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_027722353.1 H589_RS0112630 imidazole glycerol phosphate synthase subunit HisF
Query= curated2:A6UWA5 (241 letters) >NCBI__GCF_000425265.1:WP_027722353.1 Length = 259 Score = 108 bits (269), Expect = 1e-28 Identities = 63/208 (30%), Positives = 113/208 (54%), Gaps = 14/208 (6%) Query: 3 VIPAVDIKNKKCVQLIQGNPDKKHIELDNPLEVAEKWIKCGAEMIHLVDLDSAIYGTDTN 62 +IP +D++N L +G K +I++ +P+E A+ + + GA+ I D+ ++ G Sbjct: 6 IIPCLDVRNGV---LTKGVKFKDNIDIGDPVETAKLYYEQGADEIVFYDITASSEGRGIF 62 Query: 63 KETIKKIIESVPVPVEVGGGVRTVEDALNLIDLGAERVILGTSAVKNPEIITELLEKGIN 122 + ++++ + +P VGGG+ TVED ++ GAE+V + + AVKNP+II+E Sbjct: 63 LDVVERVASEIFIPFSVGGGINTVEDMRAVLLAGAEKVSVNSGAVKNPDIISE-GAAAFG 121 Query: 123 SEKIMVALDAK----------DGKVVIKGWMEKTEYTPIEIGKILEEKGAGSILFTNVDV 172 S+ I++ +D K ++VI G + +E K E GAG I ++D Sbjct: 122 SQCIVLGMDVKRVEKSELIPSGFEIVINGGRKFMGIDALEWAKTCEALGAGEICLNSIDA 181 Query: 173 EGLLDGIDIEPVKKLVDELNIPIIASGG 200 +G DG D+E + + + + +P+IASGG Sbjct: 182 DGTKDGYDLELTRLIAENVGVPVIASGG 209 Score = 50.8 bits (120), Expect = 3e-11 Identities = 33/107 (30%), Positives = 55/107 (51%), Gaps = 4/107 (3%) Query: 123 SEKIMVALDAKDGKVVIKGWMEKTEYT---PIEIGKILEEKGAGSILFTNVDVEGLLDGI 179 S++I+ LD ++G V+ KG K P+E K+ E+GA I+F ++ GI Sbjct: 3 SKRIIPCLDVRNG-VLTKGVKFKDNIDIGDPVETAKLYYEQGADEIVFYDITASSEGRGI 61 Query: 180 DIEPVKKLVDELNIPIIASGGITTYDDLLKLKEIGVDGVVVGSAIYK 226 ++ V+++ E+ IP GGI T +D+ + G + V V S K Sbjct: 62 FLDVVERVASEIFIPFSVGGGINTVEDMRAVLLAGAEKVSVNSGAVK 108 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: 181 Number of extensions: 12 Number of successful extensions: 3 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: 241 Length of database: 259 Length adjustment: 24 Effective length of query: 217 Effective length of database: 235 Effective search space: 50995 Effective search space used: 50995 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 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