Align diaminopimelate epimerase (EC 5.1.1.7) (characterized)
to candidate GFF1919 PS417_09775 DeoR faimly transcriptional regulator
Query= BRENDA::E4NI20 (295 letters) >FitnessBrowser__WCS417:GFF1919 Length = 324 Score = 62.0 bits (149), Expect = 2e-14 Identities = 69/220 (31%), Positives = 92/220 (41%), Gaps = 42/220 (19%) Query: 84 NADGSIAEMCGNGVRVFARYLVHAGH-AGSGELAVATRGGVKRVRIAADAPDGTPGDVT- 141 N DGS+AE GNG+ +FA+ L G +G+ EL V ++ V Sbjct: 86 NTDGSLAERSGNGLTIFAQALTDQGLLSGACELRVHHDKSDAVSPVSTWVEPAIREQVAG 145 Query: 142 --VDMGRAAFPGPD--GVTVTVD-------------GRSWPALN-VNMGNPHAVAFVEDL 183 +++G F GP+ G + VD W A V +GNPH V VE + Sbjct: 146 FWLELGVPGF-GPEVVGAQMEVDETELSHVSELAAINPQWAASQFVRVGNPHCVTLVEQV 204 Query: 184 A--------HAGHLYEAPATA----PAGA---YPQGVNVEFVVDRGERHVAMRVHERGSG 228 + LYE T PAG P GVN+++ + + RV ERG G Sbjct: 205 SALPDNTQMQQPALYEPLKTIAFAPPAGGGRPCPAGVNLQWAARQPGNRIIARVFERGEG 264 Query: 229 ETRSCGTGACAVAVAAIRRDGADPAATGEAVRYTVDVPGG 268 T S GT A AVA AA R A E+ V +PGG Sbjct: 265 PTASSGTSASAVACAAWR------AGWVESGEVAVVMPGG 298 Score = 24.6 bits (52), Expect = 0.003 Identities = 12/26 (46%), Positives = 15/26 (57%) Query: 107 AGHAGSGELAVATRGGVKRVRIAADA 132 AG SGE+AV GG+ VR+ A Sbjct: 283 AGWVESGEVAVVMPGGIAPVRLHTQA 308 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: 258 Number of extensions: 17 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 295 Length of database: 324 Length adjustment: 27 Effective length of query: 268 Effective length of database: 297 Effective search space: 79596 Effective search space used: 79596 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