Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate 3607199 Dshi_0620 short-chain dehydrogenase/reductase SDR (RefSeq)
Query= reanno::Burk376:H281DRAFT_00644 (263 letters) >FitnessBrowser__Dino:3607199 Length = 250 Score = 119 bits (299), Expect = 5e-32 Identities = 77/245 (31%), Positives = 122/245 (49%), Gaps = 13/245 (5%) Query: 17 VSAGAAGIGLAIAEAFIEAQAEVYICDVNQAAIDEATSRFPKLHAGIADVSKQAQVDQII 76 V+ A GIGLA + +E +V + D + A+ EA +H DVS V+ +I Sbjct: 8 VTGAARGIGLATTKLLLERGWKVAMIDRDGPALAEALQGLDGVHGIDCDVSDPEAVEGMI 67 Query: 77 DDARRKLGGLDVLVNNAGIAGPTGAVEELDPAQWESTVSTNLNSQFYFLRKAVPVLKETS 136 + R+ G +D LVNNAG+A G +EE A+W++ + TNL+ F ++ A P LK T Sbjct: 68 AETLREFGQIDALVNNAGVA-DFGPIEETSFARWKTVMETNLDGPFLCVQAATPALKATK 126 Query: 137 DCASIIAMSSVAGRLGYPFRTPYASTKWAIVGLVKSLAAELGPSNVRVNAILPGVVEGER 196 +++ ++S++G R Y ++K A++ L A ELG +R N + PG V + Sbjct: 127 --GAVVNIASISGLRASTLRVAYGTSKAAVIQLTLQQAVELGEHGIRANCVCPGPVRTKL 184 Query: 197 MDRVISARADALGIPFNAMREEYLKKISLRRMVTVDDIAAMALFLASPAGSNVTGQAISV 256 A+ + + + Y I L R + +IA LFL S S +TGQ ++ Sbjct: 185 ----------AMAVHSQEIIDAYHDAIPLNRYGSEQEIAEAILFLCSERASFITGQVLAA 234 Query: 257 DGNVE 261 DG E Sbjct: 235 DGGFE 239 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: 139 Number of extensions: 9 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: 263 Length of database: 250 Length adjustment: 24 Effective length of query: 239 Effective length of database: 226 Effective search space: 54014 Effective search space used: 54014 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 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