Align Glycerol-3-phosphate dehydrogenase SDP6, mitochondrial; Protein SUGAR-DEPENDENT 6; EC 1.1.5.3 (characterized)
to candidate WP_012470730.1 GLOV_RS13305 glycerol-3-phosphate dehydrogenase/oxidase
Query= SwissProt::Q9SS48 (629 letters) >NCBI__GCF_000020385.1:WP_012470730.1 Length = 518 Score = 355 bits (912), Expect = e-102 Identities = 220/547 (40%), Positives = 304/547 (55%), Gaps = 45/547 (8%) Query: 61 QESALIAATASDPL-DVLVIGGGATGSGVALDAVTRGLRVGLVEREDFSSGTSSRSTKLI 119 + + L+ PL D++VIGGGATG G A++A +RG R L+E+ DF+ GTSSRSTKLI Sbjct: 2 KRAKLLQQLEDGPLWDMIVIGGGATGLGTAVEAASRGYRTLLLEQGDFAQGTSSRSTKLI 61 Query: 120 HGGVRYLEKAVFNLDYGQLKLVFHALEERKQLIENAPHLCHALPCMTPCFDWFEVIYFWM 179 HGGVRYL++ G L LV AL ER LI NAPHL H + + P +DW+E ++ + Sbjct: 62 HGGVRYLQQ-------GNLSLVLEALRERGLLIRNAPHLVHNMSFVVPLYDWWEGSFYGI 114 Query: 180 GLKMYDLVAGPRLLHLSRYYSAKESIELFPTLARKGKDKNLRGTVVYYDGQMNDSRLNVG 239 GLKMYDL+AG L S S +E++ PT+ G LRG V+Y+DGQ +DSRL + Sbjct: 115 GLKMYDLLAGKLGLGPSCLLSKEETLRHIPTVEPSG----LRGGVIYHDGQFDDSRLAIS 170 Query: 240 LACTAALAGAAVLNHAEVVSLITDDATKRIIGARIRNNLTGQEFNSYAKVVVNAAGPFCD 299 LA T A G LN+ V ++I D + G + TG+EF KVV+NAAGPF D Sbjct: 171 LALTLADLGGVALNYLAVTNIIRTDGL--VSGLTALDRETGREFAIRGKVVINAAGPFID 228 Query: 300 SIRKMIDEDTKPMICPSSGVHIVLPDYYSPEGMGLIVPKTKDGRVVFMLPWLGRTVAGTT 359 +R+M+D K +I PS GVH+VL + ++VP T DGRV+F +PW GRT+ GTT Sbjct: 229 KVRRMVDPTLKELITPSQGVHLVLDGSFLNGDSAIMVPHTDDGRVLFAVPWHGRTIVGTT 288 Query: 360 DSNTSITSL-PEPHEDEIQFILDAISDYLNIKVRRTDVLSAWSGIRPLAMDPTAKSTESI 418 D+ L P P +EI F+L S YL +R+D+LS ++GIRPL T S+ Sbjct: 289 DTPIPEAGLEPRPLAEEIDFLLAHASRYLTRHPQRSDLLSIFAGIRPLVRADAGSDTASL 348 Query: 419 SRDHVVFEENPGLVTITGGKWTTYRSMAEDAVDAAIKSGQLKPTNECVTQKLQLLGSYGW 478 SRDH + E+ GL+TI GGKWTTYR M ED V AA + L+ VT +L++ +GW Sbjct: 349 SRDHTLLVESSGLITIAGGKWTTYRKMGEDTVTAAAQIAGLE-ERPSVTAELRI---HGW 404 Query: 479 EPSSFTTLAQQYVRMKKTYGGKVVPGAMDTAAAKHLSHAYGSMADRVATIAQEEGLGKRL 538 + R + YG D AA + L +A+ + L Sbjct: 405 QEGVAGD------RPLQVYGS-------DAAALEQL-------------LAENPAWREPL 438 Query: 539 AHGHPFLEAEVAYCARHEYCESAVDFIARRCRIAFLDTDAAARALQRVVEILASEHKWDK 598 P+ EV + R E + D +ARR R LD A+ A +V ++ASE D+ Sbjct: 439 HPALPYCAGEVIWGTRCEQARTVEDILARRTRALLLDARASISAAPQVAALMASELGQDQ 498 Query: 599 SRQKQEL 605 + Q+ ++ Sbjct: 499 TWQEAQV 505 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: 678 Number of extensions: 24 Number of successful extensions: 6 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: 518 Length adjustment: 36 Effective length of query: 593 Effective length of database: 482 Effective search space: 285826 Effective search space used: 285826 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