Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate CCNA_02900 CCNA_02900 N-acyl-L-amino acid amidohydrolase
Query= curated2:Q032G8 (376 letters) >FitnessBrowser__Caulo:CCNA_02900 Length = 437 Score = 155 bits (392), Expect = 2e-42 Identities = 119/367 (32%), Positives = 185/367 (50%), Gaps = 30/367 (8%) Query: 9 RQLHQIPEIGLEEHKTQKYLLTIIHQIIQNKSFIQVE-TWQTGILVYLKGSQGQKTIGWR 67 + +H PE+G +E +T K L + + F E +TG++ LK +G K + R Sbjct: 48 KDIHAHPELGFQEVETAKKLAAQMRAL----GFTVTEGVGKTGVVAVLKNGEGPKVL-IR 102 Query: 68 TDIDGLPVEELTNLPFASK-----NGRM----HACGHDIHMTVALGLLEKL--SESQPKN 116 T++DGLP++E + L +AS+ NG HACGHDIHM +G +L +++ K Sbjct: 103 TELDGLPMQEKSGLAWASQATATWNGEKVFVAHACGHDIHMAAWVGAARQLVAMKAKWKG 162 Query: 117 NLLFLFQPAEENEAGGKLMYDGGAFKN--WLPDEFYGLHVRPDLKVGDIATNEQTLFAGT 174 L+F+ QP+EE G + M D G + PD + LHV G++ L + + Sbjct: 163 TLVFVAQPSEETVRGARAMLDDGLWDKIGGKPDYGFALHVGSG-PAGEVYYKAGVLTSTS 221 Query: 175 CEVELTFVGTGGHAAFPHTANDALVAAAYFVTQVQTIVSRNVDPLDSAVVTFGKMEAGTT 234 +++TF G GGH + P D ++ AA F VQ+++SR DP VVT G ++AG+ Sbjct: 222 DGLDITFNGRGGHGSMPSATIDPVLMAARFTVDVQSVISREKDPSAFGVVTVGSIQAGSA 281 Query: 235 NNIIAERAFLHGTIRSLTQEVNELTQKRLTELAKGVAQSFDMT----IDLKLKQGGYLPV 290 NII ++A + GTIR TQ+ N + +K L + + V DM DLKL GG + V Sbjct: 282 GNIIPDKARVRGTIR--TQD-NAVREKILDGVRRTVKAVTDMAGAPPADLKLTPGGKM-V 337 Query: 291 ENNPKLAKELMDFFRNETKANLI-DIAPAMTGEDFG-YLLSKIPGVMFWLGINSEAPLHS 348 N+ L F+ A + P ED+ ++L+ +P V F +G + A L Sbjct: 338 VNDAALTDRTAVVFKAAFGARAVAQDKPGSASEDYSEFVLAGVPSVYFAIGGSDPAELAK 397 Query: 349 QKMQADE 355 K + E Sbjct: 398 AKAEGRE 404 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: 326 Number of extensions: 13 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: 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