Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (characterized)
to candidate WP_011156405.1 TX73_RS04475 type III PLP-dependent enzyme
Query= SwissProt::B4XMC6 (405 letters) >NCBI__GCF_000195775.1:WP_011156405.1 Length = 380 Score = 133 bits (335), Expect = 8e-36 Identities = 113/372 (30%), Positives = 182/372 (48%), Gaps = 30/372 (8%) Query: 14 PFYLYDFDKIKQAFLNYKEAFKGRKSLICYALKANSNLSILSLLAHLESGADCVSIGEIQ 73 P + D + ++ F+++ +A S + YA+KAN +LSLLA L S DC S+ EIQ Sbjct: 21 PCLVVDLEVVRDNFMHFAKALPD--SRVFYAIKANPAPEVLSLLASLGSCFDCASVQEIQ 78 Query: 74 RALKAGIKPYRIVFSGVGKSAFEIEQALKLNILFLNVESFMELKTIETIAQSLGIKARIS 133 AL AG P RI F K +I +A +L I +V+ E++ + A +++ Sbjct: 79 MALAAGATPDRISFGNTIKKERDIARAYELGIRLFSVDCTPEVEKVARAAPG----SKVF 134 Query: 134 IRINPNIDAKTHPYISTGLKENKFGVGEKEALEMFLWAKKSAFLEPVSVHFHIGSQLLDL 193 RI + P KFG + A+++ AK+ LE + FH+GSQ + Sbjct: 135 CRILYDCAGAEWPL------SRKFGCDPEMAVDVLDNAKRLG-LEAYGISFHVGSQQRKV 187 Query: 194 EPIIEASQKVAKIAKSLIALGIDLRFFDVGGGIGVSYENEETIKLYDYAQGILNALQ--- 250 + A A++ + GI L ++GGG Y +E + Y + I AL+ Sbjct: 188 KAWDRALAMAAQVFRDCAERGISLSMVNMGGGFPTKY-LKEVPPVVQYGRSIFRALRKHF 246 Query: 251 --GLDLTIICEPGRSIVAESGELITQVLYEKKAQNK---RFVIVDAGMNDFLRPSLYHA- 304 + TII EPGR +V +G + T+V+ K ++ R+V +D G L ++ + Sbjct: 247 GNQIPETII-EPGRGMVGNAGVIETEVVLISKKSDEDDVRWVYLDIGKFGGLAETMDESI 305 Query: 305 KHAIRVITPSKGREISPCDVVGPVCESSDTFLKDAHLP---ELEPGDKIAIEKVGAYGSS 361 ++AI+ + G E++PC + GP C+S+D + P LE GDK+ IE GAY S+ Sbjct: 306 RYAIK--SRHDGAEMTPCVLAGPTCDSADVLYEKMPYPLPVTLEIGDKLLIEGTGAYTST 363 Query: 362 MAS-QYNSRPKL 372 +S +N P L Sbjct: 364 YSSVAFNGFPPL 375 Lambda K H 0.319 0.138 0.389 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: 305 Number of extensions: 18 Number of successful extensions: 5 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: 405 Length of database: 380 Length adjustment: 31 Effective length of query: 374 Effective length of database: 349 Effective search space: 130526 Effective search space used: 130526 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 (21.7 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