Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_077276827.1 BW732_RS11280 3-oxoacyl-[acyl-carrier-protein] reductase
Query= metacyc::MONOMER-16230 (256 letters) >NCBI__GCF_001998885.1:WP_077276827.1 Length = 244 Score = 158 bits (400), Expect = 9e-44 Identities = 97/254 (38%), Positives = 150/254 (59%), Gaps = 12/254 (4%) Query: 2 LLIDKTVIVTGASRGIGRAAARECARQGARVVIGHSGSDEGRAG-ALSLAEEIAAFGGTA 60 +L +KTV++TG+SRGIG+ AR A+QGA +V+ GR + L EEI +FG Sbjct: 1 MLKNKTVVITGSSRGIGQELARSFAKQGANIVLN------GRKPISKELIEEIESFGVKT 54 Query: 61 IAVGADAADLDSGEKLVAAAVEAFGSVDVLVNNAGICPFHSFLDMPRELYLKTVGTNLNG 120 V D E+L+ A E FGSVD+L+NNAGI + M + + + NL G Sbjct: 55 HCVIGDIQYFAQAEQLILEAKEVFGSVDILINNAGITRDTLLMRMTEDDFNSVLQVNLTG 114 Query: 121 AYFTVQAAARRMKEQGRGGAIIAVSSISALVGGAMQTHYTPTKAGLLSLMQSCAIALGPY 180 + T++ A++ M +Q R G II ++S+ L G A Q +Y +KAG++ L +S A L Sbjct: 115 TFNTIKHASKIMLKQ-RSGIIINMASVVGLTGNAGQANYAASKAGVVGLTKSVARELASR 173 Query: 181 GIRCNAVLPGTIATDINKEDLSDLEKRERMTSRVPLGRLGEPDDLAGPIVFLASDMARYV 240 GI CNA+ PG I+TD+ D+ + + +E++ ++PL R+G D+A +FLA+ + Y+ Sbjct: 174 GITCNAIAPGYISTDMT--DVLNEKVKEQVVQQIPLRRIGSVTDVAQTAIFLAT--SPYI 229 Query: 241 TGASLLVDGGLFVN 254 TG + VDGG+ +N Sbjct: 230 TGQVINVDGGMVMN 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: 138 Number of extensions: 7 Number of successful extensions: 5 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: 244 Length adjustment: 24 Effective length of query: 232 Effective length of database: 220 Effective search space: 51040 Effective search space used: 51040 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