Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (characterized)
to candidate Echvi_0302 Echvi_0302 amidohydrolase
Query= SwissProt::D5E0A1 (375 letters) >FitnessBrowser__Cola:Echvi_0302 Length = 432 Score = 194 bits (492), Expect = 5e-54 Identities = 117/356 (32%), Positives = 188/356 (52%), Gaps = 22/356 (6%) Query: 3 ENEFVKIRRELHKIPELGFQEVKTQRFLLDYINTLPQERLEVKTWKTGLFVKVHGTNPTK 62 E + ++ RR++H+ PELG QE +T + + ++ +L E +E K TG+ + G +P Sbjct: 35 EPKVIEWRRDIHQNPELGNQETRTAKLIASHLRSLGLE-VEEKVAVTGVVGLLKGDHPGP 93 Query: 63 TIGYRADIDGLPITEETNYSFQS--------QHEGLMHACGHDMHMAIGLGVLTYFA--Q 112 T+ RAD+D LP+TE + F+S Q G+MHACGHD H+AI +GV + + Sbjct: 94 TVALRADMDALPVTERNDLPFKSTKKTVYNGQEIGIMHACGHDTHVAILMGVAEVLSSMK 153 Query: 113 HEIKDNVLFIFQPAEEG-------PGGAQPMLQSDIMKEWLPDFIFALHVAPEYPVGSIA 165 +++ V FIFQPAEEG GA+ M++ +M D +F LH+ + VG I Sbjct: 154 NDLHGTVKFIFQPAEEGVFEEGISSWGAKQMVEEGVMDG--VDAVFGLHINSQTEVGDIK 211 Query: 166 LKEGLLFANTSELFIDLKGKGGHAAYPHTTNDMVVAACQLVSQLQTIVARNVDPLDS-AV 224 + G A L + + G+ H AYP ++ D +V + Q++S LQTI++RNV+ ++ A+ Sbjct: 212 YRSGPAMAAVDNLKLTVNGRQAHGAYPWSSVDPIVTSSQMISALQTIISRNVNITENPAI 271 Query: 225 ITVGKIQGGTVQNIIAERARIEGTIRTLSPESMTRVKERIEAIVKGVEVGYQCETAIDYG 284 +T+G I GG QNII E+ + GT+RT + +RI I +D Sbjct: 272 VTIGSIHGGVRQNIIPEKVEMLGTVRTYGTAQQELIHQRIHDIATHTAEAAGATVDVDID 331 Query: 285 CMYHQVYNHHEVTREFMEFAKEQTDVDVIECKEAMTG-EDFGYMLKDIPGFMFWLG 339 +Y N +T + + K + + + +TG EDF Y + +PG +LG Sbjct: 332 KIYPATINDPGLTEKMVNTLKTVAGEEHVIYHDPITGAEDFSYFQQQVPGLFIFLG 387 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: 419 Number of extensions: 25 Number of successful extensions: 7 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: 432 Length adjustment: 31 Effective length of query: 344 Effective length of database: 401 Effective search space: 137944 Effective search space used: 137944 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