Align Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized)
to candidate Ac3H11_4989 Enoyl-CoA hydratase (EC 4.2.1.17)
Query= SwissProt::Q0AVM1 (260 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4989 Length = 266 Score = 133 bits (335), Expect = 3e-36 Identities = 82/255 (32%), Positives = 127/255 (49%), Gaps = 1/255 (0%) Query: 6 IILEKEEKLAVLYINRPKAMNALNKDTLLEIKDAVTAVNDDPAVELLIITGSGDKSFVAG 65 ++LE+E +A L NRP+A+NA++ AV V DPAV +++ G+G + F+AG Sbjct: 13 LLLEREGAIATLRFNRPEALNAIDVPMANAFLAAVQTVAADPAVRAVVLCGNG-RGFMAG 71 Query: 66 ADIAFMQNLSAMEAREFGALGQKVFRLIEAMEKPVIAAVNGFALGGGCELAMCCDFRIAA 125 D+A ++ A + L+ M PV+A V+G A G G L + D+ IAA Sbjct: 72 GDLATLRADPVQSAIDILTPLNAALLLLAQMNAPVVAQVHGVAAGAGLSLLLMADYVIAA 131 Query: 126 SNAKFGQPEVGLGITPGFGGTQRLPRLVGPGMAKQLLYTADVINADEAFRIGLVNKVVQP 185 + + LG + G + LPR+VG A ++ D AD+A R+GLVN+VV Sbjct: 132 EGTRLNLAYINLGTSCDVGASWALPRIVGVRQALEIALLGDAFTADDALRLGLVNRVVPA 191 Query: 186 EELLPEVKKIAGRILSKGQLAVRLSKAAANEGMQTDIDRAMSIEADAFGLCFATQDQKEG 245 EL +A R+ S LA K M + ++ E DAF C T+D + G Sbjct: 192 AELDSATAALAQRLASGPTLAYGAMKRLMRASMDHTLPEQLAAEKDAFVHCAGTEDFRAG 251 Query: 246 MTAFLEKRKANFISK 260 + AF ++ A+F + Sbjct: 252 VEAFHLRQSASFAGR 266 Lambda K H 0.319 0.136 0.378 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: 161 Number of extensions: 8 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: 260 Length of database: 266 Length adjustment: 25 Effective length of query: 235 Effective length of database: 241 Effective search space: 56635 Effective search space used: 56635 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: 47 (22.7 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