Align BadH (characterized)
to candidate WP_042117993.1 RHE_RS04605 SDR family oxidoreductase
Query= metacyc::MONOMER-893 (255 letters) >NCBI__GCF_000092045.1:WP_042117993.1 Length = 255 Score = 156 bits (395), Expect = 3e-43 Identities = 95/261 (36%), Positives = 137/261 (52%), Gaps = 22/261 (8%) Query: 3 RLQNKTAVITGGGGGIGGATCRRFAQEGAKIAVFDLNLDAAEKVAGAIRDAGGTAEAVRC 62 RL+ K A+I+GG G+GGA + FA EGA++A+ D N AA + AIRDAGG A+ Sbjct: 4 RLKGKVAIISGGATGMGGAASKLFAAEGARVAIIDRNGQAAAETVKAIRDAGGEADHWTA 63 Query: 63 DIADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWERLIAINLTGALHMH 122 D++D +V+AA+A G V +L N+AG + KPF +T EW+ L A+N+ M Sbjct: 64 DVSDEGAVNAAVAGVEERYGAVTVLFNHAGTIVIKPFLETTLQEWDWLHAVNVRSMFLMT 123 Query: 123 HAVLPGMVERRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKTLAREHARHGITVNV 182 AVLP M+ G IV +S +A + E +Y KG + F++ +A E I N Sbjct: 124 KAVLPKMIAAGGGSIVCTSSISAVAATPMEVLYDTTKGAVHMFARAIAVEFRDRNIRCNA 183 Query: 183 VCPGPTDT-----------ALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGAIAF 231 VCPG T AL DV+ A ++ GR+G+P+D+A A + Sbjct: 184 VCPGFIRTPHGLREVADLQALGVDVSDAAITAQQ-----------GRIGEPEDVARAALY 232 Query: 232 FGSDDAGFITGQVLSVSGGLT 252 SD++ F+ G L V G T Sbjct: 233 LASDESSFVNGAHLFVDNGFT 253 Lambda K H 0.318 0.135 0.398 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: 192 Number of extensions: 6 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 255 Length of database: 255 Length adjustment: 24 Effective length of query: 231 Effective length of database: 231 Effective search space: 53361 Effective search space used: 53361 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 Apr 09 2024. 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