Align L-rhamnose mutarotase; Rhamnose 1-epimerase; Type-3 mutarotase; EC 5.1.3.32 (characterized)
to candidate 3609041 Dshi_2430 L-rhamnose 1-epimerase (RefSeq)
Query= SwissProt::Q7BSH1 (106 letters) >FitnessBrowser__Dino:3609041 Length = 112 Score = 154 bits (390), Expect = 2e-43 Identities = 72/104 (69%), Positives = 81/104 (77%) Query: 3 LEKHAFKMQLNPGMEAEYRKRHDEIWPELVDLLHQSGASDYSIHLDRETNTLFGVLTRPK 62 +EK AFKM LNPG EY KRHD IWPELVDLL ++G SDYSIHLD ET+TLF VL R + Sbjct: 9 MEKIAFKMMLNPGCREEYIKRHDAIWPELVDLLRKAGVSDYSIHLDPETDTLFAVLWRKE 68 Query: 63 DHTMASLPDHPVMKKWWAHMADIMATNPDNSPVQSDLVTLFHMP 106 H M LP HPVM+KWWAHMADIM T PDN+PV + L T+FHMP Sbjct: 69 GHGMDDLPSHPVMQKWWAHMADIMQTQPDNAPVVTPLDTVFHMP 112 Lambda K H 0.319 0.132 0.419 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: 84 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: 106 Length of database: 112 Length adjustment: 12 Effective length of query: 94 Effective length of database: 100 Effective search space: 9400 Effective search space used: 9400 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.3 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