Align Alpha-glycerophosphate oxidase; EC 1.1.3.21; Exported protein 6; Glycerol-3-phosphate oxidase (uncharacterized)
to candidate 7026168 Shewana3_3310 FAD dependent oxidoreductase (RefSeq)
Query= curated2:P35596 (608 letters) >FitnessBrowser__ANA3:7026168 Length = 396 Score = 142 bits (358), Expect = 3e-38 Identities = 106/340 (31%), Positives = 171/340 (50%), Gaps = 16/340 (4%) Query: 14 KMQERTLDLLIIGGGITGAGVALQAAASGLETGLIEMQDFAEGTSSRSTKLVHGGLRYLK 73 K + D+ IIGGGI+G G+A AAA+G T LIE + TS+ S+KL+HGGLRYL+ Sbjct: 3 KADMSSYDIAIIGGGISGVGIAQYAAAAGYSTLLIEKGEIGGQTSANSSKLIHGGLRYLE 62 Query: 74 QFDVEVVSDTVSERAVVQQIAPHIPKSDPMLLPVYDEDGATFSLFRLKVAMDLYDLLAGV 133 V +V ++ ER + AP + K+ P +PVY + + + + ++ + LY LL+ Sbjct: 63 SGQVNLVRKSLQERRHLLDFAPSLVKAVPFYIPVYQD--SQRNPWTIRAGLSLYALLSEF 120 Query: 134 SNTPAANKVLSKDQVLERQPNLKKEGLVGGGVYLDFRNNDARLVIENIKRANQDGALIAN 193 P V R LK +GL Y D + +D L + A GA Sbjct: 121 D--PLGRFVSIPAVHWHRFNGLKLQGLKAVFQYWDAQTDDKLLTQAVARSAEALGA---- 174 Query: 194 HVKAEGFLFDESGKITGVVARDLLTDQVFEIKARLVINTTGPWSDKVRNLSNKGTQFSQM 253 HV AE + + L +V +I A+LVIN GPW ++V + ++ Sbjct: 175 HVYAEAEFLQLNHLSEQIDLSFRLRGEVQQIDAKLVINAAGPWVNEVIAKVSPPLAGVEL 234 Query: 254 RPTKGVHLVVDSSKIKVSQPVYFDTGLGDGRMVFVLPRENKTYFGTTDTDYTGDLEHPKV 313 +G HL++D + + + D R++FV+P + GTT+T+ T P+V Sbjct: 235 DWVQGAHLLLD---LPAPDGILYLESCFDKRVIFVMPWYGQMLIGTTETELTSLDSPPQV 291 Query: 314 TQEDVDYLLGIVNNRFPESNITIDDIES----SWAGLRPL 349 T+ +++YLLGI + FP S +ID++++ ++ G+R L Sbjct: 292 TESEINYLLGIYRHYFPLS-ASIDELKTKIVQTFCGVRVL 330 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: 446 Number of extensions: 15 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: 396 Length adjustment: 34 Effective length of query: 574 Effective length of database: 362 Effective search space: 207788 Effective search space used: 207788 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