Align Putative acetolactate synthase large subunit IlvX; ALS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; AHAS (uncharacterized)
to candidate WP_026607653.1 METAC_RS0114840 acetolactate synthase large subunit
Query= curated2:O53554 (515 letters) >NCBI__GCF_000427445.1:WP_026607653.1 Length = 514 Score = 507 bits (1306), Expect = e-148 Identities = 277/515 (53%), Positives = 343/515 (66%), Gaps = 10/515 (1%) Query: 1 MNGAQALINTLVDGGVDVCFANPGTSEMHFVAALDAVPRMRGMLTLFEGVATGAADGYAR 60 MNGA++L+ TL GGV+VCFANPGTSEMHFVAALD V MR +L LFEGV TGAADGY R Sbjct: 1 MNGAESLVRTLTAGGVEVCFANPGTSEMHFVAALDRVAGMRCILGLFEGVVTGAADGYGR 60 Query: 61 IAGRPAAVLLHLGPGLGNGLANLHNARRARVPMVVVVGDHATYHKKYDAPLESDIDAVAG 120 +A +PA LLHLGPGL NGLANLHNARRAR P++ +VG+HAT HK+YDAPL +DI+A+A Sbjct: 61 MARKPACSLLHLGPGLANGLANLHNARRARAPLINIVGEHATRHKRYDAPLTTDIEAIAR 120 Query: 121 TVSGWVRRTEAAADVGADAEAAIAASRS-GSQIATLILPADVCWSDGAHAAA--GVPAQA 177 S W+R + AAD+G+DA AI A+RS +IATLILPADV W++G AA +P+ Sbjct: 121 PYSDWLRISAHAADLGSDAADAIVAARSEPGRIATLILPADVAWTEGGAVAALPPIPSPP 180 Query: 178 AAAPVDVGPVAGVLRSGEPAMMLIGGDATRGPGLTAAARIVQATGARWLCETFPTCLERG 237 A + A +LR+ P +L+ G+A P LTAA R+ +A+GAR L +ERG Sbjct: 181 MPASATIDRAAAMLRADLPTAILLAGNALLEPALTAAGRVAEASGARLLAAYSMARIERG 240 Query: 238 AGIPAVERLAYFAEGAAAQLDGVKHLVLAGARSPVSFFAYPGMPSDLVPAGCEVHVLAEP 297 AG P V R+ Y E AAA L + L+L GA PV+FFAYP S L P GCE HVLA P Sbjct: 241 AGRPIVTRVPYVLEQAAALLREFRQLILVGAGPPVAFFAYPDKSSALTPEGCETHVLARP 300 Query: 298 G----GAADALAALADEVAPGTVAPVAGASRPQLPTGDLTSVSAADVVGALLPERAIVVD 353 G A DALA + A + V RP P+G++T A VV ALLPE +VVD Sbjct: 301 GEDCAAALDALATILG--ASPILRRVQDFDRPAAPSGEITLPGLAAVVAALLPENCVVVD 358 Query: 354 ESNTCGVLLPQATAGAPAHDWLTLTGGAIGYGIPAAVGAAVAAPDRPVLCLESDGSAMYT 413 ES T G + AT GAP HDWL TGG+IG +P AVGAAVA PDR VLCL +DGS M+T Sbjct: 359 ESMTSGRGMLAATKGAPPHDWLCNTGGSIGIAMPMAVGAAVARPDRSVLCLSADGSGMFT 418 Query: 414 ISGLWSQARENLDVTTVIYNNGAYDILRIELQRVGAGSDPGPKALDLLDISRPTMDFVKI 473 + LW+ ARENL +TTV++ N AY IL+ E +G G GP A +L+I RP +D+ + Sbjct: 419 LQALWTMARENLAITTVVFANRAYAILKGEYANLG-GGPLGPSATSMLEIGRPELDWTAL 477 Query: 474 AEGMGVPARRVTTCEEFADALRAAFAEPGPHLIDV 508 A+GMGVP RV + E FA AL A GP+LI+V Sbjct: 478 AKGMGVPGVRVESLEAFAKALDAGLRSQGPYLIEV 512 Lambda K H 0.318 0.134 0.402 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: 692 Number of extensions: 34 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: 515 Length of database: 514 Length adjustment: 35 Effective length of query: 480 Effective length of database: 479 Effective search space: 229920 Effective search space used: 229920 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 (21.7 bits) S2: 52 (24.6 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