Align 6-phospho-5-dehydro-2-deoxy-D-gluconate aldolase; DKGP aldolase; EC 4.1.2.29 (characterized)
to candidate WP_012103922.1 CKL_RS17525 fructose-1,6-bisphosphate aldolase, class II
Query= SwissProt::P42420 (290 letters) >NCBI__GCF_000016505.1:WP_012103922.1 Length = 313 Score = 180 bits (457), Expect = 3e-50 Identities = 106/302 (35%), Positives = 167/302 (55%), Gaps = 30/302 (9%) Query: 1 MAFVSMKELLEDAKREQYAIGQFNINGLQWTKAILQAAQKEQSPVIAAASDRLVDYLGGF 60 MA V+ K++ E A + Y+IG FNIN ++ + ++ A+ + S VI S + Y G Sbjct: 1 MALVTTKKMFEKAYKGHYSIGAFNINNMEIIQGVVNGAKAKNSAVILQCSASAMKYAGP- 59 Query: 61 KTIAAMVGALIEDMAITVPVVLHLDHGSSAERCRQAIDAGFSSVMIDGSHQPIDENIAMT 120 K + AMV A +ED I + LHLDHG E + I+ GF+SVM DGSH ++N++ T Sbjct: 60 KYLKAMVDAAVEDTGIDI--ALHLDHGPDFEAVKLCIETGFTSVMFDGSHLDYEDNVSQT 117 Query: 121 KEVTDYAAKHGVSVEAEVGTVGGMEDGLVGGVR-YADITECERIVKETNIDALAAALGSV 179 K+V +Y+ HGV VEAE+G + G+ED + Y D + V T +D+LA A+G+ Sbjct: 118 KQVVEYSHSHGVVVEAELGVLAGIEDEVSASDHIYTDPEQAVDFVNRTGVDSLAIAIGTS 177 Query: 180 HGKYQGEPN----LGFKEMEAI-SRMTDIPLVLHGAS---------------------GI 213 HG ++ PN L F +E I + + P+VLHGAS GI Sbjct: 178 HGAFKFPPNFKPKLRFDILEKIQENLPNFPIVLHGASAVDPKAVETCNKYGGNIADAKGI 237 Query: 214 PQDQIKKAITLGHAKININTECMVAWTDETRRMFQENSDLYEPRGYLTPGIEAVEETVRS 273 P D ++KA ++ KIN++T+ ++ T R+ F ++ +++PR YL G +A+++ V Sbjct: 238 PIDMLRKASSMAVCKINMDTDLRLSMTAAIRKTFGDSPKVFDPRKYLGAGRDAIQKVVED 297 Query: 274 KM 275 K+ Sbjct: 298 KI 299 Lambda K H 0.316 0.132 0.372 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: 232 Number of extensions: 16 Number of successful extensions: 6 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: 290 Length of database: 313 Length adjustment: 27 Effective length of query: 263 Effective length of database: 286 Effective search space: 75218 Effective search space used: 75218 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 (21.6 bits) S2: 48 (23.1 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