Align SDR family oxidoreductase (characterized, see rationale)
to candidate PP_1817 PP_1817 Oxidoreductase, short-chain dehydrogenase/reductase family
Query= uniprot:A0A4P7ABK7 (254 letters) >FitnessBrowser__Putida:PP_1817 Length = 253 Score = 135 bits (339), Expect = 1e-36 Identities = 93/255 (36%), Positives = 134/255 (52%), Gaps = 23/255 (9%) Query: 9 AGKTVLITAAAQGIGRASTELFAREGARVIATDISKTHLEELAS---IAGVETHLL--DV 63 +G+ L+T A GIGRA+ FA EG +V+ D+ E + AG E + DV Sbjct: 6 SGQVALVTGAGAGIGRATALAFAHEGMKVVVADLDPVGGEATVAQIHAAGGEALFIACDV 65 Query: 64 TDDDAIKAL----VAKVGTVDVLFNCAGY-VAAGNILECDDKAWDFSFNLNAKAMFHTIR 118 T D ++ L +A G +D FN AG + + E + +D +N K ++ ++ Sbjct: 66 TRDAEVRQLHERLMAAYGRLDYAFNNAGIEIEQHRLAEGSEAEFDAIMGVNVKGVWLCMK 125 Query: 119 AVLPGMLAKKAGSIVNIASAASSVKGVANRFA-YGASKAAVVGLTKSVAADFVSQGIRCN 177 LP +LA+ G+IVN AS A G A + + Y ASK AV+GLTKS A ++ +GIR N Sbjct: 126 YQLPLLLAQGGGAIVNTASVAGL--GAAPKMSIYSASKHAVIGLTKSAAIEYAKKGIRVN 183 Query: 178 AICPGTIESPSLNQRISTQAKETGKSEDEVRAAF-VARQPMGRIGKAEEVAALALYLASD 236 A+CP I++ + D +A F A P+GRIGK EE+A+ LYL SD Sbjct: 184 AVCPAVIDTDMFRRAYQA---------DPRKAEFAAAMHPVGRIGKVEEIASAVLYLCSD 234 Query: 237 ESNFTTGSIHMIDGG 251 + FTTG +DGG Sbjct: 235 GAAFTTGHCLTVDGG 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: 133 Number of extensions: 6 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: 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