Align SDR family oxidoreductase (characterized, see rationale)
to candidate 206645 DVU1206 3-oxoacyl-(acyl-carrier-protein) reductase (TIGR)
Query= uniprot:A0A4P7ABK7 (254 letters) >FitnessBrowser__DvH:206645 Length = 259 Score = 114 bits (284), Expect = 3e-30 Identities = 78/251 (31%), Positives = 126/251 (50%), Gaps = 24/251 (9%) Query: 12 TVLITAAAQGIGRASTELFAREGARVIATDISKTHLEELASIAGVE-------THLLDVT 64 T ++T ++GIG+A E AR G +V T +SK E A AG+ LDV+ Sbjct: 19 TAIVTGGSRGIGKAVAETLARAGLQVFLTYVSKPDEAE-AVAAGIRDAGGSATAFRLDVS 77 Query: 65 DDDAIKAL----VAKVGTVDVLFNCAGYVAAGNILECDDKAWDFSFNLNAKAMFHTIRAV 120 D A+ A + +DVL N AG G I+ D+ ++ ++N F +R Sbjct: 78 DAAAVAAFFQSEIKDKVRLDVLVNNAGITKDGLIMRMKDEDFERVLDVNLCGAFTCLREA 137 Query: 121 LPGMLAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQGIRCNAIC 180 M ++ G I+NI S + G A + Y A+KA ++GLTKS A + ++ + NA+ Sbjct: 138 SKLMTRQRLGRIINITSVVGQM-GNAGQANYCAAKAGLIGLTKSAAKELAARNVTVNAVA 196 Query: 181 PGTIESPSLNQRISTQAKETGKSEDEVRAAFVARQPMGRIGKAEEVAALALYLASDESNF 240 PG IE+ T +EVR A+V P+ R+G A+++A +LAS+ +++ Sbjct: 197 PGFIETDM-----------TAGLPEEVRKAYVEAIPLRRLGSAQDIADAVAFLASERASY 245 Query: 241 TTGSIHMIDGG 251 TG + ++GG Sbjct: 246 ITGQVLAVNGG 256 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: 134 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: 259 Length adjustment: 24 Effective length of query: 230 Effective length of database: 235 Effective search space: 54050 Effective search space used: 54050 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 Apr 09 2024. 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