Align Putative acetolactate synthase large subunit IlvX; ALS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; AHAS (uncharacterized)
to candidate YP_004140722.1 Mesci_1514 thiamine pyrophosphate TPP-binding domain-containing protein
Query= curated2:O53554 (515 letters) >NCBI__GCF_000185905.1:YP_004140722.1 Length = 517 Score = 424 bits (1090), Expect = e-123 Identities = 250/518 (48%), Positives = 312/518 (60%), Gaps = 9/518 (1%) Query: 1 MNGAQALINTLVDGGVDVCFANPGTSEMHFVAALDAVPRMRGMLTLFEGVATGAADGYAR 60 MNGA L + L+ V VCFANPGTSEMHFVAALD P+MR +L LFEGV TGAADGYAR Sbjct: 1 MNGADVLCDVLLANDVTVCFANPGTSEMHFVAALDRKPKMRCVLGLFEGVVTGAADGYAR 60 Query: 61 IAGRPAAVLLHLGPGLGNGLANLHNARRARVPMVVVVGDHATYHKKYDAPLESDIDAVAG 120 + RPAA LLH GPGL NGLAN+HNARRA PM+ +VGDHA+YH DAPL SDI+++A Sbjct: 61 MTDRPAATLLHTGPGLANGLANMHNARRAFSPMINIVGDHASYHLPLDAPLTSDIESLAA 120 Query: 121 TVSGWVRRTEAAADVGADAEAAIAASRSGSQIATLILPADVCWSDGAHAAAGVPAQAAAA 180 +S WV R + ADV AEAA AS + +ATLILPAD W + G A Sbjct: 121 PMSNWVGRVKGPADVVPAAEAAFRASLTPPGVATLILPADAAWGEVEAVLPGKVRLVPAP 180 Query: 181 PVD---VGPVAGVLRSGE-PAMMLIGGDATRGPGLTAAARIVQATGARWLCETFPTCLER 236 VD V VA +R+ A M++ G A R L A +I + R E ++R Sbjct: 181 AVDMDAVRKVAAAIRAAPGRAGMIVRGKAARADALAIAGQISAGSDVRLFGEVLIARMQR 240 Query: 237 GAGIPAVERLAYFAEGAAAQLDGVKHLVLAGARSPVSFFAYPGMPSDLVPAGCEVHVLAE 296 G G A R+ Y + A A L V L+L GA+ PV+FFAYPG P LV GCEV LA Sbjct: 241 GRGRAAPIRIPYPVDAAMAVLSDVDVLILVGAKEPVAFFAYPGKPGRLVREGCEVLTLAA 300 Query: 297 PGGAAD-ALAALADE--VAPGTVAPVAGASRPQ-LPTGDLTSVSAADVVGALLPERAIVV 352 G AL AL DE + P +A A + P G LT + A V LP AIV Sbjct: 301 HGDDLHAALEALRDELGIQPSQHKVLAAAFPDEATPNGKLTEDAVALSVARKLPADAIVC 360 Query: 353 DESNTCGVLLPQATAGAPAHDWLTLTGGAIGYGIPAAVGAAVAAPDRPVLCLESDGSAMY 412 DE+ T +A A HD++ TGG+IG GIP A GAA+A PDR V+ LE+DGS MY Sbjct: 361 DEAVTSARRFFALSAFAAPHDYMMGTGGSIGGGIPMATGAAIACPDRKVVNLEADGSGMY 420 Query: 413 TISGLWSQARENLDVTTVIYNNGAYDILRIELQRVGAGSDPGPKALDLLDISRPTMDFVK 472 T+ GLW+QARE LDV T++++N Y IL E++ VG G+ G A +LD+ P++D+V Sbjct: 421 TVQGLWTQAREKLDVVTIVFSNRTYAILHGEMKNVGVGA-IGENARRMLDLDHPSLDWVS 479 Query: 473 IAEGMGVPARRVTTCEEFADALRAAFAEPGPHLIDVVV 510 +A+GMGV A R TCE F L +A + GP LI+ V+ Sbjct: 480 LAKGMGVEAARADTCERFDALLDSALSRRGPFLIEAVL 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: 667 Number of extensions: 28 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: 517 Length adjustment: 35 Effective length of query: 480 Effective length of database: 482 Effective search space: 231360 Effective search space used: 231360 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