Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate 6938034 Sama_2167 multifunctional fatty acid oxidation complex subunit alpha (RefSeq)
Query= reanno::BFirm:BPHYT_RS17335 (258 letters) >FitnessBrowser__SB2B:6938034 Length = 706 Score = 117 bits (293), Expect = 7e-31 Identities = 70/190 (36%), Positives = 110/190 (57%), Gaps = 12/190 (6%) Query: 14 VGLVTLNRP-KALNALNDALMDELGAALREFDADDAI-GAIVVTGSEKAFAAGADIGMMS 71 + L+T++ P + +N L E+ A L+E AD +I G ++++G +F AGADI M+ Sbjct: 14 IALLTMDVPGETMNTLKAQFAPEITAILQEIKADSSIKGLVLISGKADSFVAGADISMLD 73 Query: 72 TYTYMDVYK-----GDYITRNWETVRSIRKPIIAAVAGFALGGGCELAMMCDIIFAADTA 126 + + G ++ E + P++AA+ G LGGG ELA+ C +D++ Sbjct: 74 ACETAEDARLLSRQGHHVFAELE---GLNIPVVAAIHGACLGGGLELALACHQRVCSDSS 130 Query: 127 K--FGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSRVIPAA 184 K G PE++LG++PG GGTQRLPR + AKA+DL LT + + +A + GLV V+P + Sbjct: 131 KTMLGVPEVQLGLLPGGGGTQRLPRLIGIAKALDLMLTGKQVRPKQAVKMGLVDDVVPES 190 Query: 185 SLVDEAIAAA 194 L+D AI A Sbjct: 191 ILLDTAIEMA 200 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: 392 Number of extensions: 15 Number of successful extensions: 2 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: 706 Length adjustment: 32 Effective length of query: 226 Effective length of database: 674 Effective search space: 152324 Effective search space used: 152324 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: 50 (23.9 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