Align imidazoleglycerol-phosphate dehydratase (EC 4.2.1.19) (characterized)
to candidate SMc02574 SMc02574 imidazoleglycerol-phosphate dehydratase
Query= reanno::BFirm:BPHYT_RS17700 (195 letters) >FitnessBrowser__Smeli:SMc02574 Length = 202 Score = 241 bits (615), Expect = 6e-69 Identities = 112/194 (57%), Positives = 144/194 (74%) Query: 2 RLAEVVRNTSETQIRVKINLDGTGQQKLATGVPFLDHMLDQIARHGLFDLEIEAHGDLHI 61 R +V R T+ET I V +N+DGTG K+ATGV F DHMLDQ++RH L D+EI+A GDLH+ Sbjct: 8 RTGQVSRKTNETAISVSVNVDGTGVSKIATGVGFFDHMLDQLSRHSLIDMEIKAEGDLHV 67 Query: 62 DDHHTVEDTGITLGQAVAKAIGDRKGIVRYGHSYVPLDEALSRVVIDFSGRPGLEFHVPF 121 DDHHTVEDTGI +GQA+AKA+GDR+GI RY + +DE ++R +D SGRP L ++V F Sbjct: 68 DDHHTVEDTGIAIGQALAKALGDRRGITRYASIDLAMDETMTRAAVDVSGRPFLVWNVTF 127 Query: 122 TRARIGTFDVDLSIEFFRGFVNHAGVTLHIDNLRGLNAHHQMETVFKAFGRALRMATELD 181 T +IGTFD +L EFF+ HAG+TLH+ N+ G N HH ET FK+ R LR ATE+D Sbjct: 128 TSPKIGTFDTELVREFFQALAQHAGITLHVQNIYGANNHHVAETCFKSVARVLRTATEID 187 Query: 182 ERAAGQIPSTKGSL 195 R AG++PSTKG+L Sbjct: 188 PRQAGRVPSTKGTL 201 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: 177 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: 195 Length of database: 202 Length adjustment: 20 Effective length of query: 175 Effective length of database: 182 Effective search space: 31850 Effective search space used: 31850 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 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