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_010527312.1 GQW_RS0107125 imidazole glycerol phosphate synthase subunit HisF
Query= curated2:A6UWA5 (241 letters) >NCBI__GCF_000220155.1:WP_010527312.1 Length = 251 Score = 115 bits (289), Expect = 6e-31 Identities = 70/228 (30%), Positives = 132/228 (57%), Gaps = 9/228 (3%) Query: 3 VIPAVDIKNKKCVQLIQGNPDKKHIELDNPLEVAEKWIKCGAEMIHLVDLDSAIYGTDTN 62 +IP +DI+N K V+ ++ K E+ +P+E+ + + GA+ + +D+ ++ T Sbjct: 6 IIPCLDIRNGKTVKGVKFLDIK---EVGDPVELGALYARQGADELVFLDITASHEKRKTF 62 Query: 63 KETIKKIIESVPVPVEVGGGVRTVEDALNLIDLGAERVILGTSAVKNPEIITELLEKGIN 122 + + +I + + +P VGGG+ ++DA L++ GA+++ + +SAV+NP++I++ + K Sbjct: 63 ADLVLRIAQHINIPFTVGGGISELKDAEILLNAGADKISINSSAVRNPQLISD-MAKHFG 121 Query: 123 SEKIMVALDAK-----DGKVVIKGWMEKTEYTPIEIGKILEEKGAGSILFTNVDVEGLLD 177 S+ ++VA+DAK D V + G TE + E++GAG ILFT++D +G+ Sbjct: 122 SQFVVVAIDAKQVEDDDWVVTVNGGRIPTEKRLFSWAREAEDRGAGEILFTSMDHDGVKK 181 Query: 178 GIDIEPVKKLVDELNIPIIASGGITTYDDLLKLKEIGVDGVVVGSAIY 225 G E + +L +EL+IPIIASGG + + IG + ++I+ Sbjct: 182 GFANEALARLSEELSIPIIASGGAGAKEHFKDVFTIGKADAGLAASIF 229 Lambda K H 0.314 0.139 0.384 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: 169 Number of extensions: 9 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: 241 Length of database: 251 Length adjustment: 24 Effective length of query: 217 Effective length of database: 227 Effective search space: 49259 Effective search space used: 49259 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: 42 (21.9 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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