Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate WP_011158579.1 TX73_RS15470 acetylornithine deacetylase
Query= curated2:B2FIC0 (375 letters) >NCBI__GCF_000195775.1:WP_011158579.1 Length = 426 Score = 95.9 bits (237), Expect = 2e-24 Identities = 89/304 (29%), Positives = 127/304 (41%), Gaps = 47/304 (15%) Query: 3 AVLDLTCELIARPSVTPDDAGCQALLAARLKQAGFQCDHLRLGDVDNLWATHGLGAPV-- 60 A L T + +A PS + CQ ++ L+Q G++ D + D+D+L G G P+ Sbjct: 20 AQLATTRDFVAIPSTRGAEGPCQDMIGDLLRQRGYEVDDWHI-DLDDLKDLRGYG-PIEH 77 Query: 61 ---------------------LVLLGHTDVVPTGPRESWTSDPFTPHIRDGVLYGRGAAD 99 L+L GH DVVP GP E W + PF+P I+ G +YGRGA D Sbjct: 78 DFSKARTVVGTYRPSTNAGRSLILQGHCDVVPAGPLEMWDTPPFSPVIKQGRMYGRGACD 137 Query: 100 MKGSVAAFVVAAEQFVADHPDHPGTLAVLLTSDEEGDAIDGVRHVARLFAARGQRIDWCI 159 MK + A + A G + +EE + + + RG R D C Sbjct: 138 MKSGTIGALYALDAIKAAGLRPTGRIHFQSVIEEESTGVGALSTL-----QRGYRADACF 192 Query: 160 TGEPSSTATLGDLLRVGRRGSLSAKLRVQGVQGHVAYPEKARNPI---HQAAPALAELCA 216 EP T G ++R + G + +L+V+G HVA N I + AL +L Sbjct: 193 IPEP----TGGKMVR-SQVGVIWFRLKVRGYPVHVATAGTGSNAITAAYHLIDALGKL-E 246 Query: 217 RRWDDGYESFP-------PTSLQISNIHAGTGANNVIPGELDVDFNIRYNPHWDAPKLEA 269 W+ S P P + I G A++V P DVD I P W +A Sbjct: 247 EEWNRRAASDPHFKTLAHPINFNPGIIKGGDWASSV-PAWCDVDCRIAILPGWSVADHQA 305 Query: 270 EITA 273 EI A Sbjct: 306 EILA 309 Lambda K H 0.319 0.137 0.421 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: 480 Number of extensions: 33 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: 375 Length of database: 426 Length adjustment: 31 Effective length of query: 344 Effective length of database: 395 Effective search space: 135880 Effective search space used: 135880 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 Apr 10 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