Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate SM_b20681 SM_b20681 glyoxylate carboligase
Query= curated2:O08353 (599 letters) >FitnessBrowser__Smeli:SM_b20681 Length = 594 Score = 328 bits (841), Expect = 4e-94 Identities = 189/589 (32%), Positives = 317/589 (53%), Gaps = 36/589 (6%) Query: 1 MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALH-HSDLIHLLTRHEQAAAHAADGYAR 59 M +A + LE E ++ FG PG A+ PFY AL + H+L RH + A+H A+GY R Sbjct: 4 MRAVDAAVYVLEKEGIDCAFGVPGAAINPFYSALRARGSIRHILARHVEGASHMAEGYTR 63 Query: 60 AS-GKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLF 118 A G +GVCIGTSGP T+++TG+ +A +DS P++ +TGQ P + + FQ +D + Sbjct: 64 ARHGNIGVCIGTSGPAGTDMITGLYSASADSIPILCITGQAPRARLDKEDFQAVDIAKIA 123 Query: 119 MPIVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVK 178 P+ K + + +P +F+ AF + ++GRPGPV IDLP DVQ E++ D + Sbjct: 124 APVTKWAVTVMEPALVPFVFQKAFHLMRSGRPGPVLIDLPVDVQLAEIEFDPE---TYEP 180 Query: 179 LIGYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTL 238 L Y P Q +KA+ ++ A+RP+I+AGGG++ + A++ L + E+ +PV TL Sbjct: 181 LSAYKPAAT--RAQAEKALAMLNEAERPLIVAGGGIINADASDLLTEFAEITGVPVVPTL 238 Query: 239 MGKGCISENHPLALGMVGMHGT-KPANYCLSESDVLISIGCRFSDRITGDIKSFATNAKI 297 MG G I ++HPL GM G+ + + N L SD + IG R+++R TG+I ++ K Sbjct: 239 MGWGVIPDDHPLMAGMCGLQTSHRYGNATLLASDFVFGIGNRWANRHTGNIPTYTEGRKF 298 Query: 298 IHIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIENVN 357 IH+DI+P +IG+ D IV DA LK L + + K + S W E Sbjct: 299 IHVDIEPTQIGRVFAPDFGIVSDAGAALK-----LFLDVATEWKTAGKLRDWSAWAEECR 353 Query: 358 SLKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQT 417 K+S + +D P+KPQ++ +E+ + ++T + +G +Q+ A + Sbjct: 354 ERKRSMLRKTHFDQTPLKPQRVYEEM-----NKTFGRDTCYVSTIGLSQIAGAQFLHVYK 408 Query: 418 PRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVVI 477 PR++++ G G +G+ P+A+G + A P+ +++ ++GD F +EL A++ +P + Sbjct: 409 PRNWINCGQAGPLGWTLPAALGVRAADPNRQIVALSGDYDFQFLIEELAVGAQHKLPYLH 468 Query: 478 CIFDNRTLGMVYQWQNLFYGKRQCSVNF-----------GGAPDFIKLAESYGIKARRIE 526 + +N LG++ Q Q F + S+ F G D + +AE G KA R+ Sbjct: 469 VVVNNSYLGLIRQAQRGFNMDFEVSLAFENINADGDAEKGYGVDHVAVAEGLGCKAIRVR 528 Query: 527 SPNEINEALKEA----INCDEPYLLDFAIDPSSALSMVPPGAKLTNIID 571 SPNE +A A P +++F ++ + ++M GA + +++ Sbjct: 529 SPNEFADAFDRAQALMAEHQVPVVIEFILERVTNIAM---GADINAVVE 574 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: 762 Number of extensions: 41 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: 594 Length adjustment: 37 Effective length of query: 562 Effective length of database: 557 Effective search space: 313034 Effective search space used: 313034 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 09 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