Align N-(5'-phosphoribosyl)anthranilate isomerase; PRAI; EC 5.3.1.24 (uncharacterized)
to candidate WP_041305455.1 BTUS_RS08535 phosphoribosylanthranilate isomerase
Query= curated2:C0ZCE4 (222 letters) >NCBI__GCF_000092905.1:WP_041305455.1 Length = 210 Score = 141 bits (356), Expect = 8e-39 Identities = 85/208 (40%), Positives = 121/208 (58%), Gaps = 7/208 (3%) Query: 4 LKICGIKRTETLALLKELEVDYVGLVFAPSKRQVDAQTAGQLLAAVPGHPPAVGVFVNPT 63 +K CG R E +A + L VD++GLVFAPSKR+V+ + A L A +GVFV+ Sbjct: 1 MKACGFTRAEDVAAAERLGVDWIGLVFAPSKRRVEVEQAAGLRAGT--RLRCMGVFVDAG 58 Query: 64 MEELEEVLSEAPLSVIQLHGQETPQFCQQVRERFALPVWKALAVGGEADAALAIQSYQGI 123 +E++ E + L +QLHG E+P+ C+++R+ L V KA + E A A +YQG Sbjct: 59 IEKVRETVRRVGLDGVQLHGAESPEDCRRLRDE-GLFVVKAFSALLERPGAAA--AYQGA 115 Query: 124 VSAFLFDTYDPGQAGGTGKKFSWEQIPALQAACEAADCIIAGGIHAENVGELMGQYQAGI 183 V A L D PG+ GG G+ F W+ IP + E IAGG+ ENV EL+ Y+ Sbjct: 116 VDAVLVDAGVPGERGGRGQTFRWQDIPEWRKGAEGVFLWIAGGLRPENVQELLRGYRPDG 175 Query: 184 VDVSSGVET--DGVKDAQKIKTLVERVK 209 VDVSSG+ET GVKD +++ V +V+ Sbjct: 176 VDVSSGIETGVPGVKDVARMEQFVRKVR 203 Lambda K H 0.317 0.133 0.383 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: 157 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: 222 Length of database: 210 Length adjustment: 22 Effective length of query: 200 Effective length of database: 188 Effective search space: 37600 Effective search space used: 37600 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 (21.6 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