Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate Pf6N2E2_1339 Acetylornithine deacetylase (EC 3.5.1.16)
Query= curated2:B2IDW3 (383 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1339 Length = 394 Score = 99.8 bits (247), Expect = 1e-25 Identities = 106/337 (31%), Positives = 146/337 (43%), Gaps = 33/337 (9%) Query: 55 NLYARFGSGAPC-LVFAGHTDVVPVGTATDWRFDPFAAKVEDGQLWGRGAADMKGAIAAF 113 NL A G P +V +GHTDVVPV W DPF DG+ +GRG ADMKG +A+ Sbjct: 59 NLLASIGPAVPGGVVLSGHTDVVPVDGQA-WTVDPFCLTEMDGKWFGRGTADMKGYLASV 117 Query: 114 TAAALTFIEQHKDFKGSIAFLITGDEEGPSINGTIKLLKWAAEQGEHFDHCIVGEPTNPQ 173 AA F+ + + + DEE + G LL+ + C++GEPT + Sbjct: 118 LAAVPVFLS--SPLRRPVHLAFSYDEEVGCL-GVHSLLEVLVRRIAQPALCLIGEPTQLR 174 Query: 174 VLGDMIKIGRRGSLNGILSITGKQGHVAYPHRADNPVPKLMRLIEAL--IGTPLDEGTDH 231 + +G +G L + G H AY N + + RLI L IG L E + H Sbjct: 175 PV-----LGHKGKLAMRCHVRGAACHSAYAPYGVNAIEQAARLIGRLGEIGAQLAEPSRH 229 Query: 232 ---FD--ASNLEVVALSSGTDAYNVIPAKAEARFNIR----FNDLWTPQTL----ELELL 278 FD S ++V + GT A N++PA F +R F+ L + L E LL Sbjct: 230 DPRFDPACSTVQVGVVHGGT-ALNIVPADCRFDFEVRALPDFDPLVVVEQLQGYAEQTLL 288 Query: 279 ARLDSVAEGTAYTLTFEPCNAL-AFITKPDQFTDLVANAIEKQTGRRPELSTTGGTSDAR 337 + +VA TA + FEP +A T PD A I + G + GT Sbjct: 289 PAMQAVAGDTA--IRFEPLSAYPGLATSPD---SAAARLIAQLCGSDAFGTVAFGTEGGL 343 Query: 338 FISAYCPVVEFGLVGQTM-HMVDERVSVADIATLETI 373 F A P V G H DE VSV +A + + Sbjct: 344 FHQAGVPTVVCGPGSMDQGHKPDEYVSVEQMAACDRL 380 Lambda K H 0.319 0.136 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: 360 Number of extensions: 18 Number of successful extensions: 2 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: 383 Length of database: 394 Length adjustment: 30 Effective length of query: 353 Effective length of database: 364 Effective search space: 128492 Effective search space used: 128492 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