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_055437259.1 ASC41_RS13925 imidazole glycerol phosphate synthase subunit HisF
Query= curated2:A6UWA5 (241 letters) >NCBI__GCF_001418085.1:WP_055437259.1 Length = 251 Score = 130 bits (327), Expect = 2e-35 Identities = 80/242 (33%), Positives = 140/242 (57%), Gaps = 12/242 (4%) Query: 3 VIPAVDIKNKKCVQLIQGNPDKKHIELDNPLEVAEKWIKCGAEMIHLVDLDSAIYGTDTN 62 +IP +DIKN + V+ + + + +P+E+A+++ GA+ + +D+ + + G T Sbjct: 6 IIPCLDIKNGRTVKGVNFVDLR---DAGDPVELAKQYALKGADELVFLDISATLEGRKTM 62 Query: 63 KETIKKIIESVPVPVEVGGGVRTVEDALNLIDLGAERVILGTSAVKNPEIITELLEKGIN 122 + + K+ E V +P VGGG+ ++ED L+ GA+++ + +SAVK PE++ EL K Sbjct: 63 HDMVLKVAEHVNIPFTVGGGISSIEDVDALLKCGADKISINSSAVKRPELVNELANK-FG 121 Query: 123 SEKIMVALDAK--DGK--VVIKGWMEKTEYTPIEIGKILEEKGAGSILFTNVDVEGLLDG 178 S+ ++VA+DAK DG V + G T+ + K +E++GAG ILFT++D +G DG Sbjct: 122 SQCVVVAIDAKNVDGNWIVHLAGGTIPTKLNLFDWAKEVEQRGAGEILFTSMDNDGTKDG 181 Query: 179 IDIEPVKKLVDELNIPIIASGGITTYDDLLKLKEIGVDGVVVGSAIYK----EMMDLKKA 234 + + KL ELNIPIIASGG T + + G + ++++ + +LK+A Sbjct: 182 FANDALAKLSQELNIPIIASGGAGTIQHFVDTFKKGKADAALAASVFHFGEIPISELKEA 241 Query: 235 IK 236 +K Sbjct: 242 LK 243 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: 186 Number of extensions: 14 Number of successful extensions: 3 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