Align Beta-phosphoglucomutase; Beta-PGM; EC 5.4.2.6 (characterized)
to candidate Ac3H11_2632 Beta-phosphoglucomutase (EC 5.4.2.6)
Query= SwissProt::O06995 (226 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2632 Length = 224 Score = 77.4 bits (189), Expect = 2e-19 Identities = 62/194 (31%), Positives = 89/194 (45%), Gaps = 16/194 (8%) Query: 1 MKAVIFDLDGVITDTAEYHFLAWKHIAEQ----IDIPFDRDMNERLKGISREESLESILI 56 ++A+IFD+DG + D+ +H AW A + ID+P D+ R G + E + +L Sbjct: 3 VEAIIFDMDGTMIDSMPWHAQAWVEFARRRGMDIDVP---DLMARTTGKNGTECIVELL- 58 Query: 57 FGGAETKYTNAEKQELMHRKNRDYQMLISKLTPEDLLPGIGRLLCQLKNENIKI--GLAS 114 G A ++ E L H K Y+ L + E + G + Q++ +K+ G A Sbjct: 59 -GRAVSQ---DEADALTHEKETIYRELFAPRFTE--VAGFRQFAAQVRARGLKVAVGTAG 112 Query: 115 SSRNAPKILRRLAIIDDFHAIVDPTTLAKGKPDPDIFLTAAAMLDVSPADCAAIEDAEAG 174 N L L + AIV GKP P IFL AA + PA C EDA G Sbjct: 113 DIGNVEFALGHLGLEPAPQAIVRGDEGLPGKPQPAIFLEAARRIAADPAHCIVFEDAPFG 172 Query: 175 ISAIKSAGMFAVGV 188 I A + AGM AV + Sbjct: 173 IEAARRAGMRAVAI 186 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: 113 Number of extensions: 6 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: 224 Length adjustment: 22 Effective length of query: 204 Effective length of database: 202 Effective search space: 41208 Effective search space used: 41208 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