Align imidazole glycerol-phosphate synthase (subunit 2/2) (EC 4.3.2.10) (characterized)
to candidate Ga0059261_3125 Ga0059261_3125 Imidazoleglycerol-phosphate synthase
Query= BRENDA::Q5NMD6 (255 letters) >FitnessBrowser__Korea:Ga0059261_3125 Length = 260 Score = 168 bits (426), Expect = 9e-47 Identities = 93/232 (40%), Positives = 132/232 (56%), Gaps = 3/232 (1%) Query: 6 RIIPCLDVADGRVVKGVNFTDLMDAGDPVEQAKVYDAAGADELCFLDISASHEGRGTMLD 65 RIIPCL + DG +VK V F D GDP+ ++++ DEL +I A+ GR Sbjct: 5 RIIPCLLIKDGGLVKTVKFGDAKYVGDPINAVRIFNEKQVDELIVANIDATVHGREPDYA 64 Query: 66 VVARTAEVCFMPLTVGGGVRQVEDARALLLAGADKVAVNSAAVARPELVAEIADRFGAQC 125 V+A A C MPL GGVR E ++ G +KV ++S A+ RPE+++E A R GAQ Sbjct: 65 VIANLAAECRMPLCYSGGVRTAEQVDRIISLGVEKVGISSGAIERPEMISEAARRVGAQS 124 Query: 126 VVAAIDARRNG--DHWEVYTHGGRRPTGINALDHALNLTRLGAGEILLTSMDKDGTRDGY 183 +VA +D +R G +E+ TH G R TG+ D A LGAGEIL+ S+D+DG GY Sbjct: 125 IVAVMDVKRTGLLKGYELVTHNGTRRTGLKPADWARKAQELGAGEILVNSVDRDGGMQGY 184 Query: 184 DLELTRLVADSVPVPVIASGGVGNLDHMVEGVTKGHASALLAASIFHF-GQY 234 DL+L + V +V VP+ GG G+L + + + + A S+F F G+Y Sbjct: 185 DLDLAQQVRSAVGVPITVLGGAGSLADIEAVLRRFGVIGVSAGSLFVFKGKY 236 Lambda K H 0.320 0.136 0.400 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: 214 Number of extensions: 9 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: 255 Length of database: 260 Length adjustment: 24 Effective length of query: 231 Effective length of database: 236 Effective search space: 54516 Effective search space used: 54516 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 47 (22.7 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