Align Glycerol-3-phosphate dehydrogenase SDP6, mitochondrial; Protein SUGAR-DEPENDENT 6; EC 1.1.5.3 (characterized)
to candidate WP_004308826.1 C665_RS10735 FAD-dependent oxidoreductase
Query= SwissProt::Q9SS48 (629 letters) >NCBI__GCF_000310185.1:WP_004308826.1 Length = 346 Score = 159 bits (402), Expect = 2e-43 Identities = 122/384 (31%), Positives = 183/384 (47%), Gaps = 40/384 (10%) Query: 74 LDVLVIGGGATGSGVALDAVTRGLRVGLVEREDFSSGTSSRSTKLIHGGVRYLEKAVFNL 133 ++V V+G G G+ A +G+ V L ER+ TS S+KL+HGG+RYLE Sbjct: 1 MEVAVVGAGIVGACTAWALARQGVEVTLYERKQPMGETSRASSKLLHGGLRYLET----- 55 Query: 134 DYGQLKLVFHALEERKQLIENAPHLCHALPCMTPCF--DWFEVIYFWMGLKMYDLVAGPR 191 GQ +LV AL R +E APHLCH L + P + + G+++YD++A Sbjct: 56 --GQFRLVGKALHARTDWLELAPHLCHRLEMLLPMYRDKGRSQLTISAGIRIYDVLAMGS 113 Query: 192 LLHLSRYYSAKESIELFPTLARKGKDKNLRGTVVYYDGQMNDSRLNVGLACTAALAGAAV 251 +R E + L P L+ G L G ++D QM+D L + G + Sbjct: 114 GFPRARVLKPSEVLALQPGLSADG----LVGAWAFFDAQMDDYALGNWVVEQFRQLGGEL 169 Query: 252 LNHAEVVSLITDDATKRIIGARIRNNLTGQEFNSYAKVVVNAAGPFCDSIRKMIDEDTKP 311 + EV L D RI VNA GP+ +R+ + Sbjct: 170 VTDFEVRDLAVLDGFDRI---------------------VNATGPWAMQLRETMPGKPSY 208 Query: 312 MICPSSGVHIVLPDYYSPEGMGLIVPKTKDGRVVFMLPWLGRTVAGTTDSNTSITSLPEP 371 + G HIVL D P M L VP + R+ F+LP+ GRT+ GTT+ S + P P Sbjct: 209 TLDWVRGSHIVL-DRVCPAAMLLEVPGSS--RIFFVLPYKGRTLIGTTEVRQSGPNNPGP 265 Query: 372 HEDEIQFILDAISDYLNIKVRRTDVLSAWSGIRPLAMDPTAKSTESISRDHVVFEENPGL 431 EDEI+++LDA + YL R DV+ A++G+RPL +A + +R+ FE + Sbjct: 266 SEDEIRYLLDAHNHYLAPAAMRCDVVEAFAGVRPLLR--SADNPSEATREW-AFERTGNV 322 Query: 432 VTITGGKWTTYRSMAEDAVDAAIK 455 + I GGKWTT + ++A + ++ Sbjct: 323 LHIYGGKWTTAKLQGDEAANRILQ 346 Lambda K H 0.318 0.133 0.390 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: 456 Number of extensions: 22 Number of successful extensions: 5 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: 629 Length of database: 346 Length adjustment: 33 Effective length of query: 596 Effective length of database: 313 Effective search space: 186548 Effective search space used: 186548 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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