Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_052666591.1 NITAL_RS12765 3-oxoacyl-ACP reductase
Query= metacyc::MONOMER-16230 (256 letters) >NCBI__GCF_000969705.1:WP_052666591.1 Length = 252 Score = 153 bits (387), Expect = 3e-42 Identities = 100/251 (39%), Positives = 137/251 (54%), Gaps = 9/251 (3%) Query: 1 MLLIDKTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALSLAEEIAAFGGTA 60 M + K +VTGA+RG+G A AR +GA+VV+G D G+A +A+E+ G A Sbjct: 1 MKVTGKVALVTGAARGMGEAIARRLVAEGAQVVLGDVLDDAGKA----VADEL---GEVA 53 Query: 61 IAVGADAADLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHSFLDMPRELYLKTVGTNLNG 120 V D + + VA FG +DVLVNNAGI F + + N G Sbjct: 54 RYVHLDVTSTEDWAEAVAITEREFGRLDVLVNNAGILRFGAVTADNEADLRALIEVNQLG 113 Query: 121 AYFTVQAAARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALGPY 180 + ++AA M+ G G+I+ +SSI L GGA T YT TK + + ++ A+ LG Sbjct: 114 VQWGMRAAVPAMRRAG-AGSIVNISSIEGLGGGAYLTGYTATKFAVRGMTKAAALELGGK 172 Query: 181 GIRCNAVLPGTIATDINKEDLSDLEKRER-MTSRVPLGRLGEPDDLAGPIVFLASDMARY 239 GIR N+V PG I TD+ E+ ER + S+ L R+GEPD++A VFLASD A Y Sbjct: 173 GIRVNSVHPGAIRTDMVLSQTGGNEQAERFIASKTALARMGEPDEVAAAAVFLASDDASY 232 Query: 240 VTGASLLVDGG 250 +TGA L VDGG Sbjct: 233 ITGAELSVDGG 243 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: 171 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: 252 Length adjustment: 24 Effective length of query: 232 Effective length of database: 228 Effective search space: 52896 Effective search space used: 52896 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 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