Align Glycerol-3-phosphate dehydrogenase SDP6, mitochondrial; Protein SUGAR-DEPENDENT 6; EC 1.1.5.3 (characterized)
to candidate 208651 DVU3132 glycerol-3-phosphate dehydrogenase, FAD-dependent
Query= SwissProt::Q9SS48 (629 letters) >MicrobesOnline__882:208651 Length = 546 Score = 425 bits (1092), Expect = e-123 Identities = 227/552 (41%), Positives = 332/552 (60%), Gaps = 20/552 (3%) Query: 70 ASDPLDVLVIGGGATGSGVALDAVTRGLRVGLVEREDFSSGTSSRSTKLIHGGVRYLEKA 129 A D+L++GGGATG GVALDA TRGL V LVER+DF+ GTSS+STKL+HGGVRYLEKA Sbjct: 12 ADKTFDLLIVGGGATGCGVALDAATRGLDVALVERDDFAQGTSSKSTKLVHGGVRYLEKA 71 Query: 130 VFNLDYGQLKLVFHALEERKQLIENAPHLCHALPCMTPCFDWFEVIYFWMGLKMYDLVAG 189 + D Q LV L ER L+ NAPHL H + MTP W + Y + GL MYDL+AG Sbjct: 72 ILKADKEQFALVHEGLRERGYLLRNAPHLAHPVQLMTPVDSWKDAGYLFAGLTMYDLLAG 131 Query: 190 PRLLHLSRYYSAKESIELFPTLARKGKDKNLRGTVVYYDGQMNDSRLNVGLACTAALAGA 249 L SR+ + ++ LFPTL R GK K G V+YYDGQ ND+R+ V LA TAAL GA Sbjct: 132 RLGLGHSRFVTRSKAQRLFPTL-RLGKAK---GAVLYYDGQFNDARMAVTLARTAALHGA 187 Query: 250 AVLNHAEVVSLITDDATKRIIGARIRNNLTGQEFNSYAKVVVNAAGPFCDSIRKMIDEDT 309 NH EV+ L+ ++ R+ GA +R+ +G+ + A+ ++NA GPF D +R+M D++ Sbjct: 188 TCANHVEVIDLVRENG--RLCGAVLRDVNSGETWQVRARGIINATGPFSDGLRRMDDQNA 245 Query: 310 KPMICPSSGVHIVLPDYYSPEGMGLIVPKTKDGRVVFMLPWLGRTVAGTTDSNTSITSLP 369 ++ SSG+H+V+ ++P +GL+VP+T DGRV+FM+PW G V GTTD I+ P Sbjct: 246 CDILKVSSGIHLVIDPGHTPPHLGLMVPRTDDGRVLFMIPWQGHVVFGTTDEPVDISRDP 305 Query: 370 EPHEDEIQFILDAISDYLNIKVRRTDVLSAWSGIRPLAMDPTAKSTESISRDHVVFEENP 429 P +++I ++L+ YL+ + R DV +AW G+RPL + T+ ++R HV+ Sbjct: 306 VPTQEDIDYLLNYAGRYLSRPLSRDDVRAAWCGLRPLVFEADKSCTQELARTHVIEVSPG 365 Query: 430 GLVTITGGKWTTYRSMAEDAVDAAIKSGQLKPTNECVTQKLQLLGSYGWEPSSFTTLAQQ 489 GL+TITGGKWT+YR MAED +D A + +L CVT+ L+++GS G+ + +A+ Sbjct: 366 GLLTITGGKWTSYRRMAEDTIDRADAAFELGLQRPCVTRDLRVIGSRGFVRGAHAEMARD 425 Query: 490 YVRMKKTYGGKVVPGAMDTAAAKHLSHAYGSMADRVATIAQEEGLGKRLAHGHPFLEAEV 549 + +D A A+ L +G + T+A+EEGL RL H ++ A+V Sbjct: 426 F--------------GVDPALARGLFELHGDETPLILTLAREEGLMDRLHPAHNYIGAQV 471 Query: 550 AYCARHEYCESAVDFIARRCRIAFLDTDAAARALQRVVEILASEHKWDKSRQKQELQKAK 609 A+ RHE D + RR + +D A +I+A E WD + +++E++ Sbjct: 472 AFAVRHEMAVHLTDVMVRRLPLGLVDVQHTLEASAPAADIMAQELGWDAATRQREMEALA 531 Query: 610 EFLETFKSSKNA 621 +L ++ + +A Sbjct: 532 AYLAAWRPAPDA 543 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: 762 Number of extensions: 40 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: 546 Length adjustment: 37 Effective length of query: 592 Effective length of database: 509 Effective search space: 301328 Effective search space used: 301328 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