Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate 208065 DVU2568 peptidase, M20/M25/M40 family
Query= curated2:Q5WF94 (374 letters) >MicrobesOnline__882:208065 Length = 412 Score = 231 bits (590), Expect = 2e-65 Identities = 138/374 (36%), Positives = 191/374 (51%), Gaps = 21/374 (5%) Query: 6 LIHIRRAFHQIPELGFNEFKTQKLLLDTISNME-QTRLQIKTWKTAVFVRVEGRQDYTIA 64 +I RRA H IPE GF E T + +T+S + R I T + G + + Sbjct: 30 IIAHRRALHAIPETGFEERCTAAYVAETLSGLGLPVRTGIATTGVTALLDT-GLEGPVVM 88 Query: 65 YRADMDGLPITEETGYSFASKHEGAMHACGHDFHMTIALG---LLDHFASHEP---ECHL 118 RADMD LP+TE TG FAS+HEG MHACGHD HM + LG +L EP + Sbjct: 89 LRADMDALPVTEATGLPFASRHEGRMHACGHDAHMAMLLGAAEMLSAIVREEPGRLRGKV 148 Query: 119 LFIFQPAEEGPGGAKPIIEADVLGAWQPDEIYALHIDPNLPVGSIATKPGLLFANTSELF 178 LF+FQPAEEGPGGA P+I VL + D H+ P+LPVG++ KPG L A Sbjct: 149 LFLFQPAEEGPGGAAPMIAEGVLDEPKVDVCLGAHVWPSLPVGTVGVKPGPLMAAMDRFE 208 Query: 179 IDFQGKGGHAAYPHTANDMVVACAHFVTQVQTVVARNIDPLDSAVVTLGVIAGGTKQNVI 238 + G+GGHAA PH D + V +Q VV+R DPL+ ++T+G + GT NVI Sbjct: 209 LAVHGRGGHAATPHLCVDALETATQVVGALQRVVSRMTDPLEPVILTIGELHAGTAYNVI 268 Query: 239 AATARLEGTIRTLSMASMEVVKSRLEAIAAGIEASFACKIAIDYGSNYCEVYNDPELAEA 298 AR+ GT+RT S + R+ +A G+ A+ +D+ + V N P +AE Sbjct: 269 PGEARMAGTVRTFSPDVRAAWEDRIRTVADGVCAAMGATATLDFHYCHGPVINTPRVAEV 328 Query: 299 FAAFSKTRKGITFVEAEEAMT-------GEDFGYFLKQYPGVMFWLGVDSPYGLHDSRLQ 351 R+ + E+A+T GEDF FL++ PG F++G +H+ R Sbjct: 329 ------VRRAVVEARGEQAVTTPTPTLGGEDFSCFLERIPGCFFFVGCGGDVPIHNPRFD 382 Query: 352 PSEEAIGIAIEHMV 365 E + + E V Sbjct: 383 LDERCLALGAETFV 396 Lambda K H 0.321 0.136 0.406 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: 409 Number of extensions: 11 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: 374 Length of database: 412 Length adjustment: 31 Effective length of query: 343 Effective length of database: 381 Effective search space: 130683 Effective search space used: 130683 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