Align imidazoleglycerol-phosphate dehydratase (EC 4.2.1.19) (characterized)
to candidate WP_036260734.1 DL86_RS09675 imidazoleglycerol-phosphate dehydratase HisB
Query= reanno::BFirm:BPHYT_RS17700 (195 letters) >NCBI__GCF_000746085.1:WP_036260734.1 Length = 197 Score = 231 bits (588), Expect = 8e-66 Identities = 111/195 (56%), Positives = 139/195 (71%) Query: 1 MRLAEVVRNTSETQIRVKINLDGTGQQKLATGVPFLDHMLDQIARHGLFDLEIEAHGDLH 60 MR A V R T ET+I V ++LDG+G K++TG+ F DHML+Q+ARH L D+EI+A GDLH Sbjct: 1 MRAAAVSRKTKETEIEVHVHLDGSGLAKISTGIGFFDHMLEQLARHSLIDMEIKAKGDLH 60 Query: 61 IDDHHTVEDTGITLGQAVAKAIGDRKGIVRYGHSYVPLDEALSRVVIDFSGRPGLEFHVP 120 ID HHTVEDTGI LGQAV +A+GD GI R+ +P+DE L+RV ID SGRP L F Sbjct: 61 IDQHHTVEDTGIALGQAVRRALGDMAGITRFADVLLPMDETLTRVAIDISGRPFLVFRTQ 120 Query: 121 FTRARIGTFDVDLSIEFFRGFVNHAGVTLHIDNLRGLNAHHQMETVFKAFGRALRMATEL 180 F RA+IG FD +L EFF+ F HAG+ +H++ L G N+HH E+ FK RALR+A + Sbjct: 121 FARAKIGNFDTELVREFFQAFTMHAGMNVHVETLYGENSHHISESSFKGLARALRLAVAV 180 Query: 181 DERAAGQIPSTKGSL 195 D R G IPSTKGSL Sbjct: 181 DHRQLGAIPSTKGSL 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: 167 Number of extensions: 3 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: 195 Length of database: 197 Length adjustment: 20 Effective length of query: 175 Effective length of database: 177 Effective search space: 30975 Effective search space used: 30975 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: 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