Align predicted cytochrome c component of periplasmic glucoside 3-dehydrogenase (EC 1.1.99.13) (characterized)
to candidate H281DRAFT_00126 H281DRAFT_00126 cytochrome c
Query= reanno::Pedo557:CA265_RS15360 (127 letters) >FitnessBrowser__Burk376:H281DRAFT_00126 Length = 113 Score = 65.1 bits (157), Expect = 3e-16 Identities = 37/103 (35%), Positives = 54/103 (52%), Gaps = 4/103 (3%) Query: 28 TVVATATMT---KHAAFQSNP-GEKLINKSDCLGCHNKTNKIIGPAYVEIAKKYPATEKN 83 T VA TM+ AA P G L + +C+ CH+ + +GPA ++A KY E Sbjct: 11 TAVAFVTMSIGISPAAHAEAPMGLALAQQQNCMSCHSVSRPFMGPALHDVAAKYAGREDA 70 Query: 84 INMLADKIIKGGTGVWGNMPMTAHATLKKDDAKLMVKYILSLK 126 L KI+ G TGVWG +PM A+ L + A + ++L+LK Sbjct: 71 AIYLKHKILDGSTGVWGPVPMPANTQLTPEQAAALAGWVLTLK 113 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: 45 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: 113 Length adjustment: 13 Effective length of query: 114 Effective length of database: 100 Effective search space: 11400 Effective search space used: 11400 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