Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate WP_011384771.1 AMB_RS11990 acetylornithine deacetylase
Query= curated2:B2FIC0 (375 letters) >NCBI__GCF_000009985.1:WP_011384771.1 Length = 404 Score = 103 bits (257), Expect = 8e-27 Identities = 104/346 (30%), Positives = 152/346 (43%), Gaps = 38/346 (10%) Query: 49 NLWATHGLG-APVLVLLGHTDVVPTGPRESWTSDPFTPHIRDGVLYGRGAADMKGSVAAF 107 N++AT G P +VL GHTDVVP ++ W+ DPF DG LYGRG ADMK +A Sbjct: 75 NIFATIGPSDVPGIVLSGHTDVVPVDGQD-WSRDPFHLVQADGKLYGRGTADMKSFIAIC 133 Query: 108 VVAAEQFVADHPDHPGTLAVLLTSDEEGDAIDGVRHVARLFAARGQRIDWCITGEPSSTA 167 + A QF A P A + DEE + GVR + A R CI GEP+ Sbjct: 134 LAMAPQFAAAPLRMPVHFA--FSYDEEVGCV-GVRRLIDDLAHLPVRPALCIVGEPTDMK 190 Query: 168 TLGDLLRVGRRGSLSAKLRVQGVQGHVAYPEKARNPIHQAAPALAELCARR--------W 219 + +G +G S + V+G + H A + N I AA + L A + + Sbjct: 191 AV-----IGHKGKKSVRCHVEGHECHSALNHQGVNAIEIAAEMVTRLRALQRRIREQGPF 245 Query: 220 DDGYESFPPTSLQISNIHAGTGANNVIPGELDVDFNIRYNPHWDAPKLEAEI-------- 271 D GY+ P T++ + GT A N++P +F IR P D L AE+ Sbjct: 246 DLGYQP-PYTTVHTGTMQGGT-ALNIVPKSCSFEFEIRNLPDHDPETLMAEVRGWAQDLV 303 Query: 272 ---TALLERHGLQYTLKWHRSGEPFYTPEGTLRAIARAVLAEHIGRAPEESTGGGTSDAR 328 A+ E G+ TL H S E + A R V A + A + S T++A Sbjct: 304 PEMLAVSEASGI--TLDEHNSTPGLGMDE--MDAAVRLVCA--LSGANQTSKVAFTTEAG 357 Query: 329 FIAPLGAQCIEVGPVN-ASIHQVDENVRVDDLEALPGLYQRLVERL 373 G + +GP + H+ DE + ++ + +RL+ + Sbjct: 358 LFQQAGIPAVVIGPGSITQAHRPDEFITLEQVAQCEDFLRRLLAHM 403 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: 359 Number of extensions: 20 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: 404 Length adjustment: 30 Effective length of query: 345 Effective length of database: 374 Effective search space: 129030 Effective search space used: 129030 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