Align Glycerol-3-phosphate dehydrogenase SDP6, mitochondrial; Protein SUGAR-DEPENDENT 6; EC 1.1.5.3 (characterized)
to candidate WP_017558097.1 C892_RS0116650 glycerol-3-phosphate dehydrogenase/oxidase
Query= SwissProt::Q9SS48 (629 letters) >NCBI__GCF_000341205.1:WP_017558097.1 Length = 572 Score = 282 bits (722), Expect = 2e-80 Identities = 194/561 (34%), Positives = 294/561 (52%), Gaps = 36/561 (6%) Query: 66 IAATASDPLDVLVIGGGATGSGVALDAVTRGLRVGLVEREDFSSGTSSRSTKLIHGGVRY 125 +A + LDVLV+GGG G+G ALDAV RGL+VGL+E DF+SGTSSRS+KLIHGG+RY Sbjct: 16 LARMGTGELDVLVVGGGIVGAGTALDAVARGLKVGLIEARDFASGTSSRSSKLIHGGLRY 75 Query: 126 LEKAVFNLDYGQLKLVFHALEERKQLIEN-APHLCHALPCMTPCFDWFEVIYFWMGLKMY 184 LE+ F +LV AL ER L+ APHL +P + P +E Y G+ +Y Sbjct: 76 LEQLDF-------ELVREALTERGLLLHRIAPHLVRPVPFVFPFSHHWERPYIGAGVALY 128 Query: 185 DLVA----GPRLLHLSRYYSAKESIELFPTLARKGKDKNLRGTVVYYDGQMNDSRLNVGL 240 D ++ R L R+ + ++ +FP L R L G V Y+D Q++D+R + + Sbjct: 129 DTLSLTMGTSRGLPHHRHLTRSGALRVFPALRRDA----LVGAVQYWDAQVDDARYVLTV 184 Query: 241 ACTAALAGAAVLNHAEVVSLITDDATKRIIGARIRNNLTGQEFNSYAKVVVNAAGPFCDS 300 TAA GA V + + S + + + + GAR + TGQE AK VVNAAG + D Sbjct: 185 LRTAAGLGAHVASRVQATSFLREG--EHVTGARATDLETGQELEIRAKQVVNAAGVWTDD 242 Query: 301 IRKMIDEDTKPMICPSSGVHIVLPDYYSPEGMGLIVPKTKDGRVVFMLPWLGRTVAGTTD 360 I++M+ + + S G+H+V+P GLI+ K V+F++PW + GTTD Sbjct: 243 IQEMVGGRGQIHVRASKGIHLVVPRDRVQASSGLILRTEKS--VLFVIPWGRHWIVGTTD 300 Query: 361 SNTSITSL-PEPHEDEIQFILDAISDYLNIKVRRTDVLSAWSGIRPLAMDPTAKSTESIS 419 ++ + P +I ++LD ++ L + + R DV ++G+RPL + + T +S Sbjct: 301 TSWDLDKAHPAASRRDIDYLLDEVNRVLRVPLTRDDVEGVYAGLRPL-LSGESDETSKLS 359 Query: 420 RDHVVFEENPGLVTITGGKWTTYRSMAEDAVDAAIKSGQLKPTNECVTQKLQLLGSYGWE 479 R+H V PGLV I GGK+TTYR MA+DAVD A+ G + VT +L L G+ G Sbjct: 360 REHTVAHPVPGLVLIAGGKYTTYRVMAQDAVD-AVAHGLDGRIPDSVTDRLPLAGADG-- 416 Query: 480 PSSFTTLAQQYVRMKKTYGGKVVPGAMDTAAAKHLSHAYGSMADRVATIAQEE-GLGKRL 538 F L Q + + G + + HL YGS+ V + +E+ L + L Sbjct: 417 ---FAALWNQRRSLARDAG-------LHPSRVAHLLRRYGSLVHEVLALMKEDPDLKEPL 466 Query: 539 AHGHPFLEAEVAYCARHEYCESAVDFIARRCRIAFLDTDAAARALQRVVEILASEHKWDK 598 A +L AEV Y R+E D +ARR R A D A ++A W Sbjct: 467 AGADDYLRAEVVYAVRNEGARHLDDVLARRTRAAIETWDRGIAAAPEAAALMAGPLGWSS 526 Query: 599 SRQKQELQKAKEFLETFKSSK 619 + ++E++ ++ +E ++++ Sbjct: 527 EQVEREVEYYRKRIEAERAAQ 547 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: 787 Number of extensions: 42 Number of successful extensions: 8 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: 572 Length adjustment: 37 Effective length of query: 592 Effective length of database: 535 Effective search space: 316720 Effective search space used: 316720 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