Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate N515DRAFT_3767 N515DRAFT_3767 acetylornithine deacetylase
Query= curated2:A5FYQ7 (371 letters) >FitnessBrowser__Dyella79:N515DRAFT_3767 Length = 366 Score = 62.8 bits (151), Expect = 1e-14 Identities = 91/333 (27%), Positives = 131/333 (39%), Gaps = 50/333 (15%) Query: 38 GFSIEWLRFGEVS-NLVARRGSGSPHFGFAGHTDVVPPGEGWRHDPFAAVIEDGLLFGRG 96 GF + FG + NL A RG P + F H D VP W DP +E G G Sbjct: 42 GFEVTVTDFGAGAVNLYAVRGK--PKYLFNVHLDTVPDSPHWSADPHVLRVEGDRAIGLG 99 Query: 97 AVDMKGAIAAFVAALAARPANHAGTISLLITGDEEGDAVDGTRRILDHLAASGALPEFCL 156 A D+KGA AA VA A G ++LL++ DEE + R + + E + Sbjct: 100 ACDIKGAAAALVAVANAT----QGDMALLLSTDEEAN----DARCIAGFLKDHPVYEAVI 151 Query: 157 VGEPTCRARLGDTIKIGRRGSISAHVTVRGVQGHVAYPHL-ADNPLHRL----IPALEAL 211 V EPT G+ + + RG S + G GH + +D+ +H+ + AL+ + Sbjct: 152 VAEPT----KGEAV-LAHRGIHSVQMRFSGKAGHASGEQKPSDSAVHQAVRWGVAALDYV 206 Query: 212 RATTLDEGTAWFEPSSLQITSVDTGNKAGNVIPASASARLNIRFNDRHTGPDLAAWIRDT 271 + E I V+ G KA NVI +A R Sbjct: 207 ESQA-HERFGGLTGLRFNIGKVEGGIKA-NVIAPTADVRFGF------------------ 246 Query: 272 VARHAPGAACDIGISGEAFLTEPGPVTTLFSEAVAAVTGITPKLDTGGGTSDARFIAAHC 331 R P D + L EP PV F E + P DT T++ R +AA Sbjct: 247 --RPLPSMDADRMLETFRTLVEPQPVE--FGETFRGDS--LPAGDT--ATAETRRLAARD 298 Query: 332 PVAEFGL-VGTSMHRVDEAVPVSELRALAEIYG 363 E G+ VG +++ EA S ++ +YG Sbjct: 299 LADELGIPVGNAVNFWTEAALFSAAGYISFVYG 331 Lambda K H 0.320 0.137 0.412 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: 397 Number of extensions: 26 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 371 Length of database: 366 Length adjustment: 30 Effective length of query: 341 Effective length of database: 336 Effective search space: 114576 Effective search space used: 114576 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: 49 (23.5 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