Align phosphoribosylanthranilate isomerase subunit (EC 5.3.1.24) (characterized)
to candidate WP_028585448.1 G494_RS0116855 phosphoribosylanthranilate isomerase
Query= metacyc::MONOMER-301 (205 letters) >NCBI__GCF_000429965.1:WP_028585448.1 Length = 223 Score = 167 bits (424), Expect = 1e-46 Identities = 93/209 (44%), Positives = 132/209 (63%), Gaps = 7/209 (3%) Query: 3 RVKICGITNLEDALFSVESGADAVGFVFYPKSKRYISPEDARRISVELPPFVFRVGVFVN 62 R+KICGIT L+DAL +VE G DA+GF+FY S R+I PE+A+ I +LPPFV VGVFV+ Sbjct: 8 RIKICGITRLDDALEAVEEGVDALGFIFYEGSPRFIDPEEAKLIIEQLPPFVGTVGVFVD 67 Query: 63 EEPEKILDVASYVQLNAVQLHGEEPIELCRKIAERIL---VIKAVGVSNERDMERALNYR 119 ++ +++ ++ Y L+ VQLHG E + C ++A V+KA+ V E E Y Sbjct: 68 KKRKEVEEIVEYCCLDYVQLHGSESPKYCERLARHAAPCQVLKALRVGPELSAETVAVYS 127 Query: 120 EF--PILLDTKTP-EYGGSGKTFDWSLILPYRDRFRYLVLSGGLNPENVRSAIDVVRPFA 176 +LDT +P GG+G FDW+LI + +L L+GGL+P+NV SA+ VRP+ Sbjct: 128 PHVKGFVLDTYSPLAVGGTGTAFDWNLIEKLELQKPFL-LAGGLSPDNVESALTTVRPYG 186 Query: 177 VDVSSGVEAFPGKKDHDSIKMFIKNAKGL 205 VD +SG+E PG KDH I+ FI+ + L Sbjct: 187 VDANSGLETEPGVKDHGLIRSFIRKVREL 215 Lambda K H 0.321 0.140 0.408 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: 137 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: 205 Length of database: 223 Length adjustment: 22 Effective length of query: 183 Effective length of database: 201 Effective search space: 36783 Effective search space used: 36783 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