hidden markov model (hmm) profile for the lysm domain (pf01476)  (InterPro Inc)

Journal: International Journal of Molecular Sciences

Article Title: Systematic Analysis of Cotton RING E3 Ubiquitin Ligase Genes Reveals Their Potential Involvement in Salt Stress Tolerance

doi: 10.3390/ijms26010359

Figure Lengend Snippet: The types and features of RING domains in G. hirsutum .

Article Snippet: In addition, the Hidden Markov Model (HMM) profiles of RING domains (PF00097, PF12906, PF13639, PF13923, PF13920, and PF15227) were downloaded from the InterPro database ( http://www.ebi.ac.uk/interpro/ , (accessed on 20 November 2023)) [ ], which was queried to identify RING protein sequences in the above three cotton species using the HMMER program (v3.3.2, http://www.hmmer.org/ , (accessed on 20 November 2023)), with E -value ≤ e − 10 .

Techniques: Sequencing

Journal: International Journal of Molecular Sciences

Article Title: Systematic Analysis of Cotton RING E3 Ubiquitin Ligase Genes Reveals Their Potential Involvement in Salt Stress Tolerance

doi: 10.3390/ijms26010359

Figure Lengend Snippet: Distance variation between ml pairs in G. hirsutum RING domains. ( A ) Distance variation between ml pairs ml1–ml2, ml3–ml4, ml4–ml5, ml5–ml6, and ml7–ml8. ( B ) Comparison of the number of amino acids in the loops between ml2 and ml3, and ml6 and ml7 of the RING-H2, RING-HCa, RING-HCb, RING-v, and RING-C2 domains. ml denotes metal ligand. Xn indicates the number of amino acids observed between two conserved metal ligands.

Article Snippet: In addition, the Hidden Markov Model (HMM) profiles of RING domains (PF00097, PF12906, PF13639, PF13923, PF13920, and PF15227) were downloaded from the InterPro database ( http://www.ebi.ac.uk/interpro/ , (accessed on 20 November 2023)) [ ], which was queried to identify RING protein sequences in the above three cotton species using the HMMER program (v3.3.2, http://www.hmmer.org/ , (accessed on 20 November 2023)), with E -value ≤ e − 10 .

Techniques: Comparison

Journal: International Journal of Molecular Sciences

Article Title: Systematic Analysis of Cotton RING E3 Ubiquitin Ligase Genes Reveals Their Potential Involvement in Salt Stress Tolerance

doi: 10.3390/ijms26010359

Figure Lengend Snippet: Expression profiles of the 144 G. hirsutum RING genes under salinity stress. Expression patterns of G. hirsutum RING genes determined from reanalysis of publicly available transcriptome data from the roots of cotton cultivar GX100-2 (SRP343057). The heat map was constructed based on transcript levels, calculated as fragments per kilobase of the exon model per million mapped fragments (FPKM). DEGs were identified using the DESeq2 R packages (1.16.1), with a cutoff of |log 2 FC | ≥ 1 and P -adj ≤ 0.05. The selection of these 144 RING genes was based on their differential expression in at least two salt stress time points. The values marked on round rectangles correspond to the log 2 FC values. The scale represents the relative expression levels, with red indicating higher expression and blue indicating lower expression. The RING genes highlighted in pale blue are tandemly duplicated genes.

Article Snippet: In addition, the Hidden Markov Model (HMM) profiles of RING domains (PF00097, PF12906, PF13639, PF13923, PF13920, and PF15227) were downloaded from the InterPro database ( http://www.ebi.ac.uk/interpro/ , (accessed on 20 November 2023)) [ ], which was queried to identify RING protein sequences in the above three cotton species using the HMMER program (v3.3.2, http://www.hmmer.org/ , (accessed on 20 November 2023)), with E -value ≤ e − 10 .

Techniques: Expressing, Construct, Selection, Quantitative Proteomics