Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate RR42_RS14100 RR42_RS14100 3-ketoacyl-ACP reductase
Query= metacyc::MONOMER-16230 (256 letters) >FitnessBrowser__Cup4G11:RR42_RS14100 Length = 249 Score = 158 bits (400), Expect = 9e-44 Identities = 98/252 (38%), Positives = 144/252 (57%), Gaps = 7/252 (2%) Query: 3 LIDKTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALSLAEEIAAFGGTAIA 62 L ++ +VTGASRGIGRA A E A QGA VV G+ AGA +++E +AA GG Sbjct: 5 LENQVALVTGASRGIGRAIALELAAQGATVV----GTATSEAGAAAISEYLAAAGGKGRG 60 Query: 63 VGADAADLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHSFLDMPRELYLKTVGTNLNGAY 122 + D + E L+ V+A GS+ VLVNNAGI + M E + + TN+ A Sbjct: 61 AVLNVNDAAASEALIDELVKAHGSLGVLVNNAGITQDQLAMRMKDEDWSAVIETNMT-AV 119 Query: 123 FTVQAAARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALGPYGI 182 F + A R + RGG II ++S+ G Q +Y KAG+ + ++ A +G + Sbjct: 120 FRLSRAVLRPMMKARGGRIINITSVVGSTGNPGQMNYAAAKAGVEGMSRALAREIGSRNV 179 Query: 183 RCNAVLPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLASDMARYVTG 242 N V PG I TD+ K LS+ E+ + +++PLGRLG+P+D+A + FLA A Y+TG Sbjct: 180 TVNCVAPGFIDTDMTKV-LSE-EQHAALKTQIPLGRLGQPEDIAHAVAFLAGPQAAYITG 237 Query: 243 ASLLVDGGLFVN 254 +L V+GG+++N Sbjct: 238 TTLHVNGGMYMN 249 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: 174 Number of extensions: 13 Number of successful extensions: 5 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: 249 Length adjustment: 24 Effective length of query: 232 Effective length of database: 225 Effective search space: 52200 Effective search space used: 52200 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