Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate RR42_RS00390 RR42_RS00390 amidohydrolase
Query= curated2:Q8ERA3 (371 letters) >FitnessBrowser__Cup4G11:RR42_RS00390 Length = 422 Score = 202 bits (515), Expect = 1e-56 Identities = 132/368 (35%), Positives = 195/368 (52%), Gaps = 17/368 (4%) Query: 4 QLEQIRRDLHQIPELGFQEFKTQAYL---LERINEIATENVEIKKWSTGILVYVHGKSPA 60 +LE IR +HQ PEL F E +T + LE T V TG++ + Sbjct: 47 ELEAIRHSIHQHPELAFDEVRTAELVATELEGWGYAVTRGVG----GTGVVGTLCQGDGP 102 Query: 61 RKIGFRADIDGLPILEQTNLPYASLHEGRMHACGHDLHMTIALGALEKLIQDP-INDDVI 119 R IG RAD+D LPI E+T L YAS+H G+MHACGHD H T+ LGA +L + N V Sbjct: 103 RSIGVRADMDALPIHERTGLAYASIHAGKMHACGHDGHTTVLLGAARQLARTRNFNGTVN 162 Query: 120 FVFQPAEE--GPGGAKPMLESEEFQQWKPDMMFALHIAPELPVGTVSSKAGLLFANTSEL 177 +FQPAEE GGA+ ML F+++ D +F LH P + GT +AG A + Sbjct: 163 LIFQPAEEIGAGGGAERMLADGLFERFPCDAIFGLHNHPGVEAGTFMFRAGPFMAACDTV 222 Query: 178 FIDFEGVGGHAAYPHLTKDMTVAASNFVVQLQQIVSRGLNPLDGSVITIGKMESGYVQNA 237 I G GGHAA PH + D + A + V+ LQ IVSR ++P + +V+TIG + +G+V N Sbjct: 223 AITIRGKGGHAARPHQSIDPILVAGSLVMALQSIVSRNIDPNETAVVTIGTLHAGHVANV 282 Query: 238 IAETARLEGTIRSTDADAIDMIKSKLNRLMKGFEISYDCTIKVDYGANYYQVVN---DAT 294 I E+A+LE ++RS D ++ ++ RL+ Y T+++DY Y ++N + Sbjct: 283 IPESAKLELSVRSFSPDVRRTLEDRIRRLVTSHVEGYGATVEIDYIRGYPVLINSERETE 342 Query: 295 YVQQF-ENVINQTQTITYQQADAAMTGEDFGDMLKEIPGFMFWLGVDSSYG-LHNARLNP 352 + +Q E ++ + + A EDF L++ PG +G + LHNA + Sbjct: 343 FARQVAEELVGPDKVVANFPLIAG--SEDFAYFLQQRPGCFVRMGNGAGQPLLHNAGYDF 400 Query: 353 KEEAIDVG 360 +E + VG Sbjct: 401 NDENLTVG 408 Lambda K H 0.319 0.136 0.394 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: 355 Number of extensions: 20 Number of successful extensions: 3 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: 371 Length of database: 422 Length adjustment: 31 Effective length of query: 340 Effective length of database: 391 Effective search space: 132940 Effective search space used: 132940 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 (21.7 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