Align Alpha-glycerophosphate oxidase; EC 1.1.3.21; Exported protein 6; Glycerol-3-phosphate oxidase (uncharacterized)
to candidate WP_086511672.1 BZY95_RS20125 FAD-dependent oxidoreductase
Query= curated2:P35596 (608 letters) >NCBI__GCF_002151265.1:WP_086511672.1 Length = 570 Score = 142 bits (357), Expect = 5e-38 Identities = 110/348 (31%), Positives = 170/348 (48%), Gaps = 21/348 (6%) Query: 8 RELSIKKMQERTLDLLIIGGGITGAGVALQAAASGLETGLIEMQDFAEGTSSRSTKLVHG 67 R +I K+ D+LI+GGGI GA A A G+ LIE DFA TS S+ LV G Sbjct: 4 RSSNIDKLGGEVFDVLIVGGGINGASAAAALAGKGVRVALIERGDFAGSTSMHSSNLVWG 63 Query: 68 GLRYLKQFDVEVVSDTVSERAVVQQIAPHIPKSDPMLLPVYDEDGATFSLFRLKVAMDLY 127 G++Y++ D +V R + + P + L + G + L LY Sbjct: 64 GIKYMESRDFALVRKLCRSRNHLIKSYPSTVQEIRFLTTI--TRGFRYHPRYLWAGAWLY 121 Query: 128 DLLA-GVSNTPAANKVLSKDQVLERQPNLKKEGLVGGGVYLD--FRNNDARLVIENIKRA 184 L+ G + P + LS + + + + VGG Y D +NDAR V ++ A Sbjct: 122 WLIGNGFTRIP---RFLSPQAISDNEAIIDTSSAVGGFEYSDAYLHDNDARFVFNFVRGA 178 Query: 185 NQDGALIANHVKAEGFLFDESGKITGVVARDLLTDQVFEIKARLVINTTGPWSDKVRNLS 244 GA+ N+V++ G + G +T V RD+++ + E+++R++IN GPW D+ L+ Sbjct: 179 LNYGAVAVNYVESLGARRESDGWLTRV--RDVMSGRELEVRSRVLINAAGPWVDEHNALT 236 Query: 245 NKGTQFSQMRPTKGVHLVVDSSKIKVSQPVYFDTGLGDGRMVFVLPRENKTYFGTTDTDY 304 + T + +KG+HL+V +F DGR+ FV+P +T GTTDT Sbjct: 237 GQSTNHRHVY-SKGIHLIVPRLTDSQRVLAFF---ADDGRLFFVIPMGPRTCIGTTDT-- 290 Query: 305 TGDLEHPKV--TQEDVDYLLGIVNNRFP-ESNITIDDIESSWAGLRPL 349 +E P+V TQED+ ++L +N R E + DI S G+RPL Sbjct: 291 --RVERPEVVATQEDIRFVLDNINKRLRLERPLDQQDIISIRCGVRPL 336 Score = 25.0 bits (53), Expect = 0.009 Identities = 12/29 (41%), Positives = 16/29 (55%) Query: 535 LHYAMRNELTLSPVDFLLRRTNHMLFMRD 563 LHYA R E+ DFL RR+ L + + Sbjct: 474 LHYAKRREMITRLEDFLRRRSKIALVVHE 502 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: 596 Number of extensions: 27 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 608 Length of database: 570 Length adjustment: 37 Effective length of query: 571 Effective length of database: 533 Effective search space: 304343 Effective search space used: 304343 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 Apr 09 2024. 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