Align 2-keto-3-deoxy-L-fuconate dehydrogenase; EC 1.1.1.- (characterized)
to candidate 3607950 Dshi_1358 short-chain dehydrogenase/reductase SDR (RefSeq)
Query= SwissProt::Q8P3K4 (300 letters) >FitnessBrowser__Dino:3607950 Length = 258 Score = 134 bits (336), Expect = 3e-36 Identities = 87/245 (35%), Positives = 127/245 (51%), Gaps = 12/245 (4%) Query: 57 LQGKRCLITAAGAGIGRESALACARAGAHVIATDIDAAALQALA----AESDAITTQLLD 112 L+GKR LIT A +GIG AL +AGA VI A L+A+A AE T LD Sbjct: 16 LEGKRALITGASSGIGAHLALTLGQAGAEVILAARRADRLEAVAETLRAEGIVAQTAALD 75 Query: 113 VTDAAAITALVAAHGPFDVLFNCAGYVHQGSILDCDEPAWRRSFSINVDAMYYTCKAVLP 172 VTDAA++ A V GP D+L N +G Q ++D E W R N+ + +A P Sbjct: 76 VTDAASVAAAVTTVGPLDILINNSGVSGQDMVIDTTEADWDRVLDTNLKGAWRVSRAFAP 135 Query: 173 GMLERGRGSIINMSSVASSIKGVPNRFVYGVTKAAVIGLSKAIAADYVAQGVRCNAICPG 232 G++ R +G+I+N++S+ I + Y +KA +I L++A+A + GVR NA+ PG Sbjct: 136 GLIAR-QGTILNVASIL-GIGVLKTVGPYAASKAGLIQLTRAMALELARDGVRVNALAPG 193 Query: 233 TIKTPSLGQRVQALGGDEQAVWKSFTDRQPMGRLGDPREIAQLVVYLASDESSFTTGQTH 292 I+TP + + G + P RLG P ++ V+ L + F TG T Sbjct: 194 YIETPINTEFFASEAG------QKMLRGVPQRRLGQPGDLDAAVLMLLGPGAGFVTGATV 247 Query: 293 IIDGG 297 ++DGG Sbjct: 248 VVDGG 252 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: 147 Number of extensions: 10 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: 258 Length adjustment: 25 Effective length of query: 275 Effective length of database: 233 Effective search space: 64075 Effective search space used: 64075 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