Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (uncharacterized)
to candidate WP_013820696.1 METME_RS20725 glycosyl transferase family protein
Query= curated2:Q1IZP8 (351 letters) >NCBI__GCF_000214665.1:WP_013820696.1 Length = 334 Score = 78.6 bits (192), Expect = 2e-19 Identities = 75/240 (31%), Positives = 110/240 (45%), Gaps = 23/240 (9%) Query: 26 LTQAEAAAFMHEVMEGNVSGVRLAAALAALRVRGETPEEIAGFAQAMRASAVRVQVAPRE 85 LTQ EA M ++ G V ++L A L +RV+ ET EE+AGF A + S Sbjct: 27 LTQDEAYRAMKMILAGEVQPIQLGAFLMLMRVKEETCEELAGFVSAAKESFSHAPAV--S 84 Query: 86 VLLDVVGTGGDGAHT--FNISTTTAFVVAAAGVPVAKHG-NRAASSRAGSADVLEALGVN 142 V LD G H F +ST F++A G+ V HG R + VLEALG+ Sbjct: 85 VDLDWSSYAGKRRHLPWFLLST---FLLAENGIKVFMHGAGGHTQGRVYTEKVLEALGIP 141 Query: 143 -----LDAPPQLVADGVNELGIGFMFARNYHPALRHAAPVRADLAARTVFNILGPLANPA 197 +A QL+A+ + L + R+ P L +R + R+ + L L NP Sbjct: 142 AAHSLAEAEQQLLANNFSYLSL-----RHICPMLFDMINLRPVMGLRSPVHTLVRLLNPM 196 Query: 198 GASHLVVGVYRPELTRMLAEVLRLLGAKGATVVYGSGLDEFTVCGPNT---VTGLRNGEL 254 ASH + G++ P ++ + LLG + V+ G G + T P+ V + NGEL Sbjct: 197 RASHSIQGIFHPSYRQVHQKAALLLGERNMAVLKGEGGE--TERNPDVECLVQSVCNGEL 254 Lambda K H 0.318 0.131 0.375 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: 230 Number of extensions: 12 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: 351 Length of database: 334 Length adjustment: 29 Effective length of query: 322 Effective length of database: 305 Effective search space: 98210 Effective search space used: 98210 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 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