Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate Ga0059261_2908 Ga0059261_2908 Enoyl-CoA hydratase/carnithine racemase
Query= BRENDA::O87873 (258 letters) >FitnessBrowser__Korea:Ga0059261_2908 Length = 275 Score = 95.9 bits (237), Expect = 8e-25 Identities = 82/261 (31%), Positives = 122/261 (46%), Gaps = 25/261 (9%) Query: 9 KVWLERDGSLLRLRLARP-KANIVDAAMIAAMRQALGEHLQAPALRAVLLDAEGPHFSFG 67 +V + R G++ +RL RP K N +D M A+ A P +RAV+L EG F G Sbjct: 12 RVSIGRAGAVADIRLRRPFKMNALDGPMFDALIAAAESVAVDPTIRAVVLSGEGKAFCAG 71 Query: 68 A---SVDEHMPDQCAQMLKSL-HGLVREMLDS-------PVPILVALRGQCLGGGLEVAA 116 S+ M D+ Q ++S HGL + PVP++ AL G GGGL++ Sbjct: 72 IDLESLQALMSDEGKQAMQSRSHGLANRYQQAALAWREVPVPVIAALHGVAFGGGLQIPL 131 Query: 117 AGNLLFAAPDAKFGQPEIRLGVFAP-AASCLLPPRVGQACAEDLLWSGRSIDGAEGHRIG 175 ++ +APD KF E+R G+ A + LL V + +L+++ R G E +G Sbjct: 132 GADIRISAPDTKFSLMEVRWGIVPDMAGTVLLRSIVREDVLRELIYTARVFTGIEAASMG 191 Query: 176 LIDVLAEDPEAAALRWFDEHIARLSASSLRFAVRAARCDSVPRIKQKLDTVEALYLEE-- 233 ++ LA +P AAL +A A AVRAA+ + Q + AL E Sbjct: 192 IVTQLAANPHVAAL-----ELASSIAEQGPRAVRAAK--QLLNETQSVSPQVALLSESEA 244 Query: 234 ---LMASHDAVEGLKAFLEKR 251 L+A D +E L A E+R Sbjct: 245 QVGLLAGPDQIEALNAHAEQR 265 Lambda K H 0.321 0.135 0.402 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: 173 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: 275 Length adjustment: 25 Effective length of query: 233 Effective length of database: 250 Effective search space: 58250 Effective search space used: 58250 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: 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