Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate GFF2712 PS417_13835 crotonase
Query= reanno::BFirm:BPHYT_RS17335 (258 letters) >FitnessBrowser__WCS417:GFF2712 Length = 367 Score = 94.0 bits (232), Expect = 4e-24 Identities = 58/190 (30%), Positives = 96/190 (50%), Gaps = 6/190 (3%) Query: 4 ENILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGS-EKAFA 62 + +L E R +G +TLNRP LNA+ ++ L + L+ + D + A+V+ G+ EKAF Sbjct: 17 DEVLAEVRNHIGHLTLNRPAGLNAITLNMVRRLASQLKAWADDPQVYAVVLRGAGEKAFC 76 Query: 63 AGADI-GMMSTYTYMDVYKGDYITRNWE---TVRSIRKPIIAAVAGFALGGGCELAMMCD 118 AG DI + ++ D D+ + + RKP++A + GF LGGG L D Sbjct: 77 AGGDIRSLYDSFKNGDTLHQDFFVEEYALDLAIHHYRKPVLALMDGFVLGGGMGLVQGAD 136 Query: 119 IIFAADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVS 178 + + ++ PE+ +G P GG+ LPR + + L +T + AA+A GL Sbjct: 137 LRVVTERSRLAMPEVAIGYFPDVGGSYFLPR-IPGELGIYLGVTGVQIRAADALYCGLAD 195 Query: 179 RVIPAASLVD 188 + ++ L D Sbjct: 196 WYLESSKLAD 205 Lambda K H 0.321 0.134 0.380 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: 172 Number of extensions: 10 Number of successful extensions: 3 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: 258 Length of database: 367 Length adjustment: 27 Effective length of query: 231 Effective length of database: 340 Effective search space: 78540 Effective search space used: 78540 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 (21.9 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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