Align Glycerol-3-phosphate dehydrogenase SDP6, mitochondrial; Protein SUGAR-DEPENDENT 6; EC 1.1.5.3 (characterized)
to candidate 8500048 DvMF_0811 FAD dependent oxidoreductase (RefSeq)
Query= SwissProt::Q9SS48 (629 letters) >FitnessBrowser__Miya:8500048 Length = 542 Score = 418 bits (1075), Expect = e-121 Identities = 232/546 (42%), Positives = 325/546 (59%), Gaps = 20/546 (3%) Query: 75 DVLVIGGGATGSGVALDAVTRGLRVGLVEREDFSSGTSSRSTKLIHGGVRYLEKAVFNLD 134 D+LVIGGGATG GVA+DA TRGL V LV+R DF+ GTSSRSTKL+HGGVRYLEKAV D Sbjct: 17 DLLVIGGGATGCGVAVDAATRGLDVALVDRADFAQGTSSRSTKLVHGGVRYLEKAVLQCD 76 Query: 135 YGQLKLVFHALEERKQLIENAPHLCHALPCMTPCFDWFEVIYFWMGLKMYDLVAGPRLLH 194 Q LV L ER L+ NAPHL HA+ +TP W + Y + GL +YDL+AG L Sbjct: 77 REQFGLVREGLRERGFLLANAPHLAHAVRLLTPVPTWKDAGYMFAGLTLYDLLAGRLGLG 136 Query: 195 LSRYYSAKESIELFPTLARKGKDKNLRGTVVYYDGQMNDSRLNVGLACTAALAGAAVLNH 254 S++ + + +FPTL R G + + V Y+DGQ ND+R+ V LA TA GA NH Sbjct: 137 HSKFVGKRAAERMFPTL-RMG---DYKAAVTYWDGQFNDARMAVALARTANAHGATCCNH 192 Query: 255 AEVVSLITDDATKRIIGARIRNNLTGQEFNSYAKVVVNAAGPFCDSIRKMIDEDTKPMIC 314 EV LI + R+ GA +R+ LTG+ + A+ ++NA GP D++R+M D ++ Sbjct: 193 VEVTHLIKEGG--RLRGAELRDMLTGETWTLRARGIINATGPMADTVRRMDDPGADEILK 250 Query: 315 PSSGVHIVLPDYYSPEGMGLIVPKTKDGRVVFMLPWLGRTVAGTTDSNTSITSLPEPHED 374 SSG+HIVL ++P + L++PKT+DGRV+FM+PW V GTTD + + P P Sbjct: 251 VSSGIHIVLEAGFTPPDLSLMIPKTEDGRVLFMIPWQNHVVFGTTDEHANPEHDPVPDVA 310 Query: 375 EIQFILDAISDYLNIKVRRTDVLSAWSGIRPLAMDPTAKSTESISRDHVVFEENPGLVTI 434 +I ++L S YL+ V R DV + WSG+RPL P ST+ ++R HV+ GL+TI Sbjct: 311 DIDYLLRYASKYLSRPVTRGDVRAVWSGLRPLVFAPGKGSTQELARTHVIEVSPAGLLTI 370 Query: 435 TGGKWTTYRSMAEDAVDAAIKSGQLKPTNECVTQKLQLLGSYGWEPSSFTTLAQQYVRMK 494 GGKWT+YR MA+D VD A + L T CVT+ L+++G+ G+ P +T +A++Y Sbjct: 371 AGGKWTSYRMMAQDTVDRADVAFGLNLTRPCVTRHLKVVGARGFIPGGYTEIAREY---- 426 Query: 495 KTYGGKVVPGAMDTAAAKHLSHAYGSMADRVATIAQEEGLGKRLAHGHPFLEAEVAYCAR 554 + AK L YG +V TIA++E LG R+ HP + AEVA+ R Sbjct: 427 ----------GVPVELAKALHGTYGDETGQVLTIARDENLGDRVHPDHPHIMAEVAFIVR 476 Query: 555 HEYCESAVDFIARRCRIAFLDTDAAARALQRVVEILASEHKWDKSRQKQELQKAKEFLET 614 +E VD + RR + LD + +A V I+A+E WD +R ELQ + +L Sbjct: 477 NEMAMRLVDVLVRRLPMGLLDVEHTLQAAPGVARIMAAELGWDAARTDAELQYLETYLSG 536 Query: 615 FKSSKN 620 +++ ++ Sbjct: 537 WRAPRD 542 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: 770 Number of extensions: 35 Number of successful extensions: 4 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: 542 Length adjustment: 36 Effective length of query: 593 Effective length of database: 506 Effective search space: 300058 Effective search space used: 300058 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: 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