Align Glycerol-3-phosphate dehydrogenase SDP6, mitochondrial; Protein SUGAR-DEPENDENT 6; EC 1.1.5.3 (characterized)
to candidate WP_092344240.1 BLU87_RS01915 FAD-dependent oxidoreductase
Query= SwissProt::Q9SS48 (629 letters) >NCBI__GCF_900107645.1:WP_092344240.1 Length = 538 Score = 446 bits (1146), Expect = e-129 Identities = 239/533 (44%), Positives = 333/533 (62%), Gaps = 22/533 (4%) Query: 75 DVLVIGGGATGSGVALDAVTRGLRVGLVEREDFSSGTSSRSTKLIHGGVRYLEKAVFNLD 134 D+LVIGGGATG GVALDA RGL+V LVE+ DF+ GTSSRSTKL+HGGVRYLE AV LD Sbjct: 17 DLLVIGGGATGCGVALDAAARGLKVALVEKNDFAEGTSSRSTKLVHGGVRYLEMAVKKLD 76 Query: 135 YGQLKLVFHALEERKQLIENAPHLCHALPCMTPCFDWFEVIYFWMGLKMYDLVAGPRLLH 194 Q LV L ER L++NA HL + L +TP + W +V Y + GLK YD+++G + + Sbjct: 77 RVQYNLVKDGLHERGLLLKNARHLSNRLALVTPLYKWIDVPYVFAGLKFYDVLSGKQNIG 136 Query: 195 LSRYYSAKESIELFPTLARKGKDKNLRGTVVYYDGQMNDSRLNVGLACTAALAGAAVLNH 254 SR S KE+++ FP L +G L+ V+YYDGQ +D+R+ + LA TA GA + NH Sbjct: 137 HSRLLSRKEALKRFPGLKAEG----LKAGVLYYDGQFHDARMALSLALTAEEQGAVISNH 192 Query: 255 AEVVSLITDDATKRIIGARIRNNLTGQEFNSYAKVVVNAAGPFCDSIRKMIDEDTKPMIC 314 VV+++ +D +I GA + ++L+G+ + A+ V+NA GPF D+IR M + ++ Sbjct: 193 VAVVAILKNDG--KISGAELEDSLSGERWQIKARGVINATGPFVDNIRSMDNPQAAKILS 250 Query: 315 PSSGVHIVLPDYYSPEGMGLIVPKTKDGRVVFMLPWLGRTVAGTTDSNTSITSLPEPHED 374 S+G+HI+L ++P GL++P+T+DGRV+F+LPW + GTTD +T P P E Sbjct: 251 ASTGIHIILDKRFAPPDTGLMIPETEDGRVLFVLPWEDHAIVGTTDEPAEVTEHPLPLES 310 Query: 375 EIQFILDAISDYLNIKVRRTDVLSAWSGIRPLAMDPTAKSTESISRDHVVFEENPGLVTI 434 EI+++L + Y N+KV ++D+ + WSG+RPL DP A T ++RDHV+ + GL+TI Sbjct: 311 EIEYLLRHVGRYFNLKVEKSDIKAVWSGLRPLVSDPKAADTAKLARDHVIEDSEDGLLTI 370 Query: 435 TGGKWTTYRSMAEDAVDAAIKSGQLK-PTNECVTQKLQLLGSYGWEPSSFTTLAQQYVRM 493 GGKWTTYR MA D VD AIK QL P C T++L +LGS + L Y Sbjct: 371 AGGKWTTYRKMALDTVDHAIKVFQLSAPKPTCQTEQLPILGSANYNDQGEQELINTYNL- 429 Query: 494 KKTYGGKVVPGAMDTAAAKHLSHAYGSMADRVATIAQEEGLGKRLAHGHPFLEAEVAYCA 553 A D AA +L+ YG A +VAT++ EG RL HP +EAE+ Y A Sbjct: 430 -----------APDIAA--YLNRTYGDQAAKVATLSL-EGYAARLVDNHPVIEAEILYAA 475 Query: 554 RHEYCESAVDFIARRCRIAFLDTDAAARALQRVVEILASEHKWDKSRQKQELQ 606 R E E +D +ARR +A LDT+A+ A RV+EI+A+E WD+ R +E Q Sbjct: 476 RFELAERVIDVLARRTPLALLDTEASKLAATRVLEIMANELGWDQKRMDEETQ 528 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: 716 Number of extensions: 21 Number of successful extensions: 5 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: 538 Length adjustment: 36 Effective length of query: 593 Effective length of database: 502 Effective search space: 297686 Effective search space used: 297686 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