Align SDR family oxidoreductase (characterized, see rationale)
to candidate WP_009780166.1 MED217_RS08850 3-oxoacyl-[acyl-carrier-protein] reductase
Query= uniprot:A0A4P7ABK7 (254 letters) >NCBI__GCF_000152985.1:WP_009780166.1 Length = 248 Score = 122 bits (305), Expect = 9e-33 Identities = 80/254 (31%), Positives = 136/254 (53%), Gaps = 22/254 (8%) Query: 8 LAGKTVLITAAAQGIGRASTELFAREGARVIATDISKT----HLEELASIAGVET--HLL 61 L GK +IT A++GIG ++FA+ GA V T S LE+ + GV+ + Sbjct: 4 LEGKNTIITGASRGIGNGIAKVFAQNGANVAFTYSSSAGPAEELEKELTAMGVKAKAYKS 63 Query: 62 DVTDDDAIKALVAKVG----TVDVLFNCAGYVAAGNILECDDKAWDFSFNLNAKAMFHTI 117 D + +A + L+ ++ ++DVL N AG ++ ++ +D +N K++F+ Sbjct: 64 DASSFEACQDLIKQISEDFDSIDVLVNNAGITKDNLLMRMGEEDFDKVLEVNLKSIFNMT 123 Query: 118 RAVLPGMLAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQGIRCN 177 +AV ML ++ GSI+N++S +KG A + Y ASKA ++G +KS+A + S+ IR N Sbjct: 124 KAVQRTMLKQRHGSIINMSSVVG-IKGNAGQANYAASKAGIIGFSKSMALELGSRNIRTN 182 Query: 178 AICPGTIESPSLNQRISTQAKETGKSEDEVRAAFVARQPMGRIGKAEEVAALALYLASDE 237 + PG IE+ + T K +++V A + P+ R G E++A ++L SD Sbjct: 183 VVAPGFIET-----------EMTAKLDEKVVAGWRDAIPLKRGGTPEDIANACVFLGSDM 231 Query: 238 SNFTTGSIHMIDGG 251 S + TG + +DGG Sbjct: 232 SAYVTGQVLQVDGG 245 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: 125 Number of extensions: 7 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: 248 Length adjustment: 24 Effective length of query: 230 Effective length of database: 224 Effective search space: 51520 Effective search space used: 51520 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