Align diaminopimelate epimerase (EC 5.1.1.7) (characterized)
to candidate PfGW456L13_2444 Diaminopimelate epimerase (EC 5.1.1.7)
Query= BRENDA::E4NI20 (295 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2444 Length = 330 Score = 70.1 bits (170), Expect = 6e-17 Identities = 82/260 (31%), Positives = 113/260 (43%), Gaps = 70/260 (26%) Query: 84 NADGSIAEMCGNGVRVFARYLVHAGHAGSGELAVATRGGVKRVRIAADAPDG-TPGDVTV 142 N DG++AE GNG+ +F++ L G E + +R+ D D +PG +V Sbjct: 86 NTDGTLAERSGNGLTIFSQALSDQGLLPQNEACL--------LRVHHDKADSPSPGQTSV 137 Query: 143 -------------DMGRAAFPGPD-----GVTVTV-DGRSWP------ALN--------V 169 D+G+ F GP GV T+ +GR ALN Sbjct: 138 KAAEVGGVKGFWLDLGQPGF-GPSAVSAHGVEATIFNGRELSHVEQLSALNSAWSHSQFA 196 Query: 170 NMGNPHAVAFVE---DLAHAGHLYEAPATA----------PAGA---YPQGVNVEFVVDR 213 +GNPH V VE DL + E PA P GA P G+N+++ + Sbjct: 197 RVGNPHCVTLVESAEDLPSNEQMRE-PALGEGLTRIAYAMPVGAGKPCPAGINLQWAMRV 255 Query: 214 GERHVAMRVHERGSGETRSCGTGACAVAVAAIRRDGADPAATGEAVRYTVDVPGGR---L 270 E H+A RV ERG G T S GT A AVA AA R A + GE V +PGG L Sbjct: 256 SEGHIAARVFERGEGPTASSGTSASAVACAAWR---AGWVSAGEV---KVTMPGGTAPIL 309 Query: 271 VIEEFPD-GRIEMTGPAVIV 289 + EE + R+ + G A ++ Sbjct: 310 LAEELGELSRVSLFGTARLI 329 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: 303 Number of extensions: 19 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: 330 Length adjustment: 27 Effective length of query: 268 Effective length of database: 303 Effective search space: 81204 Effective search space used: 81204 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 Aug 03 2021. The underlying query database was built on Aug 03 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