Align Anaerobic glycerol-3-phosphate dehydrogenase subunit A1; G-3-P dehydrogenase A1; G3PDH A1; EC 1.1.5.3 (characterized)
to candidate 8500375 DvMF_1126 FAD dependent oxidoreductase (RefSeq)
Query= SwissProt::D4GYI2 (586 letters) >FitnessBrowser__Miya:8500375 Length = 392 Score = 277 bits (708), Expect = 6e-79 Identities = 159/388 (40%), Positives = 216/388 (55%), Gaps = 11/388 (2%) Query: 7 VLVIGGGSTGTGIARDLAMRGLDVTLVEKGNLTHGTTGRMHGLLHSGGRYAVSDQPSAKE 66 + +IGGG T +A DL +RG V + E+G G+TGR HGLLHSG RYAV D +A+E Sbjct: 4 IAIIGGGGTAAALAHDLILRGFSVAIYERGEFFSGSTGRHHGLLHSGARYAVHDPEAARE 63 Query: 67 CIEENRVLRRIAGHCVEMTGGLFVQRPEDSDEYFEKKLEGCRECGIPAEVLSAEEAREIE 126 CIEEN +LRR+ +E GLFV ++ Y ++ + C GIP + E+AR +E Sbjct: 64 CIEENMILRRLVPQAMEQNEGLFVALDDEDMAYRQRLKDACAATGIPTRDYTPEQARSME 123 Query: 127 PYLAKDIKRAIKVPDGAVDPFRLCVANAASAVEHGARIETHSEVTDVLVEGGEVVGVEVT 186 P L + A++VPD D +RL + A+A GA I +EV + V+GG V G+ + Sbjct: 124 PGLTDTLLAAMQVPDATFDAWRLALPFLATARAGGATIHNFTEVIGIDVQGGAVRGLRLR 183 Query: 187 HQTGTGPYVHGEPGEVEEIRADYVVNATGAWAGQIGDFAGVNVEVRPSKGVMTIMNTRQV 246 T HG G AD VVNA GAWAG++ AGV+V ++P GV+ + R Sbjct: 184 TLTED---AHGARGREWSAPADMVVNAAGAWAGKVAALAGVHVPIQPGPGVLVAIEGRVT 240 Query: 247 DTVVNRCRPKGDADIIVPHETTCILGTTDEEVEDPE--DYPEEGWEVDLMIETLSELVPM 304 + V+NR R + DIIVP +LGT+ +DP+ D P E V M+ SE+VP Sbjct: 241 NMVINRMRKASEGDIIVPQRRLSVLGTSMWLTDDPDHLDIPPE--HVQRMVRLCSEMVPA 298 Query: 305 LADARTIRSFW-GVRPLYEPPGTGTEDPTDITREFFLLDHADRDDLPGMTSIVGGKLTTY 363 ADA IRS W RPL P +I+R F DH RD++ G+ SI+GGK T Sbjct: 299 CADA-PIRSAWSAARPLI--GNADAARPQEISRTFDCYDHGTRDNVSGLLSIIGGKGMTL 355 Query: 364 RMMAEQISDHVCEKLGVDAECRTADEPL 391 R MAE+ +D +C G DA CRT + PL Sbjct: 356 RAMAEKTADIICRLTGRDAPCRTRETPL 383 Lambda K H 0.316 0.134 0.400 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: 549 Number of extensions: 23 Number of successful extensions: 3 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: 586 Length of database: 392 Length adjustment: 34 Effective length of query: 552 Effective length of database: 358 Effective search space: 197616 Effective search space used: 197616 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 (21.6 bits) S2: 51 (24.3 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