Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (uncharacterized)
to candidate WP_026190940.1 M446_RS02180 type III PLP-dependent enzyme
Query= curated2:Q9JXM2 (414 letters) >NCBI__GCF_000019365.1:WP_026190940.1 Length = 388 Score = 111 bits (278), Expect = 3e-29 Identities = 105/348 (30%), Positives = 157/348 (45%), Gaps = 27/348 (7%) Query: 39 AFAALNP--LVCYAVKANGNLSIIKHFASLGSGFDIVSGGELARVLAAGGDAAKTIFSGV 96 AFA P V YAVKAN ++ ASLGS FD S E+ LAAG A + F Sbjct: 36 AFARALPDTRVFYAVKANPAPEVLGLLASLGSCFDTASVAEIQMALAAGATADRISFGNT 95 Query: 97 GKSEAEIEFALNAGVKCFNMESIPEIDRIQKVAARLGKTAP----VSLRINPDVDAKTHP 152 K E I AL GV+ F ++ E+++I + AA AP V RI D P Sbjct: 96 IKKERCIARALALGVRLFAVDCEAEVEKIARAAA-CADVAPEEVQVFCRILCDGAGAEWP 154 Query: 153 YISTGLKANKFGIAYADALEAYHYAAQQPNLKIIGIDCHIGSQLTDLSPLVEACERILIL 212 + KFG A++ +A +Q L+ G+ H+GSQ + A ++ Sbjct: 155 L------SRKFGCVPDMAVDVLEHAHRQ-GLRAYGVSFHVGSQQGNTEAWDGALASAAMI 207 Query: 213 VDALAAEGIVLEHLDLGGGVGIVYQDENVPDL----GAYAQAVQKLIGTRRLKLILEPGR 268 A GI L ++LGGG Y E VP + GA +A+ K G R + I+EPGR Sbjct: 208 FRECAERGIALAMVNLGGGFPTKYLKE-VPGVESYGGAIFRALTKHFGNRMPETIIEPGR 266 Query: 269 SLVGNAGSLLTRVEFV----KYGEEKNFVMVDAAMNDLMRPALYDAYHHIEAVETKDIAT 324 +VGNAG + V V + +E +V +D + + ++ + + + Sbjct: 267 GMVGNAGIIEAEVILVSKKSEAADEVRWVYLDIGKFGGLAETMDESIRYRIRTDHDEDRM 326 Query: 325 LTANIVGPICETGDFLGK----DRTIACEEGDLLLIRSAGAYGASMAS 368 + + GP C++ D L + ++ GD +LI AGAY + A+ Sbjct: 327 VPCVLAGPTCDSADVLYEKIPYPLPVSLSIGDKVLIEGAGAYTTTYAA 374 Lambda K H 0.319 0.136 0.388 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: 390 Number of extensions: 23 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: 414 Length of database: 388 Length adjustment: 31 Effective length of query: 383 Effective length of database: 357 Effective search space: 136731 Effective search space used: 136731 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 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 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