Align Phosphoribosyl isomerase A; 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase; EC 5.3.1.16; N-(5'-phosphoribosyl)anthranilate isomerase; PRAI; EC 5.3.1.24; Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (uncharacterized)
to candidate WP_012048927.1 SWIT_RS13765 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase
Query= curated2:P60583 (243 letters) >NCBI__GCF_000016765.1:WP_012048927.1 Length = 243 Score = 156 bits (394), Expect = 4e-43 Identities = 96/240 (40%), Positives = 134/240 (55%), Gaps = 7/240 (2%) Query: 2 LILLPAVDVVDGRAVRLVQGKAGSETEYGS-ALDAALGWQRDGAEWIHLVDLDAAF-GRG 59 +I+ PA+D+ G+ VRL +G T YG D A + GAEW+H+VDLD AF GR Sbjct: 3 IIVFPAIDLKGGQVVRLAEGDMDRATVYGDDPADQARRFAEAGAEWLHVVDLDGAFAGRA 62 Query: 60 SNRELLAEVVGKLDVRVELSGGIRDDDSLAAALATGCARVNLGTAALENPQWCARAIGEH 119 N E + ++ +VEL GGIRD + LA G RV +GTAAL+NP A E Sbjct: 63 VNAEAVEAIIKAFPGKVELGGGIRDRAGIDRWLALGVERVIIGTAALQNPDLVREAAKEL 122 Query: 120 GDKVAVGLDVQIIDGQHRLRGRGW-ETDGGDLWEVLERLERQGCSRYVVTDVTKDGTLGG 178 ++ VG+D + DG + GW E + ++ +R G + + TDV +DG L G Sbjct: 123 PGRIVVGVDAR--DGF--VATHGWAEVSTVGITDLADRFADAGVASLLFTDVGRDGLLKG 178 Query: 179 PNLDLLGAVADRTDAPVIASGGVSSLDDLRAIATLTGRGVEGAIVGKALYAGRFTLPQAL 238 N++ A+A PVIASGGV+S+ D+ A+ G G+EG I G+ALY GR L +AL Sbjct: 179 CNVEATVALARHASIPVIASGGVASIADIAALVPHAGDGIEGVITGRALYDGRLDLAEAL 238 Lambda K H 0.318 0.138 0.407 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: 239 Number of extensions: 20 Number of successful extensions: 4 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: 243 Length of database: 243 Length adjustment: 23 Effective length of query: 220 Effective length of database: 220 Effective search space: 48400 Effective search space used: 48400 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 (21.7 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