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
ULT Acco TF Acco01g3513 None None None None
ULT Acco TF Acco08g0664 None None None None
ULT Accr TF Accr13g00673 None None None None
ULT Accr TF Accr1g03196 None None None None
ULT Adu TF Adu03g01366 PF01342 SAND 3.6e-05 No_clan
ULT Adu TF Adu08g01648 PF01342 SAND 4e-05 No_clan
ULT Aed TF Aed5g0816 None None None None
ULT Aed TF Aed5g1109 None None None None
ULT Aev TF Aev10g2007 None None None None
ULT Ahy TF Ahy13g1512 PF01342 SAND 9.80E-05 No_clan
ULT Ahy TF Ahy18g0841 PF01342 SAND 4.00E-05 No_clan
ULT Ahy TF Ahy3g1251 PF01342 SAND 9.80E-05 No_clan
ULT Ahy TF Ahy8g1605 PF01342 SAND 3.90E-05 No_clan
ULT Aip TF Aip03g01690 PF01342 SAND 3.5e-05 No_clan
ULT Aip TF Aip08g00872 PF01342 SAND 2.9e-05 No_clan
ULT Alju TF Alju02g0484 None None None None
ULT Alju TF Alju10g0683 None None None None
ULT Amo TF Amo18g0845 PF01342 SAND 4e-05 No_clan
ULT Amo TF Amo18g0854 PF01342 SAND 3.9e-05 No_clan
ULT Apr TF Apr2g1947 PF01342 SAND 4.3e-05 No_clan
ULT Apr TF Apr3g1085 PF01342 SAND 8e-05 No_clan
ULT Arst TF Arst3g01750 None None None None
ULT Arst TF Arst8g02252 PF01342 SAND 2.8e-05 No_clan
ULT Bach TF Bach13g01014 PF01342 SAND 0.00017 No_clan
ULT Bach TF Bach9g00474 PF01342 SAND 4.5e-05 No_clan
ULT Bisa TF Bisa02g3311 None None None None
ULT Bisa TF Bisa12g0894 None None None None
ULT Bva TF Bva06g00048 None None None None
ULT Bva TF Bva07g02055 None None None None
ULT Bva TF Bva09g00575 PF01342 SAND 0.00017 No_clan
ULT Bva TF Bva09g00818 None None None None
ULT Car TF Car06g03177 PF01342 SAND 0.00019 No_clan
ULT Cca TF Cca04g01091 PF01342 SAND 0.0001 No_clan
ULT Cca TF Cca04g01379 None None None None
ULT Dere TF Dere07g0410 PF01342 SAND 0.00012 No_clan
ULT Dere TF Dere08g0743 None None None None
ULT Dod TF Dod10g1296 PF01342 SAND 2.6e-05 No_clan
ULT Enph TF Enph3g1165 None None None None
ULT Enph TF Enph8g0628 PF01342 SAND 3e-05 No_clan
ULT Eupl TF Eupl02g00125 PF01342 SAND 9.7e-05 No_clan
ULT Eupl TF Eupl06g00811 PF01342 SAND 0.00014 No_clan
ULT Gabi TF Gabi4579g00028 PF01342 SAND 4e-05 No_clan
ULT Gabi TF Gabi4921g00001 PF01342 SAND 8.9e-05 No_clan
ULT Glsi TF Glsi04g0730 PF01342 SAND 0.00018 No_clan
ULT Glsi TF Glsi14g1355 None None None None
ULT Gma TF Gma06g02305 None None None None
ULT Gma TF Gma06g02307 None None None None
ULT Gma TF Gma06g02656 PF01342 SAND 1.5e-05 No_clan
ULT Gma TF Gma12g00964 PF01342 SAND 0.0001 No_clan
ULT Gso TF Gso12g0885 PF01342 SAND 0.0001 No_clan
ULT Gso TF Gso6g2085 None None None None
ULT Gso TF Gso6g2086 None None None None
ULT Gso TF Gso6g2087 None None None None
ULT Gso TF Gso6g2099 None None None None
ULT Gso TF Gso6g2100 None None None None
ULT Gso TF Gso6g2439 PF01342 SAND 0.00015 No_clan
ULT Lal TF Lal10g0708 PF01342 SAND 2.7e-05 No_clan
ULT Lal TF Lal1g0478 PF01342 SAND 0.00016 No_clan
ULT Lal TF Lal2g0450 PF01342 SAND 1.2e-05 No_clan
ULT Lal TF Lal9g0497 None None None None
ULT Lan TF Lan13g0487 PF01342 SAND 0.00018 No_clan
ULT Lan TF Lan4g1000 PF01342 SAND 1.5e-05 No_clan
ULT Lan TF Lan7g0463 PF01342 SAND 2.2e-05 No_clan
ULT Lapu TF Lapu11g00172 PF01342 SAND 0.00019 No_clan
ULT Lasa TF Lasa1g06360 PF01342 SAND 0.00013 No_clan
ULT Lasa TF Lasa7g01101 PF01342 SAND 9.9e-05 No_clan
ULT Lasa TF Lasa7g01102 PF01342 SAND 9.7e-05 No_clan
ULT Lele TF Lele09g0881 None None None None
ULT Lele TF Lele10g0807 None None None None
ULT Lele TF Lele11g0887 None None None None
ULT Lele TF Lele12g0456 None None None None
ULT Lele TF Lele29g0525 None None None None
ULT Lele TF Lele30g0888 None None None None
ULT Lele TF Lele31g1020 None None None None
ULT Lele TF Lele32g0502 None None None None
ULT Lja TF Lja3g1164 PF01342 SAND 1.6e-05 No_clan
ULT Lja TF Lja3g1340 None None None None
ULT Lja TF Lja3g2445 PF01342 SAND 7.6e-05 No_clan
ULT Mal TF Mal4g1184 PF01342 SAND 4.3e-05 No_clan
ULT Mal TF Mal7g1526 PF01342 SAND 5.1e-05 No_clan
ULT Mepo TF Mepo6g03608 PF01342 SAND 1.1e-05 No_clan
ULT Mesa TF Mesa13g03857 None None None None
ULT Mesa TF Mesa14g04077 PF01342 SAND 2.9e-05 No_clan
ULT Mesa TF Mesa15g03937 PF01342 SAND 2.1e-06 No_clan
ULT Mesa TF Mesa16g04061 None None None None
ULT Mesa TF Mesa5g00831 PF01342 SAND 8.4e-06 No_clan
ULT Mesa TF Mesa6g00765 PF01342 SAND 1e-05 No_clan
ULT Mesa TF Mesa8g00834 PF01342 SAND 1e-05 No_clan
ULT Mesa TF Mesaun15407g00001 None None None None
ULT Mibi TF Mibi01g0417 None None None None
ULT Mibi TF Mibi07g0671 None None None None
ULT Mtr TF Mtr2g3059 PF01342 SAND 1.1e-05 No_clan
ULT Mtr TF Mtr4g1306 PF01342 SAND 2.7e-05 No_clan
ULT Mupr TF Mupr4334g00002 PF01342 SAND 9.9e-05 No_clan
ULT Mupr TF Mupr4667g00001 None None None None
ULT Phac TF Phac11g01642 None None None None
ULT Phco TF Phco9g01259 None None None None
ULT Pral TF Pral4073g00022 PF01342 SAND 0.00014 No_clan
ULT Pral TF Pral4115g00010 PF01342 SAND 0.00014 No_clan
ULT Pral TF Pral4649g00043 None None None None
ULT Pral TF Pral4649g00044 None None None None
ULT Prci TF Prci6g0827 PF01342 SAND 0.00019 No_clan
ULT Psa TF Psa5g6206 None None None None
ULT Psa TF Psa7g4584 PF01342 SAND 0.00012 No_clan
ULT Pste TF Pste1g03311 None None None None
ULT Pste TF Pste1g03932 None None None None
ULT Pte TF Pte10g00744 None None None None
ULT Pte TF Pte15g01683 PF01342 SAND 2.6e-05 No_clan
ULT Pte TF Pte17g00502 None None None None
ULT Pte TF Pte1g01484 None None None None
ULT Pte TF Pte6g00985 PF01342 SAND 1.7e-05 No_clan
ULT Pumo TF Pumo11g00729 None None None None
ULT Pumo TF Pumo11g01120 PF01342 SAND 9.7e-05 No_clan
ULT Pvu TF Pvu11g1155 PF01342 SAND 0.00019 No_clan
ULT Rops TF Rops3g01375 PF01342 SAND 3.8e-05 No_clan
ULT Rops TF Rops3g01818 PF01342 SAND 0.00011 No_clan
ULT Rops TF Rops7g00960 PF01342 SAND 0.00015 No_clan
ULT Sebi TF Sebi800g00006 None None None None
ULT Seca TF Seca3g04519 PF01342 SAND 7.9e-05 No_clan
ULT Seca TF Seca3g05379 None None None None
ULT Seca TF Seca3g09294 None None None None
ULT Seca TF Seca4g05029 PF01342 SAND 7.8e-05 No_clan
ULT Seca TF Seca4g05563 PF01342 SAND 0.00011 No_clan
ULT Seca TF Seca4g09459 None None None None
ULT Spst TF Spst11g01026 PF01342 SAND 8.1e-05 No_clan
ULT Ssu TF Ssu3g1859 None None None None
ULT Ssu TF Ssu3g2173 PF01342 SAND 0.00012 No_clan
ULT Sto TF Sto12g0605 PF01342 SAND 8.8e-05 No_clan
ULT Sto TF Sto7g0580 None None None None
ULT Stsc TF Stsc120831g00027 PF01342 SAND 2.8e-05 No_clan
ULT Stsc TF Stsc181372g00005 None None None None
ULT Stsc TF Stsc30940g00003 PF01342 SAND 0.00015 No_clan
ULT Stsc TF Stsc60654g00011 PF01342 SAND 2.8e-05 No_clan
ULT Tpr TF Tpr4g1341 PF01342 SAND 5.6e-06 No_clan
ULT Tpr TF Tpr7g4016 PF01342 SAND 2.3e-05 No_clan
ULT Tpr TF Tpr7g4225 PF01342 SAND 2.3e-05 No_clan
ULT Trme TF Trme30479g00001 None None None None
ULT Trme TF Trme5601g00001 None None None None
ULT Trre TF Trre11g04043 PF01342 SAND 0.00014 No_clan
ULT Trre TF Trre12g03839 PF01342 SAND 2.2e-05 No_clan
ULT Trre TF Trre7g01219 PF01342 SAND 1.6e-05 No_clan
ULT Trre TF Trre8g01239 PF01342 SAND 3.2e-05 No_clan
ULT Tsu TF Tsu02g04911 PF01342 SAND 3e-05 No_clan
ULT Tsu TF Tsu06g01123 PF01342 SAND 6.6e-06 No_clan
ULT Vian TF Vian5g00832 None None None None
ULT Vifa TF Vifa1g01780 PF01342 SAND 9.7e-05 No_clan
ULT Vifa TF Vifaun4238g00002 PF01342 SAND 0.00012 No_clan
ULT Vimu TF Vimu5g01497 None None None None
ULT Vium TF Vium7609g00001 None None None None
ULT Viun TF Viun11g01481 None None None None
ULT Vivi TF Vivi2g06902 PF01342 SAND 5.2e-05 No_clan
ULT Vivi TF Vivi5g01742 PF01342 SAND 0.00012 No_clan
ULT Vra TF Vra2g1006 PF01342 SAND 9.7e-05 No_clan
ULT Vvi TF Vvi12g0578 None None None None