Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate GFF983 PGA1_c10000 short chain dehydrogenase / reductase
Query= reanno::Burk376:H281DRAFT_00644 (263 letters) >FitnessBrowser__Phaeo:GFF983 Length = 250 Score = 109 bits (273), Expect = 5e-29 Identities = 70/247 (28%), Positives = 126/247 (51%), Gaps = 4/247 (1%) Query: 12 GLRVFVSAGAAGIGLAIAEAFIEAQAEVYICDVNQAAIDEATSRFPKLHAGIADVSKQAQ 71 G ++ G GIGLA+A+A AEV I Q ++E + LH DV +A Sbjct: 5 GKHALITGGGTGIGLAMAQALAAEGAEVTITGRRQEVLEEVATE--GLHPLAMDVRDEAD 62 Query: 72 VDQIIDDARRKLGGLDVLVNNAGIAGPTGAVEELDPAQWESTVSTNLNSQFYFLRKAVPV 131 V ID A G + + V NAGIA A+ ++ W + ++TNL+ F +R+++ Sbjct: 63 VIAKIDAATAARGPIQICVPNAGIAEGK-ALHKMSMEFWRNMMATNLDGAFLTIRESMKS 121 Query: 132 LKETSDCASIIAMSSVAGRLGYPFRTPYASTKWAIVGLVKSLAAELGPSNVRVNAILPGV 191 +++T D ++ +SS+AG G Y+++K ++GL +SL+ + + NA+ PG Sbjct: 122 MRQT-DWGRVMTVSSIAGLRGLQGAPCYSASKHGLIGLTRSLSEDYLGTPYTFNALCPGY 180 Query: 192 VEGERMDRVISARADALGIPFNAMREEYLKKISLRRMVTVDDIAAMALFLASPAGSNVTG 251 V+ +DR +++ + G+ + + +R++ D++AA L+L P ++ G Sbjct: 181 VDTPIIDRNVTSISQRAGVSEEDALKIMVSANRHKRLILPDEVAAALLWLCGPGSQSING 240 Query: 252 QAISVDG 258 Q I + G Sbjct: 241 QTIEIAG 247 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: 128 Number of extensions: 7 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