Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate BWI76_RS07340 BWI76_RS07340 amidohydrolase
Query= curated2:B1MZM9 (387 letters) >FitnessBrowser__Koxy:BWI76_RS07340 Length = 392 Score = 197 bits (500), Expect = 6e-55 Identities = 129/343 (37%), Positives = 180/343 (52%), Gaps = 18/343 (5%) Query: 13 RRELHQIPETALEEFKTHDYLLTKLKSWQQDYMTIKTVEALPTAILVYFQGTNPVRTIGY 72 R LH PE +LEEF T + + KL W T+ A + +G +P RTIG Sbjct: 20 RHYLHAHPELSLEEFNTSELVAGKLTEWGY---TVTRGLAKTGVVGTLSKGDSP-RTIGL 75 Query: 73 RTDIDALPIQEATGLDFASQHPGKMHACGHDVHMTMALGLAQYFSQHQPKDN--LIIFFQ 130 R D+DALPI EAT L +AS GKMHACGHD H T+ L A+Y + + N + + FQ Sbjct: 76 RADMDALPIFEATDLPWASTVAGKMHACGHDGHTTILLAAAKYIASPACQFNGTVHLIFQ 135 Query: 131 PAEEAESGGKVAYDMGLFEGKWRPDEFYGIHDQPNLPAGTLSTLAGTLFAGTAELKVDVI 190 PAEEA G + GLFE ++ + +G+H+ P LP G L AG A +K+ + Sbjct: 136 PAEEAIGGADLMIKDGLFE-RFPCERIFGLHNMPGLPVGKLGFYAGNFMASADTVKITIT 194 Query: 191 GTGGHAAYPHLAKDPIVIAAELIIQLQTVVSRSVDPIAGGVVSVGVINGGFANNVIPDQV 250 G GGH A+P DPIV A L++ LQ++V+R+V P A VVSVG G A+NVIP+ V Sbjct: 195 GYGGHGAHPERTVDPIVTGAALVMNLQSIVARNVPPGATAVVSVGTFQAGIASNVIPENV 254 Query: 251 HFEGTVRSMTRTGLETMLTRIRKIAE------GLAIANEVTINVSLESGSYLPVENDPIL 304 E +VR+M + ++ RI+++A+ G + EV + + + S E L Sbjct: 255 VMELSVRAMKPEIRDLLIKRIKELADFTAKSYGASSEVEVFDSYPVLTNSDEETEFAKAL 314 Query: 305 ATQVINFMQKQSDINFELAQPAMTGEDFGYLLQHIPGVMLWLG 347 A +V + E P EDF ++LQ PG LG Sbjct: 315 ALEVFG-----EEGVLESISPMNASEDFAFMLQKRPGCYFLLG 352 Lambda K H 0.319 0.135 0.398 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: 369 Number of extensions: 22 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: 387 Length of database: 392 Length adjustment: 30 Effective length of query: 357 Effective length of database: 362 Effective search space: 129234 Effective search space used: 129234 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