Align D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized)
to candidate BPHYT_RS30440 BPHYT_RS30440 short-chain dehydrogenase
Query= BRENDA::B8H1Z0 (248 letters) >FitnessBrowser__BFirm:BPHYT_RS30440 Length = 254 Score = 131 bits (330), Expect = 1e-35 Identities = 90/246 (36%), Positives = 131/246 (53%), Gaps = 11/246 (4%) Query: 9 LKGKRVVITGGGS--GIGAGLTAGFARQGAEVIFLDIADEDSRALEAELAGSPIPPVYKR 66 L GK VI+GG S GIG FA GA + D+ ++ A+EA + P Y Sbjct: 7 LDGKVAVISGGASPRGIGMATARKFAAHGARIAIFDL--DEKAAVEAAASIGPEHRGYV- 63 Query: 67 CDLMNLEAIKAVF----AEIGDVDVLVNNAGNDDRHKLADVTGAYWDERINVNLRHMLFC 122 C++ + A +A A+ G +D+L+NNAG K D+ WD ++VNLR +L+ Sbjct: 64 CNVTDRGACQAAVERTVADFGSIDILINNAGITQAAKFLDIDPESWDRILDVNLRGVLYL 123 Query: 123 TQAVAPGMKKRGGGAVINFGSISWHLGLEDL--VLYETAKAGIEGMTRALARELGPDDIR 180 +QAV P MKK+ G++ S+S G L Y AKAG+ G+ +A+ARELG D IR Sbjct: 124 SQAVVPQMKKQKSGSIGCMSSVSAQRGGGILGGPHYSAAKAGVLGLAKAMARELGNDGIR 183 Query: 181 VTCVVPGNVKTKRQEKWYTPEGEAQIVAAQCLKGRIVPENVAALVLFLASDDASLCTGHE 240 V CV PG ++T + + +I++ L VP++VA LFLASD +S TG Sbjct: 184 VNCVTPGLIQTDINAGKISDDKRVEILSGIPLNRLGVPDDVAGAFLFLASDLSSYITGAV 243 Query: 241 YWIDAG 246 ++ G Sbjct: 244 IDVNGG 249 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: 159 Number of extensions: 6 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: 254 Length adjustment: 24 Effective length of query: 224 Effective length of database: 230 Effective search space: 51520 Effective search space used: 51520 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