Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate Ga0059261_2769 Ga0059261_2769 amidohydrolase
Query= curated2:Q032G8 (376 letters) >FitnessBrowser__Korea:Ga0059261_2769 Length = 437 Score = 180 bits (456), Expect = 8e-50 Identities = 133/399 (33%), Positives = 192/399 (48%), Gaps = 40/399 (10%) Query: 3 NLIEIRRQLHQIPEIGLEEHKTQKYLLTIIHQIIQNKSFIQVETWQTGILVYLKGSQGQK 62 +L+ + ++LH PE+ E +T + + + + + TG++ +K G Sbjct: 33 SLMALYKELHAAPELSQHEVQTAARMAA---EARKAGFTVTEKVGGTGVVAVMKNGAGP- 88 Query: 63 TIGWRTDIDGLPVEELTNLPFASK----------NGRMHACGHDIHMTVALGLLEKLS-- 110 TI R D+DGLPV E T LPFASK G MHAC HD HMT +G L L+ Sbjct: 89 TILIRADMDGLPVTEETGLPFASKVRGKTPEGVETGIMHACAHDTHMTAWVGTLRNLAAM 148 Query: 111 ESQPKNNLLFLFQPAEENEAGGKLMYDGGAFKNW-LPDEFYGLHVRPDLKVGDIATNEQT 169 + + K L+ + QPAEEN AG M + G + + P H L G I Sbjct: 149 KGKWKGTLVMVAQPAEENSAGAIAMLNDGLYARFGKPSHAIAFHNSAALPAGTIGIRSGP 208 Query: 170 LFAGTCEVELTFVGTGGHAAFPHTANDALVAAAYFVTQVQTIVSRNVDPLDSAVVTFGKM 229 FA V++ G GGH A+P T D +V A V+ +QTIV+R VDPLDSAV+T G Sbjct: 209 TFASVDSVDIVVKGVGGHGAYPATTKDPIVLGARIVSALQTIVAREVDPLDSAVITVGSF 268 Query: 230 EAGTTNNIIAERAFLHGTIRSLTQEVNELTQKRLTELAKGVAQSFDMTID----LKLKQG 285 + GT +NII E+A L T+R+ T EV + + +AKG A + + + + +++ Sbjct: 269 QGGTRHNIIPEQALLLLTVRAYTPEVRKQLLDGIARIAKGEAIAAGVPEERMPVVTIREN 328 Query: 286 GYLPVENNPKLAKELMDFFRNE-TKANLIDIAPAMTGEDFG-YLLS--KIPGVMFWLGIN 341 P + A L F K + DIAP M GEDFG Y ++ I ++W+G Sbjct: 329 FTPPTVSTDPFATHLKTLFTARFGKDRVTDIAPTMAGEDFGRYHIADPSIQSAIYWVGGV 388 Query: 342 SE--------------APLHSQKMQAD-EEVLDFAVEAI 365 + LHS K D E+V+ A EA+ Sbjct: 389 PQDKWDAAKASGGKGLPSLHSSKWAPDAEKVIGTAAEAM 427 Lambda K H 0.319 0.136 0.396 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: 387 Number of extensions: 23 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: 376 Length of database: 437 Length adjustment: 31 Effective length of query: 345 Effective length of database: 406 Effective search space: 140070 Effective search space used: 140070 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 (21.7 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