Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (characterized)
to candidate WP_025273184.1 HALAL_RS0106245 amidohydrolase
Query= SwissProt::D5E0A1 (375 letters) >NCBI__GCF_000527155.1:WP_025273184.1 Length = 407 Score = 169 bits (429), Expect = 1e-46 Identities = 103/344 (29%), Positives = 165/344 (47%), Gaps = 9/344 (2%) Query: 3 ENEFVKIRRELHKIPELGFQEVKTQRFLLDYINTLPQERLEVKTWKTGLFVKVHGTNPTK 62 ++E V +RR LH+ PE+G +TQ +L I+ LP + + + + + G P Sbjct: 11 QDELVDLRRRLHREPEVGLNLPRTQEKVLQSISDLPLN-ISLGNDLSSVTAVLKGNQPGP 69 Query: 63 TIGYRADIDGLPITEETNYSFQSQHEGLMHACGHDMHMAIGLGVLTYFAQH--EIKDNVL 120 T+ R D+D LP+TE T S+ + + MHACGHD+H A+ G A+ ++ +V+ Sbjct: 70 TVLLRGDMDALPVTERTGASYAASSDR-MHACGHDLHTAMLSGAARLLAEKVDSLRGDVI 128 Query: 121 FIFQPAEEGPGGAQPMLQSDIMKEW--LPDFIFALHVAPEY-PVGSIALKEGLLFANTSE 177 F+FQP EEG GA ML+ ++ P +ALHV P G + G + + + E Sbjct: 129 FMFQPGEEGYDGAGHMLREGVLDATGDKPVAAYALHVTSAIIPGGLFVTRHGPIMSASDE 188 Query: 178 LFIDLKGKGGHAAYPHTTNDMVVAACQLVSQLQTIVARNVDPLDSAVITVGKIQGGTVQN 237 +++ ++G GGH + PH D + AC++V LQ++V R D D V+TVG GGT N Sbjct: 189 MYVTVRGAGGHGSMPHLARDPMPGACEMVLALQSMVTRRFDIHDPVVLTVGSFHGGTASN 248 Query: 238 IIAERARIEGTIRTLSPESMTRVKERIEAIVKGVEVGYQCETAIDYGCMYHQVYNHHEVT 297 +I + + TIRT S + K+ ++K + + DY Y N Sbjct: 249 VITDEVTFKATIRTYSKAARATAKDECARVIKNLAAAHGLSVDFDYDENYPVTVNSDSEA 308 Query: 298 REFMEFAKEQTDVDVIECK--EAMTGEDFGYMLKDIPGFMFWLG 339 +E + EDF ++ ++PG LG Sbjct: 309 DFVANSVRENLGEERFHWSPHPFPGSEDFSRVIGEVPGAFTMLG 352 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: 374 Number of extensions: 22 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: 375 Length of database: 407 Length adjustment: 31 Effective length of query: 344 Effective length of database: 376 Effective search space: 129344 Effective search space used: 129344 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