Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_085773067.1 B1812_RS19550 thiamine pyrophosphate-binding protein
Query= BRENDA::P00893 (574 letters) >NCBI__GCF_002117405.1:WP_085773067.1 Length = 571 Score = 229 bits (584), Expect = 2e-64 Identities = 166/560 (29%), Positives = 264/560 (47%), Gaps = 24/560 (4%) Query: 3 MLSGAEMVVRSLIDQGVKQVFGYPGGAVLDIYDALHTVGGIDHVLVRHEQAAVHMADGLA 62 M G + ++ +L ++G+ +F PGG V AL + ++ E A +MADG A Sbjct: 1 MRQGVDFILEALSEEGLDHLFMVPGGLVDPFLPALGRQTALTPIVAAQEGGAAYMADGYA 60 Query: 63 RATGEVGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQVATSLIGYDAFQEC-----D 117 RA+G +GV L GPG NA+T IATA D PL++LSG+V+TSL G FQ+ D Sbjct: 61 RASGNLGVALCIGGPGLANAVTAIATARTDGSPLLLLSGEVSTSLEGRGMFQDASPQTLD 120 Query: 118 MVGISRPVVKHSFLVKQTEDIPQVLKKAFWLAASGRPGPVVVDLPKDILNPANKLPYVWP 177 V + +P+ ++S + +++P + K+A + PV + LP D L Y Sbjct: 121 DVSMLKPIARYSSSIDNPKNLPHLFKRAMLQLRTQPSAPVHLSLPGDCLTGQLAAEYAAI 180 Query: 178 ESVSMRSYNPTTTGHKGQIKRALQTLVAAKKPVVYVGGGAITAGCHQQLKETVEALNLPV 237 + R T + + R K + G G A + L+E E +PV Sbjct: 181 DPALRRPGTLALTAAEASL-RHFDGPTPPIKIAILAGAGVEHAESARALREFAELWRIPV 239 Query: 238 VCSLMGLGAFPATHRQALGMLGMHGTYEANMTMHNA--DVIFAVGVRFDDRTTNNLAKYC 295 +L G G FP H +LG+ G GT+ A + A D++ +G ++R T + A Sbjct: 240 ATTLRGKGVFPEDHPLSLGVFGYAGTHHARSALLGAPLDLLIVLGTGLNERDTMHWALQI 299 Query: 296 PNATVLHIDIDPTSISKTVTADIPIVGDARQVLEQMLELLSQESAH----QPLDEIRDWW 351 + +++++ S+ A +VGD L+ +L+ E+ H L+ W Sbjct: 300 EPSVAINVNLSAVSLGMHAQAG-AVVGDCGAYLKFLLD--RGEALHGSLAPTLEARAQWL 356 Query: 352 QQIEQW-RARQCLKYDTHSEKIKPQAVIETLWRLTKGDAYVTSDVGQHQMFAALYYPFDK 410 +I R + + + + P VI L +L D + D G H+ FA Y+ + Sbjct: 357 SEIRSTPRLQDAANCASDATPLHPARVISELRKLFPRDGVLLVDSGAHRAFAGHYWESYE 416 Query: 411 PRRWINSGGLGTMGFGLPAALGVKMALPEETVVCVTGDGSIQMNIQELSTALQYELPVLV 470 PR +I++ LG MG+ + AA GV+ A P V +TGDG ++M+ E++TA +Y LP++ Sbjct: 417 PRTYISATNLGPMGWAIAAATGVQCASPTRRVAVITGDGCMRMSGMEVATAARYRLPIVF 476 Query: 471 VNLNNRYLGMVKQWQDMIYSGRHSQSYMQSLP--DFVRLAEAYGHVGIQISHPHELESKL 528 V +NN LG V W G + + SLP D+ +A G G + P EL S Sbjct: 477 VVINNAALGNV--WLRAHKFGA-TPDELTSLPDHDWAAFGQALGCRGETVRRPAELASAF 533 Query: 529 SEALEQVRNNRLVFVDVTVD 548 + ALE + +DV D Sbjct: 534 ARALESAEPS---VIDVKAD 550 Lambda K H 0.319 0.135 0.403 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: 721 Number of extensions: 28 Number of successful extensions: 4 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: 574 Length of database: 571 Length adjustment: 36 Effective length of query: 538 Effective length of database: 535 Effective search space: 287830 Effective search space used: 287830 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 (21.8 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