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 HSERO_RS01600 HSERO_RS01600 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase
Query= SwissProt::P23522 (256 letters) >FitnessBrowser__HerbieS:HSERO_RS01600 Length = 250 Score = 132 bits (332), Expect = 7e-36 Identities = 80/235 (34%), Positives = 123/235 (52%), Gaps = 5/235 (2%) Query: 8 NKFKAALAAKQVQIGCWSALSNPISTEVLGLAGFDWLVLDGEHAPNDISTFIPQLMALKG 67 N+ + A +Q+ + W ++ N + EV+ +G+D + +D +H P I +P L A+ Sbjct: 4 NRLRTLFAQQQLALSGWVSMGNALLAEVIAHSGYDAVTVDLQHGPFSIDAALPMLQAISS 63 Query: 68 SASAPVVRVPTNEPVIIKRLLDIGFYNFLIPFVETKEEAELAVASTRYPPEGIRGVSVSH 127 + + P+VR N I +LLD G Y + P + T +AE V + Y P G R + Sbjct: 64 TPAVPLVRCSENSLGEINKLLDAGAYGVICPLINTAADAERFVRACHYSPRGGRSYGPA- 122 Query: 128 RANMFGTVADYFAQSNKNITILVQIESQQGVDNVDAIAATEGVDGIFVGPSDLAAALGHL 187 R ++G ADYF +N + L IE+++G N +AI T +DGIF+GPSDLA LG L Sbjct: 123 RGFLYGG-ADYFTHANATLLTLAMIETREGYANAEAILQTPDLDGIFIGPSDLAIELG-L 180 Query: 188 GNASHPDVQ--KAIQHIFNRASAHGKPSGILAPVEADARRYLEWGATFVAVGSDL 240 ++ DV+ +AI H+ A GK GI A A+R G V G+D+ Sbjct: 181 APDAYDDVRLNEAIDHLLALARKLGKYVGIFAGTMEMAQRMKGIGMDLVVPGTDI 235 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: 136 Number of extensions: 6 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: 250 Length adjustment: 24 Effective length of query: 232 Effective length of database: 226 Effective search space: 52432 Effective search space used: 52432 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