Align D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized)
to candidate 207249 DVU1784 oxidoreductase, short-chain dehydrogenase/reductase family (TIGR)
Query= BRENDA::B8H1Z0 (248 letters) >FitnessBrowser__DvH:207249 Length = 253 Score = 84.3 bits (207), Expect = 2e-21 Identities = 60/184 (32%), Positives = 89/184 (48%), Gaps = 17/184 (9%) Query: 14 VVITGGGSGIGAGLTAGFARQGAEVIFLDIADEDSRALEAELAGSPIPPVYKRCDLMNLE 73 + ITG +G G FA +G +I E L AEL P+ D+ + + Sbjct: 5 ICITGATAGFGEACARRFAAEGCRLIITGRRKERLEKLAAELGEDRCLPLV--FDVRDRK 62 Query: 74 AIKAVFAEI----GDVDVLVNNAG------NDDRHKLADVTGAYWDERINVNLRHMLFCT 123 A++A FA + +VDVL+NNAG R L D W+ I+ NL+ +++CT Sbjct: 63 AVEAAFAALPEAFANVDVLINNAGLALGLEPAHRASLED-----WETMIDTNLKGLMYCT 117 Query: 124 QAVAPGMKKRGGGAVINFGSISWHLGLEDLVLYETAKAGIEGMTRALARELGPDDIRVTC 183 +A+ PGM +RG G V+N GSI+ Y KA + +R L +L +RVT Sbjct: 118 RALLPGMVERGKGHVVNLGSIAGSYPYPGGNTYGATKAFVMQFSRNLRADLHGTGVRVTN 177 Query: 184 VVPG 187 + PG Sbjct: 178 IEPG 181 Lambda K H 0.319 0.137 0.416 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: 156 Number of extensions: 8 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: 248 Length of database: 253 Length adjustment: 24 Effective length of query: 224 Effective length of database: 229 Effective search space: 51296 Effective search space used: 51296 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 (21.7 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Apr 09 2024. 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