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_011802492.1 PNAP_RS15615 imidazole glycerol phosphate synthase cyclase subunit
Query= curated2:A8AY24 (252 letters) >NCBI__GCF_000015505.1:WP_011802492.1 Length = 253 Score = 170 bits (431), Expect = 2e-47 Identities = 93/231 (40%), Positives = 141/231 (61%), Gaps = 1/231 (0%) Query: 1 MLKKRIIPCLDVKDGRVVKGINFVNLTDVGDPVDASKAYYEAGCDELVFLDITATHEERD 60 MLK R+IPCL +K+G +VK F + VGDP++ + + + DEL+ LDI A+ +R+ Sbjct: 1 MLKHRVIPCLLLKNGGLVKTKKFQDPKYVGDPINVIRIFNDKEVDELIVLDIEASKAQRE 60 Query: 61 TTIEMVRRVAEQVFIPFTVGGGIRTVEDMKRMLQAGADKVAVNSSALANPQLLADCAEKF 120 E++ + A + F+P GGGI TVE KR+ G +KV + + ALA+ QL+ D A+++ Sbjct: 61 PNYELIEQFAGECFMPLCYGGGISTVEQAKRLFTLGVEKVCIQTWALADLQLVRDIADRY 120 Query: 121 GSQCVVLAVDAKKEADGSWHVYLAGGRKDSGRELLDWVQEAVGLGAGEILLTSMDKDGTK 180 GSQ VV++VD KK S +Y + K D++ +AV GAGEI+LT++D+DGT Sbjct: 121 GSQSVVVSVDIKKNLFASHRLYASSTGKMLDLPWQDFLNKAVAAGAGEIMLTAVDRDGTL 180 Query: 181 SGFDLPMLEAVSQVVSVPIIASGGAGSSQHILEVFEKTA-ATGALAASIFH 230 +G DL ++ A SQ +P+IA+GGA + + + A A A A IFH Sbjct: 181 AGMDLALIHAASQSCPIPLIAAGGAATLSDLRAAVDAGASAIAAGAMFIFH 231 Lambda K H 0.317 0.134 0.378 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: 169 Number of extensions: 9 Number of successful extensions: 2 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: 252 Length of database: 253 Length adjustment: 24 Effective length of query: 228 Effective length of database: 229 Effective search space: 52212 Effective search space used: 52212 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: 46 (22.3 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