Align D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized)
to candidate 5209125 Shew_1603 3-oxoacyl-(acyl-carrier-protein) reductase (RefSeq)
Query= BRENDA::B8H1Z0 (248 letters) >FitnessBrowser__PV4:5209125 Length = 248 Score = 107 bits (266), Expect = 3e-28 Identities = 73/239 (30%), Positives = 118/239 (49%), Gaps = 2/239 (0%) Query: 9 LKGKRVVITGGGSGIGAGLTAGFARQGAEVIFLDIADEDSRALEAELAGSPIPPVYKRCD 68 L GK ++TG GIG + GA VI ++ + A++ L V D Sbjct: 7 LTGKVALVTGASRGIGRAVAETLVEAGALVIGTATSERGAAAIQEYLGDKGHGLVLNVTD 66 Query: 69 LMNLEAIKAVFAE-IGDVDVLVNNAGNDDRHKLADVTGAYWDERINVNLRHMLFCTQAVA 127 +++ + A E +G+VD+LVNNAG + L + W + I+ NL + ++ V Sbjct: 67 SESIDHLFASIKEKVGEVDILVNNAGITRDNLLMRMKEDEWTDIIDTNLTSLYRTSKQVL 126 Query: 128 PGMKKRGGGAVINFGSISWHLGLEDLVLYETAKAGIEGMTRALARELGPDDIRVTCVVPG 187 M K+ G +IN GS+ +G Y AKAG+ G T++LARE+ I V + PG Sbjct: 127 RAMMKKRSGRIINIGSVVGTMGNAGQTNYCAAKAGLIGFTKSLAREVASRQITVNAIAPG 186 Query: 188 NVKTKRQEKWYTPEGEAQIVAAQCLKGRIVPENVAALVLFLASDDASLCTGHEYWIDAG 246 ++T ++ T E + I++ ++ P+ +A VLFLASD A+ TG ++ G Sbjct: 187 FIQTDMTDE-LTEEQQKGIMSQVPMERLGQPQEIANAVLFLASDSAAYITGETLHVNGG 244 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: 126 Number of extensions: 7 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: 248 Length adjustment: 24 Effective length of query: 224 Effective length of database: 224 Effective search space: 50176 Effective search space used: 50176 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