Align Probable 5-dehydro-4-deoxyglucarate dehydratase; EC 4.2.1.41; 5-keto-4-deoxy-glucarate dehydratase; KDGDH (uncharacterized)
to candidate H281DRAFT_00509 H281DRAFT_00509 dihydrodipicolinate synthase
Query= curated2:B1W1P9 (320 letters) >FitnessBrowser__Burk376:H281DRAFT_00509 Length = 308 Score = 102 bits (253), Expect = 2e-26 Identities = 59/171 (34%), Positives = 93/171 (54%), Gaps = 4/171 (2%) Query: 21 VTAFGPDGAVDLAVFRAHVRAGIDAGAAAVFACCGTGEFHALTPEEFRLAVGAAVEESAG 80 +T DG++DL FR + + G A+ +GE L+ EE L V AVE +AG Sbjct: 26 ITPMLEDGSLDLPAFRKLIDWHVAEGTNALVVVGTSGESATLSVEEHVLMVKTAVEHTAG 85 Query: 81 QVPVLAGA-GYGTALAVQYARAAEEAGADGLLAMPPYLVVADQQGLLHHYAALAAATGLE 139 ++PV+AG+ G TA A++ R A+E GAD L + PY Q+G+ H+A +A L Sbjct: 86 RIPVIAGSGGNSTAEAIELTRQAKEVGADATLQVVPYYNKPTQEGIYRHFAKIAETVDLP 145 Query: 140 TIVYQ---RDNAVFTPETVVALARTPGVIGLKDGHGDLDLMQRIVSAVRTH 187 I+Y R A + ET++ A+ PG+IG+K+ G++D ++ + H Sbjct: 146 VILYNVPGRTVADMSNETILRCAQVPGIIGVKEATGNIDRAAHLIKSAPAH 196 Lambda K H 0.322 0.138 0.405 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: 186 Number of extensions: 9 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: 320 Length of database: 308 Length adjustment: 27 Effective length of query: 293 Effective length of database: 281 Effective search space: 82333 Effective search space used: 82333 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