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_004514506.1 GMET_RS11555 GMP synthase (glutamine-hydrolyzing)
Query= curated2:O28670 (178 letters) >NCBI__GCF_000012925.1:WP_004514506.1 Length = 520 Score = 59.7 bits (143), Expect = 8e-14 Identities = 49/151 (32%), Positives = 75/151 (49%), Gaps = 17/151 (11%) Query: 36 LRKMSFDGVVISPGP------GKPDRSLEFVFKMGVPVLGVCLGHQMIAEVFGGKV---G 86 +R + G+++S GP G P E +F++GVPVLG+C G Q+++ FGG+V G Sbjct: 46 IRAFAPRGIILSGGPKSVYEEGAPAVE-EALFELGVPVLGICYGMQLMSRHFGGQVVPAG 104 Query: 87 RVEPVHGKTSLVEHDG---RGIFKGVRNPLRAGRYHSLAVLEPPEGFEVCAKSEDGVVMG 143 + E H V G G F ++P+ H V P GF+V ++ + V Sbjct: 105 KREFGHADLLAVGTPGPLFDGFFVEGKSPVWMS--HGDHVSLVPAGFQVVGETANAPVCA 162 Query: 144 LR--RGKIHGVQFHPESVLTEDGVRMIRNFV 172 ++ ++GVQFHPE T G +I FV Sbjct: 163 IQDLARNLYGVQFHPEVNHTPRGELLIDTFV 193 Lambda K H 0.323 0.144 0.434 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: 277 Number of extensions: 19 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: 178 Length of database: 520 Length adjustment: 27 Effective length of query: 151 Effective length of database: 493 Effective search space: 74443 Effective search space used: 74443 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 10 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