Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (uncharacterized)
to candidate WP_011800804.1 PNAP_RS07005 DNA-binding protein YbiB
Query= curated2:Q1IZP8 (351 letters) >NCBI__GCF_000015505.1:WP_011800804.1 Length = 301 Score = 79.3 bits (194), Expect = 1e-19 Identities = 63/201 (31%), Positives = 95/201 (47%), Gaps = 9/201 (4%) Query: 26 LTQAEAAAFMHEVMEGNVSGVRLAAALAALRVRGETPEEIAGFAQAMRASAVRVQVAPRE 85 L++A+AA + +V++G V+ + + A+R++GETPEE+AGF A+ R+ + P Sbjct: 20 LSRAQAADLLGQVLDGVVTDLEIGGFCLAMRIKGETPEEMAGFLDAVHQ---RLNLLPAS 76 Query: 86 VLLDVVGTGGDGAHTFNIST-TTAFVVAAAGVPVAKHGNRAASSRAGSADVLEALGVNLD 144 VV +GA + T A ++A G+ V HG SSR S++VL ALG Sbjct: 77 DGPTVVLPSYNGARKLPVLTPLLALLLAREGLSVLVHGTPTESSRVFSSEVLSALGTQAL 136 Query: 145 APPQLVADGVNELGIGFMFARNYHPALRHAAPVRADLAARTVFNILGPLANPAGASHLVV 204 + +A G + F PAL+ VR + R + L L NP LVV Sbjct: 137 TAIKPIAPG----EVVFAPTELLSPALKRLLDVRRAVGLRNPAHSLVKLMNPVAGKALVV 192 Query: 205 GVY-RPELTRMLAEVLRLLGA 224 Y PE +A L+ A Sbjct: 193 SSYTHPEYALSMAATFELVQA 213 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: 207 Number of extensions: 17 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: 351 Length of database: 301 Length adjustment: 28 Effective length of query: 323 Effective length of database: 273 Effective search space: 88179 Effective search space used: 88179 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: 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