Align SDR family oxidoreductase (characterized, see rationale)
to candidate N515DRAFT_0334 N515DRAFT_0334 NAD(P)-dependent dehydrogenase, short-chain alcohol dehydrogenase family
Query= uniprot:A0A4P7ABK7 (254 letters) >FitnessBrowser__Dyella79:N515DRAFT_0334 Length = 249 Score = 120 bits (302), Expect = 2e-32 Identities = 83/257 (32%), Positives = 132/257 (51%), Gaps = 20/257 (7%) Query: 6 GRLAGKTVLITAAAQGIGRASTELFAREGARVIATDISKTHLEELASIAGVETHLL---- 61 G+L GK +IT + G+G A+ LF REGA VI T + LE G ++ Sbjct: 2 GKLDGKVAVITGGSAGMGLATARLFLREGATVIVTGRDEAALEAAKRDLGGGAEIVRCDN 61 Query: 62 -DVTDDDAIKALV-AKVGTVDVLFNCAGYVAAGNILECDDKAWDFSFNLNAKAMFHTIRA 119 V D +++ A V K G VD++F AG + +DF + N K + T++ Sbjct: 62 SKVADIESLSAYVETKHGRVDIVFANAGGGRPALFEHTSEDDFDFMIDTNFKGAYFTVQK 121 Query: 120 VLPGMLAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQGIRCNAI 179 +LP + KAG+ V + ++ S +G Y A+KAA+ L +S++ + +GIR NA+ Sbjct: 122 LLPLV---KAGASVILNTSTLSTQGRPYVSVYSAAKAAIRSLARSLSVELSERGIRVNAL 178 Query: 180 CPGTIESPSLNQRISTQAKETGKSEDEVRAAFV---ARQPMGRIGKAEEVAALALYLASD 236 PG I+ + QA++ G SE+ + + A+ PM R G +E+A L+LAS Sbjct: 179 APGYID--------TDQARKVGMSEEMIEQTKIQVHAQVPMHRSGTVDEIANAVLFLASH 230 Query: 237 ESNFTTGSIHMIDGGWS 253 +S + TG +DGGW+ Sbjct: 231 DSAYVTGIELCVDGGWA 247 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: 136 Number of extensions: 12 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