Align acetolactate synthase (EC 2.2.1.6) (characterized)
to candidate BPHYT_RS33355 BPHYT_RS33355 oxalyl-CoA decarboxylase
Query= BRENDA::P9WG39 (547 letters) >FitnessBrowser__BFirm:BPHYT_RS33355 Length = 580 Score = 228 bits (582), Expect = 4e-64 Identities = 175/559 (31%), Positives = 286/559 (51%), Gaps = 36/559 (6%) Query: 2 STDTAPA-QTMHAGRLIARRLKASGIDTVFTLSGGHLFSIYDGCREEGIRLIDTRHEQTA 60 +T T A +T L+ LK + I T+F L G + + + EG+R I RHEQ A Sbjct: 11 NTSTQQATETTDGFHLVIDALKLNDIKTIFGLVGIPITDLARLAQAEGMRFIGFRHEQHA 70 Query: 61 AFAAEGWSKVTRVPGVAALTAGPGITNGMSAMAAAQQNQSPLVVLGGRAPA--LRWGMGS 118 AA +T+ PG+ + PG NG++A+A A N P++++ G + + G Sbjct: 71 GNAAAVSGYMTKKPGICLTVSAPGFLNGLTALANATTNCFPMILISGSSEREIVDLQQGD 130 Query: 119 LQEIDHVPFVAPVARFAATAQSAENAGLLVDQALQAAVSAPSGVAFVDFPMDH-AFSMSS 177 +E+D + P A+ A AE+ G+ V +A++AAVS G ++D P A +M + Sbjct: 131 YEEMDQLNAAKPYAKAAYRVLHAEDIGIGVARAIRAAVSGRPGGVYLDLPAKLLAQTMDA 190 Query: 178 DNGRPGALTELPAGPT--PAGDALDRAAGLLSTAQRPVIMAGTNVWWGHAEAALLRLVEE 235 + + + A P PA +++ RA +L +A+RP+I+ G + A+A + VE+ Sbjct: 191 VKAQQSLVRVVDAAPRQLPAPESVKRAIDVLKSAKRPLILLGKGAAYAQADAEIRGFVEQ 250 Query: 236 RHIPVLMNGMARGVVPADHRLAFSRARSKALGEADVALIVGVPMDFRL--GFGGVFGSTT 293 IP L MA+G++P H + S ARS L EADV +++G +++ L G G +G+ Sbjct: 251 SGIPYLPMSMAKGLLPDTHEQSASAARSFVLQEADVVVLIGARLNWLLSHGKGKTWGAEP 310 Query: 294 QLIVADRVEPAR-EHPRPVAAGLYGDLTATLSALA-------GSGGTDHQGWIEELATAE 345 + V + P + +AA + GD+ + ++AL GT+ G A AE Sbjct: 311 KKFVQIDISPTEIDSNVAIAAPVIGDIGSCVAALREGLDASYKKPGTEWTG-----AIAE 365 Query: 346 TMARDLEKAELVDDRIPLHPMRVYAELAALLE-----RDALVVIDAGDFGSYAGRMIDSY 400 ++L K D+ P PM ++ L A+ + D VV + + YA +ID Y Sbjct: 366 RKNKNLAKMAATLDKNP-SPMNFHSALRAIRDVLKTRPDINVVNEGANTLDYARSIIDMY 424 Query: 401 LPGCWLDSGPFGCLGSGPGYALAAKLARPQRQVVLLQGDGAFGFSGMEWDTLVRHNVAVV 460 P DSG +G +G G G+A+ A + + VV ++GD AFGFSGME +T+ R+++ V Sbjct: 425 EPRKRFDSGTWGIMGIGMGFAIGAAVT-SGKPVVAIEGDSAFGFSGMELETICRYDLPVC 483 Query: 461 SVI-GNNGIW-GLEKHPMEALYGYSVVAE--LRPGTRYDEVVRALGGHGELVSVPAELRP 516 +++ NNG++ G + +P G VA RYD+++ A GG G + P EL Sbjct: 484 TIVFNNNGVYRGTDVNPT----GGKDVAPTVFVKNARYDKMIEAFGGIGYHATTPEELTK 539 Query: 517 ALERAFASGLPAVVNVLTD 535 AL + ASG P+++N + D Sbjct: 540 ALLESIASGKPSLINAVID 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: 716 Number of extensions: 38 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 09 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