Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate WP_009545707.1 CCE_RS08990 amidohydrolase
Query= curated2:B7GIC0 (378 letters) >NCBI__GCF_000017845.1:WP_009545707.1 Length = 403 Score = 266 bits (679), Expect = 1e-75 Identities = 151/372 (40%), Positives = 213/372 (57%), Gaps = 10/372 (2%) Query: 3 VNIRRDLHQIPELGFQEFKTQQYILDYLATLPSERLQIKTWRTGILVRVHGTAPTKTIGY 62 V RR LHQ PELGFQE T +I L + + +TGI+ + + P + Sbjct: 28 VEWRRYLHQRPELGFQEEITATFIAQKLTEMGIPH-ETGIAKTGIVATIDSSYPGPILAI 86 Query: 63 RADMDGLPIDEQTDVPFRSTHEGRMHACGHDMHMAIALGVLTHVVHH--PIRDDMLFIFQ 120 RADMD LPI E+ +VP+RS HEG MHACGHD H IALG +++ H + + IFQ Sbjct: 87 RADMDALPIHEENEVPYRSLHEGTMHACGHDGHTTIALGTASYLWQHRQDFKGTVKIIFQ 146 Query: 121 PAEEGPGGALPMLESDEMKQWMPDMILALHIAPAYPVGTIATKEGLLFANTSELFIDLIG 180 PAEE PGGA PM+E+ +K D I+ LH+ P+GT+ + G L A +++ G Sbjct: 147 PAEESPGGAKPMIEAGVLKNPDVDGIIGLHLWNNLPLGTVGVRSGPLMAAVECFRLNIFG 206 Query: 181 KGGHAAFPHETKDMVVAASSLIMQLQTIVSRNVNPLDSAVITIGKLTSGTVQNVIAERAR 240 KGGH A PH+T D VV ++ ++ LQ+IVSRNVNP+DSAV+TIG+L +GT NVIA+ AR Sbjct: 207 KGGHGAMPHQTIDSVVVSAQIVNALQSIVSRNVNPIDSAVVTIGELHAGTALNVIADTAR 266 Query: 241 LEGTIRTLSPEAMEKVKGRIEAIVRGIEVAYDCQAHIDYGSMYYQVYNDETLTN--EFMQ 298 + GT+R +PE RIE IV+GI Y +DY +Y V N+ET+ + + Sbjct: 267 MSGTVRYFNPEFEGYFGQRIEEIVKGICQGYGADYELDYWRLYPPVINNETMAELVKSVA 326 Query: 299 FVEKETDVHLVRCQEAMTGEDFGYMLARIPGFMFWLG-VQSPFGL----HHAKLNPNEEA 353 ET + + M GED + L +PG F+LG + GL HH + + +E Sbjct: 327 LEVVETPAGIAPTCQTMGGEDMSFFLEEVPGCYFFLGSANAEKGLNYPHHHPRFDFDETV 386 Query: 354 IDVAIQLLTRYV 365 + + +++ R V Sbjct: 387 LPLGVEMFVRCV 398 Lambda K H 0.322 0.137 0.411 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: 423 Number of extensions: 18 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: 403 Length adjustment: 31 Effective length of query: 347 Effective length of database: 372 Effective search space: 129084 Effective search space used: 129084 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 10 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