Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (characterized)
to candidate WP_011034159.1 MM_RS11540 amidohydrolase
Query= SwissProt::D5E0A1 (375 letters) >NCBI__GCF_000007065.1:WP_011034159.1 Length = 428 Score = 153 bits (387), Expect = 7e-42 Identities = 112/358 (31%), Positives = 171/358 (47%), Gaps = 23/358 (6%) Query: 3 ENEFVKIRRELHKIPELGFQEVKTQRFLLDYINTLPQERLEVKTWKTGLFVKVHGTNPTK 62 E+ +++RRE HK PEL F+E +TQ+ +L + L E ++ TG+ + GT Sbjct: 20 ESWIIRLRREFHKYPELSFKEYETQKRILKILGELGIEGRKIAD--TGVLASIRGTMSGP 77 Query: 63 TIGYRADIDGLPITEET---NYSFQSQHEGLMHACGHDMHMAIGLGVLTYFAQH-EIKDN 118 I R D DGL + EE N + S+ EG+MHACGHD HMA+ G F ++ E Sbjct: 78 CIALRTDTDGLQVQEEPAERNREYISRTEGVMHACGHDGHMAMLFGAARMFMENREFPGE 137 Query: 119 VLFIFQPAEEGPGGAQPMLQSDIMKEWLPDFIFALHVAPEYPVGSIALKEGLLFANTSEL 178 V IFQPAEE P G + ++ E + D I +H+ + GS+ + G A+T+ Sbjct: 138 VRLIFQPAEEIPPGGSERVIAEGGLEGV-DAIIGMHIFTNHESGSVGFRPGPFMASTNRF 196 Query: 179 FIDLKGKGGHAAYPHTTNDMVVAACQLVSQLQTIVARNVDPLDSAVITVGKIQGGTVQNI 238 + LKGKGGH + P D V A ++ L + + +D + V+ VG+IQGG N Sbjct: 197 EVILKGKGGHISLPAKCIDPVRMAVDFINSLNSALEERLDK-EKYVLGVGRIQGGAQFNR 255 Query: 239 IAERARIEGTIRTLSPESM----TRVKERIEAIVK-----GVEVG----YQCETAIDYGC 285 + I G+ RT E+ +KE +E I + G E Y+ + Y Sbjct: 256 TPDNVGILGSYRTFDSETTDIIDATIKECLEKIKQEYLKHGEEFSGLPDYELDILHGYPV 315 Query: 286 MYHQVYNHHEVTREFMEFAKEQTDVDVIECKEAMTGEDFGYMLKDIPGFMFWLGVQSE 343 + + + V + E E T IE + EDF L+ +PG LG +++ Sbjct: 316 LVNDPFFTEAVNLKLHESFPELTVYPEIE--KTFAAEDFASYLQVVPGVFISLGTRNQ 371 Lambda K H 0.320 0.137 0.410 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: 449 Number of extensions: 24 Number of successful extensions: 7 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: 375 Length of database: 428 Length adjustment: 31 Effective length of query: 344 Effective length of database: 397 Effective search space: 136568 Effective search space used: 136568 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 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