Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate AO353_29020 AO353_29020 amidohydrolase
Query= curated2:B1YJ90 (370 letters) >FitnessBrowser__pseudo3_N2E3:AO353_29020 Length = 389 Score = 211 bits (538), Expect = 2e-59 Identities = 130/364 (35%), Positives = 200/364 (54%), Gaps = 19/364 (5%) Query: 5 IEMRRELHKIPEPGFKEFKTQAFILDQIRSYPEDRVSYDTFETGVFVRVKGLTGNRTIGY 64 I +R+ +H PE GF+EF T + + + D VS +TGV +K G R++G Sbjct: 18 ITLRQRIHAHPELGFEEFSTSELVAQCLTQWGYD-VSTGVGKTGVVGTLKNGEG-RSLGL 75 Query: 65 RADIDGLPIEEATGLPFCSEHPGFMHACGHDVHASIALGLLRRIVELPVMDDVVFL-FQP 123 RAD+D LPI+EATGLP+ S G MHACGHD H + L + + + + + L FQP Sbjct: 76 RADMDALPIQEATGLPYASRIDGVMHACGHDGHTATLLAAAKYLAQTREFNGTLNLVFQP 135 Query: 124 AEEGPGGAEPMIKSPLFEKYRPSEMYGLHVAPEYPVGTIASRPGVLFASAREVHITIYGQ 183 AEEG GGA+ M++ LFE++ ++ +H P YP G + G ASA V I + G Sbjct: 136 AEEGLGGAKKMLEDGLFERFPCDAIFAMHNIPGYPAGQLGFYSGPFMASADTVTIKVIGT 195 Query: 184 SGHAAFPHLTIDTVVAQAALIMQLQTIVSRSINPMNCSVITIGKVDAGIRENVIAGRALL 243 GH A PH ++D VV A++++ LQ+IVSR++NP ++IT+G + AG NVI A + Sbjct: 196 GGHGAVPHKSVDPVVVCASIVIALQSIVSRNVNPQETAIITVGSIHAGNVSNVIPASAEM 255 Query: 244 DGTMRALNGTDMEKLEQRVRDIIRGIEASFGVKIDLQFGNRYYEVVNDQRVVDKFSSFVK 303 ++RAL + LE+R+ D++ G ASFG + ++ + + ++ND + ++F + Sbjct: 256 ILSVRALTPEVRQLLERRITDLVNGQAASFGAQAEIDYYRCHPVLIND----PEQTAFAR 311 Query: 304 MNA-------NYIECDAAMT-GEDFGFMLKEIPGMMFWLGVNNATSG---LHQPTLNPDE 352 A IE T EDF F+L++ PG +G N G LH P + ++ Sbjct: 312 QVAREWLGEGQLIEDLRPFTASEDFAFILEQCPGSYLVIG-NGQGEGSCLLHNPGYDFND 370 Query: 353 EAIP 356 +P Sbjct: 371 ACLP 374 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: 395 Number of extensions: 22 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: 389 Length adjustment: 30 Effective length of query: 340 Effective length of database: 359 Effective search space: 122060 Effective search space used: 122060 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