Align Fucose mutarotase; EC 5.1.3.29 (characterized)
to candidate SM_b21302 SM_b21302 hypothetical protein
Query= SwissProt::A2VDF0 (154 letters) >FitnessBrowser__Smeli:SM_b21302 Length = 151 Score = 92.0 bits (227), Expect = 4e-24 Identities = 54/148 (36%), Positives = 84/148 (56%), Gaps = 6/148 (4%) Query: 4 LKGVPALLSPELLYALARMGHGDEIVLADLNFPASSICQCGPME--IRADGLGIPQLLEA 61 LK + L+ ++L+AL MGHGD +V++D NFP+ +I + + + D + + A Sbjct: 2 LKNIDPALNADVLHALRSMGHGDTLVISDTNFPSDAIARQTTLGKLLHIDNVSSARAARA 61 Query: 62 VLKLLPLDTYVESPAAVMELVPS-DKERGLQTPVWTEYESILRRAGCVRALAKIERFEFY 120 +L +LPLDT ++ A ME++ + D+ +Q V E + R G + IERF FY Sbjct: 62 ILSVLPLDTPLQPSAGRMEVMGAPDEVPAVQREVQAEID---RAEGKPAPMYGIERFAFY 118 Query: 121 ERAKKAFAVVATGETALYGNLILRKGVL 148 E AKKA+ V+ TGE YG + KGV+ Sbjct: 119 EEAKKAYCVITTGEPRFYGCFLFTKGVI 146 Lambda K H 0.322 0.139 0.404 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: 76 Number of extensions: 5 Number of successful extensions: 3 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: 154 Length of database: 151 Length adjustment: 17 Effective length of query: 137 Effective length of database: 134 Effective search space: 18358 Effective search space used: 18358 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: 41 (21.9 bits) S2: 43 (21.2 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