Align NADH-dependent phenylglyoxylate dehydrogenase subunit epsilon; Phenylglyoxylate:NAD oxidoreductase; Phenylglyoxylate:acceptor oxidoreductase; EC 1.2.1.58 (characterized)
to candidate 5208217 Shew_0729 FAD-dependent pyridine nucleotide-disulphide oxidoreductase (RefSeq)
Query= SwissProt::Q8L3B0 (421 letters) >FitnessBrowser__PV4:5208217 Length = 566 Score = 117 bits (292), Expect = 1e-30 Identities = 101/336 (30%), Positives = 157/336 (46%), Gaps = 37/336 (11%) Query: 11 LIAGSSHAALEAINAIRMHDAEGPITVVTRDAHLPYSPTVLPYVVSGKSAPER--IFLRD 68 +I G + A A A R+ + I + R ++ ++ LPY +SG+ A + Sbjct: 6 IIGGVAGGASAAARARRLSET-AEIIMFERGEYVSFANCGLPYHISGEIAQRSALVLQTP 64 Query: 69 DDFFARNKVAYRPKAALKALHADR-----NTAELADGSSVV--YEKLLLATGASPAIPPI 121 + F AR V R K + A+ DR L DGS Y+ LLL+ GA+P +PPI Sbjct: 65 ESFKARFNVEVRVKHEVVAI--DRAAKLVTVRRLLDGSEYQESYDTLLLSPGAAPIVPPI 122 Query: 122 PGIDTVSYHVLRTLDDALKLRGAIAES--KQAVVLGAGLVGMHAAENLVKAGATVTIVEM 179 PG+D H LR + D ++ I + + A V+G G +G+ E+L G T++E+ Sbjct: 123 PGVDNPLTHSLRNIPDMDRILQTIQMNNVEHATVVGGGFIGLEMMESLHHLGIKTTLLEL 182 Query: 180 SEQLTSGYFDKVAADMIEQAFRDAGGKIMTGSRV--------VRLEPTAAGA-------- 223 ++Q+ + D+ A QA RD G + G+ + + AAG Sbjct: 183 ADQVMTPV-DREMAGFAHQAIRDQGVDLRLGTALSEVSYQVQTHVASDAAGEDTAHQHIK 241 Query: 224 ---KLTLENGTTLEADLLLVATGVKPEMDYLNGSGVEHAQ--GILVDDRMQTTAENVWAA 278 LTL NG LE DLL++A GV+PE +G+ + GI V+ MQT+ ++A Sbjct: 242 GHLSLTLSNGELLETDLLIMAIGVRPETQLARDAGLAIGELGGIKVNAMMQTSDPAIYAV 301 Query: 279 ATA-QARGFFTGTKVMNAILPDATIQGRVAGMAMAG 313 A + + F TG + + A QGR+A M G Sbjct: 302 GDAVEEQDFVTGQACLVPLAGPANRQGRMAADNMFG 337 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: 492 Number of extensions: 19 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 421 Length of database: 566 Length adjustment: 34 Effective length of query: 387 Effective length of database: 532 Effective search space: 205884 Effective search space used: 205884 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: 52 (24.6 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