Align Glyceraldehyde dehydrogenase small chain; Glyceraldehyde dehydrogenase subunit C; Glyceraldehyde dehydrogenase subunit gamma; EC 1.2.99.8 (characterized)
to candidate 5209813 Shew_2266 2Fe-2S iron-sulfur cluster binding domain-containing protein (RefSeq)
Query= SwissProt::Q4J6M5 (163 letters) >FitnessBrowser__PV4:5209813 Length = 168 Score = 120 bits (301), Expect = 1e-32 Identities = 56/148 (37%), Positives = 88/148 (59%), Gaps = 4/148 (2%) Query: 11 KVRVRVNGVWYEKYVSPRTLLVDFIRDELGLTGTKVGCDTTTCGACTVIMNGKSVKSCTV 70 K+ +++NG Y P ++ IRD LGLTGTK GC CGACT+ ++G+ ++C Sbjct: 5 KLGLKINGKDYTLDADPNMPVLWAIRDLLGLTGTKYGCGAGLCGACTIHVDGEPARACLT 64 Query: 71 LAAQADGAEITTIEGLSSDSKLHPIQEAFKDNFALQCGFCTAGMIMQTYFFLKEHPNPTE 130 Q G ++TTIEGL++D +++A++DN QCG+C AG +M L ++P P + Sbjct: 65 SLKQVQGKQVTTIEGLAADG----LKQAWRDNNVPQCGYCQAGQLMSAAALLSQYPQPND 120 Query: 131 EEVRDGIHGNICRCTGYQNIVKAVLDAS 158 ++ + + GN+CRC Y I A+ AS Sbjct: 121 AQIEEAMVGNLCRCGTYTRIKAAIKQAS 148 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: 104 Number of extensions: 4 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: 168 Length adjustment: 18 Effective length of query: 145 Effective length of database: 150 Effective search space: 21750 Effective search space used: 21750 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: 43 (21.2 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