Align predicted cytochrome c component of periplasmic glucoside 3-dehydrogenase (EC 1.1.99.13) (characterized)
to candidate BPHYT_RS04810 BPHYT_RS04810 cytochrome C
Query= reanno::Pedo557:CA265_RS15360 (127 letters) >FitnessBrowser__BFirm:BPHYT_RS04810 Length = 112 Score = 68.2 bits (165), Expect = 3e-17 Identities = 36/110 (32%), Positives = 54/110 (49%), Gaps = 7/110 (6%) Query: 24 SREKTVVATATMTKHAAFQSNP-------GEKLINKSDCLGCHNKTNKIIGPAYVEIAKK 76 S+ T +A A + A +P G L + +C+ CH+ +GPA ++A K Sbjct: 3 SKSHTALAAAVVLGAALSAGSPAAQAEAAGLALAQQQNCMSCHSVIRSFMGPALHDVAAK 62 Query: 77 YPATEKNINMLADKIIKGGTGVWGNMPMTAHATLKKDDAKLMVKYILSLK 126 Y E L KI+ G TGVWG +PM A+ L D A + ++L+LK Sbjct: 63 YAGREDAAAYLKHKILDGSTGVWGEVPMPANTQLTPDQAATLANWVLTLK 112 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: 41 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: 112 Length adjustment: 13 Effective length of query: 114 Effective length of database: 99 Effective search space: 11286 Effective search space used: 11286 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: 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