Align imidazoleglycerol-phosphate dehydratase (EC 4.2.1.19) (characterized)
to candidate WP_043747210.1 AMB_RS22940 imidazoleglycerol-phosphate dehydratase
Query= reanno::BFirm:BPHYT_RS17700 (195 letters) >NCBI__GCF_000009985.1:WP_043747210.1 Length = 199 Score = 232 bits (591), Expect = 4e-66 Identities = 111/195 (56%), Positives = 146/195 (74%) Query: 1 MRLAEVVRNTSETQIRVKINLDGTGQQKLATGVPFLDHMLDQIARHGLFDLEIEAHGDLH 60 MR A + RNT+ET I+V ++LDG+G+ ++TGV FLDHML+Q++RH L DLE++A GDLH Sbjct: 1 MRKAAITRNTNETSIKVAVDLDGSGKYAVSTGVGFLDHMLEQLSRHSLMDLEVDAKGDLH 60 Query: 61 IDDHHTVEDTGITLGQAVAKAIGDRKGIVRYGHSYVPLDEALSRVVIDFSGRPGLEFHVP 120 ID HHT ED GI +GQAV +A+GDRKGI RYG +YVP+DEAL+RV +D S RP L + V Sbjct: 61 IDAHHTTEDVGIAIGQAVNQALGDRKGICRYGSAYVPMDEALTRVALDLSNRPYLIWKVA 120 Query: 121 FTRARIGTFDVDLSIEFFRGFVNHAGVTLHIDNLRGLNAHHQMETVFKAFGRALRMATEL 180 F R ++GT D +L E+F+ F AG TLH+++L G N HH +E+ FKA RALR A E+ Sbjct: 121 FGRDKLGTMDTELFKEWFQAFAQAAGATLHVESLYGDNDHHIVESCFKALARALREAVEI 180 Query: 181 DERAAGQIPSTKGSL 195 D R A +PSTKG+L Sbjct: 181 DPRKADAVPSTKGTL 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: 154 Number of extensions: 5 Number of successful extensions: 3 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: 199 Length adjustment: 20 Effective length of query: 175 Effective length of database: 179 Effective search space: 31325 Effective search space used: 31325 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