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::Pedo557:CA265_RS15360 (127 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_952 Length = 101 Score = 78.2 bits (191), Expect = 3e-20 Identities = 36/100 (36%), Positives = 57/100 (57%) Query: 27 KTVVATATMTKHAAFQSNPGEKLINKSDCLGCHNKTNKIIGPAYVEIAKKYPATEKNINM 86 K + T MT A + L +C+ CH K++GP+Y ++A KY + ++ Sbjct: 2 KRTLITLAMTLSVAAPAMADMALATSKNCMACHAVDKKLVGPSYKDVAAKYAGQKDAVDK 61 Query: 87 LADKIIKGGTGVWGNMPMTAHATLKKDDAKLMVKYILSLK 126 LA KI+KGG+GVWG +PM A+A + DAK + ++L+ K Sbjct: 62 LAAKIVKGGSGVWGPVPMPANAQVNDADAKKLAAWVLTQK 101 Lambda K H 0.317 0.131 0.372 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: 53 Number of extensions: 2 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: 127 Length of database: 101 Length adjustment: 12 Effective length of query: 115 Effective length of database: 89 Effective search space: 10235 Effective search space used: 10235 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: 40 (21.3 bits) S2: 40 (20.0 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