Align Probable 5-dehydro-4-deoxyglucarate dehydratase; EC 4.2.1.41; 5-keto-4-deoxy-glucarate dehydratase; KDGDH (uncharacterized)
to candidate WP_011841738.1 RSPH17029_RS12825 4-hydroxy-tetrahydrodipicolinate synthase
Query= curated2:A4YNH1 (314 letters) >NCBI__GCF_000015985.1:WP_011841738.1 Length = 290 Score = 104 bits (259), Expect = 3e-27 Identities = 86/284 (30%), Positives = 124/284 (43%), Gaps = 12/284 (4%) Query: 22 VTPFKADYSFDETTYRSNMDWLCGYDVAGLFAAGGTGEFFSLTAAEVPEVVKVAVDETKG 81 VTPFK + D T + +DW GL G TGE +L+ E V++ V G Sbjct: 10 VTPFK-NGELDLDTLKKLVDWQIAEGSTGLVPVGTTGESPTLSHEEHETVIEAVVKAAAG 68 Query: 82 RVPVLAGTG-YGTAIAREIAMSAEKAGADGLLLLPPYLMHAEQEGLAAHVEAVCKSVKIG 140 RVPV+AG G TA + AE GAD L++ PY Q G+ AH A+ + Sbjct: 69 RVPVIAGAGSNSTAEGIRLIRFAETVGADAALVVTPYYNKPTQAGMIAHFTALHDCCSLP 128 Query: 141 VIVYN---RDNAILQPDTLARLCERCPNLVGYKDGIGDIELMTRVYTKMGDRLTYIGGLP 197 +++YN R + P+T+ L R P +VG KD G IE +++ G + G Sbjct: 129 IVIYNIPGRSVVDMSPETMGTLA-RLPRIVGVKDATGKIERVSQQRASCGPDFIQLSG-- 185 Query: 198 TAETFALPYLDMGVTTYSSAVFNFVPEFATNFYAAVRKRDHATIHAGLKDFILPLIAIRN 257 + AL + G S N P F A D A +D ++PL Sbjct: 186 -EDATALGFNAHGGVGCISVTANVAPRLCAEFQQATLAGDFAKA-LEYQDRLMPLHEAIF 243 Query: 258 RKKGYAVSIIKAGMKVIGRDSGPVRLPLTDLTEAEMAELTALVK 301 + G + K + +G S VRLPL LT+A A + A ++ Sbjct: 244 LEPGLVGA--KYALSKLGLCSDEVRLPLVGLTDATKARIEAAMR 285 Lambda K H 0.320 0.136 0.392 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: 228 Number of extensions: 11 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: 314 Length of database: 290 Length adjustment: 27 Effective length of query: 287 Effective length of database: 263 Effective search space: 75481 Effective search space used: 75481 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 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Sep 17 2021.
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