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Conserved domains on  [gi|15229445|ref|NP_191909|]
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fibronectin type III domain protein (DUF1423) [Arabidopsis thaliana]

Protein Classification

PHD_OBE1_like and Oberon_cc domain-containing protein( domain architecture ID 11165415)

PHD_OBE1_like and Oberon_cc domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PHD_Oberon pfam07227
PHD - plant homeodomain finger protein; PHD_oberon is a plant homeodomain finger domain of ...
 807-931 2.62e-50

PHD - plant homeodomain finger protein; PHD_oberon is a plant homeodomain finger domain of Oberon proteins from plants. Oberon is necessary for maintenance and/or establishment of both the shoot and root apical meristems in Arabidopsis. Oberon proteins are made up of a PHD finger domain and a coiled-coil domain. The PHD-finger domain is found in a wide variety of proteins involved in the regulation of chromatin structure. Oberon proteins mediate the TMO7 (the direct target of MP) expression through modification of, or binding to, chromatin at the TMO7 locus. TMO7 stands for the target of Monopteros 7 (MP) (or Auxin response factor 7).


:

Pssm-ID: 429357  Cd Length: 130  Bit Score: 173.69  E-value: 2.62e-50
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229445    807 CKNLSCRVLLPVDECDCRVCSRKDGFCSACMCLVCSNFDMASNTCSWVGC-------DVCLHWCHTDCGIKESYIrnGIN 879
Cdd:pfam07227    1 CRNIACRSQLPVDDCDCKICSQEDGFCRRCSCCICHKFDDNKDTCSWIGCsavvsegDSCGHWCHLDCALRDYKT--GTV 78

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 15229445    880 ASGAPGMTEMQFHCVACNHPSEMFGFVKEVFLNFAREWKFERFCKELEYVNK 931
Cdd:pfam07227   79 KKGGSGGLDGQFYCRACGKTSELLGHVKKVLQTCAEAWRRDVLCKELDLGRR 130
Oberon_cc super family cl24780
Coiled-coil region of Oberon; Oberon_cc is the coiled-coil region of Oberon proteins from ...
 1022-1136 5.84e-36

Coiled-coil region of Oberon; Oberon_cc is the coiled-coil region of Oberon proteins from plants. Oberon is necessary for maintenance and/or establishment of both the shoot and root apical meristems in Arabidopsis. Most Oberon proteins carry a PHD finger domain, pfam07227 and this coiled-coil domain. Oberon proteins mediate the TMO7 (the direct target of MP) expression through modification of, or binding to, chromatin at the TMO7 locus. TMO7 stands for the target of Monopteros 7 (or Auxin response factor 7).


The actual alignment was detected with superfamily member pfam16312:

Pssm-ID: 465089 [Multi-domain]  Cd Length: 129  Bit Score: 132.80  E-value: 5.84e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229445   1022 KRSASVADAFHRERQvEICAVEMELERGS-PKEPRFEELESIVRMKQAEAEMFQGRADDARREAEGLKRIAIAKKEKIEE 1100
Cdd:pfam16312    1 KRARLALDACDRELE-DKAREASELKFERqRKKQQIEELESIVRLKQAEAEMFQLKADEARREAEGLQRIALAKSEKSEE 79

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 15229445   1101 EYNRRMGKLSMEDAQERRRRRYEELEAMQRGQREFY 1136
Cdd:pfam16312   80 EYASRYLKLRLEEAEEERRYKFEELKLLENSHRDYD 115
 
Name Accession Description Interval E-value
PHD_Oberon pfam07227
PHD - plant homeodomain finger protein; PHD_oberon is a plant homeodomain finger domain of ...
 807-931 2.62e-50

PHD - plant homeodomain finger protein; PHD_oberon is a plant homeodomain finger domain of Oberon proteins from plants. Oberon is necessary for maintenance and/or establishment of both the shoot and root apical meristems in Arabidopsis. Oberon proteins are made up of a PHD finger domain and a coiled-coil domain. The PHD-finger domain is found in a wide variety of proteins involved in the regulation of chromatin structure. Oberon proteins mediate the TMO7 (the direct target of MP) expression through modification of, or binding to, chromatin at the TMO7 locus. TMO7 stands for the target of Monopteros 7 (MP) (or Auxin response factor 7).


Pssm-ID: 429357  Cd Length: 130  Bit Score: 173.69  E-value: 2.62e-50
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229445    807 CKNLSCRVLLPVDECDCRVCSRKDGFCSACMCLVCSNFDMASNTCSWVGC-------DVCLHWCHTDCGIKESYIrnGIN 879
Cdd:pfam07227    1 CRNIACRSQLPVDDCDCKICSQEDGFCRRCSCCICHKFDDNKDTCSWIGCsavvsegDSCGHWCHLDCALRDYKT--GTV 78

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 15229445    880 ASGAPGMTEMQFHCVACNHPSEMFGFVKEVFLNFAREWKFERFCKELEYVNK 931
Cdd:pfam07227   79 KKGGSGGLDGQFYCRACGKTSELLGHVKKVLQTCAEAWRRDVLCKELDLGRR 130
Oberon_cc pfam16312
Coiled-coil region of Oberon; Oberon_cc is the coiled-coil region of Oberon proteins from ...
 1022-1136 5.84e-36

Coiled-coil region of Oberon; Oberon_cc is the coiled-coil region of Oberon proteins from plants. Oberon is necessary for maintenance and/or establishment of both the shoot and root apical meristems in Arabidopsis. Most Oberon proteins carry a PHD finger domain, pfam07227 and this coiled-coil domain. Oberon proteins mediate the TMO7 (the direct target of MP) expression through modification of, or binding to, chromatin at the TMO7 locus. TMO7 stands for the target of Monopteros 7 (or Auxin response factor 7).


Pssm-ID: 465089 [Multi-domain]  Cd Length: 129  Bit Score: 132.80  E-value: 5.84e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229445   1022 KRSASVADAFHRERQvEICAVEMELERGS-PKEPRFEELESIVRMKQAEAEMFQGRADDARREAEGLKRIAIAKKEKIEE 1100
Cdd:pfam16312    1 KRARLALDACDRELE-DKAREASELKFERqRKKQQIEELESIVRLKQAEAEMFQLKADEARREAEGLQRIALAKSEKSEE 79

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 15229445   1101 EYNRRMGKLSMEDAQERRRRRYEELEAMQRGQREFY 1136
Cdd:pfam16312   80 EYASRYLKLRLEEAEEERRYKFEELKLLENSHRDYD 115
PHD_OBE1_like cd15612
PHD finger found in Arabidopsis thaliana protein OBERON 1, OBERON 2, and similar proteins ...
 837-896 4.29e-31

PHD finger found in Arabidopsis thaliana protein OBERON 1, OBERON 2, and similar proteins mainly found in plants; Included in this family are OBERON 1 (OBE1, or potyvirus VPg-interacting protein 2) and OBERON 2 (OBE2, or potyvirus VPg-interacting protein 1), which have been involved in the maintenance and/or establishment of the meristems in Arabidopsis. They interact with potyvirus VPg-interacting proteins (PVIP1 and 2) and act as central regulators in auxin-mediated control of development. Both OBE1and OBE2 contain a plant homeodomain (PHD) finger. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins.


Pssm-ID: 277084  Cd Length: 60  Bit Score: 116.18  E-value: 4.29e-31
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229445  837 MCLVCSNFDMASNTCSWVGCDVCLHWCHTDCGIKESYIRNGINASGAPGMTEMQFHCVAC 896
Cdd:cd15612    1 MCPICSKFDFAVNTCSWIGCDVCSHWTHTDCAIRSGEISMGVSLKGVEGSTEMEFHCRAC 60
 
Name Accession Description Interval E-value
PHD_Oberon pfam07227
PHD - plant homeodomain finger protein; PHD_oberon is a plant homeodomain finger domain of ...
 807-931 2.62e-50

PHD - plant homeodomain finger protein; PHD_oberon is a plant homeodomain finger domain of Oberon proteins from plants. Oberon is necessary for maintenance and/or establishment of both the shoot and root apical meristems in Arabidopsis. Oberon proteins are made up of a PHD finger domain and a coiled-coil domain. The PHD-finger domain is found in a wide variety of proteins involved in the regulation of chromatin structure. Oberon proteins mediate the TMO7 (the direct target of MP) expression through modification of, or binding to, chromatin at the TMO7 locus. TMO7 stands for the target of Monopteros 7 (MP) (or Auxin response factor 7).


Pssm-ID: 429357  Cd Length: 130  Bit Score: 173.69  E-value: 2.62e-50
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229445    807 CKNLSCRVLLPVDECDCRVCSRKDGFCSACMCLVCSNFDMASNTCSWVGC-------DVCLHWCHTDCGIKESYIrnGIN 879
Cdd:pfam07227    1 CRNIACRSQLPVDDCDCKICSQEDGFCRRCSCCICHKFDDNKDTCSWIGCsavvsegDSCGHWCHLDCALRDYKT--GTV 78

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 15229445    880 ASGAPGMTEMQFHCVACNHPSEMFGFVKEVFLNFAREWKFERFCKELEYVNK 931
Cdd:pfam07227   79 KKGGSGGLDGQFYCRACGKTSELLGHVKKVLQTCAEAWRRDVLCKELDLGRR 130
Oberon_cc pfam16312
Coiled-coil region of Oberon; Oberon_cc is the coiled-coil region of Oberon proteins from ...
 1022-1136 5.84e-36

Coiled-coil region of Oberon; Oberon_cc is the coiled-coil region of Oberon proteins from plants. Oberon is necessary for maintenance and/or establishment of both the shoot and root apical meristems in Arabidopsis. Most Oberon proteins carry a PHD finger domain, pfam07227 and this coiled-coil domain. Oberon proteins mediate the TMO7 (the direct target of MP) expression through modification of, or binding to, chromatin at the TMO7 locus. TMO7 stands for the target of Monopteros 7 (or Auxin response factor 7).


Pssm-ID: 465089 [Multi-domain]  Cd Length: 129  Bit Score: 132.80  E-value: 5.84e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229445   1022 KRSASVADAFHRERQvEICAVEMELERGS-PKEPRFEELESIVRMKQAEAEMFQGRADDARREAEGLKRIAIAKKEKIEE 1100
Cdd:pfam16312    1 KRARLALDACDRELE-DKAREASELKFERqRKKQQIEELESIVRLKQAEAEMFQLKADEARREAEGLQRIALAKSEKSEE 79

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 15229445   1101 EYNRRMGKLSMEDAQERRRRRYEELEAMQRGQREFY 1136
Cdd:pfam16312   80 EYASRYLKLRLEEAEEERRYKFEELKLLENSHRDYD 115
PHD_OBE1_like cd15612
PHD finger found in Arabidopsis thaliana protein OBERON 1, OBERON 2, and similar proteins ...
 837-896 4.29e-31

PHD finger found in Arabidopsis thaliana protein OBERON 1, OBERON 2, and similar proteins mainly found in plants; Included in this family are OBERON 1 (OBE1, or potyvirus VPg-interacting protein 2) and OBERON 2 (OBE2, or potyvirus VPg-interacting protein 1), which have been involved in the maintenance and/or establishment of the meristems in Arabidopsis. They interact with potyvirus VPg-interacting proteins (PVIP1 and 2) and act as central regulators in auxin-mediated control of development. Both OBE1and OBE2 contain a plant homeodomain (PHD) finger. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins.


Pssm-ID: 277084  Cd Length: 60  Bit Score: 116.18  E-value: 4.29e-31
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229445  837 MCLVCSNFDMASNTCSWVGCDVCLHWCHTDCGIKESYIRNGINASGAPGMTEMQFHCVAC 896
Cdd:cd15612    1 MCPICSKFDFAVNTCSWIGCDVCSHWTHTDCAIRSGEISMGVSLKGVEGSTEMEFHCRAC 60
PHD_TCF19_like cd15517
PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and ...
 837-896 1.67e-08

PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and KDM5B, and other similar proteins; TCF-19 was identified as a putative trans-activating factor with expression beginning at the late G1-S boundary in dividing cells. It functions as a novel islet factor necessary for proliferation and survival in the INS-1 beta cell line. It plays an important role in susceptibility to both Type 1 Diabetes Mellitus (T1DM) and Type 2 Diabetes Mellitus (T2DM); it has been suggested that it may positively impact beta cell mass under conditions of beta cell stress and increased insulin demand. KDM5A was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interaction with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK, and BMAL1. KDM5B has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. Both KDM5A and KDM5B function as trimethylated histone H3 lysine 4 (H3K4me3) demethylases. This family also includes Caenorhabditis elegans Lysine-specific demethylase 7 homolog (ceKDM7A). ceKDM7A (also termed JmjC domain-containing protein 1.2, PHD finger protein 8 homolog, or PHF8 homolog) is a plant homeodomain (PHD)- and JmjC domain-containing protein that functions as a histone demethylase specific for H3K9me2 and H3K27me2. The binding of the PHD finger to H3K4me3 guides H3K9me2- and H3K27me2-specific demethylation by its catalytic JmjC domain in a trans-histone regulation mechanism. In addition, this family includes plant protein OBERON 1 and OBERON 2, Alfin1-like (AL) proteins, histone acetyltransferases (HATs) HAC, and AT-rich interactive domain-containing protein 4 (ARID4).


Pssm-ID: 276992 [Multi-domain]  Cd Length: 49  Bit Score: 51.78  E-value: 1.67e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229445  837 MCLVCSNFDmASNTCSWVGCDVCLHWCHTDCGIKESYIrnginasgapGMTEMQFHCVAC 896
Cdd:cd15517    1 VCGICNLET-AAVDELWVQCDGCDKWFHQFCLGLSNER----------YADEDKFKCPNC 49
PHD_TCF19 cd15609
PHD finger found in Transcription factor 19 (TCF-19) and similar proteins; TCF-19, also termed ...
 833-893 4.99e-03

PHD finger found in Transcription factor 19 (TCF-19) and similar proteins; TCF-19, also termed transcription factor SC1, was identified as a putative trans-activating factor with expression beginning at the late G1-S boundary in dividing cells. It also functions as a novel islet factor necessary for proliferation and survival in the INS-1 beta cell line. It plays an important role in susceptibility to both Type 1 Diabetes Mellitus (T1DM) and Type 2 Diabetes Mellitus (T2DM); it has been suggested that it may positively impact beta cell mass under conditions of beta cell stress and increased insulin demand. TCF-19 contains an N-terminal fork head association domain (FHA), a proline rich region, and a C-terminal plant homeodomain (PHD) finger. The FHA domain may serve as a nuclear signaling domain or as a phosphoprotein binding domain. The proline rich region is a common characteristic of trans-activating factors. The PHD finger may allow TCF-19 to interact with chromatin via methylated histone H3.


Pssm-ID: 277082  Cd Length: 50  Bit Score: 36.29  E-value: 4.99e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15229445  833 CSACMCLVCSNfdmasNTCSWVGCDVCLHWCHTDCgikesyIRNGINASGAPgmtEMQFHC 893
Cdd:cd15609    2 CASPSCCLPQD-----ETVSWVQCDDCDQWYHVAC------VGCDYNAVKDP---DADFHC 48
PHD_SF cd15489
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 837-896 8.27e-03

PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies.


Pssm-ID: 276966 [Multi-domain]  Cd Length: 48  Bit Score: 35.37  E-value: 8.27e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229445  837 MCLVCSNFDMASNtcSWVGCDVCLHWCHTDCgikesyirngINASGAPGMTEMQFHCVAC 896
Cdd:cd15489    1 SCIVCGKGGDLGG--ELLQCDGCGKWFHADC----------LGPPLSSFVPNGKWICPVC 48
PHD_ARID4_like cd15615
PHD finger found in Arabidopsis thaliana AT-rich interactive domain-containing protein 4 ...
 838-896 9.55e-03

PHD finger found in Arabidopsis thaliana AT-rich interactive domain-containing protein 4 (ARID4) and similar proteins; This family includes A. thaliana ARID4 (ARID domain-containing protein 4) and similar proteins. Their biological roles remain unclear, but they all contain an AT-rich interactive domain (ARID) and a plant homeodomain (PHD) finger at the C-terminus. ARID is a helix-turn-helix motif-based DNA-binding domain conserved in all eukaryotes. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins.


Pssm-ID: 277087  Cd Length: 57  Bit Score: 35.53  E-value: 9.55e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15229445  838 CLVCSNFDMASNTCS--WVGCDVCLHWCHTDCGikesyIRNGINASGAPGMTEMQFHCVAC 896
Cdd:cd15615    2 CILCGQVYEENEGDEkeWVQCDSCSEWVHFECD-----GRTGLGAFKYAKSDGLQYVCPRC 57
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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