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_092055888.1 BQ4888_RS07525 imidazole glycerol phosphate synthase subunit HisF
Query= curated2:P60583 (243 letters) >NCBI__GCF_900111775.1:WP_092055888.1 Length = 255 Score = 94.0 bits (232), Expect = 3e-24 Identities = 66/215 (30%), Positives = 111/215 (51%), Gaps = 15/215 (6%) Query: 4 LLPAVDVVDGRAVRLVQGKAGSETEYGSALDAALGWQRDGAEWIHLVDLDAAFG-RGSNR 62 ++P +DV DGR V+ VQ + G ++AA + GA+ + +D+ A+ RG Sbjct: 6 IIPCLDVKDGRVVKGVQFVELRDA--GDPVEAAEAYDAQGADELTFLDITASSDKRGIIL 63 Query: 63 ELLAEVVGKLDVRVELSGGIRDDDSLAAALATGCARVNLGTAALENPQWCARAIGEHGDK 122 +++A ++ + + + GG+R+ + L G +V++ TAA+ P + A G + Sbjct: 64 DVVARTAERVFMPLTVGGGVREIADIRNLLNAGADKVSINTAAVHRPDFVREAAERFGSQ 123 Query: 123 -VAVGLDVQIIDGQHRLRGRGWE--TDGG------DLWEVLERLERQGCSRYVVTDVTKD 173 + V +D + + G R WE T GG D+ E R+E G ++T + KD Sbjct: 124 CIVVAIDARQVAGSDPRR---WEVYTHGGRNGTGIDVLEWAARMESYGAGEILLTSMDKD 180 Query: 174 GTLGGPNLDLLGAVADRTDAPVIASGGVSSLDDLR 208 GT G ++ L AV+DR PVIASGGV +L+ +R Sbjct: 181 GTKDGYDIPLTRAVSDRVKIPVIASGGVGNLEHIR 215 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: 209 Number of extensions: 14 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: 255 Length adjustment: 24 Effective length of query: 219 Effective length of database: 231 Effective search space: 50589 Effective search space used: 50589 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