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
TKL-Pl-7 Acco PK Acco05g0781 PF07714 PK_Tyr_Ser-Thr 2.5e-41 CL0016
TKL-Pl-7 Accr PK Accr3g02112 PF07714 PK_Tyr_Ser-Thr 8.2e-42 CL0016
TKL-Pl-7 Adu PK Adu07g01321 PF07714 PK_Tyr_Ser-Thr 1.8e-42 CL0016
TKL-Pl-7 Aed PK Aed3g1873 PF07714 PK_Tyr_Ser-Thr 1.3e-42 CL0016
TKL-Pl-7 Aed PK Aed4g2216 PF07714 PK_Tyr_Ser-Thr 5.2e-41 CL0016
TKL-Pl-7 Aev PK Aev07g2140 PF07714 PK_Tyr_Ser-Thr 2.7e-42 CL0016
TKL-Pl-7 Ahy PK Ahy17g1442 PF07714 PK_Tyr_Ser-Thr 1.70E-42 CL0016
TKL-Pl-7 Ahy PK Ahy7g1188 PF07714 PK_Tyr_Ser-Thr 1.70E-42 CL0016
TKL-Pl-7 Aip PK Aip07g01416 PF07714 PK_Tyr_Ser-Thr 1.7e-42 CL0016
TKL-Pl-7 Alju PK Alju07g0797 PF07714 PK_Tyr_Ser-Thr 1.5e-41 CL0016
TKL-Pl-7 Amo PK Amo07g0989 PF07714 PK_Tyr_Ser-Thr 1.7e-42 CL0016
TKL-Pl-7 Amo PK Amo07g0993 PF07714 PK_Tyr_Ser-Thr 9.1e-43 CL0016
TKL-Pl-7 Apr PK Apr10g1824 PF07714 PK_Tyr_Ser-Thr 2.4e-42 CL0016
TKL-Pl-7 Apr PK Apr9g1150 PF07714 PK_Tyr_Ser-Thr 9.2e-42 CL0016
TKL-Pl-7 Arst PK Arst7g01714 PF07714 PK_Tyr_Ser-Thr 1.8e-42 CL0016
TKL-Pl-7 Bach PK Bach12g02060 PF07714 PK_Tyr_Ser-Thr 1.5e-41 CL0016
TKL-Pl-7 Bisa PK Bisa05g2913 PF07714 PK_Tyr_Ser-Thr 4.4e-41 CL0016
TKL-Pl-7 Bisa PK Bisa09g0353 PF07714 PK_Tyr_Ser-Thr 7.6e-42 CL0016
TKL-Pl-7 Bva PK Bva12g00334 PF07714 PK_Tyr_Ser-Thr 1e-41 CL0016
TKL-Pl-7 Car PK Car02g01371 PF07714 PK_Tyr_Ser-Thr 7e-38 CL0016
TKL-Pl-7 Car PK Car05g01314 PF07714 PK_Tyr_Ser-Thr 3.1e-43 CL0016
TKL-Pl-7 Cca PK Cca01g00633 PF07714 PK_Tyr_Ser-Thr 6.7e-43 CL0016
TKL-Pl-7 Cca PK Cca05g01291 PF07714 PK_Tyr_Ser-Thr 2e-42 CL0016
TKL-Pl-7 Dere PK Dere04g1893 PF07714 PK_Tyr_Ser-Thr 1e-42 CL0016
TKL-Pl-7 Dere PK Dere05g0087 PF07714 PK_Tyr_Ser-Thr 6e-42 CL0016
TKL-Pl-7 Dod PK Dod08g1026 PF07714 PK_Tyr_Ser-Thr 3.1e-40 CL0016
TKL-Pl-7 Enph PK Enph7g1960 PF07714 PK_Tyr_Ser-Thr 3.4e-41 CL0016
TKL-Pl-7 Eupl PK Eupl01g01000 PF07714 PK_Tyr_Ser-Thr 6.4e-43 CL0016
TKL-Pl-7 Eupl PK Eupl05g02202 PF07714 PK_Tyr_Ser-Thr 6.7e-40 CL0016
TKL-Pl-7 Gabi PK Gabi4624g00090 PF07714 PK_Tyr_Ser-Thr 6.5e-39 CL0016
TKL-Pl-7 Gabi PK Gabi5000g00002 PF07714 PK_Tyr_Ser-Thr 1.4e-42 CL0016
TKL-Pl-7 Glsi PK Glsi08g0384 PF07714 PK_Tyr_Ser-Thr 4.4e-44 CL0016
TKL-Pl-7 Glsi PK Glsi10g2820 PF07714 PK_Tyr_Ser-Thr 3.2e-13 CL0016
TKL-Pl-7 Gma PK Gma02g02174 PF07714 PK_Tyr_Ser-Thr 3.4e-43 CL0016
TKL-Pl-7 Gma PK Gma11g01859 PF07714 PK_Tyr_Ser-Thr 1.4e-40 CL0016
TKL-Pl-7 Gma PK Gma14g01945 PF07714 PK_Tyr_Ser-Thr 5.1e-42 CL0016
TKL-Pl-7 Gma PK Gma18g00554 PF00899 ThiF 3.6e-75 CL0063
TKL-Pl-7 Gso PK Gso11g1679 PF07714 PK_Tyr_Ser-Thr 1.4e-40 CL0016
TKL-Pl-7 Gso PK Gso14g1655 PF07714 PK_Tyr_Ser-Thr 5.1e-42 CL0016
TKL-Pl-7 Gso PK Gso18g0521 PF07714 PK_Tyr_Ser-Thr 5.6e-40 CL0016
TKL-Pl-7 Gso PK Gso2g1955 PF07714 PK_Tyr_Ser-Thr 3.4e-43 CL0016
TKL-Pl-7 Lal PK Lal18g1250 PF07714 PK_Tyr_Ser-Thr 4.5e-38 CL0016
TKL-Pl-7 Lal PK Lal22g0344 PF07714 PK_Tyr_Ser-Thr 2.6e-42 CL0016
TKL-Pl-7 Lal PK Lal5g0988 PF07714 PK_Tyr_Ser-Thr 2.3e-40 CL0016
TKL-Pl-7 Lan PK Lan2g1017 PF07714 PK_Tyr_Ser-Thr 1.2e-42 CL0016
TKL-Pl-7 Lan PK Lan9g1211 PF07714 PK_Tyr_Ser-Thr 3.4e-44 CL0016
TKL-Pl-7 Lapu PK Lapu6g02348 PF07714 PK_Tyr_Ser-Thr 9.2e-40 CL0016
TKL-Pl-7 Lapu PK Lapu8g01934 PF07714 PK_Tyr_Ser-Thr 4.4e-41 CL0016
TKL-Pl-7 Lasa PK Lasa2g01263 PF07714 PK_Tyr_Ser-Thr 6.6e-41 CL0016
TKL-Pl-7 Lasa PK Lasa5g01419 PF07714 PK_Tyr_Ser-Thr 4.5e-43 CL0016
TKL-Pl-7 Lele PK Lele25g1672 PF07714 PK_Tyr_Ser-Thr 7.7e-42 CL0016
TKL-Pl-7 Lele PK Lele26g1672 PF07714 PK_Tyr_Ser-Thr 2.1e-41 CL0016
TKL-Pl-7 Lele PK Lele27g0414 PF07714 PK_Tyr_Ser-Thr 5.5e-42 CL0016
TKL-Pl-7 Lele PK Lele28g1675 PF07714 PK_Tyr_Ser-Thr 2.8e-41 CL0016
TKL-Pl-7 Lja PK Lja6g1054 PF07714 PK_Tyr_Ser-Thr 3.3e-41 CL0016
TKL-Pl-7 Mal PK Mal2g3232 PF07714 PK_Tyr_Ser-Thr 6e-43 CL0016
TKL-Pl-7 Mal PK Mal8g1745 PF07714 PK_Tyr_Ser-Thr 6e-40 CL0016
TKL-Pl-7 Mepo PK Mepo3g05094 PF07714 PK_Tyr_Ser-Thr 2.9e-43 CL0016
TKL-Pl-7 Mepo PK Mepo7g01858 PF00899 ThiF 4.6e-74 CL0063
TKL-Pl-7 Mesa PK Mesa10g02374 PF07714 PK_Tyr_Ser-Thr 3.3e-43 CL0016
TKL-Pl-7 Mesa PK Mesa11g02375 PF07714 PK_Tyr_Ser-Thr 2.8e-43 CL0016
TKL-Pl-7 Mesa PK Mesa12g02624 PF07714 PK_Tyr_Ser-Thr 2.8e-43 CL0016
TKL-Pl-7 Mesa PK Mesa17g03166 PF07714 PK_Tyr_Ser-Thr 2.2e-38 CL0016
TKL-Pl-7 Mesa PK Mesa18g03352 PF07714 PK_Tyr_Ser-Thr 2.2e-38 CL0016
TKL-Pl-7 Mesa PK Mesa19g03137 PF07714 PK_Tyr_Ser-Thr 2.8e-38 CL0016
TKL-Pl-7 Mesa PK Mesa20g03519 PF07714 PK_Tyr_Ser-Thr 2.3e-38 CL0016
TKL-Pl-7 Mesa PK Mesa9g02303 PF07714 PK_Tyr_Ser-Thr 4.2e-43 CL0016
TKL-Pl-7 Mibi PK Mibi08g0677 PF07714 PK_Tyr_Ser-Thr 2.8e-42 CL0016
TKL-Pl-7 Mtr PK Mtr3g1744 PF07714 PK_Tyr_Ser-Thr 8e-43 CL0016
TKL-Pl-7 Mtr PK Mtr5g2447 PF07714 PK_Tyr_Ser-Thr 2.3e-38 CL0016
TKL-Pl-7 Mupr PK Mupr3148g00001 PF07714 PK_Tyr_Ser-Thr 4e-42 CL0016
TKL-Pl-7 Phac PK Phac6g01001 PF07714 PK_Tyr_Ser-Thr 1.4e-38 CL0016
TKL-Pl-7 Phac PK Phac8g03452 PF07714 PK_Tyr_Ser-Thr 7.8e-42 CL0016
TKL-Pl-7 Phco PK Phco11g01684 PF00899 ThiF 8e-75 CL0063
TKL-Pl-7 Phco PK Phco3g00364 PF07714 PK_Tyr_Ser-Thr 8e-42 CL0016
TKL-Pl-7 Pral PK Pral1219g00001 PF07714 PK_Tyr_Ser-Thr 1.1e-41 CL0016
TKL-Pl-7 Pral PK Pral3790g00016 PF07714 PK_Tyr_Ser-Thr 1.1e-41 CL0016
TKL-Pl-7 Prci PK Prci2g2964 PF07714 PK_Tyr_Ser-Thr 8.3e-40 CL0016
TKL-Pl-7 Psa PK Psa2g1282 PF07714 PK_Tyr_Ser-Thr 2.1e-40 CL0016
TKL-Pl-7 Psa PK Psa5g3613 PF07714 PK_Tyr_Ser-Thr 4.2e-43 CL0016
TKL-Pl-7 Pste PK Pste8g01646 PF07714 PK_Tyr_Ser-Thr 1.9e-41 CL0016
TKL-Pl-7 Pte PK Pte9g00718 PF07714 PK_Tyr_Ser-Thr 9.7e-41 CL0016
TKL-Pl-7 Pte PK PteUn0120g00001 PF07714 PK_Tyr_Ser-Thr 9.7e-41 CL0016
TKL-Pl-7 Pumo PK Pumo1g00608 PF07714 PK_Tyr_Ser-Thr 1e-41 CL0016
TKL-Pl-7 Pumo PK Pumo9g01586 PF07714 PK_Tyr_Ser-Thr 1.9e-41 CL0016
TKL-Pl-7 Pvu PK Pvu6g0757 PF07714 PK_Tyr_Ser-Thr 8.4e-39 CL0016
TKL-Pl-7 Pvu PK Pvu8g2671 PF07714 PK_Tyr_Ser-Thr 7.9e-42 CL0016
TKL-Pl-7 Rops PK Rops11g02369 PF07714 PK_Tyr_Ser-Thr 5.5e-43 CL0016
TKL-Pl-7 Rops PK Rops9g01250 PF07714 PK_Tyr_Ser-Thr 2.9e-40 CL0016
TKL-Pl-7 Sebi PK Sebi777g00018 PF07714 PK_Tyr_Ser-Thr 1.4e-33 CL0016
TKL-Pl-7 Seca PK Seca6g02614 PF07714 PK_Tyr_Ser-Thr 1.1e-42 CL0016
TKL-Pl-7 Seca PK Seca7g01411 PF07714 PK_Tyr_Ser-Thr 3.8e-42 CL0016
TKL-Pl-7 Seca PK Seca8g01521 PF07714 PK_Tyr_Ser-Thr 3.8e-42 CL0016
TKL-Pl-7 Spst PK Spst6g00129 PF07714 PK_Tyr_Ser-Thr 6.5e-42 CL0016
TKL-Pl-7 Spst PK Spst8g00134 PF07714 PK_Tyr_Ser-Thr 2.6e-41 CL0016
TKL-Pl-7 Ssu PK Ssu6g2683 PF07714 PK_Tyr_Ser-Thr 5.7e-42 CL0016
TKL-Pl-7 Ssu PK Ssu9g1243 PF07714 PK_Tyr_Ser-Thr 3.4e-41 CL0016
TKL-Pl-7 Sto PK Sto9g2204 PF07714 PK_Tyr_Ser-Thr 2.2e-42 CL0016
TKL-Pl-7 Stsc PK Stsc151992g00001 PF07714 PK_Tyr_Ser-Thr 3e-16 CL0016
TKL-Pl-7 Stsc PK Stsc241878g00004 PF07714 PK_Tyr_Ser-Thr 1.7e-42 CL0016
TKL-Pl-7 Tpr PK Tpr3g3700 PF07714 PK_Tyr_Ser-Thr 1e-41 CL0016
TKL-Pl-7 Tpr PK Tpr4g2754 PF07714 PK_Tyr_Ser-Thr 4.2e-41 CL0016
TKL-Pl-7 Trme PK Trme102756g00001 PF07714 PK_Tyr_Ser-Thr 8.4e-21 CL0016
TKL-Pl-7 Trme PK Trme32359g00001 PF07714 PK_Tyr_Ser-Thr 4.3e-09 CL0016
TKL-Pl-7 Trme PK Trme36491g00001 PF07714 PK_Tyr_Ser-Thr 5.7e-08 CL0016
TKL-Pl-7 Trme PK Trme81595g00001 PF07714 PK_Tyr_Ser-Thr 3.8e-17 CL0016
TKL-Pl-7 Trme PK Trme86990g00001 PF07714 PK_Tyr_Ser-Thr 3.7e-21 CL0016
TKL-Pl-7 Trme PK Trme9733g00001 PF07714 PK_Tyr_Ser-Thr 2.1e-21 CL0016
TKL-Pl-7 Trre PK Trre10g03741 PF07714 PK_Tyr_Ser-Thr 7.7e-40 CL0016
TKL-Pl-7 Trre PK Trre5g00354 PF07714 PK_Tyr_Ser-Thr 2.2e-42 CL0016
TKL-Pl-7 Trre PK Trre5g00927 PF07714 PK_Tyr_Ser-Thr 2.2e-42 CL0016
TKL-Pl-7 Trre PK Trre5g02396 PF07714 PK_Tyr_Ser-Thr 9.4e-16 CL0016
TKL-Pl-7 Trre PK Trre6g00848 PF07714 PK_Tyr_Ser-Thr 3e-42 CL0016
TKL-Pl-7 Trre PK Trre9g03788 PF07714 PK_Tyr_Ser-Thr 7.8e-40 CL0016
TKL-Pl-7 Tsu PK Tsu03g00850 PF00899 ThiF 3.4e-73 CL0063
TKL-Pl-7 Tsu PK Tsu05g02884 PF07714 PK_Tyr_Ser-Thr 9e-41 CL0016
TKL-Pl-7 Vian PK Vian6g00654 PF07714 PK_Tyr_Ser-Thr 2.6e-39 CL0016
TKL-Pl-7 Vian PK Vian7g01901 PF07714 PK_Tyr_Ser-Thr 1.3e-40 CL0016
TKL-Pl-7 Vifa PK Vifa1g01336 PF07714 PK_Tyr_Ser-Thr 5.3e-40 CL0016
TKL-Pl-7 Vifa PK Vifa2g01321 PF07714 PK_Tyr_Ser-Thr 1.7e-42 CL0016
TKL-Pl-7 Vimu PK Vimu10g02209 None None None None
TKL-Pl-7 Vimu PK Vimu1g01442 PF07714 PK_Tyr_Ser-Thr 1.5e-41 CL0016
TKL-Pl-7 Vimu PK Vimu2g02133 PF07714 PK_Tyr_Ser-Thr 3.9e-39 CL0016
TKL-Pl-7 Vium PK Vium4775g00001 PF07714 PK_Tyr_Ser-Thr 2.9e-39 CL0016
TKL-Pl-7 Vium PK Vium9434g00004 PF07714 PK_Tyr_Ser-Thr 3.1e-41 CL0016
TKL-Pl-7 Viun PK Viun6g01183 PF07714 PK_Tyr_Ser-Thr 3.4e-40 CL0016
TKL-Pl-7 Viun PK Viun8g01836 PF07714 PK_Tyr_Ser-Thr 8.7e-42 CL0016
TKL-Pl-7 Vivi PK Vivi307g00001 PF07714 PK_Tyr_Ser-Thr 4.3e-43 CL0016
TKL-Pl-7 Vivi PK Vivi3g04734 PF07714 PK_Tyr_Ser-Thr 6.2e-43 CL0016
TKL-Pl-7 Vivi PK Vivi7g01525 PF07714 PK_Tyr_Ser-Thr 2.8e-39 CL0016
TKL-Pl-7 Vvi PK Vvi6g0735 PF07714 PK_Tyr_Ser-Thr 2.6e-41 CL0016