Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate AO353_01155 AO353_01155 3-hydroxyacyl-CoA dehydrogenase
Query= BRENDA::P76082 (255 letters) >FitnessBrowser__pseudo3_N2E3:AO353_01155 Length = 714 Score = 104 bits (260), Expect = 4e-27 Identities = 66/178 (37%), Positives = 101/178 (56%), Gaps = 9/178 (5%) Query: 9 QQRVLLLTLNRPAARNALNNALLMQLVNELEA--AATDTSISVCVITGNARFFAAGADLN 66 Q ++++LT++ P NA+ + + + A A SI+ +IT + F AG DLN Sbjct: 11 QDQIVVLTIDMPGQSANTMNAVYREAMADCVARLVADKDSITGVIITSAKKTFFAGGDLN 70 Query: 67 EMAE--KDLAATLNDTRPQLWARL---QAFNKPLIAAVNGYALGAGCELALLCDVVVAGE 121 E+ + K A D L A+L + KP++AA+NG ALG G E+ L C VA + Sbjct: 71 ELIKVGKSQAKAFYDMVLLLKAQLRTLETLGKPVVAAINGAALGGGWEICLACHHRVALD 130 Query: 122 N--ARFGLPEITLGIMPGAGGTQRLIRSVGKSLASKMVLSGESITAQQAQQAGLVSDV 177 N + GLPE+TLG++PG GG R++R +G A +L G+ + +QQA QAGLV ++ Sbjct: 131 NPSVQIGLPEVTLGLLPGGGGVVRMVRLLGLEKALPYLLEGKKVRSQQALQAGLVDEL 188 Lambda K H 0.318 0.130 0.356 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: 296 Number of extensions: 14 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: 255 Length of database: 714 Length adjustment: 32 Effective length of query: 223 Effective length of database: 682 Effective search space: 152086 Effective search space used: 152086 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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