Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate 3609637 Dshi_3020 acetylornithine deacetylase or succinyl-diaminopimelate desuccinylase (RefSeq)
Query= curated2:B6IPH8 (386 letters) >FitnessBrowser__Dino:3609637 Length = 431 Score = 130 bits (326), Expect = 9e-35 Identities = 125/420 (29%), Positives = 184/420 (43%), Gaps = 46/420 (10%) Query: 4 DPIALARDLIRCPSVTPADAGALDR---VQSVLEGLGFTCH--RLPFQEPGTERVD--NL 56 D +AL RDLIR P++ P D +++ L LGF C R +ER NL Sbjct: 17 DLVALTRDLIRIPTLNPPGRHYHDICAFLEARLAPLGFRCELVRATGAPADSERYPRWNL 76 Query: 57 YARLGDKGPNFC--FAGHTDVVPAGDAAAWTVDPFGGEIIDGRLYGRGAADMKGGVAAFI 114 AR GP C F H DVV G WT+DPFGGE+ DGR+YGRGA DMKGG+AA + Sbjct: 77 VARYEGGGPGDCVHFNSHHDVVEVGHG--WTMDPFGGEVRDGRVYGRGACDMKGGLAASV 134 Query: 115 AAVGSFLERNGPPAGSISLLITGDEEGPAVNGTRKVLDWMAAAGERIDACLVGEPTNPRA 174 A +F+ + +G+I + T DEE G + + + ER+ ++ EP N Sbjct: 135 IAAEAFIATHPEFSGAIEISATADEESGGFGGVAYLAEQGWFSPERVQHVIIPEPLNK-- 192 Query: 175 LGDMIKVGRRGSLTATLTALGAQGHTAYPHLADNPLPRLAEALH--------LLASSPLD 226 D I +G RG A + G H + P L D+ + + LH LLA+ Sbjct: 193 --DRICLGHRGVWWAEVETKGRIAHGSMPFLGDSAIRHMGAVLHEIETVLYPLLATKRTK 250 Query: 227 MGT--PHFQPSTLALTSIDVGNPASNV----IPA-----RGTARFNIRFNDLHTPESLEA 275 M + STL + S+ G P + +PA R + RF ++A Sbjct: 251 MPVVPEGARQSTLNINSVHGGEPEQDADYTGLPAPCVADRCRIVLDRRFLIEEDITEVKA 310 Query: 276 HIRDVLEEVGGAW-ELALQTSGVAFLTPPGALSDI-----VAAAVEAHTGRTPELSTSGG 329 I +LE V + + + P A D VAA++E R P+ S G Sbjct: 311 EITALLERVKATRPSFEYEIRELFEVQPTMADRDAPVVRSVAASIERVLARQPDYVVSPG 370 Query: 330 TSDARFIK-----DHCPVVEFGLVGASMHKVDENVAVADLLELTAIYRTVLERWFAGAEP 384 T D + I +C G++ + H+ DE V + D+++ + L+ +P Sbjct: 371 TYDQKHIDRIGRLKNCIAYGPGILDLA-HQPDEWVGIDDMVDSAKVMALTLQDLLVVPQP 429 Lambda K H 0.318 0.136 0.413 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: 502 Number of extensions: 38 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: 386 Length of database: 431 Length adjustment: 31 Effective length of query: 355 Effective length of database: 400 Effective search space: 142000 Effective search space used: 142000 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 (21.7 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