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 AO356_09800 AO356_09800 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
Query= curated2:Q0A5D3 (265 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_09800 Length = 245 Score = 99.8 bits (247), Expect = 5e-26 Identities = 76/247 (30%), Positives = 121/247 (48%), Gaps = 20/247 (8%) Query: 7 IIPCLDVDGGRVVKGVKFVDIRDA----GDPVEIARRYDAMGADEITFLDITASHERRDT 62 IIP +D+ G V+ ++ + D+ DPV +A ++ G + +D+ + E + Sbjct: 3 IIPAIDLKDGACVR-LRQGRMEDSTVFSDDPVSMAAKWVEGGCRRLHLVDLNGAFEGQPV 61 Query: 63 MVQVVEKVASQV-FIPLTVGGGIREVADIRRMLNAGADKVGINTAAVARPEFVAEAAERF 121 +VV +A + +P+ +GGGIR + I + AG V I T AV PEFVAEA F Sbjct: 62 NGEVVTAIAKRYPNLPIQIGGGIRSLETIEHYVKAGVSYVIIGTKAVKEPEFVAEACRAF 121 Query: 122 GSQCIVVAVDAKQVSRADEPARWEVFTHGGRKATGLDAVEWAGRMAELGAGEILLTSMDR 181 + ++V +DAK V T G + + + ++ A R G I+ T + + Sbjct: 122 PGK-VIVGLDAKD---------GFVATDGWAEVSTVQVIDLAKRFEADGVSAIVYTDIAK 171 Query: 182 DGTQAGFDLALTRAVSDAVPVPVIASGGVGTLSD---LADGVLEGGADAVLAASIFHFGR 238 DG G ++ T A++ A +PVIASGG+ L D L D G A+ +I+ G Sbjct: 172 DGMMQGCNVPFTAALAAATKIPVIASGGIHNLGDIKALLDAKAPGIIGAITGRAIYE-GT 230 Query: 239 YTVAEAK 245 VAEA+ Sbjct: 231 LDVAEAQ 237 Lambda K H 0.320 0.136 0.388 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: 166 Number of extensions: 11 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: 265 Length of database: 245 Length adjustment: 24 Effective length of query: 241 Effective length of database: 221 Effective search space: 53261 Effective search space used: 53261 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 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