Align SDR family oxidoreductase (characterized, see rationale)
to candidate 201911 SO2776 3-oxoacyl-(acyl-carrier-protein) reductase (NCBI ptt file)
Query= uniprot:A0A4P7ABK7 (254 letters) >FitnessBrowser__MR1:201911 Length = 248 Score = 130 bits (327), Expect = 3e-35 Identities = 83/250 (33%), Positives = 130/250 (52%), Gaps = 18/250 (7%) Query: 8 LAGKTVLITAAAQGIGRASTELFAREGARVIATDISKTHLEELASIAGVETH--LLDVTD 65 LAGK L+T A++GIGRA E GA VI T S+ + G + +L+VTD Sbjct: 7 LAGKVALVTGASRGIGRAIAETLVEAGAVVIGTATSEKGAAAIQEYLGDKGFGLVLNVTD 66 Query: 66 D----DAIKALVAKVGTVDVLFNCAGYVAAGNILECDDKAWDFSFNLNAKAMFHTIRAVL 121 D ++ K G VD+L N AG ++ D W+ + N ++F + V+ Sbjct: 67 SQSVTDLFDSIKEKAGDVDILVNNAGITRDNLLMRMKDDEWNDIIDTNLTSLFRLSKPVM 126 Query: 122 PGMLAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQGIRCNAICP 181 M+ K+ G I+NI S ++ G A + Y A+KA ++G TKS+A + S+ I NAI P Sbjct: 127 RTMMKKRFGRIINIGSVVGTM-GNAGQVNYSAAKAGLIGFTKSLAREVASRQITVNAIAP 185 Query: 182 GTIESPSLNQRISTQAKETGKSEDEVRAAFVARQPMGRIGKAEEVAALALYLASDESNFT 241 G I++ ++ Q K A +++ PM R+G+A+E+A L+LASD + + Sbjct: 186 GFIQTDMTDELTEDQQK-----------AIMSQVPMERLGQAQEIANAVLFLASDSAAYI 234 Query: 242 TGSIHMIDGG 251 TG ++GG Sbjct: 235 TGETLHVNGG 244 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: 151 Number of extensions: 5 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: 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 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