Align N-(5'-phosphoribosyl)anthranilate isomerase; PRAI; EC 5.3.1.24 (uncharacterized)
to candidate WP_069663041.1 BCR25_RS07710 phosphoribosylanthranilate isomerase
Query= curated2:C1CT52 (199 letters) >NCBI__GCF_001730305.1:WP_069663041.1 Length = 198 Score = 171 bits (434), Expect = 6e-48 Identities = 93/195 (47%), Positives = 128/195 (65%), Gaps = 5/195 (2%) Query: 3 KVKICGLSTKEAVETAVSAGADYIGFVFAPSKRQVTLEEAAELAKLIPADVKKVGVFVSP 62 KVKICGL+T+E V+TAV GADY+GFVFA SKR + E+ E+ K +P +VKKVGVFV+P Sbjct: 2 KVKICGLTTREQVDTAVKKGADYLGFVFAESKRAIRPEKVKEITKEVPKNVKKVGVFVTP 61 Query: 63 SRVELLEAIDKVGLDLVQVHGQVAADLFENLPCASIQAVQVDGNGHVPNSQADYLLFDAP 122 S E AI + GLD++Q+HG++ + +I + + + A+YLLFDA Sbjct: 62 SNQEAETAIREAGLDMIQIHGKLVTRSYSVPVIQAIPVGSYEQEKMMKETTAEYLLFDAL 121 Query: 123 ----VAGSGQSFDWGQLDTTGLA-QPFFIAGGLNEDNVVKAIQHFTPYAVDVSSGVETDG 177 + G+G+ FDW QL+ + L + FIAGGL +NV +A F+PYAVDVSSGVET+G Sbjct: 122 PQKFIGGNGKPFDWQQLNISKLKNKKIFIAGGLTSENVQEARATFSPYAVDVSSGVETNG 181 Query: 178 QKDHEKIRRFIERVK 192 KD KI F+++ K Sbjct: 182 IKDLAKISEFLKKAK 196 Lambda K H 0.317 0.134 0.384 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: 142 Number of extensions: 4 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: 199 Length of database: 198 Length adjustment: 20 Effective length of query: 179 Effective length of database: 178 Effective search space: 31862 Effective search space used: 31862 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 Jul 26 2024. The underlying query database was built on Jul 25 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