Align Putative acetolactate synthase large subunit IlvX; ALS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; AHAS (uncharacterized)
to candidate WP_011782354.1 MVAN_RS26215 acetolactate synthase large subunit
Query= curated2:O53554 (515 letters) >NCBI__GCF_000015305.1:WP_011782354.1 Length = 519 Score = 732 bits (1890), Expect = 0.0 Identities = 379/519 (73%), Positives = 427/519 (82%), Gaps = 7/519 (1%) Query: 1 MNGAQALINTLVDGGVDVCFANPGTSEMHFVAALDAVPRMRGMLTLFEGVATGAADGYAR 60 MNGA++L+ TLVD GVDVCFANPGTSEMHFVAALD VP MRG+LTLFEGVATGAADGYAR Sbjct: 1 MNGARSLLTTLVDQGVDVCFANPGTSEMHFVAALDTVPGMRGVLTLFEGVATGAADGYAR 60 Query: 61 IAGRPAAVLLHLGPGLGNGLANLHNARRARVPMVVVVGDHATYHKKYDAPLESDIDAVAG 120 ++G+PAAVLLHLGPGLGNGLANLHNARRA VPMVVVVGDHATYHKKYDAPLESDIDA+A Sbjct: 61 MSGKPAAVLLHLGPGLGNGLANLHNARRAHVPMVVVVGDHATYHKKYDAPLESDIDALAH 120 Query: 121 TVSGWVRRTEAAADVGADAEAAIAASRSGSQIATLILPADVCWSDGAHAAAGVPAQAAAA 180 TVSGWVRRT D+ DA A+AASR+G ++T+I+PADV W+DG +PA A Sbjct: 121 TVSGWVRRTLDVGDIAVDAVDAVAASRAGV-VSTMIVPADVSWNDG-EPTEPLPAGHPAP 178 Query: 181 PVD---VGPVAGVLRSGEPAMMLIGGDATRGPGLTAAARIVQATGARWLCETFPTCLERG 237 +D V A L SG P ++L+GGDAT PGL+AA RI + TGA+ LCETFP L+RG Sbjct: 179 GIDDDAVREAADALNSGVPTVLLVGGDATLAPGLSAAVRIAERTGAKVLCETFPARLQRG 238 Query: 238 AGIPAVERLAYFAEGAAAQLDGVKHLVLAGARSPVSFFAYPGMPSDLVPAGCEVHVLAEP 297 AG+PAVERLAYFAEGA AQL G +HL+LAGA SPVSFFAYPG PSDLVP GCEVHVLA Sbjct: 239 AGVPAVERLAYFAEGAEAQLVGAEHLILAGAASPVSFFAYPGRPSDLVPQGCEVHVLAGH 298 Query: 298 GGAADALAALADEVAPGTVAPVAGASRPQLPTGDLTSVSAADVVGALLPERAIVVDESNT 357 GAA AL LAD+VAPGT A VA RP LPTG+LT+ SAA V+GALLPE A+VVDESNT Sbjct: 299 SGAAAALEQLADDVAPGTTASVAPLMRPDLPTGELTAFSAAAVIGALLPEGAVVVDESNT 358 Query: 358 CGVLLPQATAGAPAHDWLTLTGGAIGYGIPAAVGAAVAAPDRPVLCLESDGSAMYTISGL 417 GV + ATAGAP HD LTLTGGAIGYG+PAA+GAA+AAPDRPVL L++DGSAMYT+S L Sbjct: 359 AGVGVAAATAGAPGHDVLTLTGGAIGYGMPAAIGAAMAAPDRPVLSLQADGSAMYTVSAL 418 Query: 418 WSQARENLDVTTVIYNNGAYDILRIELQRVGA--GSDPGPKALDLLDISRPTMDFVKIAE 475 W+QARENLDVTTVI+ NGAYDILRIELQRVGA + PGP AL LLD+ PT+DFVKIAE Sbjct: 419 WTQARENLDVTTVIFGNGAYDILRIELQRVGAENAATPGPSALRLLDLGSPTLDFVKIAE 478 Query: 476 GMGVPARRVTTCEEFADALRAAFAEPGPHLIDVVVPSLV 514 GMGVPARRV+T E+ A AL AFA PGPHLI+ VVPSLV Sbjct: 479 GMGVPARRVSTAEDLAAALTEAFAAPGPHLIEAVVPSLV 517 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: 867 Number of extensions: 45 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: 515 Length of database: 519 Length adjustment: 35 Effective length of query: 480 Effective length of database: 484 Effective search space: 232320 Effective search space used: 232320 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