Align 2-keto-3-deoxy-L-fuconate dehydrogenase; EC 1.1.1.- (characterized)
to candidate AZOBR_RS28175 AZOBR_RS28175 short-chain dehydrogenase
Query= SwissProt::Q8P3K4 (300 letters) >FitnessBrowser__azobra:AZOBR_RS28175 Length = 251 Score = 147 bits (370), Expect = 3e-40 Identities = 97/252 (38%), Positives = 139/252 (55%), Gaps = 15/252 (5%) Query: 55 TRLQGKRCLITAAGAGIGRESALACARAGAHVIATDI-DAAALQAL----AAESDAITTQ 109 T + G L+T +GIGR +ALA A+AGA I T +A L+ + A A+ Q Sbjct: 2 TDMSGGVALVTGGTSGIGRATALAFAKAGATAIVTGRREAEGLETVDLVRQAGGRAVFVQ 61 Query: 110 LLDVTDAAAITALVAA----HGPFDVLFNCAGYVHQGSILDCDEPAWRRSFSINVDAMYY 165 DV DA + AL A HG D FN AG S+ D E + R ++N+ ++ Sbjct: 62 A-DVADAEEVAALFARIERDHGRLDYAFNNAGIHFGRSVADTTEADFDRMVAVNIKGVWL 120 Query: 166 TCKAVLPGMLERGRGSIINMSSVASSIKGVPNRFVYGVTKAAVIGLSKAIAADYVAQGVR 225 K LP ML +G+G+I++ SV I G+ VY +KAAV G+++++A + GVR Sbjct: 121 CLKHELPIMLRQGKGAIVSTGSVLGQI-GLAGNSVYSASKAAVEGMTRSVAIEVAKSGVR 179 Query: 226 CNAICPGTIKTPSLGQRVQALGGDEQAVWKSFTDRQPMGRLGDPREIAQLVVYLASDESS 285 NA+CP I+TP + GG+E AV + P+GR+G PRE+A VV+L SD +S Sbjct: 180 VNAVCPAIIQTP---MSAGSFGGEE-AVNAALGPLHPVGRVGQPREVADTVVWLCSDAAS 235 Query: 286 FTTGQTHIIDGG 297 F TGQ+ +DGG Sbjct: 236 FITGQSINVDGG 247 Lambda K H 0.320 0.133 0.395 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: 164 Number of extensions: 6 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: 300 Length of database: 251 Length adjustment: 25 Effective length of query: 275 Effective length of database: 226 Effective search space: 62150 Effective search space used: 62150 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: 47 (22.7 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