Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate BWI76_RS20455 BWI76_RS20455 multifunctional fatty acid oxidation complex subunit alpha
Query= reanno::BFirm:BPHYT_RS17335 (258 letters) >FitnessBrowser__Koxy:BWI76_RS20455 Length = 714 Score = 98.6 bits (244), Expect = 3e-25 Identities = 58/189 (30%), Positives = 103/189 (54%), Gaps = 10/189 (5%) Query: 14 VGLVTLNRP-KALNALNDALMDELGAALREF-DADDAIGAIVVTGSEKAFAAGADIGMMS 71 + ++T++ P + +N L E+ +R+ D + GA+ ++ F AGADI M++ Sbjct: 16 IAVITIDAPGEKMNTLKAEFASEVRGIIRQIRDNKELRGAVFISAKPDNFIAGADINMIA 75 Query: 72 TYTYMDVYKGDYITRNWETVRS----IRKPIIAAVAGFALGGGCELAMMCD--IIFAADT 125 + + + R + + + + P+IAA+ G LGGG ELA+ C + D Sbjct: 76 RCH--SAQEAEALARQGQQIMAEIHGLSIPVIAAIHGACLGGGLELALACHGRVCSDDDK 133 Query: 126 AKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSRVIPAAS 185 + G PE++LG++PG+GGTQRLPR + + A+++ LT + + +A +AGLV V+ Sbjct: 134 TRLGLPEVQLGLLPGSGGTQRLPRLIGVSGALEMILTGKQLRPRQALKAGLVDEVVAQTI 193 Query: 186 LVDEAIAAA 194 L+ A+ A Sbjct: 194 LLQTAVELA 202 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: 353 Number of extensions: 15 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: 714 Length adjustment: 32 Effective length of query: 226 Effective length of database: 682 Effective search space: 154132 Effective search space used: 154132 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: 51 (24.3 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