Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate AO353_29125 AO353_29125 acetylornithine deacetylase
Query= curated2:Q6G1H9 (390 letters) >FitnessBrowser__pseudo3_N2E3:AO353_29125 Length = 382 Score = 104 bits (260), Expect = 4e-27 Identities = 103/343 (30%), Positives = 155/343 (45%), Gaps = 30/343 (8%) Query: 57 NLYAKMGGEGRH-LMFAGHTDVVPPGALEDWTYPPFEGVIDQGKLYGRGAVDMKGGIACF 115 NL+A +G R ++ +GHTDVVP + WT PF+ GKLYGRG DMKG IAC Sbjct: 52 NLFATIGPADRPGIVLSGHTDVVPVDG-QPWTVAPFQLSERDGKLYGRGTADMKGYIAC- 109 Query: 116 VAALARILEKRSIKGMVSLLITGDEEGPALNGTVKLLKWAEQKGEKWTAALVGEPTSVKT 175 V AL L ++ V + ++ DEE L G LLK EQ+ K ++GEPT +K Sbjct: 110 VLALVPSLVNAPLRRPVHIALSYDEEVGCL-GVRSLLKALEQRPVKPMLCIIGEPTELKP 168 Query: 176 VGDVIKIGRRGSLSGVVTVKGRQGHVAFPERAANPLPLAGKLIQALTQ-----TALDRGT 230 V +G +G L+ + G H A+ N + A +LI L + + Sbjct: 169 V-----LGHKGKLAMRCDIHGEACHSAYAPLGVNAIEYAAELIGELGRIGHRLKVPEHHD 223 Query: 231 ENFQPS-NLELTTIDTDNPAVNVIPAQTTIRFNIRY-----NDVWTKETLMTEIEKRLAS 284 F P + T + + A+N++PA F IR V KE ++ L Sbjct: 224 ARFDPPFSTVQTGMISGGKALNIVPADCRFDFEIRALPSQDPSVVAKELKTYAEQQVLPR 283 Query: 285 VQLKNNDYQYPYYQLEWIPSLGSVFITKNDKLIKTLSNAIESVTGNIPEYSTSGGTSDAR 344 ++ ++ + +L P L + ++ +LI S + E T + T GG DA Sbjct: 284 MRAVSDQSDIRFSELSAYPGLATDAHSEAAELIAAFSGSREFGT---VAFGTEGGLFDAA 340 Query: 345 FIKDYCPVVEFGLPG--QTMHMVDECVTLDAIETLTSVYERFI 385 I P V G PG H DE V+LD ++ ++ +R + Sbjct: 341 GI----PTVVCG-PGSMDQGHKPDEFVSLDQLKGCDAMLQRML 378 Lambda K H 0.317 0.136 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: 351 Number of extensions: 22 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: 390 Length of database: 382 Length adjustment: 30 Effective length of query: 360 Effective length of database: 352 Effective search space: 126720 Effective search space used: 126720 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 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