Align D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized)
to candidate WP_010539115.1 KCY_RS0122130 SDR family oxidoreductase
Query= reanno::Korea:Ga0059261_1894 (259 letters) >NCBI__GCF_000226135.1:WP_010539115.1 Length = 259 Score = 125 bits (313), Expect = 1e-33 Identities = 83/245 (33%), Positives = 119/245 (48%), Gaps = 5/245 (2%) Query: 17 KGKRVLVTGGGSGIGAGIVEGFARQGADVTFFDIAGAESQLLVERLSADGHKACFERVDL 76 + K V++TG SGIG +G V D + + L L+ G Sbjct: 5 ENKVVVITGAASGIGEATTRRIVSEGGKVVIADYSKERADELAAELTQSGADVRSVYFSA 64 Query: 77 TDVASLQAVIARLIKGAGGFDILVNNAANDDRHA---IDEITEAYWDERLSVNLKHIFFC 133 T++ S + +I +K G D+L+NN D I+++ Y+DE +NL + Sbjct: 65 TELQSCKELIDFAMKEYGQVDVLINNVGGTDPKRDLNIEKLDIDYFDEAFHLNLCCTMYL 124 Query: 134 AQAVVPAMRARGGGAIVNLGSISWHLGLSDLVLYQTCKAAIEGLTRSLARDLGRDGIRAT 193 +Q V+P M A GGG IVN+ SIS ++ LY KA + LT+ +A +G+ IR Sbjct: 125 SQQVIPIMTAHGGGNIVNVASISGITADANGTLYGASKAGVINLTKYIATQMGKKNIRCN 184 Query: 194 CVIPGNVRTPRQLKWYSPEGEAEIVAAQCLDGRLA-PEDVAAMVLFLASDDARLVTGHSY 252 V PG V TP + + E I QC L PEDVAA + FLAS+DAR +TG + Sbjct: 185 AVAPGLVLTPAAVNNLN-EDVRNIFLGQCATPYLGEPEDVAATIAFLASNDARYITGQTI 243 Query: 253 FVDAG 257 VD G Sbjct: 244 VVDGG 248 Lambda K H 0.321 0.137 0.409 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: 142 Number of extensions: 7 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: 259 Length of database: 259 Length adjustment: 24 Effective length of query: 235 Effective length of database: 235 Effective search space: 55225 Effective search space used: 55225 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 47 (22.7 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