Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate AZOBR_RS31030 AZOBR_RS31030 acetylornithine deacetylase
Query= curated2:Q7W8Y3 (379 letters) >FitnessBrowser__azobra:AZOBR_RS31030 Length = 398 Score = 92.4 bits (228), Expect = 2e-23 Identities = 117/395 (29%), Positives = 165/395 (41%), Gaps = 54/395 (13%) Query: 7 LDLVKDLIARPSVTPD-DVDCQMLLAQRLERIGFQCETIARGGVT--NLWARRGAGAPL- 62 L+L++DLIA + + + ++D + L +G + T NL+A G P+ Sbjct: 18 LELLRDLIAFDTTSRNSNLDLIHYIRDHLAELGVSSTLVFNEERTKANLYATIG---PMD 74 Query: 63 ---TVFAGHTDVVPPGPRDKWDSDPFVPTERDGFLYGRGAADMKSSIAAFVVAAEEFVAA 119 +GHTDVVP +D W SDPF TERDG L+GRG ADMK IAA + A +F+AA Sbjct: 75 RGGVCLSGHTDVVPVDDQD-WSSDPFTLTERDGKLFGRGTADMKGFIAAALAMAPDFLAA 133 Query: 120 HPEHPGSIALLITSDEEGPAVDGTVIVCDELRQRGEQLDYCIVGEPTSTEALGDVCKNGR 179 + P + + DEE + G + +L + CIVGEPT + G Sbjct: 134 NLTTP--VHYAFSYDEELGCL-GVPGLLTQLAGMAVKPRLCIVGEPTRMRVI-----VGH 185 Query: 180 RGSLSGRLLVKGVQGHVAYPHLARNPVHQLAPALTELVAIEWDQGNEY-----------F 228 +G ++ R V GH + LA V+ + A ELV+ G + Sbjct: 186 KGKVALRC---RVHGHACHSSLAPQGVNAVEYA-AELVSFLRGMGRRFAEQGPFDHDYDI 241 Query: 229 PPTTFQVSNLHAGTGATNVVPGEAVALFNFRFSTASTPDQLKARVHEVLDRHGLEYQ--- 285 P TT + GT A N+VP +A F R + + + E + Sbjct: 242 PYTTVHTGVMEGGT-ARNIVPSDASFEFEIRHLADHPVAPMLKELRDFAKTLEPEMRAVR 300 Query: 286 ----LDWE-LGGEPFL-TPRGSLTDALVSAIQAETGLQAELSTTGG---TSDGRFIARIC 336 WE L P L TP S LV + + G T G TS A +C Sbjct: 301 PDAGFSWETLSDSPALDTPPESEEVTLVKNLAEQNGHGKVAFGTEGALFTSIANIPAVVC 360 Query: 337 -PQVIEFGPCNATIHKVNERIELSSLAPLKNIYRR 370 P IE HK +E +ELS LA + R Sbjct: 361 GPGDIE------QAHKPDEYVELSELARAERFLHR 389 Lambda K H 0.318 0.136 0.410 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: 402 Number of extensions: 21 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: 379 Length of database: 398 Length adjustment: 30 Effective length of query: 349 Effective length of database: 368 Effective search space: 128432 Effective search space used: 128432 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