Align N-acetyldiaminopimelate deacetylase; EC 3.5.1.47 (uncharacterized)
to candidate GFF3807 PS417_19495 N-acyl-L-amino acid amidohydrolase
Query= curated2:Q04FS2 (382 letters) >FitnessBrowser__WCS417:GFF3807 Length = 448 Score = 181 bits (458), Expect = 5e-50 Identities = 135/397 (34%), Positives = 198/397 (49%), Gaps = 41/397 (10%) Query: 7 LIKIRRHLHANPEIGMQEVKTHQFLLEQIAKFPQENLTIETISEIP-TALLVRIAGSDPK 65 +++ RR +HA+PE+G E +T + + +Q+ +L +E + + T ++ + G+ P Sbjct: 48 MLETRRDIHAHPELGNTETRTAELVAKQL-----RDLGLEVKTGVARTGVVAVLKGALPG 102 Query: 66 RTIALRTDMDALPIQEETGLDFASKND--------HVMHACGHDIHMTVALG---ILSYF 114 T+ALR DMDALP++E L FASK VMHACGHD H+ + L IL+ Sbjct: 103 PTVALRADMDALPVKEVADLPFASKAKGTYLGKEVDVMHACGHDAHVAILLSTAKILTGM 162 Query: 115 AKHQPKDNLLVFFQPAEE----------NEFGGKRFYDAGGFQGEYLPDEFYALHVNPQL 164 + P + +FQPAEE N +G K G Q PD + LHV + Sbjct: 163 RERLP-GTVEFYFQPAEEGPSDFIPDGKNTWGAKMMVQEGVMQSPK-PDAVFGLHVWAGV 220 Query: 165 PAGQIASRKGTLFAGSNELRISFIGKSGHAAYPQNAKDSIVAAANFVTNVQTVVSRNVDP 224 PAGQIA R G A S++LRI +GK HA P + D I A + +QTVVSR D Sbjct: 221 PAGQIAYRSGPTLASSDDLRIKILGKQTHAGRPWDGIDPITVGAQTIVGLQTVVSRRTDI 280 Query: 225 IE-GGVVTIGKFNAGKAMNIIAGKADIEGTIRSFTQSGMEIMTKHIRMIAEGIAGAFGQE 283 VV+IG N G NII D+ GTIRS+ + + +R E IA + G + Sbjct: 281 SSFPSVVSIGTINGGTRYNIIPESMDMSGTIRSYDYGIRQKLHADVRQTVEKIAESGGAK 340 Query: 284 LKINFRQGGYMPVVNDERTTNFFIDYMKNADGVDFKIVQPAMI--AEDFGFLSNQFEGTM 341 ++ + Y P +N+ T + ++ A D +VQ ++ AEDF F + + G Sbjct: 341 AEVTIIE-KYDPTINNPALTEKMLPSLRWAAKDD--VVQGPLVGGAEDFSFYAKEAPGLF 397 Query: 342 CWLGV--NDPKHSLHSDHLNP----DESAITKGVEAI 372 +LGV D S + + NP DESA+ GV + Sbjct: 398 VFLGVTPRDQDMSKAAPNHNPGFFVDESALVVGVRTL 434 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: 427 Number of extensions: 24 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: 382 Length of database: 448 Length adjustment: 31 Effective length of query: 351 Effective length of database: 417 Effective search space: 146367 Effective search space used: 146367 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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