Align 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase; EC 5.3.1.16; Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (uncharacterized)
to candidate WP_013707444.1 DESAC_RS12530 imidazole glycerol phosphate synthase subunit HisF
Query= curated2:Q18DL2 (245 letters) >NCBI__GCF_000195295.1:WP_013707444.1 Length = 254 Score = 119 bits (299), Expect = 4e-32 Identities = 73/232 (31%), Positives = 122/232 (52%), Gaps = 10/232 (4%) Query: 6 ESFEVIPAVDMQDGDVVQLVQGERGTETRYGDPVVAAKQWVEAGAKTLHLVDLDGAFEGD 65 E +++P +DM+DG VV+ V + GDPV A+ + GA L ++D+ E Sbjct: 2 EPIKIMPCLDMKDGRVVKGVNFINLRDA--GDPVENARFYEREGADELAMLDIAATVENR 59 Query: 66 RMNATAVDAIIDAVDIPVQLGGGIRTANDAASLLDRGVNRVILGTAAVENPDLVAELAES 125 + V+ + ++IP+ +GGGI T D +L G +++ + +AAV+NPDL+ A++ Sbjct: 60 KTRLEWVEKVAAVINIPLTMGGGIATLEDIELVLTAGADKISMNSAAVKNPDLIDLAAKT 119 Query: 126 Y-PGRIIVSLDA-------ADGEVVVSGWTESTGIDPAVAAARFADYGACGILFTDVDVE 177 Y PGR+ +++D + E+V++G T+ G D A GA IL T +D + Sbjct: 120 YGPGRVTIAIDGKRNPAMPSGFELVIAGGTKPVGRDAIAWATECQQRGAGSILPTSMDGD 179 Query: 178 GKLAGIQSSVTARVIDAVDIPVIASGGVASLDDIQTLHTTGAAATVVGTALY 229 G G T + DAV +PVIASGG +L+ T G A ++ +++ Sbjct: 180 GTQKGYDLEFTRAIADAVTVPVIASGGAGTLEHFYEGATRGGARILLAASVF 231 Score = 38.5 bits (88), Expect = 1e-07 Identities = 29/107 (27%), Positives = 49/107 (45%), Gaps = 2/107 (1%) Query: 127 PGRIIVSLDAADGEVV--VSGWTESTGIDPAVAAARFADYGACGILFTDVDVEGKLAGIQ 184 P +I+ LD DG VV V+ DP A + GA + D+ + + Sbjct: 3 PIKIMPCLDMKDGRVVKGVNFINLRDAGDPVENARFYEREGADELAMLDIAATVENRKTR 62 Query: 185 SSVTARVIDAVDIPVIASGGVASLDDIQTLHTTGAAATVVGTALYEN 231 +V ++IP+ GG+A+L+DI+ + T GA + +A +N Sbjct: 63 LEWVEKVAAVINIPLTMGGGIATLEDIELVLTAGADKISMNSAAVKN 109 Lambda K H 0.316 0.133 0.375 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: 179 Number of extensions: 12 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 245 Length of database: 254 Length adjustment: 24 Effective length of query: 221 Effective length of database: 230 Effective search space: 50830 Effective search space used: 50830 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: 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