Align SDR family oxidoreductase (characterized, see rationale)
to candidate Echvi_4610 Echvi_4610 3-oxoacyl-(acyl-carrier-protein) reductase
Query= uniprot:A0A4P7ABK7 (254 letters) >FitnessBrowser__Cola:Echvi_4610 Length = 248 Score = 145 bits (365), Expect = 1e-39 Identities = 95/255 (37%), Positives = 142/255 (55%), Gaps = 22/255 (8%) Query: 6 GRLAGKTVLITAAAQGIGRASTELFAREGARVIATDISKTH----LEELASIAGVETHLL 61 G L GKT LIT A++GIGRA +A+EGA V T +S LE+ + GV+ Sbjct: 2 GLLTGKTALITGASKGIGRAIALKYAQEGANVAFTFLSSVEKGQALEKELAEFGVKAKGF 61 Query: 62 --DVTDDDAIKALVAKV----GTVDVLFNCAGYVAAGNILECDDKAWDFSFNLNAKAMFH 115 D +D A + LV +V G +DVL N AG ++ +++AWD N+N K+ F+ Sbjct: 62 RSDASDFKAAEELVNEVVKEFGALDVLINNAGVTRDNLLMRMNEEAWDDVMNINLKSCFN 121 Query: 116 TIRAVLPGMLAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQGIR 175 T++A ++ +KAGSI+NI S +KG A + Y ASKA ++G TKSVA + S+GIR Sbjct: 122 TVKAATRTLMKQKAGSIINITSVV-GIKGNAGQANYAASKAGIIGFTKSVALELGSRGIR 180 Query: 176 CNAICPGTIESPSLNQRISTQAKETGKSEDEVRAAFVARQPMGRIGKAEEVAALALYLAS 235 NA+ PG IE+ + T +++ + PM R G+ EEVA ++L S Sbjct: 181 SNAVAPGFIET-----------EMTEVLDEKTVQGWRDAIPMKRGGQPEEVANACVFLGS 229 Query: 236 DESNFTTGSIHMIDG 250 D S++ +G + +DG Sbjct: 230 DMSSYVSGQVIQVDG 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: 156 Number of extensions: 7 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