Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (uncharacterized)
to candidate WP_011879899.1 pyridoxal-dependent decarboxylase, exosortase A system-associated
Query= curated2:O29458 (419 letters) >NCBI__GCF_000016205.1:WP_011879899.1 Length = 402 Score = 155 bits (393), Expect = 2e-42 Identities = 127/402 (31%), Positives = 192/402 (47%), Gaps = 16/402 (3%) Query: 2 FSTSDGILTVEGVKVTEIVRETG-TPVYVTSRALLERNLEAYKKAF-SNEGLLYAVKANN 59 FS +GILTV GV + + G TP +V RA L+ + ++ + L Y+VKAN Sbjct: 5 FSEREGILTVGGVAINRLADRAGRTPFFVYDRATLDARVCMLRETLPTGIDLHYSVKANP 64 Query: 60 NLALMRIIASHGFGADVFSDGELYLASLAGFRKDMVLFNGNSKSRKEIEMGVTAGVKFSV 119 A++ +A G DV S E+ +A AG +++ F G KSR ++ V +GV + Sbjct: 65 LPAVVHHLAPQMDGFDVASANEMAVALNAGMPAELIGFAGPGKSRDDLRRAVASGVNIHL 124 Query: 120 DSLDELRTISKIAKEVGKEVEIAFRVNPDVDPKTHPKIATGLRESKFGIPHEMVREAYEM 179 +S+ +LR ++ + E+G + ++A RVNPD H + G S FG+ E V E Sbjct: 125 ESVTQLRLVTALGWELGVQPKVAIRVNPDFH-VDHSGMRMGGGASPFGLDAEQVPELLR- 182 Query: 180 ALKLDGVVPVGIHCHIGSQILDLSPFVHALNKVMDIAVDIE-KLGVELSFVDMGGGLGID 238 L V G H GSQ L +HA K D+ V + L V +V+ GGG GI Sbjct: 183 ELDARDVTLAGFHIFWGSQCLHAPTVIHAQRKSADLVVRLAGGLPVAPQYVNFGGGFGIP 242 Query: 239 YEGKGAPTPKDLASA--ILPEFEGRKADLTSDPQLWLEPGRSIVGNTTVLITRVNAVK-K 295 Y TP DLA+ + ++ G + LE GR +VG + + R+ K Sbjct: 243 Y--FAGETPLDLAAVADAMHDWLGVLRGRLPGTRTVLEFGRYLVGEAGIYVCRIIDRKIS 300 Query: 296 GYKNFVAVDAGF-NVLIRPAMYGSYHR----VAVANKMDAEPEEVYTVVGPICESGDVLA 350 + F+ D G + L +G R V + N+ P E +VG +C D +A Sbjct: 301 RDRTFLITDGGLHHHLAASGNFGQILRRNFPVTIGNRQTQAPTERCHIVGCLCTPLDRIA 360 Query: 351 RDRKLPKVEVGDLIAVFDAGAYGFVMSSQ-YNGRPRCAEVLV 391 D LP+ ++GD + VF +GAYG S + + G P E+LV Sbjct: 361 DDVLLPEAQIGDFVVVFQSGAYGRSASPRNFLGHPDAIEMLV 402 Lambda K H 0.318 0.137 0.395 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: 405 Number of extensions: 20 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: 419 Length of database: 402 Length adjustment: 31 Effective length of query: 388 Effective length of database: 371 Effective search space: 143948 Effective search space used: 143948 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 (21.7 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