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_013458980.1 SULKU_RS00580 imidazole glycerol phosphate synthase subunit HisF
Query= curated2:Q58927 (237 letters) >NCBI__GCF_000183725.1:WP_013458980.1 Length = 253 Score = 119 bits (297), Expect = 7e-32 Identities = 83/242 (34%), Positives = 133/242 (54%), Gaps = 18/242 (7%) Query: 3 IIPAVDLKDKKCVQLIQGDPNKKHLELNNPVEVAKKFVDEGAEYLHIIDLDAAFGTGNNR 62 IIP +D+KD + V+ + K + +PVEVAK++ +EGA+ L +D+ A+ R Sbjct: 9 IIPCLDVKDGRVVKGVNFVGLK---DAGDPVEVAKRYNEEGADELTFLDITASH---EER 62 Query: 63 DVIKNII----KEVNVPVEVGGGIRNLEIAKELISLGVDRVIVGTKAILEPKFIDDLNKE 118 D I +I+ KEV +P+ VGGGIR L+ L+++G D+V V + AI P+ ID+ K Sbjct: 63 DTIVHIVEQVAKEVFIPLTVGGGIRKLDDIYRLLAVGCDKVSVNSAAIKRPELIDEGAKR 122 Query: 119 IGKDKIVLAVECK----EGKVVIKGWKEKVDKTPIEVIKEFEDK-VGYILFTNVDVEGLL 173 G IV+A++ K + V + G + +E KE D+ G IL T++D +G Sbjct: 123 FGSQCIVVAIDVKRTGNQYNVYLNGGRVDTGINALEWAKEVVDRGAGEILLTSMDADGTK 182 Query: 174 KGINVDIIKELIEKTDIPIIYSGGITTLEDIKALKELGIYGVVIGSAL-YK--GLIDLKK 230 G ++ I +++ ++P+I SGG T+E IK E G + S YK ++DLK+ Sbjct: 183 AGFDLSITEQISRAVNVPVIASGGAGTMEHIKEAFEHGADAALAASIFHYKEIDIMDLKR 242 Query: 231 AL 232 L Sbjct: 243 YL 244 Lambda K H 0.317 0.143 0.395 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: 204 Number of extensions: 16 Number of successful extensions: 6 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: 237 Length of database: 253 Length adjustment: 24 Effective length of query: 213 Effective length of database: 229 Effective search space: 48777 Effective search space used: 48777 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 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