Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate GFF769 PGA1_c07830 acetylornithine deacetylase ArgE
Query= curated2:Q2P492 (376 letters) >FitnessBrowser__Phaeo:GFF769 Length = 384 Score = 101 bits (252), Expect = 3e-26 Identities = 113/398 (28%), Positives = 178/398 (44%), Gaps = 42/398 (10%) Query: 1 MNDVLDLTCDLIARASVTPE-DAGCQALLAGRLTAAGFACEHL--RLGEVDNLWATHGSG 57 M + DLIA +V+ + + A LA RL G + + G+ NL+AT G Sbjct: 2 MEQTTRILSDLIAYPTVSADSNLEMIAYLANRLEDCGARVDVMFDAGGQKANLFATLGPD 61 Query: 58 APV-LVLLGHTDVVPPGPREAWTSDPFDPQIRDGVLYGRGVADMKGSVAAFVVAAEQFVA 116 +VL GH+DVVP ++ WTSDPF + DG LYGRG DMKG +AA + A +F Sbjct: 62 TDGGIVLSGHSDVVPVTDQD-WTSDPFTMEEWDGRLYGRGTCDMKGFIAATLAMAPKF-- 118 Query: 117 AHRAHAGTLAVLLTSDEEGDAIDGVRRVANLFLERGQAIDWCITGEPSSTERLGDLLRV- 175 A + + T DEE I G + ERG + GEP+S +RV Sbjct: 119 AEQISRRPIHFAFTYDEEVGCI-GAGHLVQALRERGLKPRLALIGEPTS-------MRVV 170 Query: 176 -GRRGSLSGTLTVKGVQGHVAYPHKARNPIHLAAPALAELVARQWD-------DGFESFP 227 G +G + +G++GH + P + N + AA ++ L+ + D D P Sbjct: 171 EGHKGCHEYSTRFQGLEGHGSNPGRGVNAVEYAARYVSRLLDLRGDLQQRTPPDSRFDPP 230 Query: 228 PTSLQVSNIHAGTGANNVIPGELQVAFNLRYTPHWDAPRLEAEITALLDRHALDYALRWH 287 T+L + ++ G+ A+NVI + QV + +R DA ++ + R+ D L Sbjct: 231 WTTLNIGALNGGS-AHNVIASKAQVDWEMRPVQPSDADHVKDTMA----RYCRDTLLPAM 285 Query: 288 RSGEPFYTPEGRL-----------RSVAREVLGAFAGAPPEESTGGGTSDARFIAPLGAQ 336 ++ P + E + ++ ARE++ G+ E GT +A LG Sbjct: 286 QAIYPEASIETEVVGEVAGLTPTTQNEARELMADLLGSNAAELVPFGT-EAGLFQELGMD 344 Query: 337 CIEVGPVN-ASIHQVDEHVRVADLQALPALYRTLIERL 373 + GP + A H+ DE++ + L + L RL Sbjct: 345 VVVCGPGSIAQAHKADEYLSLDQLSQCLTVLNRLAGRL 382 Lambda K H 0.319 0.137 0.417 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: 370 Number of extensions: 19 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: 376 Length of database: 384 Length adjustment: 30 Effective length of query: 346 Effective length of database: 354 Effective search space: 122484 Effective search space used: 122484 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