Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate BWI76_RS12865 BWI76_RS12865 acetylornithine deacetylase
Query= curated2:Q2W0E7 (379 letters) >FitnessBrowser__Koxy:BWI76_RS12865 Length = 389 Score = 113 bits (282), Expect = 1e-29 Identities = 104/325 (32%), Positives = 152/325 (46%), Gaps = 27/325 (8%) Query: 55 NLYARLGTEAPN-LCFAGHTDVVP-PGKGWTVEPFAAGIDQGRLFGRGSADMKGAIACFV 112 NLYARLG P + +GHTDVVP G+ WTV PFA GR +GRGSADMKG IAC + Sbjct: 53 NLYARLGPSGPGGVMLSGHTDVVPVDGQAWTVPPFALTERDGRYYGRGSADMKGFIACVL 112 Query: 113 AAVARLLEDGAP-KGSLSLLITGDEEGPAVDGTVKVLDWLAARGERIDCCIVGEPTNPRK 171 A++ L AP + L L + DEE + G ++D+L A E+ CI+GEPT+ R Sbjct: 113 ASLEAFL--AAPLRMPLHLAFSYDEEVGCL-GVRSLVDFLRASAEKPALCIIGEPTDMRP 169 Query: 172 LGDMMKIGRRGSLNCRLTVFGTQGHSAYPHLADNPIPRLLDILRRLTEAPLDEGTPHFQ- 230 + G +G L R V G HSAY N I ++ RL +A + + H Sbjct: 170 V-----YGHKGKLAVRCRVEGHACHSAYAPQGVNAISYAAKLIYRL-DALGESFSQHLDR 223 Query: 231 -----ASTLALTTVDVGNPATNVIPAEARAGFNIRF----NDLHSGASLERWIRDTVAQA 281 + TL + T+ G A N++P F IR+ +L + R+ + A Sbjct: 224 RFSPPSGTLQVGTIR-GGEALNIVPQSCWFDFEIRYLPGTRPQAVTDALGDYAREQLLPA 282 Query: 282 GGEVEIKVEVSGESFLTPPGALSD---ALAEAAFEVTGLRPELSTSGGTSDARFIKNHCP 338 +V ++ ++ PG LSD A A + G + + GT F + Sbjct: 283 MRKVAQCSDIHFQTLSHYPGLLSDPQSAFARWLAQWCGSDDFTTVAYGTEGGLFDEAGVA 342 Query: 339 VVEFGLVGQTM-HKSDEHVSVADME 362 + G H++DE++S+ E Sbjct: 343 TLICGPGSMAQGHRADEYISIPQTE 367 Lambda K H 0.319 0.137 0.412 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: 382 Number of extensions: 18 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: 379 Length of database: 389 Length adjustment: 30 Effective length of query: 349 Effective length of database: 359 Effective search space: 125291 Effective search space used: 125291 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 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