Align 2-keto-3-deoxy-L-fuconate dehydrogenase; EC 1.1.1.- (characterized)
to candidate WP_008486155.1 B3C1_RS16220 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase KduD
Query= SwissProt::Q8P3K4 (300 letters) >NCBI__GCF_000299915.1:WP_008486155.1 Length = 249 Score = 123 bits (308), Expect = 5e-33 Identities = 81/249 (32%), Positives = 123/249 (49%), Gaps = 13/249 (5%) Query: 57 LQGKRCLITAAGAGIGRESALACARAGAHVIAT-------DIDAAALQALAAESDAITTQ 109 L GKR L+T A G+G+ AL A GA VI D A + AL ++ A+ Sbjct: 4 LNGKRALVTGASRGLGQAMALGLAENGAEVICASSREGGCDDTVAKILALGGKARALAAD 63 Query: 110 LLDVTDAAAITALVAAHGPFDVLFNCAGYVHQGSILDCDEPAWRRSFSINVDAMYYTCKA 169 L D A+ A GP DVL N G +++ + LD A+ +N++A + + Sbjct: 64 LGDSQAVQALAEQALAAGPVDVLVNNGGCIYREAALDFPLDAFDAVIKVNLNAAFQLSQL 123 Query: 170 VLPGMLERGRGSIINMSSVASSIKGVPNRFVYGVTKAAVIGLSKAIAADYVAQGVRCNAI 229 + M+ +G G I+N++S+ S G+ Y +K A+ GL+KA+A ++ G++ NAI Sbjct: 124 LGRAMVTKGSGKIVNIASMLSYSGGI-RVPAYTASKHAIAGLTKALANEWGQHGIQVNAI 182 Query: 230 CPGTIKTPSLGQRVQALGGDEQAVWKSFTDRQPMGRLGDPREIAQLVVYLASDESSFTTG 289 PG +T QAL D + R P GR G+P ++ VV+LAS S + G Sbjct: 183 APGYFRT----DNTQALQDDAERS-SEIEKRIPAGRWGNPDDLKGAVVFLASKASDYVNG 237 Query: 290 QTHIIDGGW 298 +DGGW Sbjct: 238 HILAVDGGW 246 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: 7 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: 249 Length adjustment: 25 Effective length of query: 275 Effective length of database: 224 Effective search space: 61600 Effective search space used: 61600 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 24 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