Align N-(5'-phosphoribosyl)anthranilate isomerase; Short=PRAI; EC 5.3.1.24 (characterized, see rationale)
to candidate WP_012048933.1 SWIT_RS13795 phosphoribosylanthranilate isomerase
Query= uniprot:A0A1L6JC25_9SPHN (212 letters) >NCBI__GCF_000016765.1:WP_012048933.1 Length = 217 Score = 259 bits (662), Expect = 3e-74 Identities = 135/212 (63%), Positives = 158/212 (74%), Gaps = 3/212 (1%) Query: 3 VTAKICGLSTAATLDTALAGGASHVGFVFFPPSPRHVTFDQAGSLSTRVPAQTGKVGVFV 62 VTAKICGLST +D A+ GASH GFVFFP SPRHVTF+QA SL+ R+P G+VGVFV Sbjct: 7 VTAKICGLSTPDAVDAAVRHGASHAGFVFFPKSPRHVTFEQAASLTMRLPRHVGRVGVFV 66 Query: 63 DPEDALLESAIRAARLDAIQLH-RVTPERAAAIGAR-TRLPVWAAVAVKTRADLDAANGF 120 DPE+A+++ AIR +D +QLH PER AA+ AR + VW AV V+TRADLDAA + Sbjct: 67 DPEEAVVDQAIRIGGIDTVQLHGHEPPERLAALAARHPGVAVWKAVPVRTRADLDAAARY 126 Query: 121 RGAVQRILYDAKVPEDAKLPGGMGIRFDWTLLQGFAHPLPWALSGGLDPANVAEAVGITG 180 R ILYDAK PE LPGGMG+RFDW LL GF HP WALSGG+D NVA+A G TG Sbjct: 127 RPVADLILYDAKTPE-GTLPGGMGLRFDWALLDGFRHPQRWALSGGIDADNVADAAGRTG 185 Query: 181 ARLVDVSSGVESAPGVKDEAKIAAFLKTVATL 212 ARL+D+SSGVESAPG+K KIAAFL+ VATL Sbjct: 186 ARLIDISSGVESAPGIKAVDKIAAFLQRVATL 217 Lambda K H 0.320 0.134 0.398 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: 209 Number of extensions: 9 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: 212 Length of database: 217 Length adjustment: 22 Effective length of query: 190 Effective length of database: 195 Effective search space: 37050 Effective search space used: 37050 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 45 (21.9 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