Align Glycerol-3-phosphate dehydrogenase; EC 1.1.5.3 (characterized, see rationale)
to candidate GFF810 PGA1_c08240 aerobic glycerol-3-phosphate dehydrogenase GlpD
Query= uniprot:Q92LM5 (503 letters) >FitnessBrowser__Phaeo:GFF810 Length = 529 Score = 575 bits (1482), Expect = e-168 Identities = 294/516 (56%), Positives = 351/516 (68%), Gaps = 21/516 (4%) Query: 2 SEQTIFDVFVIGGGINGCGIARDAAGRGYSVALAEMSDFASGTSSGSTKLIHGGLRYLEH 61 ++ I D+F+IGGGINGCGIARDAAGRG SVALAEM+D AS TSS STKL HGGLRYLE+ Sbjct: 6 AQDQITDLFIIGGGINGCGIARDAAGRGLSVALAEMNDLASATSSASTKLFHGGLRYLEY 65 Query: 62 YEFRLVREALMEREVLWAMAPHVIWPMRFVLPFHKG---------------------GPR 100 +EFRLVREAL+EREVL PH+ WPMRFVLPFHK G R Sbjct: 66 FEFRLVREALIEREVLLKAMPHISWPMRFVLPFHKDMRFDNTTPTSKLLTTIMPWMKGRR 125 Query: 101 PAWLIRLGLFLYDHIGGRKLLPATKTLDMTRDPAGAPLKGLFTKAFEYSDGWVDDARLVV 160 PAWLIRLGLF+YD +G R +LP T LD+ DPAG PL F AFEYSD W++DARLVV Sbjct: 126 PAWLIRLGLFMYDSLGKRGILPGTSKLDLASDPAGRPLDPKFKTAFEYSDCWIEDARLVV 185 Query: 161 LNARDAADRGARIMARTRVVSARREGGRWAIEIESTETGARETMRARMLVNAAGPWVDRV 220 LNARDA RGA IM RT+V A R W I++E TG RA+MLVNA GPWV V Sbjct: 186 LNARDAEARGAEIMTRTKVTGATRNADHWVIDLEDITTGETSQRRAKMLVNAGGPWVADV 245 Query: 221 LSEAVGNNDVRNVRLVQGSHIVVKKKFDDPRAYFFQNPDGRIMFAIPYQDEFTLIGTTDR 280 L + +G N +VRLV+GSHIVV K +D R YFFQ DGRI+FAIPY++++TLIGTTD Sbjct: 246 LRQKLGQNSRESVRLVRGSHIVVPKLYDHGRCYFFQGTDGRIIFAIPYEEDYTLIGTTDA 305 Query: 281 DFTGNPADVRISDAEIDYLCRAASEYFSDPVGREDIVWTYSAVRPLFDDGASKAQEATRD 340 D + E DYL AS+YF++P+ R+DIVWTYS VRPL+DDGAS A ATR+ Sbjct: 306 DHPDPQTAPTCTPEEQDYLINFASQYFANPLSRDDIVWTYSGVRPLYDDGASSATAATRE 365 Query: 341 YVLRVENGDAPLLNVFGGKLTTYRRLAESALEKIGETIGEKGRKWTAVSHLPGGDFPAAG 400 YVL + + APLLNVFGGK+TTYR+LAE+ALEKI + WTA LPGGDFP Sbjct: 366 YVLTLNDSAAPLLNVFGGKITTYRKLAEAALEKIATVFPDLPADWTAGVALPGGDFPVGD 425 Query: 401 YDDEVAKLRTRYPFLTASHARRLVRLYGTRAAQLLGNAASEADLGKHFGADLYAAEVDWL 460 AKL YPFL+ RRL+R YGT A ++LG A + ADLG+ FGA + A E+DW Sbjct: 426 VAKLTAKLAQDYPFLSPYATRRLIRAYGTEAWEVLGKATTAADLGEAFGATVTARELDWT 485 Query: 461 IVQEWALRAEDVLWRRTKLGLKFSRAQTAELEEYMR 496 I EW ED L RRTKL L+ + A+ A ++ Y+R Sbjct: 486 IAHEWVRTGEDYLLRRTKLALRLTEAERAAVDSYIR 521 Lambda K H 0.321 0.137 0.417 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: 837 Number of extensions: 32 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 503 Length of database: 529 Length adjustment: 35 Effective length of query: 468 Effective length of database: 494 Effective search space: 231192 Effective search space used: 231192 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (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