Align L-rhamnose mutarotase; EC 5.1.3.32; Rhamnose 1-epimerase; Type-3 mutarotase (uncharacterized)
to candidate YP_001313688.1 Smed_4974 hypothetical protein
Query= curated2:A5FC30 (107 letters) >NCBI__GCF_000017145.1:YP_001313688.1 Length = 109 Score = 57.4 bits (137), Expect = 5e-14 Identities = 28/79 (35%), Positives = 47/79 (59%), Gaps = 3/79 (3%) Query: 6 RNAFTMKVKSGFETEYKIRHDQIWPELTALLSESGICDYSIFLDEETGILFGV-QKLSSG 64 R + ++S EYK H +WP++ AL+SE I +YSIFL E +LFG + + Sbjct: 3 RMGMVIGLESAKLAEYKRLHAAVWPDILALISECNITNYSIFLKEPENLLFGYWEYVGQD 62 Query: 65 F--DRSQLSSHPLMRKWWN 81 F D +++++HP ++WW+ Sbjct: 63 FDADMAKMAAHPKNQEWWS 81 Lambda K H 0.317 0.132 0.401 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: 4 Number of successful extensions: 2 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: 107 Length of database: 109 Length adjustment: 12 Effective length of query: 95 Effective length of database: 97 Effective search space: 9215 Effective search space used: 9215 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 (21.2 bits) S2: 40 (20.0 bits)
This GapMind analysis is from Sep 24 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