Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate CA265_RS23900 CA265_RS23900 N-acyl-L-amino acid amidohydrolase
Query= curated2:B1YJ90 (370 letters) >FitnessBrowser__Pedo557:CA265_RS23900 Length = 394 Score = 205 bits (522), Expect = 1e-57 Identities = 125/366 (34%), Positives = 190/366 (51%), Gaps = 13/366 (3%) Query: 8 RRELHKIPEPGFKEFKTQAFILDQIRSYPEDRVSYDTFETGVFVRVKG-LTGNRTIGYRA 66 R+ +H PE FKEF+T FI D+++ + + D TGV +KG L ++ I RA Sbjct: 21 RQHIHANPELSFKEFETSLFIKDKLKKWGIEYT--DCANTGVVGLIKGNLPSDQVIALRA 78 Query: 67 DIDGLPIEEATGLPFCSEHPGFMHACGHDVHASIALGLLRRIVELP--VMDDVVFLFQPA 124 D+D LPI E P+ S++ G MHACGHDVH S LG + +L + +FQPA Sbjct: 79 DMDALPIHETNDKPYRSKNHGVMHACGHDVHTSSLLGTAHILNQLKDEFGGTIKLIFQPA 138 Query: 125 EEG-PGGAEPMIKSPLFEKYRPSEMYGLHVAPEYPVGTIASRPGVLFASAREVHITIYGQ 183 EE PGGA MIK + E +P+ + G HV P G + R G+ AS E+++T+ G+ Sbjct: 139 EELLPGGASIMIKEGVLENPKPNAIVGQHVMPLIDAGKVGFRSGIYMASTDELYVTVTGK 198 Query: 184 SGHAAFPHLTIDTVVAQAALIMQLQTIVSRSINPMNCSVITIGKVDAGIRENVIAGRALL 243 GH A PH ID V+ + +I+ LQ IVSR+ +P SV++ GKV A NVI + Sbjct: 199 GGHGAQPHQNIDPVLIASHIIVALQQIVSRNADPRLPSVLSFGKVIANGATNVIPNEVKI 258 Query: 244 DGTMRALNGTDMEKLEQRVRDIIRGIEASFGVKIDLQFGNRYYEVVNDQRVVDKFSSFVK 303 +GT R L+ ++ +R++ + G+ S G D Y ++N++++ +F + Sbjct: 259 EGTFRTLDENWRDEAHKRMKKMAEGMAESMGGSCDFDIHRGYPFLINEEKLTANARAFAE 318 Query: 304 ---MNANYIECDAAMTGEDFGFMLKEIPGMMFWLGVNNATS----GLHQPTLNPDEEAIP 356 N ++ D M EDF F + + LG NA +H P + DE+A+ Sbjct: 319 DFLGKENVVDLDIWMAAEDFSFYSQVTDACFYRLGTGNAAKDTQYSVHTPRFDIDEDALK 378 Query: 357 FVINLL 362 L+ Sbjct: 379 ISTGLM 384 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: 349 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: 394 Length adjustment: 30 Effective length of query: 340 Effective length of database: 364 Effective search space: 123760 Effective search space used: 123760 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