Align N-(5'-phosphoribosyl)anthranilate isomerase; PRAI; EC 5.3.1.24 (uncharacterized)
to candidate WP_011319309.1 AVA_RS12855 phosphoribosylanthranilate isomerase
Query= curated2:B7KC08 (220 letters) >NCBI__GCF_000204075.1:WP_011319309.1 Length = 210 Score = 268 bits (684), Expect = 7e-77 Identities = 132/206 (64%), Positives = 155/206 (75%) Query: 1 MRVKICGITQPEQGRAIANLGANTLGFICVAQSPRYVTPNQIREIIEQLPPLVDKIGVFV 60 MRVKICGITQP+Q AIA+LGA LGFICV SPRYVT QI + LP +DKIGVF Sbjct: 1 MRVKICGITQPQQSVAIASLGATALGFICVPSSPRYVTAAQIWAAVAPLPKNIDKIGVFA 60 Query: 61 NAPATEIINIVAQTGLTGVQLHGDETPEMCQQLKISLPDVEIIRALRIKSSQSLREVALY 120 N+ EI V GLTGVQLHGDETPE C QL+ SLP VEI++ALR++S + L + +Y Sbjct: 61 NSSIAEIKQTVIDCGLTGVQLHGDETPEFCDQLRRSLPQVEILKALRVRSLEHLEQAIIY 120 Query: 121 FDSVNTLLLDAYHPHLFGGTGATIDWEILAQFKSPIPWLLAGGLKPDNLVSALSQLSPHG 180 +NTLLLDAYHP GGTG T+DW++L +F PWLLAGGL PDN++ ALSQL+P G Sbjct: 121 TQYINTLLLDAYHPQQLGGTGQTLDWQMLHKFHPSCPWLLAGGLTPDNILEALSQLNPDG 180 Query: 181 IDLSSGVERAPGDKDLDKVAELFQQL 206 IDLSSGVER PGDKDLDKVA LF++L Sbjct: 181 IDLSSGVERKPGDKDLDKVALLFEKL 206 Lambda K H 0.319 0.137 0.406 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: 193 Number of extensions: 6 Number of successful extensions: 1 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: 220 Length of database: 210 Length adjustment: 22 Effective length of query: 198 Effective length of database: 188 Effective search space: 37224 Effective search space used: 37224 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 (21.7 bits) S2: 45 (21.9 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