Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (uncharacterized)
to candidate Ga0059261_4188 Ga0059261_4188 pyridoxal-dependent decarboxylase, exosortase A system-associated
Query= curated2:O29458 (419 letters) >FitnessBrowser__Korea:Ga0059261_4188 Length = 407 Score = 142 bits (359), Expect = 1e-38 Identities = 122/377 (32%), Positives = 174/377 (46%), Gaps = 15/377 (3%) Query: 7 GILTVEGVKVTEIVRETGTPVYVTSRALLERNLEAYKKAFSNE-GLLYAVKANNNLALMR 65 G LT+ G + V E G+P++V ++ L + A + + +A+KAN + Sbjct: 15 GELTIAGRAAADWVAEAGSPLFVYDMGIVHERLRGLRAALPDACEIHFAIKANPLPEFIA 74 Query: 66 IIASHGFGADVFSDGELYLASLAGFRKDM--VLFNGNSKSRKEIEMGVTAGVKFSVDSLD 123 +A G DV S GEL A KD + F G K E+E + AG +++S Sbjct: 75 AVAPLVGGLDVASGGELAKALKV---KDAAHISFAGPGKRDAELEAAIVAGATLNLESEG 131 Query: 124 ELRTISKIAKEVGKEVEIAFRVNPDVDPKTHPKIATGLRESKFGIPHEMVREAYEMALKL 183 E I + +G +A RVNPD + + + G R S FG+ V A L Sbjct: 132 EAERALTIGRVLGTTPRLAVRVNPDFELRGSG-MKMGGRASPFGVDAARV-PALVNRLIA 189 Query: 184 DGVVPVGIHCHIGSQILDLSPFVHALNKVMDIAVDI-EKLGVELSFVDMGGGLGIDYEGK 242 G G H GSQ LD + + + +A + ++ GV V++GGG GI Y Sbjct: 190 AGADWRGFHIFAGSQSLDTAAIIETQAATVALAARLAQEAGVSPPLVNLGGGFGIPYFSG 249 Query: 243 GAPTPKDLASAILPEFEGRKADLTSDPQLWLEPGRSIVGNTTVLITRVNAVK-KGYKNFV 301 P D A L + + ++ + +E GR I G V + RV K G + F+ Sbjct: 250 DMPIDIDAVGAALGKTLESRQEILAQSGFAIELGRWIAGECGVYLMRVIDRKISGDETFL 309 Query: 302 AVDAGFN-VLIRPAMYGSYHR----VAVANKMDAEPEEVYTVVGPICESGDVLARDRKLP 356 D G + L +G+ R VAVA KMDAEP E +VVGP+C D LA LP Sbjct: 310 ICDGGLHHQLAASGNFGTVVRRNYPVAVAEKMDAEPVETVSVVGPLCTPLDRLADRVALP 369 Query: 357 KVEVGDLIAVFDAGAYG 373 + E GD+IAVF AGAYG Sbjct: 370 RTEPGDVIAVFLAGAYG 386 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: 390 Number of extensions: 18 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: 407 Length adjustment: 31 Effective length of query: 388 Effective length of database: 376 Effective search space: 145888 Effective search space used: 145888 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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