Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate WP_011383077.1 AMB_RS03265 enoyl-CoA hydratase
Query= BRENDA::D3RXI0 (252 letters) >NCBI__GCF_000009985.1:WP_011383077.1 Length = 258 Score = 112 bits (280), Expect = 7e-30 Identities = 82/259 (31%), Positives = 125/259 (48%), Gaps = 8/259 (3%) Query: 1 MEYKKIKVEKDERVARIKIANPP-VNVLDMETMKEIISAIDEVEGVD---VIVFSGEGKS 56 M ++ I VE V I + P +N L + E+ A+D E D +V +G K+ Sbjct: 1 MAFENITVETRGNVGVIALNRPKAMNALCAALISELGQALDAFEADDSIGAVVLTGSEKA 60 Query: 57 FSAGAEIKEHFPDKAPE--MIRWFTQLIDKVLRCKAITVAAVKGFALGGGFELAIACDFV 114 F+AGA+IKE + + + T ++V +C+ VAAV GFALGGG E+A+ CDF+ Sbjct: 61 FAAGADIKEMASKSYMDVYLANFITDGWERVTKCRKPIVAAVAGFALGGGCEMAMMCDFI 120 Query: 115 LASKNAKLGVPEITLAHYPPV-AIALLPRMIGWKNAYELILTGEAITAERAFEIGLVNKV 173 +A NAK G PEIT+ P L R +G A E+ LTG + A A GLV+++ Sbjct: 121 IAGDNAKFGQPEITIGTIPGAGGTQRLTRAVGKSKAMEMCLTGRMMDAAEAERAGLVSRI 180 Query: 174 FEDENFEESVNDFVNSLLEKSSVALRLTKKALLFSTEKEYLSLFDVINDVYLSQLVKSED 233 + + S + L K+++ + E ++ S +ED Sbjct: 181 VPVAELLDEAVKAAGKIASLSRPIVMLCKESVNAAFETTLAQGVTFERRLFHSTF-STED 239 Query: 234 AVEGLKAFLEKRKPEWKGR 252 EG+ AF+EKR +K R Sbjct: 240 QKEGMAAFVEKRPAAFKNR 258 Lambda K H 0.318 0.136 0.382 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: 160 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: 252 Length of database: 258 Length adjustment: 24 Effective length of query: 228 Effective length of database: 234 Effective search space: 53352 Effective search space used: 53352 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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