Align Alpha-glycerophosphate oxidase; EC 1.1.3.21; Exported protein 6; Glycerol-3-phosphate oxidase (uncharacterized)
to candidate CA265_RS07875 CA265_RS07875 FAD-dependent oxidoreductase
Query= curated2:P35596 (608 letters) >FitnessBrowser__Pedo557:CA265_RS07875 Length = 530 Score = 221 bits (563), Expect = 6e-62 Identities = 171/582 (29%), Positives = 269/582 (46%), Gaps = 101/582 (17%) Query: 21 DLLIIGGGITGAGVALQAAASGLETGLIEMQDFAEGTSSRSTKLVHGGLRYLKQFDVEVV 80 D +IIGGG TG G AL AA+ G +T L+E DFA+GTSSRSTKLVHGG+RYL Q D+ +V Sbjct: 16 DFIIIGGGATGLGTALDAASRGFKTLLVEQSDFAKGTSSRSTKLVHGGVRYLAQGDIGLV 75 Query: 81 SDTVSERAVVQQIAPHIPKSDPMLLPVYDEDGATFSLFRLKVAMDLYDLLAGVSNTPAAN 140 + ER ++QQ A H+ + L+P YD FS+ + + LYD LAG + + Sbjct: 76 KHALKERGLLQQNAKHLVNKEEFLIPCYD----WFSVVKYLTGLTLYDWLAG-KYSFGKS 130 Query: 141 KVLSKDQVLERQPNLKKEGLVGGGVYLDFRNNDARLVIENIKRANQDGALIANHVKAEGF 200 K SK + L P +K++GL G Y D + +DARL I + A ++GA + N+ K G Sbjct: 131 KFFSKKETLTMMPGIKEKGLKGSIRYYDGKFDDARLAINIAQTAIENGASLLNYTKVTG- 189 Query: 201 LFDESGKITGVVARDLLTDQVFEIKARLVINTTGPWSDKVRNLSNKGTQFSQMRPTKGVH 260 L ++TG+ D +T + ++VIN TG + D + ++N ++ +RP++GVH Sbjct: 190 LLKSGDQVTGIETEDTITGLTAKYNGKIVINATGVFVDDILQMNNPNSK-KMVRPSQGVH 248 Query: 261 LVVDSSKIKVSQPVYFDTGLGDGRMVFVLPRENKTYFGTTDTDYTGDLEHPKVTQEDVDY 320 +V+D S + S+ DGR++F +P + GTTDT P+ +++VD+ Sbjct: 249 VVLDKSFLN-SESALMIPKTSDGRVLFAVPWHDHLLVGTTDTPLDEHSLEPRALKKEVDF 307 Query: 321 LLGIVNNRFPESNITIDDIESSWAGLRPLIAGNSASDYNGGNNGTISDESFDNLIATVES 380 ++ + F + DI S ++GLRPL A+ NG N T Sbjct: 308 IMSTAASYFNRKPLE-KDILSVFSGLRPL-----AAPTNGDGNST--------------- 346 Query: 381 YLSKEKTREDVESAVSKLESSTSEKHLDPSAVSRGSSLDRDDNGLLTLAGGKITDYRKMA 440 +SR L GL+T+ GGK T YR+MA Sbjct: 347 -----------------------------KEISRDHKLIVSAKGLITITGGKWTTYRRMA 377 Query: 441 EGAMERVVDILKAEFDRSFKLINSKTYPVSGGELNPANVDSEIEAFAQLGVSRGLDSKEA 500 E ++ + GG ++S+ L + + Sbjct: 378 EETVDLAI--------------------THGG------LESKACVTQNLSIHGSSTTTGD 411 Query: 501 HYLANLYGSNAPKVFALAHSLEQAPGLSLA-------DTLSLHYAMRNELTLSPVDFLLR 553 H+LA +YG++ K+ AL + Q PGL + ++ RNE+ + D L R Sbjct: 412 HHLA-IYGTDRSKIEAL---IVQDPGLGNKLNPAFPFTEAEVIWSARNEMAETVEDILSR 467 Query: 554 RTNHMLFM-----RDSLDSIVEPILDEMGRFYDWTEEEKATY 590 R +LF+ +D + + E+ +W + T+ Sbjct: 468 RL-RILFINAQAAKDMAPRVASLLAQELSADKNWETNQIETF 508 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: 730 Number of extensions: 39 Number of successful extensions: 6 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: 530 Length adjustment: 36 Effective length of query: 572 Effective length of database: 494 Effective search space: 282568 Effective search space used: 282568 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