Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate RR42_RS07840 RR42_RS07840 acetylornithine deacetylase
Query= curated2:B7GXA3 (377 letters) >FitnessBrowser__Cup4G11:RR42_RS07840 Length = 401 Score = 78.2 bits (191), Expect = 4e-19 Identities = 79/248 (31%), Positives = 112/248 (45%), Gaps = 41/248 (16%) Query: 47 GDVDNLW-----ARRGTEGPVFCFAGHTDVVPTGRLDAWNSDPFAPEIRDGKLYGRGSAD 101 GD NL+ A T+G + +GHTDVVP + W +DPF P IRDG+LYGRG+ D Sbjct: 62 GDKANLFVTVPAASGSTDGGIV-LSGHTDVVPVDGQN-WTTDPFKPVIRDGRLYGRGTCD 119 Query: 102 MK----TALAAMVVASERFVAKHPNHKGSIAFLITSDEEGPAVNGTVKVIETLEKRNEKI 157 MK T+LA + E + + P H + ++ DEE + G ++ L +R Sbjct: 120 MKGFIGTSLALLPTLLEARL-REPVH-----YALSFDEEIGCM-GAPYLLAELRERGVTP 172 Query: 158 TWCLVGEPSSTHKLGDIVKNGRRGSLNAV-LKVQGKQGHVAYPHLARNPIHEASPALAEL 216 C+VGEP+S + + G +NA V+G+ H + N I A A L Sbjct: 173 GGCIVGEPTSMRVI--VAHKG----INAYRCCVKGQAAHSSLTPKGVNAIEYA----ARL 222 Query: 217 CQTVWDNGNEY-----------FPATSFQISNIHAGTGATNVIPGALEVTFNFRYSTEVT 265 + D +E+ P T+ Q IH G A N IP E F FR V Sbjct: 223 ICHIRDIADEFKANGPYDRDFDVPFTTAQTGTIHGGI-ALNTIPALCEFVFEFRNLPGVD 281 Query: 266 AEQLKQRV 273 E + R+ Sbjct: 282 PEAIFARI 289 Lambda K H 0.317 0.134 0.399 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: 310 Number of extensions: 20 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: 377 Length of database: 401 Length adjustment: 30 Effective length of query: 347 Effective length of database: 371 Effective search space: 128737 Effective search space used: 128737 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 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