Align BadI (characterized)
to candidate Dsui_2807 Dsui_2807 enoyl-CoA hydratase/carnithine racemase
Query= metacyc::MONOMER-892 (260 letters) >FitnessBrowser__PS:Dsui_2807 Length = 262 Score = 103 bits (256), Expect = 5e-27 Identities = 77/249 (30%), Positives = 118/249 (47%), Gaps = 13/249 (5%) Query: 12 NGVAWIIINRPDKMNAFRGTTCDELIKALYKAGYDKDVGAIVLAGAGDRAFCTGGDQSTH 71 +G +++NRP + N+ + L+ L DK V +VL GAG +AFC G D Sbjct: 15 DGRTTLVLNRPAQFNSLSNAMLETLLAELQSIAADKTVRVVVLQGAG-KAFCAGHDLKEM 73 Query: 72 DGNYDGRGTVGL--PMEELHTAIRDVPKPVIARVQGYAIGGGNVLATICDLTICSEKAIF 129 N+D L ++ I+++P+PVIAR+ G A G L ++CDL + ++ A F Sbjct: 74 RSNHDKAFMQALFKLCAKVMLTIQEMPQPVIARIHGIATAAGCQLVSMCDLAVAADVAKF 133 Query: 130 GQVGPKMG--SVDPGYGTAFLARVVGEKKAREIWYMCKRYSGKEAEAMGLANLCVPHDEL 187 G +G P G LAR +G K+A E+ + EA+ GL N V +L Sbjct: 134 AVSGINVGLFCSTPAVG---LARNMGRKEALEMLLTGEFIDAGEAQRRGLVNRVVALGDL 190 Query: 188 DAEVQKWGEELCERSPTALAIAKRSFNMDTAHQAGIAGMGMYA---LKLYYDTDESREGV 244 D V+ + + +SP A+A K+ F + GI YA + ++ EG+ Sbjct: 191 DEAVEHLVQSILAKSPVAVATGKQMFYKQL--EMGIEAAYQYAGEVMACNMMAGDAAEGI 248 Query: 245 KALQEKRKP 253 A EKRKP Sbjct: 249 DAFIEKRKP 257 Lambda K H 0.319 0.138 0.418 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: 8 Number of successful extensions: 5 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: 260 Length of database: 262 Length adjustment: 25 Effective length of query: 235 Effective length of database: 237 Effective search space: 55695 Effective search space used: 55695 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 (21.7 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