Align 6-phospho-5-dehydro-2-deoxy-D-gluconate aldolase; DKGP aldolase; EC 4.1.2.29 (characterized)
to candidate SM_b20199 SM_b20199 fructose-1,6-bisphosphate aldolase
Query= SwissProt::P42420 (290 letters) >FitnessBrowser__Smeli:SM_b20199 Length = 359 Score = 152 bits (385), Expect = 8e-42 Identities = 104/336 (30%), Positives = 168/336 (50%), Gaps = 49/336 (14%) Query: 1 MAFVSMKELLEDAKREQYAIGQFNINGLQWTKAILQAAQKEQSPVIAAASDRLVDYLGGF 60 MA +++++LL+ A Y + FNIN ++ AI++AA+ +PVI S Y Sbjct: 1 MARITLRQLLDHAAERSYGVPAFNINNMEQGLAIMEAARASDAPVILQVSRGARSYANDV 60 Query: 61 KTIAAMVGALIEDMAITVPVVLHLDHGSSAERCRQAIDAGFSSVMIDGSHQP-------I 113 +A M+ AL E+M +P+ +H DHG++ C AI GF+SVM+DGS + Sbjct: 61 M-LAKMMEAL-EEMYPDIPLCIHQDHGNNVATCLTAIQHGFTSVMMDGSLKEDAKTPADY 118 Query: 114 DENIAMTKEVTDYAAKHGVSVEAEVGTVGGMEDG-------------LVGGVRYADITEC 160 D N+++T EV+ A G SVE E+G +G +E G L D E Sbjct: 119 DYNVSITAEVSRLAHMVGASVEGELGCLGSLETGHGEAEDGHGFEGALDRSQLLTDPDEA 178 Query: 161 ERIVKETNIDALAAALGSVHGKYQ--GEPNLGFKEMEAIS----RMTDIPLVLHGASGIP 214 R V ET +DALA A+G+ HG Y+ +P M+ I R+ D +V+HG+S +P Sbjct: 179 ARFVAETGVDALAVAIGTSHGAYKFTRKPTGEVLAMDVIEKIHERLPDTHIVMHGSSSVP 238 Query: 215 QD---------------------QIKKAITLGHAKININTECMVAWTDETRRMFQENSDL 253 Q+ +I + I G K+NI+T+ +A RR+ + Sbjct: 239 QEWQDVFNAHGGQMRETYGVPVEEIVRGIRFGVRKVNIDTDLRLAAAAAFRRVADTSRSE 298 Query: 254 YEPRGYLTPGIEAVEETVRSKMREFGSAGKAAKQQV 289 ++PR +L P ++A+ +++ FG+AG A++ +V Sbjct: 299 FDPRKFLKPAMDAMSAVCKARFEAFGTAGNASRIKV 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: 275 Number of extensions: 13 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: 359 Length adjustment: 28 Effective length of query: 262 Effective length of database: 331 Effective search space: 86722 Effective search space used: 86722 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