Align Glutamine amidotransferase of anthranilate synthase (characterized, see rationale)
to candidate Ga0059261_0317 Ga0059261_0317 GMP synthase (glutamine-hydrolyzing), C-terminal domain or B subunit/GMP synthase (glutamine-hydrolyzing), N-terminal domain or A subunit
Query= uniprot:B8DM46_DESVM (192 letters) >FitnessBrowser__Korea:Ga0059261_0317 Length = 518 Score = 57.8 bits (138), Expect = 3e-13 Identities = 43/122 (35%), Positives = 59/122 (48%), Gaps = 7/122 (5%) Query: 74 VPVLGVCLGHQVLGLFAGATVDVGPRIMHGKTSDITHDGQGLFHGVPSPMQVGRYHSLIV 133 +PVLG+C G QV+ G V +G G+ D LF G+ + G H + + Sbjct: 78 LPVLGICYGQQVMMQQLGGNVQLGDSGEFGRAFIEIADSCVLFDGLWAE---GETHQVWM 134 Query: 134 HAEERPDLLAVTAR---APEGEVMALRYTD-RPWVGVQFHPESVLTPDGVRMLANFPAHV 189 ++ LA R A G A+ D R + +QFHPE V TPDG ++LANF HV Sbjct: 135 SHGDKVTSLAPGFRPVAASAGAPFAVIADDTRRYYAMQFHPEVVHTPDGAKLLANFVRHV 194 Query: 190 AG 191 G Sbjct: 195 CG 196 Lambda K H 0.325 0.142 0.453 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: 276 Number of extensions: 23 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: 192 Length of database: 518 Length adjustment: 27 Effective length of query: 165 Effective length of database: 491 Effective search space: 81015 Effective search space used: 81015 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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