVAESNASSVPVILLTIDIPLPGEGRGVLTELDCARLF 120 Query: 119 MPIVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVK 178 PI K + Q++ ++PEI R AF +A +G+PG VH+ +P+D+ E+D + + + + Sbjct: 121 EPITKMSVQVKSAEKLPEILRRAFRVACSGKPGAVHLQIPEDMLRAEVDPARVSLHVEEE 180 Query: 179 LIGYNP-TTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTT 237 + T+ P + + + L+++++RP+I++GGGV S A E+ L E LNIPVCTT Sbjct: 181 CASFPAFPTLPTPDTLHRLMALLSASERPLIVSGGGVNRSCAGPEVTALAERLNIPVCTT 240 Query: 238 LMGKGCISENHPLALGMVGMHGTKP-ANYCLSESDVLISIGCRFSDRIT--GDIKSFATN 294 + G+G + ++H LA+G++G +G P AN+ L +D ++ +G + +T N Sbjct: 241 MTGQGTMPDDHRLAVGVIGDNGFHPHANWALEHADFVLFVGSKMGSVVTIGWTFPKITLN 300 Query: 295 AKIIHIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIE 354 ++ IDIDP + N + + GDAKL L ++I + ++D+ W++ Sbjct: 301 KRVAQIDIDPEIMANNYENVLSVPGDAKLTLAQLIDL--------APADHDRGKTQPWVD 352 Query: 355 NVNSLK----KSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMA 410 +N L+ +++ P+++ D +P++P+++V+ ++ K I +D G +M Sbjct: 353 ELNGLRAEFWRNAEPLLNSDSLPLRPERVVRCFNEALE--AHGKPAHIYSDAGTPTPYMT 410 Query: 411 HYFKTQTPRS-FLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIA 469 + K + R+ F G +G P+ +GA A + + I + GDG F M EL T+ Sbjct: 411 RFLKLKDRRTRFAIPRAFGGLGSALPATVGAWFADKERRPIGMFGDGSFGMAVGELETLV 470 Query: 470 EYNIPVVICIFDNRTLGMVYQWQNLFYGKRQC-SVNFGGAPDFIKLAESYGIKARRIESP 528 +P ++ +F+N T G + L G QC SV+F P +AE++G++A + Sbjct: 471 RLQVPAILLLFNNGTFGWIKGLHRL-RGHNQCFSVDF-MPPQGQAIAEAFGVRAWTARTS 528 Query: 529 NEINEALKEAINCDE-PYLLDFAIDPSSALSMVPP 562 E+++AL EA D P L+D ++ S VPP Sbjct: 529 VELDKALAEAFAYDSGPCLIDIHVE--SIADRVPP 561 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: 804 Number of extensions: 47 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: 584 Length adjustment: 37 Effective length of query: 562 Effective length of database: 547 Effective search space: 307414 Effective search space used: 307414 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