Align SDR family oxidoreductase (characterized, see rationale)
to candidate SMc01635 SMc01635 oxidoreductase
Query= uniprot:A0A4P7ABK7 (254 letters) >FitnessBrowser__Smeli:SMc01635 Length = 253 Score = 145 bits (366), Expect = 8e-40 Identities = 91/253 (35%), Positives = 137/253 (54%), Gaps = 15/253 (5%) Query: 8 LAGKTVLITAAAQGIGRASTELFAREGARVIATDIS-KTHLEELASIAG----VETHLLD 62 L + ++T A GIGRA + AREGA V+ D S + + +A+IA E +D Sbjct: 3 LNNRIAIVTGAGSGIGRAGAAIMAREGAHVVVVDRSVEAAGDTVAAIAAGGGSAEALAVD 62 Query: 63 VTDDDAIKALVAKV----GTVDVLFNCAGYVAAGNILECDDKAWDFSFNLNAKAMFHTIR 118 VTDDDA+ +A + G +D+L N AG AG++ E + +D S+NLN +A F R Sbjct: 63 VTDDDALADGIADILYRHGRIDILHNHAGAQVAGDLEEVEVAGFDRSWNLNVRAHFMAAR 122 Query: 119 AVLPGMLAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQGIRCNA 178 V+P M G IVN S++S V AY +K AV+ +T+ +A D+ G+R NA Sbjct: 123 LVMPSMKKAGRGVIVN-TSSSSGVLYDREMIAYTTTKHAVIAMTRQMAGDYAKYGVRVNA 181 Query: 179 ICPGTIESPSLNQRISTQAKETGKSEDEVRAAFVARQPMGRIGKAEEVAALALYLASDES 238 +CPG +++P N+ Q + + A R P+GR +E+A L+L SD S Sbjct: 182 LCPGWVDTP-FNEPFIDQM----GGREAIEAYIRERVPLGRWASVDEIAESILFLVSDRS 236 Query: 239 NFTTGSIHMIDGG 251 ++ TG I ++DGG Sbjct: 237 SYMTGQILVVDGG 249 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: 143 Number of extensions: 8 Number of successful extensions: 5 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: 253 Length adjustment: 24 Effective length of query: 230 Effective length of database: 229 Effective search space: 52670 Effective search space used: 52670 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