Align SDR family oxidoreductase (characterized, see rationale)
to candidate Ac3H11_2257 Short-chain dehydrogenase/reductase SDR
Query= uniprot:A0A4P7ABK7 (254 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2257 Length = 267 Score = 133 bits (335), Expect = 3e-36 Identities = 84/246 (34%), Positives = 126/246 (51%), Gaps = 13/246 (5%) Query: 10 GKTVLITAAAQGIGRASTELFAREGARVIATDISKTHLEELASIAGVETHLLDVTDDDAI 69 G+ ++T AQGIG A FA EGA+ + D+ + LA+ G DV D + Sbjct: 20 GRVCIVTGGAQGIGEACVRRFAAEGAKPVIVDVDDARGQALAAELGALYVRCDVGDKAQV 79 Query: 70 KALVAKV----GTVDVLFNCAGYVAAGNILECDDKAWDFSFNLNAKAMFHTIRAVLPGML 125 ALVA+V G +DVL N AG A + LE + +D +N K F +AV M+ Sbjct: 80 DALVAQVLAAHGRIDVLVNNAGIFRAADFLEVTEADFDAVLRVNLKGSFLVGQAVARAMV 139 Query: 126 AKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQGIRCNAICPGTIE 185 G+IVN+ S+ + V + N +Y SK V LT+ +A + IR NA+ PGTI Sbjct: 140 TSGGGAIVNM-SSVNGVLAIPNIASYNVSKGGVNQLTRVMALALADKNIRVNAVAPGTIA 198 Query: 186 SPSLNQRISTQAKETGKSEDEVRAAFVARQPMGRIGKAEEVAALALYLASDESNFTTGSI 245 + + + T DE + ++R PM R+G+ E+A + +LASD +++ TG I Sbjct: 199 TELAAKAVLT--------SDEAKRKIMSRTPMKRLGQPSEIADVVAWLASDAASYVTGEI 250 Query: 246 HMIDGG 251 +DGG Sbjct: 251 VTVDGG 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: 148 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: 267 Length adjustment: 24 Effective length of query: 230 Effective length of database: 243 Effective search space: 55890 Effective search space used: 55890 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