Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_051327156.1 G491_RS30200 thiamine pyrophosphate-binding protein
Query= curated2:Q02137 (575 letters) >NCBI__GCF_000429905.1:WP_051327156.1 Length = 573 Score = 210 bits (535), Expect = 1e-58 Identities = 167/547 (30%), Positives = 253/547 (46%), Gaps = 19/547 (3%) Query: 12 GSQLVLQTLKELGVEIIFGYPGGAMLPLYDAIHNFEGIQHILARHEQGATHEAEGYAKSS 71 G +L+ + + GVE +F PG ++ P+ A GI + ARHEQ AT AE Y + + Sbjct: 15 GWELIAEAFAQKGVEYLFTVPGESISPIQRAAEA-SGIPIVSARHEQAATFMAETYGRMT 73 Query: 72 GKVGVVVVTSGPGATNAVTGIADAYLDSVPLLVFTGQVGPLSIGKDAFQEADTVGITAPI 131 GK G+V VT GPG TN ++ I +A L + PL++ G G S + Q+ I I Sbjct: 74 GKPGLVAVTFGPGFTNTLSAIQNANLSNSPLILMAGAHGAPSPDRLGLQDMKQEPIIESI 133 Query: 132 TKYNYQIRETADIPRIVTEAYYLARTGRPGPVEIDLPKDVSTLEVTEINDPSLNLPHYHE 191 K + R+T +P + A+ A TGRPGPV ++LP DV L+ ++ ++ L Sbjct: 134 VKKSLVCRQTERLPDYIDMAFRYAGTGRPGPVFLELPIDV--LDGAVESENAVRLHTEVA 191 Query: 192 SEKATDEQLQELLTELSVSKKPVIIAGGGINYSGSVDIFRAFVEKYQIPVVSTLLGLGTL 251 S + +++T + S KPVI+AG G +S + FVEK IPV + G G + Sbjct: 192 SRPIDPNDVVKMMTLIKESLKPVIMAGSGAYFSQAGPELAQFVEKAGIPVFTGKFGRGIV 251 Query: 252 PISHELQLGMAGMHGSYAANMALVEADYIINLGSRFDDRVVSNPAKVAKNAVVAHIDIDA 311 P SH L + AA +A +++D II LG+R + + +A + +DI+ Sbjct: 252 PDSHPLCFESSVGLRPGAAALATIDSDCIILLGNRL-CLYNATGSLYRPDAKIIQVDIEP 310 Query: 312 AELGKIVKTDIPILSDLKAALSRLLQL-------NKVRTDFNDWIKTVTK----NKEKAP 360 E+G+ D I D+K L +R F WI + K NKE + Sbjct: 311 EEIGRNRSVDAAIFGDVKRLLEACTHWIDAKGAGESLRERFAPWIAQLQKEHDNNKELSK 370 Query: 361 FTYEPQNHDIRPQETIKLIGEY-TQGDAIIVTDVGQHQMWVAQYYPYKNARQLITSGGMG 419 F Y I P K I + + D IIV D G W+ Y + + SG G Sbjct: 371 FHYTSDQVPIHPARLAKEIDRFMDRPDDIIVYDGGDMPTWMLSYRTCEAPWNEMASGLYG 430 Query: 420 TMGFGIPAAIGAKLAQPNKNVIVFVGDGGFQMTNQELALLNGYGIAIKVVLINNHSLGMV 479 +G G+P A +KL +P V++ GDG + EL G+ I VV+ NN+ GM Sbjct: 431 CLGCGLPYAAASKLIRPQSRVMLCTGDGSIGFSFMELETCVRKGLPIVVVIGNNNLWGMT 490 Query: 480 RQWQESFYEERRSQSV-FDVEPNFQLLAEAYGIKHVKLDNPKTLADDLKIITE-DEPMLI 537 + +V D P + L EA GI+ ++NP + LK + P ++ Sbjct: 491 ANSMMLKFRHHIPNTVELDFVP-YHKLMEAIGIQGFFVENPADIGPALKAAFDTGGPAIV 549 Query: 538 EVLISKS 544 V+ S Sbjct: 550 NVMTDPS 556 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: 661 Number of extensions: 32 Number of successful extensions: 5 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: 573 Length adjustment: 36 Effective length of query: 539 Effective length of database: 537 Effective search space: 289443 Effective search space used: 289443 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