Align Succinyl-diaminopimelate desuccinylase 2; SDAP desuccinylase 2; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase 2 (uncharacterized)
to candidate WP_043752928.1 MNOD_RS35275 acetylornithine deacetylase
Query= curated2:A3QGR1 (377 letters) >NCBI__GCF_000022085.1:WP_043752928.1 Length = 394 Score = 71.6 bits (174), Expect = 3e-17 Identities = 63/208 (30%), Positives = 91/208 (43%), Gaps = 17/208 (8%) Query: 53 RPAQLALAGHTDVVPPGDLSRWQTPPFAATLVDGMLIGRGAVDMKSGLAVMLAAVEDHIA 112 R + L+GHTDVV P W PF + DG +IGRGAVDMK A+ LA V + +A Sbjct: 67 RDGGVVLSGHTDVVSPAGQD-WSGDPFRLRVADGRVIGRGAVDMKGFCALCLALVPEMLA 125 Query: 113 CYGLPKANWQFIVTSDEEGEAEHGTRTLVERLKAQSRLPKYCVVAEPTADKQAGDVIKIG 172 + +++ DEE G ++ RL A P +V EPT G + Sbjct: 126 AE--LRTPIHILLSYDEETTC-LGVVDVIARLGADLPRPGAVIVGEPT-----GLDVADA 177 Query: 173 RRGAISARLTLKGKQGHVAYPKNAVNALHMAARVMQALEALIWD-------EGSDDFPGT 225 + + T+ G + H A P NA+ AA ++ L + G D P T Sbjct: 178 HKSVATYVTTVHGHEAHSAKPALGANAIMAAAELVAELNRIADQMIARGDPSGRFDPPYT 237 Query: 226 SLQVTHVDSGAFTDNIVPGSCEICFNIR 253 ++ V V G NI+P +C + R Sbjct: 238 TVHV-GVIGGGTVRNILPKTCAFEWEFR 264 Lambda K H 0.320 0.135 0.405 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: 327 Number of extensions: 18 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: 377 Length of database: 394 Length adjustment: 30 Effective length of query: 347 Effective length of database: 364 Effective search space: 126308 Effective search space used: 126308 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