Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_005456689.1 SACCYDRAFT_RS12715 glyoxylate carboligase
Query= curated2:O08353 (599 letters) >NCBI__GCF_000244975.1:WP_005456689.1 Length = 591 Score = 330 bits (845), Expect = 1e-94 Identities = 190/591 (32%), Positives = 321/591 (54%), Gaps = 42/591 (7%) Query: 1 MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALH-HSDLIHLLTRHEQAAAHAADGYAR 59 M +A + LE E FG PG A+ PFY AL H + H+L RH + A+H A+GY R Sbjct: 4 MRAVDAAVLILEKEGSTQAFGLPGAAINPFYSALRAHGGIRHVLARHVEGASHMAEGYTR 63 Query: 60 A-SGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLF 118 A +G +GVC+GTSGP T+++TG+ +A +DS P++ +TGQ P + + FQ ++ + Sbjct: 64 AEAGNIGVCVGTSGPAGTDMITGLYSASADSIPILCITGQAPVDKLHKEDFQAVNIASIA 123 Query: 119 MPIVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVK 178 P+ K + + Q+P F AF+I + GRPGPV IDLP DVQ E++ D Sbjct: 124 APVTKWAVTVLEPAQVPGTFAKAFQIMREGRPGPVLIDLPLDVQLAEIEFDPDT------ 177 Query: 179 LIGYNPTTIGHP----RQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPV 234 Y P + P +QI++A+ ++ +A RP+I++GGGV+ + A++ L++ E +PV Sbjct: 178 ---YEPLPVVKPAATRKQIERALSMLVAADRPLIVSGGGVINADASDLLVEFAEATGVPV 234 Query: 235 CTTLMGKGCISENHPLALGMVGMHGT-KPANYCLSESDVLISIGCRFSDRITGDIKSFAT 293 TLMG G I ++HPL GMVG+ + + N L SD ++ +G R+++R TG I ++ Sbjct: 235 VPTLMGWGTIPDDHPLTAGMVGLQTSHRYGNATLLASDFVLGVGNRWANRHTGGIDTYTA 294 Query: 294 NAKIIHIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWI 353 +H+DI+P +IG+ D IV DAK L+ ++ + ++ K + + + W Sbjct: 295 GRTFVHVDIEPTQIGRVFAPDYGIVSDAKAALELFVE-----VAREWKRDGRLPDYTGWA 349 Query: 354 ENVNSLKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYF 413 E +++ +D +PIKPQ++ +E+ + + T +G +Q+ A Sbjct: 350 EECRRRRRTMQRKTHFDTVPIKPQRVYEEM-----NRAFGPDVRYVTTIGLSQIQAAQLL 404 Query: 414 KTQTPRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNI 473 PR ++++G G +G+ P+A+G A PDS V+ ++GD F +EL A++NI Sbjct: 405 HVYKPRHWINAGQAGPLGWTVPAALGVATADPDSTVVALSGDYDFQFLIEELAVGAQFNI 464 Query: 474 PVVICIFDNRTLGMVYQWQNLFYGKRQCSVNF---------GGAPDFIKLAESYGIKARR 524 P V + +N LG++ Q Q F ++F G D +K+AE G KA R Sbjct: 465 PYVHVVVNNAYLGLIRQAQRNFDMDYCVQLSFDNINAPELGGYGVDHVKVAEGLGCKALR 524 Query: 525 IESPNEINEALKEAINCDE----PYLLDFAIDPSSALSMVPPGAKLTNIID 571 + P +I AL++A E P +++ ++ + +SM G ++ ++++ Sbjct: 525 VFEPEDIRPALEKAKTLAEEQRVPVVVEVVLERITNVSM---GMEIDDVVE 572 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: 798 Number of extensions: 36 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: 591 Length adjustment: 37 Effective length of query: 562 Effective length of database: 554 Effective search space: 311348 Effective search space used: 311348 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