Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (uncharacterized)
to candidate BPHYT_RS00645 BPHYT_RS00645 diaminopimelate decarboxylase
Query= curated2:P19572 (415 letters) >FitnessBrowser__BFirm:BPHYT_RS00645 Length = 402 Score = 146 bits (368), Expect = 1e-39 Identities = 122/388 (31%), Positives = 191/388 (49%), Gaps = 27/388 (6%) Query: 3 TFSYRDAELFAEGVALSRIAERFG-TPTYVYSRAHIEAQYRAYADALAGMPHLVCFAVKA 61 TF R L G+ + ++A+R G TP + Y R+ I+ + R L L +++KA Sbjct: 4 TFLQRPPGLQFNGIDVRQLADRAGQTPFFAYDRSAIDTRVRELRSLLPSAMQLH-YSIKA 62 Query: 62 NSNLGVLNVLARLGAGFDIVSRGELERVLAAGGDPAKVVFSGVGKTRDDMRRALEVGVHC 121 N V++ LA+ GFD+ S E+ L AG P + F+G GK+ DD+RRA+ GV+ Sbjct: 63 NPMPAVIHYLAQRVDGFDVASAQEMALALDAGATPDSIGFAGPGKSHDDLRRAVASGVN- 121 Query: 122 FNVESGEELERLQRVAAELGVKAPVSLRVNPDVDAQTHPYISTGLKENKFGIAIDEAEAV 181 +VES +L + + ELGV+ V +R+NPD H + G FG+ +D+ A+ Sbjct: 122 VHVESDTQLRLVTALGWELGVQPNVVIRINPDFQV-GHSGMRMGGSAAPFGVDVDQIPAL 180 Query: 182 YARAAELDHLEVIGVDCHI--GSQLTQLEPFLDALERLLGLVDRLAGK-GIGIRHLDLGG 238 EL+ EV H+ GSQ ++A + + L+ RLA +R ++LGG Sbjct: 181 ---LHELETREVALAGFHVFWGSQCLHASTIIEAQRQSVDLILRLASDLPRPLRFVNLGG 237 Query: 239 GLGVRYRDEQPPL--------AGDYIRAIRERLHGRDLTLVFEPGRSIVANAGVLLTRVE 290 G G+ Y + PL D++ + ERL G T + E GR +V AG+ + RV Sbjct: 238 GFGIPYFPGETPLDTKVVCEAMHDWLPRLCERLPG--TTPILELGRYLVGEAGIYVCRVI 295 Query: 291 YLKHTEHKDFAIVDAAMNDLIRPA------LYQAWMDVQAVRPRDAAPRRYDLVGPICET 344 K + + F I D ++ + + L + + V RP + R +VG +C Sbjct: 296 DRKVSRGRTFVITDGGLHHHLAASGNFGQVLRRNFPVVIGNRPDGISRERCYVVGCLCTP 355 Query: 345 GDFLAKDRDLALAE-GDLLAVRSAGAYG 371 D LA D +L A GD + V+ +GAYG Sbjct: 356 LDRLADDVELPEAHIGDFVVVKQSGAYG 383 Lambda K H 0.321 0.139 0.400 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: 382 Number of extensions: 22 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: 415 Length of database: 402 Length adjustment: 31 Effective length of query: 384 Effective length of database: 371 Effective search space: 142464 Effective search space used: 142464 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 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 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