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 GFF156 Psest_0156 imidazoleglycerol phosphate synthase, cyclase subunit
Query= curated2:Q18DL2 (245 letters) >FitnessBrowser__psRCH2:GFF156 Length = 256 Score = 124 bits (311), Expect = 2e-33 Identities = 80/240 (33%), Positives = 131/240 (54%), Gaps = 13/240 (5%) Query: 10 VIPAVDMQDGDVVQLVQGERGTETRYGDPVVAAKQWVEAGAKTLHLVDLDGAFEGDRMNA 69 +IP +D+ +G VV+ VQ E + GDPV A+++ E GA + +D+ + + Sbjct: 7 IIPCLDVDNGRVVKGVQFENIRDA--GDPVEIARRYDEQGADEITFLDITASVDNRDTTL 64 Query: 70 TAVDAIIDAVDIPVQLGGGIRTANDAASLLDRGVNRVILGTAAVENPDLVAELAESYPGR 129 V+ + V IP+ +GGG+R+ D +LL+ G ++V + TAAV NPD V E A+ + + Sbjct: 65 HTVERMASQVFIPLTVGGGVRSVQDIRNLLNAGADKVSINTAAVFNPDFVGEAADRFGSQ 124 Query: 130 -IIVSLDA----ADG-----EVVVSGWTESTGIDPAVAAARFADYGACGILFTDVDVEGK 179 I+V++DA A G E+ G + TG+D A + D GA IL T +D +G Sbjct: 125 CIVVAIDAKKVSAPGEPGRWEIFTHGGRKPTGLDAVAWAKKMEDLGAGEILLTSMDQDGV 184 Query: 180 LAGIQSSVTARVIDAVDIPVIASGGVASLDDIQTLHTTGAAATVVGTALYE-NKFTLADA 238 +G VT + +A+ IPVIASGGV +L + G A V+ +++ ++T+ +A Sbjct: 185 KSGYDLGVTRAISEALCIPVIASGGVGNLQHLADGILEGKADAVLAASIFHFGEYTIPEA 244 Score = 45.4 bits (106), Expect = 1e-09 Identities = 35/114 (30%), Positives = 48/114 (42%), Gaps = 2/114 (1%) Query: 129 RIIVSLDAADGEVVVSGWTEST--GIDPAVAAARFADYGACGILFTDVDVEGKLAGIQSS 186 RII LD +G VV E+ DP A R+ + GA I F D+ Sbjct: 6 RIIPCLDVDNGRVVKGVQFENIRDAGDPVEIARRYDEQGADEITFLDITASVDNRDTTLH 65 Query: 187 VTARVIDAVDIPVIASGGVASLDDIQTLHTTGAAATVVGTALYENKFTLADAME 240 R+ V IP+ GGV S+ DI+ L GA + TA N + +A + Sbjct: 66 TVERMASQVFIPLTVGGGVRSVQDIRNLLNAGADKVSINTAAVFNPDFVGEAAD 119 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: 144 Number of extensions: 10 Number of successful extensions: 4 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: 256 Length adjustment: 24 Effective length of query: 221 Effective length of database: 232 Effective search space: 51272 Effective search space used: 51272 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 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