Align Histidine biosynthesis bifunctional protein HisB; EC 3.1.3.15; EC 4.2.1.19 (characterized)
to candidate WP_057506750.1 ABB28_RS00540 bifunctional histidinol-phosphatase/imidazoleglycerol-phosphate dehydratase HisB
Query= SwissProt::Q9S5G5 (355 letters) >NCBI__GCF_001431535.1:WP_057506750.1 Length = 357 Score = 374 bits (960), Expect = e-108 Identities = 188/354 (53%), Positives = 248/354 (70%), Gaps = 5/354 (1%) Query: 6 LFIDRDGTLISEPPSDFQVDRFDKLAFEPGVIPQLLKLQKAGYKLVMITNQDGLGTQSFP 65 LFIDRDGTLI EP +D Q+D ++KL F VIP L+KL+ AG++ V+++NQDGLG++S+P Sbjct: 5 LFIDRDGTLIEEP-ADHQIDAYEKLRFVRDVIPALIKLRDAGWQFVIVSNQDGLGSESYP 63 Query: 66 QADFDGPHNLMMQIFTSQGVQFDEVLICPHLPADECDCRKPKVKLVERYLAEQAMDRANS 125 QA FD PH LMM +F SQG+ F +VLI P + RKP + L+ YL ++++D A S Sbjct: 64 QAIFDAPHALMMHVFESQGITFRDVLIDTSWPHENLPTRKPGIGLMTAYLQDRSIDWARS 123 Query: 126 YVIGDRATDIQLAENMGINGLRYDRETL----NWPMIGEQLTRRDRYAHVVRNTKETQID 181 ++GDR TDIQ A+N+ I G + E +WP I L R A V RNTKET+I Sbjct: 124 AMVGDRLTDIQFAQNLNIRGFQLRTEEFGGDWDWPAIAHALADAPRTAVVQRNTKETRIR 183 Query: 182 VQVWLDREGGSKINTGVGFFDHMLDQIATHGGFRMEINVKGDLYIDDHHTVEDTGLALGE 241 V++ LD + +I+TG+ FFDHML+QI HGG + I +GDL+ID+HHT+EDTGLALG+ Sbjct: 184 VELDLDAQAEPRIHTGLPFFDHMLEQIGKHGGISVRIQAEGDLHIDEHHTIEDTGLALGQ 243 Query: 242 ALKIALGDKRGICRFGFVLPMDECLARCALDISGRPHLEYKAEFTYQRVGDLSTEMIEHF 301 AL+ ALGDKRGI R+GF LPMDE LA ALD SGRP+ + EF +RVGDL TE++ HF Sbjct: 244 ALREALGDKRGIGRYGFTLPMDETLASAALDFSGRPYFVFDGEFKRERVGDLPTELVPHF 303 Query: 302 FRSLSYTMGVTLHLKTKGKNDHHRVESLFKAFGRTLRQAIRVEGDTLPSSKGVL 355 FRSL G+ L+L+ +G NDHH+VE+ FKA R LR A+ +G LPS+KG L Sbjct: 304 FRSLCEAAGLNLNLQVRGDNDHHKVEACFKALARALRTAVARQGTELPSTKGAL 357 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: 400 Number of extensions: 11 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: 357 Length adjustment: 29 Effective length of query: 326 Effective length of database: 328 Effective search space: 106928 Effective search space used: 106928 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: 49 (23.5 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