Align imidazoleglycerol-phosphate dehydratase (EC 4.2.1.19) (characterized)
to candidate 3607380 Dshi_0794 Imidazoleglycerol-phosphate dehydratase (RefSeq)
Query= reanno::BFirm:BPHYT_RS17700 (195 letters) >FitnessBrowser__Dino:3607380 Length = 195 Score = 227 bits (578), Expect = 1e-64 Identities = 110/195 (56%), Positives = 136/195 (69%) Query: 1 MRLAEVVRNTSETQIRVKINLDGTGQQKLATGVPFLDHMLDQIARHGLFDLEIEAHGDLH 60 MR A + R T+ET I V+I+LDGTG TGV F DHMLDQ++RH L D+ + GDLH Sbjct: 1 MRRATITRKTAETDISVEIDLDGTGVYDNRTGVGFFDHMLDQLSRHALIDMTVRCDGDLH 60 Query: 61 IDDHHTVEDTGITLGQAVAKAIGDRKGIVRYGHSYVPLDEALSRVVIDFSGRPGLEFHVP 120 IDDHHTVED GI LGQA+A+A+GD++GIVRYG +P+D+AL R +D SGRP L + V Sbjct: 61 IDDHHTVEDVGIALGQALAEAVGDKRGIVRYGSCLLPMDDALVRAALDISGRPYLVWDVA 120 Query: 121 FTRARIGTFDVDLSIEFFRGFVNHAGVTLHIDNLRGLNAHHQMETVFKAFGRALRMATEL 180 A+IGTFD +L EFF+ H G+TLH+ L G+N+HH E FK+ RALR A E Sbjct: 121 LPTAKIGTFDTELVREFFQALATHGGLTLHVTRLAGINSHHIAEAAFKSVARALRAALET 180 Query: 181 DERAAGQIPSTKGSL 195 D R A IPSTKGSL Sbjct: 181 DPRKANAIPSTKGSL 195 Lambda K H 0.323 0.140 0.408 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: 156 Number of extensions: 4 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: 195 Length of database: 195 Length adjustment: 20 Effective length of query: 175 Effective length of database: 175 Effective search space: 30625 Effective search space used: 30625 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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