Align acetolactate synthase (EC 2.2.1.6) (characterized)
to candidate WP_011996144.1 XAUT_RS02450 oxalyl-CoA decarboxylase
Query= BRENDA::P9WG39 (547 letters) >NCBI__GCF_000017645.1:WP_011996144.1 Length = 584 Score = 236 bits (601), Expect = 2e-66 Identities = 171/551 (31%), Positives = 284/551 (51%), Gaps = 21/551 (3%) Query: 4 DTAPAQTMHAG-RLIARRLKASGIDTVFTLSGGHLFSIYDGCREEGIRLIDTRHEQTAAF 62 D A Q + G L+ LK +GI+T++ + G + + +EEGIR+I RHEQ A Sbjct: 17 DPAAEQELTDGFHLVIDALKLNGIETIYGVPGIPITDLGRMAQEEGIRVISFRHEQNAGN 76 Query: 63 AAEGWSKVTRVPGVAALTAGPGITNGMSAMAAAQQNQSPLVVLGGRA--PALRWGMGSLQ 120 AA +T+ PGV + PG NG++A+A A N P++++ G + + G + Sbjct: 77 AAAIAGFLTKKPGVCLTVSAPGFLNGLTALANATTNCFPMILISGSSEREIVDLQQGDYE 136 Query: 121 EIDHVPFVAPVARFAATAQSAENAGLLVDQALQAAVSAPSGVAFVDFPMD-HAFSMSSDN 179 E+D + P+ + A A + G+ V +A++AAVS G ++D P + +M ++ Sbjct: 137 EMDQLAIAKPLCKAAFRVLHAADIGIGVARAIRAAVSGRPGGVYLDLPAKLFSQAMDAEA 196 Query: 180 GRPGALTELPAGPT--PAGDALDRAAGLLSTAQRPVIMAGTNVWWGHAEAALLRLVEERH 237 G + + A P P+ A+DRA LL A++P+I+ G + A+ + VE Sbjct: 197 GAKSLVKVIDAAPAQIPSPAAVDRAIDLLKGAKKPLIILGKGAAYAQADEEIRAFVENSG 256 Query: 238 IPVLMNGMARGVVPADHRLAFSRARSKALGEADVALIVGVPMDFRL--GFGGVFGSTTQL 295 IP L MA+G++P H + ARS AL +ADV L+VG +++ L G G +G + Sbjct: 257 IPFLPMSMAKGLLPDTHPQSAGAARSTALKDADVVLLVGARLNWLLSHGKGKTWGDKPKQ 316 Query: 296 IVADRVEPAR-EHPRPVAAGLYGDLTATLSAL----AGSGGTDHQGWIEELATAETMARD 350 + +EP + + A L GD+ + ++AL GS W+E + + + Sbjct: 317 FIQVDIEPREMDSNVEIKAPLVGDIGSVIAALNARIDGSWQAPPAEWVETIRSKKEANIA 376 Query: 351 LEKAELVDDRIPLHPMRVYAELAALLER--DALVVIDAGDFGSYAGRMIDSYLPGCWLDS 408 +L+ + +P+ L +++ DA++V + + A +ID + P LD Sbjct: 377 KMAPKLLKNSVPMDFHSALGALKNVIKERPDAILVNEGANTLDLARGIIDMHQPRKRLDV 436 Query: 409 GPFGCLGSGPGYALAAKLARPQRQVVLLQGDGAFGFSGMEWDTLVRHNVAVVSVI-GNNG 467 G +G +G G G+A+ A + + V+ ++GD AFGFSGME +T+ R+++ V VI NNG Sbjct: 437 GTWGVMGIGMGFAVGAAV-ETGKPVLAVEGDSAFGFSGMEVETICRYDLPVTIVIFNNNG 495 Query: 468 IW-GLEKHPMEALYGYSVVAELRPGTRYDEVVRALGGHGELVSVPAELRPALERAFASGL 526 I+ G + P G +V PG RYD+++ A GG G V+ P EL A+ A SG Sbjct: 496 IYRGTDTDPTGRDPGTTVFV---PGARYDKMMEAFGGVGVHVTSPDELYRAVSAAMDSGK 552 Query: 527 PAVVNVLTDPS 537 P ++N + DP+ Sbjct: 553 PTLINAVIDPA 563 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: 747 Number of extensions: 47 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: 584 Length adjustment: 36 Effective length of query: 511 Effective length of database: 548 Effective search space: 280028 Effective search space used: 280028 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