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_066920093.1 ACG33_RS07630 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
Query= curated2:Q7W2X9 (269 letters) >NCBI__GCF_001579945.1:WP_066920093.1 Length = 252 Score = 76.3 bits (186), Expect = 6e-19 Identities = 68/210 (32%), Positives = 98/210 (46%), Gaps = 12/210 (5%) Query: 18 IIPCLDVTAGRVV---KGVNFVNLTDAGDPVEIARRYNEQGADELTFLDITATSDGHDLI 74 +IP +D+ GR V KG + DP + RY GA + +D+ DG Sbjct: 3 LIPAIDLRQGRCVRLFKGDFAAETVYSDDPSSVLERYLALGARHVHVVDLDGARDGTQAN 62 Query: 75 LPIIEQVASQVFIPLTVGGGVRQVSDVQRLLNAGADKISINSAAVANPELVRAAADYHGS 134 I +A+ V + L VGGG+R ++ V+ LL G ++ I S AV P V G Sbjct: 63 RDAIIAMAADVRVKLQVGGGLRSLARVRDLLEQGVERAVIGSLAVTAPGQVSEWMRELGP 122 Query: 135 QCIVVAIDARRSSAEGEPARWEVFTHGGRKATGLDAVAWARRMAAYGAG--EILLTSMDR 192 Q IV+A+D R A G P + THG + + + V W + AG +L T + R Sbjct: 123 QRIVLALDVRLDGA-GRPL---LTTHGWQHTS--EVVLWDVLESYLQAGLRHVLCTDIAR 176 Query: 193 DGTKSGFDLEL-TRAVSDAVPVPVIASGGV 221 DG +G +L L +AV + ASGGV Sbjct: 177 DGALNGPNLALYAQAVKRFPELQWQASGGV 206 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: 158 Number of extensions: 10 Number of successful extensions: 1 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: 252 Length adjustment: 24 Effective length of query: 245 Effective length of database: 228 Effective search space: 55860 Effective search space used: 55860 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