Align NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family) (characterized, see rationale)
to candidate WP_009780078.1 MED217_RS08410 SDR family oxidoreductase
Query= uniprot:A0A4R8NY47 (263 letters) >NCBI__GCF_000152985.1:WP_009780078.1 Length = 293 Score = 87.8 bits (216), Expect = 2e-22 Identities = 76/253 (30%), Positives = 120/253 (47%), Gaps = 8/253 (3%) Query: 16 SLAGKRVVITGGGSGIGAALVEAFVGQGAQVCFLDIATEPSEALVASLKDAAVAPRFFP- 74 +L GK +V+TGGGSG+G A+ + F+ GAQV E + +L +A FP Sbjct: 12 ALQGKTIVVTGGGSGLGKAMTKYFMELGAQVAITSRNLEKLKTTAEAL-EAETCGTCFPV 70 Query: 75 -CNLMNLEALRATFTEIETVMGGVDILINNAANDDRHKSEDVTPAYWDERLAVNLRHQFF 133 C++ + E + A + G VD+L+NNAA + +E ++ +D + + L+ Sbjct: 71 QCDVRDYEQVVAMRDAVIEQFGSVDVLLNNAAGNFISPTERLSANAFDVVIDIVLKGSKN 130 Query: 134 CAQAVLPGMRERK--GGVILNFGSISWHLGLPDLTLYMTAKAGIEGMTHGMARDFGRDGV 191 C A ++K ILN + G + TAKAG+ MT +A ++ + G+ Sbjct: 131 CTLAFGKHWIDKKVTNKTILNIVTTYAWTGSAYVVPSATAKAGVLAMTRSLAVEWAKYGI 190 Query: 192 RVNAIIPGAIRTPRQTLLWHTPEEEAKILAAQCLPV-RVDPH-DVAALALFLSSDSGAKC 249 R NAI PG T + K ++ +P+ RV H ++A LA +L SD A Sbjct: 191 RSNAIAPGPFPTKGAWERLLPGDLAEKFDLSKKVPLRRVGAHQELANLAAYLVSDFSAYI 250 Query: 250 TGREYYVDAG-WL 261 G +D G WL Sbjct: 251 NGEVVTIDGGEWL 263 Lambda K H 0.322 0.137 0.417 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: 186 Number of extensions: 12 Number of successful extensions: 3 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: 263 Length of database: 293 Length adjustment: 25 Effective length of query: 238 Effective length of database: 268 Effective search space: 63784 Effective search space used: 63784 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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