Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_043879520.1 AZC_RS17235 3-oxoacyl-ACP reductase
Query= metacyc::MONOMER-16231 (254 letters) >NCBI__GCF_000010525.1:WP_043879520.1 Length = 269 Score = 159 bits (402), Expect = 6e-44 Identities = 102/252 (40%), Positives = 140/252 (55%), Gaps = 5/252 (1%) Query: 4 LEGKTVLVTGASTGIGRAAAIGAAQHGADVAINYAHSDGPAQSCVAEIEALGQRAIAVKG 63 L GK+VLVTGASTGIG A A G A GA VA++Y S PA+ V I+A G A+ ++G Sbjct: 18 LAGKSVLVTGASTGIGAAVAEGFAASGAKVAVHYNASREPAEQLVDRIQAAGSEAVLIQG 77 Query: 64 DVADPQTAQDFVAKAVETFGKVDVMVSNA-GICPFHAFLDMPVDVVERTFKVNLHGAYFM 122 DV +P V AV+ FG++DV+V+NA G+ D + R +N+ Sbjct: 78 DVTEPGAPARIVKAAVDAFGRLDVLVNNAGGLVERVPIPDYTPEFATRVLDLNVTQVIAF 137 Query: 123 VQAAAQQMVRQ-GHGGSIVAVSSISAL-VGGEYQTHYTPTKAGVHSLMQSTAIALGKHGI 180 V AA QQM Q GGSI+ VSS++A GG Y K + + A L K GI Sbjct: 138 VTAAVQQMTGQPDPGGSIINVSSVAARNGGGNGAVLYAAAKGFISTATHGWAKELAKSGI 197 Query: 181 RCNSVLPGTILTEINKDDLADQEKREYMEARTPLGRLGAPEDLAGPIVFLASDMAA-YVT 239 R N+V PG I T + + + ++ M+A P+ R+G PE+ G +FLASD A+ Y+T Sbjct: 198 RVNAVAPGVIATPFH-ERFSTPQQMAAMQATIPMDRIGIPEECVGAFLFLASDAASGYIT 256 Query: 240 GAALLVDGGMYV 251 G L V+GG Y+ Sbjct: 257 GQILEVNGGQYM 268 Lambda K H 0.318 0.133 0.379 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: 140 Number of extensions: 6 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: 254 Length of database: 269 Length adjustment: 25 Effective length of query: 229 Effective length of database: 244 Effective search space: 55876 Effective search space used: 55876 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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