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TranScout Classification

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TranScout Classification


1.    BASIC DNA-BINDING DOMAINS

1.1.    bZIP factors
1.1.1.    Jun
Basic DNA-binding domains: this class contains proteins which bind DNA with a basic amino-acidic segment. bZIP factors contain a unconserved dimerization leucine zipper domain. Subclass Jun contain factors homologous to Jun.

2.    HELIX-TURN-HELIX

2.1.    Homeodomain

2.1.1.    Abd-b
2.1.2.    Antennapedia
2.1.3.    Caudal
2.1.4.    Distal-less
2.1.5.    Engrailed
2.1.6.    Even-skipped
2.1.7.    HD-ZIP
2.1.8.    Lim
2.1.9.    MSH
2.1.10.    NK-1
2.1.11.    NK-2
2.1.12.    NK-3
2.1.13.    Paired
2.1.14.    POU
2.2.    Fork-head/Winged-helix
2.3.    Heat shock factors
2.4.    Myb factors
2.4.1.    Myb 1
2.4.2.    Myb 2
2.4.3.    Myb 3
2.5.    Bacterial factors
2.5.1.    AsnC-like
2.5.2.    MarR-like
2.5.3.    LuxR-like
2.5.4.    GntR-like
2.5.5.    LysR-like
2.5.6.    AraC-like
2.5.7.    ArsR-like
2.5.8.    IclR-like
2.5.9.    LacI-like
2.5.10.    TetR-like
2.5.11.    MerR-like
2.6.    RF-X
Helix-turn-helix: this motif cannot bind DNA isolated from the rest of the protein. The Homeodomain class is very well-characterized. Abdominal-b (abd-b) family contains five Hox vertebrate groups (Hox9 to Hox13). Antennapedia (antp) family contains factors related to Hox7, Hox6 and Hox8. Members of Caudal family are homolgous to Drosophila Caudal factor. Engrailed is a very conserved family. Members of HD-ZIP family are plant factors that contain a leucine zipper. The LIM family contain the LIM non-transcriptional motif.. The MSH family contains proteins homologus to Msh transcription factor of Drosophila. NK-2 and NK-1 families present some homology between them and some less with NK-1 family. Members of the POU family show a basic DNA-binding motif known as POU. The Fork-head/Winged helix class contains a highly conserved 100-aa long motif which binds DNA through an helical structucture. The Heat shock factors class contains proteins which bind promoters related to temprature stress. All Myb factors bind a common DNA target sequence through a motif build out of three different sequences. RF-X factors have a DNA-binding structure similar to that of fork-head factor altough bind DNA with a ?-hairpin. Each family within bacterial factors class gather different bacterial repressors and activators named after the most prominent of them.

3.    B-SCAFFOLD FACTORS

3.1.    MADS box
3.2.    TATA binding
3.3.    CBF-A
3.4.    Runt
B-sheet factors bind DNA through their ?-sheets. MADS class gathers together factors with different functions but with the same DNA-binding sequence that has been related both to DNA-binding and dimerization. TATA-binding proteins (TBP) class also contains the TBP-related factors (TRF). CCAAT-box factors (CBF) are heterodimeric factors binding DNA by their two DNA-binding segments combined. TranScout detects segment A. The Runt class contains transcription factors that can both bind DNA and heterodimerize by the Runt domain.

4.    METAL-COORDINATING DNA-BINDING DOMAINS

4.1.    Cys4 Zn fingers
4.1.1.    Corticoid receptors
4.1.2.    Progesterone receptors
4.1.3.    Estrogen receptors
4.1.4.    Retinoic acid receptors
4.1.5.    Thyroid horm. receptors
4.1.6.    Vitamin D receptor
4.1.7.    PPAR
4.1.8.    Ecdisone receptor
4.1.9.    HNF

4.2.    C2H2 Zn fingers
4.3.    Cys6 Zn fingers
4.4.    RING Zn fingers
4.5.    CCHC
4.6.    PARP
4.7.    GATA
4.8.    Zinc ribbon
4.9.    Copper fist
Metal-coordinating DNA-binding domains superclass contains several classes classified by the number and position of the Cys and His residues in the metal-binding segment. Zinc fingers bind one or more Zn ions and copper fist factor bind one Cu ion.
Zinc fingers usually contain more than one copy of the motif. Cys4 Zn fingers class contains factors that coordinate the Zn with four Cys residues. This class contains the thyroidal and stheroidal vertebrate hormones (Corticoid, Progesterone and Estrogen receptors) and the DNA-binding domain is really two C4 zinc finger single domains in tandem.
Other Cys4 zinc fingers class includes zinc finger motifs with four Cys in their sequence but too different from the canonical C4 consensus, such as Zinc ribbon (TFIIS) factor and GATA.
Members of the C2H2 class bind a Zn ion with two Cys and two His.
The Cys6 class inclued fungical factors which bind two Zn ions with six Cys.
The next classes of Other Zn fingers include Zn fingers with a composition or distribution of Cys and His which does not match any of the previous classes.
The CCHC class transcription factors are found in retroviruses.
The RING (C3HC4) proteins bind DNA with seven Cys and one Hi.
PARP (Poly(ADP-ribose) polymerase) class members have a special zinc finger that bind single-stranded DNA.
Copper fist class transcription factors have a DNA-binding domain that bind copper ions through three Cys and two His (in a structure that reminds of zinc fingers).

5.    NON-TRANSCRIPTIONAL MOTIFS

5.1.    LIM
5.2.    NHL
5.3.    Bromodomain
5.4.    RFX-D
5.5.    RFX-B
5.6.    RFX-C
LIM domain is present in the LIM family of  homeotic transcription factors.
NHL domain is present in some members of the RING class of zinc finger proteins.
Bromodomain is a motif present in a variety of different transcription factors.
RFX-D, RFX-B and RFX-C domains are present in RF-X class of proteins.

A link to the classification of transcription factors present in TRANSFAC can be found here.



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