Align Alpha-glycerophosphate oxidase; EC 1.1.3.21; Exported protein 6; Glycerol-3-phosphate oxidase (uncharacterized)
to candidate 200162 SO0978 FAD-dependent glycerol-3-phosphate dehydrogenase, family protein (NCBI ptt file)
Query= curated2:P35596 (608 letters) >FitnessBrowser__MR1:200162 Length = 391 Score = 127 bits (320), Expect = 7e-34 Identities = 98/333 (29%), Positives = 166/333 (49%), Gaps = 16/333 (4%) Query: 21 DLLIIGGGITGAGVALQAAASGLETGLIEMQDFAEGTSSRSTKLVHGGLRYLKQFDVEVV 80 D+ IIGGGI+G G+A AAA+G T LIE + TS+ S+KL+HGGLRYL+ + +V Sbjct: 5 DIAIIGGGISGVGIAQYAAAAGYSTLLIEKGEIGGQTSANSSKLIHGGLRYLESGQINLV 64 Query: 81 SDTVSERAVVQQIAPHIPKSDPMLLPVYDEDGATFSLFRLKVAMDLYDLLAGVSNTPAAN 140 ++ ER + +AP + K +PVY + + + ++ + LY LL+ P Sbjct: 65 RKSLLERRNLLDLAPSLVKPVAFYIPVYQD--SRRNPLTIRAGLSLYALLSEFD--PLGR 120 Query: 141 KVLSKDQVLERQPNLKKEGLVGGGVYLDFRNNDARLVIENIKRANQDGALIANHVKAEGF 200 V R LK GL Y D + +D +L+ + + R+ Q + H+ AE Sbjct: 121 FVSIPAVHWHRFKGLKLSGLKAVFQYWDAQTDD-KLLTQAVARSAQ---ALGAHIYAEAE 176 Query: 201 LFDESGKITGVVARDLLTDQVFEIKARLVINTTGPWSDKVRNLSNKGTQFSQMRPTKGVH 260 + + +V +I+ +LVIN GPW ++V ++ +G H Sbjct: 177 FLQLNHLKEQIELSFRHRGEVQQIETKLVINAAGPWVNEVLAHVEPPLAGVEIDWVQGAH 236 Query: 261 LVVDSSKIKVSQPVYFDTGLGDGRMVFVLPRENKTYFGTTDTDYTGDLEHPKVTQEDVDY 320 L++D + + + + D R++FV+P + GTT+T T P+VT+ + Y Sbjct: 237 LLLD---LPAPEGILYLESCFDKRVIFVMPWYGQMLIGTTETVLTSIDTPPQVTESETQY 293 Query: 321 LLGIVNNRFPESNITIDDIES----SWAGLRPL 349 LLGI + FP S +I+++++ ++ G+R L Sbjct: 294 LLGIYCHYFPLSP-SIEELKTKIVQTYCGVRVL 325 Lambda K H 0.314 0.133 0.368 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: 438 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: 608 Length of database: 391 Length adjustment: 34 Effective length of query: 574 Effective length of database: 357 Effective search space: 204918 Effective search space used: 204918 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 52 (24.6 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