Align Anthranilate synthase component 2; AS; ASII; EC 4.1.3.27; Anthranilate synthase, GATase component; Anthranilate synthase, glutamine amidotransferase component (uncharacterized)
to candidate 353791 BT4265 GMP synthase (glutamine-hydrolyzing) (NCBI ptt file)
Query= curated2:Q02003 (198 letters) >FitnessBrowser__Btheta:353791 Length = 507 Score = 66.2 bits (160), Expect = 9e-16 Identities = 44/141 (31%), Positives = 68/141 (48%), Gaps = 5/141 (3%) Query: 48 SPGPGWPADAGKMETLIQQFAGQKPILGICLGFQAIVEVFGGKLRLAHQVMHGKNSQVRQ 107 SP + DA K++ + + G+ PILGIC G Q + GK+ A +G+ Sbjct: 52 SPFSVYDKDAFKVD--LSEIRGKYPILGICYGAQFMAYTNNGKVEPAGTREYGRAHLTSF 109 Query: 108 TSGNLIFNHLPSKFLVMRYHSIVMDEAVALPDFAITAVATDDGEIMAIENEKEQIYGLQF 167 N++F + V H D A+PD +TD +I A + E E+++G+QF Sbjct: 110 CKDNVLFKGVRENTQVWMSHG---DTITAIPDNFKKIASTDKVDIAAYQVEGEKVWGVQF 166 Query: 168 HPESIGTLDGMTMIENFVNQV 188 HPE + DG ++ NFV V Sbjct: 167 HPEVFHSEDGTQILRNFVVDV 187 Lambda K H 0.318 0.136 0.389 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: 209 Number of extensions: 9 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 198 Length of database: 507 Length adjustment: 27 Effective length of query: 171 Effective length of database: 480 Effective search space: 82080 Effective search space used: 82080 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 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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