Align Imidazole glycerol phosphate synthase subunit HisF; EC 4.3.2.10; IGP synthase cyclase subunit; IGP synthase subunit HisF; ImGP synthase subunit HisF; IGPS subunit HisF (uncharacterized)
to candidate 201226 SO2069 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (NCBI ptt file)
Query= curated2:Q03VY0 (254 letters) >FitnessBrowser__MR1:201226 Length = 245 Score = 83.6 bits (205), Expect = 4e-21 Identities = 68/214 (31%), Positives = 108/214 (50%), Gaps = 13/214 (6%) Query: 7 IVPALDIKNGRVVKGVNFVNLREVG---DPVESAKAYQAAGADELVFLDITATLEERDTI 63 I+PA+D+ +G+VV+ ++ P+ ++YQA A L +D+T + Sbjct: 2 IIPAIDLIDGKVVRLYQGDYGQQTTFDLSPLAQLQSYQAQDASWLHIVDLTGAKDPAKRQ 61 Query: 64 MSVVDAVSREVFIPLTVGGGIRTTEDMGRLIKAGADKIFVNSEAVKNPALITDGAKIFGS 123 +++ A++ + + VGGGIRT E + L+ G ++ + S AVK P L+ FG+ Sbjct: 62 TALIAALTAGLSANIQVGGGIRTEEQVAELLSLGVKRVVIGSLAVKEPELVKGWFNKFGN 121 Query: 124 QAIVGAIDAKWDESAGIYRVYVS----GGSKPTSLDAIEWAFELVARGAGELLVTSMDAD 179 +AI A+D S G V VS GG K +L++I F V G LVT + D Sbjct: 122 EAICLALDINITPS-GEKIVAVSGWQNGGGK--NLESIVEDFSQV--GLKHALVTDISRD 176 Query: 180 GTKKGYDIQLYDQLADAV-NVPVVASGGAGSTQD 212 GT G + +LY +L+ N+ ASGG S +D Sbjct: 177 GTLTGANTELYCELSSRYPNIAWQASGGIASLED 210 Lambda K H 0.317 0.135 0.376 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: 169 Number of extensions: 13 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: 1 Length of query: 254 Length of database: 245 Length adjustment: 24 Effective length of query: 230 Effective length of database: 221 Effective search space: 50830 Effective search space used: 50830 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 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