Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate WP_013646093.1 METBO_RS12525 amidohydrolase
Query= curated2:Q88V24 (384 letters) >NCBI__GCF_000191585.1:WP_013646093.1 Length = 417 Score = 157 bits (396), Expect = 7e-43 Identities = 118/381 (30%), Positives = 183/381 (48%), Gaps = 28/381 (7%) Query: 12 YQHLHQIPEIGLQEHETQAYLLSIIGKMPQEWLTIKTIPTLDTAILVKVSGLKHDYRIGY 71 +Q LHQ PE+ QE E+ Y+ S + + + L + P T I + G + Sbjct: 25 FQWLHQHPELAYQEFESGRYIASYLETL--DGLEV-IYPFAKTGIKAVLKGENSKNAVAI 81 Query: 72 RTDIDALPVTENTGLPFASTHPG--------VMHACGHDIHMSVALGILSYFAENRPAT- 122 R D DALPV E+TGL +AS G V H CGHD + A+G + + + Sbjct: 82 RADFDALPVKEDTGLSYASRSKGTYNGQETYVSHVCGHDASAATAMGTATVLNQLKDDLN 141 Query: 123 -DMVFMFQPAEENASGGQR-----LYESGALDGDWMPD--EIFAFHDNPNLPTGAIGCRM 174 D+VF+FQPAEE G + + GAL PD IFA H G + Sbjct: 142 GDVVFLFQPAEEGVPDGMKAGADLMVSEGALKN---PDVSAIFALHPYSKAYPGTVLLSK 198 Query: 175 GTLFAGTCEIHAHLSGKSGHAAYPHQANDMVVAGAALVSQLQTIVARNVDPIQ-SGVVTL 233 T AG ++ + G H + P D +VAGAA+++ LQTIV+R D ++ + VVT+ Sbjct: 199 NTTHAGLNDLVIKIKGVQAHGSMPWVGRDPIVAGAAIINSLQTIVSREADLMRGAAVVTV 258 Query: 234 GHFTAGTIGNVIAGEAQIDGTIRALTQEMNMHIQRRVRTITEGIALAYDCNIDLKLNQGG 293 G+F G N+I A++ TIRAL + + +RV IT+ ++ A+ C ++ + Q Sbjct: 259 GYFHGGIKVNIIPDHAEMGLTIRALDENNLKLLVKRVTEITKLVSKAHGCEAEIIMGQ-- 316 Query: 294 YYPVENNDA-ITADFIKYMQEDDDVNFIETEPAMTG-EDFGYLIHQIPGTMFWLGVDSPY 351 + P+ ND + + +K +++ + +PA TG EDF Y +++PG G Sbjct: 317 HDPMNKNDPDLCKNMLKTIRQVAGDGNMILKPATTGSEDFSYFSNKVPGLYLHFGTAPQN 376 Query: 352 SLHSENMVPHTAAIMSGVNAM 372 SE+ H M +A+ Sbjct: 377 KPLSESRPNHHPGFMVDDDAL 397 Lambda K H 0.320 0.136 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: 441 Number of extensions: 26 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: 384 Length of database: 417 Length adjustment: 31 Effective length of query: 353 Effective length of database: 386 Effective search space: 136258 Effective search space used: 136258 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