Align Glycerol-3-phosphate dehydrogenase SDP6, mitochondrial; Protein SUGAR-DEPENDENT 6; EC 1.1.5.3 (characterized)
to candidate WP_143148086.1 P735_RS0108625 FAD-dependent oxidoreductase
Query= SwissProt::Q9SS48 (629 letters) >NCBI__GCF_000283015.1:WP_143148086.1 Length = 520 Score = 330 bits (845), Expect = 1e-94 Identities = 203/546 (37%), Positives = 306/546 (56%), Gaps = 50/546 (9%) Query: 75 DVLVIGGGATGSGVALDAVTRGLRVGLVEREDFSSGTSSRSTKLIHGGVRYLEKAVFNLD 134 DV+VIGGGATG GVALD++TRG + L+E+ DF+ GTSSRSTKL+HGGVRYL + Sbjct: 18 DVIVIGGGATGLGVALDSITRGYKTLLLEQVDFAKGTSSRSTKLVHGGVRYLAQ------ 71 Query: 135 YGQLKLVFHALEERKQLIENAPHLCHALPCMTPCFDWFEVIYFWMGLKMYDLVAGPRLLH 194 G + LV AL ER L++NA HL + P ++W++ + + +GLK+YD +AG Sbjct: 72 -GNIDLVKEALYERGLLLKNASHLVSNQSFIIPNYNWWDNLKYTIGLKIYDALAGKLSFG 130 Query: 195 LSRYYSAKESIELFPTLARKGKDKNLRGTVVYYDGQMNDSRLNVGLACTAALAGAAVLNH 254 S S KE+++ T+ K+ L+G VVY+DGQ +DSRL V +A T GA VLNH Sbjct: 131 KSTRISKKETLKRLSTI----KNGKLKGGVVYHDGQFDDSRLAVNIAQTCIEHGATVLNH 186 Query: 255 AEVVSLITDDATKRIIGARIRNNL-TGQEFNSYAKVVVNAAGPFCDSIRKMIDEDTKPMI 313 +V L+ +D + ++ A + + T + + KVV+NA G F D I KM + + K ++ Sbjct: 187 FKVKQLLKND--RGVVNAVVAEDAETHKSYTLKTKVVINATGVFTDEILKMDNAEAKDIV 244 Query: 314 CPSSGVHIVLPDYYSPEGMGLIVPKTKDGRVVFMLPWLGRTVAGTTDSNTSITSL-PEPH 372 PS G+H+V+ + P +++PKT DGRV+F++PW + V GTTD+ SL P+ Sbjct: 245 RPSQGIHLVIDKSFLPGNDAIMIPKTNDGRVLFLVPWHNKIVVGTTDTLLDSHSLEPKAL 304 Query: 373 EDEIQFILDAISDYLNIKVRRTDVLSAWSGIRPLAMDPTAKS--TESISRDHVVFEENPG 430 + E+ FI+ ++YL + + DVLS ++G+RPLA P KS T+ ISR H + + Sbjct: 305 DAEVDFIIATANNYLTKTLAKEDVLSIFAGLRPLAA-PKDKSEKTKEISRSHKIIVSDSD 363 Query: 431 LVTITGGKWTTYRSMAEDAVDAAIKSGQLKPTNECVTQKLQLLGSYGWEPSSFTTLAQQY 490 L+TITGGKWTTYR MA+D ++ AI G+L P C T+ ++ Sbjct: 364 LITITGGKWTTYRRMAQDTINKAIFIGKL-PKVACETKAIK------------------- 403 Query: 491 VRMKKTYGGKVVPGAMDTAAAKHLSHAYGSMADRVAT-IAQEEGLGKRLAHGHPFLEAEV 549 + GA+ + K + YGS + I + LG +L PF + EV Sbjct: 404 -----------IHGAIKPSEKKSHQYVYGSDETNIQNLIKKHPELGAQLHKSLPFTKGEV 452 Query: 550 AYCARHEYCESAVDFIARRCRIAFLDTDAAARALQRVVEILASEHKWDKSRQKQELQKAK 609 + R+E + D +ARR R FLD A + V +IL+ E D ++Q++++ K Sbjct: 453 VWAIRNEMARTIEDVLARRVRTLFLDAKATLEIIPIVAKILSEELNKDAIWEQQQIEEFK 512 Query: 610 EFLETF 615 + + Sbjct: 513 SIAKQY 518 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: 674 Number of extensions: 36 Number of successful extensions: 7 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: 520 Length adjustment: 36 Effective length of query: 593 Effective length of database: 484 Effective search space: 287012 Effective search space used: 287012 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 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