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_012402124.1 BPHY_RS14005 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase
Query= curated2:Q7W2X9 (269 letters) >NCBI__GCF_000020045.1:WP_012402124.1 Length = 250 Score = 103 bits (256), Expect = 5e-27 Identities = 75/237 (31%), Positives = 120/237 (50%), Gaps = 31/237 (13%) Query: 18 IIPCLDVTAGRVVKGVNFVNLTDAG----DPVEIARRYNEQGADELTFLDITATSDG--- 70 +IP +D+ G+ V+ + ++ A +P +AR + ++GA L +D+ G Sbjct: 3 LIPAIDLKDGQCVR-LKQGDMDQATIFHEEPAVMARHWVDRGARRLHLVDLNGAFAGKPK 61 Query: 71 -HDLILPIIEQVASQVFIPLTVGGGVRQVSDVQRLLNAGADKISINSAAVANPELVRAAA 129 D I IIE+V + IP+ +GGG+R ++ ++R L+ G + + I +AAV NP + A Sbjct: 62 NEDAIRAIIEEVGGE--IPVQLGGGIRDLNTIERYLDDGLEYVIIGTAAVKNPGFLLEAC 119 Query: 130 DYHGSQCIVVAIDARRSSAEGEPARWEVFTHGGRKATGLDAVAWARRMAAYGAGEILLTS 189 G I+V +DA+ +V T G K TG + AR+ YG I+ T Sbjct: 120 TAFGGH-IIVGLDAKDG---------KVATDGWSKLTGHEVADLARKFEDYGCESIIYTD 169 Query: 190 MDRDGTKSGFDLELTRAVSDAVPVPVIASGGVGNLQHL----------ADGVTTGRA 236 + RDG G ++E T ++ AV +PVIASGG+ NL + +GV GRA Sbjct: 170 IGRDGMLQGINIEATVRLARAVKIPVIASGGLSNLGDIEALCEVEDEGIEGVICGRA 226 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: 185 Number of extensions: 12 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: 269 Length of database: 250 Length adjustment: 24 Effective length of query: 245 Effective length of database: 226 Effective search space: 55370 Effective search space used: 55370 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