Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate YP_004143559.1 Mesci_4399 amidohydrolase
Query= curated2:Q04FS2 (382 letters) >NCBI__GCF_000185905.1:YP_004143559.1 Length = 409 Score = 206 bits (523), Expect = 1e-57 Identities = 127/378 (33%), Positives = 200/378 (52%), Gaps = 18/378 (4%) Query: 5 EQLIKIRRHLHANPEIGMQEVKTHQFLLEQIAKFPQENLTIETISEIPTALLVRIAGSDP 64 +++I++RRHLH NPE+ QE T ++L + + Q + I ++ A+ + AG Sbjct: 27 DRMIEVRRHLHRNPELSNQEAGTQRYLRQMLVD--QGIVDIRDVAGFGLAVDIVGAGRPS 84 Query: 65 KRTIALRTDMDALPIQEETGLDFASKNDHVMHACGHDIHMTVALGILSYFAKHQPKDN-- 122 R IA+R D+DALPI+EE+G+D+AS N VMHACGHD H ++A + ++ HQ +D+ Sbjct: 85 NRKIAIRADIDALPIEEESGVDYASTNPGVMHACGHDAHASMAFAVAAHL--HQSRDSFG 142 Query: 123 --LLVFFQPAEENE-FGGKRFYDAGGFQGEYLPDEFYALHVNPQLPAGQIASRKGTLFAG 179 + + FQPAEE+E GGKR + G D +HV+P P G+IA G Sbjct: 143 GTVRLIFQPAEEDEPSGGKRVVEEGLLDDI---DAAICVHVDPYTPTGKIAVGSGPYTLA 199 Query: 180 SNELRISFIGKSGHAAYPQNAKDSIVAAANFVTNVQTVVSRNVDPIEGGVVTIGKFNAGK 239 + ++ IG + HAA P D++ A + V+ +Q +VSR DP + V+++ N G Sbjct: 200 CDTFDVAVIGSAAHAAKPHEGVDALAVACSLVSELQKIVSRETDPYDPLVISVTAINGGN 259 Query: 240 AMNIIAGKADIEGTIRSFTQSGMEIMTKHIRMIAEGIAGAFGQELKINFRQGGYMPVVND 299 A N+ AG+ ++GTIRS + + E +R IA G+A + G ++++ + G VVND Sbjct: 260 AYNVTAGRVTLKGTIRSGSDATRERAWHRVRTIAAGMATSHGARVEVDIHK-GEPGVVND 318 Query: 300 ERTTNFFIDYMKNADGVDFKIVQPA-MIAEDFGFLSNQFEGTMCWLGVNDPK----HSLH 354 T K G D + P IA+DFG+ S + LG+ + + LH Sbjct: 319 VEMTELIAASAKACIGADNVLNTPGWTIADDFGYYSEKRPSVYFRLGIRNEEIGSVFPLH 378 Query: 355 SDHLNPDESAITKGVEAI 372 DE+A+ G + Sbjct: 379 HARFRIDEAALKVGATTL 396 Lambda K H 0.320 0.137 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: 392 Number of extensions: 23 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: 382 Length of database: 409 Length adjustment: 31 Effective length of query: 351 Effective length of database: 378 Effective search space: 132678 Effective search space used: 132678 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 (21.8 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