Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate AZOBR_RS32390 AZOBR_RS32390 amidohydrolase
Query= curated2:B1YJ90 (370 letters) >FitnessBrowser__azobra:AZOBR_RS32390 Length = 399 Score = 201 bits (511), Expect = 3e-56 Identities = 126/350 (36%), Positives = 183/350 (52%), Gaps = 11/350 (3%) Query: 6 EMRRELHKIPEPGFKEFKTQAFILDQIRSYPEDRVSYDTFETGVFVRVKGLT-GNRTIGY 64 + R LH PE F+E +T AF+ D++R++ + V+ TG+ +KG G R I Sbjct: 22 QWRHHLHAHPETAFEEHETAAFVADKLRAFGLE-VATGLGRTGLVGTLKGRRPGGRAIAL 80 Query: 65 RADIDGLPIEEATGLPFCSEHPGFMHACGHDVHASIALGLLRRIVELPVMDDVVF-LFQP 123 RAD+D L I E S +PG MHACGHD H ++ LG + + + P + +FQP Sbjct: 81 RADMDALHIHETNDFAHRSVNPGRMHACGHDGHTTMLLGATKVLADDPDFAGTLHVIFQP 140 Query: 124 AEEGPGGAEPMIKSPLFEKYRPSEMYGLHVAPEYPVGTIASRPGVLFASAREVHITIYGQ 183 AEE GGA M+ LFE++ +YG+H P P+G IA RPG + S +T++G+ Sbjct: 141 AEENEGGAREMVAEGLFERFPVDGVYGMHNWPGLPLGQIALRPGPMMGSYDIFEVTVHGK 200 Query: 184 SGHAAFPHLTIDTVVAQAALIMQLQTIVSRSINPMNCSVITIGKVDAGIRENVIAGRALL 243 HAA PHL D + A L+ LQTI RS++P++ +V++ + G NVI L Sbjct: 201 GSHAAMPHLGHDPMTAAGHLLTTLQTIPGRSLHPLDSAVVSTTWITGGDTWNVIPAEVTL 260 Query: 244 DGTMRALNGTDMEKLEQRVRDIIRGIEASFGVKIDLQFGNRYYEVVND--QRVVDKFSSF 301 GT+RA + +E R+R + A+FG +++ RY VN + + + Sbjct: 261 RGTVRAFKEGVQDVVEARLRALAEHTAAAFGCTASVRYERRYPATVNSAAETALCARVAA 320 Query: 302 VKMNANYIECD--AAMTGEDFGFMLKEIPGMMFWLGVNNATSG---LHQP 346 + I+ D +M EDF FMLKE PG WLG N T G LH P Sbjct: 321 TLVGEENIDHDPMPSMGAEDFAFMLKERPGCYVWLG-NGPTDGGCLLHNP 369 Lambda K H 0.323 0.140 0.417 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: 438 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: 370 Length of database: 399 Length adjustment: 30 Effective length of query: 340 Effective length of database: 369 Effective search space: 125460 Effective search space used: 125460 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