Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate WP_012044335.1 BBTA_RS20040 acetylornithine deacetylase
Query= curated2:B7KVW2 (385 letters) >NCBI__GCF_000015165.1:WP_012044335.1 Length = 432 Score = 82.4 bits (202), Expect = 2e-20 Identities = 73/236 (30%), Positives = 101/236 (42%), Gaps = 37/236 (15%) Query: 7 LALAQALIRCPSVTPEEGGALSFLADRLSRAGFSVER------PVFSEPGTPDIQNL--- 57 +A Q L++ S+ E +LA G+ V+R + P + N+ Sbjct: 28 VAFLQQLVQFRSLRGAEAPVQDWLAGEFETRGYEVDRFSLADVDLMRHPKAAPMDNIALD 87 Query: 58 -----YARIGTAGP--VLVFAGHTDVVPPGETEAWTHGPFSGEVADGFLYGRGAVDMKGG 110 A + AG L+ GH DVVP G T+ W P+ V DG++ GRGA DMK G Sbjct: 88 GSKQVVATLDGAGKGRSLILQGHIDVVPEGPTDLWNDPPYEAIVRDGWMIGRGAQDMKAG 147 Query: 111 IACMLAA-----TLAFLDRHRPDFGGSIAFLVTGDEEGPAVNGTVKLLDWAKARGERFDH 165 ++ M+ A T F+ PD G I L T EE NG + L RG D Sbjct: 148 VSAMIFALDAIKTAGFV----PD--GRI-HLETVTEEESTGNGALSTL----MRGYTADA 196 Query: 166 CLLGEPTNPDTLGEMIKIGRRGSLTGRITVHGRQGHVAYPHRAENPIPGLLRLASA 221 CL+ EPT G + + G++ R+ V G HVAY N I + L A Sbjct: 197 CLIPEPT-----GHTLTRAQVGAIWFRLRVRGTPVHVAYAETGTNAILSAMHLIRA 247 Lambda K H 0.319 0.137 0.415 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: 429 Number of extensions: 20 Number of successful extensions: 1 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: 385 Length of database: 432 Length adjustment: 31 Effective length of query: 354 Effective length of database: 401 Effective search space: 141954 Effective search space used: 141954 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 Apr 10 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