Align Imidazoleglycerol-phosphate dehydratase; Short=IGPD; EC 4.2.1.19 (characterized, see rationale)
to candidate WP_013517771.1 ALIDE2_RS04150 imidazoleglycerol-phosphate dehydratase HisB
Query= uniprot:Q9HU41 (197 letters) >NCBI__GCF_000204645.1:WP_013517771.1 Length = 210 Score = 309 bits (791), Expect = 3e-89 Identities = 146/196 (74%), Positives = 166/196 (84%) Query: 2 AERKASVARDTLETQIKVSIDLDGTGKARFDTGVPFLDHMMDQIARHGLIDLDIECKGDL 61 A+R A V+R+T ET+I V ++LDGTG+A TG+ F DHM+DQIARHGLIDLD+ C GDL Sbjct: 15 ADRTAEVSRNTAETRISVRVNLDGTGQASLHTGIGFFDHMLDQIARHGLIDLDVRCDGDL 74 Query: 62 HIDDHHTVEDIGITLGQAFAKAIGDKKGIRRYGHAYVPLDEALSRVVIDFSGRPGLQMHV 121 HID HHTVED+GITLGQAFA+A+GDKKGIRRYGHAYVPLDEALSRVV+DFSGRPGL +H+ Sbjct: 75 HIDGHHTVEDVGITLGQAFARAVGDKKGIRRYGHAYVPLDEALSRVVVDFSGRPGLHLHI 134 Query: 122 PFTRASVGGFDVDLFMEFFQGFVNHAQVTLHIDNLRGHNTHHQIETVFKAFGRALRMAIE 181 PFT AS+GGFD L EFFQGFVNHA VTLHIDNL+G N HHQ ETVFKAF RALR A+E Sbjct: 135 PFTAASIGGFDTQLTYEFFQGFVNHAGVTLHIDNLKGINAHHQCETVFKAFARALRAALE 194 Query: 182 LDERMAGQMPSTKGCL 197 D R AG +PSTKG L Sbjct: 195 RDPRAAGVIPSTKGSL 210 Lambda K H 0.325 0.141 0.421 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: 228 Number of extensions: 5 Number of successful extensions: 1 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: 197 Length of database: 210 Length adjustment: 21 Effective length of query: 176 Effective length of database: 189 Effective search space: 33264 Effective search space used: 33264 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 45 (21.9 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