Align L-rhamnose mutarotase; P21_mutarotase; Polysaccharide utilization locus H protein P21; PUL H protein P21; Rhamnose 1-epimerase; Type-3 mutarotase; EC 5.1.3.32 (characterized)
to candidate Echvi_1620 Echvi_1620 L-rhamnose 1-epimerase
Query= SwissProt::T2KM13 (104 letters) >FitnessBrowser__Cola:Echvi_1620 Length = 104 Score = 137 bits (345), Expect = 4e-38 Identities = 61/100 (61%), Positives = 81/100 (81%) Query: 2 ERLAFKMKLNKGQKQAYKERHDQLWPELKQLLKDNGVSEYSIFIDEETNTLFAFQKVSGH 61 +++AFKMKL G + Y++RH ++WPEL +LLKD+GV +YSI++D ET+TLFA Q V+G Sbjct: 3 KQIAFKMKLLPGYEAEYEQRHREIWPELVKLLKDSGVQDYSIYLDRETSTLFAVQTVTGD 62 Query: 62 GGSQDLANNEIVKKWWDFMADIMQVNPDNSPVSIPLEEVF 101 SQDL N IV+KWW +MADIM+ NPDNSPVS+PL+EVF Sbjct: 63 SNSQDLGNTTIVQKWWAYMADIMETNPDNSPVSLPLKEVF 102 Lambda K H 0.316 0.133 0.397 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: 65 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: 104 Length of database: 104 Length adjustment: 11 Effective length of query: 93 Effective length of database: 93 Effective search space: 8649 Effective search space used: 8649 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: 40 (21.1 bits) S2: 40 (20.0 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