Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_083509394.1 APY04_RS01590 3-oxoacyl-ACP reductase
Query= metacyc::MONOMER-16231 (254 letters) >NCBI__GCF_001541235.1:WP_083509394.1 Length = 287 Score = 144 bits (362), Expect = 3e-39 Identities = 91/246 (36%), Positives = 131/246 (53%), Gaps = 3/246 (1%) Query: 4 LEGKTVLVTGASTGIGRAAAIGAAQHGADVAINYAHSDGPAQSCVAEIEALGQRAIAVKG 63 L+GK +VTGAS GIG A A GA V +NYA S A VA+I A G +AIAV G Sbjct: 42 LDGKVAVVTGASKGIGAEVARALAAEGASVVVNYASSREGADRVVADITAAGGKAIAVGG 101 Query: 64 DVADPQTAQDFVAKAVETFGKVDVMVSNAGICPFHAFLDMPVDVVERTFKVNLHGAYFMV 123 DV+ A + +G+VD++++NAG+ F ++ ER F++N+ G Sbjct: 102 DVSKSNDVTALFDAAKQAYGRVDILINNAGVFDFKPLEEITEAHFERHFRINVLGPILTT 161 Query: 124 QAAAQQMVRQGHGGSIVAVSSISALVGGEYQTHYTPTKAGVHSLMQSTAIALGKHGIRCN 183 QAA + GG I+ VSS+ A + Y+ TK + +L ++ A LG IR Sbjct: 162 QAAVKHFPIS--GGVIINVSSVVAFSPVPNSSVYSATKGALDTLTRTYAQELGPRNIRVV 219 Query: 184 SVLPGTILTEINKD-DLADQEKREYMEARTPLGRLGAPEDLAGPIVFLASDMAAYVTGAA 242 S+ PG + TE ++ + + + A TPL R+G P D+A VFLASD A ++TG Sbjct: 220 SLNPGLVSTEGSQSLGVIGSPFEQQVIAETPLRRIGLPTDIAKVAVFLASDDAGWITGEI 279 Query: 243 LLVDGG 248 + V GG Sbjct: 280 ITVSGG 285 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: 116 Number of extensions: 6 Number of successful extensions: 2 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: 287 Length adjustment: 25 Effective length of query: 229 Effective length of database: 262 Effective search space: 59998 Effective search space used: 59998 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