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 7024671 Shewana3_1849 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase (RefSeq)
Query= curated2:B2A6X0 (251 letters) >FitnessBrowser__ANA3:7024671 Length = 245 Score = 97.1 bits (240), Expect = 3e-25 Identities = 72/239 (30%), Positives = 113/239 (47%), Gaps = 10/239 (4%) Query: 6 IIPCLDVKDGQVVK---GVKFNELKLAGDPVELAQKYDREGADELVFLDITASIEDRGTM 62 IIP +D+ DGQ+V+ G + P Q Y +GA L +D+T + E Sbjct: 2 IIPAIDLIDGQIVRLYQGDYGQQTTFDLSPQTQLQSYQDQGASWLHIVDLTGAKEPAKRQ 61 Query: 63 LEVVEKTAKNVFIPFTVGGGIKTVDDMRRLLQAGADKVSINSAAVKNPELISQGSDRFGS 122 ++ K + VGGGI+T + + LL G +V I S AVK PEL+ ++FGS Sbjct: 62 TALIAKLTAGLNANIQVGGGIRTEEQVAELLSLGVKRVVIGSLAVKEPELVKGWFNKFGS 121 Query: 123 QCIVVAIDTKKTEEGYQ-VFINGGTKNTGIPLMDWVKEVKYRGAGEILLTSIDHDGGKNG 181 + I +A+D + G + V ++G G L V++ G L+T I+ DG G Sbjct: 122 EAICLALDVNINQNGEKIVAVSGWQSGGGKSLESIVEDFSQVGLKHALVTDINRDGTLTG 181 Query: 182 YDNDIINQVARVSNIPVI---ASGGAGTIEDFYNVFHKGQASGALAASVFHFEEISVKE 237 + + +++ S+ P I ASGG T+ED V G A+G + + +V E Sbjct: 182 ANTALYRELS--SHYPHIAWQASGGIATLEDVAAVRDSG-AAGIIIGKALLINQFNVAE 237 Lambda K H 0.316 0.137 0.383 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: 147 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: 251 Length of database: 245 Length adjustment: 24 Effective length of query: 227 Effective length of database: 221 Effective search space: 50167 Effective search space used: 50167 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 09 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