Align Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized)
to candidate WP_067476779.1 BJL86_RS10875 SDR family oxidoreductase
Query= reanno::Koxy:BWI76_RS01745 (267 letters) >NCBI__GCF_001659785.1:WP_067476779.1 Length = 246 Score = 84.0 bits (206), Expect = 3e-21 Identities = 79/257 (30%), Positives = 116/257 (45%), Gaps = 24/257 (9%) Query: 10 KIITVTGGASGIGLAIVDELLAQGANVQMIDI---HGGDKHQSSGNYNFWPTDISSASEV 66 K I +TGG SGIGLA +L +GA+V + H + G+ D + E Sbjct: 7 KTILITGGTSGIGLAGAAKLADEGADVIVTGRSTEHLARAAEVLGDRAMVVNDDQLSPES 66 Query: 67 HKTVDHIIQRFGRIDGLVNNAGVNFPRLLVDEKAPSGRYELNEAAFEKMVNINQKGVFLM 126 + + + + G +DG+ NAG A S +L + E M +N L Sbjct: 67 PQRLARVAREAGGLDGIWLNAGY---------AAASPIEDLTRSETESMFAVNTVAPMLQ 117 Query: 127 SQAVARQMVKQRSGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSKELGKHGIRVV 186 A++ MV+ V+V SS + EG + S Y+ATKAAL S R W+ EL IRV Sbjct: 118 MGALS-PMVRSGGSVLVT-SSTATYEGGKDLSLYSATKAALLSSARCWATELSPRNIRVN 175 Query: 187 GVAPGILEKTGLRTPEYEEALAWTRNITVEQLREGYSKNSIPLGRSGRLTEVADFVCYLL 246 + PG + + LRT E + E + + L R G E A F +LL Sbjct: 176 TLVPGPI-TSNLRTGLPAE---------IRSTFESELADQVLLRRVGDAKEAAAFAAFLL 225 Query: 247 SERASYMTGVTTNIAGG 263 S+ AS++TG + + GG Sbjct: 226 SDDASFVTGSSHYVDGG 242 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: 139 Number of extensions: 7 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: 267 Length of database: 246 Length adjustment: 24 Effective length of query: 243 Effective length of database: 222 Effective search space: 53946 Effective search space used: 53946 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 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