Align SDR family oxidoreductase (characterized, see rationale)
to candidate WP_077276827.1 BW732_RS11280 3-oxoacyl-[acyl-carrier-protein] reductase
Query= uniprot:A0A4P7ABK7 (254 letters) >NCBI__GCF_001998885.1:WP_077276827.1 Length = 244 Score = 124 bits (310), Expect = 2e-33 Identities = 87/253 (34%), Positives = 136/253 (53%), Gaps = 24/253 (9%) Query: 8 LAGKTVLITAAAQGIGRASTELFAREGARVIATD---ISKTHLEELASIAGVETHLL--D 62 L KTV+IT +++GIG+ FA++GA ++ ISK +EE+ S GV+TH + D Sbjct: 2 LKNKTVVITGSSRGIGQELARSFAKQGANIVLNGRKPISKELIEEIESF-GVKTHCVIGD 60 Query: 63 VTDDDAIKALVAKV----GTVDVLFNCAGYVAAGNILECDDKAWDFSFNLNAKAMFHTIR 118 + + L+ + G+VD+L N AG ++ + ++ +N F+TI+ Sbjct: 61 IQYFAQAEQLILEAKEVFGSVDILINNAGITRDTLLMRMTEDDFNSVLQVNLTGTFNTIK 120 Query: 119 AVLPGMLAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQGIRCNA 178 ML +++G I+N+AS + G A + Y ASKA VVGLTKSVA + S+GI CNA Sbjct: 121 HASKIMLKQRSGIIINMASVVG-LTGNAGQANYAASKAGVVGLTKSVARELASRGITCNA 179 Query: 179 ICPGTIESPSLNQRISTQAKETGKSEDEVRAAFVARQPMGRIGKAEEVAALALYLASDES 238 I PG I + T ++V+ V + P+ RIG +VA A++LA+ S Sbjct: 180 IAPGYISTDM-----------TDVLNEKVKEQVVQQIPLRRIGSVTDVAQTAIFLAT--S 226 Query: 239 NFTTGSIHMIDGG 251 + TG + +DGG Sbjct: 227 PYITGQVINVDGG 239 Lambda K H 0.316 0.129 0.359 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: 160 Number of extensions: 10 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: 254 Length of database: 244 Length adjustment: 24 Effective length of query: 230 Effective length of database: 220 Effective search space: 50600 Effective search space used: 50600 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: 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