Align SDR family oxidoreductase (characterized, see rationale)
to candidate 15215 b1093 3-oxoacyl-[acyl-carrier-protein] reductase (NCBI)
Query= uniprot:A0A4P7ABK7 (254 letters) >FitnessBrowser__Keio:15215 Length = 244 Score = 137 bits (345), Expect = 2e-37 Identities = 82/248 (33%), Positives = 133/248 (53%), Gaps = 18/248 (7%) Query: 10 GKTVLITAAAQGIGRASTELFAREGARVIATDISKTHLEELASIAGVETH--LLDVTDDD 67 GK L+T A++GIGRA E A GA+VI T S+ + ++ G +L+VTD Sbjct: 5 GKIALVTGASRGIGRAIAETLAARGAKVIGTATSENGAQAISDYLGANGKGLMLNVTDPA 64 Query: 68 AIKALVAKV----GTVDVLFNCAGYVAAGNILECDDKAWDFSFNLNAKAMFHTIRAVLPG 123 +I++++ K+ G VD+L N AG ++ D+ W+ N ++F +AV+ Sbjct: 65 SIESVLEKIRAEFGEVDILVNNAGITRDNLLMRMKDEEWNDIIETNLSSVFRLSKAVMRA 124 Query: 124 MLAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQGIRCNAICPGT 183 M+ K+ G I+ I S ++ G + Y A+KA ++G +KS+A + S+GI N + PG Sbjct: 125 MMKKRHGRIITIGSVVGTM-GNGGQANYAAAKAGLIGFSKSLAREVASRGITVNVVAPGF 183 Query: 184 IESPSLNQRISTQAKETGKSEDEVRAAFVARQPMGRIGKAEEVAALALYLASDESNFTTG 243 IE+ T D+ RA +A+ P GR+G A+E+A +LASDE+ + TG Sbjct: 184 IETDM-----------TRALSDDQRAGILAQVPAGRLGGAQEIANAVAFLASDEAAYITG 232 Query: 244 SIHMIDGG 251 ++GG Sbjct: 233 ETLHVNGG 240 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: 154 Number of extensions: 9 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: 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 17 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