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_022948099.1 H035_RS0106015 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
Query= curated2:Q7W2X9 (269 letters) >NCBI__GCF_000421465.1:WP_022948099.1 Length = 243 Score = 92.0 bits (227), Expect = 1e-23 Identities = 70/235 (29%), Positives = 111/235 (47%), Gaps = 28/235 (11%) Query: 18 IIPCLDVTAGRVVK---GVNFVNLTDAGDPVEIARRYNEQGADELTFLDITATSDGHDLI 74 +IP +D+ AG+ V+ G + + DPV +ARR+ E GA L +D+ G Sbjct: 3 LIPAIDLKAGKCVRLRQGRMEDDTVFSDDPVAVARRWVEMGAKRLHLVDLDGAFAGKPRN 62 Query: 75 LPIIEQVASQVF--IPLTVGGGVRQVSDVQRLLNAGADKISINSAAVANPELVR-AAADY 131 +I + ++ F + + VGGG+R +Q L+AG + + AV P V A ++ Sbjct: 63 ADVIRAI-TEAFPEVAVQVGGGIRDGDTIQAYLDAGVQYAILGTRAVTAPHFVEDMAMEF 121 Query: 132 HGSQCIVVAIDARRSSAEGEPARWEVFTHGGRKATGLDAVAWARRMAAYGAGEILLTSMD 191 G I+V +DA+ V G K + D + ARR G I+ T + Sbjct: 122 PGH--IIVGLDAKEG---------RVAIDGWSKLSRHDVIDLARRFEDEGVEAIIYTDIS 170 Query: 192 RDGTKSGFDLELTRAVSDAVPVPVIASGGVGNLQHLAD----------GVTTGRA 236 RDG G ++E T +++A+ +PVIASGG+ +L + G TGRA Sbjct: 171 RDGMLQGVNVEATARLAEAIQIPVIASGGIRSLDDVRSVGKIAENGVIGAITGRA 225 Lambda K H 0.319 0.133 0.382 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: 173 Number of extensions: 13 Number of successful extensions: 5 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: 269 Length of database: 243 Length adjustment: 24 Effective length of query: 245 Effective length of database: 219 Effective search space: 53655 Effective search space used: 53655 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 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