Align Probable 5-dehydro-4-deoxyglucarate dehydratase; EC 4.2.1.41; 5-keto-4-deoxy-glucarate dehydratase; KDGDH (uncharacterized)
to candidate N515DRAFT_1147 N515DRAFT_1147 4-hydroxy-tetrahydrodipicolinate synthase
Query= curated2:B1W1P9 (320 letters) >FitnessBrowser__Dyella79:N515DRAFT_1147 Length = 297 Score = 112 bits (281), Expect = 8e-30 Identities = 98/302 (32%), Positives = 132/302 (43%), Gaps = 21/302 (6%) Query: 13 VAGPLFFPVTAFGPDGAVDLAVFRAHVRAGIDAGAAAVFACCGTGEFHALTPEEFRLAVG 72 + G + T F DGA+DL F + + G AV TGE H L +E+ + Sbjct: 3 IGGSICALATPFTSDGALDLDAFGRLLDYQVAGGTQAVVVAGSTGEAHMLEHDEYETLLS 62 Query: 73 AAVEESAGQVPVLAGAG-YGTALAVQYARAAEEAGADGLLAMPPYLVVADQQGLLHHYAA 131 AV+ AG++PVLAG G GTA V R A E GAD L + P+ V Q+GL H+ Sbjct: 63 FAVKRIAGRIPVLAGTGEAGTARTVALTRRARELGADAALVVAPFYVRPTQEGLRRHFLE 122 Query: 132 LAAATGLETIVYQ---RDNAVFTPETVVALARTPGVIGLKDGHGDLDLMQRIVSAVRTHR 188 +A GL ++Y R PETV AL P ++G+K+ G + ++ + R Sbjct: 123 VAEHGGLPVLLYNVPGRTACDLLPETVAALREHPAIVGIKEAVGSDERIRALAELAR--- 179 Query: 189 PGGDFLYFNG-LPTAELTGPAYRGIGVTLYSSAVFAFAPDIALAFYRALDSGDDALVDGL 247 DF+Y +G PTA G A G S V AP A SG DA Sbjct: 180 --ADFVYLSGDDPTA---GKAMLA-GAAGTISVVANLAPKAFRELCDAATSG-DAAATTR 232 Query: 248 LDHFYRPLVELRAQGRGYAVSLVKAGVRLQGLDVGEVRTPLTE----PTAAHVKDLIEII 303 D PLV+ A VKAG+ GL R PL E P + + + + Sbjct: 233 CDDVLAPLVQ--ALNCAPNPIAVKAGLPALGLGSAAPRLPLVELQDGPERTRIAEALAAL 290 Query: 304 AS 305 AS Sbjct: 291 AS 292 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: 220 Number of extensions: 12 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: 320 Length of database: 297 Length adjustment: 27 Effective length of query: 293 Effective length of database: 270 Effective search space: 79110 Effective search space used: 79110 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