Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate WP_041098458.1 SUTH_RS08230 3-oxoacyl-ACP reductase FabG
Query= reanno::Burk376:H281DRAFT_00644 (263 letters) >NCBI__GCF_000828635.1:WP_041098458.1 Length = 248 Score = 107 bits (267), Expect = 2e-28 Identities = 84/252 (33%), Positives = 126/252 (50%), Gaps = 17/252 (6%) Query: 14 RVFVSAGAA-GIGLAIAEAFIEAQAEVYICDVNQAAIDEATSRFPKLHA---GIA-DVSK 68 RV + GA GIG ++A A+ A+V + D+N A ++ + G+A DVS Sbjct: 6 RVAIVTGAGQGIGASVAAAYAREGAKVAVVDMNGEAAEKVAAAIVGAGGTAIGVACDVSS 65 Query: 69 QAQVDQIIDDARRKLGGLDVLVNNAGIAGPTGAVEELDPAQWESTVSTNLNSQFYFLRKA 128 + QV+ + + G +D+LVNNAGI T + ++ QW V +L F L+ Sbjct: 66 REQVEAMAAKVNAEWGRIDILVNNAGITR-TAMLHKMTIEQWNQVVGVHLTGAFNCLQAV 124 Query: 129 VPVLKETSDCASIIAMSSVAGRLGYPFRTPYASTKWAIVGLVKSLAAELGPSNVRVNAIL 188 V + E II ++S AG LG + Y++ K I+G+ KS A EL N+ NAI Sbjct: 125 VGGMIERK-YGRIIYVTSAAGVLGTIGQINYSAAKAGILGMTKSTAKELARYNITANAIA 183 Query: 189 PGVVEGERMDRVISARADALGIPFNAMREEYLKKISLRRMVTVDDIAAMALFLASPAGSN 248 PG M VI R D +++YL +I L R ++IA + LF AS A + Sbjct: 184 PGA--ATPMTEVI--RTD------EKFKDKYLDRIPLGRWAEPEEIAPVFLFFASDASAY 233 Query: 249 VTGQAISVDGNV 260 VTGQ ++ DG + Sbjct: 234 VTGQILAADGGM 245 Lambda K H 0.318 0.134 0.375 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: 131 Number of extensions: 5 Number of successful extensions: 3 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: 263 Length of database: 248 Length adjustment: 24 Effective length of query: 239 Effective length of database: 224 Effective search space: 53536 Effective search space used: 53536 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. 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