Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase; EC 3.5.1.18 (characterized)
to candidate CCNA_03746 CCNA_03746 acetylornithine deacetylase
Query= SwissProt::Q9JYL2 (381 letters) >FitnessBrowser__Caulo:CCNA_03746 Length = 391 Score = 79.3 bits (194), Expect = 2e-19 Identities = 67/205 (32%), Positives = 95/205 (46%), Gaps = 19/205 (9%) Query: 63 VCFAGHTDVVPTGPVEKWDSPPFEPAERDGRLYGRGAADMKTSIACFVTACERFVAKHPN 122 V +GHTDVVP + W + P+ ERDGRLYGRG DMK +A + A N Sbjct: 73 VVLSGHTDVVPVDG-QPWSTDPWTLTERDGRLYGRGTCDMKGFLALALAAAPDLA--QAN 129 Query: 123 HQGSIALLITSDEEGDALDGTTKVVDVLKARDELIDYCIVGEPTAVDKLGDMIK-NGRRG 181 + + L + DEE L G ++DV+ +VGEPT DM+ +G Sbjct: 130 LRKPVHLAFSYDEEVGCL-GAPDMIDVIAREVPRPALVVVGEPT------DMVAVRAHKG 182 Query: 182 SLSGNLTVKGKQGHIAYPHLAI--NPVHTFAPALLELTQEVWD---EGNEYFPP--TSFQ 234 S +TV G++ H + HL + N V A+L E + + N F P + Sbjct: 183 IASFKVTVTGREAHSSLTHLGVSANMVAIKLMAMLVGLSEKLEREADPNSPFTPKGATLT 242 Query: 235 ISNINGGTGATNVIPGELNVKFNFR 259 I +NGGT A N++ E F+ R Sbjct: 243 IGQVNGGT-AVNILARECVFIFDLR 266 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: 364 Number of extensions: 24 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: 391 Length adjustment: 30 Effective length of query: 351 Effective length of database: 361 Effective search space: 126711 Effective search space used: 126711 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