Align D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized)
to candidate Dsui_0694 Dsui_0694 dehydrogenase of unknown specificity, short-chain alcohol dehydrogenase like protein
Query= BRENDA::B8H1Z0 (248 letters) >FitnessBrowser__PS:Dsui_0694 Length = 251 Score = 96.3 bits (238), Expect = 5e-25 Identities = 84/252 (33%), Positives = 119/252 (47%), Gaps = 24/252 (9%) Query: 8 SLKGKRVVITGGGSGIGAGLTAGFARQGAE-VIFLDIADEDSRALEAEL-AGSPIPPVYK 65 +L+GK +++TGG +GA + GA V+ A ++R+L AEL A V Sbjct: 6 NLQGKAILVTGGAKRVGAAIARRLHAAGASLVLHYRSAAAEARSLAAELNAQRDGSAVCI 65 Query: 66 RCDLMNLEAIKAVFAE----IGDVDVLVNNAGNDDRHKLADVTGAYWDERINVNLRHMLF 121 + DL+ A+ + + G +D LVNNA + R L + A WD+ + N + LF Sbjct: 66 QADLLQTSALPGLVEQSVTAFGRLDGLVNNASSFFRTPLGSIDEAAWDDLVGSNFKAPLF 125 Query: 122 CTQAVAPGMKKRGGGAVINFGSISWHLGLEDLVLYETAKAGIEGMTRALARELGPDDIRV 181 TQA AP + + GGAV+N + L LY AK + +TRALA EL P +RV Sbjct: 126 LTQAAAPHL-RASGGAVVNITDVHAERPLVGYPLYCAAKGALLTLTRALAAELAP-VVRV 183 Query: 182 TCVVPGNVKTKRQEKWYTPEGE------AQIVAAQCLKGRI-VPENVAALVLFLASDDAS 234 V PG + W PEG Q + A L GR P ++A V FL D Sbjct: 184 NAVAPGPI------LW--PEGSDFDSAARQAIVADTLLGREGSPADIARAVHFLLVDSPY 235 Query: 235 LCTGHEYWIDAG 246 + TG +D G Sbjct: 236 I-TGQVINVDGG 246 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: 140 Number of extensions: 9 Number of successful extensions: 2 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: 251 Length adjustment: 24 Effective length of query: 224 Effective length of database: 227 Effective search space: 50848 Effective search space used: 50848 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 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