Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate RR42_RS35270 RR42_RS35270 3-hydroxyacyl-CoA dehydrogenase
Query= BRENDA::O87873 (258 letters) >FitnessBrowser__Cup4G11:RR42_RS35270 Length = 693 Score = 80.9 bits (198), Expect = 7e-20 Identities = 58/177 (32%), Positives = 83/177 (46%), Gaps = 7/177 (3%) Query: 15 DGSLLRLRLARPKANIVDAAMIAAMRQALGEHLQAPALRAVLLDAEGPHFSFGASVDEHM 74 +G + L L P N + AA+ A + + + +R ++L G F GA + E Sbjct: 13 EGEIAILTLNSPPVNALSAAVRAGILAGIERAIADSNVRGIVLTCAGKTFIAGADITEFG 72 Query: 75 PDQCAQMLKSLHGLVREMLDSPVPILVALRGQCLGGGLEVAAAGNLLFAAPDAKFGQPEI 134 L + + SP P++ A+ G LGGGLEVA + AA A+ G PE+ Sbjct: 73 KPPVGPSLADVQAAIE---GSPKPVVAAIHGTALGGGLEVALVCHYRVAARSARCGLPEV 129 Query: 135 RLGVFAPAASCLLPPR-VGQACAEDLLWSGRSIDGAEGHRIGLIDVLAEDPEAAALR 190 LG+ A PR VG A A D++ SG I A +GL D++ ED AALR Sbjct: 130 NLGLLPGAGGTQRLPRIVGPAKALDMVTSGAHIGAAAAAEMGLFDLVTED---AALR 183 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: 353 Number of extensions: 15 Number of successful extensions: 2 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: 693 Length adjustment: 32 Effective length of query: 226 Effective length of database: 661 Effective search space: 149386 Effective search space used: 149386 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: 50 (23.9 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