Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate GFF3695 PS417_18910 acetylornithine deacetylase
Query= curated2:Q2P492 (376 letters) >FitnessBrowser__WCS417:GFF3695 Length = 385 Score = 97.1 bits (240), Expect = 7e-25 Identities = 103/342 (30%), Positives = 151/342 (44%), Gaps = 33/342 (9%) Query: 49 NLWATHGSG-APVLVLLGHTDVVPPGPREAWTSDPFDPQIRDGVLYGRGVADMKGSVAAF 107 NL AT G P +VL GHTDVVP + W+ PFD +DG LYGRG ADMKG +A Sbjct: 51 NLLATIGPAEVPGIVLSGHTDVVPV-EGQRWSVAPFDLTEKDGKLYGRGTADMKGYIACV 109 Query: 108 VVAAEQFVAAHRAHAGTLAVLLTSDEEGDAIDGVRRVANLFLERGQAIDWCITGEPSSTE 167 + V A + + + L+ DEE + GVR + F E+ C+ GEP+ + Sbjct: 110 LACVPALVKA--SLRMPVHIALSYDEEVGCL-GVRSLIERFHEQPVKPLLCVIGEPTELK 166 Query: 168 RLGDLLRVGRRGSLSGTLTVKGVQGHVAYPHKARNPIHLAAPALAELV-------ARQWD 220 + +G +G L+ V G H AY N I AA ++ELV A Q Sbjct: 167 PV-----LGHKGKLAMRCHVHGAACHSAYAPAGVNAIEYAACLISELVRLGETLKAPQHL 221 Query: 221 DGFESFPP--TSLQVSNIHAGTGANNVIPGELQVAFNLRYTPHWDAPRLEAEITALLDRH 278 D + F P +++Q I+ G A N++P + F +R P D ++ ++ A ++ Sbjct: 222 D--QRFAPAFSTVQTGLINGGK-ALNIVPQDCSFDFEVRSLPAQDPWQVARQLQAYAEQT 278 Query: 279 ALDYALRWHRSGEPFYTPE--------GRLRSVAREVLGAFAGAPPEESTGGGTSDARFI 330 L A+R E L S A E + F G+ + GT F Sbjct: 279 LLP-AMRAVSEQSAISLSELSSYPGLATSLESQAAEWVAQFCGSREFATVAFGTEGGLF- 336 Query: 331 APLGAQCIEVGPVNASI-HQVDEHVRVADLQALPALYRTLIE 371 G + GP + H+ DE + VA LQA + ++E Sbjct: 337 DQAGIPTVVCGPGSMEQGHKPDEFISVAQLQACDRMLARVLE 378 Lambda K H 0.319 0.137 0.417 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: 328 Number of extensions: 19 Number of successful extensions: 2 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: 376 Length of database: 385 Length adjustment: 30 Effective length of query: 346 Effective length of database: 355 Effective search space: 122830 Effective search space used: 122830 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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