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_013460753.1 SULKU_RS09510 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
Query= curated2:A4YI34 (251 letters) >NCBI__GCF_000183725.1:WP_013460753.1 Length = 232 Score = 100 bits (249), Expect = 3e-26 Identities = 62/233 (26%), Positives = 109/233 (46%), Gaps = 10/233 (4%) Query: 6 IIACLDVKDGKVVKGVRFL--DLKLKGD-PAELASRYEEEGADEIVFLDISATVEGRKTL 62 I +D+KDGK V+ + L K+ D P EL +EE GA + +D++ G Sbjct: 3 IFPAIDLKDGKAVRLTKGLMESAKIYSDTPWELVKTFEEMGAKWVHLVDLNGAFAGEPKN 62 Query: 63 LEKVRETASVLSIPLTVGGGVRTVEDVSNLLSNGADKVSLNTVAAENPSVVSMASREFGA 122 LE++R ++ L +GGG+R + L G D++ L ++A +P V + ++ Sbjct: 63 LEQIRAIRENCNVKLQLGGGIRDEATIQRYLELGIDRLILGSIALRDPEFVKSMAAKYPI 122 Query: 123 QAVVVAIDAKRVGNGWRVFVRSGTKDTGLDAVDWAKRVEEMGAGEILLTSIDRDGTRDGY 182 + AID GW + + + A D A+ + G I+ T + RDGT G Sbjct: 123 VVGIDAIDGYVAVEGW-------GEVSSMRATDLARAFADAGVEAIICTDVGRDGTLSGV 175 Query: 183 DLELTKAVVRATKVPVIASGGAGKPDHFLSVFRQAGADAALAAGIFHDGVIRI 235 +++ T + RA+ +P IASGG +++ + + F++G I + Sbjct: 176 NVDFTLEIARASGIPTIASGGVKDDSDIVALQKSGEVSGVIIGKAFYEGRINL 228 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: 149 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: 251 Length of database: 232 Length adjustment: 23 Effective length of query: 228 Effective length of database: 209 Effective search space: 47652 Effective search space used: 47652 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 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