Align 2-deoxy-D-ribonate dehydrogenase (characterized)
to candidate GFF900 HP15_879 short-chain dehydrogenase/reductase SDR
Query= metacyc::MONOMER-20835 (262 letters) >FitnessBrowser__Marino:GFF900 Length = 224 Score = 78.2 bits (191), Expect = 1e-19 Identities = 57/186 (30%), Positives = 85/186 (45%), Gaps = 5/186 (2%) Query: 15 VLISGGAAGIGEVLAAAYLEAGAQVHVCDVSESALAVFRDKYPG---TVATRADVSDAAQ 71 +LI+G ++GIG A A + G ++ + SE L + + G + + DV Sbjct: 1 MLITGASSGIGAETARAAAKQGYRLVLAARSEDKLKGLQQELGGEEKVLTVQCDVQSGDD 60 Query: 72 IEAVFKVQREHLGGLDVLVNNAGIAGPTGGIDAISDAEWQATININLTAQYRFAHHAVPM 131 + + + G +D + NAG G GG W+ I N+ H +P Sbjct: 61 QKNMVDQALKTFGRIDAVFANAGRGGEPGGFSGADPDVWKDMILTNIYGVGLTLQHCMPA 120 Query: 132 LKESSHGHLLHIASVAGRLGYAWRTPYAATKWAIVGLMKSLASELGESDIRVNALLPGIV 191 LKES GHLL S AGR + Y+ATKWA+ + + EL S IRV + PG+V Sbjct: 121 LKESK-GHLLLTGSAAGRATIPG-SMYSATKWAVTAIGYGVREELRGSGIRVTLIEPGMV 178 Query: 192 EGPRMD 197 + P D Sbjct: 179 DTPFFD 184 Lambda K H 0.318 0.133 0.383 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: 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: 262 Length of database: 224 Length adjustment: 23 Effective length of query: 239 Effective length of database: 201 Effective search space: 48039 Effective search space used: 48039 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 (21.7 bits) S2: 46 (22.3 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