Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (characterized)
to candidate GFF999 PGA1_c10160 amidohydrolase
Query= SwissProt::D5E0A1 (375 letters) >FitnessBrowser__Phaeo:GFF999 Length = 388 Score = 220 bits (561), Expect = 4e-62 Identities = 131/372 (35%), Positives = 197/372 (52%), Gaps = 5/372 (1%) Query: 5 EFVKIRRELHKIPELGFQEVKTQRFLLDYINTLPQERLEVKTWKTGLFVKVHGTNPT--K 62 E RR++H+ PE+ ++ +T + + + T + + +TG+ + G + T + Sbjct: 13 EITAWRRDIHQNPEILYETHRTSASVAEKLRTFGCDEVVTGIGRTGVVGVIRGRSDTQNR 72 Query: 63 TIGYRADIDGLPITEETNYSFQSQHEGLMHACGHDMHMAIGLGVLTYFAQHEIKDNV-LF 121 IG RAD+D LP+ E+T SQ EG MHACGHD H A+ LG Y A+ D + Sbjct: 73 AIGLRADMDALPMAEDTGLPHASQIEGAMHACGHDGHTAMLLGAAKYLAETRNFDGTAVV 132 Query: 122 IFQPAEEGPGGAQPMLQSDIMKEWLPDFIFALHVAPEYPVGSIALKEGLLFANTSELFID 181 IFQPAEEG GA+ M + +M + D ++A+H +P +G AL+ G + A+ E I Sbjct: 133 IFQPAEEGGNGAEAMCKDGLMDRFGIDEVYAIHNSPGLELGKFALRPGPILASVDEFIIR 192 Query: 182 LKGKGGHAAYPHTTNDMVVAACQLVSQLQTIVARNVDPLDSAVITVGKIQ-GGTVQNIIA 240 L+G+GGHAA P T D V CQL++ LQ+IV+RNVDP+ AV++V + N+I Sbjct: 193 LQGRGGHAAKPQETVDTTVMMCQLITALQSIVSRNVDPVMQAVLSVTSAETSSKAYNVIP 252 Query: 241 ERARIEGTIRTLSPESMTRVKERIEAIVKGVEVGYQCETAIDYGCMYHQVYNHHEVTREF 300 +RA ++GTIRT SP+ + ER+ A+ G+ + + +++ N E T Sbjct: 253 DRAEVKGTIRTHSPDVRAHIPERLRAVTAGIALTFGGSAEVEFVNGVPVTINDAEATGH- 311 Query: 301 MEFAKEQTDVDVIECKEAMTGEDFGYMLKDIPGFMFWLGVQSEYGLHHAKLQPHEGAIDI 360 A D E AM GEDF +ML++ PG M +G S GLHH ++ AI Sbjct: 312 AHAAALAVAGDCEEVALAMGGEDFSFMLEERPGAMIRVGNGSSAGLHHPAYDFNDDAIPA 371 Query: 361 AISLITKYFEHK 372 S E + Sbjct: 372 GCSWFVTLIEQR 383 Lambda K H 0.320 0.137 0.410 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: 363 Number of extensions: 15 Number of successful extensions: 5 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: 375 Length of database: 388 Length adjustment: 30 Effective length of query: 345 Effective length of database: 358 Effective search space: 123510 Effective search space used: 123510 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 (21.8 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