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
TLK Acco PK Acco05g0069 PF00069 Pkinase 8.9e-60 CL0016
TLK Accr PK Accr3g02771 PF00069 Pkinase 1.1e-24 CL0016
TLK Accr PK Accr3g02772 PF00069 Pkinase 1.4e-59 CL0016
TLK Accr PK Accr3g02773 PF00069 Pkinase 1.5e-59 CL0016
TLK Accr PK Accr3g02774 PF00069 Pkinase 1.1e-24 CL0016
TLK Accr PK Accr3g02775 PF00069 Pkinase 1.4e-59 CL0016
TLK Accr PK Accr3g02776 PF00069 Pkinase 1.1e-24 CL0016
TLK Adu PK Adu07g00587 PF00069 Pkinase 9.1e-60 CL0016
TLK Aed PK Aed3g2291 PF00069 Pkinase 3.5e-10 CL0016
TLK Aev PK Aev07g0456 PF00069 Pkinase 9.4e-60 CL0016
TLK Ahy PK Ahy17g0686 PF00069 Pkinase 9.10E-60 CL0016
TLK Ahy PK Ahy7g0538 PF00069 Pkinase 9.10E-60 CL0016
TLK Aip PK Aip07g00628 PF00069 Pkinase 9.1e-60 CL0016
TLK Alju PK Alju07g0080 PF00069 Pkinase 1.4e-59 CL0016
TLK Amo PK Amo15g0874 PF00069 Pkinase 9.1e-60 CL0016
TLK Apr PK Apr9g1550 PF00069 Pkinase 9.3e-60 CL0016
TLK Arst PK Arst26235483g00001 PF00069 Pkinase 3.9e-60 CL0016
TLK Arst PK Arst7g00875 PF00069 Pkinase 9.1e-60 CL0016
TLK Arst PK Arst7g00876 PF00069 Pkinase 9.1e-60 CL0016
TLK Bach PK Bach12g01689 PF00069 Pkinase 1.4e-59 CL0016
TLK Bach PK Bach3g00586 PF00069 Pkinase 3.8e-60 CL0016
TLK Bisa PK Bisa05g2257 PF00069 Pkinase 2.5e-60 CL0016
TLK Bva PK Bva12g00756 PF00069 Pkinase 9.6e-61 CL0016
TLK Bva PK Bva12g03053 PF00069 Pkinase 3.5e-60 CL0016
TLK Car PK Car02g01836 PF02463 SMC_N 1.3e-47 CL0023
TLK Cca PK Cca05g01733 PF00069 Pkinase 6e-59 CL0016
TLK Dere PK Dere05g0643 PF00069 Pkinase 8.2e-60 CL0016
TLK Dod PK Dod08g0546 PF00069 Pkinase 5.4e-59 CL0016
TLK Enph PK Enph7g1591 PF00069 Pkinase 2.3e-58 CL0016
TLK Eupl PK Eupl05g00935 PF00069 Pkinase 9.5e-37 CL0016
TLK Gabi PK Gabi3807g00049 PF00069 Pkinase 1.1e-51 CL0016
TLK Gabi PK Gabi3807g00050 PF00069 Pkinase 1e-59 CL0016
TLK Glsi PK Glsi10g2479 PF00069 Pkinase 9.6e-60 CL0016
TLK Gma PK Gma02g02541 PF00069 Pkinase 2.9e-59 CL0016
TLK Gma PK Gma14g00373 PF00069 Pkinase 4e-59 CL0016
TLK Gso PK Gso14g0389 PF00069 Pkinase 4.1e-59 CL0016
TLK Gso PK Gso2g2305 PF00069 Pkinase 2.9e-59 CL0016
TLK Lal PK Lal18g1445 PF00069 Pkinase 1.1e-59 CL0016
TLK Lal PK Lal6g0180 PF00069 Pkinase 4.2e-58 CL0016
TLK Lan PK Lan11g0189 PF00069 Pkinase 4.8e-59 CL0016
TLK Lan PK Lan2g1197 PF00069 Pkinase 3.1e-59 CL0016
TLK Lapu PK Lapu8g01486 PF00069 Pkinase 2.6e-60 CL0016
TLK Lasa PK Lasa2g01941 PF00069 Pkinase 7.2e-62 CL0016
TLK Lele PK Lele25g2023 PF00069 Pkinase 8.3e-60 CL0016
TLK Lele PK Lele26g2075 PF00069 Pkinase 2.1e-27 CL0016
TLK Lele PK Lele27g0054 PF00069 Pkinase 1.5e-59 CL0016
TLK Lele PK Lele28g2076 PF00069 Pkinase 9.5e-22 CL0016
TLK Lja PK Lja2g3255 PF00069 Pkinase 1.7e-59 CL0016
TLK Mal PK Mal8g0883 PF00069 Pkinase 2.6e-59 CL0016
TLK Mepo PK Mepo7g02456 PF00069 Pkinase 5.4e-59 CL0016
TLK Mesa PK Mesa17g03945 PF00069 Pkinase 5.4e-59 CL0016
TLK Mesa PK Mesa17g03947 PF00069 Pkinase 2e-12 CL0016
TLK Mesa PK Mesa17g03952 PF00069 Pkinase 1.3e-12 CL0016
TLK Mesa PK Mesa18g04142 PF00069 Pkinase 5.4e-59 CL0016
TLK Mesa PK Mesa18g04150 PF00069 Pkinase 8.4e-60 CL0016
TLK Mesa PK Mesa18g04158 PF00069 Pkinase 3.9e-19 CL0016
TLK Mesa PK Mesa18g04159 PF00069 Pkinase 3.2e-12 CL0016
TLK Mesa PK Mesa18g04161 PF00069 Pkinase 1.3e-50 CL0016
TLK Mesa PK Mesa18g04162 PF00069 Pkinase 7.5e-58 CL0016
TLK Mesa PK Mesa19g03882 PF00069 Pkinase 3.3e-51 CL0016
TLK Mesa PK Mesa19g03886 PF00069 Pkinase 6.9e-33 CL0016
TLK Mesa PK Mesa19g03891 PF00069 Pkinase 4.4e-10 CL0016
TLK Mesa PK Mesa19g03893 PF00069 Pkinase 9.8e-30 CL0016
TLK Mesa PK Mesa19g03895 PF00069 Pkinase 6.2e-31 CL0016
TLK Mesa PK Mesa20g03951 PF00069 Pkinase 3.3e-51 CL0016
TLK Mesa PK Mesa20g03954 PF00069 Pkinase 1.1e-45 CL0016
TLK Mibi PK Mibi08g0064 PF00069 Pkinase 1.3e-59 CL0016
TLK Mtr PK Mtr5g3005 PF00069 Pkinase 5.5e-59 CL0016
TLK Mtr PK Mtr5g3007 PF00069 Pkinase 1.5e-57 CL0016
TLK Mtr PK Mtr5g3014 PF00069 Pkinase 5e-59 CL0016
TLK Mtr PK Mtr5g3019 PF00069 Pkinase 5.3e-58 CL0016
TLK Mtr PK Mtr5g3020 PF00069 Pkinase 2.6e-58 CL0016
TLK Mupr PK Mupr12770g00003 PF00069 Pkinase 1.5e-59 CL0016
TLK Phac PK Phac8g02795 PF00069 Pkinase 2.2e-16 CL0016
TLK Phac PK Phac8g02796 PF00069 Pkinase 5e-33 CL0016
TLK Phco PK Phco3g00894 PF00069 Pkinase 2.5e-60 CL0016
TLK Pral PK Pral4451g00025 PF00069 Pkinase 5e-55 CL0016
TLK Pral PK Pral4451g00026 PF00069 Pkinase 2.5e-57 CL0016
TLK Pral PK Pral4451g00027 PF00069 Pkinase 2.6e-59 CL0016
TLK Pral PK Pral736g00001 PF00069 Pkinase 8.8e-60 CL0016
TLK Prci PK Prci2g3849 PF00069 Pkinase 3.9e-57 CL0016
TLK Prci PK Prci2g3850 PF00069 Pkinase 3.9e-57 CL0016
TLK Prci PK Prci2g3851 PF00069 Pkinase 4.1e-59 CL0016
TLK Psa PK Psa2g0551 PF00069 Pkinase 3.6e-62 CL0016
TLK Pste PK Pste8g00887 PF00069 Pkinase 2.5e-55 CL0016
TLK Pte PK Pte8g00258 PF00069 Pkinase 3.3e-57 CL0016
TLK Pte PK Pte8g00263 PF00069 Pkinase 3.3e-57 CL0016
TLK Pumo PK Pumo9g02144 PF00069 Pkinase 2.9e-59 CL0016
TLK Pvu PK Pvu8g2175 PF00069 Pkinase 2.5e-60 CL0016
TLK Rops PK Rops9g00650 PF00069 Pkinase 6.9e-58 CL0016
TLK Sebi PK Sebi45g00110 PF00069 Pkinase 2.9e-60 CL0016
TLK Sebi PK Sebi575g00013 PF00069 Pkinase 5.3e-60 CL0016
TLK Seca PK Seca7g00639 PF00069 Pkinase 3.1e-34 CL0016
TLK Seca PK Seca8g00685 PF00069 Pkinase 3.1e-34 CL0016
TLK Spst PK Spst8g00629 PF00069 Pkinase 1.5e-60 CL0016
TLK Ssu PK Ssu6g3215 PF00069 Pkinase 3.8e-12 CL0016
TLK Sto PK Sto5g2159 PF00069 Pkinase 2.4e-59 CL0016
TLK Stsc PK Stsc120965g00004 PF00069 Pkinase 4e-59 CL0016
TLK Stsc PK Stsc200g00002 PF00069 Pkinase 9.3e-59 CL0016
TLK Tpr PK Tpr1g3012 PF00069 Pkinase 1.7e-57 CL0016
TLK Tpr PK Tpr4g2119 PF00069 Pkinase 2.9e-60 CL0016
TLK Tpr PK Tpr4g2214 PF00069 Pkinase 2.9e-60 CL0016
TLK Trme PK Trme48732g00001 PF00069 Pkinase 9.2e-17 CL0016
TLK Trme PK Trme8684g00001 PF00069 Pkinase 1.1e-40 CL0016
TLK Trre PK Trre10g04458 PF00069 Pkinase 5.1e-60 CL0016
TLK Trre PK Trre10g04459 PF00069 Pkinase 5e-60 CL0016
TLK Trre PK Trre1g01157 PF00069 Pkinase 1.5e-41 CL0016
TLK Trre PK Trre9g04598 PF00069 Pkinase 5.1e-60 CL0016
TLK Trre PK Trre9g04599 PF00069 Pkinase 5e-60 CL0016
TLK Tsu PK Tsu05g03508 PF02463 SMC_N 1.9e-63 CL0023
TLK Vian PK Vian7g01425 PF00069 Pkinase 2.3e-60 CL0016
TLK Vifa PK Vifa1g02683 PF00069 Pkinase 1.1e-61 CL0016
TLK Vifa PK Vifa1g02684 PF00069 Pkinase 1e-59 CL0016
TLK Vimu PK Vimu1g00707 PF00069 Pkinase 8.2e-24 CL0016
TLK Viun PK Viun8g02516 PF00069 Pkinase 2.3e-60 CL0016
TLK Viun PK Viun8g02517 PF00069 Pkinase 2.2e-60 CL0016
TLK Vivi PK Vivi7g03083 PF00069 Pkinase 2e-61 CL0016
TLK Vivi PK Vivi7g03084 PF00069 Pkinase 1.7e-61 CL0016
TLK Vra PK Vra6g0449 PF00069 Pkinase 2.2e-60 CL0016
TLK Vvi PK Vvi6g0946 PF00069 Pkinase 3.3e-59 CL0016