Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate RR42_RS07685 RR42_RS07685 amidohydrolase
Query= curated2:B1YJ90 (370 letters) >FitnessBrowser__Cup4G11:RR42_RS07685 Length = 396 Score = 203 bits (516), Expect = 7e-57 Identities = 124/359 (34%), Positives = 189/359 (52%), Gaps = 8/359 (2%) Query: 5 IEMRRELHKIPEPGFKEFKTQAFILDQIRSYPEDRVSYDTFETGVFVRVKGLTGNRTIGY 64 + +RR++H PE F+E +T + + + ++ + V TGV R++ G RT+G Sbjct: 24 VAIRRQIHAHPELAFEERRTGDLVAELLTAWGYE-VHRGLGTTGVVGRLRKGLGTRTLGI 82 Query: 65 RADIDGLPIEEATGLPFCSEHPGFMHACGHDVHASIALGLLRRIVELPVMDDVV-FLFQP 123 RAD+D LPI+E TGL + S PG MHACGHD H +I L R + E + + +FQP Sbjct: 83 RADMDALPIQEKTGLDYASTLPGKMHACGHDGHTAILLCAARYLAESVDFNGTLNLIFQP 142 Query: 124 AEEGPGGAEPMIKSPLFEKYRPSEMYGLHVAPEYPVGTIASRPGVLFASAREVHITIYGQ 183 AEE GGA M++ LFE++ E+Y LH AP PVG I G AS +T+ G+ Sbjct: 143 AEENEGGALRMLEDGLFERFPCDEIYALHNAPGLPVGQIGLIAGPAMASFDRATVTLTGR 202 Query: 184 SGHAAFPHLTIDTVVAQAALIMQLQTIVSRSINPMNCSVITIGKVDAGIRENVIAGRALL 243 S H A PH ID + A++++ LQ+IVSR I+ + +VIT+G + AG NV+ A + Sbjct: 203 SAHGAMPHHGIDVMQGAASMVLGLQSIVSREIDALKSAVITVGSIQAGATYNVVPESATI 262 Query: 244 DGTMRALNGTDMEKLEQRVRDIIRGIEASFGVKIDLQFGNRYYEVVNDQRVVDKFSSFVK 303 +RAL+ +E R+RD + SF ++ ++ + +Y +VN R ++ Sbjct: 263 KIGVRALDPKVRTYIETRLRDFVAAQAQSFQLQAEVVYERKYPVLVNHDRQTERAREVAV 322 Query: 304 M---NANYIECDAAMTGEDFGFMLKEIPGMMFWLGVNNATSG---LHQPTLNPDEEAIP 356 N + M EDF ML+ PG LG G +H P + ++ A+P Sbjct: 323 RLLGEDNVVSRGPVMGSEDFACMLEHRPGAYIRLGNGLGQDGGCMVHNPLYDFNDRALP 381 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: 377 Number of extensions: 15 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: 396 Length adjustment: 30 Effective length of query: 340 Effective length of database: 366 Effective search space: 124440 Effective search space used: 124440 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