Align 2-dehydro-3-deoxy-phosphogluconate aldolase (EC 4.1.2.14) (characterized)
to candidate GFF2758 PGA1_c28010 KHG/KDPG aldolase
Query= BRENDA::Q0K1X1 (214 letters) >FitnessBrowser__Phaeo:GFF2758 Length = 215 Score = 208 bits (529), Expect = 7e-59 Identities = 105/195 (53%), Positives = 131/195 (67%), Gaps = 1/195 (0%) Query: 16 PVIPVLEFHSVDEALHVSEALVTGGLPLLEITLRTPVALEAIKAVAAALPQACVGAGTVL 75 P++PVL H V A ++EAL+ GGLP LE+TLRTP AL+ I A A + VGAGT++ Sbjct: 20 PIVPVLVVHDVAHARPLAEALIAGGLPALEVTLRTPAALDVI-AEMAKVKGGVVGAGTLI 78 Query: 76 NVEQLHAVRDAGAQFAVSPGLTPALAEGAQGAGISLLPGVATASEAMAALEAGFTFLKFF 135 E + AGAQF VSPG T L + A+ AG+ +LPG ATASEAM L+ G+ LKFF Sbjct: 79 TPEDVTRAVAAGAQFGVSPGATDTLLDAAEAAGLPMLPGAATASEAMRLLDRGYDMLKFF 138 Query: 136 PAQAAGGVPMLKSLGGPLPQLRFCPTGGIDAALAPTYLALPNVVCVGGSWVVPKDAVASG 195 PA+A+GG P LK++G PLPQ+ FCPTGG+ A +YL+L NVVC GGSWV P V +G Sbjct: 139 PAEASGGAPALKAIGAPLPQISFCPTGGVSPDNADSYLSLSNVVCAGGSWVAPAKLVEAG 198 Query: 196 DWGRIRTLAEQARAL 210 DW IR LA A L Sbjct: 199 DWDGIRDLARAASQL 213 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: 203 Number of extensions: 6 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: 214 Length of database: 215 Length adjustment: 22 Effective length of query: 192 Effective length of database: 193 Effective search space: 37056 Effective search space used: 37056 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