Align NADH-dependent phenylglyoxylate dehydrogenase subunit epsilon; Phenylglyoxylate:NAD oxidoreductase; Phenylglyoxylate:acceptor oxidoreductase; EC 1.2.1.58 (characterized)
to candidate WP_043744649.1 AMB_RS14715 NAD(P)/FAD-dependent oxidoreductase
Query= SwissProt::Q8L3B0 (421 letters) >NCBI__GCF_000009985.1:WP_043744649.1 Length = 421 Score = 165 bits (418), Expect = 2e-45 Identities = 122/409 (29%), Positives = 194/409 (47%), Gaps = 13/409 (3%) Query: 10 YLIAGSSHAALEAINAIRMHDAEGPITVVTRDAHLPYSPTVLPYVVSGKSAPERIFLRDD 69 +LI G+ A + A IR + IT+V + PYS +PY++ GK + +LR Sbjct: 3 HLIVGAGPAGVTAAEIIRELEPGATITLVGDEPEPPYSRMAIPYMLVGKVGEDGTYLRKG 62 Query: 70 -DFFARNKVAYRPKAALKALHADRNTAELADGSSVVYEKLLLATGASPAIPPIPGIDTVS 128 + + R + P + L L G ++ Y++LLLA GA P P I G+D Sbjct: 63 PNHYERLGITLMPGRRMSGLDPAARRIVLDGGETLAYDRLLLALGARPLRPDIEGLDLPG 122 Query: 129 YHVLRTLDDALKLRGAIAESKQAVVLGAGLVGMHAAENLVKAGATVTIVEMSEQLTSGYF 188 H TL DA K+ V++GAG VG E L ++T+VEM +++ Sbjct: 123 IHTCWTLADARKIAAQAIPGSHVVLMGAGFVGTIVLEALALRQVSLTVVEMGDRMVPRMM 182 Query: 189 DKVAADMIEQAFRDAGGKIMTGSRVVRLEPTAAGAK------LTLENGTTLEADLLLVAT 242 D+ A M+++ G +++TG+ + R+ A A + L +GT+L A L++V+ Sbjct: 183 DETAGGMLKRWCEAKGVRVLTGTGIRRITQAQAAADTRDSLVVELSDGTSLPAHLVVVSA 242 Query: 243 GVKPEMDYLNGSGVEHAQGILVDDRMQTTAENVWAAA-TAQARGFFTGTKVMNAILPDAT 301 GV+ + + SG+ GILVDD M+T+ +V+AA AQ R F +G ++AI A Sbjct: 243 GVRSNTEAVAASGIALGNGILVDDHMRTSLPDVFAAGDVAQGRDFMSGEAHVHAIQITAA 302 Query: 302 IQGRVAGMAMAGDPGVKDYAGAVPLNTYHFFGRHAISVGSSTVPEGGEVVTRFDEKTGRY 361 GR+A M G+ + Y G++ +N G S G S GG+ DE RY Sbjct: 303 AHGRIAAYNMTGND--QAYHGSLNMNVLDTLGLITCSFG-SWQGNGGDCARLVDEAGFRY 359 Query: 362 LKAIF-AADGPLTGIFGVNEFFDGGVMAQLILRRTDL-TPLRSRFVANP 408 L+ F + G V G + LI + L T ++ + +A+P Sbjct: 360 LRLEFDGTSDVVIGAQAVGTTDHVGALRGLIQSKRRLGTAVKEQMMADP 408 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: 405 Number of extensions: 19 Number of successful extensions: 4 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: 421 Length adjustment: 32 Effective length of query: 389 Effective length of database: 389 Effective search space: 151321 Effective search space used: 151321 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