Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate WP_086508437.1 BZY95_RS02550 acetylornithine deacetylase
Query= curated2:B7KVW2 (385 letters) >NCBI__GCF_002151265.1:WP_086508437.1 Length = 432 Score = 88.6 bits (218), Expect = 3e-22 Identities = 123/406 (30%), Positives = 163/406 (40%), Gaps = 52/406 (12%) Query: 7 LALAQALIRCPSVTPEEGGALSFLADRLSRAGFSVERPVFSEPG-------------TPD 53 LAL L+R SV E GAL + R V R PG Sbjct: 21 LALTCDLVRGYSVLGREHGALETMERWFERLELPVTRVPLDAPGFAAHAHRVPTEWDCAG 80 Query: 54 IQNLYARIG--TAGPVLVFAGHTDVVPPGETEAWTHGPFSGEVADGFLYGRGAVDMKGGI 111 NL A++ + GP LVF GH DVVP T+ WT P+ DG+LYGRGA DMK GI Sbjct: 81 RYNLVAQLNADSPGPHLVFNGHLDVVPAEPTDMWTRLPWEPWEKDGWLYGRGAGDMKAGI 140 Query: 112 ACMLAATLAFLDRHRPDFGGSIAF---LVTGDEEGPAVNGTVKLLDWAKARGERFDHCLL 168 A M A A G I F L T EE NG + L +G D L+ Sbjct: 141 AAMTLAVQAVRQA-----GVVIDFPLTLQTVIEEECTGNGALACLH----QGFSGDFVLI 191 Query: 169 GEPTNPDTLGEMIKIGRRGSLTGRITVHGRQGHVAYPHRAENPIPGLLRLASALTA--DP 226 EP G I G+ G L R+ + G HV N I L+ A A Sbjct: 192 PEP-----FGARIYAGQVGVLWFRMRLDGVPAHVLDTRAGRNAIETLIEYLPAFKALEAE 246 Query: 227 LDG--GTAHFDA----SNLEFTTIDVGNPATNVIPASAKAVFNVRFNDDWTADTLGAEIR 280 ++G A +DA NL I+ GN A++V PA A V F T D + +R Sbjct: 247 INGLPRQAPYDALDSPFNLSIGKIEGGNWASSV-PAHAILEGRVGFPPGMTPDEVMERVR 305 Query: 281 -----RRLEAA-AGNAVRFSLDLQPSNSPAFLTQPDA-FVDRVADAIEAETGRRPALSTT 333 R E A AG A R ++ S L +A ++ ++ + G PA + Sbjct: 306 HCVATRHAELADAGPAPR--VEFHGFRSEGHLVDLEAPGIELLSRCHQDLLGEPPATYLS 363 Query: 334 GGTSDAR--FIKDACPVIEFGLVGRTMHETDERVAVADLDRLTAIY 377 T+D R + A +G V + +H DE V + + + Y Sbjct: 364 TCTTDLRAFHVSGAINGTCYGPVAQRIHGVDECVEIDSIRHVLTTY 409 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: 467 Number of extensions: 26 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: 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