Align D-gluconate dehydrogenase 21.7 kD subunit (EC 1.1.99.3) (characterized)
to candidate BPHYT_RS30775 BPHYT_RS30775 gluconate 2-dehydrogenase
Query= metacyc::MONOMER-12747 (251 letters) >FitnessBrowser__BFirm:BPHYT_RS30775 Length = 251 Score = 216 bits (549), Expect = 5e-61 Identities = 113/243 (46%), Positives = 153/243 (62%), Gaps = 13/243 (5%) Query: 10 RREFLRKSLTLIPVVT-VASTGLGGSLLAAASETAIAATPATPGKQPAGSGQGYEPGYFT 68 RR FL KS+ ++PV +A+ G L A+AS + ++ A P Y+P +F Sbjct: 18 RRRFLIKSVAVLPVAGGLAACDRPGGLTASASASTADSSNAAP----------YQPKFFK 67 Query: 69 AEEWAFIKAAVERLIPADEMGPGALEAGVPEYIDRQMNTPYAAGALWYMQGPFKADAAPE 128 +EW+ ++AA++RLIPAD GPGALE V +IDRQM + A WYM GPF DA P Sbjct: 68 PDEWSVLQAAIDRLIPADAEGPGALELDVATFIDRQMEGAFGHAAAWYMHGPFHPDATPL 127 Query: 129 MGWQSKLVPKDIYRLGIAATDAWCK-ELKGQTFAAQDSATRDDLLKQLEAGTPQFDAVPA 187 G+QS + P+D+YR GIAA DA CK G+ F +A +D LL +++G +F+ A Sbjct: 128 AGYQSPMSPRDLYRTGIAALDAHCKAHFGGKPFVQLTTAQQDTLLHAMDSGKVKFEQTSA 187 Query: 188 KLFFNLLLQNTKEGFFSDPIHGGNKGLVGWTLIGFPGARADFMDWV-ERNEQYPFPAVSI 246 + F LL QNTKEG+FSDPIHGGNK WT+IGFPGARAD++DWV + + YP V+I Sbjct: 188 RHFIALLWQNTKEGYFSDPIHGGNKHAASWTMIGFPGARADYLDWVAQPGKVYPLGPVTI 247 Query: 247 RGE 249 G+ Sbjct: 248 EGK 250 Lambda K H 0.317 0.135 0.414 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: 230 Number of extensions: 10 Number of successful extensions: 3 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: 251 Length of database: 251 Length adjustment: 24 Effective length of query: 227 Effective length of database: 227 Effective search space: 51529 Effective search space used: 51529 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: 46 (22.3 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