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_012673675.1 SULAZ_RS07265 imidazole glycerol phosphate synthase subunit HisF
Query= curated2:Q0W0J3 (240 letters) >NCBI__GCF_000021545.1:WP_012673675.1 Length = 252 Score = 125 bits (315), Expect = 6e-34 Identities = 77/231 (33%), Positives = 127/231 (54%), Gaps = 16/231 (6%) Query: 5 VIPAIDLKGGKCVQLVQGVPGTEMVSIDDAVEVAAGWVGQGAKTLHIIDLDGAFSGSRKN 64 +IP +D+ G+ +V+GV ++ D VE+AA + +GA + +D+ + S ++ Sbjct: 6 IIPCLDVNKGR---VVKGVNFVNLIDAGDPVEIAAAYDKEGADEIVFLDI----TASAED 58 Query: 65 AYIMEDIVSKFDVDV----QVGGGIRDYETAKYLLSLGIDRVILGTAAIKNPDLVRQLAD 120 I+ D+V K V VGGG+R E + LL G D+V + TAA+KNP LV A Sbjct: 59 RNIILDVVKKTAETVFMPLTVGGGVRSLEDIRKLLENGADKVSINTAAVKNPSLVESAAV 118 Query: 121 EFGSETVMVSLDSK-----QGEVVIEGWTESSGKTTNEMGKFFSEIGAGSILYTNVDVEG 175 FGS T++V++D+K + EV I G +G + K ++GAG IL T++D +G Sbjct: 119 RFGSSTIVVAIDAKKVSESKWEVYINGGRTPTGIDAVQWAKAVEDLGAGEILLTSMDKDG 178 Query: 176 LLKGVNEDPVRSLVNSVTIPVIASGGVAKIDDLVKIKNTGAAGVVVGSALY 226 G + + +++ +V IPVIASGG K +D ++ G A + ++L+ Sbjct: 179 TKSGYDIELTKAVSQAVKIPVIASGGAGKKEDFYQVFEEGKADAALAASLF 229 Lambda K H 0.315 0.136 0.378 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: 160 Number of extensions: 6 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: 240 Length of database: 252 Length adjustment: 24 Effective length of query: 216 Effective length of database: 228 Effective search space: 49248 Effective search space used: 49248 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: 42 (22.0 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