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 GFF3489 PS417_17865 2-keto-3-deoxy-L-rhamnonate aldolase
Query= SwissProt::P23522 (256 letters) >FitnessBrowser__WCS417:GFF3489 Length = 266 Score = 221 bits (564), Expect = 9e-63 Identities = 117/253 (46%), Positives = 160/253 (63%), Gaps = 1/253 (0%) Query: 4 DVFPNKFKAALAAKQVQIGCWSALSNPISTEVLGLAGFDWLVLDGEHAPNDISTFIPQLM 63 D+ N+FK L +VQIG W L++ E+ AGFDWL++DGEHAPN + + QL Sbjct: 2 DMPVNRFKQRLRNGEVQIGLWLGLADAYCAELAANAGFDWLLIDGEHAPNHLQGMLAQLQ 61 Query: 64 ALKGSASAPVVRVPTNEPVIIKRLLDIGFYNFLIPFVETKEEAELAVASTRYPPEGIRGV 123 A+ S ++R + +IK+LLDIG L+P VE+ +A V + RYPPEGIRGV Sbjct: 62 AVAPYPSQALIRPVIGDSALIKQLLDIGAQTLLVPMVESAAQARELVRAMRYPPEGIRGV 121 Query: 124 -SVSHRANMFGTVADYFAQSNKNITILVQIESQQGVDNVDAIAATEGVDGIFVGPSDLAA 182 S RA+ + ++ Y Q++ + +LVQIE+ +G+ N+D IAA EGVDG+F+GP+DL+A Sbjct: 122 GSALARASRWNSIQGYLDQADDQMCLLVQIENLEGLANLDEIAAVEGVDGVFIGPADLSA 181 Query: 183 ALGHLGNASHPDVQKAIQHIFNRASAHGKPSGILAPVEADARRYLEWGATFVAVGSDLGV 242 ++GH GN HP+VQ AI+ R GK +GIL+ E ARRY+E GATFVAVG D V Sbjct: 182 SMGHRGNPGHPEVQVAIEDAIGRIVQSGKAAGILSADENLARRYIELGATFVAVGVDTTV 241 Query: 243 FRSATQKLADTFK 255 Q LA FK Sbjct: 242 LMRGLQALAGKFK 254 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: 222 Number of extensions: 7 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: 256 Length of database: 266 Length adjustment: 25 Effective length of query: 231 Effective length of database: 241 Effective search space: 55671 Effective search space used: 55671 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: 47 (22.7 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