Align Putative acetolactate synthase large subunit IlvX; ALS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; AHAS (uncharacterized)
to candidate WP_013721544.1 ALIDE2_RS05100 acetolactate synthase large subunit
Query= curated2:O53554 (515 letters) >NCBI__GCF_000204645.1:WP_013721544.1 Length = 550 Score = 568 bits (1463), Expect = e-166 Identities = 302/516 (58%), Positives = 362/516 (70%), Gaps = 6/516 (1%) Query: 1 MNGAQALINTLVDGGVDVCFANPGTSEMHFVAALDAVPRMRGMLTLFEGVATGAADGYAR 60 MNGAQAL+ TL D GV+VCF NPGTSEMHFVAALD PRMR +L LFEGVATGAADGYAR Sbjct: 1 MNGAQALLQTLADAGVEVCFTNPGTSEMHFVAALDTEPRMRAVLALFEGVATGAADGYAR 60 Query: 61 IAGRPAAVLLHLGPGLGNGLANLHNARRARVPMVVVVGDHATYHKKYDAPLESDIDAVAG 120 +AG+PAA LLHLG GLGNGLANLHNAR+ +VP+V +VGDHATYH +YDA L+SDI+ VA Sbjct: 61 MAGKPAATLLHLGCGLGNGLANLHNARKGKVPVVNIVGDHATYHTRYDAQLQSDIETVAR 120 Query: 121 TVS-GWVRRTEAAADVGADAEAAIAASRS-GSQIATLILPADVCWSDGAHAAAGVPAQAA 178 VS G+VR ++ A +G DA AIAA+R Q+ATLILPADV W +G P Sbjct: 121 NVSPGFVRTAQSTAALGRDAADAIAAARGLPGQVATLILPADVSWGEGGQPCPPPPPPTP 180 Query: 179 AAPVD--VGPVAGVLRSGEPAMMLIGGDATRGPGLTAAARIVQATGARWLCETFPTCLER 236 AA D V A +RSGE ++L+GG A R L AARI +GA+ L E FPT +ER Sbjct: 181 AAASDEAVQAAAQAIRSGEKTIVLLGGHALREGALRTAARIAAHSGAQLLAEVFPTRMER 240 Query: 237 GAGIPAVERLAYFAEGAAAQLDGVKHLVLAGARSPVSFFAYPGMPSDLVPAGCEVHVLAE 296 GAG+PAVER+AY AE A QL G +HLVL A+SPVSFFAYPG SDLVP GC VH L Sbjct: 241 GAGLPAVERVAYLAELAGVQLAGARHLVLVDAKSPVSFFAYPGKASDLVPEGCTVHTLCS 300 Query: 297 PG-GAADALAALADEVAPGTVAPVAGASRPQLPTGDLTSVSAADVVGALLPERAIVVDES 355 P AA +L LA + P+A A RP+ P G LT+ VG LLPE AIV+DE+ Sbjct: 301 PAQDAAASLDKLAAALGATAEPPLAPARRPERPRGPLTAPKVCKAVGHLLPENAIVIDEA 360 Query: 356 NTCGVLLPQATAGAPAHDWLTLTGGAIGYGIPAAVGAAVAAPDRPVLCLESDGSAMYTIS 415 T G++L TAG P HD LTLTGGAIG G+P AVGAA+A PDRPVL L DG+AMYTI Sbjct: 361 ITSGLMLGAMTAGCPRHDLLTLTGGAIGQGLPNAVGAAIACPDRPVLALIGDGTAMYTIQ 420 Query: 416 GLWSQARENLDVTTVIYNNGAYDILRIELQRVGAGSDPGPKALDLLDISRPTMDFVKIAE 475 LW+ ARE L V +VI+NN +Y +L +EL+RVGA + G KA LD+ P ++F ++A+ Sbjct: 421 ALWTMAREKLHVVSVIFNNASYSVLNVELERVGA-DEAGSKAKSQLDLKGPVLNFAQLAQ 479 Query: 476 GMGVPARRVTTCEEFADALRAAFAEPGPHLIDVVVP 511 GMGV A R T E+F AL A A+PGPHLI+ +VP Sbjct: 480 GMGVHAVRARTAEDFCQALEYALAQPGPHLIEALVP 515 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: 747 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: 550 Length adjustment: 35 Effective length of query: 480 Effective length of database: 515 Effective search space: 247200 Effective search space used: 247200 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