Align Glycerol-3-phosphate dehydrogenase; EC 1.1.5.3 (characterized, see rationale)
to candidate 3607214 Dshi_0630 FAD dependent oxidoreductase (RefSeq)
Query= uniprot:Q92LM5 (503 letters) >FitnessBrowser__Dino:3607214 Length = 531 Score = 570 bits (1470), Expect = e-167 Identities = 292/519 (56%), Positives = 362/519 (69%), Gaps = 22/519 (4%) Query: 2 SEQTIFDVFVIGGGINGCGIARDAAGRGYSVALAEMSDFASGTSSGSTKLIHGGLRYLEH 61 ++ + D+F+IGGGINGCGIARDAAGRG SVALAEM+D ASGTSSGSTKL HGGLRYLE+ Sbjct: 4 TDAKLHDLFIIGGGINGCGIARDAAGRGLSVALAEMNDLASGTSSGSTKLFHGGLRYLEY 63 Query: 62 YEFRLVREALMEREVLWAMAPHVIWPMRFVLPFHKG---------------------GPR 100 +EFRLVREAL+EREVL PH+ WP RFVLP+H G R Sbjct: 64 FEFRLVREALIEREVLLRAMPHISWPKRFVLPYHPDMRFEGQTPTSKLLGIFMPWMKGRR 123 Query: 101 PAWLIRLGLFLYDHIGGRKLLPATKTLDMTRDPAGAPLKGLFTKAFEYSDGWVDDARLVV 160 PAWLIRLGLFLYD++GGRK+LP T+TL + P GAPL+ F KAFEYSD WV+D+RLVV Sbjct: 124 PAWLIRLGLFLYDNLGGRKILPGTETLSLQGTPEGAPLEPRFEKAFEYSDCWVEDSRLVV 183 Query: 161 LNARDAADRGARIMARTRVVSARREGGRWAIEIESTETGARETMRARMLVNAAGPWVDRV 220 LNARDA RGA I RT+VV+ R W IE + +TG R + RA+MLVNA GPWV + Sbjct: 184 LNARDAEARGAEIHMRTKVVATERHADHWRIETQEADTGTRRSFRAKMLVNAGGPWVAEL 243 Query: 221 LSEAVGNNDVRNVRLVQGSHIVVKKKFDDPRAYFFQNPDGRIMFAIPYQDEFTLIGTTDR 280 L+ + N VRLV+GSHIVV K +D + YFFQ DGRI+FAIPY+ +FTLIGTTD Sbjct: 244 LTGTLRLNVPDTVRLVRGSHIVVPKLYDHDKCYFFQGTDGRIIFAIPYETDFTLIGTTDA 303 Query: 281 DFTGNPADVRISDAEIDYLCRAASEYFSDPVGREDIVWTYSAVRPLFDDGASKAQEATRD 340 + + E DYL A++YF + ED+VWTYS VRPL+DDGAS ATRD Sbjct: 304 EHPDPSQKPECTPEERDYLLAFANQYFKQDITAEDVVWTYSGVRPLYDDGASSVTAATRD 363 Query: 341 YVLRVE-NGDAPLLNVFGGKLTTYRRLAESALEKIGETIGEKGRKWTAVSHLPGGDFPAA 399 Y L+ + AP+LNVFGGK+TTYRRLAESAL +IG + WTA LPGG+FP Sbjct: 364 YTLKTDAAAGAPVLNVFGGKITTYRRLAESALAQIGAQLPVGAGPWTAGVALPGGNFPVD 423 Query: 400 GYDDEVAKLRTRYPFLTASHARRLVRLYGTRAAQLLGNAASEADLGKHFGADLYAAEVDW 459 G ++ +A+LR YPFL+A A RL+R YG A ++LG+A +EADLG+ FGA L A EV W Sbjct: 424 GVEELIAQLRAAYPFLSARWATRLIRAYGRDAWEVLGDAKTEADLGEGFGATLTAREVRW 483 Query: 460 LIVQEWALRAEDVLWRRTKLGLKFSRAQTAELEEYMRGA 498 L+ +E+A +AEDV+WRR+KLGL+ S + L+ +M+ A Sbjct: 484 LMTREYARQAEDVVWRRSKLGLRMSAEEIVTLDRWMQAA 522 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: 850 Number of extensions: 29 Number of successful extensions: 3 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: 531 Length adjustment: 35 Effective length of query: 468 Effective length of database: 496 Effective search space: 232128 Effective search space used: 232128 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