Align Beta-phosphoglucomutase; Beta-PGM; EC 5.4.2.6 (characterized)
to candidate SMc01502 SMc01502 hydrolase phosphatase
Query= SwissProt::O06995 (226 letters) >FitnessBrowser__Smeli:SMc01502 Length = 224 Score = 58.9 bits (141), Expect = 8e-14 Identities = 57/200 (28%), Positives = 86/200 (43%), Gaps = 43/200 (21%) Query: 2 KAVIFDLDGVITDTAEYHF------LAWKHIAEQIDIPFDRDMNERLKGIS----REESL 51 + VIFD DGV+ D+ LA ++ + +R + LK +S E L Sbjct: 9 RLVIFDCDGVLVDSEPISLGVLVDALAAAGVSMTAEEASERFLGRSLKTMSTILHEEHGL 68 Query: 52 ESILIFGGAETKYTNAEKQELMHRKNRDYQMLISKLTP----EDLLPGIGRLLCQLKN-- 105 + +F L + R Y +L P + + G+G C + Sbjct: 69 ATDEVF--------------LEGMRTRLYARFREELRPIARIREAVEGLGTAHCVASSSQ 114 Query: 106 -ENIKIGLASSSRNAPKILRRLAIIDDFHA-IVDPTTLAKGKPDPDIFLTAAAMLDVSPA 163 E I++ L + +ID F I + +A+GKP PD+FL A+A + P+ Sbjct: 115 PERIRLSLTVTG-----------LIDLFEPNIFSASMVARGKPAPDLFLHASAEMGYHPS 163 Query: 164 DCAAIEDAEAGISAIKSAGM 183 DC IED+ AGI A KSAGM Sbjct: 164 DCIVIEDSPAGIEAAKSAGM 183 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: 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: 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