Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate Ac3H11_2048 Catalyzes the cleavage of p-aminobenzoyl-glutamate to p-aminobenzoate and glutamate, subunit A
Query= curated2:Q836H7 (378 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2048 Length = 405 Score = 187 bits (474), Expect = 6e-52 Identities = 120/368 (32%), Positives = 186/368 (50%), Gaps = 11/368 (2%) Query: 8 ELIAIRRQLHQIPEIGLEEKETQAFLLNEIDKMKQPYLQVRTWQTGILVFIEGKNPQK-- 65 EL A+RR LH PE+G EE T + + + +TG++ I G++ Sbjct: 22 ELTALRRDLHAHPELGFEEVYTSKRVKEALTLCGVDEIHDGIGRTGVVGVIRGRSTSSGS 81 Query: 66 TIGWRADIDGLPIQEEVVSAFQSKRPGFMHACGHDFHMTIGLGVLKELSQQQP-DNNFLF 124 +G RAD+D LP+ E +++S +PG MH CGHD H + +G + L++ + D + Sbjct: 82 MVGLRADMDALPLAEHNDFSWKSCKPGLMHGCGHDGHTAMLVGAARYLAETRNFDGTAVL 141 Query: 125 LFQPAEENEAGGMLMYEDHAFGEWLPDEFYALHVNPDLPVGTISTRVGTLFAATCEVNIT 184 +FQP EE AG +M ED F + YA+H P + GT+ G + AA I Sbjct: 142 VFQPGEEGFAGARVMMEDGLFDRFPVQSIYAMHNWPAMKPGTVGINAGPMMAAADRFTIE 201 Query: 185 LKGKGGHAAFPHQANDMVLAATNLIQQAQTIVSRNVDPVVGAVVTFGTFHAGT--ACNVI 242 + G+GGH A +Q D+++ A ++I AQ+IVSRNV P+ AVV+ AG A +V+ Sbjct: 202 ITGRGGHGAHAYQTVDVLVVAAHIITAAQSIVSRNVRPIESAVVSICAAQAGDLGAFSVL 261 Query: 243 AEEATLSGTIRTLTAETNEQTQRRIREISEGIAQSFQCEVTVHLDQKGYLPVVN--EPAC 300 ATL GT+RT E ++R++E+ IA F TVH ++ Y +N A Sbjct: 262 PGSATLVGTVRTFDPVVQEMVEKRLKELCNAIALGFGATATVHY-ERIYPATINSESEAI 320 Query: 301 TTNFIEYMSKQATVQFQQAPVAMTGEDFGYLLSKVPGTMFWLGV---ASPYSLHSAKFEP 357 + A + +M EDF ++L PG LG AS +LH+++++ Sbjct: 321 FAGDVAESLLGADHVVRDLEPSMGAEDFAFMLQTRPGAYLRLGQGTGASGSALHNSRYDF 380 Query: 358 NEEALLFG 365 N++ L G Sbjct: 381 NDDILPLG 388 Lambda K H 0.319 0.135 0.398 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: 360 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: 378 Length of database: 405 Length adjustment: 31 Effective length of query: 347 Effective length of database: 374 Effective search space: 129778 Effective search space used: 129778 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 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