Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (uncharacterized)
to candidate WP_041379088.1 SWIT_RS07570 diaminopimelate decarboxylase
Query= curated2:O29458 (419 letters) >NCBI__GCF_000016765.1:WP_041379088.1 Length = 402 Score = 128 bits (321), Expect = 4e-34 Identities = 120/402 (29%), Positives = 184/402 (45%), Gaps = 34/402 (8%) Query: 7 GILTVEGVKVTEIVRETGTPVYVTSRALLERNLEAYKKAFSNEG----LLYAVKANNNLA 62 G L G V + R P++V + NL + A G + YA+K N Sbjct: 18 GRLIFAGADVETLARAHDGPLFVYGAGRVRANLNRLRGALGASGCAHRIYYAMKCNRFAP 77 Query: 63 LMRIIASHG-FGADVFSDGELYLASLAGFRKDMVLFNGNSKSRKEIE-MGVTAGVKFSVD 120 L+ ++A+ G G D+ S EL LA GFR + F G S + ++++ + V + + D Sbjct: 78 LLEMLAADGAVGVDICSPDELDLALACGFRAGDISFTGTSVADRDLDRLLVHDDLHINCD 137 Query: 121 SLDELRTISKIAKEVGKEVEIAFRVNPDVDPKTHPKIA---TGLRESKFGIPHEMVREAY 177 SL ++R I + + G+ + I R+NP G R +KFGI E EA Sbjct: 138 SLGQIRRIGE--RRPGRAIGI--RINPGFGTGYGDSARLTYAGARTTKFGIYREQWAEAL 193 Query: 178 EMALKLDGVVPVGIHCHIGSQILD--LSPFVHALNKVMDIAVDIEKLGVELSFVDMGGGL 235 +A + D + IH H+G L L + A+ D D+ E + V++GGGL Sbjct: 194 GLAARHDLRI-TAIHFHVGCGYLSGQLDAWDRAVGAAADFLADLP----EATTVNIGGGL 248 Query: 236 GIDYEGKGAPTPKDLA---SAILPEFEGRKADLTSDPQLWLEPGRSIVGNTTVLITRVNA 292 G+ + AP DLA S + F GR + +EPG +V + +L+ V Sbjct: 249 GLPHRAGDAPL--DLARWSSIVARHFGGRGLTVA------IEPGDYLVKDAGLLLLSVVG 300 Query: 293 VKKGYKN-FVAVDAGFNVLIRPAMYGSYHRVAVANKMDAEPE--EVYTVVGPICESGDVL 349 V++ FVAVD GFN+ PA Y + +P + +V G I E+ D+ Sbjct: 301 VERKRDTLFVAVDGGFNLHPEPAHYDLPCEPVACVLREPDPARWQPVSVAGNINEALDLW 360 Query: 350 ARDRKLPKVEVGDLIAVFDAGAYGFVMSSQYNGRPRCAEVLV 391 A D +P +E GD +A+ +AG YG MSS + R E+LV Sbjct: 361 AEDHPMPPLEEGDHVALINAGGYGSAMSSNHCMRGAFTELLV 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: 398 Number of extensions: 26 Number of successful extensions: 4 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