Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_019556958.1 F612_RS0106535 thiamine pyrophosphate-binding protein
Query= curated2:Q02137 (575 letters) >NCBI__GCF_000381085.1:WP_019556958.1 Length = 611 Score = 271 bits (693), Expect = 6e-77 Identities = 189/573 (32%), Positives = 292/573 (50%), Gaps = 37/573 (6%) Query: 23 LGVEIIFGYPGGAMLPLYDAIHNFEGIQHILARHEQGATHEAEGYAKSSGKVGVVVVTSG 82 LGV+ +F GG + L D + E + I HEQ + A YAK + V + TSG Sbjct: 26 LGVKDVFLVTGGGAMFLNDGVAKHEKLNPICNHHEQASAMAAVAYAKYNNSYSVAMTTSG 85 Query: 83 PGATNAVTGIADAYLDSVPLLVFTGQV--------GPLSIGKDAFQEADTVGITAPITKY 134 GATNAVTG+ DA+ D+ P+ +GQV PLS+ + QEA+ + I + I+KY Sbjct: 86 CGATNAVTGLLDAWQDNTPVFFISGQVKRKETVHNSPLSLRQVGVQEANIIPIVSSISKY 145 Query: 135 NYQIRETADIPRIVTEAYYLARTGRPGPVEIDLPKDVSTLEVTEINDPSLNLPHYHESEK 194 + + E + I + +A +LA +GRPGPV +D+P+DV + E + L H+ E+ Sbjct: 146 SVMVNEPSQIAYHLEKAAFLAISGRPGPVWVDIPQDVQGAMIEECD-----LIHFSPLEE 200 Query: 195 AT-------DEQLQELLTELSVSKKPVIIAGGGINYSGSVDIFRAFVEKYQIPVVSTLLG 247 D+ L ++ +L +++P+++AG GI +V F F+ KY++PVV+T LG Sbjct: 201 GLAYTDNLLDKDLITIIKDLDNAQRPIVLAGNGIRLGNAVSEFIEFINKYRLPVVTTYLG 260 Query: 248 LGTLPISHELQLGMAGMHGSYAANMALVEADYIINLGSRFDDRVVSNPAKV-AKNAVVAH 306 + + +L +G G+ G A N AL +D ++ LGSR V + A+NA + Sbjct: 261 IDLIASEDDLCVGRVGIKGDRAGNFALQNSDLVLVLGSRLSVAVSGFEYDLFARNAKIIV 320 Query: 307 IDIDAAELGK-IVKTDIPILSDLKAALSRLLQLNKVRTDFND---WIKTVTKNKEKAPF- 361 +DIDA E K VK D+ I +D+K+ L+ LN + +F+D WI+ + K P Sbjct: 321 VDIDAIEHKKNTVKIDVFINADIKSFLN---VLNSQKMNFSDRKKWIERCNIWRNKWPVA 377 Query: 362 --TYEPQNHDIRPQETIKLIGEYTQGDAIIVTDVGQHQMWVAQYYPYKNARQLITSGGMG 419 YE ++ I IK +G Y D+ IV D G AQ +++ ITSG Sbjct: 378 LNAYEDRDGAINMYTFIKYLGRYLLPDSTIVADAGSAYYVTAQALRISGSQRYITSGAQA 437 Query: 420 TMGFGIPAAIGAKLAQPNKNVIVFVGDGGFQMTNQELALLNGYGIAIKVVLINNHSLGMV 479 MGF IPAAIGA +A+ + V+ GDG FQM QEL + Y + IK+ + NN + Sbjct: 438 DMGFTIPAAIGASIAKKGE-VVAITGDGSFQMNIQELQTIVHYQLPIKIFVWNNDGYLSI 496 Query: 480 RQWQESFYEER---RSQSVFDVEPNFQLLAEAYGIKHVKLDNPKTLADDLKIITE-DEPM 535 R Q+ F+E R S P+ +AEAYG+++ L LK + P+ Sbjct: 497 RTTQKKFFEGRLMGTEASTGISFPDLHKIAEAYGLQYFIAKTFVALEGTLKETMDFVGPV 556 Query: 536 LIEVLISKSEHVLPMIPAGLHSD-EMIGLHFTD 567 + E++ + ++P + A D M+ F D Sbjct: 557 ICEIICPPFQEIIPAVSAMKKDDGTMVSKPFED 589 Lambda K H 0.316 0.135 0.385 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: 748 Number of extensions: 31 Number of successful extensions: 6 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: 575 Length of database: 611 Length adjustment: 37 Effective length of query: 538 Effective length of database: 574 Effective search space: 308812 Effective search space used: 308812 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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