Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase; EC 3.5.1.18 (characterized)
to candidate WP_012114603.1 XAUT_RS13000 acetylornithine deacetylase
Query= SwissProt::Q9JYL2 (381 letters) >NCBI__GCF_000017645.1:WP_012114603.1 Length = 397 Score = 105 bits (262), Expect = 2e-27 Identities = 104/331 (31%), Positives = 143/331 (43%), Gaps = 33/331 (9%) Query: 61 PVVCFAGHTDVVPTGPVEKWDSPPFEPAERDGRLYGRGAADMKTSIACFVTACERFVAKH 120 P + + HTDVV + W S PF A RDGRLYGRG +DMK IAC + A F A Sbjct: 65 PGIVLSAHTDVVAVEG-QPWTSNPFRIAARDGRLYGRGTSDMKGFIACVLAALPAFAAAD 123 Query: 121 PNHQGSIALLITSDEEGDALDGTTKVVDVLKARDELIDYCIVGEPTAVDKLGDMIKNGRR 180 P +AL S +E G +V + A CIVGEPTA+ +K + Sbjct: 124 PLTPVHVAL---SYDEEIGCKGAGDLVAAVAALPARPLMCIVGEPTAM-----KVKRAHK 175 Query: 181 GSLSGNLTVKGKQGHIAYPHLAINPVHT---FAPALLELTQEV--WDEGNEYFPP-TSFQ 234 G T G+ GH A PH A N V A L +L E+ + + PP + Sbjct: 176 GKTGWRATALGRTGHSALPHQAANAVTALARLAARLADLADELKTGAQDRAFDPPYATLH 235 Query: 235 ISNINGGTGATNVIPGELNVKFNFRFSTESTE-------AGLKQRVHAILDKHGVQYDLQ 287 I +++GG GA NV+P ++F R S L Q A+L + DL Sbjct: 236 IGSLHGG-GALNVVPDRAVMEFELRTIPGSDTNTLFRRIEALVQEARAVLKAQAPEADLL 294 Query: 288 W-SCSGQPFLTQAGKLTDVARAAIAETCGIEAELSTTG-GTSDGRFIKAIAQELIELGPS 345 S P L A + AA+A G T GT G + +A L+ GP Sbjct: 295 LEELSAYPALATASDAPEA--AAVARLTGDNGVPGTIAFGTEAGLYAQAGIPTLV-CGPG 351 Query: 346 N-ATIHQINENVRLNDIPKLSAVYEGILARL 375 + A H+ +E + ++ + A +LARL Sbjct: 352 DIARAHKADEWIGREELAQCDA----MLARL 378 Lambda K H 0.317 0.135 0.400 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: 384 Number of extensions: 23 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: 381 Length of database: 397 Length adjustment: 30 Effective length of query: 351 Effective length of database: 367 Effective search space: 128817 Effective search space used: 128817 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 (21.6 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