Align 2-keto-3-deoxy-L-fuconate dehydrogenase; EC 1.1.1.- (characterized)
to candidate AO356_20240 AO356_20240 short-chain dehydrogenase
Query= SwissProt::Q8P3K4 (300 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_20240 Length = 272 Score = 149 bits (377), Expect = 5e-41 Identities = 103/261 (39%), Positives = 139/261 (53%), Gaps = 13/261 (4%) Query: 49 IPTTPN-TRLQGKRCLITAAGAGIGRESALACARAGAHVIATDIDAAALQALAAE----- 102 +P P RL+ K L+T A GIG A A A ++ +DI A ++A+AA Sbjct: 10 VPEPPKGERLKDKVVLLTGAAQGIGEAIVAAFASQQARLVISDIQAQKVEAVAAHWRERG 69 Query: 103 SDAITTQLLDVTDAAAITAL----VAAHGPFDVLFNCAGYVHQGSILDCDEPAWRRSFSI 158 +D Q DV+ + A+ V HG DVL NCAG L+ E WRR F+I Sbjct: 70 ADVHALQA-DVSKQQDLQAMARRAVELHGRIDVLVNCAGVNVFRDPLEMTEEDWRRCFAI 128 Query: 159 NVDAMYYTCKAVLPGMLERGRGSIINMSSVASSIKGVPNRFVYGVTKAAVIGLSKAIAAD 218 ++D +Y CKAVLP M+E+G GSIIN++SV SS +P F Y V K ++GL++A+ + Sbjct: 129 DLDGAWYGCKAVLPQMIEQGVGSIINIASVHSS-HIIPGCFPYPVAKHGLLGLTRALGIE 187 Query: 219 YVAQGVRCNAICPGTIKTPSLGQRVQALGGDEQAVWKSFTDRQPMGRLGDPREIAQLVVY 278 Y +GVR NAI PG I+T L D A + D P R+G P E+A V+ Sbjct: 188 YAPKGVRVNAIAPGYIET-QLNVDYWNGFADPHAERQRALDLHPPRRVGQPIEVAMTAVF 246 Query: 279 LASDESSFTTGQTHIIDGGWS 299 LASDE+ F IDGG S Sbjct: 247 LASDEAPFINASCITIDGGRS 267 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: 178 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: 272 Length adjustment: 26 Effective length of query: 274 Effective length of database: 246 Effective search space: 67404 Effective search space used: 67404 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