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
SCY1_SCYL2 Acco PK Acco01g2335 PF00069 Pkinase 3e-24 CL0016
SCY1_SCYL2 Accr PK Accr1g02026 PF00069 Pkinase 3e-24 CL0016
SCY1_SCYL2 Adu PK Adu10g02124 PF00069 Pkinase 4.1e-24 CL0016
SCY1_SCYL2 Aev PK Aev08g1441 PF00069 Pkinase 1.6e-21 CL0016
SCY1_SCYL2 Ahy PK Ahy10g1868 PF00069 Pkinase 7.00E-24 CL0016
SCY1_SCYL2 Ahy PK Ahy20g2340 PF00069 Pkinase 4.50E-24 CL0016
SCY1_SCYL2 Aip PK Aip10g02766 PF00069 Pkinase 4.5e-24 CL0016
SCY1_SCYL2 Alju PK Alju02g1714 PF00069 Pkinase 5.2e-24 CL0016
SCY1_SCYL2 Amo PK Amo02g1345 PF00069 Pkinase 4.3e-24 CL0016
SCY1_SCYL2 Amo PK Amo20g3087 PF00069 Pkinase 4.5e-24 CL0016
SCY1_SCYL2 Apr PK Apr1g0014 PF00069 Pkinase 8.1e-23 CL0016
SCY1_SCYL2 Arst PK Arst10g02709 PF00069 Pkinase 4.1e-24 CL0016
SCY1_SCYL2 Bach PK Bach9g01814 PF00069 Pkinase 3.3e-22 CL0016
SCY1_SCYL2 Bisa PK Bisa02g2312 PF00069 Pkinase 2.2e-22 CL0016
SCY1_SCYL2 Bisa PK Bisa12g1974 PF00069 Pkinase 1.4e-22 CL0016
SCY1_SCYL2 Bva PK Bva07g00055 PF00069 Pkinase 9.2e-23 CL0016
SCY1_SCYL2 Car PK Car06g02874 PF00069 Pkinase 5.5e-20 CL0016
SCY1_SCYL2 Cca PK Cca04g01973 PF00069 Pkinase 2.8e-23 CL0016
SCY1_SCYL2 Dere PK Dere07g1606 PF00069 Pkinase 8.1e-12 CL0016
SCY1_SCYL2 Dere PK Dere08g1823 PF00069 Pkinase 6e-24 CL0016
SCY1_SCYL2 Dod PK Dod09g0557 PF00069 Pkinase 1e-23 CL0016
SCY1_SCYL2 Enph PK Enph3g0266 PF00069 Pkinase 1.5e-22 CL0016
SCY1_SCYL2 Eupl PK Eupl02g00858 PF00069 Pkinase 1e-19 CL0016
SCY1_SCYL2 Gabi PK Gabi3912g00004 PF00069 Pkinase 3.9e-23 CL0016
SCY1_SCYL2 Glsi PK Glsi14g0076 PF00069 Pkinase 2.7e-24 CL0016
SCY1_SCYL2 Gma PK Gma09g00024 PF00069 Pkinase 1.8e-22 CL0016
SCY1_SCYL2 Gma PK Gma12g02261 PF00069 Pkinase 1.2e-24 CL0016
SCY1_SCYL2 Gso PK Gso12g2040 PF00069 Pkinase 1.2e-24 CL0016
SCY1_SCYL2 Gso PK Gso9g0015 PF00069 Pkinase 1.8e-22 CL0016
SCY1_SCYL2 Lal PK Lal2g0850 PF00069 Pkinase 1.1e-24 CL0016
SCY1_SCYL2 Lal PK Lal9g0715 PF00069 Pkinase 1.6e-24 CL0016
SCY1_SCYL2 Lan PK Lan7g0865 PF00069 Pkinase 2.3e-24 CL0016
SCY1_SCYL2 Lan PK Lan8g1239 PF00069 Pkinase 1.3e-23 CL0016
SCY1_SCYL2 Lapu PK Lapu11g01168 PF00069 Pkinase 1.8e-24 CL0016
SCY1_SCYL2 Lasa PK Lasa7g00766 PF00069 Pkinase 4.6e-21 CL0016
SCY1_SCYL2 Lele PK Lele10g0004 PF00069 Pkinase 2.2e-22 CL0016
SCY1_SCYL2 Lele PK Lele11g0006 PF00069 Pkinase 9e-20 CL0016
SCY1_SCYL2 Lele PK Lele12g1241 PF00069 Pkinase 4.9e-23 CL0016
SCY1_SCYL2 Lja PK Lja3g4757 PF00069 Pkinase 1.8e-22 CL0016
SCY1_SCYL2 Mal PK Mal7g0968 PF00069 Pkinase 3e-21 CL0016
SCY1_SCYL2 Mepo PK Mepo2g00912 PF00069 Pkinase 5.7e-21 CL0016
SCY1_SCYL2 Mesa PK Mesa13g04442 PF00069 Pkinase 2e-21 CL0016
SCY1_SCYL2 Mesa PK Mesa14g04660 PF00069 Pkinase 2.5e-21 CL0016
SCY1_SCYL2 Mesa PK Mesa15g04534 PF00069 Pkinase 2.5e-21 CL0016
SCY1_SCYL2 Mesa PK Mesa16g04644 PF00069 Pkinase 2.5e-21 CL0016
SCY1_SCYL2 Mibi PK Mibi01g1594 PF00069 Pkinase 5.5e-24 CL0016
SCY1_SCYL2 Mtr PK Mtr4g0870 PF00069 Pkinase 2e-21 CL0016
SCY1_SCYL2 Mupr PK Mupr1738g00002 PF00069 Pkinase 1.2e-24 CL0016
SCY1_SCYL2 Phac PK Phac11g02798 PF00069 Pkinase 5.6e-23 CL0016
SCY1_SCYL2 Phco PK Phco16g00009 PF00069 Pkinase 1.1e-23 CL0016
SCY1_SCYL2 Pral PK Pral3429g00020 PF00069 Pkinase 5e-24 CL0016
SCY1_SCYL2 Prci PK Prci7g0295 PF00069 Pkinase 3.2e-24 CL0016
SCY1_SCYL2 Psa PK Psa7g5227 PF00069 Pkinase 5.7e-21 CL0016
SCY1_SCYL2 Pste PK Pste1g04210 PF00069 Pkinase 1.5e-24 CL0016
SCY1_SCYL2 Pte PK Pte7g01368 PF00069 Pkinase 2.5e-23 CL0016
SCY1_SCYL2 Pumo PK Pumo10g02737 PF00069 Pkinase 4e-24 CL0016
SCY1_SCYL2 Pvu PK Pvu11g2247 PF00069 Pkinase 5e-23 CL0016
SCY1_SCYL2 Rops PK Rops3g02823 PF00069 Pkinase 2.2e-23 CL0016
SCY1_SCYL2 Sebi PK Sebi210g00020 PF00069 Pkinase 4.5e-23 CL0016
SCY1_SCYL2 Sebi PK Sebi891g00019 PF00069 Pkinase 1.2e-22 CL0016
SCY1_SCYL2 Seca PK Seca3g09849 PF00069 Pkinase 3.5e-23 CL0016
SCY1_SCYL2 Seca PK Seca4g10013 PF00069 Pkinase 5.1e-23 CL0016
SCY1_SCYL2 Ssu PK Ssu2g0150 PF00069 Pkinase 6.1e-25 CL0016
SCY1_SCYL2 Sto PK Sto4g2520 PF00069 Pkinase 3e-25 CL0016
SCY1_SCYL2 Sto PK Sto7g2489 PF00069 Pkinase 1.7e-22 CL0016
SCY1_SCYL2 Stsc PK Stsc241812g00003 PF00069 Pkinase 1.7e-23 CL0016
SCY1_SCYL2 Stsc PK Stsc60419g00006 PF00069 Pkinase 8.6e-24 CL0016
SCY1_SCYL2 Tpr PK Tpr4g1082 PF00069 Pkinase 1.6e-20 CL0016
SCY1_SCYL2 Trme PK Trme15098g00001 PF00069 Pkinase 5.1e-09 CL0016
SCY1_SCYL2 Trre PK Trre7g00868 PF00069 Pkinase 1.7e-20 CL0016
SCY1_SCYL2 Trre PK Trre8g00921 PF00069 Pkinase 1.7e-20 CL0016
SCY1_SCYL2 Tsu PK Tsu06g00803 PF00069 Pkinase 6.6e-20 CL0016
SCY1_SCYL2 Vian PK Vian5g00017 PF00069 Pkinase 7.1e-26 CL0016
SCY1_SCYL2 Vifa PK Vifa2g04968 PF00069 Pkinase 8e-21 CL0016
SCY1_SCYL2 Vium PK Vium2446g00016 PF00069 Pkinase 7.1e-26 CL0016
SCY1_SCYL2 Viun PK Viun11g00009 PF00069 Pkinase 1.7e-24 CL0016
SCY1_SCYL2 Vivi PK Vivi554g00008 PF00069 Pkinase 3.3e-20 CL0016
SCY1_SCYL2 Vivi PK Vivi5g01425 PF00069 Pkinase 5.6e-20 CL0016
SCY1_SCYL2 Vra PK Vra2g1633 PF00069 Pkinase 7.2e-26 CL0016
SCY1_SCYL2 Vvi PK Vvi18g2001 PF00069 Pkinase 1.1e-19 CL0016