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_011613118.1 TERY_RS17895 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase
Query= curated2:C4L176 (255 letters) >NCBI__GCF_000014265.1:WP_011613118.1 Length = 257 Score = 112 bits (280), Expect = 8e-30 Identities = 69/212 (32%), Positives = 118/212 (55%), Gaps = 8/212 (3%) Query: 6 IIPCLDVKEGRVVKGIE--FVQLRDIGD-PVEIAKYYDESGADELVFLDITASTERRQTM 62 IIP +D+ GR V+ + + Q + D PV++AK + + GA +L +D+ A+ + Sbjct: 3 IIPAIDILGGRCVRLYQGDYKQTQIFNDNPVDVAKRWADEGATKLHLVDLDAAKVGQPVN 62 Query: 63 LDVVSAVARKVFIPLTVGGGIRSLEDISSLLKAGADKVSLNTLAVESPSLIREAADRFGS 122 + A+ + V IP+ VGGG+R+ ++SLL G + L T+A+E P L+ + +F Sbjct: 63 QKTIEAIIKAVDIPIQVGGGLRNYSTVASLLALGVQQAILGTVAIEQPELVSDFCQKFPG 122 Query: 123 QCIVVAIDVKFKDGEYYVYTYGGKQKTDLLAVEWAKQVAALGAGELLVTSMNQDGKQSGY 182 Q I+V ID +DG+ V T G + + +LA + A Q+A L ++ T +++DG G Sbjct: 123 Q-IIVGIDA--RDGK--VATKGWLETSQVLATDLALQMAKLKVAAIIYTDIHRDGTLKGP 177 Query: 183 DLSILEQLREVVDIPIIASGGAGNAEHVVEAL 214 ++ L +L V IP+IASGG + ++ L Sbjct: 178 NIEALRELATAVSIPVIASGGISSINDLLNLL 209 Lambda K H 0.318 0.135 0.373 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: 157 Number of extensions: 9 Number of successful extensions: 4 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: 255 Length of database: 257 Length adjustment: 24 Effective length of query: 231 Effective length of database: 233 Effective search space: 53823 Effective search space used: 53823 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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