Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate PP_3571 PP_3571 putative Acetylornithine deacetylase
Query= curated2:Q2W0E7 (379 letters) >FitnessBrowser__Putida:PP_3571 Length = 391 Score = 102 bits (254), Expect = 2e-26 Identities = 112/364 (30%), Positives = 154/364 (42%), Gaps = 43/364 (11%) Query: 34 LEELGFACHHIRSATGGPEIRNLYARLGT-EAPNLCFAGHTDVVP-PGKGWTVEPFAAGI 91 L ELG C + G NL+A +G + + +GHTDVVP G+ WTVEPFA Sbjct: 40 LAELGVECELFHNPEGTKA--NLFATVGPRDVGGVVLSGHTDVVPVDGQAWTVEPFALSE 97 Query: 92 DQGRLFGRGSADMKGAIACFVAAVARLLEDGAPKGSLSLLITGDEEGPAVDGTVKVLDWL 151 GRL+GRG+ADMKG IA +AAV L + + L + DEE + G +L L Sbjct: 98 RDGRLYGRGTADMKGFIASVLAAVPAFLAQPL-RMPVHLAFSYDEEVGCL-GVRSMLAAL 155 Query: 152 AARGERIDCCIVGEPTNPRKLGDMMKIGRRGSLNCRLTVFGTQGHSAYPHLADNPIPRLL 211 R + C++GEPT + + +G +G L R V G HSAY N I Sbjct: 156 QQRPCKPRLCLIGEPTELKPV-----LGHKGKLAMRCQVQGAACHSAYAPYGVNAIEYAA 210 Query: 212 DILRRLTEAPLDEGTP--HFQASTLALTTVDV----GNPATNVIPAEARAGFNIRFNDLH 265 ++ +L E P H + +TV G A N++P E F +R Sbjct: 211 KLIGKLGEIGEALALPVHHDERFDPPFSTVQAGVIKGGRALNIVPDECEFDFEVR----- 265 Query: 266 SGASLERWIRDTVA---QAGGEVEI-----KVEVSGESFLTP----PGALSDALAEAAFE 313 +L + VA Q E E+ KV + L P PG + +EAA Sbjct: 266 ---ALPGFEAQAVADQLQTYAEAELLPRMRKVNTASAIRLAPLSAYPGLATPEDSEAA-R 321 Query: 314 VTGLRPELSTSG----GTSDARFIKNHCPVVEFGLVGQTM-HKSDEHVSVADMEALTEIY 368 + L T G GT F + P V G HK DE VSV + + Sbjct: 322 LVALLSGSDTFGTVAFGTEGGLFDQAGIPTVVCGPGSMDQGHKPDEFVSVEQLRGCDAML 381 Query: 369 RRVL 372 R++ Sbjct: 382 LRLV 385 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: 370 Number of extensions: 21 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: 379 Length of database: 391 Length adjustment: 30 Effective length of query: 349 Effective length of database: 361 Effective search space: 125989 Effective search space used: 125989 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