Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate AZOBR_RS30425 AZOBR_RS30425 acetylornithine deacetylase
Query= curated2:A7HPQ6 (395 letters) >FitnessBrowser__azobra:AZOBR_RS30425 Length = 385 Score = 103 bits (257), Expect = 8e-27 Identities = 100/337 (29%), Positives = 148/337 (43%), Gaps = 27/337 (8%) Query: 15 LDIAVELIRCPSVTPDEGGALGVLEKWLAPLGFKCERMRFSAEGTPDVDNLYARLG-SGH 73 LDI L+ P+V+ D L + K R+ S +G NL+A +G + Sbjct: 8 LDILERLVAFPTVSRDSNLDLILWAKERLEAAGATTRLVPSEDGRKA--NLFASVGPADR 65 Query: 74 PHFCFAGHTDVVPVGQADAWSVDPFAADIKDGRLYGRGAADMKSAVASFVAAAERISREG 133 P +GHTDVVPV AW+ DPF + G LYGRG ADMK VA+ +A A+R S Sbjct: 66 PGVLLSGHTDVVPV-DGQAWTSDPFRLTRRAGNLYGRGTADMKGFVAAAMALAQRASGRT 124 Query: 134 FQGSISLLITGDEEGPSINGTRKMLEKLAARNETIDHCIVGEPTSVEKLGDMIKVGRRGS 193 + L ++ DEE + G R++++ +AA CIVGEPT ++ + +G Sbjct: 125 LSQPLHLALSYDEEVGCL-GVRRLIDMMAALPVRPRFCIVGEPTLMQ-----VVTAHKGK 178 Query: 194 INGWLTVQGTQGHVAYPHLADNPVPRLLEM---LRRLDAHVLDEGT---DHFQPSNLEVT 247 + +G + H + N + +M LRRL V EG+ D+ P Sbjct: 179 TALRIDCRGVECHSSLAPQGMNAIHMACDMLTGLRRLQERVQTEGSRDADYDVPWTTIHA 238 Query: 248 TVDIGNTATNVIPGSARATVNIRFNDLHTGASLDKWMRGVLDAVTAEMGGSYSFKTSV-- 305 V G +A N++P R + IR + +LDAV AE + S Sbjct: 239 GVIQGGSALNIVPNHCRLDMEIRHLPQDP-------VEPLLDAVRAEAAAIETRARSAFP 291 Query: 306 SGEAFITEPGAFSALIAEAAKEVTGITPELSTTGGTS 342 + I E ++ +L + EV L TGG S Sbjct: 292 AAAVEIAELSSYPSLDTDGDSEVVSFVKAL--TGGNS 326 Lambda K H 0.316 0.134 0.395 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: 374 Number of extensions: 20 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: 395 Length of database: 385 Length adjustment: 31 Effective length of query: 364 Effective length of database: 354 Effective search space: 128856 Effective search space used: 128856 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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