Align SDR family oxidoreductase (characterized, see rationale)
to candidate WP_025331338.1 SALWKB2_RS08960 3-oxoacyl-ACP reductase FabG
Query= uniprot:A0A4P7ABK7 (254 letters) >NCBI__GCF_000600005.1:WP_025331338.1 Length = 247 Score = 123 bits (309), Expect = 3e-33 Identities = 79/251 (31%), Positives = 124/251 (49%), Gaps = 19/251 (7%) Query: 8 LAGKTVLITAAAQGIGRASTELFAREGARVIATDISK---THLEELASIAGVETHLLDVT 64 L GK L+T A +GIG A A +GA+VI T S T + E + G E L + Sbjct: 5 LTGKIALVTGATRGIGAAIARFLAEKGAKVIGTATSAAGVTSINEALADFGGEGRELRIA 64 Query: 65 DDDAIKALVA----KVGTVDVLFNCAGYVAAGNILECDDKAWDFSFNLNAKAMFHTIRAV 120 ++++I+ L+A +G + +L N AG ++ + WD +N K+ F +AV Sbjct: 65 EENSIENLIADIESNIGNIAILVNNAGITRDNLLMRMKESEWDEIMQINLKSAFRASKAV 124 Query: 121 LPGMLAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQGIRCNAIC 180 M+ + G I+N+ S + G A + Y A+KA +VG +KS+A + S+GI N + Sbjct: 125 TRSMMKARWGRIINVTSVVGFI-GNAGQANYAAAKAGLVGFSKSMAREVGSRGITVNCVA 183 Query: 181 PGTIESPSLNQRISTQAKETGKSEDEVRAAFVARQPMGRIGKAEEVAALALYLASDESNF 240 PG IE+ T E R F + + G E+VAA L+LAS+E+ + Sbjct: 184 PGFIETDM-----------TKVLPQEQRDFFAGQTALNHFGTVEDVAAAVLFLASEEARY 232 Query: 241 TTGSIHMIDGG 251 TG ++GG Sbjct: 233 ITGQTLHVNGG 243 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: 142 Number of extensions: 8 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: 247 Length adjustment: 24 Effective length of query: 230 Effective length of database: 223 Effective search space: 51290 Effective search space used: 51290 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