Align Putative acetolactate synthase large subunit IlvX; ALS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; AHAS (uncharacterized)
to candidate WP_011157556.1 TX73_RS10205 acetolactate synthase large subunit
Query= curated2:O53554 (515 letters) >NCBI__GCF_000195775.1:WP_011157556.1 Length = 514 Score = 484 bits (1245), Expect = e-141 Identities = 268/518 (51%), Positives = 336/518 (64%), Gaps = 12/518 (2%) Query: 1 MNGAQALINTLVDGGVDVCFANPGTSEMHFVAALDAVPRMRGMLTLFEGVATGAADGYAR 60 MNGAQ+++ TLV+ GV+VCFANPGTSEMHFVAALD+V MR +L LFEGV TGAADGY R Sbjct: 1 MNGAQSVVRTLVNCGVEVCFANPGTSEMHFVAALDSVSGMRPVLCLFEGVVTGAADGYGR 60 Query: 61 IAGRPAAVLLHLGPGLGNGLANLHNARRARVPMVVVVGDHATYHKKYDAPLESDIDAVAG 120 IAG+PA LLHLGPGL NGLANLHNARRA P+V +VGDHA YH +YDAPL SDI A Sbjct: 61 IAGKPAVNLLHLGPGLANGLANLHNARRAATPIVNIVGDHAAYHLQYDAPLTSDIAGFAR 120 Query: 121 TVSGWVRRTEAAADVGAD-AEAAIAASRSGSQIATLILPADVCWSDGAHAAAGVP--AQA 177 VS W+ +++A V +D A A AAS + IATLI+PADV W+ A AA +P A Sbjct: 121 PVSSWIHESKSAGAVASDTARAVQAASAAPGGIATLIMPADVAWNPAARAAQKLPEIGPA 180 Query: 178 AAAPVDVGPVAGVLRSGEPAMMLIGGDATRGPGLTAAARIVQATGARWLCETFPTCLERG 237 A V +A +L +G+ + +L+ G A G L AA R+ TG R LC+TF E G Sbjct: 181 KVAAETVEAIAKLLANGKKSALLLRGSALLGDVLEAAGRVAAKTGVRLLCDTFAPQTELG 240 Query: 238 AGIPAVERLAYFAEGAAAQLDGVKHLVLAGARSPVSFFAYPGMPSDLVPAGCEVHVLAEP 297 AG +ER+ YF+E A L V+ L+L GA+ PVSFFAYPG PS P GC + LA+P Sbjct: 241 AGRVPLERIPYFSEQITAFLKDVEQLILVGAKPPVSFFAYPGKPSWGAPEGCLIDYLAQP 300 Query: 298 GGAADALAALADEVAPGTVAPVAGASR-----PQLPTGDLTSVSAADVVGALLPERAIVV 352 D A+ D +A AP A+R P+LP G L S+ A + L P+ AI Sbjct: 301 --HEDGAQAVRD-LAAALDAPAEPAARTQLVLPELPKGKLNSLGVAQAIAHLTPDHAIYA 357 Query: 353 DESNTCGVLLPQATAGAPAHDWLTLTGGAIGYGIPAAVGAAVAAPDRPVLCLESDGSAMY 412 +E+NT G+ A H L LTGG+IG G+P A+GAA+AAPDR V+C DG A Y Sbjct: 358 EEANTSGLPFQMILPKARPHTHLPLTGGSIGQGLPLAIGAAIAAPDRKVVCPHGDGGAAY 417 Query: 413 TISGLWSQARENLDVTTVIYNNGAYDILRIELQRVGAGSDPGPKALDLLDISRPTMDFVK 472 T+ LW+ ARE LDVT VIY N +Y IL IELQRVGA S G AL +LD+ P M+++K Sbjct: 418 TMQALWTMAREKLDVTVVIYANRSYAILNIELQRVGA-SGAGANALSMLDLHNPEMNWMK 476 Query: 473 IAEGMGVPARRVTTCEEFADALRAAFAEPGPHLIDVVV 510 IAEG+GV A R TT EEF+ +A ++ GP LI+ ++ Sbjct: 477 IAEGLGVEASRATTAEEFSAQYASAMSQRGPRLIEALI 514 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: 629 Number of extensions: 30 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