Align 6-phospho-5-dehydro-2-deoxy-D-gluconate aldolase; DKGP aldolase; EC 4.1.2.29 (uncharacterized)
to candidate WP_013402102.1 CALHY_RS00635 class II fructose-bisphosphate aldolase
Query= curated2:Q5WKY5 (293 letters) >NCBI__GCF_000166355.1:WP_013402102.1 Length = 278 Score = 175 bits (443), Expect = 1e-48 Identities = 104/279 (37%), Positives = 156/279 (55%), Gaps = 5/279 (1%) Query: 4 VPMAPLLADAKKDSYAIGQFNINGLQWAKAILAGAESQQSPVIAAASDRLIDYLGGFQTV 63 V + +L+ K + +G FN + + ++ AE + P+I +DR +D L F+ + Sbjct: 3 VNLNEVLSYTKVKKFGVGMFNGLSADFYEGLIDAAEQLRCPIIIGVADRFVDRLD-FEMI 61 Query: 64 VAMMGALTDELGITVPVVLHLDHGLSIERCKKAVDAGFSSVMFDGSHYPINENIDMTKEV 123 +M L +VPV +HLDH S++ +A+ AGF+SVMFDGS P ENI TKE+ Sbjct: 62 AEVMIFLAKRA--SVPVCVHLDHAKSLKNIMRAIKAGFTSVMFDGSSLPFEENIKRTKEI 119 Query: 124 VAYAHAHNVSVEGEVGTVGGMEDGLMAEIKYADVEECQRFVCETNVDALAAALGSVHGKY 183 V AH+ VSVEGE+G VG + Y +E + F +T VDALA ++G+VHG Y Sbjct: 120 VEIAHSVGVSVEGELGVVGRGDFDFKNPEFYTKPDEAEEFAQKTQVDALAVSIGTVHGVY 179 Query: 184 KGEPKLGFNEMAAISASTNVPLVLHGASGIPDEQLQRAIKLGHAKININTECMIAWSDAC 243 KGEPKL F ++ I + LVLHG SG+ DE ++ I+ G K+NI T+ +A +A Sbjct: 180 KGEPKLDFERLSEIRKRVDCYLVLHGGSGLSDEDFKKCIEYGINKVNIFTDLTLA-INAQ 238 Query: 244 RTTFAEQETAFEPRLLLQEGLAMVQATVEKKIKQFGAAN 282 F +Q P + ++ +V+ KK+K FG+ N Sbjct: 239 LPEFIKQTEDLTP-AIFEKIREIVKQEAIKKLKIFGSYN 276 Lambda K H 0.317 0.132 0.378 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: 184 Number of extensions: 10 Number of successful extensions: 4 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: 293 Length of database: 278 Length adjustment: 26 Effective length of query: 267 Effective length of database: 252 Effective search space: 67284 Effective search space used: 67284 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 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