Regulatory proteins (RPs)

  In this study, we systemically compared TF/TR classification rules used in different databases, and derived a set of consensus rules based on the available literature for accurate plant TF/TR identification and classification. For plant PKs, we directly used the HMM profiles developed by Lehti-Shiu and Shiu (2012) to provide a comprehensive classification system. These consensus rules for TF/TR classification and HMM profiles for PK classification were implemented in iTAK, a computational program that provides consistency and uniformity on the identification and classification of plant TFs, TRs, and PKs.
  The relevant gene ids can be obtained from the legume blast and match under the Tools module.This link is Legume blast and match.

Regulatory proteins (RPs)

Transcription factors (TFs)

Column 1 Column 2 Column 3 Column 4 Column 5 Column 6 Column 7 Column 8
AP2 or ERF-AP2 AP2 or ERF-ERF AP2 or ERF-RAV Alfin-like B3 B3-ARF BBR-BPC BES1
BSD C2C2-CO-like C2C2-Dof C2C2-GATA C2C2-LSD C2C2-YABBY C2H2 C3H
CAMTA CPP CSD DBB DBP E2F-DP EIL FAR1
GARP-ARR-B GARP-G2-like GRAS GRF GeBP HB-BELL HB-HD-ZIP HB-KNOX
HB-PHD HB-WOX HB-other HRT HSF LFY LIM LOB
MADS-M-type MADS-MIKC MYB MYB-related NAC NF-X1 NF-YA NF-YB
NF-YC NOZZLE OFP PLATZ RWP-RK S1Fa-like SAP SBP
SRS STAT TCP TUB Tify Trihelix ULT VOZ
WRKY Whirly bHLH bZIP zf-HD --- --- ---

Transcription regulators (TRs)

Column 1 Column 2 Column 3 Column 4 Column 5 Column 6 Column 7 Column 8
ARID AUX or IAA Coactivator p15 DDT GNAT HMG IWS1 Jumonji
LUG MBF1 MED6 MED7 Others PHD Pseudo ARR-B RB
Rcd1-like SET SNF2 SOH1 SWI or SNF-BAF60b SWI or SNF-SWI3 TAZ TRAF
mTERF --- --- --- --- --- --- ---

Protein kinases (PKs)

Column 1 Column 2 Column 3 Column 4 Column 5 Column 6 Column 7 Column 8
AGC-Pl AGC_MAST AGC_NDR AGC_PDK1 AGC_PKA-PKG AGC_RSK-2 Aur AurL-Cr-1
BUB CAMK_AMPK CAMK_CAMK1-DCAMKL CAMK_CAMK1-Tthe CAMK_CAMKL-CHK1 CAMK_CAMKL-LKB CAMK_CDPK CAMK_Cr-1
CAMK_OST1L CK1_CK1 CK1_CK1-Pl CMGC_CDK-CCRK CMGC_CDK-CDK7 CMGC_CDK-CDK8 CMGC_CDK-CRK7-CDK9 CMGC_CDK-PITSLRE
CMGC_CDK-Pl CMGC_CDKL-Cr CMGC_CDKL-Os CMGC_CK2 CMGC_CLK CMGC_DYRK-PRP4 CMGC_DYRK-YAK CMGC_GSK
CMGC_GSKL CMGC_MAPK CMGC_Pl-Tthe CMGC_RCK CMGC_SRPK Group-Cr-1 Group-Pl-2 Group-Pl-3
Group-Pl-4 Group-other IRE1 NAK NEK PEK_GCN2 PEK_PEK RLK-Pelle_C-LEC
RLK-Pelle_CR4L RLK-Pelle_CrRLK1L-1 RLK-Pelle_DLSV RLK-Pelle_DSLV RLK-Pelle_Extensin RLK-Pelle_L-LEC RLK-Pelle_LRK10L-2 RLK-Pelle_LRR-I-1
RLK-Pelle_LRR-I-2 RLK-Pelle_LRR-II RLK-Pelle_LRR-III RLK-Pelle_LRR-IV RLK-Pelle_LRR-IX RLK-Pelle_LRR-V RLK-Pelle_LRR-VI-1 RLK-Pelle_LRR-VI-2
RLK-Pelle_LRR-VII-1 RLK-Pelle_LRR-VII-2 RLK-Pelle_LRR-VII-3 RLK-Pelle_LRR-VIII-1 RLK-Pelle_LRR-XI-1 RLK-Pelle_LRR-XI-2 RLK-Pelle_LRR-XII-1 RLK-Pelle_LRR-XIIIa
RLK-Pelle_LRR-XIIIb RLK-Pelle_LRR-XIV RLK-Pelle_LRR-XV RLK-Pelle_LRR-Xa RLK-Pelle_LRR-Xb-1 RLK-Pelle_LRR-Xb-2 RLK-Pelle_LysM RLK-Pelle_PERK-1
RLK-Pelle_PERK-2 RLK-Pelle_RKF3 RLK-Pelle_RLCK-II RLK-Pelle_RLCK-IV RLK-Pelle_RLCK-IXa RLK-Pelle_RLCK-IXb RLK-Pelle_RLCK-Os RLK-Pelle_RLCK-V
RLK-Pelle_RLCK-VI RLK-Pelle_RLCK-VIII RLK-Pelle_RLCK-VIIa-1 RLK-Pelle_RLCK-VIIa-2 RLK-Pelle_RLCK-VIIb RLK-Pelle_RLCK-X RLK-Pelle_RLCK-XI RLK-Pelle_RLCK-XII-1
RLK-Pelle_RLCK-XII-2 RLK-Pelle_RLCK-XIII RLK-Pelle_RLCK-XV RLK-Pelle_RLCK-XVI RLK-Pelle_SD-2b RLK-Pelle_Singleton RLK-Pelle_URK-1 RLK-Pelle_URK-2
RLK-Pelle_URK-3 RLK-Pelle_URK-Pp-1 RLK-Pelle_WAK RLK-Pelle_WAK_LRK10L-1 SCY1_SCYL1 SCY1_SCYL2 STE_STE-Pl STE_STE11
STE_STE20-Fray STE_STE20-Pl STE_STE20-YSK STE_STE7 TKL-Cr-3 TKL-Cr-4 TKL-Cr-Single TKL-Pl-1
TKL-Pl-2 TKL-Pl-3 TKL-Pl-4 TKL-Pl-5 TKL-Pl-6 TKL-Pl-7 TKL-Pl-8 TKL_CTR1-DRK-1
TKL_CTR1-DRK-2 TKL_Gdt TLK TTK ULK_Fused ULK_ULK4 WEE WNK_NRBP

Results

Select RPs_name Species RPs_type Gene ID Hmm_acc Hmm_name E-value Clan
RB Acco TR Acco08g1910 PF01858 RB_A 7.9e-64 CL0065
RB Accr TR Accr15g00423 PF01858 RB_A 1.8e-63 CL0065
RB Accr TR Accr15g00424 PF01858 RB_A 1.8e-63 CL0065
RB Adu TR Adu06g02882 PF01858 RB_A 1.2e-64 CL0065
RB Aed TR Aed4g1472 PF01858 RB_A 6.9e-65 CL0065
RB Aev TR Aev08g1428 PF01858 RB_A 2.9e-64 CL0065
RB Ahy TR Ahy16g3179 PF01858 RB_A 1.20E-64 CL0065
RB Ahy TR Ahy6g2484 PF01858 RB_A 1.20E-64 CL0065
RB Aip TR Aip06g03429 PF01858 RB_A 1.2e-64 CL0065
RB Alju TR Alju1000051g0002 PF01857 RB_B 3.8e-25 CL0065
RB Alju TR Alju10g1896 PF01858 RB_A 6.2e-64 CL0065
RB Alju TR Alju10g1898 PF01858 RB_A 6.3e-64 CL0065
RB Amo TR Amo06g2815 PF01858 RB_A 6.9e-65 CL0065
RB Amo TR Amo16g3700 PF01858 RB_A 1.2e-64 CL0065
RB Apr TR Apr5g0904 PF01858 RB_A 1.4e-63 CL0065
RB Arst TR Arst6g03743 PF01858 RB_A 1.2e-64 CL0065
RB Arst TR Arst6g03744 PF01858 RB_A 1.2e-64 CL0065
RB Bach TR Bach13g00365 PF01858 RB_A 8.7e-64 CL0065
RB Bach TR Bach9g01288 PF01858 RB_A 5.6e-64 CL0065
RB Bisa TR Bisa02g2538 PF01858 RB_A 5.1e-65 CL0065
RB Bisa TR Bisa12g1619 PF01858 RB_A 1.4e-64 CL0065
RB Bva TR Bva07g01118 PF01858 RB_A 1.9e-63 CL0065
RB Bva TR Bva09g01443 PF01858 RB_A 2e-64 CL0065
RB Car TR Car07g02512 PF01858 RB_A 4.8e-65 CL0065
RB Cca TR Cca04g01805 PF01858 RB_A 5.2e-65 CL0065
RB Dere TR Dere07g1831 PF01858 RB_A 6.5e-65 CL0065
RB Dod TR Dod09g0693 PF01858 RB_A 4.8e-64 CL0065
RB Dod TR Dod10g0059 PF01857 RB_B 9.2e-34 CL0065
RB Enph TR Enph8g1412 PF01858 RB_A 3.9e-50 CL0065
RB Eupl TR Eupl04g00087 PF01858 RB_A 9.9e-66 CL0065
RB Eupl TR Eupl11g00043 PF01858 RB_A 1.2e-63 CL0065
RB Gabi TR Gabi3544g00004 PF01858 RB_A 2.1e-63 CL0065
RB Gabi TR Gabi3544g00005 PF01858 RB_A 2.1e-63 CL0065
RB Gabi TR Gabi745g00001 PF01858 RB_A 3.1e-64 CL0065
RB Glsi TR Glsi04g1837 PF01858 RB_A 4.7e-65 CL0065
RB Glsi TR Glsi14g0358 PF01858 RB_A 2.5e-65 CL0065
RB Gma TR Gma04g01863 PF01858 RB_A 7.8e-64 CL0065
RB Gma TR Gma13g01695 PF01858 RB_A 5.1e-65 CL0065
RB Gma TR Gma15g02221 PF01858 RB_A 9.7e-65 CL0065
RB Gso TR Gso11g2240 PF01858 RB_A 5.1e-65 CL0065
RB Gso TR Gso15g1932 PF01858 RB_A 9.7e-65 CL0065
RB Gso TR Gso4g1621 PF01858 RB_A 7.8e-64 CL0065
RB Lal TR Lal2g0714 PF01858 RB_A 4.1e-64 CL0065
RB Lal TR Lal9g0623 PF01858 RB_A 5.4e-64 CL0065
RB Lan TR Lan7g0709 PF01858 RB_A 4e-64 CL0065
RB Lapu TR Lapu11g01269 PF01858 RB_A 1.8e-64 CL0065
RB Lasa TR Lasa4g01221 PF01858 RB_A 1.6e-62 CL0065
RB Lasa TR Lasa4g01222 PF01858 RB_A 1.6e-62 CL0065
RB Lele TR Lele10g0192 PF01858 RB_A 1e-63 CL0065
RB Lele TR Lele11g0193 PF01857 RB_B 7.7e-28 CL0065
RB Lele TR Lele29g1300 PF01858 RB_A 1.6e-64 CL0065
RB Lele TR Lele30g0238 PF01858 RB_A 1.5e-64 CL0065
RB Lele TR Lele31g0277 PF01858 RB_A 7.5e-64 CL0065
RB Lele TR Lele32g1146 PF01858 RB_A 2.2e-64 CL0065
RB Lja TR Lja1g0138 PF01858 RB_A 2.3e-63 CL0065
RB Lja TR Lja3g2504 PF01858 RB_A 2.1e-64 CL0065
RB Mal TR Mal4g3868 PF01857 RB_B 1.6e-30 CL0065
RB Mal TR Mal5g1814 PF01858 RB_A 9e-62 CL0065
RB Mepo TR Mepo1g03406 PF01858 RB_A 1.5e-62 CL0065
RB Mepo TR Mepo6g01493 PF01857 RB_B 1.1e-26 CL0065
RB Mesa TR Mesa29g03898 PF01858 RB_A 2.5e-62 CL0065
RB Mesa TR Mesa30g03817 PF01858 RB_A 1.5e-62 CL0065
RB Mesa TR Mesa30g03818 PF01858 RB_A 1.5e-62 CL0065
RB Mesa TR Mesa31g03665 PF01858 RB_A 1.4e-62 CL0065
RB Mesa TR Mesa5g03126 PF01857 RB_B 2e-34 CL0065
RB Mesa TR Mesa5g03127 PF01857 RB_B 8e-30 CL0065
RB Mesa TR Mesa6g02805 PF01857 RB_B 2e-34 CL0065
RB Mesa TR Mesa6g02806 PF01857 RB_B 1.5e-29 CL0065
RB Mesa TR Mesa7g03009 PF01858 RB_A 1e-23 CL0065
RB Mesa TR Mesa8g03036 PF01857 RB_B 2.4e-34 CL0065
RB Mesa TR Mesa8g03037 PF01857 RB_B 6.1e-29 CL0065
RB Mibi TR Mibi07g1780 PF01858 RB_A 3.8e-64 CL0065
RB Mtr TR Mtr8g1261 PF01858 RB_A 1.5e-62 CL0065
RB Mupr TR Mupr10045g00001 PF01858 RB_A 7.4e-65 CL0065
RB Phac TR Phac11g02617 PF01858 RB_A 5.2e-64 CL0065
RB Phac TR Phac11g02618 PF01858 RB_A 5.1e-64 CL0065
RB Phco TR Phco9g02141 PF01858 RB_A 5.2e-64 CL0065
RB Pral TR Pral1253g00021 PF01858 RB_A 3.3e-64 CL0065
RB Pral TR Pral2545g00007 PF01858 RB_A 3.4e-64 CL0065
RB Pral TR Pral2545g00008 PF01858 RB_A 3.3e-64 CL0065
RB Prci TR Prci6g2361 PF01858 RB_A 2.4e-64 CL0065
RB Psa TR Psa4g3365 PF01858 RB_A 1.6e-62 CL0065
RB Pste TR Pste1g00182 PF01858 RB_A 9.9e-65 CL0065
RB Pte TR Pte17g00175 PF01858 RB_A 3.9e-64 CL0065
RB Pte TR Pte1g00990 PF01858 RB_A 1.2e-64 CL0065
RB Pte TR Pte1g00991 PF01858 RB_A 1.3e-61 CL0065
RB Pumo TR Pumo10g02834 PF01857 RB_B 4.8e-40 CL0065
RB Pumo TR Pumo3g01397 PF01858 RB_A 1.6e-64 CL0065
RB Pvu TR Pvu11g2095 PF01858 RB_A 5.2e-64 CL0065
RB Rops TR Rops3g02590 PF01858 RB_A 5.7e-62 CL0065
RB Sebi TR Sebi174g00016 PF01858 RB_A 1e-64 CL0065
RB Seca TR Seca3g09635 PF01858 RB_A 1e-64 CL0065
RB Seca TR Seca4g09791 PF01858 RB_A 6.4e-65 CL0065
RB Spst TR Spst11g00073 PF01858 RB_A 9.5e-65 CL0065
RB Ssu TR Ssu2g0277 PF01858 RB_A 5.2e-65 CL0065
RB Sto TR Sto4g2334 PF01858 RB_A 1.4e-64 CL0065
RB Sto TR Sto7g2298 PF01858 RB_A 1.3e-64 CL0065
RB Stsc TR Stsc121354g00002 PF01857 RB_B 7.5e-15 CL0065
RB Stsc TR Stsc90699g00008 PF01858 RB_A 8.8e-65 CL0065
RB Tpr TR Tpr7g1592 PF01858 RB_A 2.1e-61 CL0065
RB Trme TR Trme1834g00001 PF01857 RB_B 2.1e-28 CL0065
RB Trme TR Trme35608g00001 PF01857 RB_B 1e-11 CL0065
RB Trre TR Trre13g05258 PF01857 RB_B 3e-30 CL0065
RB Trre TR Trre15g01497 PF01858 RB_A 2.5e-61 CL0065
RB Trre TR Trre16g01534 PF01858 RB_A 2.2e-61 CL0065
RB Tsu TR Tsu04g04449 PF01857 RB_B 4.3e-30 CL0065
RB Tsu TR Tsu04g04450 PF01858 RB_A 2e-26 CL0065
RB Tsu TR Tsu08g01436 PF01858 RB_A 1.2e-61 CL0065
RB Vian TR Vian5g00158 PF01858 RB_A 3.4e-64 CL0065
RB Vifa TR Vifa4g00782 PF01858 RB_A 8.3e-62 CL0065
RB Vimu TR Vimu5g00270 PF01858 RB_A 1.5e-64 CL0065
RB Vium TR Vium2233g00001 PF01858 RB_A 1.8e-64 CL0065
RB Viun TR Viun11g00212 PF01858 RB_A 2e-64 CL0065
RB Viun TR Viun11g00213 PF01858 RB_A 2e-64 CL0065
RB Viun TR Viun11g00214 PF01858 RB_A 1.9e-64 CL0065
RB Vivi TR Vivi1497g00004 PF01858 RB_A 1.6e-62 CL0065
RB Vivi TR Vivi3g03920 PF01857 RB_B 2e-26 CL0065
RB Vivi TR Vivi7g04824 PF01858 RB_A 1.6e-62 CL0065
RB Vvi TR Vvi14g1301 PF01858 RB_A 1.4e-61 CL0065
RB Vvi TR Vvi4g0264 PF01858 RB_A 6.1e-66 CL0065