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 GFF3066 HP15_3010 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
Query= curated2:Q67KI0 (254 letters) >FitnessBrowser__Marino:GFF3066 Length = 245 Score = 108 bits (269), Expect = 1e-28 Identities = 71/243 (29%), Positives = 121/243 (49%), Gaps = 11/243 (4%) Query: 7 IIPCLDIRDGRVVKNVQFHLN--TWDAGDPVALAAEYDRQGADEIVFLDINASWEGRSAT 64 IIP +D++DG+ V+ Q ++ T DPV +A + GA + +D+N ++ G Sbjct: 3 IIPAIDLKDGKCVRLRQGRMDDSTVFGDDPVDMATRWVEAGARRLHLVDLNGAFAGEPVN 62 Query: 65 LDVLSRAAEQV-FVPLTIGGGVSAVEHVKAYLRAGADKVSVNTAAVQRPDLIDEIADLFG 123 +++ A + +P+ IGGG+ + E ++AYL+AG V + T AV+ P+ + E+ F Sbjct: 63 GEIVQAIARKYPDLPIQIGGGIRSAETIEAYLKAGVQWVIIGTKAVKEPEFVTEMCKKF- 121 Query: 124 SSTLVVAIDCKRRPEGGWEVYLHGGRTPTGIDAVAWAEEAARRGAGELLVTSMDADGTRQ 183 ++V +D K V G + + A A+ A G ++ T + DG Q Sbjct: 122 PGHIIVGLDAK-----DGRVATDGWAEVSEVMATDLAKRFANDGVDAIVYTDISRDGMMQ 176 Query: 184 GYDIALHQALADAVGVPVIASGGAGSPEDILEVLTVGRAD--AALAASIFHSGRHTVGEV 241 G ++ ALA+ G+PVIASGG + +D+ + TV A+ + G V E Sbjct: 177 GVNVEATAALAEEGGIPVIASGGVTNMDDLKRLATVADKGILGAITGRAIYEGTLDVAEA 236 Query: 242 KAF 244 +AF Sbjct: 237 QAF 239 Lambda K H 0.319 0.136 0.398 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: 177 Number of extensions: 11 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: 254 Length of database: 245 Length adjustment: 24 Effective length of query: 230 Effective length of database: 221 Effective search space: 50830 Effective search space used: 50830 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