Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_048040261.1 MM_RS14740 thiamine pyrophosphate-binding protein
Query= curated2:O85293 (571 letters) >NCBI__GCF_000007065.1:WP_048040261.1 Length = 570 Score = 346 bits (887), Expect = 2e-99 Identities = 204/569 (35%), Positives = 313/569 (55%), Gaps = 10/569 (1%) Query: 1 MEILSGAEMVIRSLINQGIQHIFGYPGGAVLDIYDALKTVGGVEHILVRHEQAATHMADG 60 M+ ++GAE++I+ L + G++HIFGY G A+L ++ AL+ +E I+ +EQ+A A G Sbjct: 1 MKEMNGAEVLIKCLEDLGVKHIFGYTGAAILPVFHALRH-SDIEIIVNSNEQSAAFSAAG 59 Query: 61 YARSTGKIGVVLVTSGPGATNAITGIATAYMDSIPMVVISGQVASSLIGYDAFQECDMIG 120 Y+RS+ ++GV +VTSGP TN +T +A AY DSIP++V +GQV IG D+FQ ++ G Sbjct: 60 YSRSSNRVGVAIVTSGPAITNTLTSVADAYGDSIPLLVFAGQVPEHKIGTDSFQHINVRG 119 Query: 121 ISRPIVKHSFLVKRTEDIPIIFKKAFWLASTGRPGPVVIDLPKDILKKTNKYNFIWPKNI 180 I R K + +DI I K A++ + +G+PGPVVID P D K ++Y+ + K Sbjct: 120 IFRDAAKKVIQLSNGDDIETIIKDAYYFSKSGKPGPVVIDFPLDKQIKNHEYHGMDVKRF 179 Query: 181 HIRSYNPTTKGHQGQIKKALRILLKAKKPIIYAGGGIISSNSSEELRIFAEKINCPVTTS 240 SY+ +GQ + ++LL +++P++Y GGG+ S + S+ +R F E P + Sbjct: 180 E-GSYHDDRHLSEGQCENFFKLLLNSRRPLLYLGGGLNSESGSQAVREFNELFGIPSVNT 238 Query: 241 LMGLGAFPGNHIQSISMLGMHGTYEANMAMHYSDVIFAIGVRFDDRTTNNLKKYCPNATI 300 LM G H ++ MLGM GT ANM + +D+ FAIGVR+DDR + + I Sbjct: 239 LMAKGVVDERHDMNLGMLGMFGTPYANMLIQENDLFFAIGVRWDDRVAEKVG-FAIGTDI 297 Query: 301 LHVDIDPTSISKTV---SADIPIVGDAKQVLKEMIELIKKEKQIHSLKEWWSSIGKWKKI 357 ++DI+P + + S +GDA L++++ +K ++EW KK Sbjct: 298 AYIDINPEKMHQIKIERSPKFTFIGDAATALRDLLNYARKHNIRLDIREWQIRARYLKKS 357 Query: 358 KSLEYNKKSNKIKPQKIIQTLFKLTKGTSYITSDVGQHQMFTALYYQFNKPRRWINSGGL 417 L YN+ S I+ K+I L ++ IT+ VG HQM A Y P+ ++ SG Sbjct: 358 WPLNYNRSSEYIQAAKVISMLANHVDESTKITTGVGNHQMLAAQYLSMQCPKSFMTSGSF 417 Query: 418 GTMGFGLPAALGVKLALPKATVICVTGDGSIQMNIQELSTARQYNLAVLILNLNNSSLGM 477 GTMGF LP A+GV A P + VI + GDGS++MN+ EL T +L + IL LNN S GM Sbjct: 418 GTMGFSLPTAIGVHYANPHSGVIAIDGDGSLRMNLGELHTIASLDLPIKILMLNNRSDGM 477 Query: 478 VKQWQDMIYSGRHSHSYMDSLPDFVKLVESYG-HIGLKVKTNEELEEKLILALKKLSEGN 536 V+ QD Y G + + +F ++ S+G +V +L K+ + +EG Sbjct: 478 VQNLQDAAYEGVRTGTQRPKDVNFAEIARSFGFSYAERVSNRNDLNVKMEAFID--AEGP 535 Query: 537 LVFLDIQIDDSEHVYPMQIQGGGMNEMWL 565 FL+ D E +YP GG +M L Sbjct: 536 -CFLEACTDREEVLYPKVPAGGSYKDMIL 563 Lambda K H 0.319 0.136 0.398 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: 682 Number of extensions: 29 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: 571 Length of database: 570 Length adjustment: 36 Effective length of query: 535 Effective length of database: 534 Effective search space: 285690 Effective search space used: 285690 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