Align acetolactate synthase (EC 2.2.1.6) (characterized)
to candidate WP_013094652.1 BC1002_RS34920 oxalyl-CoA decarboxylase
Query= BRENDA::P9WG39 (547 letters) >NCBI__GCF_000092885.1:WP_013094652.1 Length = 580 Score = 234 bits (598), Expect = 5e-66 Identities = 175/552 (31%), Positives = 284/552 (51%), Gaps = 35/552 (6%) Query: 8 AQTMHAGRLIARRLKASGIDTVFTLSGGHLFSIYDGCREEGIRLIDTRHEQTAAFAAEGW 67 ++T L+ LK + I+T+F L G + + + EG+R I RHEQ A AA Sbjct: 18 SETTDGFHLVIDALKLNDINTIFGLVGIPITDLARLAQAEGMRFIGFRHEQHAGNAAAIA 77 Query: 68 SKVTRVPGVAALTAGPGITNGMSAMAAAQQNQSPLVVLGGRAPA--LRWGMGSLQEIDHV 125 +T+ PG+ + PG NG++A+A A N P++++ G + + G +E+D + Sbjct: 78 GYITKKPGICLTVSAPGFLNGLTALANATTNCFPMILISGSSEREIVDLQQGDYEEMDQL 137 Query: 126 PFVAPVARFAATAQSAENAGLLVDQALQAAVSAPSGVAFVDFPMDH-AFSMSSDNGRPGA 184 P A+ A AE+ G+ V +A++AAVS G ++D P A ++ + + Sbjct: 138 NAARPYAKAAYRVLHAEDIGIGVARAIRAAVSGRPGGVYLDLPAKLLAQTLDTLKAQQSL 197 Query: 185 LTELPAGPT--PAGDALDRAAGLLSTAQRPVIMAGTNVWWGHAEAALLRLVEERHIPVLM 242 + + A P+ PA +++ RA +L +A+RP+I+ G + A+A + VE+ IP L Sbjct: 198 VKVVDAAPSQLPARESVKRAIDVLKSAKRPLILLGKGAAYAQADAEIRAFVEQSGIPYLP 257 Query: 243 NGMARGVVPADHRLAFSRARSKALGEADVALIVGVPMDFRL--GFGGVFGSTTQLIVADR 300 MA+G++P H S ARS L EADV +++G +++ L G G +G + V Sbjct: 258 MSMAKGLLPDTHEQCASAARSFVLQEADVVVLIGARLNWLLSHGKGKTWGGAPKQFVQVD 317 Query: 301 VEPAR-EHPRPVAAGLYGDLTATLSALAGS-------GGTDHQGWIEELATAETMARDLE 352 + P + +AA + GD+ + ++AL G+ G + G A AE ++L Sbjct: 318 ISPTEIDSNVAIAAPVIGDIGSCVTALRGALDANFVKPGVEWTG-----AIAERKNKNLA 372 Query: 353 KAELVDDRIPLHPMRVYAELAALLE-----RDALVVIDAGDFGSYAGRMIDSYLPGCWLD 407 K + D+ P PM ++ L A+ + D VV + + YA +ID P D Sbjct: 373 KMAALLDKNP-SPMNFHSALRAIRDVLKTRPDINVVNEGANTLDYARSIIDMAEPRKRFD 431 Query: 408 SGPFGCLGSGPGYALAAKLARPQRQVVLLQGDGAFGFSGMEWDTLVRHNVAVVSVI-GNN 466 SG +G +G G G+A+ A + Q VV ++GD AFGFSGME +T+ R+N+ V +++ NN Sbjct: 432 SGTWGIMGIGMGFAIGAAVTTGQ-PVVAIEGDSAFGFSGMELETICRYNLPVCTIVFNNN 490 Query: 467 GIW-GLEKHPMEALYGYSVVAE--LRPGTRYDEVVRALGGHGELVSVPAELRPALERAFA 523 G++ G + +P G VA G RYD ++ A GG G S P EL AL A A Sbjct: 491 GVYRGTDVNPT----GGKDVAPTVFVKGARYDRMIEAFGGIGYHASTPEELTQALLEAIA 546 Query: 524 SGLPAVVNVLTD 535 SG P+++N + D Sbjct: 547 SGKPSLINAVID 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: 749 Number of extensions: 45 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: 580 Length adjustment: 36 Effective length of query: 511 Effective length of database: 544 Effective search space: 277984 Effective search space used: 277984 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