Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate PP_1817 PP_1817 Oxidoreductase, short-chain dehydrogenase/reductase family
Query= reanno::BFirm:BPHYT_RS04775 (263 letters) >FitnessBrowser__Putida:PP_1817 Length = 253 Score = 105 bits (263), Expect = 7e-28 Identities = 77/255 (30%), Positives = 120/255 (47%), Gaps = 21/255 (8%) Query: 12 GLRVLISGAAAGIGAAIAQAFLDVGANVYICDVDPAAIDRARTAHPQLHAG-------VA 64 G L++GA AGIG A A AF G V + D+DP Q+HA Sbjct: 7 GQVALVTGAGAGIGRATALAFAHEGMKVVVADLDPVG---GEATVAQIHAAGGEALFIAC 63 Query: 65 DVSDCAQVDRIIDDARSKLGGLDLLINNAGIAGPTGAVEDLDPAEWERTIGTNLNSQFYF 124 DV+ A+V ++ + + G LD NNAGI + + AE++ +G N+ + Sbjct: 64 DVTRDAEVRQLHERLMAAYGRLDYAFNNAGIEIEQHRLAEGSEAEFDAIMGVNVKGVWLC 123 Query: 125 LRKAVPLLKETSANPGIIAMASVAGRLGYAFRTPYAASKWAIVGMVKSLAIELGPNNVRV 184 ++ +PLL I+ ASVAG + Y+ASK A++G+ KS AIE +RV Sbjct: 124 MKYQLPLLLAQGGG-AIVNTASVAGLGAAPKMSIYSASKHAVIGLTKSAAIEYAKKGIRV 182 Query: 185 NAILPGVVEGERMDRVISARAESLGIGFDQMKGEYLQKI-SLRRMVTVHDVAAMALFLAS 243 NA+ P V++ + R A D K E+ + + R+ V ++A+ L+L S Sbjct: 183 NAVCPAVIDTDMFRRAYQA---------DPRKAEFAAAMHPVGRIGKVEEIASAVLYLCS 233 Query: 244 PAGQNISGQAISVDG 258 +G ++VDG Sbjct: 234 DGAAFTTGHCLTVDG 248 Lambda K H 0.320 0.136 0.391 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: 138 Number of extensions: 8 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: 253 Length adjustment: 24 Effective length of query: 239 Effective length of database: 229 Effective search space: 54731 Effective search space used: 54731 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