Align Glyceraldehyde dehydrogenase small chain; Glyceraldehyde dehydrogenase subunit C; Glyceraldehyde dehydrogenase subunit gamma; EC 1.2.99.8 (characterized)
to candidate 14424 b0286 predicted xanthine dehydrogenase, 2Fe-2S subunit (NCBI)
Query= SwissProt::Q4J6M5 (163 letters) >FitnessBrowser__Keio:14424 Length = 229 Score = 140 bits (354), Expect = 1e-38 Identities = 73/171 (42%), Positives = 100/171 (58%), Gaps = 15/171 (8%) Query: 8 EGVKVRVRVNGVWYEKYVSPRTLLVDFIRDELGLTGTKVGCDTTTCGACTVIMNGKSVKS 67 E + + ++VNG + V RT L+D +R+ L L GTK GCD CGACTV++NG+ + + Sbjct: 59 EIMPLTLKVNGKTEQLEVDTRTTLLDTLRENLHLIGTKKGCDHGQCGACTVLVNGRRLNA 118 Query: 68 CTVLAAQADGAEITTIEGLSSDSKLHPIQEAFKDNFALQCGFCTAGMIMQTYFFLKE--- 124 C LA GAEITTIEGL S LHP+Q AF + QCG+CT+G I + LKE Sbjct: 119 CLTLAVMHQGAEITTIEGLGSPDNLHPMQAAFIKHDGFQCGYCTSGQICSSVAVLKEIQD 178 Query: 125 ------------HPNPTEEEVRDGIHGNICRCTGYQNIVKAVLDASKRLRS 163 P T +E+R+ + GNICRC Y NI+ A+ DA+ ++S Sbjct: 179 GIPSHVTVDLVSAPETTADEIRERMSGNICRCGAYANILAAIEDAAGEIKS 229 Lambda K H 0.321 0.136 0.412 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: 121 Number of extensions: 6 Number of successful extensions: 2 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: 163 Length of database: 229 Length adjustment: 20 Effective length of query: 143 Effective length of database: 209 Effective search space: 29887 Effective search space used: 29887 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 (21.9 bits) S2: 44 (21.6 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