Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate Pf6N2E2_1185 Acetylornithine deacetylase (EC 3.5.1.16)
Query= curated2:B9KHC9 (381 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1185 Length = 413 Score = 94.4 bits (233), Expect = 5e-24 Identities = 83/274 (30%), Positives = 126/274 (45%), Gaps = 24/274 (8%) Query: 7 VSLACRLMSYPSVTPDRSGA--IPFLAELLSDLGFRCEILSFGNGDVEVKNLYAQYGNGH 64 + +A L+ +PSV+ DRS I +++ L G + +IL +G NL+A G Sbjct: 27 LEIARTLIGFPSVS-DRSNLDLIEWVSGYLHGFGVQAQILPDASG--RKANLFASLGPPR 83 Query: 65 PN-LCFAGHTDVVPPGG-TWRTDPFSPQVKDGMLYGRGASDMKAAICAYISAVARL-DSV 121 P + +GHTDVVP G W DPFS + LYGRG+SDMK I ++ V L S Sbjct: 84 PGGIILSGHTDVVPVAGQAWAQDPFSAYLDQDRLYGRGSSDMKGFIAVVLAMVPELMASA 143 Query: 122 PGCLSFLITGDEEGRWREYGTKSVLDWMTKNGICPDYCVLGEPSSRKRLGDCISIGRRGS 181 ++ DEE G K + ++T+ + P C++GEP+S + IG +G Sbjct: 144 RQSFHLALSYDEE--VGAMGAKHLAPFITQAQLEPAGCIVGEPTSM-----ALVIGHKGR 196 Query: 182 LNFELSCRGVQGHVAYPELAHNPID-------DVLCILRKIKDTTLDSGTDHFPPSHCEI 234 G H + P N ID + + R++ LDSG D P + ++ Sbjct: 197 HEINCCVHGKVAHSSLPNEGVNAIDYAARVQMQLQHVARRLSQGPLDSGFD-VPYTTVQV 255 Query: 235 TSIDVGNDVENLIPSSATAAFNIRFNDLHTAESL 268 ++ G N+IP + F IR+ AE L Sbjct: 256 CRVN-GGVAGNVIPGQCSFDFEIRYLPGCDAEQL 288 Lambda K H 0.321 0.137 0.430 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: 386 Number of extensions: 23 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: 413 Length adjustment: 31 Effective length of query: 350 Effective length of database: 382 Effective search space: 133700 Effective search space used: 133700 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 (21.9 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