Align Alpha-glycerophosphate oxidase; Glycerol-3-phosphate oxidase; EC 1.1.3.21 (characterized)
to candidate 5208288 Shew_0800 FAD dependent oxidoreductase (RefSeq)
Query= SwissProt::O86963 (609 letters) >FitnessBrowser__PV4:5208288 Length = 413 Score = 132 bits (333), Expect = 2e-35 Identities = 103/339 (30%), Positives = 169/339 (49%), Gaps = 19/339 (5%) Query: 21 DVLIIGGGITGAGVAVQTAAAGMKTVLLEMQDFAEGTSSRSTKLVHGGIRYLKTFDVEVV 80 D+++IGGGITG G+A AAG VLLE + E TSS S+KL+HGG+RYL++ + +V Sbjct: 5 DLVVIGGGITGVGIAQCVQAAGYSVVLLEKDNLGEKTSSNSSKLIHGGLRYLESGQLGLV 64 Query: 81 ADTVRERAIVQQIAPHIPKPDPMLLPIYDEPGATFSLFSVKVAMDLYDRLANVTG-SKYE 139 ++ ER + +AP + KP P +PIY G+ +++ + LY L+ + +++ Sbjct: 65 RQSLSERKALLTLAPELVKPVPFYIPIY--RGSQRGPLAIRAGLSLYALLSELDPLGQFQ 122 Query: 140 NYLLTKEEVLAREPQLQAENLVGGGVYLDFRNNDARLVIENIKRAQADGAAMISKAKVVG 199 + ++ LA L+ + L Y D + +D L + A+A GA ++++ + Sbjct: 123 SVPASRWSELA---GLKLKGLRAVFRYWDAQTDDGALTRAVAQSARALGAELLTQVSLEQ 179 Query: 200 ILHDEQGIINGVEVEDQLTNERFEVHAKVVINTTGPW-SDIVRQLDKNDELPPQMRPTKG 258 I H I V E + ++ VIN TGPW + + ++ E+ P + +G Sbjct: 180 IEHRPDSCI----VSFSHKGETRRLSSRCVINATGPWVNQTLERVTPKVEVSP-VELVQG 234 Query: 259 VHLVVDREKLKVPQPTYFDTGKNDGRMVFVVPRENKTYFGTTDTDYTGDFAHPTVTQEDV 318 HLV+D + P ++ D R+VFV+P + KT GTT+T A VT + Sbjct: 235 SHLVLD---IPAPSGIFYLESIFDKRVVFVMPWQGKTMIGTTETPIDAVDA-AGVTPAEE 290 Query: 319 DYLLTIVNERFPHAQ---ITLDDIEASWAGLRPLITNNG 354 YLL I FP ++ + I + G+R L G Sbjct: 291 AYLLGIYRHYFPLSENDGALEERITGRYCGVRVLPKQGG 329 Lambda K H 0.314 0.132 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: 441 Number of extensions: 22 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 609 Length of database: 413 Length adjustment: 34 Effective length of query: 575 Effective length of database: 379 Effective search space: 217925 Effective search space used: 217925 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