Align 5-keto-4-deoxy-D-glucarate aldolase; KDGluc aldolase; KDGlucA; 2-dehydro-3-deoxy-D-glucarate aldolase; 2-keto-3-deoxy-D-glucarate aldolase; 5-dehydro-4-deoxy-D-glucarate aldolase; Alpha-keto-beta-deoxy-D-glucarate aldolase; EC 4.1.2.20 (characterized)
to candidate N515DRAFT_2292 N515DRAFT_2292 4-hydroxy-2-oxoheptanedioate aldolase
Query= SwissProt::P23522 (256 letters) >FitnessBrowser__Dyella79:N515DRAFT_2292 Length = 242 Score = 108 bits (269), Expect = 1e-28 Identities = 78/236 (33%), Positives = 118/236 (50%), Gaps = 9/236 (3%) Query: 21 IGCWSALSNPISTEVLGLAGFDWLVLDGEHAPNDISTFIPQLMALKGSASAPVVRVPTNE 80 IG ++ +P+ E+LG AG+D+++LD EH + A + AP VRVP + Sbjct: 5 IGLLQSVPSPLLCEMLGHAGYDFVLLDLEHVLLSPDQLQHAIRACELGGCAPWVRVPEVD 64 Query: 81 PVIIKRLLDIGFYNFLIPFVETKEEAELAVASTRYPPEGIRGVSVSHRANMFGTVA--DY 138 +I R+LD G +I +ET E+AE AVA+ R+PP G RG++ R FG A DY Sbjct: 65 EKLIGRVLDAGARGVVISRLETVEQAERAVAAARFPPLGRRGIT-GGRVTGFGKTALPDY 123 Query: 139 FAQSNKNITILVQIESQQGVDNVDAIAATEGVDGIFVGPSDLAAALGHLGNASHPDVQKA 198 Q+N+ I ++ IES+ GV + I A G+ + G DLA LG H DV + Sbjct: 124 IEQANREIHVVPMIESEAGVRALPQILAVPGISLVMEGALDLALDLGLGPQPLHADVWQR 183 Query: 199 IQHIFNRASAHGKPSGILAPVEADARRYLEWGA---TFVAVGSDLGVFRSATQKLA 251 +Q I + G P P + ++ W A ++ G D G+ +A + A Sbjct: 184 LQDIADCCDTAGIP---FCPNPRNEQQLRYWAAREVRWMLAGEDRGLLLAALRDRA 236 Lambda K H 0.318 0.134 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: 137 Number of extensions: 8 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: 256 Length of database: 242 Length adjustment: 24 Effective length of query: 232 Effective length of database: 218 Effective search space: 50576 Effective search space used: 50576 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 (21.7 bits) S2: 46 (22.3 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