Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (uncharacterized)
to candidate WP_085770944.1 B1812_RS06935 type III PLP-dependent enzyme
Query= curated2:Q9Z661 (421 letters) >NCBI__GCF_002117405.1:WP_085770944.1 Length = 380 Score = 125 bits (314), Expect = 2e-33 Identities = 113/372 (30%), Positives = 168/372 (45%), Gaps = 31/372 (8%) Query: 28 PCYVYSHSYLTERARRFTKALDGAGKGKSLVAFAVKANPSQAILASFAKEGLGADVVSAG 87 PC V + + R F++AL + V +AVKANP+ +L+ A G D S Sbjct: 21 PCLVVDLDVVRDNYRDFSRALPD-----TRVYYAVKANPAPEVLSLLASLGSSFDTASVA 75 Query: 88 EIRRAVHAGIPPERIVFSGVGKTAEEMRYALEIGIGQFNIESVSEIEMLAEVATSLGKKA 147 EI A+ AG PERI F K ++ A ++G+ F ++S +E+E +A VA ++ Sbjct: 76 EIELALAAGASPERISFGNTIKKERDVARAYQLGVRLFAVDSEAEVEKIARVA----PRS 131 Query: 148 AVALRINPDVDPHTHAKIATGKADTKFGIAAEDALSAYEKLASYPSLKIQGIASHIGSQI 207 V RI D A KFG A E A E LA L G++ H+GSQ Sbjct: 132 KVFCRILCD------GSGAEWPLSRKFGCAPEMAPRVLE-LAQANGLIAYGLSFHVGSQQ 184 Query: 208 TDLAPFEAAAERIYEIITALEKAGHAIETADLGGGLGVRYKDDQPEPPSVEAYGEMIKR- 266 + ++ A E I L + G ++ +LGGG RY P+ V YG I R Sbjct: 185 PNPRMWDKALESCANIFRELAERGVYLQMVNLGGGFPTRYLKSVPK---VRIYGNAIFRA 241 Query: 267 VTKGWNCRL---IFEPGRSLIANAGVLLSKVIRI---KESKTARFVILD-AAMNDLVRPT 319 ++K + RL I EPGR ++ NAG++ ++V+ I + R+V LD N L T Sbjct: 242 LSKHFGNRLPETIIEPGRGMVGNAGIIEAEVVLISKKSDDDPLRWVFLDIGKFNGLAETT 301 Query: 320 LYDAYHEIKAVTPSAQTYQADIVGPVCETGDIFARNRSIS---AVKADDLMAIMSAGAYG 376 + I+ A I GP C++ DI +++ + I GAY Sbjct: 302 DEMIRYPIRTPVDGAAVGPCVIAGPSCDSVDILYEKTPYELPVSLEIGAKVLIEGTGAYT 361 Query: 377 ATMAS-AYNSRP 387 T +S A+N P Sbjct: 362 TTYSSIAFNGFP 373 Lambda K H 0.317 0.132 0.372 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: 342 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: 421 Length of database: 380 Length adjustment: 31 Effective length of query: 390 Effective length of database: 349 Effective search space: 136110 Effective search space used: 136110 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 (21.6 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