Align Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized)
to candidate 8502394 DvMF_3100 3-oxoacyl-(acyl-carrier-protein) reductase (RefSeq)
Query= reanno::Koxy:BWI76_RS01745 (267 letters) >FitnessBrowser__Miya:8502394 Length = 247 Score = 112 bits (281), Expect = 6e-30 Identities = 78/258 (30%), Positives = 130/258 (50%), Gaps = 31/258 (12%) Query: 14 VTGGASGIGLAIVDELLAQGANVQMIDIHGGDKHQS--------SGNYNFWPTDISSASE 65 VTGG+ GIG A+ + L +G V + + ++ ++ G+ + D+S A+ Sbjct: 10 VTGGSRGIGKAVAETLAREGFQVYLTYVSKPEEAEAVAAGINAAGGSARAFRLDVSDAAA 69 Query: 66 VHKTVDHIIQRFGRIDGLVNNAGVNFPRLLVDEKAPSGRYELNEAAFEKMVNINQKGVFL 125 V I+ +D LVNNAG+ L++ + + F++++++N G F Sbjct: 70 VAAFFQEEIREKVTLDVLVNNAGITKDGLIL---------RMKDDDFDRVLDVNLSGAFT 120 Query: 126 MSQAVARQMVKQRSGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSKELGKHGIRV 185 + A+ M +QR G IVN++S G G+ GQ Y+A KA L T+S +KEL + V Sbjct: 121 CLREAAKLMTRQRKGRIVNITSVVGQMGNAGQVNYSAAKAGLIGMTKSAAKELAGRNVTV 180 Query: 186 VGVAPGILEKTGLRTPEYEEALAWTRNITVEQLREGYSKNSIPLGRSGRLTEVADFVCYL 245 VAPG +E T +T +++R Y + +IPL R G+ ++AD V +L Sbjct: 181 NAVAPGFIETD------------MTAKLT-DEVRAAYIE-AIPLRRLGQPQDIADAVAFL 226 Query: 246 LSERASYMTGVTTNIAGG 263 S++A Y+TG + GG Sbjct: 227 ASDKAGYITGQVIAVNGG 244 Lambda K H 0.315 0.132 0.378 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: 153 Number of extensions: 11 Number of successful extensions: 4 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: 267 Length of database: 247 Length adjustment: 24 Effective length of query: 243 Effective length of database: 223 Effective search space: 54189 Effective search space used: 54189 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: 42 (22.0 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