Align Alpha-glycerophosphate oxidase; Glycerol-3-phosphate oxidase; EC 1.1.3.21 (characterized)
to candidate 3607214 Dshi_0630 FAD dependent oxidoreductase (RefSeq)
Query= SwissProt::O86963 (609 letters) >FitnessBrowser__Dino:3607214 Length = 531 Score = 163 bits (413), Expect = 1e-44 Identities = 148/524 (28%), Positives = 228/524 (43%), Gaps = 90/524 (17%) Query: 14 ETAKTTYDVLIIGGGITGAGVAVQTAAAGMKTVLLEMQDFAEGTSSRSTKLVHGGIRYLK 73 ET +D+ IIGGGI G G+A A G+ L EM D A GTSS STKL HGG+RYL+ Sbjct: 3 ETDAKLHDLFIIGGGINGCGIARDAAGRGLSVALAEMNDLASGTSSGSTKLFHGGLRYLE 62 Query: 74 TFDVEVVADTVRERAIVQQIAPHIPKPDPMLLPIYDE---PGAT-----FSLFS------ 119 F+ +V + + ER ++ + PHI P +LP + + G T +F Sbjct: 63 YFEFRLVREALIEREVLLRAMPHISWPKRFVLPYHPDMRFEGQTPTSKLLGIFMPWMKGR 122 Query: 120 -----VKVAMDLYDRLAN---VTGSKYENYLLTKEEVLAREPQLQAENLVGGGVYLDFRN 171 +++ + LYD L + G++ + T E EP+ + Y D Sbjct: 123 RPAWLIRLGLFLYDNLGGRKILPGTETLSLQGTPEGA-PLEPRFEK-----AFEYSDCWV 176 Query: 172 NDARLVIENIKRAQADGAAMISKAKVVGILHDEQGIINGVEVEDQLTNERFEVHAKVVIN 231 D+RLV+ N + A+A GA + + KVV + +E ++ T R AK+++N Sbjct: 177 EDSRLVVLNARDAEARGAEIHMRTKVVAT--ERHADHWRIETQEADTGTRRSFRAKMLVN 234 Query: 232 TTGPWSDIVRQLDKNDELPPQMRPTKGVHLVVDREKLKVPQPTYFDTGKNDGRMVFVVPR 291 GPW + +P +R +G H+VV KL YF G DGR++F +P Sbjct: 235 AGGPWVAELLTGTLRLNVPDTVRLVRGSHIVV--PKLYDHDKCYFFQG-TDGRIIFAIPY 291 Query: 292 ENK-TYFGTTDTDYTGDFAHPTVTQEDVDYLLTIVNERFPHAQITLDDIEASWAGLRPLI 350 E T GTTD ++ P T E+ DYLL N+ F IT +D+ +++G+RPL Sbjct: 292 ETDFTLIGTTDAEHPDPSQKPECTPEERDYLLAFANQYFKQ-DITAEDVVWTYSGVRPLY 350 Query: 351 TNNGGSDYNGGGKGKLSDESFEQIVESVKEYLADERQRPVVEKAVKQAQERVEASKVDPS 410 D+ + + ++Y + +A+ P Sbjct: 351 -----------------DDGASSVTAATRDYTL-----------------KTDAAAGAP- 375 Query: 411 QVSRGSSLERSKDGLLTLAGGKITDYRLMAEGAVKRINELLQESGASFELVDSTTYPVSG 470 +L + GGKIT YR +AE A+ +I L + + + G Sbjct: 376 --------------VLNVFGGKITTYRRLAESALAQIGAQLPVGAGPW----TAGVALPG 417 Query: 471 GELDAANVEEELAKLADQAQTAGFNEAAATYLAHLYGSNLPQVL 514 G VEE +A+L +A + AT L YG + +VL Sbjct: 418 GNFPVDGVEELIAQL--RAAYPFLSARWATRLIRAYGRDAWEVL 459 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: 587 Number of extensions: 28 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 609 Length of database: 531 Length adjustment: 36 Effective length of query: 573 Effective length of database: 495 Effective search space: 283635 Effective search space used: 283635 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