Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate Synpcc7942_0256 Synpcc7942_0256 Peptidase M20D, amidohydrolase
Query= curated2:B7GIC0 (378 letters) >FitnessBrowser__SynE:Synpcc7942_0256 Length = 408 Score = 243 bits (619), Expect = 9e-69 Identities = 143/368 (38%), Positives = 204/368 (55%), Gaps = 9/368 (2%) Query: 6 RRDLHQIPELGFQEFKTQQYILDYLATLPSERLQIKTWRTGILVRVHGTAPTKTIGYRAD 65 R+ LH+ PELGFQE +T +I L L Q TGI+ + G T+ RAD Sbjct: 37 RQQLHRRPELGFQEQETAAFIAARLTEL-GVSFQAGVAGTGIVAEIAGQRSGPTLAIRAD 95 Query: 66 MDGLPIDEQTDVPFRSTHEGRMHACGHDMHMAIALGVLTHV-VHHPIRDDMLFIFQPAEE 124 MD LPI E ++P+RS +GRMHACGHD H+AIALG + + + IFQPAEE Sbjct: 96 MDALPILEANEIPYRSEIDGRMHACGHDGHVAIALGTAACLQANSDFAGRVKIIFQPAEE 155 Query: 125 GPGGALPMLESDEMKQWMPDMILALHIAPAYPVGTIATKEGLLFANTSELFIDLIGKGGH 184 GPGGA PM+ ++ D I+ LH+ P+G + + G L A + + G+GGH Sbjct: 156 GPGGAAPMIAEGVLENPAVDAIIGLHLWNYLPLGKVGVRSGPLMAAVELFDLTIQGRGGH 215 Query: 185 AAFPHETKDMVVAASSLIMQLQTIVSRNVNPLDSAVITIGKLTSGTVQNVIAERARLEGT 244 AA P D V+ AS ++ LQ+IVSRNV+PL SAV+TIG L +GT NVIA+RA+L+GT Sbjct: 216 AAIPQNCIDAVLVASQIVTLLQSIVSRNVDPLHSAVVTIGSLHAGTTYNVIADRAQLKGT 275 Query: 245 IRTLSPEAMEKVKGRIEAIVRGIEVAYDCQAHIDYGSMYYQVYNDETLTNEFMQFVEK-- 302 +R ++ RIE IV G+ ++ ++Y +Y V ND + + E+ Sbjct: 276 VRYFDDRYQGFLQERIEQIVAGVCNSHGATYELNYRKLYPAVINDSAIADLVRSVAEEVL 335 Query: 303 ETDVHLVRCQEAMTGEDFGYMLARIPGFMFWLGVQS-----PFGLHHAKLNPNEEAIDVA 357 E + +V + M ED Y L ++PG F+LG + F HH + N +E A+ + Sbjct: 336 EPPLGVVPDCQTMGAEDMSYFLQKVPGCYFFLGSANLDRGLNFPHHHPRFNFDETALALG 395 Query: 358 IQLLTRYV 365 ++L R V Sbjct: 396 VELFLRCV 403 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: 381 Number of extensions: 13 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: 408 Length adjustment: 31 Effective length of query: 347 Effective length of database: 377 Effective search space: 130819 Effective search space used: 130819 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