Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate BPHYT_RS07500 BPHYT_RS07500 amidohydrolase
Query= curated2:B7GIC0 (378 letters) >FitnessBrowser__BFirm:BPHYT_RS07500 Length = 390 Score = 211 bits (538), Expect = 2e-59 Identities = 125/345 (36%), Positives = 183/345 (53%), Gaps = 22/345 (6%) Query: 3 VNIRRDLHQIPELGFQEFKTQQYILDYLATLPSERLQIKTW---------RTGILVRVHG 53 + +RR +H PEL ++EF T L +ERLQ W +TG++ ++ Sbjct: 18 IALRRQIHAHPELAYEEFAT--------GDLVAERLQ--EWGYTVHRGLGQTGVVGQLKV 67 Query: 54 TAPTKTIGYRADMDGLPIDEQTDVPFRSTHEGRMHACGHDMHMAIALGVLTHVVHHPIRD 113 T+ +G RADMD LPI E T +P+ S G+MHACGHD H A+ L H+ D Sbjct: 68 GNGTRKLGLRADMDALPIHETTGLPYASKLPGKMHACGHDGHTAMLLAAAKHLAQEKCFD 127 Query: 114 DML-FIFQPAEEGPGGALPMLESDEMKQWMPDMILALHIAPAYPVGTIATKEGLLFANTS 172 L IFQPAEEG GA MLE ++ D + A+H P YP G G A++ Sbjct: 128 GTLNLIFQPAEEGLAGAKKMLEDGLFDKFPCDAVFAMHNMPGYPAGKFGFLPGSFMASSD 187 Query: 173 ELFIDLIGKGGHAAFPHETKDMVVAASSLIMQLQTIVSRNVNPLDSAVITIGKLTSGTVQ 232 + I + G+GGH A PH+ D VV + +++ LQ+IVSRN+ PLD A+IT+G + +G Sbjct: 188 TVIIKVTGRGGHGAVPHKAVDPVVVCAQIVLALQSIVSRNIAPLDMAIITVGAIHAGEAP 247 Query: 233 NVIAERARLEGTIRTLSPEAMEKVKGRIEAIVRGIEVAYDCQAHIDYGSMYYQVYNDETL 292 NVI E A + ++R L PE + ++ RI A+ G + +A +DY Y + ND + Sbjct: 248 NVIPETAEMRLSVRALKPEVRDYLQERITAVACGQAAVFGARADVDYQRRYPVLVNDPAM 307 Query: 293 TNEFMQF-VEKETDVHLVRCQEAMTG-EDFGYMLARIPGFMFWLG 335 T Q ++ D L+ + +TG EDF ++L R G +G Sbjct: 308 TGLARQVALDWLGDDGLIADMQPLTGSEDFAFLLERCAGSYLIIG 352 Lambda K H 0.322 0.137 0.411 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: 371 Number of extensions: 14 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: 378 Length of database: 390 Length adjustment: 30 Effective length of query: 348 Effective length of database: 360 Effective search space: 125280 Effective search space used: 125280 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