Align Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized)
to candidate BPHYT_RS11930 BPHYT_RS11930 3-hydroxybutyrate dehydrogenase
Query= reanno::Koxy:BWI76_RS22230 (259 letters) >FitnessBrowser__BFirm:BPHYT_RS11930 Length = 260 Score = 103 bits (257), Expect = 4e-27 Identities = 82/262 (31%), Positives = 125/262 (47%), Gaps = 12/262 (4%) Query: 2 NQVAVVIGGGQTLGEFLCRGLAAEGYRVAVVDIQSDKATRVAQSINAEYGEGTAWGFGAD 61 ++VA+V G +GE R LAA+G V + D+ A +VA+ I + A G D Sbjct: 5 DKVALVTGAASGIGEQCARKLAADGATVVIADLNLVNAQKVAEDIVKTGAKAIA--IGMD 62 Query: 62 ATSEASVVALARGVDDIFSRVDLLVYSAGIAKAAFISDFALGDFDRSLQVNLVGYFLCAR 121 TSE SV A +D+LV +AGI I ++ D+ + L ++L G FL + Sbjct: 63 VTSEESVNAGVAETVRRLGSLDVLVSNAGIQIVNRIEEYPFADWKKMLAIHLDGAFLTTK 122 Query: 122 EFSRLMIRDGIKGRIIQINSKSGKVGSKHNSGYSAAKFGGVGLTQSLALDLAEYGITVHS 181 R M G +I + S S+ S Y AK G +GL + +A + +G+ + Sbjct: 123 AAIRHMYASKKGGAVIYMGSVHSHEASQLKSAYVTAKHGLLGLARVVAKEGGPHGVRANV 182 Query: 182 LMLGNLLKSPMFQSLLPQYATKLGIPEEQVEQYYIDKVPLKRGCD-----YQDVLNVLMF 236 + G +++P+ +P+ A LGI E+QV + V LK D DV N + F Sbjct: 183 VCPG-FVRTPLVDKQIPEQAKALGISEQQV----VSDVMLKDTVDGEFTSVDDVANTVAF 237 Query: 237 YASPQASYCTGQSINVTGGQVM 258 A ++S TGQSI V+ G M Sbjct: 238 LAGFESSALTGQSIVVSHGWFM 259 Lambda K H 0.320 0.137 0.392 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: 13 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: 259 Length of database: 260 Length adjustment: 24 Effective length of query: 235 Effective length of database: 236 Effective search space: 55460 Effective search space used: 55460 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 (21.8 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