Align Putative acetolactate synthase large subunit IlvX; ALS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; AHAS (uncharacterized)
to candidate WP_012332558.1 M446_RS12985 acetolactate synthase large subunit
Query= curated2:O53554 (515 letters) >NCBI__GCF_000019365.1:WP_012332558.1 Length = 515 Score = 486 bits (1250), Expect = e-141 Identities = 269/515 (52%), Positives = 332/515 (64%), Gaps = 7/515 (1%) Query: 1 MNGAQALINTLVDGGVDVCFANPGTSEMHFVAALDAVPRMRGMLTLFEGVATGAADGYAR 60 MNGA++L+ TLV GGV+VCF NPGTSEMHFVAALD V MR +L LFEG ATGAADGYAR Sbjct: 3 MNGAESLVRTLVAGGVEVCFTNPGTSEMHFVAALDRVEGMRAVLCLFEGGATGAADGYAR 62 Query: 61 IAGRPAAVLLHLGPGLGNGLANLHNARRARVPMVVVVGDHATYHKKYDAPLESDIDAVAG 120 + RPA+ LLHLGPGLGNG+ANLHNARRAR PMV +VG+HATYH+ +DAPL SDI+ +A Sbjct: 63 MTDRPASTLLHLGPGLGNGIANLHNARRARSPMVNIVGEHATYHRAFDAPLTSDIEGLAR 122 Query: 121 TVSGWVRRTEAAADVGADAEAAIAASRS-GSQIATLILPADVCWSDGAHAA--AGVPAQA 177 VS W+R +A +V D AA+AA+ + +ATLILPAD W +G A +PA+A Sbjct: 123 PVSAWLRTGLSAREVARDGAAAVAAALTPPGGVATLILPADTAWEEGGGVAPVPAIPARA 182 Query: 178 AAAPVDVGPVAGVLRSGEPAMMLIGGDATRGPGLTAAARIVQATGARWLCETFPTCLERG 237 + A L SGEP ++ +G A RG G AARI TGA+ L T ++RG Sbjct: 183 RVPDEAITHAAAALASGEPVLLHLGDRAVRGEGRRIAARIAARTGAQLLAMTSNARIDRG 242 Query: 238 AGIPAVERLAYFAEGAAAQLDGVKHLVLAGARSPVSFFAYPGMPSDLVPAGCEVHVLAEP 297 AG +ERL Y + A A L +H++L GA PV+FFAYPG PS L C+V LA P Sbjct: 243 AGSVPIERLPYPVDPARAVLAPFRHIMLVGATLPVAFFAYPGKPSALAAPTCDVFALAAP 302 Query: 298 -GGAADALAALADEVAPGTVAPVAGASRPQLPTGD-LTSVSAADVVGALLPERAIVVDES 355 DAL LA+ V A + +RP LP G+ L S V+GAL+PE AI+ DES Sbjct: 303 EQDQIDALERLAEAVGAPAAADLPAPARPVLPGGERLDQDSVGQVLGALIPEGAIICDES 362 Query: 356 NTCGVLLPQATAGAPAHDWLTLTGGAIGYGIPAAVGAAVAAPDRPVLCLESDGSAMYTIS 415 T G T GA H WL L+GGAIG GIP A GAAVA PDR V+ L++DGSA+YT Sbjct: 363 ITTGRNFFPVTQGAAPHTWLQLSGGAIGLGIPMATGAAVACPDRKVIALQADGSALYTAQ 422 Query: 416 GLWSQARENLDVTTVIYNNGAYDILRIELQRVGAGSDPGPKALDLLDISRPTMDFVKIAE 475 LW+QARE LDV T+I++N +Y ILR EL VGA +PG KALD+L + P +D+ +A Sbjct: 423 SLWTQAREGLDVVTLIWSNRSYAILRAELAHVGA--NPGRKALDMLTLDDPPIDWPSLAR 480 Query: 476 GMGVPARRVTTCEEFADALRAAFAEPGPHLIDVVV 510 G GV RV T D L A A GP LI+V + Sbjct: 481 GYGVEGCRVETLPRLVDVLTRALARRGPFLIEVAL 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: 719 Number of extensions: 31 Number of successful extensions: 6 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: 515 Length adjustment: 35 Effective length of query: 480 Effective length of database: 480 Effective search space: 230400 Effective search space used: 230400 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