Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate Ac3H11_3202 Metal-dependent amidase/aminoacylase/carboxypeptidase
Query= curated2:B1YJ90 (370 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3202 Length = 397 Score = 206 bits (523), Expect = 1e-57 Identities = 125/345 (36%), Positives = 182/345 (52%), Gaps = 7/345 (2%) Query: 7 MRRELHKIPEPGFKEFKTQAFILDQIRSYPEDRVSYDTFETGVFVRVKGLTGNRTIGYRA 66 +RR+LH+ PE F+E +T A + +++ + V+ TGV ++ G++ +G RA Sbjct: 30 LRRDLHEHPELSFQEHRTSAIVAERLAHWGYS-VTTGIAGTGVVGTLRKGQGSKALGIRA 88 Query: 67 DIDGLPIEEATGLPFCSEHPGFMHACGHDVHASIALGLLRRIVELPVMDDVV-FLFQPAE 125 D+D LPI EATGLP+ S + G MHACGHD H ++ L R + E D + +FQPAE Sbjct: 89 DMDALPITEATGLPYASRNAGVMHACGHDGHTTVLLAAARFLAESGRFDGTLNLIFQPAE 148 Query: 126 EGPGGAEPMIKSPLFEKYRPSEMYGLHVAPEYPVGTIASRPGVLFASAREVHITIYGQSG 185 E GGA MI LFE++ ++GLH P G G AS ++ IT+ G+ G Sbjct: 149 EHGGGANRMIGEGLFERFPCDAVFGLHNWPCVGEGHFGCVTGPAMASVDQITITVRGKGG 208 Query: 186 HAAFPHLTIDTVVAQAALIMQLQTIVSRSINPMNCSVITIGKVDAGIRENVIAGRALLDG 245 H A PH T+D VVA A +I LQT+VSR+++P++ V+T+G + G NV+ L Sbjct: 209 HGAAPHETVDPVVASAHIITALQTVVSRNVDPLDMGVVTVGSIHGGNAPNVVPESVELKL 268 Query: 246 TMRALNGTDMEKLEQRVRDIIRGIEASFGVKIDLQFGNRYYEVVNDQRVVDKFSSFVKMN 305 T RA E L+QR+ I R SFG ++ + Y V+N + + S + Sbjct: 269 TARAFKPEVREILKQRIPAIARAQAESFGATAEVLYLPGYPAVLNHEAETELARSVARDT 328 Query: 306 ANYIECDAAM----TGEDFGFMLKEIPGMMFWLGVNNATSGLHQP 346 DA EDF FML + PG ++G N + LH P Sbjct: 329 FGDARVDAGFRPRTASEDFAFMLLKRPGSYVFVG-NGDGASLHSP 372 Lambda K H 0.323 0.140 0.417 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: 404 Number of extensions: 23 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: 370 Length of database: 397 Length adjustment: 30 Effective length of query: 340 Effective length of database: 367 Effective search space: 124780 Effective search space used: 124780 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