Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (characterized)
to candidate WP_012968083.1 KVAR_RS11965 amidohydrolase
Query= SwissProt::O34916 (374 letters) >NCBI__GCF_000025465.1:WP_012968083.1 Length = 373 Score = 229 bits (583), Expect = 1e-64 Identities = 139/364 (38%), Positives = 203/364 (55%), Gaps = 12/364 (3%) Query: 4 EELIAIRRDLHRIPELGFQEFKTQQYLLNVLEQYPQDRIEIEKWRTGLFVKVNGTAPEKM 63 ++LI+ RR+LH+ PEL QE T + + L+ + + +TGL +V + +K+ Sbjct: 5 QQLISWRRELHQNPELSLQEVATTARIRDWLQSGGLTLLPFDL-KTGLVAEVG--SGDKV 61 Query: 64 LAYRADIDALSIEEQTGLPFASEHHGNMHACGHDLHMTIALG----IIDHFVHHPVKHDL 119 +A RADIDAL IEE TGLP+ S++ G MHACGHD+H ++ LG + + P + + Sbjct: 62 IALRADIDALPIEEATGLPYRSQNEGVMHACGHDIHTSVMLGAALLLKEREAELPGR--V 119 Query: 120 LFLFQPAEEGPGGAEPMLESDVLKKWQPDFITALHIAPELPVGTIATKSGLLFANTSELV 179 LFQPAEE GGA+ ++ + L+ F +H P LPVG AT+ G +AN V Sbjct: 120 RILFQPAEENFGGAKTLIRAGALEDVSAIF--GMHNEPGLPVGEFATRGGAFYANVDRFV 177 Query: 180 IDLEGKGGHAAYPHLAEDMVVAASTLVTQLQTIISRNTDPLDSAVITVGTITGGSAQNII 239 + GKG HAA PH +D ++ AS LVT LQ++ SR + LDS V++V I GG+ N++ Sbjct: 178 FKVTGKGAHAARPHEGKDAILLASQLVTVLQSVASREVNTLDSVVLSVTRIQGGNTWNVL 237 Query: 240 AETAHLEGTIRTLSEESMKQVKERIEDVVKGIEIGFRCKGKVTYPSVYHQVYNTSGLTEE 299 E+ LEGT+RT S E ++VK R+ ++ G F + V + + + N + + Sbjct: 238 PESVELEGTLRTHSSEVQQRVKARVSEIAAGFASAFGAQIDVFWYAGPTALVNDARWA-D 296 Query: 300 FMSFVAEHQLATVIEAKEAMTGEDFGYMLKKYPGFMFWLGADSEHGLHHAKLNPDENAIE 359 F S VA A + GEDF L+ PG +G+ SE+GLHH NPDE I Sbjct: 297 FASDVAAQAGYRTHHADLHLGGEDFAVYLQHIPGAFVSIGSASEYGLHHPAFNPDERLIA 356 Query: 360 TAVH 363 A H Sbjct: 357 PAAH 360 Lambda K H 0.319 0.135 0.397 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: 372 Number of extensions: 22 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: 374 Length of database: 373 Length adjustment: 30 Effective length of query: 344 Effective length of database: 343 Effective search space: 117992 Effective search space used: 117992 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