Align Histidine biosynthesis bifunctional protein HisB; EC 3.1.3.15; EC 4.2.1.19 (characterized)
to candidate RR42_RS18905 RR42_RS18905 imidazoleglycerol-phosphate dehydratase
Query= SwissProt::Q9S5G5 (355 letters) >FitnessBrowser__Cup4G11:RR42_RS18905 Length = 197 Score = 196 bits (497), Expect = 5e-55 Identities = 100/194 (51%), Positives = 130/194 (67%), Gaps = 5/194 (2%) Query: 167 RYAHVVRNTKETQIDVQVWLDREGGSKINTGVGFFDHMLDQIATHGGFRMEINVKGDLYI 226 R A V RNT ETQI V + LD G K+ +GV F DHMLDQIA HG F +E+ GD +I Sbjct: 2 RVAEVTRNTSETQIRVSLNLDGTGRQKLASGVPFLDHMLDQIARHGMFDLEVEASGDTHI 61 Query: 227 DDHHTVEDTGLALGEALKIALGDKRGICRFGF-VLPMDECLARCALDISGRPHLEYKAEF 285 DDHHTVED G+ALG+A+ A+GDK+GI R+G +P+DECL+R +D SGRP LE+ F Sbjct: 62 DDHHTVEDVGIALGQAVAKAIGDKKGITRYGHSYVPLDECLSRVVIDFSGRPGLEFHVPF 121 Query: 286 TYQRVGDLSTEMIEHFFRSLSYTMGVTLHL-KTKGKNDHHRVESLFKAFGRTLRQAIRVE 344 T RVG ++ FFR VTLH+ +G N HH+ E++FKAFGR LR A+ ++ Sbjct: 122 TRARVGSFDVDLTIEFFRGFVNHAAVTLHIDNLRGINAHHQCETVFKAFGRALRMAVEMD 181 Query: 345 ---GDTLPSSKGVL 355 G+T+PS+KG L Sbjct: 182 PRAGNTIPSTKGTL 195 Lambda K H 0.322 0.140 0.420 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: 199 Number of extensions: 9 Number of successful extensions: 5 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: 355 Length of database: 197 Length adjustment: 25 Effective length of query: 330 Effective length of database: 172 Effective search space: 56760 Effective search space used: 56760 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 47 (22.7 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