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 Pf6N2E2_3839 Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (EC 5.3.1.16)
Query= curated2:Q7UKJ9 (262 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3839 Length = 245 Score = 102 bits (253), Expect = 1e-26 Identities = 69/222 (31%), Positives = 116/222 (52%), Gaps = 16/222 (7%) Query: 9 CLDVHGGRVVKGTNFVNLRDAGDPVEVARRYEAEGADELVFLDITASHEERAILLDVVRR 68 C+ + GR+ T F + DPV +A ++ G L +D+ + E + + +VV Sbjct: 14 CVRLRQGRMEDSTVF-----SDDPVSMAAKWVEGGCRRLHLVDLNGAFEGQPVNGEVVTA 68 Query: 69 TAEQV-FMPLTVGGGVRTVEDVRALLSAGCDKVSINSSAVTNPDFIRQAADRFGRQCIVV 127 A++ +P+ +GGG+R++E + + AG V I + AV P+F+ +A F + ++V Sbjct: 69 IAKRYPNLPIQIGGGIRSLETIEHYVKAGVSYVIIGTKAVKEPEFVAEACRAFPGK-VIV 127 Query: 128 NIDPKRVQKDGEEFWEVHINGGRKPTGLQAVQWAKRVEELGAGEIVLTSMDADGTCDGYD 187 +D K DG V +G + + +Q + AKR E G IV T + DG G + Sbjct: 128 GLDAK----DGF----VATDGWAEVSTVQVIDLAKRFEADGVSAIVYTDIAKDGMMQGCN 179 Query: 188 IPITRAVSEAVRIPVVASGGAGNPDHLVEAIRDGKADAVLAA 229 +P T A++ A RIPV+ASGG N ++A+ D KA ++ A Sbjct: 180 VPFTAALAAATRIPVIASGGIHNLGD-IKALLDAKAPGIIGA 220 Lambda K H 0.320 0.137 0.404 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: 186 Number of extensions: 7 Number of successful extensions: 3 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: 262 Length of database: 245 Length adjustment: 24 Effective length of query: 238 Effective length of database: 221 Effective search space: 52598 Effective search space used: 52598 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: 46 (22.3 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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