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:Q9HN14 (242 letters) >FitnessBrowser__psRCH2:GFF156 Length = 256 Score = 129 bits (324), Expect = 6e-35 Identities = 81/242 (33%), Positives = 132/242 (54%), Gaps = 13/242 (5%) Query: 8 VLPAVDMQDGQVVQLVQGERGTERTYGDPVDAATDWVAAGAEALHLVDLDGAFEGARANA 67 ++P +D+ +G+VV+ VQ E R GDPV+ A + GA+ + +D+ + + Sbjct: 7 IIPCLDVDNGRVVKGVQFEN--IRDAGDPVEIARRYDEQGADEITFLDITASVDNRDTTL 64 Query: 68 TAVEDILDATDVSVQVGGGIRSAEDATALLDRGVDRVILGTAAIETPDIVGEIAAAY-SD 126 VE + + + VGGG+RS +D LL+ G D+V + TAA+ PD VGE A + S Sbjct: 65 HTVERMASQVFIPLTVGGGVRSVQDIRNLLNAGADKVSINTAAVFNPDFVGEAADRFGSQ 124 Query: 127 GVLVSLDAKD---------GEVVVEGWTEGTGMDPVAAAQRYADLGAAGILFTDVDVEGK 177 ++V++DAK E+ G + TG+D VA A++ DLGA IL T +D +G Sbjct: 125 CIVVAIDAKKVSAPGEPGRWEIFTHGGRKPTGLDAVAWAKKMEDLGAGEILLTSMDQDGV 184 Query: 178 QEGVRTDPVRDLVDSVDIPVIASGGVATVDDVRALEAAGAAGAVVGTALYE-GNFTLADA 236 + G R + +++ IPVIASGGV + + G A AV+ +++ G +T+ +A Sbjct: 185 KSGYDLGVTRAISEALCIPVIASGGVGNLQHLADGILEGKADAVLAASIFHFGEYTIPEA 244 Query: 237 QA 238 +A Sbjct: 245 KA 246 Lambda K H 0.314 0.133 0.369 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: 174 Number of extensions: 13 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: 242 Length of database: 256 Length adjustment: 24 Effective length of query: 218 Effective length of database: 232 Effective search space: 50576 Effective search space used: 50576 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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