Align SDR family oxidoreductase (characterized, see rationale)
to candidate 5210422 Shew_2863 short-chain dehydrogenase/reductase SDR (RefSeq)
Query= uniprot:A0A4P7ABK7 (254 letters) >FitnessBrowser__PV4:5210422 Length = 248 Score = 119 bits (297), Expect = 8e-32 Identities = 83/251 (33%), Positives = 128/251 (50%), Gaps = 18/251 (7%) Query: 10 GKTVLITAAAQGIGRASTELFAREGARVIATDISKTHLEELAS-----IAGVETHLLDVT 64 GK VLIT AA G G+ + A +GA+++ DI+ T L+ L S G+ + Sbjct: 7 GKVVLITGAASGFGKLLAQRLAPQGAKLVLGDINDTALDALCSELGECAVGLRCDVSIEA 66 Query: 65 DDDAIKALVAK-VGTVDVLFNCAGYVAA-GNILECDDKAWDFSFNLNAKAMFHTIRAVLP 122 + A+ L + G +D+ N AG A ++L + D SF +N K +F ++A +P Sbjct: 67 EQLALAQLAEESFGRLDIAINNAGISAPMKSLLATTEADMDLSFAINTKGVFFGMKAQIP 126 Query: 123 GMLAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQGIRCNAICPG 182 M K G+I+N+AS A + G Y A+K AVVG+T++ A +F +QGI+ NAICP Sbjct: 127 LMQKHKCGAILNVASMAG-INGAPKLTPYVAAKHAVVGITRTAALEFAAQGIQVNAICPF 185 Query: 183 TIESPSLNQRISTQAKETGKSEDEVRAAFVARQPMGRIGKAEEVAALALYLASDESNFTT 242 +P + T+ + E RA PM R+ EV + L++ + ++ F T Sbjct: 186 FTPTPMV-----TEGVDPALIEQLTRAV-----PMRRLADPNEVVSAMLHMVNPDNGFMT 235 Query: 243 GSIHMIDGGWS 253 G IDGG S Sbjct: 236 GQAIAIDGGVS 246 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: 119 Number of extensions: 4 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