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_017600194.1 D471_RS0119655 imidazole glycerol phosphate synthase subunit HisF
Query= curated2:Q18DL2 (245 letters) >NCBI__GCF_000341125.1:WP_017600194.1 Length = 257 Score = 113 bits (283), Expect = 3e-30 Identities = 84/245 (34%), Positives = 119/245 (48%), Gaps = 18/245 (7%) Query: 7 SFEVIPAVDMQDGDVVQLVQGERGTETRYGDPVVAAKQWVEAGAKTLHLVDLDGAFEGDR 66 + VIP +D+ G VV+ V E + GDPV A + GA L +D+ A GDR Sbjct: 4 AIRVIPCLDVDAGRVVKGVNFENLRDA--GDPVELAGTYDAGGADELTFLDVT-ASSGDR 60 Query: 67 MNA-TAVDAIIDAVDIPVQLGGGIRTANDAASLLDRGVNRVILGTAAVENPDLVAELAES 125 V D V IP+ +GGG+RT +D +LL G ++V + TAA+ P+L+ E+AE Sbjct: 61 ETTYDVVRRTADQVFIPLTVGGGVRTTDDVDTLLRAGADKVGVNTAAIARPELIGEIAER 120 Query: 126 YPGRIIVSLDA-----ADG--------EVVVSGWTESTGIDPAVAAARFADYGACGILFT 172 + GR ++ L A DG EV G TGID R A GA IL Sbjct: 121 F-GRQVLVLSADVRRVRDGDEPTPSGFEVTTHGGRRGTGIDALEWCERAAALGAGEILLN 179 Query: 173 DVDVEGKLAGIQSSVTARVIDAVDIPVIASGGVASLDDIQTLHTTGAAATVVGTALYENK 232 +D +G G + V VD+P+IASGG +++ GA A + T + + Sbjct: 180 SMDADGTKEGFDLELIRAVRARVDVPLIASGGAGAVEHFVPAVAAGADAVLAATVFHFGE 239 Query: 233 FTLAD 237 FT+AD Sbjct: 240 FTIAD 244 Lambda K H 0.316 0.133 0.375 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: 188 Number of extensions: 15 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: 245 Length of database: 257 Length adjustment: 24 Effective length of query: 221 Effective length of database: 233 Effective search space: 51493 Effective search space used: 51493 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