Align L-fucose dehydrogenase (EC 1.1.1.122) (characterized)
to candidate Ga0059261_2677 Ga0059261_2677 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases)
Query= reanno::BFirm:BPHYT_RS34225 (346 letters) >FitnessBrowser__Korea:Ga0059261_2677 Length = 336 Score = 293 bits (751), Expect = 3e-84 Identities = 159/329 (48%), Positives = 213/329 (64%), Gaps = 11/329 (3%) Query: 25 LGLGTAPLGGLYRDLSDEEAHATIAAAWDAGVRYFDTAPHYGNTKAEHRLGDALRRY-PR 83 L G A +G LYR + + +A +A AWDAGVR FDTAPHYG +E RLG AL P Sbjct: 11 LAFGAASIGNLYRAVPEAQARDVVARAWDAGVRTFDTAPHYGFGLSEKRLGAALAELDPA 70 Query: 84 ADYVLSTKVGRRFVPRTTPFDD----KEGWQNPLPFEAIYDYTHDGILRSFEDSQQRLGI 139 ++STK+GRR PR P D ++ + +P P+E+++DY++D ++RS+E S +RL Sbjct: 71 QSAIVSTKIGRRLDPR--PDADLSAMRQAFVSPEPYESVFDYSYDAVMRSYEGSLKRLRR 128 Query: 140 VDIDILLVHDIGRVTHGDNHPHYWRQLTEGGGFRALDALRSSGAIKAVGLGVNEGAAILD 199 IDIL HDIG HG HP + + GGG+RA+ LR SGA+ A+G+GVNE A ++ Sbjct: 129 DRIDILYAHDIGVFAHGAAHPRRFAEFM-GGGYRAMLKLRDSGAVGAIGIGVNEVAVCIE 187 Query: 200 AMAEFDIDCALLAGRYTLLEQTTLDDLLPACEKRGVSILLGGAFNSGILARGVQ--GDL- 256 + +ID +LAGRYTLLEQ LDDLLP C +RGV +++ G +NSGILA+GV+ G + Sbjct: 188 MLGAGEIDLIMLAGRYTLLEQDPLDDLLPLCARRGVRLVIAGPYNSGILAKGVRHGGAIP 247 Query: 257 KFNYGEAPPEVIERVARLEAVCRTHGVPLAAAALQFPYAHPTVATVLTGARSADELRENA 316 FNY APP ++ERV +E VC HGVPLAAAALQFP AHP VA+V+ G S ++ + Sbjct: 248 NFNYEPAPPAILERVGAIEDVCAKHGVPLAAAALQFPLAHPQVASVVPGMGSVRQVDDAL 307 Query: 317 ASFELPIPAALWFALREEGLLDSRAPAPE 345 A IP LW LR+ GL+ AP P+ Sbjct: 308 ALMARVIPVTLWEELRDAGLIRRDAPLPQ 336 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: 333 Number of extensions: 14 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: 346 Length of database: 336 Length adjustment: 29 Effective length of query: 317 Effective length of database: 307 Effective search space: 97319 Effective search space used: 97319 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