Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate WP_108358580.1 B9Z44_RS13785 3-oxoacyl-ACP reductase FabG
Query= BRENDA::Q8GR61 (262 letters) >NCBI__GCF_003063475.1:WP_108358580.1 Length = 255 Score = 164 bits (415), Expect = 2e-45 Identities = 91/261 (34%), Positives = 144/261 (55%), Gaps = 17/261 (6%) Query: 2 SKKFNGKVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREALEKAEASVREKGVEARSY 61 +++ GKV L+TGA IGLATAL+ A EG + + D+ + A+++A + G +A + Sbjct: 9 AQRLQGKVSLITGAAQGIGLATALKFAREGAIVIVCDVKQAAVDEAVKQCQALGAQALGF 68 Query: 62 VCDVTSEEAVIGTVDSVVRDFGKIDFLFNNAGYQGAFAPVQDYPSDDFARVLTINVTGAF 121 V DVT + V TV +V+ FG+ID L NNAG A +Q + F RV+ +N+ G F Sbjct: 69 VVDVTQRDMVDATVKAVLDKFGRIDVLVNNAGIT-QDARLQKMTLEQFDRVIDVNLRGVF 127 Query: 122 HVLKAVSRQMITQNYGRIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYNIR 181 H +AV+ M+ Q G I+N +S+ G+ G Y +K +I T+T + +L P IR Sbjct: 128 HCAQAVTEAMVAQGSGVILNASSVVGIYGNFGQTNYAATKFGVIGFTKTWSRELGPKGIR 187 Query: 182 VNAISPGYMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPGVV 241 VNA++PG+ + + ST P+ V +M VP++R G +I V Sbjct: 188 VNAVAPGF----------------IQTPILSTIPEKVIHEMTDRVPLKRLGQPEDIANVY 231 Query: 242 AFLLGDDSSFMTGVNLPIAGG 262 AFL D+++++ G + +AGG Sbjct: 232 AFLASDEAAYINGTVIEVAGG 252 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: 161 Number of extensions: 5 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: 255 Length adjustment: 24 Effective length of query: 238 Effective length of database: 231 Effective search space: 54978 Effective search space used: 54978 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 24 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