Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate SMa1836 SMa1836 acetylornithine deacetylase
Query= curated2:A0L3N2 (380 letters) >FitnessBrowser__Smeli:SMa1836 Length = 374 Score = 96.3 bits (238), Expect = 1e-24 Identities = 96/331 (29%), Positives = 148/331 (44%), Gaps = 33/331 (9%) Query: 45 GHVENFYARLGSK-GRNFTFAGHTDVVGAGDTSRWSSDPFAATLEEGYITGRGAVDMKGG 103 G N +A +G K R + +GH DVV A +T W+SDPF +E + GRG DMKG Sbjct: 47 GDRSNIFATIGPKEARGYIISGHMDVVPAAETG-WTSDPFRLRVEADRLYGRGTTDMKGF 105 Query: 104 LACMVAATARFLAARPHFAQQHSLSFLITGDEEGDALDGTLKVLQWLESQQEKMDYCLVG 163 LA ++AA + LAA P + L ++ DEE + + E ++ + ++G Sbjct: 106 LAAVLAAVPK-LAAMP---LRRPLHLALSYDEEAGCRGVPHMIARLPELCRQPLG-AIIG 160 Query: 164 EPTSAAQLGDCIKNGRRGSVNGRLTIRGVQGHVAYPHLVDNPIHRAAPVL----AAISSM 219 EPT + +G RLT+RG GH + P N IH A VL A + Sbjct: 161 EPTGMRAI-----RAHKGKAAARLTVRGRSGHSSRPDQGLNAIHGVAGVLTQAVAEADRL 215 Query: 220 TFDQGDRFFQP--TSLQFTAVQSGGSATNVVPGELTAGFNIRFSAMHTPESLEARIRQVL 277 + F+P +SLQ V+ GG A N++P F R + P L A +R+ Sbjct: 216 VGGPFEHVFEPPYSSLQIGTVK-GGQAVNIIPDSCEVEFEARAISGVDPAELLAPVRKTA 274 Query: 278 D-----GAEVDYDLQMMTSGLPFITEGGPLVEAVKATVAQVTGLEPQLSTGGGTSDARFI 332 + G EV++ ++ + PL A + ++TG E + GT +A Sbjct: 275 EALTTLGFEVEWQ-ELSAYPALSLEPDAPLA----ALLEELTGREALPAVSYGT-EAGLF 328 Query: 333 SRHCVQTVEFGL--VGSTMHKVDERVPVADL 361 R + + G +G HK DE + + +L Sbjct: 329 QRAGIDAIICGPGDIGRA-HKPDEYILIDEL 358 Lambda K H 0.320 0.136 0.404 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: 359 Number of extensions: 22 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: 380 Length of database: 374 Length adjustment: 30 Effective length of query: 350 Effective length of database: 344 Effective search space: 120400 Effective search space used: 120400 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 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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