Align Imidazoleglycerol-phosphate dehydratase; Short=IGPD; EC 4.2.1.19 (characterized, see rationale)
to candidate PfGW456L13_362 Imidazoleglycerol-phosphate dehydratase (EC 4.2.1.19)
Query= uniprot:Q9HU41 (197 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_362 Length = 197 Score = 366 bits (940), Expect = e-106 Identities = 179/197 (90%), Positives = 188/197 (95%) Query: 1 MAERKASVARDTLETQIKVSIDLDGTGKARFDTGVPFLDHMMDQIARHGLIDLDIECKGD 60 MAERKASV RDTLETQIK SI+LDGTGKARFD GVPFL+HM+DQIARHGLIDLDI KGD Sbjct: 1 MAERKASVERDTLETQIKASINLDGTGKARFDIGVPFLEHMLDQIARHGLIDLDIVSKGD 60 Query: 61 LHIDDHHTVEDIGITLGQAFAKAIGDKKGIRRYGHAYVPLDEALSRVVIDFSGRPGLQMH 120 LHIDDHHTVED+GITLGQAFAKAIGDKKGIRRYGHAYVPLDEALSRVVIDFSGRPGLQMH Sbjct: 61 LHIDDHHTVEDVGITLGQAFAKAIGDKKGIRRYGHAYVPLDEALSRVVIDFSGRPGLQMH 120 Query: 121 VPFTRASVGGFDVDLFMEFFQGFVNHAQVTLHIDNLRGHNTHHQIETVFKAFGRALRMAI 180 VP+TRA+VGGFDVDLF EFFQGFVNHA V+LHIDNLRG NTHHQIETVFKAFGRALRMA+ Sbjct: 121 VPYTRATVGGFDVDLFQEFFQGFVNHALVSLHIDNLRGTNTHHQIETVFKAFGRALRMAV 180 Query: 181 ELDERMAGQMPSTKGCL 197 ELD+RMAGQMPSTKG L Sbjct: 181 ELDDRMAGQMPSTKGVL 197 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: 270 Number of extensions: 8 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: 197 Length adjustment: 20 Effective length of query: 177 Effective length of database: 177 Effective search space: 31329 Effective search space used: 31329 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 Jul 25 2024. The underlying query database was built on Jul 25 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