Align SDR family oxidoreductase (characterized, see rationale)
to candidate HSERO_RS19050 HSERO_RS19050 3-oxoacyl-ACP reductase
Query= uniprot:A0A4P7ABK7 (254 letters) >FitnessBrowser__HerbieS:HSERO_RS19050 Length = 266 Score = 127 bits (319), Expect = 2e-34 Identities = 88/260 (33%), Positives = 141/260 (54%), Gaps = 17/260 (6%) Query: 8 LAGKTVLITAAAQ-----GIGRASTELFAREGARVIATDIS-KTHLEE---LASIAGV-E 57 + GK +++T A G G+A+ L+AREG RV+A D S + L+ + S GV E Sbjct: 5 MQGKAIIVTGAGSVGEGWGNGKAAAVLYAREGGRVLAVDRSIEAALQTQDIIRSEGGVCE 64 Query: 58 THLLDVTDDDAIKALVAKV----GTVDVLFNCAGYVAAGNILECDDKAWDFSFNLNAKAM 113 DV+ + +KA+ G VDVL N G G +E +++W+ +N ++ Sbjct: 65 VLAADVSRNTEVKAIAEAAMDHFGRVDVLHNNVGIADVGGPVETSEESWNRLVAVNQTSL 124 Query: 114 FHTIRAVLPGMLAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQG 173 F T + VLP M ++ G+IVNI+S A+ Y A+KAA++ TK+VA + G Sbjct: 125 FLTHKHVLPIMEKQRKGAIVNISSLAALRWIGFPYLGYTATKAAILAFTKNVAMQYAPMG 184 Query: 174 IRCNAICPGTIESPSLNQRISTQAKETGKSEDEVRAAFVARQPMGRIGKAEEVAALALYL 233 IR N + PG +++P + + + G +++RA A+ PMG +G A +VA +L+L Sbjct: 185 IRANCVLPGMMDTPMIREPLKA---SYGGDIEQMRAKRNAQCPMGFMGDAWDVAHASLFL 241 Query: 234 ASDESNFTTGSIHMIDGGWS 253 ASD + + TG ++DGG S Sbjct: 242 ASDHARYITGLDMIVDGGLS 261 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: 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: 266 Length adjustment: 24 Effective length of query: 230 Effective length of database: 242 Effective search space: 55660 Effective search space used: 55660 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: 47 (22.7 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