Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; EC 3.5.1.18; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase (uncharacterized)
to candidate Pf6N2E2_367 Acetylornithine deacetylase (EC 3.5.1.16)
Query= curated2:Q5F812 (381 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_367 Length = 385 Score = 85.5 bits (210), Expect = 2e-21 Identities = 68/223 (30%), Positives = 106/223 (47%), Gaps = 22/223 (9%) Query: 47 GDTKNIWLRRGTK-APVVCFAGHTDVVPTGPVEKWDSPPFEPTERDGRLYGRGAADMKTS 105 G N++ G + P V +GHTDVVP + W P F+ T RDGR+YGRG+ DMK Sbjct: 49 GKKANLFASTGPRDLPGVLLSGHTDVVPAAG-QAWTVPAFQATVRDGRVYGRGSCDMKGF 107 Query: 106 IACFVTACERFVAEHPDH--QGSIALLITSDEEGDALDGTTKVVDVLKARGELIDYCIVG 163 IA + A + + DH + L ++ DEE + G +++DVL C++G Sbjct: 108 IALAIDA----MLDAADHSLNRPLQLALSHDEEIGCV-GVRRLLDVLHLAPVRPFLCVIG 162 Query: 164 EPTAVDKLGDMIKNGRRGSLSGSLTVKGKQGHIAYPHLAVNPIHT---FAPALLELTQEI 220 EPT + G +G S +G + H + +VN IH F AL + Q++ Sbjct: 163 EPTNM-----QFVLGHKGKGSYRTYCRGLEAHSSLAPRSVNAIHVACDFIAALRQSQQQL 217 Query: 221 WDEGNE----YFPPTSFQISNINGGTGATNVIPGELNVKFNFR 259 ++G + P ++ + I GG A N++P + F R Sbjct: 218 QEQGAQDADYDVPYSTVHVGQIVGGK-ALNIVPNLCTLDFEVR 259 Lambda K H 0.317 0.135 0.400 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: 345 Number of extensions: 21 Number of successful extensions: 2 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: 385 Length adjustment: 30 Effective length of query: 351 Effective length of database: 355 Effective search space: 124605 Effective search space used: 124605 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