Align 2-dehydro-3-deoxy-phosphogluconate aldolase (EC 4.1.2.14) (characterized)
to candidate Ac3H11_2083 4-Hydroxy-2-oxoglutarate aldolase (EC 4.1.3.16) @ 2-dehydro-3-deoxyphosphogluconate aldolase (EC 4.1.2.14)
Query= BRENDA::Q0K1X1 (214 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2083 Length = 209 Score = 227 bits (579), Expect = 1e-64 Identities = 112/197 (56%), Positives = 139/197 (70%) Query: 16 PVIPVLEFHSVDEALHVSEALVTGGLPLLEITLRTPVALEAIKAVAAALPQACVGAGTVL 75 PVIPV+ V++AL ++EAL+ GG+ +LE+TLRT L AI+A+A LP+A VG GTVL Sbjct: 11 PVIPVIVIDRVEDALPLAEALLAGGVKVLEVTLRTAAGLPAIEAIARHLPEAVVGVGTVL 70 Query: 76 NVEQLHAVRDAGAQFAVSPGLTPALAEGAQGAGISLLPGVATASEAMAALEAGFTFLKFF 135 N + +AGA+FAVSPG T + +G + LLPGVAT+SE M AL GF+FLK F Sbjct: 71 NADDARRASEAGARFAVSPGYTSEVGSACKGLNLPLLPGVATSSEIMTALADGFSFLKLF 130 Query: 136 PAQAAGGVPMLKSLGGPLPQLRFCPTGGIDAALAPTYLALPNVVCVGGSWVVPKDAVASG 195 PA+A GG+P+LKS P Q+ FCPTGGI A AP YLALPNV CVGGSW+ P DAV +G Sbjct: 131 PAEAVGGIPLLKSWASPFGQVSFCPTGGITNATAPNYLALPNVRCVGGSWLTPTDAVRAG 190 Query: 196 DWGRIRTLAEQARALRN 212 DW RI LA +ALRN Sbjct: 191 DWARITELARATQALRN 207 Lambda K H 0.319 0.135 0.396 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: 204 Number of extensions: 7 Number of successful extensions: 1 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: 214 Length of database: 209 Length adjustment: 21 Effective length of query: 193 Effective length of database: 188 Effective search space: 36284 Effective search space used: 36284 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 (21.8 bits) S2: 45 (21.9 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