Align Beta-phosphoglucomutase; Beta-PGM; EC 5.4.2.6 (characterized)
to candidate SM_b21214 SM_b21214 2-deoxyglucose-6-phosphate phosphatase
Query= SwissProt::O06995 (226 letters) >FitnessBrowser__Smeli:SM_b21214 Length = 240 Score = 47.4 bits (111), Expect = 2e-10 Identities = 41/127 (32%), Positives = 57/127 (44%), Gaps = 5/127 (3%) Query: 93 LPGIGRLLCQLKNENIKIGLASSSRNAPKILRRLAIIDDFHAIVDPTTLAKGKPDPDIFL 152 +PG L L E I ++ A + L I H +V ++ GKPDP +L Sbjct: 108 IPGAVSFLKTLPPERWAIVTSAPLELAARRLEAAGIPVPRH-MVTGEDVSVGKPDPQGYL 166 Query: 153 TAAAMLDVSPADCAAIEDAEAGISAIKSAGMFAVGVGQGQPMLGAD---LVVRQTSDLTL 209 AA L V DC EDA AG+ A KSAG V V G A+ +++ SD+ Sbjct: 167 LAAQRLGVRAEDCLVFEDAPAGVLAGKSAGA-EVAVITGAHAAAAEMPHIMLSHYSDVEA 225 Query: 210 ELLHEEW 216 L+ + W Sbjct: 226 RLVEDGW 232 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: 126 Number of extensions: 7 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: 226 Length of database: 240 Length adjustment: 23 Effective length of query: 203 Effective length of database: 217 Effective search space: 44051 Effective search space used: 44051 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