Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate BPHYT_RS04770 BPHYT_RS04770 short-chain dehydrogenase
Query= BRENDA::Q8GR61 (262 letters) >FitnessBrowser__BFirm:BPHYT_RS04770 Length = 246 Score = 160 bits (404), Expect = 3e-44 Identities = 95/259 (36%), Positives = 138/259 (53%), Gaps = 17/259 (6%) Query: 4 KFNGKVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREALEKAEASVREKGVEARSYVC 63 + NGKV +VTGAG IG ATAL+ A+EG +A+ D+N +A+ + A+ G +A + Sbjct: 2 RLNGKVTIVTGAGQGIGAATALKFAKEGARVAVCDVNHDAVSRVVAACHAAGAQALGFTL 61 Query: 64 DVTSEEAVIGTVDSVVRDFGKIDFLFNNAGYQGAFAPVQDYPSDDFARVLTINVTGAFHV 123 DVT+ AV G V V F +ID L NNAG A +Q F V+ +N+ G FH Sbjct: 62 DVTNRAAVDGMVADVRERFRQIDVLVNNAGIT-RDARLQKMTLQQFDDVIDVNLRGVFHA 120 Query: 124 LKAVSRQMITQNYGRIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYNIRVN 183 +AV MI Q G I+N +S+ G+ G Y +K +I T+T + +L P IRVN Sbjct: 121 AQAVVDTMIAQGSGVILNASSVVGLYGNYGQTNYAAAKFGVIGFTKTWSRELGPKGIRVN 180 Query: 184 AISPGYMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPGVVAF 243 AI+PG+ + + ST P+ V +M VP+RR G EI + AF Sbjct: 181 AIAPGF----------------IDTPILSTVPQEVLAKMREQVPLRRLGTPEEIANIYAF 224 Query: 244 LLGDDSSFMTGVNLPIAGG 262 L D++S++ G + +GG Sbjct: 225 LASDEASYINGAVIEASGG 243 Lambda K H 0.318 0.135 0.384 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: 172 Number of extensions: 6 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: 262 Length of database: 246 Length adjustment: 24 Effective length of query: 238 Effective length of database: 222 Effective search space: 52836 Effective search space used: 52836 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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