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_012400708.1 BPHY_RS06660 glutamine-hydrolyzing GMP synthase
Query= curated2:O28670 (178 letters) >NCBI__GCF_000020045.1:WP_012400708.1 Length = 527 Score = 65.5 bits (158), Expect = 1e-15 Identities = 48/154 (31%), Positives = 72/154 (46%), Gaps = 18/154 (11%) Query: 36 LRKMSFDGVVISPGPGK-----PDRSLEFVFKMGVPVLGVCLGHQMIAEVFGGKV--GRV 88 +R G+++S GP R+ + VF+ GVPVLG+C G Q +AE GGKV G + Sbjct: 41 IRDFKPTGIILSGGPNSVTETDTPRAPQAVFEAGVPVLGICYGMQTMAEQLGGKVDSGHL 100 Query: 89 EPVHGKTSLVEHDGRGIFKGVRN--------PLRAGRYHSLAVLEPPEGFEVCAKSEDGV 140 G + + G+++ L+ H VLE P+GF++ A +E Sbjct: 101 RE-FGYAEVRARNHTSFLDGIQDFATPEGHGMLKVWMSHGDKVLEMPQGFQLMASTESCP 159 Query: 141 VMGLRRGKIH--GVQFHPESVLTEDGVRMIRNFV 172 + + H GVQ+HPE T G M+ FV Sbjct: 160 IAAMADETRHFYGVQWHPEVTHTVQGRAMLERFV 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: 267 Number of extensions: 21 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: 178 Length of database: 527 Length adjustment: 27 Effective length of query: 151 Effective length of database: 500 Effective search space: 75500 Effective search space used: 75500 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 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