Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate WP_051243215.1 H537_RS0124680 amidohydrolase
Query= curated2:B1YJ90 (370 letters) >NCBI__GCF_000430725.1:WP_051243215.1 Length = 390 Score = 222 bits (566), Expect = 1e-62 Identities = 129/359 (35%), Positives = 205/359 (57%), Gaps = 9/359 (2%) Query: 5 IEMRRELHKIPEPGFKEFKTQAFILDQIRSYPEDRVSYDTFETGVFVRVKGLTGNRTIGY 64 + +RR++H+ PE GF+E +T A + ++++++ +V TGV +++ R +G Sbjct: 15 VRLRRDIHRHPELGFEENRTSALVAEKLQAWGY-QVERGLGGTGVVGQLRRGGSARRLGL 73 Query: 65 RADIDGLPIEEATGLPFCSEHPGFMHACGHDVHASIALGLLRRIVELPVMDDVVFLFQPA 124 RAD+D LPI+EATGL S PG MHACGHD H ++ L R + + +FQPA Sbjct: 74 RADMDALPIQEATGLAHASCRPGLMHACGHDGHTAMLLAAARLLAATDFDGTLNLVFQPA 133 Query: 125 EEGPGGAEPMIKSPLFEKYRPSEMYGLHVAPEYPVGTIASRPGVLFASAREVHITIYGQS 184 EE GGA MI+ LF+KY ++ +H P G + R G + AS+ V IT++G Sbjct: 134 EESLGGAVRMIEDGLFDKYPCDAIFSMHNMPGIAQGRLVLREGAMMASSDYVTITLHGTG 193 Query: 185 GHAAFPHLTIDTVVAQAALIMQLQTIVSRSINPMNCSVITIGKVDAGIRENVIAGRALLD 244 GH A PH T D +VA A+++M LQ+IV+R+++P+ +V+T+G V AG NVI +A L+ Sbjct: 194 GHGAMPHHTADPIVAAASIVMALQSIVARNVDPLQTAVVTVGAVHAGQANNVIPQQARLE 253 Query: 245 GTMRALNGTDMEKLEQRVRDIIRGIEASFGVKIDLQFGNRYYEVVND--QRVVDKFSSFV 302 ++RAL+ L+QR+RD++ S+GV+ ++ + + Y +VND Q + + + Sbjct: 254 LSVRALDREVRALLQQRIRDLVTAQAQSYGVRAEIDYRSGYTVLVNDAAQTALAREVALE 313 Query: 303 KMNANYIECDA-AMTG-EDFGFMLKEIPGMMFWLGVNNATSG--LHQP--TLNPDEEAI 355 + +E +TG EDF FML+ +PG +G + +H P N D AI Sbjct: 314 LLGPQRVELQGPPLTGSEDFAFMLERVPGSYVLIGNGDGQGNCMVHNPGYDFNDDNIAI 372 Lambda K H 0.323 0.140 0.417 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: 384 Number of extensions: 17 Number of successful extensions: 3 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: 370 Length of database: 390 Length adjustment: 30 Effective length of query: 340 Effective length of database: 360 Effective search space: 122400 Effective search space used: 122400 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 (21.9 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