Align Anthranilate synthase component 2; AS; ASII; Anthranilate synthase, GATase component; Anthranilate synthase, glutamine amidotransferase component; EC 4.1.3.27 (characterized)
to candidate GFF4214 Psest_4287 Predicted glutamine amidotransferases
Query= SwissProt::P26922 (196 letters) >FitnessBrowser__psRCH2:GFF4214 Length = 248 Score = 53.1 bits (126), Expect = 4e-12 Identities = 45/146 (30%), Positives = 65/146 (44%), Gaps = 23/146 (15%) Query: 55 DPDKAGICLPLIDAAAKAAVPLMGVCLGHQAIGQPFGGTVVRA----------------P 98 DP + + LPLI AA +A +P+ G+C G Q + FGG++ + P Sbjct: 86 DPLRDRLTLPLIRAAVEAGIPVFGICRGFQEMNVAFGGSLHQKVHEAGPYQDHRERPDDP 145 Query: 99 VPMHGKVDRMFH-QGRGVLK--DLPSPFRATRYHSLIVERATLPACLEVTGETEDGLIMA 155 + + + H Q G+L+ LP+ + H VER L L + DGLI A Sbjct: 146 LDVQYGLSHALHVQPGGLLERLGLPAQIQVNSVHGQGVER--LGGGLRIEALAPDGLIEA 203 Query: 156 LSHRELPIH--GVQFHPESIESEHGH 179 S + GVQ+HPE EH H Sbjct: 204 FSVEQARSFALGVQWHPEWQVHEHPH 229 Lambda K H 0.321 0.140 0.420 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: 166 Number of extensions: 10 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: 196 Length of database: 248 Length adjustment: 22 Effective length of query: 174 Effective length of database: 226 Effective search space: 39324 Effective search space used: 39324 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 (21.8 bits) S2: 45 (21.9 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