Align BadK (characterized)
to candidate N515DRAFT_0416 N515DRAFT_0416 3-hydroxyacyl-CoA dehydrogenase / enoyl-CoA hydratase / 3-hydroxybutyryl-CoA epimerase
Query= metacyc::MONOMER-943 (258 letters) >FitnessBrowser__Dyella79:N515DRAFT_0416 Length = 686 Score = 93.6 bits (231), Expect = 1e-23 Identities = 62/182 (34%), Positives = 93/182 (51%), Gaps = 5/182 (2%) Query: 17 ITLNRPDV-LNALNDALMDALGGALLAFDADDGIGAIVIAGNTRAFAAGADIASMAAWSY 75 +TL+R + +NAL+ ++D LG + + G ++ + FA GADI ++ Sbjct: 22 LTLDRANSSVNALSREVLDELGQIVERLSIEKPAGVLIHSAKPGGFAVGADIKEFVEYAR 81 Query: 76 SDVYGSNFIT--RNWETIRQIRKPVLAAVAGLAYGGGCELALACDIVIAGRSAK--FALP 131 N R +E++ ++ P +AA+ G GGG EL LAC IA K LP Sbjct: 82 DGTVLQNIENGQRVFESLARLPCPTVAAIHGACMGGGTELVLACRQRIAADDEKTRIGLP 141 Query: 132 EIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRVVDDDRLRDETV 191 E+ LG+ PG GGT RLPR IG A+ + L+ + L+A A G+V R+ + L E Sbjct: 142 EVMLGIHPGWGGTARLPRLIGALDALPVMLTGKALSARRAAALGVVDRLAPPNELLAEAR 201 Query: 192 AL 193 AL Sbjct: 202 AL 203 Lambda K H 0.321 0.135 0.389 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: 271 Number of extensions: 7 Number of successful extensions: 1 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: 686 Length adjustment: 31 Effective length of query: 227 Effective length of database: 655 Effective search space: 148685 Effective search space used: 148685 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