Align Beta-phosphoglucomutase; Beta-PGM; EC 5.4.2.6 (characterized)
to candidate 16779 b2690 predicted hydrolase (NCBI)
Query= SwissProt::P77366 (219 letters) >FitnessBrowser__Keio:16779 Length = 188 Score = 85.5 bits (210), Expect = 6e-22 Identities = 56/188 (29%), Positives = 93/188 (49%), Gaps = 11/188 (5%) Query: 5 GVIFDLDGVITDTAHLHFQAWQQIAAEIGISIDAQFNESLKGISRDESLRRILQHGGKEG 64 G+IFD+DG I DT H +AW+++ G+ D Q +L G + I++ + Sbjct: 7 GLIFDMDGTILDTEPTHRKAWREVLGHYGLQYDIQAMIALNGSPTWRIAQAIIELNQADL 66 Query: 65 DFNSQERAQLAYRKNLLYVHSLRELTVNAV--LPGIRSLLADLRAQQISVGLASVSLNAP 122 D ++ R + ++R + +++V LP + + + + ++VG S S A Sbjct: 67 DPHALAREK---------TEAVRSMLLDSVEPLPLVDVVKSWHGRRPMAVGTGSESAIAE 117 Query: 123 TILAALELREFFTFCADASQLKNSKPDPEIFLAACAGLGVPPQACIGIEDAQAGIDAINA 182 +LA L LR +F A +K+ KP P+ FL +GV P C+ EDA GI A A Sbjct: 118 ALLAHLGLRHYFDAVVAADHVKHHKPAPDTFLLCAQRMGVQPTQCVVFEDADFGIQAARA 177 Query: 183 SGMRSVGI 190 +GM +V + Sbjct: 178 AGMDAVDV 185 Lambda K H 0.320 0.135 0.392 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: 103 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: 219 Length of database: 188 Length adjustment: 21 Effective length of query: 198 Effective length of database: 167 Effective search space: 33066 Effective search space used: 33066 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 (21.8 bits) S2: 45 (21.9 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