Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate WP_003562887.1 RLEG_RS24935 acetylornithine deacetylase
Query= curated2:B2FIC0 (375 letters) >NCBI__GCF_000023185.1:WP_003562887.1 Length = 373 Score = 103 bits (256), Expect = 1e-26 Identities = 115/342 (33%), Positives = 151/342 (44%), Gaps = 31/342 (9%) Query: 45 GDVDNLWATHG-LGAPVLVLLGHTDVVPTGPRESWTSDPFTPHIRDGVLYGRGAADMKGS 103 GD NL+AT G P +L GH DVVP WTSDPF +LYGRGA DMKG Sbjct: 47 GDRSNLFATIGPKETPGYILSGHMDVVPAAGG-GWTSDPFRLRAEADILYGRGATDMKGF 105 Query: 104 VAAFVVAAEQFVADHPDHPGTLAVLLTSDEEGDAIDGVRH-VARLFAARGQRIDWCITGE 162 +AA + A VA P LA + DEE GV H +ARL + I GE Sbjct: 106 LAAVLAAVPALVASPLRQPVHLA--FSYDEEA-GCRGVPHMIARLPELCATPLG-AIIGE 161 Query: 163 PSSTATLGDLLRVGRRGSLSAKLRVQGVQGHVAYPEKARNPIHQAAPALAELCAR----R 218 PS + +G +A+L V+G GH + P++ N IH LA CAR R Sbjct: 162 PSGMRAIR-----AHKGKAAARLTVRGRSGHSSRPDQGLNAIHAITDILA--CARAEAER 214 Query: 219 WDDG-YESF---PPTSLQISNIHAGTGANNVIPGELDVDFNIRYNPHWDAPKLEAEITAL 274 G YE P +SLQ+ + G A N+IP + +F R D L A + A Sbjct: 215 LTRGPYEPVFEPPYSSLQVGTLKGGQ-AVNIIPDSCEAEFEARAISGVDPITLLAPLRAS 273 Query: 275 LE-RHGLQYTLKWHRSGEPFYTPEGTLRAIA--RAVLAEHIGRAPEESTGGGTSDARFIA 331 E L + + W E P +L A A A+L+E G P + GT +A Sbjct: 274 AEGLSQLGFQIDWR---ELSAYPALSLAADAPLAALLSELTGIEPLAAVSYGT-EAGLFQ 329 Query: 332 PLGAQCIEVGPVN-ASIHQVDENVRVDDLEALPGLYQRLVER 372 G I GP + H+ DE + +L A + + L R Sbjct: 330 RAGIDAIICGPGDIGRAHKPDEFILTGELLACQAMVEALGRR 371 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: 425 Number of extensions: 34 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: 375 Length of database: 373 Length adjustment: 30 Effective length of query: 345 Effective length of database: 343 Effective search space: 118335 Effective search space used: 118335 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 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