Align 2-keto-3-deoxy-L-fuconate dehydrogenase; EC 1.1.1.- (characterized)
to candidate Pf1N1B4_412 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)
Query= SwissProt::Q8P3K4 (300 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_412 Length = 272 Score = 140 bits (353), Expect = 3e-38 Identities = 96/265 (36%), Positives = 134/265 (50%), Gaps = 14/265 (5%) Query: 47 VSIPTTPNT----RLQGKRCLITAAGAGIGRESALACARAGAHVIATDIDAAALQALAA- 101 +S+P P RL+ K L+T A GIG A A ++ +DI ++ +AA Sbjct: 5 LSLPPVPEPPKGERLKNKVVLLTGAAQGIGEAIVATFASQQARLVISDIQGEKVEKVAAH 64 Query: 102 ------ESDAITTQLLDVTDAAAITAL-VAAHGPFDVLFNCAGYVHQGSILDCDEPAWRR 154 + AI + D A+ L + HG DVL NCAG L E W R Sbjct: 65 WREQGADVVAIKADVSRQQDLHAMARLAIELHGRIDVLVNCAGVNVFRDPLQMTEEDWHR 124 Query: 155 SFSINVDAMYYTCKAVLPGMLERGRGSIINMSSVASSIKGVPNRFVYGVTKAAVIGLSKA 214 F+I++D +Y CKAVLP M+E+G GSIIN++S S+ +P F Y V K ++GL++A Sbjct: 125 CFAIDLDGAWYGCKAVLPQMIEQGIGSIINIASTHST-HIIPGCFPYPVAKHGLLGLTRA 183 Query: 215 IAADYVAQGVRCNAICPGTIKTPSLGQRVQALGGDEQAVWKSFTDRQPMGRLGDPREIAQ 274 + +Y +G+R NAI PG I+T L D A + D P R+G P E+A Sbjct: 184 LGIEYAPKGIRVNAIAPGYIET-QLNVDYWNGFADPHAERQRAFDLHPPRRIGQPIEVAM 242 Query: 275 LVVYLASDESSFTTGQTHIIDGGWS 299 V+LASDE+ F IDGG S Sbjct: 243 TAVFLASDEAPFINASCITIDGGRS 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: 14 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