Align Glyceraldehyde dehydrogenase small chain; Glyceraldehyde dehydrogenase subunit C; Glyceraldehyde dehydrogenase subunit gamma; EC 1.2.99.8 (characterized)
to candidate AO356_26655 AO356_26655 (2Fe-2S)-binding protein
Query= SwissProt::Q4J6M5 (163 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_26655 Length = 166 Score = 154 bits (389), Expect = 7e-43 Identities = 71/147 (48%), Positives = 100/147 (68%) Query: 12 VRVRVNGVWYEKYVSPRTLLVDFIRDELGLTGTKVGCDTTTCGACTVIMNGKSVKSCTVL 71 +R+ +NG E PRT L DF+R +LG TG VGC+ CGACTV+++G +++SC +L Sbjct: 11 IRLELNGRSREALAEPRTQLCDFLRHDLGATGVHVGCEHGVCGACTVLVDGVAMRSCLML 70 Query: 72 AAQADGAEITTIEGLSSDSKLHPIQEAFKDNFALQCGFCTAGMIMQTYFFLKEHPNPTEE 131 A Q I T+E L+ D L +Q+AF+ + ALQCGFCTAG++M FL+ PNP E Sbjct: 71 AVQGHERRIETVESLADDDTLSDLQQAFRRHHALQCGFCTAGILMSCVDFLERIPNPDET 130 Query: 132 EVRDGIHGNICRCTGYQNIVKAVLDAS 158 +VRD + G++CRCTGY IV+AVL+ + Sbjct: 131 QVRDMLSGHLCRCTGYTGIVQAVLEVA 157 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: 106 Number of extensions: 5 Number of successful extensions: 1 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: 166 Length adjustment: 18 Effective length of query: 145 Effective length of database: 148 Effective search space: 21460 Effective search space used: 21460 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 Apr 09 2024. 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