Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate PfGW456L13_4129 Oxidoreductase, short chain dehydrogenase/reductase family
Query= metacyc::MONOMER-16230 (256 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4129 Length = 248 Score = 146 bits (369), Expect = 3e-40 Identities = 94/252 (37%), Positives = 136/252 (53%), Gaps = 16/252 (6%) Query: 3 LIDKTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALSLAEEIAAFGGTAIA 62 L K ++ G SRGIG A + A +GA V + S A A L + I A GG A+A Sbjct: 6 LSGKVALIQGGSRGIGAAIVKRLAAEGATVAFTYVSST---AKAEELQDSITAKGGKALA 62 Query: 63 VGADAADLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHSFLDMPRELYLKTVGTNLNGAY 122 + AD+AD D+ V+A VEAFG +D+LVNNAG+ + E + +T+ N+ + Sbjct: 63 IKADSADADAIRSAVSATVEAFGRLDILVNNAGVLAVAPLAEFKLEDFDQTLAINVRSVF 122 Query: 123 FTVQAAARRMKEQGRGGAIIAVSSISA----LVGGAMQTHYTPTKAGLLSLMQSCAIALG 178 QAAAR M E GG II + S +A GG Y +K+ L+ L + A LG Sbjct: 123 IATQAAARHMTE---GGRIINIGSTNADRMPFAGGG---PYAMSKSALVGLTKGLARDLG 176 Query: 179 PYGIRCNAVLPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLASDMAR 238 P GI N V PG + TD+N ++ + E + + +GR G+ +++A + +L S A Sbjct: 177 PQGITINNVQPGPVDTDMNP---AEGDFAESLIPLMAVGRYGKAEEIASFVAYLVSPEAG 233 Query: 239 YVTGASLLVDGG 250 Y+TGASL +DGG Sbjct: 234 YITGASLTIDGG 245 Lambda K H 0.319 0.136 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: 165 Number of extensions: 12 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: 256 Length of database: 248 Length adjustment: 24 Effective length of query: 232 Effective length of database: 224 Effective search space: 51968 Effective search space used: 51968 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: 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