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_026595513.1 A3OQ_RS0105065 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
Query= curated2:P60583 (243 letters) >NCBI__GCF_000385335.1:WP_026595513.1 Length = 248 Score = 144 bits (362), Expect = 2e-39 Identities = 92/242 (38%), Positives = 139/242 (57%), Gaps = 9/242 (3%) Query: 2 LILLPAVDVVDGRAVRLVQGKAGSETEYGSALDA-ALGWQRDGAEWIHLVDLDAAF-GRG 59 +IL PA+D+ +G+ VRLVQG + T + + A A ++R G +H+VDLD AF G+ Sbjct: 1 MILFPAIDLKEGQCVRLVQGDMQAATVFNADPAAQAQSFERQGFTHLHVVDLDGAFAGKP 60 Query: 60 SNRELLAEVVGKLDVRVELSGGIRDDDSLAAALATGCARVNLGTAALENPQWCARAIGEH 119 N + + ++ K+ + V+L GGIRD ++ A L G +RV +GTAA+ +P + A H Sbjct: 61 MNAQAVEGILAKVKMPVQLGGGIRDLSTIEAWLGKGVSRVIIGTAAVRDPDFVRAAAKAH 120 Query: 120 GDKVAVGLDVQIIDGQHRLRG--RGWETDGGDLWEVLERLERQGCSRYVVTDVTKDGTLG 177 +VAVG+D + DG + G + E DL + R E G + + TD+ +DG L Sbjct: 121 PGRVAVGIDAR--DGYVAVEGWAKTSELSAADLGK---RFEDAGVAAVIYTDIARDGVLK 175 Query: 178 GPNLDLLGAVADRTDAPVIASGGVSSLDDLRAIATLTGRGVEGAIVGKALYAGRFTLPQA 237 G N++ A+AD PVIASGG++SL D+ + + GAI G+ALY GR +A Sbjct: 176 GLNIEATLALADAIAIPVIASGGLASLADIERLIQPDCAKLAGAITGRALYDGRIDPGEA 235 Query: 238 LA 239 LA Sbjct: 236 LA 237 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: 198 Number of extensions: 17 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: 248 Length adjustment: 24 Effective length of query: 219 Effective length of database: 224 Effective search space: 49056 Effective search space used: 49056 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