Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate 5208470 Shew_0982 hypothetical protein (RefSeq)
Query= curated2:A7IH44 (375 letters) >FitnessBrowser__PV4:5208470 Length = 508 Score = 59.7 bits (143), Expect = 2e-13 Identities = 59/188 (31%), Positives = 80/188 (42%), Gaps = 24/188 (12%) Query: 46 PIPNLYARIGTDG--PNLCFAGHVDVVPEGDAT--QWHHAPFAGTVEDGVLHGRGAVDMK 101 P LY G D P F H DVVP + QW PFAG V+DG + GRG +D K Sbjct: 105 PFSLLYTWKGKDPSLPPALFYAHQDVVPVPSESRDQWAVDPFAGAVQDGYIWGRGVLDDK 164 Query: 102 GAVAAFLAAA---LAFGRPQRGSLSFLITGDEEGPALDGTVKVVEWLKARGETIDHCVLG 158 + L AA + G +L F+ DEE +G + + L+ RG V+ Sbjct: 165 NQIHGILEAAEMKIKEGWQPSRTLYFVFGQDEEVGGPEGAKYIADVLEQRGIKRFAFVID 224 Query: 159 E------------PTNPDALGDAFKVGRRGSLSGILTVKGVQGHVAYPHLADNPIPRLLK 206 E P N +G + ++G +S L + G+ GH + P N I L K Sbjct: 225 ESAPLTPGIFPGIPDNTALIG----IAQKGFVSLELAMNGIGGHSSQPPEESN-IGILAK 279 Query: 207 LIGDLTAA 214 I L AA Sbjct: 280 AITKLEAA 287 Lambda K H 0.320 0.138 0.411 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: 411 Number of extensions: 19 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: 375 Length of database: 508 Length adjustment: 32 Effective length of query: 343 Effective length of database: 476 Effective search space: 163268 Effective search space used: 163268 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: 51 (24.3 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