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_012473801.1 CPHAMN1_RS01750 GMP synthase (glutamine-hydrolyzing)
Query= curated2:O28670 (178 letters) >NCBI__GCF_000020545.1:WP_012473801.1 Length = 514 Score = 67.0 bits (162), Expect = 5e-16 Identities = 49/157 (31%), Positives = 76/157 (48%), Gaps = 24/157 (15%) Query: 36 LRKMSFDGVVISPGPGK--------PDRSLEFVFKMGVPVLGVCLGHQMIAEVFGGKV-- 85 +R+ + +++S GP PD E +FK+GVP+LG+C G Q+IA FGG V Sbjct: 40 IREHNPGAIILSGGPSSVYGESAFHPD---EGIFKLGVPILGICYGLQVIATHFGGSVDS 96 Query: 86 -GRVEPVHGKTSLVEHDGRG---IFKGVRNPLRAGRYHSLAVLEPPEGFEVCAKSEDGVV 141 + E + + HDG +FK + + H V+ PEGF V A S + + Sbjct: 97 SAKQEFGRAEIQVERHDGNPQSMLFKDIPDS-HVWMSHGDKVVRMPEGFRVTASSGNSEM 155 Query: 142 MGLRRG------KIHGVQFHPESVLTEDGVRMIRNFV 172 + K+ G+QFHPE T G +++ NF+ Sbjct: 156 CAIEASGDKAALKVFGLQFHPEVQHTLYGKQLLSNFL 192 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: 257 Number of extensions: 9 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: 514 Length adjustment: 27 Effective length of query: 151 Effective length of database: 487 Effective search space: 73537 Effective search space used: 73537 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