Align D-sorbitol dehydrogenase small subunit (EC 1.1.99.21) (characterized)
to candidate Pf1N1B4_821 Glucose dehydrogenase, PQQ-dependent (EC 1.1.5.2)
Query= metacyc::MONOMER-13709 (126 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_821 Length = 802 Score = 73.6 bits (179), Expect = 6e-18 Identities = 44/102 (43%), Positives = 59/102 (57%), Gaps = 2/102 (1%) Query: 14 LTLLLGVIVLLVGLFFVIGGADLAMLGGSTYYVLCGILLVASGVFMLMGRTLGAFLYLGA 73 L LLG+++LL+GL + GG L+MLGGS YY+L GI L+ +G +L R LY Sbjct: 13 LPSLLGIVLLLMGLALLAGGIKLSMLGGSLYYLLAGIGLMLTGGLLLADRYAALSLYAVV 72 Query: 74 LAYTWVWSFWEVGFSPIDLLPRAFGPTILGILVALTIPVLRR 115 L + VW+ WEVG L+PR LGI++ L P RR Sbjct: 73 LFASTVWALWEVGLDWWQLVPRLALLFALGIVMLL--PWFRR 112 Lambda K H 0.331 0.148 0.471 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: 231 Number of extensions: 14 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: 126 Length of database: 802 Length adjustment: 27 Effective length of query: 99 Effective length of database: 775 Effective search space: 76725 Effective search space used: 76725 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 48 (23.1 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