Align cyclohexa-1,5-dienecarbonyl-CoA hydratase monomer (EC 4.2.1.100) (characterized)
to candidate CCNA_01891 CCNA_01891 enoyl-CoA hydratase/carnithine racemase
Query= metacyc::MONOMER-18320 (256 letters) >FitnessBrowser__Caulo:CCNA_01891 Length = 275 Score = 96.3 bits (238), Expect = 6e-25 Identities = 81/259 (31%), Positives = 122/259 (47%), Gaps = 21/259 (8%) Query: 9 EKKDKVATITLNVPNSNWLTIPMMKEINEALMDVKKDPTIQLLVFDHAGDKAFCDGVDVA 68 E +D VAT+TL P N ++ MM E+ A + P ++ ++ G K FC G D+ Sbjct: 27 EVEDFVATVTLANPPVNSASVDMMLELTAAFDAFNESPDVRAVLLTAEG-KTFCAGADLK 85 Query: 69 DHV-PEKVDEMIDLFHGMFRNMAAMDVTS----VCLVNGRSLGGGCELMAFCDIVIASEK 123 + P+ M R M+ V V VNG +LG G ++A CDI++ASE+ Sbjct: 86 NRPGPDAPAGTAFARQRMAREMSWSMVECSKPVVVAVNGAALGAGLGIVASCDIIVASER 145 Query: 124 AKIGQPEIN--LAVFPPVAAAWFPKIMGLKKAMELILTGKIISAKEAEAIGLVNVVLPVE 181 A G PEI+ LA A + P + A ++LTG + A+E GL+ LP E Sbjct: 146 AVFGLPEIDVGLAGGAKHAVRFIPHSL----ARRMVLTGWRVPAEELYRRGLIEAALPHE 201 Query: 182 GFREAAQKFMADFTSKSRPVAMWARRAIMAGLNLDFLQALKASEIIYMQG----CMATED 237 F + A+ + SKS A+ ++ NL + Y QG +ED Sbjct: 202 EFLDYARGIAKEIASKSPVAVAAAKDSLNVIDNLSLRDGYR-----YEQGNTYKLSKSED 256 Query: 238 ANEGLASFLEKRKPVFKDK 256 A E + +F+EKR PVF+ + Sbjct: 257 AKEAVRAFIEKRPPVFQGR 275 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: 155 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: 275 Length adjustment: 25 Effective length of query: 231 Effective length of database: 250 Effective search space: 57750 Effective search space used: 57750 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