Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate HSERO_RS09605 HSERO_RS09605 3-ketoacyl-ACP reductase
Query= metacyc::MONOMER-16230 (256 letters) >FitnessBrowser__HerbieS:HSERO_RS09605 Length = 251 Score = 137 bits (346), Expect = 2e-37 Identities = 90/250 (36%), Positives = 137/250 (54%), Gaps = 10/250 (4%) Query: 6 KTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALSLAEEIAAFGGTAIAVGA 65 + +VTGASRGIGRA A E ARQGA+V+ G+ +GA ++ E +AA G A GA Sbjct: 9 QVALVTGASRGIGRAIATELARQGAKVI----GTATSESGAAAITEYLAALGPEA-GRGA 63 Query: 66 --DAADLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHSFLDMPRELYLKTVGTNLNGAYF 123 + D ++ LV + FGS+ +LVNNAGI + M E + + TNL Sbjct: 64 VLNVNDAEASVALVEQVQKDFGSLSILVNNAGITQDQLAMRMKDEEWDSVIATNLTAVGR 123 Query: 124 TVQAAARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALGPYGIR 183 +A R M + R G II ++S+ G Q +Y KAG+ + ++ A +G I Sbjct: 124 LSRAVLRGMMK-ARTGRIINITSVVGEAGNPGQMNYAAAKAGVAGMSRALAREIGSRNIT 182 Query: 184 CNAVLPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLASDMARYVTGA 243 N V PG I TD+ + + ++ + ++PLGRLG +++A + FLAS A Y+TG Sbjct: 183 VNCVAPGFIDTDMTRA--LNEQQSAAILQQIPLGRLGAAEEIAYAVAFLASPQAAYITGT 240 Query: 244 SLLVDGGLFV 253 +L V+GG+++ Sbjct: 241 TLNVNGGMYM 250 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: 164 Number of extensions: 8 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: 256 Length of database: 251 Length adjustment: 24 Effective length of query: 232 Effective length of database: 227 Effective search space: 52664 Effective search space used: 52664 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