Align 6-phospho-5-dehydro-2-deoxy-D-gluconate aldolase; DKGP aldolase; EC 4.1.2.29 (uncharacterized)
to candidate 200117 SO0933 fructose-bisphosphate aldolase, class II, Calvin cycle subtype (NCBI ptt file)
Query= curated2:Q5WKY5 (293 letters) >FitnessBrowser__MR1:200117 Length = 355 Score = 152 bits (383), Expect = 1e-41 Identities = 111/332 (33%), Positives = 160/332 (48%), Gaps = 49/332 (14%) Query: 1 MGFVPMAPLLADAKKDSYAIGQFNINGLQWAKAILAGAESQQSPVIAAASDRLIDYLGGF 60 M + + LL A + Y + FN+N L+ +AI+ AE+ SPVI AS Y Sbjct: 1 MALISLRQLLDHAAEHGYGVPAFNVNNLEQMRAIMQAAEATDSPVIVQASAGARKYARPQ 60 Query: 61 QTVVAMMGALTDELGITVPVVLHLDHGLSIERCKKAVDAGFSSVMFDGSHYPINE----- 115 M AL E +PV +H DHG + C++++ G SSVM DGS + Sbjct: 61 FLKYLMTAAL--EQYPDIPVCIHQDHGTDPDICQRSIQLGMSSVMMDGSLMADGKTPASY 118 Query: 116 --NIDMTKEVVAYAHAHNVSVEGEVGTVG-------GMEDGLMAE------IKYADVEEC 160 N+D+T+ VA+AHA VSVEGE+G +G G EDG+ AE EE Sbjct: 119 EYNVDVTRRTVAFAHACGVSVEGEIGCLGSLETGTAGEEDGVGAEGVLSHDQLLTSPEEA 178 Query: 161 QRFVCETNVDALAAALGSVHGKYKGEPK-----LGFNEMAAISAS-TNVPLVLHGAS--- 211 RFV +T+VDALA A+G+ HG YK K L + + I A N LV+HG+S Sbjct: 179 ARFVADTHVDALAIAIGTSHGAYKFSRKPTGDVLRIDRIKEIHARIPNTHLVMHGSSSVP 238 Query: 212 ------------------GIPDEQLQRAIKLGHAKININTECMIAWSDACRTTFAEQETA 253 G+P E++ IK G K+NI+T+ +A + A R AE + Sbjct: 239 QEWLKIINQYGGQIPETYGVPLEEIVEGIKHGVRKVNIDTDLRLASTGAVRKYLAEHPSE 298 Query: 254 FEPRLLLQEGLAMVQATVEKKIKQFGAANKAA 285 F+PR L+ + + + + FG A +A+ Sbjct: 299 FDPRKFLKASMEAMADICTVRYEAFGCAGQAS 330 Lambda K H 0.317 0.132 0.378 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: 10 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: 293 Length of database: 355 Length adjustment: 28 Effective length of query: 265 Effective length of database: 327 Effective search space: 86655 Effective search space used: 86655 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 (21.7 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