Align Sorbitol dehydrogenase (EC 1.1.1.14) (characterized)
to candidate 8501727 DvMF_2444 short-chain dehydrogenase/reductase SDR (RefSeq)
Query= reanno::Phaeo:GFF1301 (257 letters) >FitnessBrowser__Miya:8501727 Length = 306 Score = 117 bits (294), Expect = 2e-31 Identities = 84/283 (29%), Positives = 133/283 (46%), Gaps = 43/283 (15%) Query: 4 LSGKRALITGAARGIGAAFAEAYANEGARVVIADIDTAR----AEATAAQIGAAAIA--- 56 L+G+ AL+TG A+GIG E G RV D D A A +A++ A +A Sbjct: 25 LAGRVALVTGGAQGIGRGIVEHLLACGMRVAAMDADAEALAELAGALSAELAAEPVADNE 84 Query: 57 ----------------------VELDVTDQASIDRALSRTVECFGGLDILINNAAVFTA- 93 + V DQA DR ++ TV FGGL +L+NNA + Sbjct: 85 ASLPAHPDASAAPHSPTFPMLTLHGSVADQADADRCVAATVARFGGLHLLVNNAGIANPH 144 Query: 94 ---APLVEVTREAYQRTFDINVSGTLFMMQAAAQQMITQGTGGKIINMASQAGRRGEPLV 150 A + + + +Q D+N++G + M++AA + + G ++N+AS + EP Sbjct: 145 SGPADVAAMDMDRWQHMLDVNLTGPMRMVRAAVPHL--RAARGAVVNIASTRAVQSEPHT 202 Query: 151 SVYCATKAAVISLTQSAGLNLISHGINVNAIAPGVVDGEHWDGVDAFFAKYEGKAPGQKK 210 Y A+K +++LT + ++L + VN I+PG ++ H + P Sbjct: 203 EAYAASKGGLVALTHALAVSL-GPEVPVNCISPGWIEVRH------LRKAAHRETPVHTD 255 Query: 211 AEVAQSVPYGRMGTAADLTGMAVFLASEDADYVVAQTYNVDGG 253 A+ AQ P GR+GT D+ + FLA +DA +V Q + VDGG Sbjct: 256 ADRAQH-PVGRVGTVRDVAALVAFLAGDDAGFVTGQNWLVDGG 297 Lambda K H 0.317 0.130 0.365 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: 135 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: 257 Length of database: 306 Length adjustment: 26 Effective length of query: 231 Effective length of database: 280 Effective search space: 64680 Effective search space used: 64680 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