Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (uncharacterized)
to candidate WP_012971010.1 ALVIN_RS08985 pyridoxal-dependent decarboxylase, exosortase A system-associated
Query= curated2:O67262 (420 letters) >NCBI__GCF_000025485.1:WP_012971010.1 Length = 410 Score = 165 bits (418), Expect = 2e-45 Identities = 128/404 (31%), Positives = 197/404 (48%), Gaps = 19/404 (4%) Query: 9 PYLEYRDGELFIEGVSLKELAQTFG-TPLYVYSSNFIKERFEAYRKAFPDAL-ICYAVKA 66 P D +L I + + LA+ G TP Y Y I R R+A PD + + YA+KA Sbjct: 10 PLFPVADNQLVIGALPIARLAERVGRTPFYAYDRALISARVAQLRQALPDDIHLHYAIKA 69 Query: 67 NFNPHLVKLLGELGAGADIVSGGELYLAKKAGIPPERIVYAGVGKTEKELTDAVDSEILM 126 N P +V+ L L G D+ SGGEL A +PP +I +AG KT EL A+ + I++ Sbjct: 70 NPMPAVVQHLAGLVDGFDVASGGELKTALDTSMPPHQISFAGPAKTPGELRQAIAAGIVI 129 Query: 127 FNVESRQELDVLNEIAGKLGKKARIAIRVNPDVDPKTHPYIATGMQKSKFGVDIREAQKE 186 N+ES +EL + LG + R+A+RVNPD + K+ +G K +FG+D E Sbjct: 130 -NLESERELRAAVQAGEALGIRPRVAVRVNPDFELKSAGMKMSGGPK-QFGID-AERVPA 186 Query: 187 YEYASKLENLEIVGIHCHIGSQILDISPYREAVEKVVSLYESLT-QKGFDIKYLDIGGGL 245 K +LE +G H G+Q L EA EK + L L ++ L++GGG Sbjct: 187 VLAEMKCLDLEFIGFHIFSGAQNLRAEAISEAQEKTLELAMRLALDVPSPVRALNLGGGF 246 Query: 246 GIKYKPEDKEPAPQDLADLLKDLLENVK-----AKIILEPGRSIMGNAGILITQVQFLKD 300 GI Y P + + + L +LL + ++I+E GR +G AG+ + +V K Sbjct: 247 GIPYFPGEPPLDLVAVGERLSELLPAARRALPDTELIIELGRFFVGEAGVYVCRVVERKV 306 Query: 301 KGSKHFIIVDAGMNDLIRPS------IYNAYHHIIPVETK-ERKKVVADIVGPICETGDF 353 + F++ D G++ + S I Y ++ + + A +VGP+C D Sbjct: 307 SRGQVFLVTDGGLHHHLAASGNFGQVIRKNYPVLVANRVESDGDPETASVVGPLCTPLDL 366 Query: 354 LALDREIEEVQRGEYLAVLSAGAYGFAMS-SHYNMRPRAAEVLV 396 LA + + G+ +AV+ +GAYG S + + P A EVLV Sbjct: 367 LADRMPLGHAREGDLVAVMQSGAYGLTASPTAFLGHPTAVEVLV 410 Lambda K H 0.317 0.139 0.392 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: 389 Number of extensions: 22 Number of successful extensions: 7 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: 420 Length of database: 410 Length adjustment: 31 Effective length of query: 389 Effective length of database: 379 Effective search space: 147431 Effective search space used: 147431 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