Align 6-phospho-5-dehydro-2-deoxy-D-gluconate aldolase; DKGP aldolase; EC 4.1.2.29 (characterized)
to candidate WP_011383790.1 AMB_RS06985 fructose-bisphosphate aldolase class II
Query= SwissProt::P42420 (290 letters) >NCBI__GCF_000009985.1:WP_011383790.1 Length = 354 Score = 168 bits (426), Expect = 1e-46 Identities = 122/337 (36%), Positives = 177/337 (52%), Gaps = 51/337 (15%) Query: 1 MAFVSMKELLEDAKREQYAIGQFNINGLQWTKAILQAAQKEQSPVIAAASDRLVDYLGGF 60 M+ VSM++LL+ A Y I FN+N ++ KAI++AA +PVI AS Y G Sbjct: 1 MSLVSMRQLLDHAAENSYGIPAFNVNNMEQVKAIMEAASACDAPVILQASAGARKYAGE- 59 Query: 61 KTIAAMVGALIEDMAITVPVVLHLDHGSSAERCRQAIDAGFSSVMIDGSHQPI------- 113 + ++ A IE +PV +H DHG+S +AI +GFSSVM+DGS + Sbjct: 60 PFLRHLILAAIEAYP-QIPVCMHQDHGTSPAINVRAIQSGFSSVMMDGSLREDGKTPSDW 118 Query: 114 DENIAMTKEVTDYAAKHGVSVEAEVGTVGGMEDGLVG---GVR----------YADITEC 160 D N+A+TK+V D A GVSVE E+G +G +E G G GV D E Sbjct: 119 DYNVAVTKQVVDIAHACGVSVEGELGCLGSLETGTAGKEDGVGAEGKLDHSQLLTDPDEA 178 Query: 161 ERIVKETNIDALAAALGSVHGKYQ------GEPNLGFKEMEAI-SRMTDIPLVLHGASGI 213 VK T +DALA A+G+ HG Y+ GE L K ++ I +R+ + LV+HG+S + Sbjct: 179 AEFVKLTQVDALAIAIGTSHGAYKFTRPPTGEV-LAIKRIKEIHARIPNTHLVMHGSSSV 237 Query: 214 PQDQIK---------------------KAITLGHAKININTECMVAWTDETRRMFQENSD 252 PQD +K + I G KINI+T+ +A T R+ F +N Sbjct: 238 PQDLLKIVNDYGGALGETYGVPVGEIVEGIKHGVRKINIDTDLRLAVTGCIRKYFHDNPK 297 Query: 253 LYEPRGYLTPGIEAVEETVRSKMREFGSAGKAAKQQV 289 ++PR YL P I A+ E +S+ FG++G+A+K +V Sbjct: 298 KFDPRDYLKPSIAAMVEVCKSRYDAFGTSGQASKIKV 334 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: 265 Number of extensions: 11 Number of successful extensions: 7 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: 354 Length adjustment: 28 Effective length of query: 262 Effective length of database: 326 Effective search space: 85412 Effective search space used: 85412 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 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