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 CA265_RS03610 CA265_RS03610 imidazole glycerol phosphate synthase subunit HisF
Query= curated2:Q18DL2 (245 letters) >FitnessBrowser__Pedo557:CA265_RS03610 Length = 379 Score = 98.6 bits (244), Expect = 2e-25 Identities = 64/208 (30%), Positives = 115/208 (55%), Gaps = 9/208 (4%) Query: 7 SFEVIPAVDMQDGDVVQLVQGERGTETR-YGDPVVAAKQWVEAGAKTLHLVDLDGAFEGD 65 S +IP +D++DG + V+G + R GDPV A Q+ + GA L +D+ E Sbjct: 131 SKRIIPCLDVKDG---RTVKGVNFVDLRDAGDPVELAAQYAQQGADELVFLDITATHERR 187 Query: 66 RMNATAVDAIIDAVDIPVQLGGGIRTANDAASLLDRGVNRVILGTAAVENPDLVAELAES 125 + V ++ ++IP +GGGI DA +LL+ G +++ + +AAV NP L+ +LA++ Sbjct: 188 KTMIEMVKSVARQLNIPFTIGGGITEIADAEALLNAGADKISINSAAVRNPKLIEDLAKT 247 Query: 126 YPGR-IIVSLDA--ADGE--VVVSGWTESTGIDPAVAAARFADYGACGILFTDVDVEGKL 180 + + +++++D DG+ V ++G T ++ + D GA IL T +D +G Sbjct: 248 FGVQFVVLAVDTKYVDGKNMVHLNGGRLITELETENWIKQAEDLGAGEILLTSMDHDGTK 307 Query: 181 AGIQSSVTARVIDAVDIPVIASGGVASL 208 AG + ++V ++IP+IASGG ++ Sbjct: 308 AGFDCGLLSKVNQMINIPIIASGGAGNM 335 Score = 42.0 bits (97), Expect = 2e-08 Identities = 30/111 (27%), Positives = 46/111 (41%), Gaps = 2/111 (1%) Query: 129 RIIVSLDAADGEVV--VSGWTESTGIDPAVAAARFADYGACGILFTDVDVEGKLAGIQSS 186 RII LD DG V V+ DP AA++A GA ++F D+ + Sbjct: 133 RIIPCLDVKDGRTVKGVNFVDLRDAGDPVELAAQYAQQGADELVFLDITATHERRKTMIE 192 Query: 187 VTARVIDAVDIPVIASGGVASLDDIQTLHTTGAAATVVGTALYENKFTLAD 237 + V ++IP GG+ + D + L GA + +A N + D Sbjct: 193 MVKSVARQLNIPFTIGGGITEIADAEALLNAGADKISINSAAVRNPKLIED 243 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: 194 Number of extensions: 11 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 245 Length of database: 379 Length adjustment: 27 Effective length of query: 218 Effective length of database: 352 Effective search space: 76736 Effective search space used: 76736 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: 48 (23.1 bits)
This GapMind analysis is from Apr 09 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