Align Beta-phosphoglucomutase; Beta-PGM; EC 5.4.2.6 (characterized)
to candidate BPHYT_RS16100 BPHYT_RS16100 HAD family hydrolase
Query= SwissProt::P77366 (219 letters) >FitnessBrowser__BFirm:BPHYT_RS16100 Length = 237 Score = 64.7 bits (156), Expect = 1e-15 Identities = 44/119 (36%), Positives = 63/119 (52%), Gaps = 10/119 (8%) Query: 83 VHSLRELTVNAVL--PGIRSLLADLRAQQISVGLASVSLN--APTILAALELREFF---T 135 + S+R+ A + P + + A L + G AS S T+L L FF Sbjct: 80 IDSIRQAVEAAAMQAPTVEGIEAALAQVPLPKGCASNSFRPYVETVLTRTGLVRFFGDRL 139 Query: 136 FCADASQLKNSKPDPEIFLAACAGLGVPPQACIGIEDAQAGIDAINASGMRSVG-IGAG 193 FCADA + N KP P+++LAA GLG+ P AC+ +ED+ G+ A A+GM +G IG G Sbjct: 140 FCADA--VPNPKPAPDVYLAAAKGLGLAPSACLVVEDSVTGVTAATAAGMTVLGFIGGG 196 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: 123 Number of extensions: 9 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: 219 Length of database: 237 Length adjustment: 23 Effective length of query: 196 Effective length of database: 214 Effective search space: 41944 Effective search space used: 41944 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: 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