Align L-fucose dehydrogenase (EC 1.1.1.122) (characterized)
to candidate AZOBR_RS23565 AZOBR_RS23565 D-threo-aldose 1-dehydrogenase
Query= reanno::BFirm:BPHYT_RS34225 (346 letters) >FitnessBrowser__azobra:AZOBR_RS23565 Length = 316 Score = 275 bits (703), Expect = 1e-78 Identities = 147/320 (45%), Positives = 192/320 (60%), Gaps = 5/320 (1%) Query: 25 LGLGTAPLGGLYRDLSDEEAHATIAAAWDAGVRYFDTAPHYGNTKAEHRLGDALRRYPRA 84 +G G APLG ++ ++ D+ A AT+AAAWDAG+RYFDTAP YG +EHR G LR PR Sbjct: 1 IGFGGAPLGNMFEEVPDDVAEATLAAAWDAGIRYFDTAPEYGPGISEHRFGHVLRNRPRD 60 Query: 85 DYVLSTKVGRRFVPRTTPFDDKEGWQNPLPFEAIYDYTHDGILRSFEDSQQRLGIVDIDI 144 ++VLSTKVGR ++ + LPF YDYT DG+ RS EDS QRLG+ IDI Sbjct: 61 EFVLSTKVGRLLRADSSKGGKHGPFVKGLPFRVDYDYTADGVRRSIEDSLQRLGMARIDI 120 Query: 145 LLVHDIGRVTHGDNHPHYWRQLTEGGGFRALDALRSSGAIKAVGLGVNEGAAILDAMAEF 204 +HD HGD + +G AL LR G I+A GLGVN + AM Sbjct: 121 AYIHDCAEDAHGDRWLEVFDTAMKGAAV-ALTQLREEGVIRAWGLGVNRVEPCVMAMERA 179 Query: 205 DIDCALLAGRYTLLEQTTLDDLLPACEKRGVSILLGGAFNSGILARGVQGDLKFNYGEAP 264 D D LLAGRY+LL Q LD L P C++RGV +++GG +NSG++A G F Y EAP Sbjct: 180 DPDVFLLAGRYSLLNQPALDTLFPRCQERGVHVVVGGPYNSGLIA----GGKTFEYQEAP 235 Query: 265 PEVIERVARLEAVCRTHGVPLAAAALQFPYAHPTVATVLTGARSADELRENAASFELPIP 324 P+ + RL + + HGV L AAALQF AHP VA+V+ G ++ ++EN A + PIP Sbjct: 236 PDKVAARDRLAEIAKRHGVDLRAAALQFCAAHPVVASVIPGTKNPPRVQENMALMKQPIP 295 Query: 325 AALWFALREEGLLDSRAPAP 344 A W L++ G+L + P P Sbjct: 296 ADFWRELKQAGVLPEQVPTP 315 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: 308 Number of extensions: 13 Number of successful extensions: 4 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: 316 Length adjustment: 28 Effective length of query: 318 Effective length of database: 288 Effective search space: 91584 Effective search space used: 91584 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