Align cyclohexa-1,5-dienecarbonyl-CoA hydratase monomer (EC 4.2.1.100) (characterized)
to candidate WP_011365963.1 GMET_RS11115 enoyl-CoA hydratase/isomerase family protein
Query= metacyc::MONOMER-18320 (256 letters) >NCBI__GCF_000012925.1:WP_011365963.1 Length = 265 Score = 133 bits (335), Expect = 3e-36 Identities = 93/265 (35%), Positives = 138/265 (52%), Gaps = 15/265 (5%) Query: 1 MGFNTILFEKKDKVATITLNVPNS-NWLTIPMMKEINEALMDVKKDPTIQLLVFDHAGDK 59 M F TI+ +KKD +ATIT N P N + M +E+ A+ DV D ++++LV +G+ Sbjct: 1 MSFETIILDKKDGIATITFNRPKVFNAYSEQMSQELKAAVADVGSDTSLRVLVLKGSGEN 60 Query: 60 AFCDGVDV----------ADHVPEKVDEMIDLFHGMFRNMAAMDVTSVCLVNGRSLGGGC 109 F G D+ A+ EKV E++D H ++ + + + V+G + G G Sbjct: 61 -FLAGADINMLNSWSKISAEQGWEKVKEILD-HHFSPTSLEKIPLPVIAAVDGMAWGMGS 118 Query: 110 ELMAFCDIVIASEKAKIGQPEINLAVFPPVAAAW-FPKIMGLKKAMELILTGKIISAKEA 168 E+ CD I + +A QPEINL + A+ P+I+G KAME+ILTGK I+A +A Sbjct: 119 EIALGCDFRICTTRASFAQPEINLGIITGGGASQRLPRIVGKAKAMEMILTGKPINAADA 178 Query: 169 EAIGLVNVVLPVEGFREAAQKFMADFTSKSRPVAMWARRAIMAGLNLDFLQALKASEIIY 228 GLVN V+ EG A + KS + WA+ + L+ D L + E+ Sbjct: 179 CKWGLVNEVVEPEGLDAAVARLAKAIMGKSPLMVKWAKDCVNLVLDHDLLSGID-KELTQ 237 Query: 229 MQGCMATEDANEGLASFLEKRKPVF 253 AT+D+ EG A+FLEKRK F Sbjct: 238 FAKTFATQDSKEGTAAFLEKRKANF 262 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: 171 Number of extensions: 10 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: 265 Length adjustment: 24 Effective length of query: 232 Effective length of database: 241 Effective search space: 55912 Effective search space used: 55912 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 24 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