Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate BWI76_RS10270 BWI76_RS10270 acetylornithine deacetylase
Query= curated2:B2FIC0 (375 letters) >FitnessBrowser__Koxy:BWI76_RS10270 Length = 391 Score = 111 bits (277), Expect = 4e-29 Identities = 99/313 (31%), Positives = 141/313 (45%), Gaps = 24/313 (7%) Query: 66 HTDVVPTGPRESWTSDPFTPHIRDGVLYGRGAADMKGSVAAFVVAAEQFVADHPDHPGTL 125 H D VP G WTSDPFT R G LYGRGA D KG + A V A A GTL Sbjct: 77 HIDTVPAG--SGWTSDPFTLAERGGRLYGRGACDAKGPLVAMVEALRLLAATRQRWSGTL 134 Query: 126 AVLLTSDEEGDAIDGVRHVARLFAARGQRIDWCITGEPSSTATLGDLLRVGRRGSLSAKL 185 + T+DEE A +G + R ID+ + GEP+S AT +GSL ++ Sbjct: 135 MGVFTADEE-VASEGAKFYVR---DNPPAIDFAVIGEPTSNATFS-----AHKGSLRPRV 185 Query: 186 RVQGVQGHVAYPEKARNPIHQAAPALAELCARRWDD----GYESFPPTSLQISNIHAGTG 241 RV+GV H PE N I+Q+A L + ++ SL ++ IH G Sbjct: 186 RVKGVTAHSGTPELGVNAIYQSARLLGLIEEAHHQQVRCRCHDLVGNASLTVTRIHGG-H 244 Query: 242 ANNVIPGELDVDFNIRYNPHWDAPKLEAEITALLE----RHGLQYTLKWHRSGEPFYTPE 297 A+NV+P ++ + R P D ++AE+ LL+ G++ + + T Sbjct: 245 ADNVVPDSCELLLDRRMVPGEDEAVVKAELQQLLDHAHAHAGVEAEIIAWQPTTGGATQT 304 Query: 298 GTLRAIARAVLA---EHIGRAPEESTGGGTSDARFIAPLGAQCIEVGPVNASI-HQVDEN 353 + AI LA H P G D LGA+ + +GP + ++ H+ DE Sbjct: 305 DSSEAIVEQSLAACRRHGQSEPGPFGFQGGCDLVHFRSLGAKGVVIGPGSLAVAHKPDEF 364 Query: 354 VRVDDLEALPGLY 366 V VD+ A +Y Sbjct: 365 VPVDEFIAAAYIY 377 Lambda K H 0.319 0.137 0.421 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: 428 Number of extensions: 28 Number of successful extensions: 4 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: 391 Length adjustment: 30 Effective length of query: 345 Effective length of database: 361 Effective search space: 124545 Effective search space used: 124545 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 (21.7 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