Align D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized)
to candidate Ac3H11_2257 Short-chain dehydrogenase/reductase SDR
Query= BRENDA::B8H1Z0 (248 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2257 Length = 267 Score = 139 bits (349), Expect = 8e-38 Identities = 87/252 (34%), Positives = 132/252 (52%), Gaps = 11/252 (4%) Query: 1 MSSAIYPSLKGKRVVITGGGSGIGAGLTAGFARQGAEVIFLDIADEDSRALEAELAGSPI 60 + S+IY G+ ++TGG GIG FA +GA+ + +D+ D +AL AEL Sbjct: 10 LPSSIYFGHTGRVCIVTGGAQGIGEACVRRFAAEGAKPVIVDVDDARGQALAAELGA--- 66 Query: 61 PPVYKRCDLMNLEAIKAVFAEI----GDVDVLVNNAGNDDRHKLADVTGAYWDERINVNL 116 +Y RCD+ + + A+ A++ G +DVLVNNAG +VT A +D + VNL Sbjct: 67 --LYVRCDVGDKAQVDALVAQVLAAHGRIDVLVNNAGIFRAADFLEVTEADFDAVLRVNL 124 Query: 117 RHMLFCTQAVAPGMKKRGGGAVINFGSISWHLGLEDLVLYETAKAGIEGMTRALARELGP 176 + QAVA M GGGA++N S++ L + ++ Y +K G+ +TR +A L Sbjct: 125 KGSFLVGQAVARAMVTSGGGAIVNMSSVNGVLAIPNIASYNVSKGGVNQLTRVMALALAD 184 Query: 177 DDIRVTCVVPGNVKTKRQEKWYTPEGEA--QIVAAQCLKGRIVPENVAALVLFLASDDAS 234 +IRV V PG + T+ K EA +I++ +K P +A +V +LASD AS Sbjct: 185 KNIRVNAVAPGTIATELAAKAVLTSDEAKRKIMSRTPMKRLGQPSEIADVVAWLASDAAS 244 Query: 235 LCTGHEYWIDAG 246 TG +D G Sbjct: 245 YVTGEIVTVDGG 256 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: 158 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: 248 Length of database: 267 Length adjustment: 24 Effective length of query: 224 Effective length of database: 243 Effective search space: 54432 Effective search space used: 54432 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: 47 (22.7 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