Table 1 Classification of putative transcription factors of Medicago into families and sub-families
TF Family | No. of Genes | Characteristic Domain (InterPro No.) | Domain Function | Domain Description |
|---|---|---|---|---|
MYB/HD-like | 76 | IPR001005, IPR009057 | D | Myb, DNA-binding; homeodomain like |
MYB | 58 | IPR001005 | D | Myb, DNA-binding |
C2H2 (Zn) | 64 | IPR007087 | NA | Zn-finger, C2H2 type |
AP2/EREBP | 55 | IPR001471 | D | Pathogenesis-related transcriptional factor and ethylene response factor |
BHLH | 49 | IPR001092 | D | Basic helix-loop-helix dimerisation region bHLH |
HD-like | 50 | IPR009057 | D | Homeodomain like |
HD family | IPR001356 | D | Homeobox | |
HD | 25 | |||
HD-ZIP | 5 | IPR006712 | P | HD-ZIP protein, N terminus |
HD-PHD finger | 2 | IPR001965 | P | Zn-finger like, PHD-finger |
MADS | 48 | IPR002100 | D | TF, MADS-box |
BZIP | 41 | IPR004827 | D | Basic Leu zipper (bZIP) TF |
PHD | 34 | IPR001965 | P | Zn-finger like, PHD-finger |
WRKY family | IPR003657 | D | DNA-binding WRKY | |
WRKY | 29 | |||
LLR WRKY | 1 | IPR001611 | Leu-rich repeat | |
ABI3/VP1 | 29 | IPR003340 | D | TF B3 |
NAC | 29 | IPR003441 | D | No apical meristem (NAM) protein |
C3H-type1(Zn) | 27 | IPR000571 | D | Zn-finger, C-x8-C-x5-C-x3-H type |
ARF | 23 | IPR003340, IPR010525, IPR011525 | D | |
JUMONJI | 20 | IPR003347 | D | TF jumonji, jmjC |
GRAS | 19 | IPR005202 | P | GRAS TF |
HMG | 15 | IPR000637 | D | HMG-I and HMG-Y, DNA binding |
AS2 | 14 | IPR004883 | P | Lateral organ boundaries |
C2C2 (Zn) | ||||
Dof | 13 | IPR003851 | D | Zn-finger, Dof type |
GATA | 7 | IPR000679 | D | Zn-finger, GATA type |
CO-like | 6 | IPR000315 | D | Zn-finger, B-box |
YABBY | 5 | IPR006780 | D | YABBY protein |
CCAAT-HAP3 type | 12 | IPR003958 | D | TF CBF/NF-Y/archaeal histone |
GRF | 8 | IPR010666 | D | Zn-finger, GRF type |
SBP | 8 | IPR004333 | D | SBP |
EIL | 7 | IPR006957 | D | Ethylene insensitive 3 |
LIM | 7 | IPR001781 | P | Zn-binding protein, LIM |
SNF2 | 6 | IPR000330 | D | SNF2 family N-terminal domain |
E2F/DP | 5 | IPR003316 | D | TF E2F/dimerisation partner (TDP) |
TCP | 5 | IPR005333 | D | TCP TF |
FHA | 5 | IPR000253 | D | Forkhead-associated |
ARID | 4 | IPR001606 | D | AT-rich interaction region |
HSF | 4 | IPR000232 | D | Heat shock factor (HSF)-type, DNA binding |
AUX/IAA | 3 | IPR003311 | D | AUX/IAA protein |
SRS | 3 | IPR006510 | D | Zn-finger, LRP1 type |
TUB | 3 | IPR000007 | D | Tubby |
ZIM | 3 | IPR010399 | D | ZIM |
DDT | 3 | IPR004022 | D | DDT |
ZF-HD | 2 | IPR006455 | D | Homeobox domain, ZF-HD class |
MBF1 | 2 | IPR001387 | D | Helix-turn-helix type 3 |
S1Fa-like | 2 | IPR006779 | D | DNA binding protein S1FA |
CAMTA | 2 | IPR005559 | D | CG-1 |
LFY | 1 | IPR002910 | D | Floricaula/leafy protein |
Nin-like | 1 | IPR003035 | D | Plant regulator RWP-RK |
TAZ | 1 | IPR000197 | P | Zn-finger, TAZ-type |
Potentially novel plant TFs and transcriptional regulators | ||||
CCHC (Zn) | 112 | IPR001878 | NA | Zn-finger, CCHC-type |
RR | 16 | IPR001789, IPR011006 | RD | Response regulator receiver |
DHHC (Zn) | 14 | IPR001594 | D or P | Zn-finger, DHHC-type |
HTH | ||||
FIS | 11 | IPR002197 | D | Helix-turn-helix, Fis-type |
AraC | 2 | IPR000005 | D | Helix-turn-helix, AraC type |
BTB/POZ | 7 | IPR000210 | P | BTB |
TTF-type (Zn) | 6 | IPR006580 | D | Zn-finger, TTF-type |
BD | 6 | IPR001487 | P | Bromodomain |
Lambda-DB | 3 | IPR010982 | D | Lambda_DNA_bd |
TrpR | 3 | IPR010921 | D | Trp repressor/replication initiator |
TPR | 3 | IPR001440 | P | Tetratricopeptide TPR_1 |
KRAB-box | 2 | IPR001909 | P | KRAB box |
NRs | 2 | IPR008946 | LBD | Steroid nuclear receptor, ligand binding |
R3H | 2 | IPR001374 | NA | Single-stranded nucleic acid binding R3H |
YEATS | 2 | IPR005033 | TA | YEATS |
U1-type (Zn) | 2 | IPR003604 | NA | Zn-finger, U1-type |
A20-like | 2 | IPR002653 | P | Zn-finger, A20-type |
Euk_TF | 1 | IPR008917 | D | Euk_TF, DNA binding |
NGN | 1 | IPR006645 | D | NGN |
p53-like | 1 | IPR008967 | D | p53-like TF, DNA binding |
SSB protein | 1 | IPR011344 | D | Single-strand binding protein |
ssDB TR | 1 | IPR009044 | D | Single-strand DNA binding transcriptional regulator |
TCoAp15 | 1 | IPR003173 | D | Transcriptional coactivator p15 |
BED-type (Zn) | 1 | IPR003656 | D | Zn-finger, BED-type predicted |
TCoA | 1 | IPR009255 | TA | Transcriptional coactivation |
Tc/PD | 1 | IPR001533 | TA | Transcriptional coactivator |