Align acetolactate synthase (EC 2.2.1.6) (characterized)
to candidate WP_012168999.1 AZC_RS02375 oxalyl-CoA decarboxylase
Query= BRENDA::P9WG39 (547 letters) >NCBI__GCF_000010525.1:WP_012168999.1 Length = 579 Score = 226 bits (577), Expect = 1e-63 Identities = 168/540 (31%), Positives = 275/540 (50%), Gaps = 23/540 (4%) Query: 16 LIARRLKASGIDTVFTLSGGHLFSIYDGCREEGIRLIDTRHEQTAAFAAEGWSKVTRVPG 75 L+ LK +GI+T++ + G + + + EGIR++ RHEQ A AA +T+ PG Sbjct: 24 LVIDALKLNGIETIYGVPGIPITDLGRMAQAEGIRVVSFRHEQNAGNAAAIAGFLTKKPG 83 Query: 76 VAALTAGPGITNGMSAMAAAQQNQSPLVVLGGRA--PALRWGMGSLQEIDHVPFVAPVAR 133 V + PG NG++A+A A N P++++ G + + G +E+D + P+ + Sbjct: 84 VCLTVSAPGFLNGLTALANATTNCFPMILISGSSEREIVDLQQGDYEEMDQLAIAKPLCK 143 Query: 134 FAATAQSAENAGLLVDQALQAAVSAPSGVAFVDFPMDHAFS--MSSDNGRPGALTELPAG 191 A A + G+ V +A++AAVS G ++D P FS M + G + + Sbjct: 144 AAFRVLHAADIGIGVARAIRAAVSGRPGGVYLDLPA-KLFSQVMDAAAGEKSLVKVIDPA 202 Query: 192 PT--PAGDALDRAAGLLSTAQRPVIMAGTNVWWGHAEAALLRLVEERHIPVLMNGMARGV 249 P P A+DRA LL A+RP+I+ G + A+ + VE+ IP L MA+G+ Sbjct: 203 PAQIPGPAAVDRAINLLKGAKRPLIILGKGAAYAQADEEIRAFVEKSGIPFLPMSMAKGL 262 Query: 250 VPADHRLAFSRARSKALGEADVALIVGVPMDFRL--GFGGVFG--STTQLIVADRVEPAR 305 +P H + ARS AL ++DV +++G +++ L G G +G + Q I D Sbjct: 263 LPDTHPQSAGAARSTALKDSDVVILLGARLNWLLSHGKGKTWGEPGSKQFIQVDIEPKEM 322 Query: 306 EHPRPVAAGLYGDLTATLSALA----GSGGTDHQGWIEELATAETMARDLEKAELVDDRI 361 + +AA L GD+ + +SAL GS WIE + + + +L+ + Sbjct: 323 DSNVEIAAPLVGDIGSVVSALLDRIDGSWQAPPADWIESIRSKKEANIAKMAPKLLKNSS 382 Query: 362 PLHPMRVYAELAALLER--DALVVIDAGDFGSYAGRMIDSYLPGCWLDSGPFGCLGSGPG 419 P+ L ++ DA++V + + A +ID Y P LD G +G +G G G Sbjct: 383 PMDFHGALGSLKKVIAERPDAILVNEGANTLDLARGIIDMYQPRKRLDVGTWGVMGIGMG 442 Query: 420 YALAAKLARPQRQVVLLQGDGAFGFSGMEWDTLVRHNVAVVSVI-GNNGIW-GLEKHPME 477 +A+AA + + V+ ++GD AFGFSGME +T+ R+++ V VI NNGI+ G + P Sbjct: 443 FAIAAAV-ETGKPVLAVEGDSAFGFSGMEVETICRYDLPVTIVIFNNNGIYRGTDTDPTG 501 Query: 478 ALYGYSVVAELRPGTRYDEVVRALGGHGELVSVPAELRPALERAFASGLPAVVNVLTDPS 537 G +V + +RYD+++ A GG G V+ P EL A+ A SG P ++N + DP+ Sbjct: 502 RDPGTTVFVK---DSRYDKMMEAFGGVGVNVTTPDELYRAVSAAMDSGKPTLINAVIDPA 558 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: 761 Number of extensions: 41 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: 579 Length adjustment: 36 Effective length of query: 511 Effective length of database: 543 Effective search space: 277473 Effective search space used: 277473 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