Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate H281DRAFT_06512 H281DRAFT_06512 hippurate hydrolase
Query= curated2:B1YJ90 (370 letters) >FitnessBrowser__Burk376:H281DRAFT_06512 Length = 403 Score = 202 bits (514), Expect = 1e-56 Identities = 123/374 (32%), Positives = 194/374 (51%), Gaps = 13/374 (3%) Query: 6 EMRRELHKIPEPGFKEFKTQAFILDQIRSYPEDRVSYDTFETGVFVRVKGLTGNRTIGYR 65 ++RR+LH PE F+E +T + ++ + VS TGV + G+ + I R Sbjct: 20 KLRRDLHAYPELRFEEHRTADVVARELEEFGYT-VSRGLGGTGVVASLPGVNPHWGIVLR 78 Query: 66 ADIDGLPIEEATGLPFCSEHPGFMHACGHDVHASIALGLLRRIVELPVMDDVV-FLFQPA 124 AD+D LPI+EA S G MHACGHD H + LG R + +P + V F+FQP Sbjct: 79 ADMDALPIQEANDFTHASCTHGIMHACGHDGHTVMLLGAARILRGMPQLPGSVHFVFQPG 138 Query: 125 EEGPGGAEPMIKSPLFEKYRPSEMYGLHVAPEYPVGTIASRPGVLFASAREVHITIYGQS 184 EEG GA MI LF +Y ++G+H P P G R G + A+ IT+ G+ Sbjct: 139 EEGGAGARKMIDDGLFVQYPTEAVFGMHNWPSLPGGHFGLRVGPIMAAGSRFRITVTGKG 198 Query: 185 GHAAFPHLTIDTVVAQAALIMQLQTIVSRSINPMNCSVITIGKVDAGIRENVIAGRALLD 244 HAA PHL +D + ++++ QTI +R +P++ +VI++ + AG +NVI A L Sbjct: 199 AHAAQPHLGLDPIPLACSMVLHCQTIAARHKDPVDPAVISVCMIHAGDTDNVIPDSAELR 258 Query: 245 GTMRALNGTDMEKLEQRVRDIIRGIEASFGVKIDLQFGNRYYEVVNDQRVVDKFSSFVKM 304 GT+R L+ +KL++ ++ + G+ A+ G ++++ F Y +N + + ++ Sbjct: 259 GTIRTLSSELQQKLQRDIQLMCEGLAAAHGAQVEVTFFQYYPATINTRAETQLCEAVIRE 318 Query: 305 ----NANYIECDAAMTGEDFGFMLKEIPGMMFWLG---VNNATSGLHQPTLNPDEEAIP- 356 + + A MT EDFGFML+E PG +G V GLH P + +++ IP Sbjct: 319 TFGDERTHADVPANMTSEDFGFMLEERPGTYVLIGNAHVGETAPGLHNPKYDFNDDIIPA 378 Query: 357 ---FVINLLDHYFR 367 + I L YF+ Sbjct: 379 GVQYWITLAQQYFQ 392 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: 448 Number of extensions: 31 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: 403 Length adjustment: 30 Effective length of query: 340 Effective length of database: 373 Effective search space: 126820 Effective search space used: 126820 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