Align N-(5'-phosphoribosyl)anthranilate isomerase 2; PRAI 2; EC 5.3.1.24 (uncharacterized)
to candidate WP_084056126.1 B9A12_RS02940 phosphoribosylanthranilate isomerase
Query= curated2:Q8PRX4 (226 letters) >NCBI__GCF_900176285.1:WP_084056126.1 Length = 226 Score = 133 bits (335), Expect = 2e-36 Identities = 84/218 (38%), Positives = 119/218 (54%), Gaps = 6/218 (2%) Query: 3 IKVCGIKRVEDAVMAAYCGADAIGLVVGRKHNSDDFIDKHLAQKIVRECPPYISPVLVTE 62 ++V GI ++A G +G + + +D ++ A++++ PP PVL+T Sbjct: 7 VQVAGIIDAQEAQALCAVGIRWLGFPLRLDVHPEDLSEEE-ARRVIAALPPESMPVLITY 65 Query: 63 LDDAEEISGLVHETGVTSVQLHSDCTVDSIISLRKTFPNIKIIKNFHVIGPG----VIHA 118 D + L GV +VQ+H D VDS+ + R P++ +IK+ V+G G ++ Sbjct: 66 EPDPRSLKELALFLGVRAVQVHGDLDVDSLRAFRSACPDLFLIKSL-VVGRGPWQELLKT 124 Query: 119 MKPFESVVDAFILDTLDLANDKVGSTGLVHDWSISRKIVKEVSRPVILAGGLTPENVGEA 178 M +VDAFI DT D G+TG VHDWS S +IV +PVILAGGL ENV EA Sbjct: 125 MDLMAPLVDAFITDTYDPETGACGATGKVHDWSWSARIVARSPKPVILAGGLHGENVAEA 184 Query: 179 IRVVNPYGVDASSGLKDSNGFKDEMKVINFVHRAKNDF 216 IRVV P GVDA +GL+ +G KD KV F +A F Sbjct: 185 IRVVRPAGVDAHTGLEGPDGRKDMEKVKRFHRKALEAF 222 Lambda K H 0.320 0.138 0.402 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: 144 Number of extensions: 2 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: 226 Length of database: 226 Length adjustment: 22 Effective length of query: 204 Effective length of database: 204 Effective search space: 41616 Effective search space used: 41616 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: 46 (22.3 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