Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate BWI76_RS16785 BWI76_RS16785 peptidase M20
Query= curated2:B7GIC0 (378 letters) >FitnessBrowser__Koxy:BWI76_RS16785 Length = 383 Score = 202 bits (513), Expect = 2e-56 Identities = 130/367 (35%), Positives = 182/367 (49%), Gaps = 10/367 (2%) Query: 6 RRDLHQIPELGFQEFKTQQYILDYLATLPSERLQIKTWRTGI-LVRVHGTAPTKTIGYRA 64 RRD H PELG+QE +T + + + LA+ LQ+ G +V P IG RA Sbjct: 15 RRDFHACPELGYQEQETSRRVAELLASFG---LQVHRGLAGTGVVATLENGPGPVIGLRA 71 Query: 65 DMDGLPIDEQTDVPFRSTHEGRMHACGHDMHMAIALGVLTHVVH-HPIRDDMLFIFQPAE 123 DMD LPI EQ+DV ++S + G MHACGHD H A+ L H+ R + F+FQPAE Sbjct: 72 DMDALPIAEQSDVGYKSRNPGVMHACGHDGHSAMLLATAAHLAQTRRFRGTVHFVFQPAE 131 Query: 124 EGPGGALPMLESDEMKQWMPDMILALHIAPAYPVGTIATKEGLLFANTSELFIDLIGKGG 183 E GGA M+E +++ D I ALH P P+G +A G + A+ I L GK Sbjct: 132 ENLGGARKMVEEGLFERFPMDAIYALHNWPGMPLGQVAIGSGAMMASLDAFEITLTGKSC 191 Query: 184 HAAFPHETKDMVVAASSLIMQLQTIVSRNVNPLDSAVITIGKLTSGTVQNVIAERARLEG 243 HAA P D +VAA+ LIM LQTI SR ++P +S V++I ++ G NV+ ++ L G Sbjct: 192 HAAMPERGADPIVAAAQLIMALQTIPSRRLSPQESTVVSITQIAGGEAINVLPDKVVLRG 251 Query: 244 TIRTLSPEAMEKVKGRIEAIVRGIEVAYDCQAHIDYGSMYYQVYNDETLTNEFMQFVEKE 303 T R L + +V+G IE+ V + + I + Y N + + Sbjct: 252 TFRCLDNQVRARVRGLIESYVAAQPQVSEVEGAIAWYPGYPVTTNHPAEAQKVREVATAL 311 Query: 304 TDVHLV--RCQEAMTGEDFGYMLARIPGFMFWLGVQSPFG---LHHAKLNPNEEAIDVAI 358 V +M EDF ML PG FW+G LH+A + N+E + + Sbjct: 312 LGESAVSWNGNPSMASEDFACMLEACPGAYFWIGADGETASKPLHNAGYDFNDELLPHGV 371 Query: 359 QLLTRYV 365 L T V Sbjct: 372 ALWTALV 378 Lambda K H 0.322 0.137 0.411 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: 371 Number of extensions: 24 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: 378 Length of database: 383 Length adjustment: 30 Effective length of query: 348 Effective length of database: 353 Effective search space: 122844 Effective search space used: 122844 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 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