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_028321552.1 H567_RS0111765 imidazole glycerol phosphate synthase subunit HisF
Query= curated2:Q2RGW1 (243 letters) >NCBI__GCF_000422285.1:WP_028321552.1 Length = 252 Score = 108 bits (271), Expect = 8e-29 Identities = 72/235 (30%), Positives = 117/235 (49%), Gaps = 15/235 (6%) Query: 3 VMPAIDLREGRCVRLYQGRIEAETVYSTDPVAVARGWVERGARWLHVVDLDGAFAGRPRN 62 +MP +D++ GR V+ Q + + DPVA + GA L ++D+ GR Sbjct: 5 IMPCLDMQNGRVVKGVQF---VDIRDAGDPVACCVAYCHAGADELALLDITATVEGRATM 61 Query: 63 LEVIAAIIRAAGVPVQVGGGIRSLESLAGVLAAGASRVVLGTVAITNPEVVATAVERYG- 121 L+V+ + RAA +P VGGGI + S VL AGA ++ + A PEV+ V+ +G Sbjct: 62 LDVVEKVARAATIPFTVGGGISDVASAEAVLRAGADKISTSSAAFRKPEVIRDMVKAFGT 121 Query: 122 ERVVVGIDSLDG-------QVAIEGWEATVARGAVEFARQMASLGVTRAVFTDIGRDGTL 174 +R+ V ID+ +V I+G AVE+A+Q+A GV + T DG Sbjct: 122 DRITVAIDAAVNDRLPSGYEVYIDGGRTATGADAVEWAKQVAGYGVKTILPTSKSTDGMK 181 Query: 175 QGPNIAATREMARSGGLKIIASGGIASLDDLRKLKELAAEGVEGAILGRSLYNGN 229 QG ++ R++ + G+ ++ASGG L+ E A+ +L S+++ N Sbjct: 182 QGFDLPLIRKIKEATGVDVVASGGAGKLEHFYDAVEAGAD----ILLAASVFHFN 232 Lambda K H 0.319 0.136 0.386 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: 176 Number of extensions: 12 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: 252 Length adjustment: 24 Effective length of query: 219 Effective length of database: 228 Effective search space: 49932 Effective search space used: 49932 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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