Align predicted cytochrome c component of periplasmic glucoside 3-dehydrogenase (EC 1.1.99.13) (characterized)
to candidate Ac3H11_952 Cytochrome c551/c552
Query= reanno::Cola:Echvi_1841 (141 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_952 Length = 101 Score = 86.3 bits (212), Expect = 1e-22 Identities = 36/80 (45%), Positives = 56/80 (70%) Query: 61 LALVKESDCPSCHMVERKIVGPAYKDVAEKYESTDENIETLAKRVVDGNNGVWGQVPMPA 120 +AL +C +CH V++K+VGP+YKDVA KY + ++ LA ++V G +GVWG VPMPA Sbjct: 22 MALATSKNCMACHAVDKKLVGPSYKDVAAKYAGQKDAVDKLAAKIVKGGSGVWGPVPMPA 81 Query: 121 HPGLSEDDAKKMVKYILMLK 140 + +++ DAKK+ ++L K Sbjct: 82 NAQVNDADAKKLAAWVLTQK 101 Lambda K H 0.309 0.127 0.361 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: 45 Number of extensions: 4 Number of successful extensions: 1 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: 141 Length of database: 101 Length adjustment: 13 Effective length of query: 128 Effective length of database: 88 Effective search space: 11264 Effective search space used: 11264 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.3 bits) S2: 41 (20.4 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