Align Beta-phosphoglucomutase; Beta-PGM; EC 5.4.2.6 (characterized)
to candidate 5210999 Shew_3425 2-deoxyglucose-6-phosphatase (RefSeq)
Query= SwissProt::O06995 (226 letters) >FitnessBrowser__PV4:5210999 Length = 223 Score = 80.5 bits (197), Expect = 2e-20 Identities = 58/189 (30%), Positives = 96/189 (50%), Gaps = 10/189 (5%) Query: 1 MKAVIFDLDGVITDTAEYHFLAWKHIAEQIDIPFDRDMNERLKGISREESLESILIFGGA 60 + AVIFD+DGV+ D+ A + Q+ +P E+ G+ ++ +E + Sbjct: 6 LAAVIFDMDGVLIDSEPSWQAAEYKVLSQLGLPISLSDTEQTTGLRIDQVVE--YWYRRH 63 Query: 61 ETK-YTNAEKQELMHRKNRDYQMLISKLTPEDLLPGIGRLLCQLKNENIKIGLASSSRNA 119 K Y NA E + Q+ L+ +++ G+ L K +K+GLA+SS Sbjct: 64 PWKGYDNAATAEAIVT-----QVAGEILSHGEVMSGVKEALEACKQRGLKLGLATSSPTL 118 Query: 120 --PKILRRLAIIDDFHAIVDPTTLAKGKPDPDIFLTAAAMLDVSPADCAAIEDAEAGISA 177 ++++LAI + F AIV LA GKP P+++L A L V+P+ C A+ED+ G+ A Sbjct: 119 LIDAVMQKLAIRELFDAIVSAEALALGKPHPEVYLNCAKALGVTPSQCLAVEDSFNGLIA 178 Query: 178 IKSAGMFAV 186 ++A M V Sbjct: 179 ARAANMHTV 187 Lambda K H 0.319 0.136 0.390 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: 106 Number of extensions: 5 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: 226 Length of database: 223 Length adjustment: 22 Effective length of query: 204 Effective length of database: 201 Effective search space: 41004 Effective search space used: 41004 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 (21.7 bits) S2: 46 (22.3 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