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_013841340.1 DESRU_RS06615 imidazole glycerol phosphate synthase subunit HisF
Query= curated2:Q3Z6V7 (237 letters) >NCBI__GCF_000215085.1:WP_013841340.1 Length = 252 Score = 125 bits (315), Expect = 6e-34 Identities = 77/241 (31%), Positives = 131/241 (54%), Gaps = 10/241 (4%) Query: 3 IIPAIDILGGRCVRLLQGDYAQETVYSPDPVGTAMRWQSLGAPRLHVVDLDGAADGESVN 62 IIP +D+ GGR V+ G + DPV A + GA + +D+ ++DG + Sbjct: 6 IIPCLDVTGGRVVK---GTNFVNLRDAGDPVELAALYDREGADEVIFLDITASSDGRATM 62 Query: 63 FELIREIANSALIPVEVGGGIRSMDTVKKLLTAGVDRVILGTVAVENPELVREICARY-A 121 +++R A IP VGGGIR+++ ++ +L AG D++ + T A++NP ++ E ++ + Sbjct: 63 LDVVRRTAEEVFIPFTVGGGIRTVEDMRLMLQAGADKIGINTAAIKNPRVISEGALKFGS 122 Query: 122 DSVAVSIDA-----RNGKVATRGWVNSTEVDALELARSMKKLGVKRFIYTDISRDGTLSE 176 V V+IDA R +V G T +DA+E A ++LG + T + RDGT Sbjct: 123 QCVVVAIDARQTGPRKWEVYIHGGRTPTGMDAVEWAAKAEELGAGEILLTSMDRDGTKEG 182 Query: 177 PNFAAIRDLISAINMPVIASGGVSSLSHL-RLLKDIGAEGAIVGKAIYTGDLNLKRAFEE 235 + A R + A+ +PVIASGGV +L H+ + L + A+ A+ + G+ ++++A E Sbjct: 183 FDLALTRTIAQAVKIPVIASGGVGTLEHMAQGLTEGMADAALAASIFHFGEYSVRQAKEY 242 Query: 236 L 236 L Sbjct: 243 L 243 Lambda K H 0.318 0.136 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: 172 Number of extensions: 9 Number of successful extensions: 5 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: 252 Length adjustment: 24 Effective length of query: 213 Effective length of database: 228 Effective search space: 48564 Effective search space used: 48564 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 (21.7 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Jul 25 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