Align imidazoleglycerol-phosphate dehydratase (EC 4.2.1.19) (characterized)
to candidate WP_012411760.1 NPUN_RS27880 imidazoleglycerol-phosphate dehydratase HisB
Query= reanno::BFirm:BPHYT_RS17700 (195 letters) >NCBI__GCF_000020025.1:WP_012411760.1 Length = 213 Score = 232 bits (591), Expect = 4e-66 Identities = 114/194 (58%), Positives = 140/194 (72%) Query: 2 RLAEVVRNTSETQIRVKINLDGTGQQKLATGVPFLDHMLDQIARHGLFDLEIEAHGDLHI 61 R+A V R T ET ++V INLDG G ATG+PFLDHML QIA HGL D++++A GDL I Sbjct: 20 RIATVHRTTGETDVQVTINLDGRGTCTAATGIPFLDHMLHQIASHGLIDIDVQAKGDLEI 79 Query: 62 DDHHTVEDTGITLGQAVAKAIGDRKGIVRYGHSYVPLDEALSRVVIDFSGRPGLEFHVPF 121 DDHHT ED GITLGQA +A+GDRKGIVR+G+ PLDEAL +V +DFSGRP L + + Sbjct: 80 DDHHTNEDVGITLGQAFNQALGDRKGIVRFGNFLAPLDEALVQVALDFSGRPHLSYGLQI 139 Query: 122 TRARIGTFDVDLSIEFFRGFVNHAGVTLHIDNLRGLNAHHQMETVFKAFGRALRMATELD 181 R+GT+D L EFF VNH+ +TLHI L G+N+HH +E FKAF RA R+A E+D Sbjct: 140 PTQRVGTYDTQLVREFFVALVNHSQMTLHIRQLDGINSHHIIEATFKAFARATRLAVEID 199 Query: 182 ERAAGQIPSTKGSL 195 R AG IPS+KG L Sbjct: 200 PRRAGLIPSSKGVL 213 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: 158 Number of extensions: 4 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: 213 Length adjustment: 21 Effective length of query: 174 Effective length of database: 192 Effective search space: 33408 Effective search space used: 33408 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