Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (characterized)
to candidate WP_003542992.1 RLEG_RS18215 type III PLP-dependent enzyme
Query= SwissProt::B4XMC6 (405 letters) >NCBI__GCF_000023185.1:WP_003542992.1 Length = 377 Score = 127 bits (319), Expect = 5e-34 Identities = 108/363 (29%), Positives = 173/363 (47%), Gaps = 29/363 (7%) Query: 14 PFYLYDFDKIKQAFLNYKEAFKGRKSLICYALKANSNLSILSLLAHLESGADCVSIGEIQ 73 P + D D ++ F ++ A S I YA+KAN +L LLA L S DC S+ EI+ Sbjct: 18 PCLVVDLDVVRDNFHAFRHAMPD--SAIYYAVKANPAPEVLKLLAGLGSNFDCASVAEIE 75 Query: 74 RALKAGIKPYRIVFSGVGKSAFEIEQALKLNILFLNVESFMELKTIETIAQSLGIKARIS 133 AL+AG RI + K ++ +A L + V+S E++ I A AR+ Sbjct: 76 MALEAGATAARISYGNTIKKERDVARAHALGVSLFAVDSHEEVEKISRAAPG----ARVF 131 Query: 134 IRINPNIDAKTHPYISTGLKENKFGVGEKEALEMFLWAKKSAFLEPVSVHFHIGSQLLDL 193 R+ + + P KFG + A+++ ++A + L+ V FH+GSQ+ + Sbjct: 132 CRVLTDGEGAEWPL------SRKFGCVPQMAVDVLVYAHQLG-LQSYGVSFHVGSQMTKV 184 Query: 194 EPIIEASQKVAKIAKSLIALGIDLRFFDVGGGIGVSYENEETIKLYDYAQGILNALQ--- 250 + A ++ SL GI L+ ++GGG Y + Y + I AL+ Sbjct: 185 DAWDSALADAKRVFVSLAKQGIHLQMVNMGGGFPTKY-LRDVPSAEAYGKSIYQALRTHF 243 Query: 251 --GLDLTIICEPGRSIVAESGELITQ-VLYEKKAQN--KRFVIVDAGMNDFLRPSLYHA- 304 + TII EPGR +V +G + + VL KK+ N R+V +D G L ++ A Sbjct: 244 GNQIPQTII-EPGRGMVGNAGVIKAEVVLISKKSDNDDARWVFLDIGKFGGLAETMDEAI 302 Query: 305 KHAIRVITPSKGREISPCDVVGPVCESSDTFLKDAHLP---ELEPGDKIAIEKVGAYGSS 361 ++ IR T G E+ PC + GP C+S+D + P L GD++ IE GAY ++ Sbjct: 303 RYPIR--TEHDGDEMEPCVIAGPTCDSADVLYEKNLYPLPISLSIGDEVLIEGTGAYTTT 360 Query: 362 MAS 364 ++ Sbjct: 361 YSA 363 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: 301 Number of extensions: 17 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: 377 Length adjustment: 31 Effective length of query: 374 Effective length of database: 346 Effective search space: 129404 Effective search space used: 129404 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