Align cyclohexa-1,5-dienecarbonyl-CoA hydratase monomer (EC 4.2.1.100) (characterized)
to candidate GFF3794 PGA1_262p01980 putative enoyl-CoA hydratase
Query= metacyc::MONOMER-18320 (256 letters) >FitnessBrowser__Phaeo:GFF3794 Length = 263 Score = 108 bits (271), Expect = 9e-29 Identities = 82/260 (31%), Positives = 131/260 (50%), Gaps = 16/260 (6%) Query: 6 ILFEKKDKVATITLNVPNS-NWLTIPMMKEINEALMDVKKDPTIQLLVFDHAGDKAFCDG 64 I +E+ VA +TLN P N L + L ++ DP+I+ ++ AG++AF G Sbjct: 5 ITYERNGAVAVLTLNRPEKLNALNYATNDCLLSLLNAIEIDPSIRAIILTGAGERAFSAG 64 Query: 65 VDV---ADHVPEKVDEMIDLF----HGMFRNMAAMDVTSVCLVNGRSLGGGCELMAFCDI 117 D+ + V VDE + F M + A + VNG + GGGCE+ + Sbjct: 65 GDIHEFTESVKAGVDEAVRDFCKRGQTMTARLEAFQKPIIAAVNGIAFGGGCEITEAVHL 124 Query: 118 VIASEKAKIGQPEINLAVFPPVAAAW-FPKIMGLKKAMELILTGKIISAKEAEAIGLVNV 176 +ASE+A +PEIN+ + P P++ G K+A+EL+LTG SA+ A +GLVN Sbjct: 125 AVASERAMFAKPEINIGIPPTFGGTQRLPRLAGRKRALELLLTGDTFSAQRACEMGLVNR 184 Query: 177 VLPVEGFREAAQKFMADFTSKSRPVAMWARRAIMA---GLNLDFLQALKASEIIYMQGCM 233 ++P + AA +AD + P+A A R I A G+N + L + + Sbjct: 185 IVPHDELMPAAFD-LADRIIRHSPLA--ASRIITAVTRGINTTIDEGLLIEREQFAR-MA 240 Query: 234 ATEDANEGLASFLEKRKPVF 253 AT+D +EGL +++ +R P + Sbjct: 241 ATKDVHEGLGAWIARRTPEY 260 Lambda K H 0.322 0.136 0.401 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: 146 Number of extensions: 11 Number of successful extensions: 4 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: 256 Length of database: 263 Length adjustment: 24 Effective length of query: 232 Effective length of database: 239 Effective search space: 55448 Effective search space used: 55448 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 Apr 09 2024. 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