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_SCYL1 Acco PK Acco02g0016 PF00069 Pkinase 4e-08 CL0016
SCY1_SCYL1 Accr PK Accr2g03698 PF00069 Pkinase 9.4e-08 CL0016
SCY1_SCYL1 Adu PK Adu09g01630 PF00069 Pkinase 9.2e-08 CL0016
SCY1_SCYL1 Aev PK Aev09g1519 None None None None
SCY1_SCYL1 Ahy PK Ahy19g1802 PF00069 Pkinase 9.40E-08 CL0016
SCY1_SCYL1 Ahy PK Ahy9g1447 PF00069 Pkinase 9.30E-08 CL0016
SCY1_SCYL1 Aip PK Aip09g02080 PF00069 Pkinase 9.3e-08 CL0016
SCY1_SCYL1 Alju PK Alju01g0022 None None None None
SCY1_SCYL1 Amo PK Amo09g1677 PF00069 Pkinase 9.3e-08 CL0016
SCY1_SCYL1 Amo PK Amo19g2010 PF00069 Pkinase 9.3e-08 CL0016
SCY1_SCYL1 Apr PK Apr4g2296 None None None None
SCY1_SCYL1 Apr PK Apr8g1589 None None None None
SCY1_SCYL1 Arst PK Arst9g02155 PF00069 Pkinase 9.2e-08 CL0016
SCY1_SCYL1 Bach PK Bach1g03414 PF00069 Pkinase 2.4e-10 CL0016
SCY1_SCYL1 Bach PK Bach8g00035 PF00069 Pkinase 8.9e-08 CL0016
SCY1_SCYL1 Bisa PK Bisa03g1596 PF00069 Pkinase 3.4e-08 CL0016
SCY1_SCYL1 Bva PK Bva04g03459 PF00069 Pkinase 4.8e-09 CL0016
SCY1_SCYL1 Bva PK Bva13g03537 PF00069 Pkinase 1.9e-08 CL0016
SCY1_SCYL1 Car PK Car04g00410 None None None None
SCY1_SCYL1 Cca PK Cca07g01982 None None None None
SCY1_SCYL1 Dere PK Dere01g3996 None None None None
SCY1_SCYL1 Dod PK Dod06g1581 None None None None
SCY1_SCYL1 Eupl PK Eupl05g02374 PF06814 Lung_7-TM_R 1.7e-105 CL0192
SCY1_SCYL1 Gabi PK Gabi1662g00023 None None None None
SCY1_SCYL1 Gabi PK Gabi1662g00024 None None None None
SCY1_SCYL1 Gabi PK Gabi4176g00040 PF00069 Pkinase 1.1e-08 CL0016
SCY1_SCYL1 Glsi PK Glsi02g3899 PF00069 Pkinase 3.6e-09 CL0016
SCY1_SCYL1 Gma PK Gma18g02218 None None None None
SCY1_SCYL1 Gso PK Gso18g1903 None None None None
SCY1_SCYL1 Lapu PK Lapu7g01471 None None None None
SCY1_SCYL1 Lasa PK Lasa4g00346 None None None None
SCY1_SCYL1 Lja PK Lja5g1648 None None None None
SCY1_SCYL1 Mal PK Mal8g3959 None None None None
SCY1_SCYL1 Mepo PK Mepo7g00464 None None None None
SCY1_SCYL1 Mesa PK Mesa1g03479 None None None None
SCY1_SCYL1 Mesa PK Mesa21g02805 None None None None
SCY1_SCYL1 Mesa PK Mesa22g03237 None None None None
SCY1_SCYL1 Mesa PK Mesa23g03159 None None None None
SCY1_SCYL1 Mesa PK Mesa24g02112 None None None None
SCY1_SCYL1 Mesa PK Mesa2g03764 None None None None
SCY1_SCYL1 Mibi PK Mibi02g0017 PF00069 Pkinase 6.8e-08 CL0016
SCY1_SCYL1 Mtr PK Mtr6g2235 None None None None
SCY1_SCYL1 Mupr PK Mupr6957g00002 None None None None
SCY1_SCYL1 Phac PK Phac8g00808 None None None None
SCY1_SCYL1 Phco PK Phco3g02659 None None None None
SCY1_SCYL1 Phco PK Phco6g01917 PF00069 Pkinase 4.9e-08 CL0016
SCY1_SCYL1 Pral PK Pral2018g00023 PF00069 Pkinase 5e-08 CL0016
SCY1_SCYL1 Prci PK Prci1g4641 None None None None
SCY1_SCYL1 Prci PK Prci1g4642 None None None None
SCY1_SCYL1 Psa PK Psa4g5083 PF07714 PK_Tyr_Ser-Thr 2.5e-05 CL0016
SCY1_SCYL1 Pste PK Pste5g01221 None None None None
SCY1_SCYL1 Pte PK Pte13g00023 None None None None
SCY1_SCYL1 Pte PK Pte18g02152 None None None None
SCY1_SCYL1 Pumo PK Pumo3g01788 PF07714 PK_Tyr_Ser-Thr 1.3e-05 CL0016
SCY1_SCYL1 Pumo PK Pumo5g00172 None None None None
SCY1_SCYL1 Pvu PK Pvu7g1218 None None None None
SCY1_SCYL1 Pvu PK Pvu8g0565 None None None None
SCY1_SCYL1 Rops PK Rops6g01661 None None None None
SCY1_SCYL1 Sebi PK Sebi213g00028 None None None None
SCY1_SCYL1 Seca PK Seca1g00864 PF00069 Pkinase 3.9e-08 CL0016
SCY1_SCYL1 Seca PK Seca2g00888 PF00069 Pkinase 1.1e-08 CL0016
SCY1_SCYL1 Seca PK Seca8g06178 None None None None
SCY1_SCYL1 Spst PK Spst1g01147 None None None None
SCY1_SCYL1 Ssu PK Ssu3g0647 None None None None
SCY1_SCYL1 Ssu PK Ssu7g1528 PF00069 Pkinase 2.6e-08 CL0016
SCY1_SCYL1 Sto PK Sto8g0032 PF00069 Pkinase 8e-08 CL0016
SCY1_SCYL1 Stsc PK Stsc271925g00012 PF00069 Pkinase 8.8e-08 CL0016
SCY1_SCYL1 Tpr PK Tpr5g0036 None None None None
SCY1_SCYL1 Trre PK Trre3g04022 None None None None
SCY1_SCYL1 Trre PK Trre3g04023 None None None None
SCY1_SCYL1 Trre PK Trre4g03921 None None None None
SCY1_SCYL1 Trre PK Trre4g03922 None None None None
SCY1_SCYL1 Tsu PK Tsu03g03308 None None None None
SCY1_SCYL1 Vian PK Vian3g01239 None None None None
SCY1_SCYL1 Vifa PK Vifaun6657g00001 None None None None
SCY1_SCYL1 Vifa PK Vifaun6657g00002 None None None None
SCY1_SCYL1 Viun PK Viun5g00783 None None None None
SCY1_SCYL1 Viun PK Viun7g02322 None None None None
SCY1_SCYL1 Vivi PK Vivi7g03806 PF07714 PK_Tyr_Ser-Thr 2.8e-05 CL0016
SCY1_SCYL1 Vra PK Vra4g0876 None None None None
SCY1_SCYL1 Vra PK Vra8g1652 None None None None
SCY1_SCYL1 Vvi PK Vvi13g0203 PF00069 Pkinase 2.2e-08 CL0016