Align predicted cytochrome c component of periplasmic glucoside 3-dehydrogenase (EC 1.1.99.13) (characterized)
to candidate BPHYT_RS01960 BPHYT_RS01960 cytochrome C
Query= reanno::Cola:Echvi_1841 (141 letters) >FitnessBrowser__BFirm:BPHYT_RS01960 Length = 115 Score = 76.3 bits (186), Expect = 1e-19 Identities = 31/82 (37%), Positives = 52/82 (63%) Query: 56 DYVEGLALVKESDCPSCHMVERKIVGPAYKDVAEKYESTDENIETLAKRVVDGNNGVWGQ 115 D G + + C CH V+RK+VGP+++ +A KY+ + L+++V DG +GVWG Sbjct: 28 DAPRGQLVANANACMGCHAVDRKLVGPSFQQIAGKYKGDAQAPAKLSRKVKDGGSGVWGM 87 Query: 116 VPMPAHPGLSEDDAKKMVKYIL 137 +PMPAH +S+ D + +V ++L Sbjct: 88 IPMPAHQSMSDADIRAVVDWVL 109 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: 43 Number of extensions: 1 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: 115 Length adjustment: 14 Effective length of query: 127 Effective length of database: 101 Effective search space: 12827 Effective search space used: 12827 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