Align Succinyl-diaminopimelate desuccinylase 2; SDAP desuccinylase 2; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase 2 (uncharacterized)
to candidate HSERO_RS13940 HSERO_RS13940 acetylornithine deacetylase
Query= curated2:Q1GMM6 (395 letters) >FitnessBrowser__HerbieS:HSERO_RS13940 Length = 390 Score = 74.3 bits (181), Expect = 6e-18 Identities = 61/199 (30%), Positives = 89/199 (44%), Gaps = 14/199 (7%) Query: 77 NGHTDVVPIGDPKDWTVDPFGAEIRDGILYGRGSTDMKSGVAAFAAAAIEFVNETPPDGR 136 +GHTDVVP+ D + W DPF +DG LY RGS DMK +A A E++ P Sbjct: 74 SGHTDVVPV-DGQKWDTDPFKLTEKDGALYARGSCDMKGFIATALALVPEYL-AMPRVKP 131 Query: 137 VIIAITGAEETGSPDGTRAIVQWMEANDIRADHFIVGEPTSLKSIGDAIKIGRRGTITVF 196 + +A + EE G G +++ + I+ D +VGEPTS+ + + +G Sbjct: 132 IHLAFSFDEEIGC-IGAPVMLEEIVKRGIKVDGCVVGEPTSMN-----VVVAHKGINVFA 185 Query: 197 LTVTGVQGHSGYPEKANNPL---PALVDLLQGF--GQAAMDEGTEFF-APSTLAITTIDT 250 V G HS + N + L+ ++ F G A +FF P + T Sbjct: 186 CKVHGKSAHSSLTPQGCNAIEHAARLICAIRDFADGYKANGPYDQFFDVPFSTMTTNQIR 245 Query: 251 GNPARNVIPATCKATLSIR 269 G A N IP C+ T R Sbjct: 246 GGIAVNTIPELCEFTYEFR 264 Lambda K H 0.318 0.135 0.407 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: 348 Number of extensions: 16 Number of successful extensions: 3 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: 395 Length of database: 390 Length adjustment: 31 Effective length of query: 364 Effective length of database: 359 Effective search space: 130676 Effective search space used: 130676 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 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