Align NADH-dependent phenylglyoxylate dehydrogenase subunit epsilon; Phenylglyoxylate:NAD oxidoreductase; Phenylglyoxylate:acceptor oxidoreductase; EC 1.2.1.58 (characterized)
to candidate WP_011384088.1 AMB_RS08490 FAD-dependent oxidoreductase
Query= SwissProt::Q8L3B0 (421 letters) >NCBI__GCF_000009985.1:WP_011384088.1 Length = 411 Score = 389 bits (998), Expect = e-112 Identities = 205/414 (49%), Positives = 277/414 (66%), Gaps = 9/414 (2%) Query: 9 KYLIAGSSHAALEAINAIRMHDAEGPITVVTRDAHLPYSPTVLPYVVSGKSAPERIFLRD 68 KYL+ GSSHAALEA+ AIR+ D +G + ++TRD LPYSPT+LPYVVSG+SAP+++ LRD Sbjct: 6 KYLLVGSSHAALEALRAIRLVDPDGSMAMLTRDDRLPYSPTILPYVVSGRSAPDKVLLRD 65 Query: 69 DDFFARNKVAYRPKAALKALHADRNTAELADGSSVVYEKLLLATGASPAIPPIPGIDTVS 128 FFA N AY P A +L A L +G Y+ LL+A+GA+PAIPP+ G+D V+ Sbjct: 66 PAFFAANNCAYVPNARAVSLDAKARAVTLENGEVWRYQSLLIASGAAPAIPPVKGLDGVT 125 Query: 129 YHVLRTLDDALKLRGAIAESKQAVVLGAGLVGMHAAENLVKAGATVTIVEMSEQLTSGYF 188 YHVLR+L DA LRGA+ +K AVVLGAGLVG+HAAEN+ +AG VT+VEM + GYF Sbjct: 126 YHVLRSLADAEGLRGAMGAAKTAVVLGAGLVGLHAAENMAEAGLKVTVVEMQGHVLPGYF 185 Query: 189 DKVAADMIEQAFRDAGGKIMTGSRVVRLEPTAAGAKLTLENGTTLEADLLLVATGVKPEM 248 D A+ IE AF G ++ G +VV + P K+ +++GTT+ ADLLLVATGV+P Sbjct: 186 DAKASTRIEDAFTTHGVELKLGRKVVEVAP----GKVMVDDGTTIAADLLLVATGVRPVT 241 Query: 249 DYLNGSGVEHAQGILVDDRMQTTAENVWAAA-TAQARGFFTGTKVMNAILPDATIQGRVA 307 D+L GSGV +G++VD+ M+T + VWAA AQA F +G K + I+P A QG++A Sbjct: 242 DWLEGSGVLVDRGVVVDEAMRTNIDGVWAAGDVAQATDFASGNKALIGIIPTAVEQGKIA 301 Query: 308 GMAMAGDPGVKDYAGAVPLNTYHFFGRHAISVGSSTVPEGGEVVTRFDEKTGRYLKAIFA 367 G MAGD KDYAG +P+NTY FFGR A+S+G + +G E V + +G Y + + Sbjct: 302 GQGMAGDSYRKDYAGGLPVNTYRFFGRVALSIGRAAATDGVEAV---ETASGAYRRLVLE 358 Query: 368 ADGPLTGIFGVNEFFDGGVMAQLILRRTDLTPLRSRFVANPLAVGREIMSQTWR 421 + L G V+E FD G+M +LI RR DL+ + F+A P+ GR +MS+ WR Sbjct: 359 GN-RLVGYASVDEPFDVGIMGELIRRRVDLSECKDAFLARPVETGRRLMSEQWR 411 Lambda K H 0.318 0.134 0.382 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: 454 Number of extensions: 18 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: 421 Length of database: 411 Length adjustment: 31 Effective length of query: 390 Effective length of database: 380 Effective search space: 148200 Effective search space used: 148200 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 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