Align 6-phospho-5-dehydro-2-deoxy-D-gluconate aldolase; DKGP aldolase; EC 4.1.2.29 (characterized)
to candidate 6938653 Sama_2756 fructose-1,6-bisphosphate aldolase (RefSeq)
Query= SwissProt::P42420 (290 letters) >FitnessBrowser__SB2B:6938653 Length = 355 Score = 154 bits (389), Expect = 3e-42 Identities = 105/333 (31%), Positives = 168/333 (50%), Gaps = 49/333 (14%) Query: 1 MAFVSMKELLEDAKREQYAIGQFNINGLQWTKAILQAAQKEQSPVIAAASDRLVDYLGGF 60 MA +S+++LL+ A Y + FN+N L+ +AI+QAA+ SPVI AS Y Sbjct: 1 MALISLRQLLDHAAEHGYGVPAFNVNNLEQMRAIMQAAEATDSPVIVQASAGARKYARP- 59 Query: 61 KTIAAMVGALIEDMAITVPVVLHLDHGSSAERCRQAIDAGFSSVMIDGSHQP-------I 113 + + ++ A +E +PV +H DHG+ + C+++I G SSVM+DGS Sbjct: 60 QFLKYLMNAALEQYP-DIPVCIHQDHGTHPDVCQRSIQLGMSSVMMDGSLMSDGKTPASY 118 Query: 114 DENIAMTKEVTDYAAKHGVSVEAEVGTVGGMEDGLVG--------GVRYAD-----ITEC 160 D N+ +T++ +A GVSVE E+G +G +E G G GV D E Sbjct: 119 DYNVDVTRKTVAFAHACGVSVEGEIGCLGSLETGTAGEEDGIGAVGVLSHDQLLTTAEEA 178 Query: 161 ERIVKETNIDALAAALGSVHG--KYQGEPNLGFKEMEAI----SRMTDIPLVLHGASGIP 214 R V +T++DALA A+G+ HG K+ +P ++ I +R+ + LV+HG+S +P Sbjct: 179 ARFVADTHVDALAIAIGTSHGAYKFSRKPTGDVLRIDRIKEIHARIPNTHLVMHGSSSVP 238 Query: 215 Q---------------------DQIKKAITLGHAKININTECMVAWTDETRRMFQENSDL 253 Q ++I + I G K+NI+T+ +A T R+ EN Sbjct: 239 QYWLEIINQYGGEIPETYGVPLEEIVEGIKHGVRKVNIDTDLRLASTGAVRKFLAENPSE 298 Query: 254 YEPRGYLTPGIEAVEETVRSKMREFGSAGKAAK 286 ++PR +L +EA+ + + FG AG A+K Sbjct: 299 FDPRKFLKASMEAMADICTERYEAFGCAGMASK 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: 249 Number of extensions: 14 Number of successful extensions: 8 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: 355 Length adjustment: 28 Effective length of query: 262 Effective length of database: 327 Effective search space: 85674 Effective search space used: 85674 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