Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_011952841.1 SWIT_RS10120 3-oxoacyl-ACP reductase
Query= metacyc::MONOMER-16230 (256 letters) >NCBI__GCF_000016765.1:WP_011952841.1 Length = 252 Score = 149 bits (377), Expect = 4e-41 Identities = 97/257 (37%), Positives = 140/257 (54%), Gaps = 12/257 (4%) Query: 1 MLLIDKTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAGALSLAEEIAAFGGTA 60 M L + +VTGA+ GIGRA AR A +GARV + +D AG + A+ A G A Sbjct: 1 MTLAGRAALVTGAASGIGRAVARAFAGEGARVWL----ADMDAAGVAAAAD---AIGPPA 53 Query: 61 IAVGADAADLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHSFLDMPRELYLKTVGTNLNG 120 A+ D +D + + VAA G +D+LVN AG +L++ E + + N G Sbjct: 54 RAIELDVSDPAAVGRTVAAIDAEAGGIDLLVNAAGRYALQPWLEIEPETWDRIFAVNTRG 113 Query: 121 AYFTVQAAARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALGPY 180 T QA AR M +G+GG+II ++S + G Y+ +KA +S+ QS A+ L P+ Sbjct: 114 IMLTTQAVARVMAARGKGGSIINIASAAGRRGDPNSVAYSASKAAAISITQSAALGLAPH 173 Query: 181 GIRCNAVLPGTIATDINKEDLSDLEKR-----ERMTSRVPLGRLGEPDDLAGPIVFLASD 235 GIR NA+ PG + T + E + R E+M +RVPLGR+ P++ A +FLA Sbjct: 174 GIRVNAIAPGPVDTPMWDEVVRLRAGRGDHSAEQMAARVPLGRISAPEEQARVALFLAGA 233 Query: 236 MARYVTGASLLVDGGLF 252 + YVTG + VDGGLF Sbjct: 234 DSGYVTGQTFNVDGGLF 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: 165 Number of extensions: 9 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: 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