Align L-fucose dehydrogenase (EC 1.1.1.122) (characterized)
to candidate SMa1403 SMa1403 oxidoreductase
Query= reanno::BFirm:BPHYT_RS34225 (346 letters) >FitnessBrowser__Smeli:SMa1403 Length = 338 Score = 339 bits (870), Expect = 5e-98 Identities = 168/335 (50%), Positives = 221/335 (65%), Gaps = 1/335 (0%) Query: 10 GQRRRIGRGPLQVTGLGLGTAPLGGLYRDLSDEEAHATIAAAWDAGVRYFDTAPHYGNTK 69 G++R+ GR L VT G GTAPLG ++R++ +E + + AWDAGVR+FDTAP YG+ Sbjct: 4 GEKRKFGRVDLDVTAFGFGTAPLGNIFREIDEETSQSMFELAWDAGVRFFDTAPMYGHGL 63 Query: 70 AEHRLGDALRRYPRADYVLSTKVGRRFVPRTTPFDDKEGWQNPLPFEAIYDYTHDGILRS 129 AE R G LR R +YVLS+KVGR P D W N PF +DY++DG +RS Sbjct: 64 AELRTGQGLRWRDRDEYVLSSKVGRLLTPAKRSTIDFAPWVNAAPFSMRFDYSYDGTMRS 123 Query: 130 FEDSQQRLGIVDIDILLVHDIGRVTHGDNHPHYWRQLTEGGGFRALDALRSSGAIKAVGL 189 FEDS QRLG+ +DI +HDI T G P + Q +G +RAL+ LRS G +KA+G+ Sbjct: 124 FEDSLQRLGLERMDICFIHDIDVFTRGSEQPEVFGQAMDGT-WRALEKLRSEGLVKAIGV 182 Query: 190 GVNEGAAILDAMAEFDIDCALLAGRYTLLEQTTLDDLLPACEKRGVSILLGGAFNSGILA 249 GVNE +A+ + D DC LLAGRYTLLEQ L++ LP CE+RG ++++GG FNSGILA Sbjct: 183 GVNEWEVCHEALKQRDFDCFLLAGRYTLLEQDALEEFLPLCEERGAAVVVGGGFNSGILA 242 Query: 250 RGVQGDLKFNYGEAPPEVIERVARLEAVCRTHGVPLAAAALQFPYAHPTVATVLTGARSA 309 G + K+NY AP ++E+VAR+EAVCRTH VPL AAALQF AHP V + + G R+ Sbjct: 243 TGAREGAKYNYAPAPKAILEKVARIEAVCRTHDVPLGAAALQFVVAHPAVPSFMAGTRTI 302 Query: 310 DELRENAASFELPIPAALWFALREEGLLDSRAPAP 344 ++LR+N + F PIPA W L+ +GLL AP P Sbjct: 303 EQLRQNLSWFSHPIPAGFWTELKSKGLLREDAPIP 337 Lambda K H 0.320 0.139 0.421 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: 334 Number of extensions: 10 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: 346 Length of database: 338 Length adjustment: 29 Effective length of query: 317 Effective length of database: 309 Effective search space: 97953 Effective search space used: 97953 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 (21.8 bits) S2: 49 (23.5 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