Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate RR42_RS27930 RR42_RS27930 amidohydrolase
Query= curated2:Q032G8 (376 letters) >FitnessBrowser__Cup4G11:RR42_RS27930 Length = 387 Score = 183 bits (464), Expect = 8e-51 Identities = 115/341 (33%), Positives = 177/341 (51%), Gaps = 14/341 (4%) Query: 6 EIRRQLHQIPEIGLEEHKTQKYLLTIIHQIIQNKSFIQVETWQTGILVYLKGSQGQKTIG 65 E+R ++H PE+G + +T + ++ + + + G++ LK G +TIG Sbjct: 14 EVRHRIHAHPELGADVPRTAEMAAALLREWGYSVHTLGGH----GLVAQLKVGNGARTIG 69 Query: 66 WRTDIDGLPVEELTNLPFASK-NGRMHACGHDIHMTVALGLLEKLSESQPKNNLL-FLFQ 123 R D+D LP++E T LP+AS+ GRMHACGHD H L E L+ ++ + L +FQ Sbjct: 70 IRADMDALPLQERTGLPYASQVAGRMHACGHDGHTATLLAAAEYLAATRHFDGTLNLIFQ 129 Query: 124 PAEENEAGGKLMYDGGAFKNWLPDEFYGLHVRPDLKVGDIATNEQTLFAGTCEVELTFVG 183 P EE G M + G F+ + D Y H P L VG + + +TF G Sbjct: 130 PDEEGMTGALAMMNDGLFERFPCDAIYAFHNAPGLPVGMAVVQSGPMGGSSDRATITFRG 189 Query: 184 TGGHAAFPHTANDALVAAAYFVTQVQTIVSRNVDPLDSAVVTFGKMEAGTTNNIIAERAF 243 GGH A PH A D +A A V +Q IV+RNV P+D+AV++ G+M+AG+T NII E A Sbjct: 190 KGGHGAMPHRATDPTLALASTVVALQGIVARNVAPVDAAVISVGEMQAGSTYNIIPETAT 249 Query: 244 LHGTIRSLTQEVNELTQKRLTELAKGVAQSFDMTIDL---KLKQGGYLPVENNPKLAKEL 300 L ++R+ EV +L + R+ E+ A S + +D+ +L VE + + Sbjct: 250 LKLSVRATVAEVRDLLETRIREVVTHQAASCGVAVDIAYERLAPAICNTVEETAIARQAV 309 Query: 301 MDFFRNETKANLIDIAPAMT--GEDFGYLLSKIPGVMFWLG 339 N+ +I + P+M EDF ++L ++PG F LG Sbjct: 310 ASVLGND---KVIQVPPSMQMGSEDFAWMLERMPGCYFALG 347 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: 317 Number of extensions: 13 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: 387 Length adjustment: 30 Effective length of query: 346 Effective length of database: 357 Effective search space: 123522 Effective search space used: 123522 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