Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_013721657.1 ALIDE2_RS06745 glyoxylate carboligase
Query= curated2:O08353 (599 letters) >NCBI__GCF_000204645.1:WP_013721657.1 Length = 596 Score = 332 bits (852), Expect = 2e-95 Identities = 193/595 (32%), Positives = 330/595 (55%), Gaps = 45/595 (7%) Query: 1 MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALH-HSDLIHLLTRHEQAAAHAADGYAR 59 M EA + LE E V + FG PG A+ P Y A+ H + H+L RH + A+H A+GY R Sbjct: 4 MKAIEAAVCVLEKEGVSVAFGVPGAAINPLYAAMKAHGGIGHILARHVEGASHMAEGYTR 63 Query: 60 A-SGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLF 118 A +G +GVCIGTSGP T+++TG+ +A +DS P++ +TGQ P + + FQ +D + Sbjct: 64 AVAGNIGVCIGTSGPAGTDMITGLYSASADSIPILCITGQAPRARLHKEDFQAVDIAAIA 123 Query: 119 MPIVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQ--ELELDIDKH-PIPS 175 P+ K + + Q+P F+ AF + ++GRPGPV IDLP DVQ E+E DI+ + P+P+ Sbjct: 124 KPVTKWATTVLEPAQVPRAFQQAFHLMRSGRPGPVLIDLPIDVQLAEIEFDIETYEPLPA 183 Query: 176 KVKLIGYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVC 235 Y P + Q +KAI ++ A+RP+I++GGGV+ + A+ L++L ELL++PV Sbjct: 184 ------YKPAATRN--QAEKAISMLNEAERPLIVSGGGVINADASALLVELAELLHVPVI 235 Query: 236 TTLMGKGCISENHPLALGMVGMHGT-KPANYCLSESDVLISIGCRFSDRITGDIKSFATN 294 TLMG G I ++HPL GM G+ + + N + SD ++ IG R+++R TG + + Sbjct: 236 PTLMGWGSIPDDHPLMAGMCGLQTSHRYGNATMLASDFVLGIGNRWANRHTGSVDVYTKG 295 Query: 295 AKIIHIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIE 354 K +H+DI+P +IG+ D IV DA LK ++ + ++ K ++ S W+ Sbjct: 296 RKFVHVDIEPTQIGRVFAPDYGIVSDAGAALKLFVE-----VAREWKAAGRLKDRSGWVA 350 Query: 355 NVNSLKKS--SIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHY 412 K S + +DD+P+KPQ++ + + + N++K+T + +G +Q+ A + Sbjct: 351 ECQGRKNSVEYLRKTQFDDVPMKPQRVYQCM-----NRNLDKDTCYVSTIGLSQIAGAQF 405 Query: 413 FKTQTPRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYN 472 PR +++ G G +G+ P+A+G +VA P+ +++ ++GD F +EL A++ Sbjct: 406 LHVYKPRHWINCGQAGPLGWTVPAALGVRVADPERRIVALSGDYDFQFMIEELAVGAQFK 465 Query: 473 IPVVICIFDNRTLGMVYQWQNLF------------YGKRQCSVNFGGAPDFIKLAESYGI 520 +P V + +N LG++ Q Q F + + G D +K+ E G Sbjct: 466 LPYVHVLVNNSYLGLIRQAQRAFSIDYCVQLAFDNINMDEGEASRGYGVDHVKVVEGLGC 525 Query: 521 KARRIESPNEINEALKEA----INCDEPYLLDFAIDPSSALSMVPPGAKLTNIID 571 KA R+ P + A+++A P +++ ++ + +SM G ++ N+I+ Sbjct: 526 KAIRVHRPEDFAPAMRQAEAWMAEHRTPVVIECILERVTNISM---GTEIDNVIE 577 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: 43 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: 596 Length adjustment: 37 Effective length of query: 562 Effective length of database: 559 Effective search space: 314158 Effective search space used: 314158 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