Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate WP_012405267.1 BPHY_RS30215 acetylornithine deacetylase
Query= curated2:B2FIC0 (375 letters) >NCBI__GCF_000020045.1:WP_012405267.1 Length = 389 Score = 103 bits (257), Expect = 8e-27 Identities = 79/232 (34%), Positives = 114/232 (49%), Gaps = 20/232 (8%) Query: 49 NLWATHGLG-APVLVLLGHTDVVPTGPRESWTSDPFTPHIRDGVLYGRGAADMKGSVAAF 107 NL+AT G +VL GHTDVVP + WT +PF +G LYGRG ADMKG +A+ Sbjct: 54 NLFATIGPDEGGGIVLSGHTDVVPVDG-QPWTVEPFRLSETEGRLYGRGTADMKGFIASA 112 Query: 108 VVAAEQFVADHPDHPGTLAVLLTSDEEGDAIDGVRHVARLFAARGQRIDWCITGEPSSTA 167 + A FVA P LA + DEE + GVR + A R + C+ GEP+ Sbjct: 113 LAAVPTFVARDLRVPVHLA--FSYDEEVGCL-GVRPMLAELAQRAHKPALCLIGEPTELK 169 Query: 168 TLGDLLRVGRRGSLSAKLRVQGVQGHVAYPEKARNPIHQAAPALAEL--------CARRW 219 + +G +G L+ + +V+G H AY N I AA + L R Sbjct: 170 PV-----LGHKGKLAMRCQVKGAPCHSAYAPNGVNAIQYAARLVNRLEEIGDQLAAPERH 224 Query: 220 DDGYESFPPTSLQISNIHAGTGANNVIPGELDVDFNIRYNPHWDAPKLEAEI 271 D+ ++ PP S + + G A N++P E + DF +R P +DA ++ E+ Sbjct: 225 DERFD--PPYSTVQTGVIKGGRALNIVPAECEFDFEVRALPGYDATEVADEL 274 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: 398 Number of extensions: 25 Number of successful extensions: 5 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: 375 Length of database: 389 Length adjustment: 30 Effective length of query: 345 Effective length of database: 359 Effective search space: 123855 Effective search space used: 123855 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