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_011386876.1 AMB_RS22930 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase
Query= curated2:P60583 (243 letters) >NCBI__GCF_000009985.1:WP_011386876.1 Length = 239 Score = 145 bits (365), Expect = 9e-40 Identities = 94/241 (39%), Positives = 133/241 (55%), Gaps = 9/241 (3%) Query: 2 LILLPAVDVVDGRAVRLVQGKAGSETEYGSALDA-ALGWQRDGAEWIHLVDLDAAF-GRG 59 + L PA+D+ DG VRL G T + + A A + GAEWIH+VDL+ AF G+ Sbjct: 1 MFLFPAIDLKDGACVRLKLGLMEESTVFNTDPGAQARDFAAAGAEWIHVVDLNGAFAGKP 60 Query: 60 SNRELLAEVVGKLDVRVELSGGIRDDDSLAAALATGCARVNLGTAALENPQWCARAIGEH 119 N + ++ + V V+L GGIR+ ++ LA G RV LGT AL+NP A Sbjct: 61 VNGAAVDSILKSVSVPVQLGGGIREMATIEDWLARGIRRVILGTVALKNPALVKEACQRF 120 Query: 120 GDKVAVGLDVQIIDGQHRLRGRGW-ETDGGDLWEVLERLERQGCSRYVVTDVTKDGTLGG 178 +VAVG+D + ++ GW ET + E+ + E G + + TD+ +DG L G Sbjct: 121 PGRVAVGIDAK----GGKVAVEGWAETSDLTVLELARKFEDCGVAALIYTDIDRDGVLAG 176 Query: 179 PNLDLLGAVADRTDAPVIASGGVSSLDDLRAIATLTGRGVEGAIVGKALYAGRFTLPQAL 238 PN+ A+AD PVIASGGVSSL DL+A+ +EG I G+A+Y GR + QA+ Sbjct: 177 PNVAATAALADAISIPVIASGGVSSLVDLKALKAYP--KLEGVISGRAIYDGRIDVAQAI 234 Query: 239 A 239 A Sbjct: 235 A 235 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: 212 Number of extensions: 16 Number of successful extensions: 5 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: 239 Length adjustment: 23 Effective length of query: 220 Effective length of database: 216 Effective search space: 47520 Effective search space used: 47520 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 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