Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_017599575.1 D471_RS0116105 glyoxylate carboligase
Query= curated2:O08353 (599 letters) >NCBI__GCF_000341125.1:WP_017599575.1 Length = 571 Score = 387 bits (995), Expect = e-112 Identities = 218/586 (37%), Positives = 333/586 (56%), Gaps = 36/586 (6%) Query: 1 MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHH-SDLIHLLTRHEQAAAHAADGYAR 59 M A+I+ L+ E V+ FG PG A+LP Y A+ + HL RHE+ A H ADG++R Sbjct: 4 MPAMNAVIEVLKDEGVDTAFGCPGAAILPLYKAMEDVGGIEHLTVRHEEGATHMADGWSR 63 Query: 60 ASGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFM 119 +GKVGV IGTSGP TN++TG+ TA +DS P+V +TGQ T L+ + FQ +D + + Sbjct: 64 TTGKVGVAIGTSGPAGTNMITGLYTAMADSVPIVCITGQAMTSLLDKEGFQAVDIVEIAK 123 Query: 120 PIVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKL 179 P+ K QI++ P IFR AF +AQ GRPGPV +D+P DV + ++ D I + +++ Sbjct: 124 PVTKWAVQIREAATAPWIFREAFRVAQEGRPGPVLVDIPLDVAKQVIEYDP-AIDAPLRI 182 Query: 180 IGYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLM 239 P H ++++A+ ++ +A+RP++LAGGGV+LS A+EEL +L E LN+PV TLM Sbjct: 183 NSVEP----HQPRVERALDMLLAAERPLLLAGGGVILSEASEELKELAEYLNVPVQVTLM 238 Query: 240 GKGCISENHPLALGMVGMH-GTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNAKII 298 GKG E+ PL GM G+ + N ESD+++++G RF DR TG I + + I Sbjct: 239 GKGSFDEDSPLYSGMTGVQTSQRYGNASFLESDLVLAVGARFGDRHTGQIDVYRGDRTFI 298 Query: 299 HIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIENVNS 358 H+DI+P +IG+ D+ +V DAKL L +++ +K +K + W++ V Sbjct: 299 HVDIEPTQIGRVFEPDLGVVSDAKLFLSALLEA--------AKARGEKAEVQPWVDRVGE 350 Query: 359 LKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQTP 418 LK++ D+D +PIK ++ KE+ V D +T T +G Q+W + K P Sbjct: 351 LKRTMTRREDFDSVPIKAPRVYKEINEVFD-----ADTYFVTAIGLYQIWGGQHQKAYKP 405 Query: 419 RSFLSSGGLGTMGFGFPSAIGAKVA----KPDSKVICITGDGGFMMNCQELGTIAEYNIP 474 R + G G +G+ P+AIG K A +PD++V+ I GD GF +EL A+YN+P Sbjct: 406 RHYQICGQAGPLGWEIPAAIGVKKALKNTEPDAEVVGIVGDYGFQYMVEELAVAAQYNVP 465 Query: 475 VVICIFDNRTLGMVYQWQNLFYGKRQCSVNFGG-APDFIKLAESYGIKARRIESPNEINE 533 VI + +N LG++ Q + Q +++ D +K+ E+YG RR+ PN+I E Sbjct: 466 YVIIMINNEYLGLIRQASIPYEMNYQVDIHYDEFGTDNVKIMEAYGCSGRRVADPNDIRE 525 Query: 534 AL----KEAINCDEPYLLDFAIDPSSALSMVPPGAKLTNIIDAVQE 575 +L KEA P L++ I+ + P IDAV+E Sbjct: 526 SLEWARKEAKATSRPVLVEIMIEREANTPHGPS-------IDAVKE 564 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: 816 Number of extensions: 43 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: 571 Length adjustment: 37 Effective length of query: 562 Effective length of database: 534 Effective search space: 300108 Effective search space used: 300108 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