Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate WP_041098343.1 SUTH_RS07745 M20 aminoacylase family protein
Query= curated2:Q836H7 (378 letters) >NCBI__GCF_000828635.1:WP_041098343.1 Length = 387 Score = 223 bits (568), Expect = 7e-63 Identities = 133/367 (36%), Positives = 196/367 (53%), Gaps = 12/367 (3%) Query: 8 ELIAIRRQLHQIPEIGLEEKETQAFLLNEIDKMKQPYLQVRTW--QTGILVFIEGKNPQK 65 ++ A RR +H PE+ +EK T + + +D + L+V +TG++ + + ++ Sbjct: 12 KIAAFRRDIHAHPELAFDEKRTATKVADYLDGLG---LEVHRGIARTGVVAKLSLGSGKR 68 Query: 66 TIGWRADIDGLPIQEEVVSAFQSKRPGFMHACGHDFHMTIGLGVLKELSQQQP-DNNFLF 124 IG RAD+D LP+ E +S G MHACGHD H + LG + LS+ + D F Sbjct: 69 AIGLRADMDALPLSELNSFPHRSTHHGKMHACGHDGHTAMLLGAAEALSRLRNFDGTVYF 128 Query: 125 LFQPAEENEAGGMLMYEDHAFGEWLPDEFYALHVNPDLPVGTISTRVGTLFAATCEVNIT 184 +FQPAEE+E GG +M E+ F + D + LH P LP G+ G + A I Sbjct: 129 IFQPAEEHEGGGRVMVEEGLFERFPMDMVFGLHNWPGLPAGSFGVTEGPVMAGADRFEIE 188 Query: 185 LKGKGGHAAFPHQANDMVLAATNLIQQAQTIVSRNVDPVVGAVVTFGTFHAGTACNVIAE 244 + G+GGHAA PHQA D+VLA ++L+Q Q++VSRN DP+ AVV+ FHAG A NV+ E Sbjct: 189 ITGRGGHAAMPHQAVDVVLAGSSLVQATQSLVSRNTDPLAAAVVSVTRFHAGHADNVLPE 248 Query: 245 EATLSGTIRTLTAETNEQTQRRIREISEGIAQSFQCEVTVHLDQKGYLPVVN--EPACTT 302 A L GT+RTL AE + + +R I GI +++ + + ++GY P VN EP+ Sbjct: 249 TAVLGGTVRTLKAELQDALEEGLRRICNGIEATYRVSIDLRY-ERGYPPTVNAPEPSFIA 307 Query: 303 NFIEYMSKQATVQFQQAPVAMTGEDFGYLLSKVPGTMFWLGVA---SPYSLHSAKFEPNE 359 + + F +M EDF YL VP WLG LHS ++ N+ Sbjct: 308 REVARQVAEEGQVFTHLNPSMGAEDFAYLARVVPACYVWLGNGPGEGGCMLHSPHYDFND 367 Query: 360 EALLFGV 366 E + G+ Sbjct: 368 EVIATGI 374 Lambda K H 0.319 0.135 0.398 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: 367 Number of extensions: 24 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: 378 Length of database: 387 Length adjustment: 30 Effective length of query: 348 Effective length of database: 357 Effective search space: 124236 Effective search space used: 124236 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 (21.8 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