Align diaminopimelate epimerase (EC 5.1.1.7) (characterized)
to candidate Pf6N2E2_33 Diaminopimelate epimerase (EC 5.1.1.7)
Query= BRENDA::E4NI20 (295 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_33 Length = 333 Score = 65.5 bits (158), Expect = 2e-15 Identities = 71/226 (31%), Positives = 99/226 (43%), Gaps = 48/226 (21%) Query: 84 NADGSIAEMCGNGVRVFARYLVHAG-HAGSGELAVATR----GGVKRVRIAADAPD--GT 136 N DG++AE GNG+ +F++ L G AG+G+ + G+ ++ + A + G Sbjct: 86 NTDGTLAERSGNGLTIFSQALQEQGLMAGTGDCLLQVHHDKPDGLSPLQTSVRAAEFEGA 145 Query: 137 PGDVTVDMGRAAF-PGPDGVTVTV-------DGRSWPALN-----------VNMGNPHAV 177 G +D+G+ F PG G V D AL VN+GNPH V Sbjct: 146 QG-FWLDLGKPLFGPGAVGAQDVVRVMFNQCDVSRVAALERLNPAWGNSQFVNIGNPHCV 204 Query: 178 AFVE--DLAHAGHLYEAPATA----------PAGA---YPQGVNVEFVVDRGERHVAMRV 222 V+ + + APA P GA P GVN+++ E +A RV Sbjct: 205 TLVDSAEALPSNPQMRAPALCQSLTRIAYAPPGGAGMPCPMGVNLQWAWLEAEGRIAARV 264 Query: 223 HERGSGETRSCGTGACAVAVAAIRRDGADPAATGEAVRYTVDVPGG 268 ERG G T S GT A AVA AA R A +A +V +PGG Sbjct: 265 FERGEGPTASSGTSASAVACAAWR------AGWVQAGPVSVMMPGG 304 Lambda K H 0.318 0.135 0.408 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: 326 Number of extensions: 15 Number of successful extensions: 3 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: 295 Length of database: 333 Length adjustment: 27 Effective length of query: 268 Effective length of database: 306 Effective search space: 82008 Effective search space used: 82008 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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