Align Sugar transporter SemiSWEET (characterized)
to candidate 8501181 DvMF_1915 hypothetical protein (RefSeq)
Query= SwissProt::B0SR19 (85 letters) >FitnessBrowser__Miya:8501181 Length = 98 Score = 66.2 bits (160), Expect = 8e-17 Identities = 31/81 (38%), Positives = 48/81 (59%) Query: 4 LIGYVAAFLTTVSFLPQVLRVVMTKQTRDISRNMYIMFFLGVVLWFVYGILRSDLPIILA 63 +IGY A LT++++LPQV+R+ T+ DIS + + +GV LW VYGI P++ A Sbjct: 17 IIGYAAGLLTSLAYLPQVVRIARTRSADDISLPTFRLLAVGVALWLVYGIGIGSWPVMAA 76 Query: 64 NVVTLFFVTIILYYKLTEGNQ 84 N V L + +++ KL Q Sbjct: 77 NAVGLALILAVIWLKLRYSRQ 97 Lambda K H 0.334 0.147 0.429 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: 26 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: 85 Length of database: 98 Length adjustment: 9 Effective length of query: 76 Effective length of database: 89 Effective search space: 6764 Effective search space used: 6764 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: 39 (21.6 bits) S2: 39 (19.6 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