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 WP_004307342.1 C665_RS09715 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
Query= curated2:A4YI34 (251 letters) >NCBI__GCF_000310185.1:WP_004307342.1 Length = 249 Score = 104 bits (259), Expect = 2e-27 Identities = 65/203 (32%), Positives = 104/203 (51%), Gaps = 10/203 (4%) Query: 6 IIACLDVKDGKVVK---GVRFLDLKLKGDPAELASRYEEEGADEIVFLDISATVEGRKTL 62 +I +D+KDG+ V+ G DP +A + E GA + +D++ G+ Sbjct: 3 LIPAIDLKDGQCVRLKQGEMDDATVFSSDPGAMARHWLEAGARRLHLVDLNGAFAGKPKN 62 Query: 63 LEKVRETASVLS--IPLTVGGGVRTVEDVSNLLSNGADKVSLNTVAAENPSVVSMASREF 120 +R V+ IP+ +GGG+R ++ + + L NG V + T A +NP + A F Sbjct: 63 GAAIRSITDVVGDDIPVQLGGGIRDLDTIEHYLDNGISYVIIGTAAVKNPGFLHDACSAF 122 Query: 121 GAQAVVVAIDAKRVGNGWRVFVRSGTKDTGLDAVDWAKRVEEMGAGEILLTSIDRDGTRD 180 ++V +DAK +V V +K TG D VD A++ E+ G ++ T I RDG Sbjct: 123 PGH-IIVGLDAK----DGKVAVDGWSKLTGHDVVDLARKFEDYGVESVIYTDIGRDGMLS 177 Query: 181 GYDLELTKAVVRATKVPVIASGG 203 G ++E T + RA ++PVIASGG Sbjct: 178 GVNIEATVRLARALRIPVIASGG 200 Score = 42.4 bits (98), Expect = 9e-09 Identities = 34/94 (36%), Positives = 48/94 (51%), Gaps = 16/94 (17%) Query: 6 IIACLDVKDGKV-VKGVRFLDLKLKG-DPAELASRYEEEGADEIVFLDISATVEGRKTLL 63 II LD KDGKV V G KL G D +LA ++E+ G + +++ DI GR +L Sbjct: 126 IIVGLDAKDGKVAVDGWS----KLTGHDVVDLARKFEDYGVESVIYTDI-----GRDGML 176 Query: 64 EKVRETASV-----LSIPLTVGGGVRTVEDVSNL 92 V A+V L IP+ GG+ + D+ L Sbjct: 177 SGVNIEATVRLARALRIPVIASGGITDLRDIDAL 210 Lambda K H 0.317 0.135 0.374 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: 170 Number of extensions: 12 Number of successful extensions: 3 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: 251 Length of database: 249 Length adjustment: 24 Effective length of query: 227 Effective length of database: 225 Effective search space: 51075 Effective search space used: 51075 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 10 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