Align imidazole glycerol-phosphate synthase (subunit 2/2) (EC 4.3.2.10) (characterized)
to candidate WP_011973909.1 MAEO_RS06090 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
Query= BRENDA::Q8ZY16 (253 letters) >NCBI__GCF_000017185.1:WP_011973909.1 Length = 241 Score = 141 bits (355), Expect = 1e-38 Identities = 81/241 (33%), Positives = 145/241 (60%), Gaps = 6/241 (2%) Query: 7 IIPCLDIDGKAGV-VVKGVNFQGIREVGDPVEMAVRYEEEGADEIAILDITAAPEGRATF 65 +IP +DI K V +++G + E+ +P+E+A ++ + GA+ I ++D+ +A G T Sbjct: 3 VIPAVDIKNKKCVQLIQGNPDKKHIELDNPLEVAEKWIKCGAEMIHLVDLDSAIYGTDTN 62 Query: 66 IDSVKRVAEAVSIPVLVGGGVRSLEDATTLFRAGADKVSVNTAAVRNPQLVA-LLAREFG 124 +++K++ E+V +PV VGGGVR++EDA L GA++V + T+AV+NP+++ LL + Sbjct: 63 KETIKKIIESVPVPVEVGGGVRTVEDALNLIDLGAERVILGTSAVKNPEIITELLEKGIN 122 Query: 125 SQSTVVAIDAKWNGEYYEVYVKGGREATGLDAVKWAKEVEELGAGEILLTSIDRDGTGLG 184 S+ +VA+DAK +V +KG E T ++ K +EE GAG IL T++D +G G Sbjct: 123 SEKIMVALDAKDG----KVVIKGWMEKTEYTPIEIGKILEEKGAGSILFTNVDVEGLLDG 178 Query: 185 YDVELIRRVADSVRIPVIASGGAGRVEHFYEAAAAGADAVLAASLFHFRVLSIAQVKRYL 244 D+E ++++ D + IP+IASGG + + G D V+ S + ++ + + + + Sbjct: 179 IDIEPVKKLVDELNIPIIASGGITTYDDLLKLKEIGVDGVVVGSAIYKEMMDLKKAIKIV 238 Query: 245 K 245 K Sbjct: 239 K 239 Lambda K H 0.318 0.137 0.381 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: 192 Number of extensions: 16 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: 253 Length of database: 241 Length adjustment: 24 Effective length of query: 229 Effective length of database: 217 Effective search space: 49693 Effective search space used: 49693 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 (21.7 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