Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate BPHYT_RS29435 BPHYT_RS29435 amidohydrolase
Query= curated2:B1YJ90 (370 letters) >FitnessBrowser__BFirm:BPHYT_RS29435 Length = 396 Score = 200 bits (508), Expect = 6e-56 Identities = 127/373 (34%), Positives = 197/373 (52%), Gaps = 14/373 (3%) Query: 6 EMRRELHKIPEPGFKEFKTQAFILDQIRSYPEDRVSYDTFETGVFVRVKGLTGNRTIGYR 65 E+R +H PE ++E +T A + ++ + +V+ +TGV +K G R+IG R Sbjct: 22 EIRHHIHHHPELAYEEHQTSALVAQKLEEWGW-QVTRGVGKTGVVGTLKVGDGKRSIGIR 80 Query: 66 ADIDGLPIEEATGLPFCSEHPGFMHACGHDVHASIALGLLRRIVELPVMDDVVFL-FQPA 124 AD+D LPI E TGLP+ S G MHACGHD H ++ LG +R+ V L FQPA Sbjct: 81 ADMDALPIIEQTGLPYASGTHGKMHACGHDGHTTMLLGAAQRLAATRNFSGTVHLYFQPA 140 Query: 125 EEG--PGGAEPMIKSPLFEKYRPSEMYGLHVAPEYPVGTIASRPGVLFASAREVHITIYG 182 EE GA MI LFE++ ++G+H P G + R G ++ + +TI G Sbjct: 141 EESGIDSGALKMINDGLFERFPCDAVFGVHNHPGEEPGVLLFRKGPFMSAGDKAIVTIEG 200 Query: 183 QSGHAAFPHLTIDTVVAQAALIMQLQTIVSRSINPMNCSVITIGKVDAGIRENVIAGRAL 242 GHAA PHLT+D VV A+++M LQTIV+R+++P +V+T+G + AG NVI+ A Sbjct: 201 VGGHAARPHLTVDPVVVAASIVMALQTIVARNVDPSQPAVVTVGSMHAGTANNVISSSAK 260 Query: 243 LDGTMRALNGTDMEKLEQRVRDIIRGIEASFGVKIDLQFGNRYYEVVNDQR----VVDKF 298 L+ ++R+ + L++R+ ++ AS+G K +++ Y VVN V+ Sbjct: 261 LELSVRSFSPEVRALLKKRITELAESQAASYGGKAVVEYIEGYPVVVNSDAETDFAVEVA 320 Query: 299 SSFVKMNANYIECDAAMTGEDFGFMLKEIPGMMFWLGVNNATSG--LHQPTLNPDEEAIP 356 V + + D M EDF FML++ PG +G G +H P + ++ +P Sbjct: 321 RELVGDDKVVAQTDILMGSEDFAFMLQKRPGTFLRIGNGAGEDGCMVHNPHYDFNDRNLP 380 Query: 357 ----FVINLLDHY 365 F L++ Y Sbjct: 381 VGAAFWTRLVERY 393 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: 384 Number of extensions: 21 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: 370 Length of database: 396 Length adjustment: 30 Effective length of query: 340 Effective length of database: 366 Effective search space: 124440 Effective search space used: 124440 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