Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (characterized)
to candidate WP_008804517.1 KVAR_RS10890 amidohydrolase
Query= SwissProt::D5E0A1 (375 letters) >NCBI__GCF_000025465.1:WP_008804517.1 Length = 385 Score = 211 bits (536), Expect = 4e-59 Identities = 132/367 (35%), Positives = 192/367 (52%), Gaps = 10/367 (2%) Query: 5 EFVKIRRELHKIPELGFQEVKTQRFLLDYINTLPQERLEVKTWKTGLFVKVHGTN-PTKT 63 E V RRE H PELG+QE +T R + + + + L+V G V N P Sbjct: 10 EAVGWRREFHAAPELGYQEQETSRRVAELLASFG---LQVHRGLAGTGVVATLENGPGPV 66 Query: 64 IGYRADIDGLPITEETNYSFQSQHEGLMHACGHDMHMAIGLGVLTYFAQ-HEIKDNVLFI 122 IG RAD+D LPITE + S++S+ G+MHACGHD H A+ L + AQ + V F+ Sbjct: 67 IGLRADMDALPITELGSVSYRSRRPGVMHACGHDGHTAMLLAAAAHLAQTRQFSGTVHFV 126 Query: 123 FQPAEEGPGGAQPMLQSDIMKEWLPDFIFALHVAPEYPVGSIALKEGLLFANTSELFIDL 182 FQPAEE GGA+ M++ + + + D I+ALH P P+G +AL +G + A+ I L Sbjct: 127 FQPAEENLGGARKMVEEGLFERFPMDAIYALHNWPGIPLGEVALSDGAMMASLDAFEITL 186 Query: 183 KGKGGHAAYPHTTNDMVVAACQLVSQLQTIVARNVDPLDSAVITVGKIQGGTVQNIIAER 242 +GK HAA P + D +VAA QL+ LQTI +R + P DSAV+++ +I GG N++ + Sbjct: 187 RGKSCHAAMPESGADPIVAAAQLIMALQTIPSRRLSPQDSAVVSITQINGGEAINVLPDT 246 Query: 243 ARIEGTIRTLSPESMTRVKERIEAIVKGVEVGYQCETAIDYGCMYHQVYNHHEVTREFME 302 + GT R LS RV+E IE+ V + I + Y NH ++ E Sbjct: 247 VVLRGTFRCLSNRVRARVRELIESYVATQPQVSDVQGEISWFPGYPVTKNHALQAQQVRE 306 Query: 303 FAKEQTDVDVIECKEA--MTGEDFGYMLKDIPGFMFWLGVQSE---YGLHHAKLQPHEGA 357 A + + +A M EDF ML+ PG FW+G E LH+A ++ Sbjct: 307 VAVATLGAEAVRWNQAPSMASEDFACMLEACPGAYFWIGTDGETPSKPLHNASYDFNDAL 366 Query: 358 IDIAISL 364 I +++ Sbjct: 367 ISPGVAM 373 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: 358 Number of extensions: 14 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: 375 Length of database: 385 Length adjustment: 30 Effective length of query: 345 Effective length of database: 355 Effective search space: 122475 Effective search space used: 122475 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