Align SDR family oxidoreductase (characterized, see rationale)
to candidate H281DRAFT_06507 H281DRAFT_06507 NAD(P)-dependent dehydrogenase, short-chain alcohol dehydrogenase family
Query= uniprot:A0A4P7ABK7 (254 letters) >FitnessBrowser__Burk376:H281DRAFT_06507 Length = 249 Score = 137 bits (344), Expect = 3e-37 Identities = 93/254 (36%), Positives = 144/254 (56%), Gaps = 20/254 (7%) Query: 7 RLAGKTVLITAAAQGIGRASTELFAREGARVIATDISKTHLEEL-----ASIAGVETHLL 61 +L+GK +IT G+G A+ +LFA+EGA+VI T + L+E A+ GV + Sbjct: 3 KLSGKIAVITGGNSGMGLATAQLFAKEGAKVIITGRRQKELDEAVESIGANAEGVLGDVS 62 Query: 62 DVTDDDAIKALV-AKVGTVDVLFNCAGYVAAGNILECDDKAWDFSFNLNAKAMFHTIRAV 120 ++D D + V AK G VDV+F AG + I + + +D +FN+N K + T++ + Sbjct: 63 RLSDLDKLNDHVKAKYGRVDVIFANAGLGSLAPIDQVTEAQFDETFNVNVKGTYFTVQKL 122 Query: 121 LPGMLAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQGIRCNAIC 180 LP L GSI+ S ASS KG+ Y A+KAAV L +++ D ++ IR NAI Sbjct: 123 LP--LVPDGGSIILNTSIASS-KGMEAFSVYSATKAAVRSLARTLTTDLKARKIRVNAIS 179 Query: 181 PGTIESPSLNQRISTQAKETGKSEDEV---RAAFVARQPMGRIGKAEEVAALALYLASDE 237 PG I++P + TG +E E+ ++ ++ P+GRIG EE+A AL+LASD+ Sbjct: 180 PGPIDTPIFGK--------TGLTEQEIEGFKSGITSQVPLGRIGLPEEIAKPALFLASDD 231 Query: 238 SNFTTGSIHMIDGG 251 S++ +G +DGG Sbjct: 232 SSYISGIELTVDGG 245 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: 152 Number of extensions: 10 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: 249 Length adjustment: 24 Effective length of query: 230 Effective length of database: 225 Effective search space: 51750 Effective search space used: 51750 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