Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate WP_027723082.1 H589_RS0116710 3-oxoacyl-ACP reductase FabG
Query= BRENDA::Q8GR61 (262 letters) >NCBI__GCF_000425265.1:WP_027723082.1 Length = 240 Score = 122 bits (306), Expect = 7e-33 Identities = 80/258 (31%), Positives = 139/258 (53%), Gaps = 26/258 (10%) Query: 8 KVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREA-LEKAEASVREKGVEARSYVCDVT 66 K+ L+TGA IG A A++LAE+G I L + +A K +++ G + DVT Sbjct: 3 KIALITGASKGIGAAIAVQLAEDGYDIWLNYRSDDAGAHKTAEQIKQHGQQCTLLKFDVT 62 Query: 67 SEEAVIGTVDSVVRDFGKIDFLF-NNAGY-QGAFAPVQDYPSDDFARVLTINVTGAFHVL 124 E+AV + S++ K+ ++ NNAG+ + + + D S D+ +VL +++TG F+V Sbjct: 63 DEKAVEENLSSLLEK--KVPYIVVNNAGFTRDSIMMMMD--SSDWNKVLQVHLTGFFNVT 118 Query: 125 KAVSRQMITQNYGRIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYNIRVNA 184 K V +M+ + GRI+N AS +G G Y +K +I T++ A+++A NI VNA Sbjct: 119 KPVVSRMLRKRTGRIINIASTSGETGVAGQTNYCAAKAGLIGATKSLAMEVAKRNILVNA 178 Query: 185 ISPGYMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPGVVAFL 244 ++PG++ + E V+ ++ ++P++R G E+ GVV+FL Sbjct: 179 VTPGFIDTDMLSELPVD-------------------EIKNTIPLKRLGTPKEVAGVVSFL 219 Query: 245 LGDDSSFMTGVNLPIAGG 262 D +S++TG + + GG Sbjct: 220 CSDKASYITGQTIAVNGG 237 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: 134 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: 240 Length adjustment: 24 Effective length of query: 238 Effective length of database: 216 Effective search space: 51408 Effective search space used: 51408 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: 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