Align Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized)
to candidate PP_2723 PP_2723 Uncharacterized oxidoreductase YhdF
Query= reanno::Koxy:BWI76_RS01745 (267 letters) >FitnessBrowser__Putida:PP_2723 Length = 285 Score = 105 bits (262), Expect = 1e-27 Identities = 83/266 (31%), Positives = 121/266 (45%), Gaps = 31/266 (11%) Query: 7 LKEKIITVTGGASGIGLAIVDELLAQGANVQMIDIHGGDKHQSSGNYN--------FWPT 58 L KI +TG SGIG A+ +GA+V + ++ D Q + + P Sbjct: 40 LAGKIALITGADSGIGRAVAIAYAREGADVAIAYLNEHDDAQETARWVKAAGRQCLLLPG 99 Query: 59 DISSASEVHKTVDHIIQRFGRIDGLVNNAGVNFPRLLVDEKAPSGRYELNEAAFEKMVNI 118 D++ H VD + +FGRID LVNNA +D+ +++ + K + Sbjct: 100 DLAQKQHCHDIVDKTVAQFGRIDILVNNAAFQMAHESLDD--------IDDDEWVKTFDT 151 Query: 119 NQKGVFLMSQAVARQMVKQRSGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSKEL 178 N +F + Q M K G I+N SS + + S YAATK A+ +FT ++ L Sbjct: 152 NITAIFRICQRALPSMPK--GGSIINTSSVNSDDPSPSLLAYAATKGAIANFTAGLAQLL 209 Query: 179 GKHGIRVVGVAPGILEKTGLRTPEYEEALAWTRNITVEQLREGYSKNSIPLGRSGRLTEV 238 GK GIRV VAPG + + +EA V GY P+GR G+ EV Sbjct: 210 GKQGIRVNSVAPGPIWTPLIPATMPDEA--------VRNFGSGY-----PMGRPGQPVEV 256 Query: 239 ADFVCYLLSERASYMTGVTTNIAGGK 264 A L S+ ASY++G + GGK Sbjct: 257 APIYVLLGSDEASYISGSRYAVTGGK 282 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: 174 Number of extensions: 8 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: 285 Length adjustment: 25 Effective length of query: 242 Effective length of database: 260 Effective search space: 62920 Effective search space used: 62920 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