Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (characterized)
to candidate WP_004512931.1 GMET_RS10195 pyridoxal-dependent decarboxylase, exosortase A system-associated
Query= SwissProt::B4XMC6 (405 letters) >NCBI__GCF_000012925.1:WP_004512931.1 Length = 419 Score = 163 bits (413), Expect = 8e-45 Identities = 122/400 (30%), Positives = 203/400 (50%), Gaps = 22/400 (5%) Query: 4 YEELFQTHKTPFYLYDFDKIKQAFLNYKEAFKGRKSLICYALKANSNLSILSLLAHLESG 63 +EEL + TPFYLYD DK+K+ ++AF L+ YA+KAN N +L+ + G Sbjct: 17 FEELAARYGTPFYLYDLDKVKEKCAAVRKAFGDSLELL-YAVKANPNRELLAAMRGEVDG 75 Query: 64 ADCVSIGEIQRALKAGIKPYRIVFSGVGKSAFEIEQALKLNILFLNVESFMELKTIETIA 123 D S GE++RAL+ G I F+G GK+ E+ ++L+ + ++VES EL + + Sbjct: 76 LDIASAGELERALETGYDAGCISFAGPGKTRDELRRSLEAGVGCISVESLRELNDLRDLV 135 Query: 124 QSLGIKARISIRINPNIDAKTHPYISTGLKENKFGVGEKE---ALEMFLWAKKSAFLEPV 180 ++ +A I +R+NP + + + G K ++FG+ E+E AL+ F+ A AF + Sbjct: 136 RAGSHRAYILVRVNPQLLIRDFA-VKMGGKASQFGIDEEELPSALD-FIKANADAF-DFK 192 Query: 181 SVHFHIGSQLLDLEPIIE-ASQKVAKIAKSLIALGIDLRFFDVGGGIGVSYENEETIKLY 239 +H + G+Q L+ E + + + +A A+ G++ R ++GGG+GVSY E Sbjct: 193 GIHIYAGTQCLNEEALAQNLANTLAIAARITTDYGMECRVINIGGGLGVSYYEEHPGLDL 252 Query: 240 DYAQGILNA-------LQGLDLTIICEPGRSIVAESGELITQVLYEKKAQNKRFVIVDAG 292 D + A G I+ E GR +VAE+G +T+V+ EK ++ ++F ++D G Sbjct: 253 DKLALLFRAEFDRYREATGTKPRILLELGRFLVAEAGIYVTRVVSEKLSRGEQFYVLDGG 312 Query: 293 MNDFLRPS-----LYHAKHAIRVITPSKGREISPCDVVGPVCESSDTFLKDAHLPELEPG 347 MN L S + +R ++ G E C +VGP+C D K + E G Sbjct: 313 MNHHLSASGNLGMTIRKNYLVRNLS-RPGAERIICTLVGPLCTPLDLMGKGVTVEVPEVG 371 Query: 348 DKIAIEKVGAYG-SSMASQYNSRPKLLELALEDHKIRVIR 386 D + G+YG S+ + + EL +E +R R Sbjct: 372 DLVGFLNSGSYGYSASPLLFLGHGEPCELLVEGKDVRPCR 411 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: 383 Number of extensions: 23 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: 419 Length adjustment: 31 Effective length of query: 374 Effective length of database: 388 Effective search space: 145112 Effective search space used: 145112 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