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BTB Domain Analysis

This page presents our analysis of the BTB domain sequence superfamily. This includes:

  • sequences separated by organism, and then clustered into subfamilies
  • viewable phylogenetic trees of each subfamily via ATVapp applet
  • viewable sequence alignments of each subfamily via Jalview applet

  • Steps in sequence clustering

    1. Structure superposition of all BTB domain structures. Download superposition (18 structures in one PDB file)
    2. Generation of profile HMM from superposition. Download HMM based on superposition
    3. Search of SWISSPROT/SpTrEMBL and Ensembl databases (selected genomes) using HMM from superposition.
    4. Global alignment of high-scoring sequences and separation by species.
    5. Generation of species-specific profile HMMs.
    5. Phylogenetic clustering of all sequences on a per-species basis.
    6. Assignment of subfamily by inspection of phylogenetic clustering pattern.
    7. Generation of species+subfamily-specific profile HMMs and calculation of sequence statistics per subfamily.
    8. Analysis of subfamily sequence patterns by visual inspection of alignment.

    Results

    Analysis is divided into BTB domains from each species analyzed.

    Subfamilies are listed. The following is tabulated:
  • viewable alignments (with short and SWISSPROT FASTA definition lines)
  • species and species+subfamily-specific profile HMMs
  • phylogenetic tree (with short and SWISSPROT FASTA definition lines)

    H. sapiens BTB Domains
    Choose alignment format:
    short swissprot
    Number of Sequences: 205
    human_all.hmm
    Choose tree format:
    short swissprot

    SubfamilyAlignment and Alignment Statistics*NJ phylogenetic tree***
    BTB domains from BTB-ZnF proteins
    Choose alignment format:
    short swissprot
    Number of Sequences: 47
    Profile HMM**: human_BTB_ZF.hmm
    Choose tree format:
    short swissprot
    BTB domains from BTB-kelch proteins
    Choose alignment format:
    short swissprot
    Number of Sequences: 53
    Profile HMM**: human_BTB_KL.hmm
    Choose tree format:
    short swissprot
    BTB/T1 domains
    Choose alignment format:
    short swissprot
    Number of Sequences: 57
    Profile HMM**: human_BTB_KT.hmm
    Choose tree format:
    short swissprot
    BTB/Skp1 domains
    Choose alignment format:
    short swissprot
    Number of Sequences: 8
    Profile HMM**: human_BTB_Skp1.hmm
    Choose tree format:
    short swissprot
    Other BTB domains (1)
    Choose alignment format:
    short swissprot
    Number of Sequences: 8
    Profile HMM**: human_other_BTBs_1.hmm
    Choose tree format:
    short swissprot
    Other BTB domains (2)
    Choose alignment format:
    short swissprot
    Number of Sequences: 20
    Profile HMM**: human_other_BTBs_2.hmm
    Choose tree format:
    short swissprot
    C. elegans BTB Domains
    Choose alignment format:
    short swissprot
    Number of Sequences: 183
    c.elegans_all.hmm
    Choose tree format:
    short swissprot
    SubfamilyAlignment and Alignment Statistics*NJ phylogenetic tree***
    BTB/T1 domains
    Choose alignment format:
    short swissprot
    Number of Sequences: 46
    Profile HMM**: c.elegans_BTB_KT.hmm
    Choose tree format:
    short swissprot
    BTB domains from BTB-Kelch and some BTB-MATH proteins
    Choose alignment format:
    short swissprot
    Number of Sequences: 21
    Profile HMM**: c.elegans_BTB_KL_MA.hmm
    Choose tree format:
    short swissprot
    BTB domains from main BTB-MATH protein cluster
    Choose alignment format:
    short swissprot
    Number of Sequences: 39
    Profile HMM**: c.elegans_BTB_MA.hmm
    Choose tree format:
    short swissprot
    BTB/Skp1 domains
    Choose alignment format:
    short swissprot
    Number of Sequences: 25
    Profile HMM**: c.elegans_BTB_Skp1.hmm
    Choose tree format:
    short swissprot
    BTB domains from proteins with no other known domains
    Choose alignment format:
    short swissprot
    Number of Sequences: 34
    Profile HMM**: c.elegans_BTB_NO.hmm
    Choose tree format:
    short swissprot
    Other BTB domains (1)
    Choose alignment format:
    short swissprot
    Number of Sequences: 13
    Profile HMM**: c.elegans_other_BTBs_1.hmm
    Choose tree format:
    short swissprot
    Other BTB domains (2)
    Choose alignment format:
    short swissprot
    Number of Sequences: 6
    Profile HMM**: c.elegans_other_BTBs_2.hmm
    Choose tree format:
    short swissprot
    M. musculus BTB Domains
    Choose alignment format:
    short swissprot
    Number of Sequences: 202
    m.musculus_all.hmm
    Choose tree format:
    short swissprot
    SubfamilyAlignment and Alignment Statistics*NJ phylogenetic tree***
    BTB/T1 domains
    Choose alignment format:
    short swissprot
    Number of Sequences: 58
    Profile HMM**: m.musculus_BTB_KT.hmm
    Choose tree format:
    short swissprot
    BTB domains from most BTB-Kelch proteins, plus a few BTB-ZF proteins
    Choose alignment format:
    short swissprot
    Number of Sequences: 40
    Profile HMM**: m.musculus_BTB_KL_ZF.hmm
    Choose tree format:
    short swissprot
    BTB domains from BTB-MATH proteins
    Choose alignment format:
    short swissprot
    Number of Sequences: 10
    Profile HMM**: m.musculus_BTB_MA.hmm
    Choose tree format:
    short swissprot
    BTB domains from BTB-ZF proteins, plus a few BTB-Kelch proteins
    Choose alignment format:
    short swissprot
    Number of Sequences: 52
    Profile HMM**: m.musculus_BTB_ZF_KL.hmm
    Choose tree format:
    short swissprot
    BTB domains from other proteins (1)
    Choose alignment format:
    short swissprot
    Number of Sequences: 10
    Profile HMM**: m.musculus_other_BTBs_1.hmm
    Choose tree format:
    short swissprot



    *Alignment and Alignment Statistics notes:
  • Alignment viewing provided by Jalview applet (Michele Clamp)
  • Average pairwise sequence identities calculated by Bioperl::SimpleAlign::average_percentage_identity module
  • Conservation profile: calculated by AL2CO, using the following settings:
    -weighted amino acid frequencies, to down-weight highly similar sequences in the calculation of amino acid frequencies. This is a method based on Henikoff and Henikoff, and Altshul's implementation in PSI-BLAST. (equation here)
    -sum-of-pairs conservation index, using BLOSUM62. The conservation index will be higher for more similar amino acids. See Pei, J and Grishin NV. (2001) AL2CO: calculation of positional conservation in a protein sequence alignment. Bioinformatics, 17 , 700-712.



    **Profile HMM notes:
  • Profile HMM generated by HMMER 2.3 with hmmbuild, then hmmcalibrate, both with default parameters.


    ***NJ phylogenetic tree notes:
  • Neighbor-joining (NJ) trees calculated using PAUP* 4.0, with distance criterion = P (uncorrected) distance.
  • Tree viewing applet: Zmasek C.M. and Eddy S.R. (2001) ATV: display and manipulation of annotated phylogenetic trees. Bioinformatics, 17, 383-384. ATV - phylogenetic tree display tool






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