Align L-fucose dehydrogenase (EC 1.1.1.122) (characterized)
to candidate GFF2306 Psest_2353 Predicted oxidoreductases (related to aryl-alcohol dehydrogenases)
Query= reanno::BFirm:BPHYT_RS34225 (346 letters) >FitnessBrowser__psRCH2:GFF2306 Length = 323 Score = 236 bits (603), Expect = 5e-67 Identities = 132/321 (41%), Positives = 185/321 (57%), Gaps = 7/321 (2%) Query: 25 LGLGTAPLGGLYRDLSDEEAHATIAAAWDAGVRYFDTAPHYGNTKAEHRLGDALRRYPRA 84 +GLG APLG ++ LS+E A AT+ AAWDAG RY+D +PHYG AE R G L PR Sbjct: 8 IGLGGAPLGNMFHPLSEETADATLNAAWDAGFRYYDVSPHYGAGLAEQRFGRLLSGKPRD 67 Query: 85 DYVLSTKVGRRFVPRTTPFDDKEGWQNPLPFEAIYDYTHDGILRSFEDSQQRLGIVDIDI 144 +YVLSTKVGR P ++ + + + LP + + DY+ DG RS EDS +R+G+ +D+ Sbjct: 68 EYVLSTKVGRLLQSAGQP-ENAKPFVDELPNKRVPDYSADGARRSIEDSLERMGVDHLDV 126 Query: 145 LLVHDIGRVTHGDNHPHYWRQLTEGGGFRALDALRSSGAIKAVGLGVNEGAAILDAMAEF 204 + +HD+ G Y++Q G +AL LR G I+ GLGVN A+ + Sbjct: 127 VFIHDVSEDQWGPQWKEYFQQAMNGAA-KALTQLRDEGVIRGWGLGVNLVEPCRMALEQS 185 Query: 205 DIDCALLAGRYTLLE-QTTLDDLLPACEKRGVSILLGGAFNSGILARGVQGDLKFNYGEA 263 D + LLAGRY+LLE LD L P C+ R V +++GG FNSG+LA G + Y + Sbjct: 186 DPNVFLLAGRYSLLEHDEALDTLFPTCQARDVGVVVGGPFNSGVLAGGDH----YEYDQI 241 Query: 264 PPEVIERVARLEAVCRTHGVPLAAAALQFPYAHPTVATVLTGARSADELRENAASFELPI 323 PP++ +R +L+A GV L AAAL F A+P VA+V+ G + + ++ F + Sbjct: 242 PPQIAQRREQLKAAAERCGVDLRAAALHFCLANPVVASVIPGTANPERPKQYMDYFNTQV 301 Query: 324 PAALWFALREEGLLDSRAPAP 344 P W L+ EGLL AP P Sbjct: 302 PREFWQTLKREGLLREDAPVP 322 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: 304 Number of extensions: 17 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: 323 Length adjustment: 28 Effective length of query: 318 Effective length of database: 295 Effective search space: 93810 Effective search space used: 93810 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