Align D-gluconate dehydrogenase 21.7 kD subunit (EC 1.1.99.3) (characterized)
to candidate WP_057507642.1 ABB28_RS05335 gluconate 2-dehydrogenase
Query= metacyc::MONOMER-12747 (251 letters) >NCBI__GCF_001431535.1:WP_057507642.1 Length = 243 Score = 211 bits (538), Expect = 8e-60 Identities = 111/255 (43%), Positives = 160/255 (62%), Gaps = 18/255 (7%) Query: 1 MSDQDRD---NPRREFLRKSLTLIPVVTVASTGLGGSLLAAASETAIAATPATPGKQPAG 57 MS+++ + +P R ++LTL+PVV L A E A A+ G PA Sbjct: 1 MSNENNEASASPSRRRFFQALTLVPVVAA---------LPACKE---APKGASAGASPAQ 48 Query: 58 SGQGYEPGYFTAEEWAFIKAAVERLIPADEMGPGALEAGVPEYIDRQMNTPYAAGALWYM 117 Y+P +F+A EWAF+ AA +RLIPAD++GPGA+E+GVPE++DR M TPYA+GA+WYM Sbjct: 49 DSAPYQPAFFSAAEWAFVVAACDRLIPADDIGPGAVESGVPEFLDRHMQTPYASGAIWYM 108 Query: 118 QGPFKADAAPEMGWQSKLVPKDIYRLGIAATDAWCKE-LKGQTFAAQDSATRDDLLKQLE 176 QGPF +A E G+Q +L +DI ++GIAA DA C+ G+ FAA ++ LL Q + Sbjct: 109 QGPF-LEAPSEFGYQGRLALRDILKVGIAAMDAHCRRAFDGKGFAALTVEQQEQLLTQAQ 167 Query: 177 AGTPQFDAVPAKLFFNLLLQNTKEGFFSDPIHGGNKGLVGWTLIGFPGARADFMDWVE-R 235 G + + K+FF+ LL K G+F+DP +GGNK + W +IG+PG RAD++DW+ R Sbjct: 168 DGKLGLEEISDKVFFSNLLNEVKNGYFADPKYGGNKDMGAWKMIGYPGMRADYIDWISVR 227 Query: 236 NEQYPFPAVSIRGER 250 ++ YP V + G R Sbjct: 228 DKPYPLGPVDLSGRR 242 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: 239 Number of extensions: 13 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: 243 Length adjustment: 24 Effective length of query: 227 Effective length of database: 219 Effective search space: 49713 Effective search space used: 49713 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 24 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