Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate WP_106713043.1 CU102_RS20965 acetylornithine deacetylase
Query= curated2:Q5FPX5 (381 letters) >NCBI__GCF_003010955.1:WP_106713043.1 Length = 374 Score = 91.7 bits (226), Expect = 3e-23 Identities = 76/209 (36%), Positives = 102/209 (48%), Gaps = 27/209 (12%) Query: 69 PALCFAGHTDVVPPGE-GWAHDPFAAVIEGDRLYGRGIADMKGGVACFVAAVARRLEQGP 127 P +GH DVVP GE GW DPF +G RL GRG DMKG +AC +AA+ +L Sbjct: 62 PGYILSGHLDVVPAGEAGWKTDPFQLQRDGKRLCGRGTTDMKGFLACALAALP-KLAASN 120 Query: 128 LKGSVSLLITGDEEGPAHFGTKPVIEWLAERGELPDFC------VLGEPTNPQALGDVIK 181 L+ V L + DEE G + V LA LPD C ++GEP+ QA+ Sbjct: 121 LQRPVHLAFSYDEEA----GCRGVPHLLA---ALPDLCAKPLGAIIGEPSRMQAVR---- 169 Query: 182 IGRRGSMNAVVTVHGTQGHVAYPHLADNPVHRL--LAAFSELTARELDAG--SEWFDP-- 235 +G A + V G GH + P L N VH + + A + + R L+ G + F+P Sbjct: 170 -AHKGKAAARLEVAGRSGHSSRPDLGLNAVHAMANVIAQAVVYGRSLEQGPFDDNFEPPY 228 Query: 236 SSLQVTSIDVGNGATNIIPGSAVGRLNIR 264 SSLQ + G A NIIP + +R Sbjct: 229 SSLQFGVVS-GGQAVNIIPDRCTADIEVR 256 Lambda K H 0.319 0.138 0.422 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: 413 Number of extensions: 29 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: 381 Length of database: 374 Length adjustment: 30 Effective length of query: 351 Effective length of database: 344 Effective search space: 120744 Effective search space used: 120744 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 Jul 26 2024. The underlying query database was built on Jul 25 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