Align NADH-dependent phenylglyoxylate dehydrogenase subunit epsilon; Phenylglyoxylate:NAD oxidoreductase; Phenylglyoxylate:acceptor oxidoreductase; EC 1.2.1.58 (characterized)
to candidate WP_004300499.1 C665_RS03645 NAD(P)/FAD-dependent oxidoreductase
Query= SwissProt::Q8L3B0 (421 letters) >NCBI__GCF_000310185.1:WP_004300499.1 Length = 429 Score = 178 bits (452), Expect = 2e-49 Identities = 134/413 (32%), Positives = 203/413 (49%), Gaps = 13/413 (3%) Query: 9 KYLIAGSSHAALEAINAIRMHDAEGPITVVTRDAHLPYSPTVLPYVVSGKSAPERIFLRD 68 K+LI G+ A + A +R I +V + PYS +PY++ G +LR Sbjct: 2 KHLILGNGPAGVVAAEILRKVAPADDILMVGHEDAPPYSRMAIPYLLEGNIDESGTWLRK 61 Query: 69 DD-FFARNKVAYRPKAALKALHADRNTAELADGSSVVYEKLLLATGASPAIPPIPGIDTV 127 D F R ++ A+ AL AD+ DG Y++LL+ATG+ P PPIPG+D Sbjct: 62 DPGHFERLRIRQLRGRAV-ALDADKRKVLFDDGHFEHYDRLLIATGSHPVRPPIPGVDLP 120 Query: 128 SYHVLRTLDDALKLRGAIAESKQAVVLGAGLVGMHAAENLVKAGATVTIVEMSEQLTSGY 187 S H TL DA + + + LGAG +G E L K G +T+VEM +++ Sbjct: 121 SVHTCWTLADARAIAAHARPGARVLQLGAGFIGCIIMEALAKCGVQLTVVEMGDRMVPRM 180 Query: 188 FDKVAADMIEQAFRDAGGKIMTGSRVVRLE-PTAAGAK----LTLENGTTLEADLLLVAT 242 A MI++ + G +++T + V R++ + AG+ ++L G L+ DL++VA Sbjct: 181 MTPKAGGMIKRWVEEKGIRVLTSAGVQRIDRGSEAGSDAPLVVSLSTGDRLDCDLVIVAA 240 Query: 243 GVKPEMDYLNGSGVEHAQGILVDDRMQTTAENVWAAA-TAQARGFFTGTKVMNAILPDAT 301 GV P + +L+ + V A+G+LVDD M+T+ ++AA A+A FTG +++AI P+A Sbjct: 241 GVAPNVGFLDETPVHVAKGVLVDDHMETSVPGIFAAGDVAEAPDLFTGAHLVSAIQPNAA 300 Query: 302 IQGRVAGMAMAGDPGVKD-YAGAVPLNTYHFFGRHAISVGS--STVPE-GGEVVTRFDEK 357 Q R+A MA D + G + +N G + S G PE GG V DE Sbjct: 301 DQARIAATNMARDRVHESRLNGVLAINVLDTLGLISSSFGQWWGEKPEAGGSGVEMVDEA 360 Query: 358 TGRYLKAIFAADGPLTGIFGVNEFFDGGVMAQLILRRTDLTPLRSRFVANPLA 410 RYL F D L G + G + LI + L + R +ANPLA Sbjct: 361 RYRYLSLQF-KDDVLVGATSIGLTQHVGALRGLIHGQVKLGDWKERLLANPLA 412 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: 416 Number of extensions: 24 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: 429 Length adjustment: 32 Effective length of query: 389 Effective length of database: 397 Effective search space: 154433 Effective search space used: 154433 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: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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