Align 6-phospho-5-dehydro-2-deoxy-D-gluconate aldolase; DKGP aldolase; EC 4.1.2.29 (characterized)
to candidate Synpcc7942_1443 Synpcc7942_1443 fructose-1,6-bisphosphate aldolase
Query= SwissProt::P42420 (290 letters) >FitnessBrowser__SynE:Synpcc7942_1443 Length = 357 Score = 150 bits (379), Expect = 4e-41 Identities = 107/334 (32%), Positives = 169/334 (50%), Gaps = 51/334 (15%) Query: 1 MAFVSMKELLEDAKREQYAIGQFNINGLQWTKAILQAAQKEQSPVIAAASDRLVDYLGGF 60 MA V ++ +L+ A +Y I FN+N L+ ++ILQAA + SPVI AS Y G Sbjct: 1 MALVPLRLMLDHAAENEYGIPAFNVNNLEQVQSILQAADETDSPVILQASRGARSYAGE- 59 Query: 61 KTIAAMVGALIEDMAITVPVVLHLDHGSSAERCRQAIDAGFSSVMIDGSHQP-------I 113 + ++ A +E +P+ +H DHG+S C AI GF+SVM+DGS + Sbjct: 60 NFLRHLILAAVETYP-HIPIAMHQDHGNSPATCYSAIKNGFTSVMMDGSLEADAKTPASY 118 Query: 114 DENIAMTKEVTDYAAKHGVSVEAEVGTVGGMEDG-------------LVGGVRYADITEC 160 + N+ +T++V D A GVSVE E+G +G +E G L D + Sbjct: 119 EYNVEVTRQVVDVAHSIGVSVEGELGCLGSLETGKGEAEDGHGFEGTLDHSQLLTDPDQA 178 Query: 161 ERIVKETNIDALAAALGSVHGKYQ------GEPNLGFKEMEAISR-MTDIPLVLHGASGI 213 V++T +DALA A+G+ HG Y+ GE L +E I R + + LV+HG+S + Sbjct: 179 VDFVEKTQVDALAVAIGTSHGAYKFTRKPTGEI-LAISRIEEIHRRLPNTHLVMHGSSSV 237 Query: 214 PQD---------------------QIKKAITLGHAKININTECMVAWTDETRRMFQENSD 252 PQ+ +I+KAI LG KINI+T+ +A+T R ++ Sbjct: 238 PQELLELINEYGGQIPETYGVPVEEIQKAIKLGVRKINIDTDNRLAFTAAVREAAAKDPS 297 Query: 253 LYEPRGYLTPGIEAVEETVRSKMREFGSAGKAAK 286 ++PR + P I+ +++ + F +AG+A+K Sbjct: 298 NFDPRHFNKPAIKYMKQVCVDRYVAFNTAGQASK 331 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: 273 Number of extensions: 15 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: 357 Length adjustment: 28 Effective length of query: 262 Effective length of database: 329 Effective search space: 86198 Effective search space used: 86198 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