Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate WP_012168732.1 AZC_RS01015 acetylornithine deacetylase
Query= curated2:B2FIC0 (375 letters) >NCBI__GCF_000010525.1:WP_012168732.1 Length = 382 Score = 127 bits (319), Expect = 5e-34 Identities = 130/396 (32%), Positives = 180/396 (45%), Gaps = 42/396 (10%) Query: 3 AVLDLTCELIARPSVTPD-DAGCQALLAARLKQAGFQCDHLRLGD--VDNLWATHG-LGA 58 + LDL LIA P+V+ D + A + A L Q G + + D NL+AT G Sbjct: 2 STLDLLDRLIAFPTVSRDPNRELIAFVQAFLGQHGIASEIIATPDGRKANLFATIGPTDR 61 Query: 59 PVLVLLGHTDVVPTGPRESWTSDPFTPHIRDGVLYGRGAADMKGSVAAFVVAAEQFVADH 118 P ++L GHTDVVP ++WT+DPF + DG YGRGAADMKG +AA + A + A Sbjct: 62 PGIMLSGHTDVVPV-EGQAWTADPFRLRVADGRAYGRGAADMKGFLAAALALAARAAARP 120 Query: 119 PDHPGTLAVLLTSDEEGDAIDGVRHVARLFAARGQRIDWCITGEPSSTATLGDLLRVGRR 178 + P L + L+ DEE + GVR + + R CI GEP+S + G + Sbjct: 121 LETP--LHLALSHDEEVGCV-GVRSLIERLSTASVRPRLCIIGEPTSLR-----VATGHK 172 Query: 179 GSLSAKLRVQGVQGHVAYPEKARNPIHQAA----------PALAELCARRWDDGYESFPP 228 G L+A+ GV+GH A KA N IH A +AE AR D P Sbjct: 173 GKLAARATCCGVEGHSALAPKALNAIHLACDFVGLLRTHQDRIAESGAR---DADYDIPY 229 Query: 229 TSLQISNIHAGTGANNVIPGELDVDFNIRYNPHWDAPK-----LEAEITALLERH----G 279 T+L I GT A N++P VDF IR DA + L+ + ER Sbjct: 230 TTLHAGVIAGGT-ALNIVPNRCTVDFEIRNIAQDDASEVLTRLLDDAARLVAERRAAFPA 288 Query: 280 LQYTLKWHRSGEPFYTP-EGTLRAIARAVLAEHIGRAPEESTGGGTSDARFIAPLGAQCI 338 ++ TP E + A +A++ + T GG DAR P + Sbjct: 289 ADIAVEVVNDYPGLATPKEAEVVAFVQALVDDASTFKVAFGTEGGLFDARLSIP----TV 344 Query: 339 EVGPVNASI-HQVDENVRVDDLEALPGLYQRLVERL 373 GP + H+ DE + +D LEA + RL+ RL Sbjct: 345 ICGPGSMDQGHKPDEFIALDQLEACDRMMDRLLHRL 380 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: 373 Number of extensions: 27 Number of successful extensions: 5 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: 382 Length adjustment: 30 Effective length of query: 345 Effective length of database: 352 Effective search space: 121440 Effective search space used: 121440 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