Align acetolactate synthase (EC 2.2.1.6) (characterized)
to candidate WP_020173438.1 A3OQ_RS0100770 oxalyl-CoA decarboxylase
Query= BRENDA::P9WG39 (547 letters) >NCBI__GCF_000385335.1:WP_020173438.1 Length = 605 Score = 228 bits (581), Expect = 5e-64 Identities = 167/540 (30%), Positives = 278/540 (51%), Gaps = 23/540 (4%) Query: 16 LIARRLKASGIDTVFTLSGGHLFSIYDGCREEGIRLIDTRHEQTAAFAAEGWSKVTRVPG 75 L+ LK +GIDT++ + G + + + EG+R+I RHEQ A AA +T+ PG Sbjct: 48 LVIDALKLNGIDTIYGVPGIPVTDLGRLAQAEGMRVISFRHEQHAGNAAAIAGYLTKKPG 107 Query: 76 VAALTAGPGITNGMSAMAAAQQNQSPLVVLGGRAPA--LRWGMGSLQEIDHVPFVAPVAR 133 + + PG NG++A+A A N P++ + G + + G +E+D + P+ + Sbjct: 108 ICLTVSAPGFLNGLTALANATTNCFPMIQISGSSEREIVDLQQGDYEEMDQLAIAKPLCK 167 Query: 134 FAATAQSAENAGLLVDQALQAAVSAPSGVAFVDFPMDHAFS--MSSDNGRPGALTELPAG 191 A A + G+ V +A++AAVS G ++D P FS M + G + + Sbjct: 168 AAFRVLHAADIGIGVARAIRAAVSGRPGGVYLDLPAK-LFSQVMDAKAGAKSLVKVIDPA 226 Query: 192 PT--PAGDALDRAAGLLSTAQRPVIMAGTNVWWGHAEAALLRLVEERHIPVLMNGMARGV 249 P PA A++RA +L +A+RP+I+ G + A++ + LVE+ IP L MA+G+ Sbjct: 227 PAVLPAPAAVERALDVLKSAKRPLIILGKGAAYAQADSEIRALVEQSGIPYLPMSMAKGL 286 Query: 250 VPADHRLAFSRARSKALGEADVALIVGVPMDFRL--GFGGVFGST-TQLIVADRVEPAR- 305 +P H + S ARS L EADV +++G +++ L G G +G TQ + +EP Sbjct: 287 LPDTHPQSASAARSMVLKEADVVMLIGARLNWLLSHGKGKTWGEPGTQKFIQIDIEPKEM 346 Query: 306 EHPRPVAAGLYGDLTATLSALA----GSGGTDHQGWIEELATAETMARDLEKAELVDDRI 361 + +AA L GD+ + +SAL G+ W + + ++L+ + Sbjct: 347 DSNIEIAAPLVGDIGSCVSALLKGIDGNWSVPPVEWTSAINARKEANLAKMASKLLKNSS 406 Query: 362 PLHPMRVYAELAALLER--DALVVIDAGDFGSYAGRMIDSYLPGCWLDSGPFGCLGSGPG 419 P+ L +++ DA++V + + A +ID Y P LD G +G +G G G Sbjct: 407 PMDFHSALGALRTVIKERPDAILVNEGANTLDLARGVIDMYQPRKRLDVGTWGVMGIGMG 466 Query: 420 YALAAKLARPQRQVVLLQGDGAFGFSGMEWDTLVRHNVAV-VSVIGNNGIW-GLEKHPME 477 +A+AA + + V+ ++GD AFGFSGME +T+ R+N+ + + V NNGI+ G + P Sbjct: 467 FAVAAAV-ETGKPVLAIEGDSAFGFSGMEVETICRYNLPICIVVFNNNGIYRGTDTDPTG 525 Query: 478 ALYGYSVVAELRPGTRYDEVVRALGGHGELVSVPAELRPALERAFASGLPAVVNVLTDPS 537 G +V + +RYD+++ A GG G V+ P EL A+ A SG P ++N DP+ Sbjct: 526 RDPGTTVFVK---DSRYDKMMEAFGGVGVHVATPDELSRAVNEAMDSGRPTLINAAIDPA 582 Lambda K H 0.319 0.135 0.405 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: 763 Number of extensions: 42 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: 547 Length of database: 605 Length adjustment: 36 Effective length of query: 511 Effective length of database: 569 Effective search space: 290759 Effective search space used: 290759 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 53 (25.0 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