Align NADH-dependent phenylglyoxylate dehydrogenase subunit epsilon; Phenylglyoxylate:NAD oxidoreductase; Phenylglyoxylate:acceptor oxidoreductase; EC 1.2.1.58 (characterized)
to candidate WP_011385301.1 AMB_RS14720 NAD(P)/FAD-dependent oxidoreductase
Query= SwissProt::Q8L3B0 (421 letters) >NCBI__GCF_000009985.1:WP_011385301.1 Length = 416 Score = 198 bits (504), Expect = 2e-55 Identities = 135/409 (33%), Positives = 206/409 (50%), Gaps = 19/409 (4%) Query: 9 KYLIAGSSHAALEAINAIRMHDAEGPITVVTRDAHLPYSPTVLPYVVSGKSAPERIFLRD 68 +Y+I G A + A +R DA G +T+V + PYS +PY ++GK +LR Sbjct: 4 RYVIVGGGPAGVIAAETLRHQDASGSVTLVCGEPGPPYSRMAIPYAMAGKIDEAGTWLRK 63 Query: 69 DDFFARNKVAYRPKAALKALHADRNTAE-------LADGSSVVYEKLLLATGASPAIPPI 121 D + ++ LH T E LA G + Y+ LL+ATG+SPA P I Sbjct: 64 D-------WNHYEALGIRLLHDRVATVEPAAKRVRLAAGGELSYDALLIATGSSPARPRI 116 Query: 122 PGIDTVSYHVLRTLDDALKLRGAIAESKQAVVLGAGLVGMHAAENLVKAGATVTI-VEMS 180 PG+D H TL+D ++ + ++ ++LGAG V ++LV+ G VT+ S Sbjct: 117 PGLDLPGVHSCWTLEDLRRIDPMLQPGRRVLLLGAGFVACIILQSLVQRGVKVTVSCGAS 176 Query: 181 EQLTSGYFDKVAADMIEQAFRDAGGKIMTGSRVVRLEPTAAGAKLTLENGTTLEADLLLV 240 ++ D+ A MI + R G +++T R +E G ++TL++G T EADL++V Sbjct: 177 GRMVRSMMDETAGGMIMRWCRAKGVEVLTAGRPTAIEQRDTGLRITLDSGKTTEADLVIV 236 Query: 241 ATGVKPEMDYLNGSGVEHAQGILVDDRMQTTAENVWAAA-TAQARGFFTGTKVMNAILPD 299 TGVK +L+GSG+ GI+VD ++T+ + +WAA AQ TG + ++AI P Sbjct: 237 GTGVKTNTAFLDGSGIAVDDGIVVDQYLRTSVDGIWAAGDVAQGFNCCTGLREVHAIQPT 296 Query: 300 ATIQGRVAGMAMAGDPGVKDYAGAVPLNTYHFFGRHAISVGSSTVPEGGEVVTRFDEKTG 359 A GR+A M M+G P ++ G++ +NT G + S G +GGE V DE Sbjct: 297 AVEHGRIAAMNMSGIP--TEFGGSLSMNTLETLGLISCSFGQWMGRDGGEQVRVVDEDHF 354 Query: 360 RYLKAIFAADGPLTGIFGVNEFFDGGVMAQLILRRTDLTPLRSRFVANP 408 RYL+ F DG L G V + G++ LI R L R +P Sbjct: 355 RYLRLEF-FDGRLVGANTVGMTNEIGIIRGLIQTRLRLGAWLERLKRDP 402 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: 413 Number of extensions: 23 Number of successful extensions: 6 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: 416 Length adjustment: 32 Effective length of query: 389 Effective length of database: 384 Effective search space: 149376 Effective search space used: 149376 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