Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_011952819.1 SWIT_RS10010 3-oxoacyl-ACP reductase
Query= metacyc::MONOMER-16230 (256 letters) >NCBI__GCF_000016765.1:WP_011952819.1 Length = 246 Score = 153 bits (387), Expect = 3e-42 Identities = 97/249 (38%), Positives = 144/249 (57%), Gaps = 10/249 (4%) Query: 6 KTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALSLAEEIAAFGGTAIAVGA 65 K I+TGA+ G+G + AR AR+GARVV+ EGRA + E+I A GG A+ Sbjct: 6 KVTIITGAASGMGASHARLFAREGARVVVADILEAEGRA----VVEDIVARGGEAVFERL 61 Query: 66 DAADLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHSFLDMPRELYLKTVGTNLNGAYFTV 125 D + ++++ AA FG +D+LVNNAG+ L+ + + TNL G + V Sbjct: 62 DISSEADWDRVMDAATARFGPLDILVNNAGLTGSGVQEVDEIALFDRLIATNLRGPFLGV 121 Query: 126 QAAARRMKEQGRGGAIIAVSSISALVGG-AMQTHYTPTKAGLLSLMQSCAIALGPYGIRC 184 +AA RRM +GRGGAI+ V+SISA +G + Y +K G+ +L ++ A GP IR Sbjct: 122 RAAVRRM--EGRGGAIVNVASISANIGNPGVHIGYNASKGGVRTLTRAAAAEYGPRKIRV 179 Query: 185 NAVLPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLASDMARYVTGAS 244 N+V PG + I + + + E + +RVPL R G+ ++++ ++FLASD A Y+ G Sbjct: 180 NSVNPGVLPPMIGSKRV---DVAEGLLARVPLNRTGQVEEVSNAVLFLASDEASYINGVE 236 Query: 245 LLVDGGLFV 253 L VDGGL V Sbjct: 237 LDVDGGLVV 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: 178 Number of extensions: 13 Number of successful extensions: 6 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: 246 Length adjustment: 24 Effective length of query: 232 Effective length of database: 222 Effective search space: 51504 Effective search space used: 51504 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 24 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