Align Alpha-glycerophosphate oxidase; EC 1.1.3.21; Exported protein 6; Glycerol-3-phosphate oxidase (uncharacterized)
to candidate Echvi_1771 Echvi_1771 Glycerol-3-phosphate dehydrogenase
Query= curated2:P35596 (608 letters) >FitnessBrowser__Cola:Echvi_1771 Length = 521 Score = 216 bits (549), Expect = 2e-60 Identities = 166/545 (30%), Positives = 259/545 (47%), Gaps = 92/545 (16%) Query: 21 DLLIIGGGITGAGVALQAAASGLETGLIEMQDFAEGTSSRSTKLVHGGLRYLKQFDVEVV 80 D++IIGGG +G GVAL A + GL L E DFA+GTSSRSTKLVHGG+RYL Q D+ +V Sbjct: 17 DIVIIGGGASGLGVALDALSRGLSVALFERADFAKGTSSRSTKLVHGGVRYLAQGDILLV 76 Query: 81 SDTVSERAVVQQIAPHIPKSDPMLLPVYDEDGATFSLFRLKVAMDLYDLLAGVSNTPAAN 140 + + ER + + APH+ + P ++P+Y + + V + YD ++G + + Sbjct: 77 WEALRERGRILKNAPHLAHAQPFIIPIYSH----ATKYYYTVGLKFYDWMSGWLSL-GDS 131 Query: 141 KVLSKDQVLERQPNLKKEGLVGGGVYLDFRNNDARLVIENIKRANQDGALIANHVKAEGF 200 +SK + ++R P +K EGL+GG VY D +DARL I + + G I N++K Sbjct: 132 SFISKKETIKRLPEIKTEGLLGGVVYHDGAFDDARLAIAVAQTCDDMGGCILNYMKVTSL 191 Query: 201 LFDESGKITGVVARDLLTDQVFEIKARLVINTTGPWSDKVRNLSNKGTQFSQMRPTKGVH 260 D +G ITGV RD + + +++KA++V+N TG ++DK+ + KG ++P++GVH Sbjct: 192 TKDGAGIITGVKVRDAIHKKSYDVKAKMVVNATGVFADKILQMDQKGAP-RMIQPSQGVH 250 Query: 261 LVVDSSKIKVSQPVYFDTGLGDGRMVFVLPRENKTYFGTTDTDYTGDLEHPKVTQEDVDY 320 LV+ + Q DGR++F +P + K GTTDT P+ ++++ Sbjct: 251 LVLPQHFLG-GQDALMIPKTSDGRVLFAVPWQGKLVVGTTDTIRAKTKMEPEALSREINF 309 Query: 321 LLGIVNNRFPESNITIDDIESSWAGLRPLIAGNSASDYNGGNNGTISDESFDNLIATVES 380 +L ++ T D+ + +AGLRPL A S Sbjct: 310 ILANA-GQYLSKKPTRKDVLTVYAGLRPLAAPKGES------------------------ 344 Query: 381 YLSKEKTREDVESAVSKLESSTSEKHLDPSAVSRGSSLDRDDNGLLTLAGGKITDYRKMA 440 KT+E +SR + D+GL TL GGK T +RKM Sbjct: 345 ----VKTKE----------------------ISRNHKVIISDSGLTTLTGGKWTTFRKMG 378 Query: 441 EGAMERVVDILKAEFDRSFKLINSKTYPVSGGELNPANVDSEIEAFAQLGVSRGLDSKEA 500 E ++ F R V+G E+ ++ EI+ + LD K Sbjct: 379 EDTVD--------HFPR-----------VTGEEIKESH-SWEIKLHGHGDPT--LDDK-- 414 Query: 501 HYLANLYGSNAPKVFALAHSLEQAPGLSLADTL------SLHYAMRNELTLSPVDFLLRR 554 H+ +YG++A K+ L E P L + +A+R E+ + DFL RR Sbjct: 415 HW--KIYGTDAVKILQLIK--ENPPYAKLLHPQYPYVAGEVIWAIREEMAMHIEDFLARR 470 Query: 555 TNHML 559 +L Sbjct: 471 IRILL 475 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: 662 Number of extensions: 37 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 608 Length of database: 521 Length adjustment: 36 Effective length of query: 572 Effective length of database: 485 Effective search space: 277420 Effective search space used: 277420 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: 53 (25.0 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