Align Anaerobic glycerol-3-phosphate dehydrogenase subunit A1; G-3-P dehydrogenase A1; G3PDH A1; EC 1.1.5.3 (characterized)
to candidate 208172 DVU2673 anaerobic glycerol-3-phosphate dehydrogenase, subunit A, truncation
Query= SwissProt::D4GYI2 (586 letters) >MicrobesOnline__882:208172 Length = 389 Score = 285 bits (730), Expect = 2e-81 Identities = 162/391 (41%), Positives = 219/391 (56%), Gaps = 20/391 (5%) Query: 7 VLVIGGGSTGTGIARDLAMRGLDVTLVEKGNLTHGTTGRMHGLLHSGGRYAVSDQPSAKE 66 + +IGGG T +A DL +RG V+L E+G G TGR HGLLHSGGRYAV+D+ +A+E Sbjct: 4 IAIIGGGGTAAALAHDLVLRGFAVSLFERGEFFSGATGRHHGLLHSGGRYAVNDKEAARE 63 Query: 67 CIEENRVLRRIAGHCVEMTGGLFVQRPEDSDEYFEKKLEGCRECGIPAEVLSAEEAREIE 126 CIEENR+LR + +E GGLFV ++ +Y +E C ECGIP +S + ARE+E Sbjct: 64 CIEENRLLRTLVPEAIEQNGGLFVAMDDEDMDYLPVFVESCAECGIPTRQMSGDAARELE 123 Query: 127 PYLAKDIKRAIKVPDGAVDPFRLCVANAASAVEHGARIETHSEVTDVLVEGGEVVGVEVT 186 P L+ ++ A++VPD D +RL + A+A +GA+ +EV V G V G+ V Sbjct: 124 PALSASVRAAVQVPDATFDAWRLPLPFLATARANGAQTHHFTEVVGVHTRAGAVHGLRVR 183 Query: 187 HQTGTGPYVHGEPGEVEEIRADYVVNATGAWAGQIGDFAGVNVEVRPSKGVMTIMNTRQV 246 G ++ AD V+NA GAWAG I AG+ V ++P GV+ + R Sbjct: 184 DI---------RLGTERDVAADVVINAAGAWAGNIAALAGIEVPIQPGPGVLVAIEGRVT 234 Query: 247 DTVVNRCRPKGDADIIVPHETTCILGTTDEEVEDPE--DYPEEGWEVDLMIETLSELVPM 304 + V+NR R G+ DIIVP +LGT+ + P+ PEE V M++ S +VP Sbjct: 235 EMVINRLRRPGEGDIIVPQRILSVLGTSLWLADAPDRLSIPEE--HVQRMVDNCSHMVPA 292 Query: 305 LADARTIRSFW-GVRPLYEPPGTGTEDPTDITREFFLLDHADRDDLPGMTSIVGGKLTTY 363 AD R RS W RPL PG DI+R F DH RD + G SI+GGK T Sbjct: 293 CAD-RPRRSAWSAARPLIRDPGASRLQ--DISRTFDCYDHGKRDGVRGFFSIIGGKAMTL 349 Query: 364 RMMAEQISDHVCEKLGVDA---ECRTADEPL 391 R MAE+ +D +C LG+DA CRT PL Sbjct: 350 RAMAEKTADVICASLGLDAGAHPCRTRTTPL 380 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: 524 Number of extensions: 21 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: 389 Length adjustment: 33 Effective length of query: 553 Effective length of database: 356 Effective search space: 196868 Effective search space used: 196868 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