Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (uncharacterized)
to candidate Ac3H11_3240 Anthranilate phosphoribosyltransferase like (EC 2.4.2.18)
Query= curated2:Q6AFI7 (349 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3240 Length = 307 Score = 80.9 bits (198), Expect = 4e-20 Identities = 60/208 (28%), Positives = 95/208 (45%), Gaps = 5/208 (2%) Query: 20 LSVADASWAMRQVMTGEATDAQIAAFLIALRAKGETVDEIVGFRDAVLDHAVGLPVNSMA 79 LS A+ QV+ G+ +D +I AF +A+R KGET +E+ GF DA LP Sbjct: 20 LSREQATDLFGQVLDGQVSDLEIGAFCLAMRIKGETAEEMCGFLDATHSRLALLPATDRP 79 Query: 80 LDIVGTGGDRFGTVNISTTAAIVAAGAGVPVIKHGNRAASSSSGSSDVLAALGIDLTLPP 139 L ++ + ++ A++ A G+PV+ HG R + +SDVL AL + P Sbjct: 80 LIVLPSYNGARKLPVLTPLLALLLAREGLPVLLHGMRTEARRILASDVLLALDVPALTAP 139 Query: 140 ERVAEVLRATGITFAFASAFHPGFANAAAVRSQLGVPTVFNILGPLCNP-ARPEASAVGV 198 E+VA + H G A AVR +G+ + + L +P A Sbjct: 140 EKVAN----GTVRHIHTQHLHAGLARLLAVREVVGLRNPGHSVVKLMSPCAGASVVVTAY 195 Query: 199 APLDRVPLIVGVFQTRGATALVFRGDDG 226 + ++ F+T G +AL+ RG +G Sbjct: 196 THPEYFEMLQTTFRTLGMSALLSRGLEG 223 Lambda K H 0.318 0.132 0.376 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: 200 Number of extensions: 13 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: 349 Length of database: 307 Length adjustment: 28 Effective length of query: 321 Effective length of database: 279 Effective search space: 89559 Effective search space used: 89559 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 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