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_029132003.1 A3GO_RS0102155 imidazole glycerol phosphate synthase subunit HisF
Query= curated2:Q3Z6V7 (237 letters) >NCBI__GCF_000428045.1:WP_029132003.1 Length = 256 Score = 126 bits (317), Expect = 4e-34 Identities = 77/231 (33%), Positives = 124/231 (53%), Gaps = 13/231 (5%) Query: 3 IIPAIDILGGRCVRLLQGDYAQETVYSPDPVGTAMRWQSLGAPRLHVVDLDGAADGESVN 62 IIP +D+ GR V+ G + + DPV A R+ S GA + +D+ ++D Sbjct: 6 IIPCLDVDAGRVVK---GVKFVDIRDAGDPVEVARRYNSEGADEITFLDITASSDDRETI 62 Query: 63 FELIREIANSALIPVEVGGGIRSMDTVKKLLTAGVDRVILGTVAVENPELVREICARY-A 121 ++ ++A+ IP+ VGGGIR+ + V+++L AG D+V + T AV NPE V+E +R+ + Sbjct: 63 VHVVEQVASEVFIPLTVGGGIRTTEDVRRMLNAGADKVAINTAAVFNPEFVKEATSRFGS 122 Query: 122 DSVAVSIDAR---------NGKVATRGWVNSTEVDALELARSMKKLGVKRFIYTDISRDG 172 + V+IDA+ ++ T G T +DA+E AR M + G + T + RDG Sbjct: 123 QCIVVAIDAKRTSAEGEPAKWEIFTHGGRKPTGLDAIEWARKMVEYGAGEILLTSMDRDG 182 Query: 173 TLSEPNFAAIRDLISAINMPVIASGGVSSLSHLRLLKDIGAEGAIVGKAIY 223 T + R + A+ +PVIASGGV +L HL G A++ +I+ Sbjct: 183 TKIGFDLELTRAISDAVTVPVIASGGVGNLQHLVDGVAQGGADAVLAASIF 233 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: 14 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: 237 Length of database: 256 Length adjustment: 24 Effective length of query: 213 Effective length of database: 232 Effective search space: 49416 Effective search space used: 49416 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 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