Align Probable 5-dehydro-4-deoxyglucarate dehydratase; EC 4.2.1.41; 5-keto-4-deoxy-glucarate dehydratase; KDGDH (uncharacterized)
to candidate GFF1410 PS417_07165 dihydrodipicolinate synthase
Query= curated2:B9KW45 (301 letters) >FitnessBrowser__WCS417:GFF1410 Length = 292 Score = 88.2 bits (217), Expect = 2e-22 Identities = 76/229 (33%), Positives = 107/229 (46%), Gaps = 13/229 (5%) Query: 19 VTPFDAENRFAAAPYQKHVEWLSGFDAPVLFAAGGTGEFFSLTPDE-IPAIVRAAKESAG 77 VTP DA+ K V++ + A G TGE +L +E I I K AG Sbjct: 10 VTPMDAQGHLDWDSLGKLVDFHLQEGTNAIVAVGTTGESATLDVEEHIQVIEFVVKRVAG 69 Query: 78 KTAIVSGCGYG-TEIARGIARSVEAAGGDGILLLPHYLIDAPQEGLYAHVRAVCQATGMG 136 + A+++G G T A + ++ + AG D LL+ Y QEGLY H RA+ +A + Sbjct: 70 RIAVIAGTGANSTREAIELTKNAKKAGADACLLVTPYYNKPTQEGLYQHFRAIAEAVDIP 129 Query: 137 VMVYN---RDNAVLQADTLARLCDDCPNLVGFKDGTGDIGLVRQITAKM-GDRLTYLGGM 192 ++YN R +QA T+ RL PN++G K+ TGD+ + I A + D L Y G Sbjct: 130 QILYNVPGRTACDMQAATVIRL-STVPNIIGIKEATGDLQRAKDILAGVSSDFLVYSGDD 188 Query: 193 PTA-ELFAEAYLGASFTTYSSAVFNFVPALANKFYAALRAGDRATCESI 240 TA EL LG S N P ++ AA AGD T +I Sbjct: 189 ATAVELI---LLGGKGNI--SVTANVAPRAMSEMCAAAIAGDAVTARAI 232 Lambda K H 0.321 0.138 0.407 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: 195 Number of extensions: 15 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: 301 Length of database: 292 Length adjustment: 26 Effective length of query: 275 Effective length of database: 266 Effective search space: 73150 Effective search space used: 73150 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: 48 (23.1 bits)
This GapMind analysis is from Sep 17 2021. 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