Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate WP_012542544.1 KVAR_RS19155 amidohydrolase
Query= curated2:A8YUT2 (384 letters) >NCBI__GCF_000025465.1:WP_012542544.1 Length = 392 Score = 196 bits (498), Expect = 9e-55 Identities = 124/352 (35%), Positives = 193/352 (54%), Gaps = 14/352 (3%) Query: 5 TESELIQIRRHLHEIPELALQEKETHDYLLKIIKGFNSEFLTIKVPEELPTAILV--LIK 62 TE E+I IR +LH PEL+L+E T + ++ G +E+ +V L +V L K Sbjct: 12 TEDEMISIRHYLHANPELSLEEFNTSE----LVAGKLAEW-GYQVTRGLGKTGVVGSLSK 66 Query: 63 GSNPQRTIGYRTDIDALPVEEKTNLPFSSTHPGIMHACGHDIHMSVALGLLSYFSENQPK 122 G +P RTIG R D+DALP+ E T+LP++ST PG MHACGHD H ++ L Y + + Sbjct: 67 GDSP-RTIGLRADMDALPIHETTDLPWASTVPGKMHACGHDGHTTILLAAAKYIASPACQ 125 Query: 123 DN--LLFFFQPAEESESGGKKAYEDGIFEGKFRPDEFYGLHDNPELPAGAIGCREGTLFA 180 N + FQPAEE+ G +DG+FE +F + +GLH+ P LP G +G G A Sbjct: 126 FNGTVHLIFQPAEEAIGGADLMIKDGLFE-QFPCERIFGLHNMPGLPVGKLGFYAGNFMA 184 Query: 181 GTTEVNIDLIGKGGHAAFPQNANDTVVAAASLIMQIQTVISRSIDPIQSGVITLGKVRAG 240 V I + G GGH A P+ D +VA A+L+M +Q++++R++ P ++ V+++G +AG Sbjct: 185 SADTVKITITGYGGHGAHPERTVDPIVAGAALVMALQSIVARNVPPGETAVVSVGTFQAG 244 Query: 241 TIRNVIAGQTRIEGTIRGLTQKMILQIDQRLQDLCEGIARSYNMKVNLELNQGGYWPVEN 300 NVI +E ++R + + + +R+ +L + A+SY +E+ Y + N Sbjct: 245 IASNVIPESVVMELSVRAMKPDIRDLLIKRIHELADFTAKSYGASSVVEV-YDSYPVLTN 303 Query: 301 NPELT--KNFISYMKNNPEVDFVETKPKMTGEDFGFLLAKFPGTMFWLGVGD 350 +PE T ++ E P EDF F+L + PG+ F LG G+ Sbjct: 304 SPEETDFARALALEVFGREGVLESVSPMNASEDFAFMLRERPGSYFLLGNGE 355 Lambda K H 0.318 0.138 0.403 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: 409 Number of extensions: 26 Number of successful extensions: 6 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: 384 Length of database: 392 Length adjustment: 30 Effective length of query: 354 Effective length of database: 362 Effective search space: 128148 Effective search space used: 128148 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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