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_093428505.1 BM272_RS09255 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
Query= curated2:A4YI34 (251 letters) >NCBI__GCF_900112605.1:WP_093428505.1 Length = 249 Score = 100 bits (248), Expect = 4e-26 Identities = 72/235 (30%), Positives = 113/235 (48%), Gaps = 26/235 (11%) Query: 6 IIACLDVKDGKVVKGVR--FLDLKLKGD-PAELASRYEEEGADEIVFLDISATVEGRKTL 62 II +D++DG+ V+ + D + GD PA +A R+ +EGA + +D+ V G Sbjct: 3 IIPAIDIQDGRCVRLRQGDLADATVYGDDPAVMADRWVDEGARRLHLVDLDGAVAGTPRN 62 Query: 63 LEKVRET-ASVLSIPLTVGGGVRTVEDVSNLLSNGADKVSLNTVAAENPSVVSMASREFG 121 + +R A+ +P VGGG+R E + L G +V + T A +P V R+F Sbjct: 63 ADIIRRIRANHPELPTQVGGGIRDAETAAGYLEAGVGRVIIGTRAVADPDFVGDLCRDFP 122 Query: 122 AQAVVVAIDAKR---VGNGWRVFVRSGTKDTGLDAVDWAKRVEEMGAGEILLTSIDRDGT 178 + V+V +DA+ +GW + + +D A+R E G I+ T I RDG Sbjct: 123 GR-VIVGLDARDGLVATDGWE-------QTSQWSVIDLARRFEGDGVAAIIYTDIGRDGM 174 Query: 179 RDGYDLELTKAVVRATKVPVIASGGAGKPDHFLSVFRQAGADAALAAGIFHDGVI 233 G LE T A+ RAT++P+IASGG + D G+ DG++ Sbjct: 175 LAGLALEETAALARATEIPIIASGGVSSLE-----------DIRALCGVAEDGIV 218 Lambda K H 0.317 0.135 0.374 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: 180 Number of extensions: 12 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: 251 Length of database: 249 Length adjustment: 24 Effective length of query: 227 Effective length of database: 225 Effective search space: 51075 Effective search space used: 51075 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 (21.6 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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