Align Imidazoleglycerol-phosphate dehydratase; Short=IGPD; EC 4.2.1.19 (characterized, see rationale)
to candidate WP_007474426.1 CMTB2_RS04715 imidazoleglycerol-phosphate dehydratase HisB
Query= uniprot:Q9HU41 (197 letters) >NCBI__GCF_000170735.1:WP_007474426.1 Length = 189 Score = 155 bits (392), Expect = 4e-43 Identities = 81/190 (42%), Positives = 115/190 (60%), Gaps = 4/190 (2%) Query: 8 VARDTLETQIKVSIDLDGTGKARFDTGVPFLDHMMDQIARHGLIDLDIECKGDLHIDDHH 67 + R T ET+I+V +++ GTGK TG+ F DHM++ ++H ID+DI C+GD+ +D HH Sbjct: 4 IKRKTKETKIEVKVNIKGTGKNNISTGIGFFDHMLETFSKHSGIDIDIYCEGDIEVDYHH 63 Query: 68 TVEDIGITLGQAFAKAIGDKKGIRRYGHAYVPLDEALSRVVIDFSGRPGLQMHVPFTRAS 127 TVED+GI LGQA + K I R+ +A LDEA V +D GR L +P + Sbjct: 64 TVEDVGIVLGQALNNEVFPIKNIERFSNAVAILDEAAVEVDLDIGGRAYLVYEMP-REGA 122 Query: 128 VGGFDVDLFMEFFQGFVNHAQVTLHIDNLRGHNTHHQIETVFKAFGRALRMAIELDERMA 187 + FD++L EFF+ FV + ++ HI RG N HH +E+ FK+F ALR A+ E Sbjct: 123 IRDFDLELVEEFFKSFVFNFKIAAHIIYKRGTNKHHIVESAFKSFAIALRRALTYRE--- 179 Query: 188 GQMPSTKGCL 197 +PSTKG L Sbjct: 180 SGIPSTKGIL 189 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: 144 Number of extensions: 11 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: 197 Length of database: 189 Length adjustment: 20 Effective length of query: 177 Effective length of database: 169 Effective search space: 29913 Effective search space used: 29913 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: 44 (21.6 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