Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate AO353_28160 AO353_28160 amidohydrolase
Query= curated2:B1YJ90 (370 letters) >FitnessBrowser__pseudo3_N2E3:AO353_28160 Length = 391 Score = 218 bits (556), Expect = 2e-61 Identities = 126/338 (37%), Positives = 192/338 (56%), Gaps = 12/338 (3%) Query: 6 EMRRELHKIPEPGFKEFKTQAFILDQIRSYPEDRVSYDTFETGVFVRVKGLTGNRTIGYR 65 E+R LH PE G++E +T + +++ + V+ ET V +K T R +G R Sbjct: 17 ELRHHLHANPELGYQEVETSELVAERLTRWGY-AVTRGYAETAVIATLKKGTSPRVLGIR 75 Query: 66 ADIDGLPIEEATGLPFCSEHPGFMHACGHDVHASIALGLLRRIVELPVMDDVVFL-FQPA 124 AD+D LPI E TGLP+ S PG MHACGHD H + L + D V L FQPA Sbjct: 76 ADMDALPILEKTGLPYASRIPGKMHACGHDGHTVMLLAAAYALAHGHPFDGTVHLIFQPA 135 Query: 125 EEGPGGAEPMIKSPLFEKYRPSEMYGLHVAPEYPVGTIASRPGVLFASAREVHITIYGQS 184 EEG GA MI+ + +K+ ++ H P YPVG + R G ASA +V++TI+G+ Sbjct: 136 EEGLAGARRMIQEGVLQKFPCDAVFAAHNMPGYPVGKLGFRAGPFMASADQVNVTIHGKG 195 Query: 185 GHAAFPHLTIDTVVAQAALIMQLQTIVSRSINPMNCSVITIGKVDAGIRENVIAGRALLD 244 GH A PHL++D VV A++IM LQTIVSR+++P + SVIT+G ++AG NVI A + Sbjct: 196 GHGAMPHLSVDPVVVCASIIMALQTIVSRNVSPQDMSVITVGAINAGKASNVIPDSAHML 255 Query: 245 GTMRALNGTDMEKLEQRVRDIIRGIEASFGVKIDLQFGNRYYEVVNDQRVVDKFSSFVKM 304 ++R+LN ++LE +++ +I +FG ++ + Y +VND+ + +F+S V + Sbjct: 256 MSVRSLNNAVRDRLESQIKRLIHAQAEAFGATAEIHYSADYPLLVNDEEMT-RFASQVAI 314 Query: 305 NANYIECDAAMT-------GEDFGFMLKEIPGMMFWLG 335 +++ D M EDF + L++ PG +G Sbjct: 315 --DWLGEDEVMRDIVPFNGSEDFAYFLQQCPGCYLIIG 350 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: 355 Number of extensions: 18 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: 391 Length adjustment: 30 Effective length of query: 340 Effective length of database: 361 Effective search space: 122740 Effective search space used: 122740 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