Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate WP_008805236.1 KVAR_RS14965 amidohydrolase
Query= curated2:Q032G8 (376 letters) >NCBI__GCF_000025465.1:WP_008805236.1 Length = 389 Score = 187 bits (476), Expect = 3e-52 Identities = 118/348 (33%), Positives = 180/348 (51%), Gaps = 18/348 (5%) Query: 5 IEIRRQLHQIPEIGLEEHKTQKYLLTIIHQIIQNKSFIQVETWQTGILVYLKGSQGQKTI 64 I +RRQ HQ PEIG EEH+T + ++ + + TG++ L+ G+K + Sbjct: 17 IALRRQFHQQPEIGFEEHQTSNEVARLLGEWGYE---VHRGLAGTGVVGTLRVGHGKKRL 73 Query: 65 GWRTDIDGLPVEELTNLPFASK-NGRMHACGHDIHMTVALGLLEKLSES-QPKNNLLFLF 122 G R D+D LP++E + P+AS+ +GR H CGHD H T L E L+ + Q L +F Sbjct: 74 GLRADMDALPMQERSGKPWASQVDGRFHGCGHDGHTTTLLYAAEYLARTRQFTGTLQLIF 133 Query: 123 QPAEENEAGGKLMYDGGAFKNWLPDEFYGLHVRPDLKVGDIATNEQTLFAGTCEVELTFV 182 QPAEE GG++M + G F + D +GLH P +G I + + A + + + Sbjct: 134 QPAEELLYGGRVMVEDGLFDRFPCDAIFGLHNMPGQPLGKIGLRDGAMMASSDTLHIEVK 193 Query: 183 GTGGHAAFPHTANDALVAAAYFVTQVQTIVSRNVDPLDSAVVTFGKMEAGTTNNIIAERA 242 G GGH A P DA + A + +Q+IVSRN+ P + AVVT G ++AG NII + Sbjct: 194 GVGGHGAVPEHTVDATLVACHITLALQSIVSRNITPFEPAVVTVGSIQAGHAPNIINDHV 253 Query: 243 FLHGTIRSLTQEVNELTQKRLTELAKGVAQSFDMTIDLKLKQGGYLPVENNPKLAKELMD 302 + T+R+L ++V E +R+ ++A A+SF+ T L G PV N A ++ Sbjct: 254 LMKLTVRTLNEQVRETVLQRIHDIAVAQAESFNATATLTHVNGS--PVLRNDPAANAMV- 310 Query: 303 FFRNETKANLI------DIAPAMTGEDFGYLLSKIP-GVMFWLGINSE 343 E +L ++ P M EDF ++L + P G F +G E Sbjct: 311 ---REVATSLFGAEQVGEVKPFMGSEDFAFMLEQHPHGSYFTIGAGDE 355 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: 373 Number of extensions: 20 Number of successful extensions: 4 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: 389 Length adjustment: 30 Effective length of query: 346 Effective length of database: 359 Effective search space: 124214 Effective search space used: 124214 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 10 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