Align 2-dehydro-3-deoxy-phosphogluconate aldolase (EC 4.1.2.14) (characterized)
to candidate WP_028312695.1 H566_RS0119085 keto-deoxy-phosphogluconate aldolase
Query= BRENDA::Q0K1X1 (214 letters) >NCBI__GCF_000482785.1:WP_028312695.1 Length = 206 Score = 193 bits (490), Expect = 2e-54 Identities = 97/191 (50%), Positives = 126/191 (65%) Query: 17 VIPVLEFHSVDEALHVSEALVTGGLPLLEITLRTPVALEAIKAVAAALPQACVGAGTVLN 76 V+PV+ + A+ ++EAL+ GG+ +EITLRTP + AI+ VA A+P VGAGT+ Sbjct: 11 VMPVVVIDDAEAAVPLAEALLAGGIDAIEITLRTPAGIIAIERVAKAVPGMVVGAGTLTR 70 Query: 77 VEQLHAVRDAGAQFAVSPGLTPALAEGAQGAGISLLPGVATASEAMAALEAGFTFLKFFP 136 E VRDAG FAVSPGLTPALA+ A+ G+ L+PG TASE +AA+E GF F+K FP Sbjct: 71 PEHFRHVRDAGGVFAVSPGLTPALAQAARFTGLPLIPGTQTASEIIAAMEEGFGFVKLFP 130 Query: 137 AQAAGGVPMLKSLGGPLPQLRFCPTGGIDAALAPTYLALPNVVCVGGSWVVPKDAVASGD 196 A AGG+ LK+ G +++FCPTGG+ A YLALPNV VGG+W+ P V +GD Sbjct: 131 ANLAGGITALKAYGSVFGEMKFCPTGGVTAETLADYLALPNVPIVGGTWLTPPALVKAGD 190 Query: 197 WGRIRTLAEQA 207 W I LA A Sbjct: 191 WAAITALAAAA 201 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: 198 Number of extensions: 8 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: 206 Length adjustment: 21 Effective length of query: 193 Effective length of database: 185 Effective search space: 35705 Effective search space used: 35705 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 24 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