Align L-fucose dehydrogenase (EC 1.1.1.122) (characterized)
to candidate H281DRAFT_03531 H281DRAFT_03531 D-threo-aldose 1-dehydrogenase
Query= reanno::BFirm:BPHYT_RS34225 (346 letters) >FitnessBrowser__Burk376:H281DRAFT_03531 Length = 346 Score = 629 bits (1621), Expect = 0.0 Identities = 310/345 (89%), Positives = 324/345 (93%) Query: 1 MTATIGSKIGQRRRIGRGPLQVTGLGLGTAPLGGLYRDLSDEEAHATIAAAWDAGVRYFD 60 MTAT GSKI QRRR+GR LQVTGL LGTAPLGGLYRDLS+EEAHAT+AAAW+AGVRYFD Sbjct: 1 MTATNGSKIQQRRRVGRSALQVTGLSLGTAPLGGLYRDLSEEEAHATVAAAWNAGVRYFD 60 Query: 61 TAPHYGNTKAEHRLGDALRRYPRADYVLSTKVGRRFVPRTTPFDDKEGWQNPLPFEAIYD 120 TAPHYG+TKAEHRLGDALRRYPR++YVLSTKVGRRFVPRT P+D EGWQ+PLPFEAIYD Sbjct: 61 TAPHYGHTKAEHRLGDALRRYPRSEYVLSTKVGRRFVPRTNPYDGSEGWQDPLPFEAIYD 120 Query: 121 YTHDGILRSFEDSQQRLGIVDIDILLVHDIGRVTHGDNHPHYWRQLTEGGGFRALDALRS 180 YTHDGILRSFEDSQQRLGIVDIDILLVHDIGRVTHG+N+ HYWRQLTEGGGFRALD LRS Sbjct: 121 YTHDGILRSFEDSQQRLGIVDIDILLVHDIGRVTHGENNTHYWRQLTEGGGFRALDELRS 180 Query: 181 SGAIKAVGLGVNEGAAILDAMAEFDIDCALLAGRYTLLEQTTLDDLLPACEKRGVSILLG 240 GA+KAVGLGVNEGA ILDAMAEFDIDCALLAGRYTLLEQ TLDDLLPACEKRGVSILLG Sbjct: 181 GGAVKAVGLGVNEGAVILDAMAEFDIDCALLAGRYTLLEQATLDDLLPACEKRGVSILLG 240 Query: 241 GAFNSGILARGVQGDLKFNYGEAPPEVIERVARLEAVCRTHGVPLAAAALQFPYAHPTVA 300 GAFNSGILARGV+GDLKFNYGEAP EVIERVARLE VCR GVPLAAAALQFPYAHP VA Sbjct: 241 GAFNSGILARGVEGDLKFNYGEAPREVIERVARLETVCRNLGVPLAAAALQFPYAHPAVA 300 Query: 301 TVLTGARSADELRENAASFELPIPAALWFALREEGLLDSRAPAPE 345 TVLTGARSADELRENAASFELPIP ALW ALREEGLLD RAPAP+ Sbjct: 301 TVLTGARSADELRENAASFELPIPGALWSALREEGLLDPRAPAPQ 345 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: 502 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: 346 Length of database: 346 Length adjustment: 29 Effective length of query: 317 Effective length of database: 317 Effective search space: 100489 Effective search space used: 100489 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