Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate AZOBR_RS31030 AZOBR_RS31030 acetylornithine deacetylase
Query= curated2:B2FIC0 (375 letters) >FitnessBrowser__azobra:AZOBR_RS31030 Length = 398 Score = 96.3 bits (238), Expect = 1e-24 Identities = 103/343 (30%), Positives = 149/343 (43%), Gaps = 39/343 (11%) Query: 49 NLWATHG-LGAPVLVLLGHTDVVPTGPRESWTSDPFTPHIRDGVLYGRGAADMKGSVAAF 107 NL+AT G + + L GHTDVVP ++ W+SDPFT RDG L+GRG ADMKG +AA Sbjct: 65 NLYATIGPMDRGGVCLSGHTDVVPVDDQD-WSSDPFTLTERDGKLFGRGTADMKGFIAAA 123 Query: 108 VVAAEQFVADHPDHPGTLAVLLTSDEEGDAIDGVRHVARLFAARGQRIDWCITGEPSSTA 167 + A F+A + P A + DEE + GV + A + CI GEP+ Sbjct: 124 LAMAPDFLAANLTTPVHYA--FSYDEELGCL-GVPGLLTQLAGMAVKPRLCIVGEPTRMR 180 Query: 168 TLGDLLRVGRRGSLSAKLRVQGVQGHVAYPEKARNPIHQAAPALAEL--CARR------W 219 + VG +G ++ + RV G H + + N + AA ++ L RR + Sbjct: 181 VI-----VGHKGKVALRCRVHGHACHSSLAPQGVNAVEYAAELVSFLRGMGRRFAEQGPF 235 Query: 220 DDGYESFPPTSLQISNIHAGTGANNVIPGELDVDFNIRY-NPHWDAP----------KLE 268 D Y+ P T++ + GT A N++P + +F IR+ H AP LE Sbjct: 236 DHDYD-IPYTTVHTGVMEGGT-ARNIVPSDASFEFEIRHLADHPVAPMLKELRDFAKTLE 293 Query: 269 AEITALLERHGLQY-TLKWHRSGEPFYTPEGTLRAIARAVLAEHIGRAPEESTGGGTSDA 327 E+ A+ G + TL TP + LAE G GT A Sbjct: 294 PEMRAVRPDAGFSWETLS---DSPALDTPPESEEVTLVKNLAEQNGHG---KVAFGTEGA 347 Query: 328 RFIAPLGAQCIEVGPVN-ASIHQVDENVRVDDLEALPGLYQRL 369 F + + GP + H+ DE V + +L RL Sbjct: 348 LFTSIANIPAVVCGPGDIEQAHKPDEYVELSELARAERFLHRL 390 Lambda K H 0.319 0.137 0.421 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: 403 Number of extensions: 18 Number of successful extensions: 3 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: 375 Length of database: 398 Length adjustment: 30 Effective length of query: 345 Effective length of database: 368 Effective search space: 126960 Effective search space used: 126960 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