Align Glutamine amidotransferase of anthranilate synthase (characterized, see rationale)
to candidate SMc00394 SMc00394 GMP synthase
Query= uniprot:B8DM46_DESVM (192 letters) >FitnessBrowser__Smeli:SMc00394 Length = 520 Score = 53.9 bits (128), Expect = 5e-12 Identities = 37/122 (30%), Positives = 55/122 (45%), Gaps = 7/122 (5%) Query: 74 VPVLGVCLGHQVLGLFAGATVDVGPRIMHGKTSDITHDGQGLFHGVPSPMQVGRYHSLIV 133 +PV G+C G Q + G V+ G G+ LF G+ S +G H + + Sbjct: 80 LPVFGICYGQQTMCAQLGGKVESGHHREFGRAFLEVEKDCPLFDGLWS---LGSRHQVWM 136 Query: 134 HAEER----PDLLAVTARAPEGEVMALRYTDRPWVGVQFHPESVLTPDGVRMLANFPAHV 189 +R P+ V A + + R + VQFHPE V TPDG +++ANF + Sbjct: 137 SHGDRVTALPEGFEVVATSSNAPFAFIADEKRKYYAVQFHPEVVHTPDGAKLIANFVHKI 196 Query: 190 AG 191 AG Sbjct: 197 AG 198 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: 293 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: 520 Length adjustment: 27 Effective length of query: 165 Effective length of database: 493 Effective search space: 81345 Effective search space used: 81345 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