Align Anthranilate synthase component 2; AS; ASII; EC 4.1.3.27; Anthranilate synthase, GATase component; Anthranilate synthase, glutamine amidotransferase component (uncharacterized)
to candidate WP_011317902.1 AVA_RS05340 glutamine-hydrolyzing GMP synthase
Query= curated2:Q57690 (197 letters) >NCBI__GCF_000204075.1:WP_011317902.1 Length = 540 Score = 73.2 bits (178), Expect = 8e-18 Identities = 50/165 (30%), Positives = 82/165 (49%), Gaps = 11/165 (6%) Query: 31 KLVDNKITLDEIKKINPDRIIISPGPKT--PKEAGNCIKIIQEVDIPILGVCLGHQCIVE 88 +++ + + + ++++NP II+S GP + A +C I + +PILGVC G Q +V Sbjct: 52 EVLSYRTSAEHLRQLNPKGIILSGGPSSVYSDRAPHCDPEIWNLGVPILGVCYGMQLMVN 111 Query: 89 AFGGEVGRAKRVMHGKASLINHDGEGIFKDIPNPFYGGRYHSLIAKEVPKELKITAKSLD 148 GGEV +A R +GKASL D + ++ + H ++P ++ A + D Sbjct: 112 QLGGEVAKADRGEYGKASLHIDDPTDLLTNVEDGTTMWMSHGDSVTKMPPGFEVLAHT-D 170 Query: 149 DNYIMGVRHKKLPIEGVQFHPESILTESDNLKFPDLGLKLIKNFV 193 + V + GVQFHPE + + GL LI+NFV Sbjct: 171 NTPCAAVADHDKKLYGVQFHPEVVHSIG--------GLALIRNFV 207 Lambda K H 0.319 0.142 0.421 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: 261 Number of extensions: 16 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: 197 Length of database: 540 Length adjustment: 28 Effective length of query: 169 Effective length of database: 512 Effective search space: 86528 Effective search space used: 86528 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 Jul 25 2024. The underlying query database was built on Jul 25 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