Align Glyceraldehyde dehydrogenase small chain; Glyceraldehyde dehydrogenase subunit C; Glyceraldehyde dehydrogenase subunit gamma; EC 1.2.99.8 (characterized)
to candidate WP_011937928.1 GURA_RS05055 molybdopterin cofactor-binding domain-containing protein
Query= SwissProt::Q4J6M5 (163 letters) >NCBI__GCF_000016745.1:WP_011937928.1 Length = 931 Score = 153 bits (387), Expect = 7e-42 Identities = 82/156 (52%), Positives = 103/156 (66%), Gaps = 3/156 (1%) Query: 10 VKVRVRVNGVWYEKYVSPRTLLVDFIRDELGLTGTKVGCDTTTCGACTVIMNGKSVKSCT 69 +K + VNG+ V LL D +R +L LTGTKVGC T CGAC VIM+GK V+SC Sbjct: 2 IKKVMVVNGIERTLIVDQEALLSDVLRKQLHLTGTKVGCGTGQCGACNVIMDGKLVRSCV 61 Query: 70 VLAAQADG-AEITTIEGLSSDSKLHPIQEAFKDNFALQCGFCTAGMIMQTYFFLKEHPNP 128 V + + A+ITTIEG+ + LHPIQ+AF + ALQCGFCT G I+ T L E+PNP Sbjct: 62 VKMKKVENLAKITTIEGIGTPLNLHPIQKAFIFHGALQCGFCTPGFIVSTKALLDENPNP 121 Query: 129 TEEEVRDGI--HGNICRCTGYQNIVKAVLDASKRLR 162 T E+VRD + N CRCTGY IV AV+DA+K +R Sbjct: 122 TREDVRDWFQKYRNACRCTGYSMIVDAVMDAAKVMR 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: 388 Number of extensions: 20 Number of successful extensions: 3 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: 931 Length adjustment: 30 Effective length of query: 133 Effective length of database: 901 Effective search space: 119833 Effective search space used: 119833 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: 50 (23.9 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