Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (uncharacterized)
to candidate WP_011383798.1 AMB_RS07020 type III PLP-dependent enzyme
Query= curated2:O69203 (437 letters) >NCBI__GCF_000009985.1:WP_011383798.1 Length = 376 Score = 132 bits (333), Expect = 1e-35 Identities = 113/371 (30%), Positives = 173/371 (46%), Gaps = 36/371 (9%) Query: 50 TPCQVLDEGTVRARARAFREALPEAEVVFAGKALPCREVYRWVADEGLSLDVCSAGELAI 109 TPC V+D VR R LP AEV +A KA P E+ R + +EG DV S GE+ + Sbjct: 16 TPCVVVDLDVVRDNYHGLRRWLPLAEVYYAVKANPAPEIVRMLTEEGSRFDVASRGEIDL 75 Query: 110 ARSVGFPAERVLLHGNVKTPEDLKAALGYGVGRVVVDSFDEIEQLGALAEGPQDVLVRVT 169 + G PAER+ +K D+ A GV DS E+E+L A G + V R+ Sbjct: 76 CLANGAPAERISFGNTIKKQSDIAYAYAKGVRLYAFDSEAELEKLAEAAPGSR-VFCRIL 134 Query: 170 PGVDPRTHRAVATGVEDQKFGFSLAGGDALEAVLRVVEQPSLRLVGLHCHVGSQVRHVAV 229 D A +KFG + D + +L + L G+ HVGSQ + Sbjct: 135 MTCDG------AEWPLSRKFGCEI---DMAKDLLVKAREMGLDPYGVSFHVGSQQTDLRQ 185 Query: 230 YEEAARRVVGLIA---SCGVRIEQLDLGGGFAVPYLPGEGEFD-LGGFAHRVRVALSHEC 285 ++ A + L + + G+ + ++LGGGF Y E D L +A V A++ Sbjct: 186 WDIAVGKAAMLFSALDAAGIELRMVNLGGGFPARY---RKEVDGLERYAEAVMDAMTKHF 242 Query: 286 ALRRVPVPRLSIEPGRAVVARAGVTLYRVAAVKR-----GVRRVFVAVD--GGMSDNPRP 338 +P + IEPGR++V AG+ V + R VR V++ V GG+++ Sbjct: 243 GNN---IPSMIIEPGRSLVGDAGILETEVVLISRKGYDDDVRWVYLDVGKFGGLAETMDE 299 Query: 339 ALYGSRYAVRLVRRGGRRAPVTVVGRHCEAGDVLAEDV--PLPEDVRAGDLLAVPVTGAY 396 A+ +Y + R G APV + G C++ D+L E +P ++ GD + + TGAY Sbjct: 300 AI---KYRIVTTRDGDDTAPVVLAGPTCDSADILYEKAGYEMPLSLKVGDKVRILSTGAY 356 Query: 397 HHALASNYNAV 407 ++Y+AV Sbjct: 357 ----TTSYSAV 363 Lambda K H 0.321 0.140 0.415 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: 329 Number of extensions: 18 Number of successful extensions: 4 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: 437 Length of database: 376 Length adjustment: 31 Effective length of query: 406 Effective length of database: 345 Effective search space: 140070 Effective search space used: 140070 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 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