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Conserved domains on  [gi|15234667|ref|NP_194749|]
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vernalization5/VIN3-like protein [Arabidopsis thaliana]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PHD_SF super family cl22851
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 146-264 7.59e-40

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.


The actual alignment was detected with superfamily member pfam07227:

Pssm-ID: 473978  Cd Length: 130  Bit Score: 142.87  E-value: 7.59e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234667   146 CKNLACRAVL----------RQEDSFCRRCSCCICRKYDDNKDPSLWLTCSsDPPFEGESCGFSCHLECAFNTEKSGLGK 215
Cdd:pfam07227   1 CRNIACRSQLpvddcdckicSQEDGFCRRCSCCICHKFDDNKDTCSWIGCS-AVVSEGDSCGHWCHLDCALRDYKTGTVK 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 15234667   216 DKQSEG--CCFYCVSCGKANSLLECWKKQLTIAKETRRVEVLCYRLFLVQK 264
Cdd:pfam07227  80 KGGSGGldGQFYCRACGKTSELLGHVKKVLQTCAEAWRRDVLCKELDLGRR 130
FN3 smart00060
Fibronectin type 3 domain; One of three types of internal repeat within the plasma protein, ...
 368-445 9.15e-06

Fibronectin type 3 domain; One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins.


:

Pssm-ID: 214495 [Multi-domain]  Cd Length: 83  Bit Score: 44.53  E-value: 9.15e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15234667    368 TKIRFEDVNATSLTVVLasnEIPSPPNIVHYSIWHRKVPEKDYPEKSTCTLFIPNTRFVVSGLAPASEYCFKVVSYSG 445
Cdd:smart00060   5 SNLRVTDVTSTSVTLSW---EPPPDDGITGYIVGYRVEYREEGSEWKEVNVTPSSTSYTLTGLKPGTEYEFRVRAVNG 79
 
Name Accession Description Interval E-value
PHD_Oberon pfam07227
PHD - plant homeodomain finger protein; PHD_oberon is a plant homeodomain finger domain of ...
 146-264 7.59e-40

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: 142.87  E-value: 7.59e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234667   146 CKNLACRAVL----------RQEDSFCRRCSCCICRKYDDNKDPSLWLTCSsDPPFEGESCGFSCHLECAFNTEKSGLGK 215
Cdd:pfam07227   1 CRNIACRSQLpvddcdckicSQEDGFCRRCSCCICHKFDDNKDTCSWIGCS-AVVSEGDSCGHWCHLDCALRDYKTGTVK 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 15234667   216 DKQSEG--CCFYCVSCGKANSLLECWKKQLTIAKETRRVEVLCYRLFLVQK 264
Cdd:pfam07227  80 KGGSGGldGQFYCRACGKTSELLGHVKKVLQTCAEAWRRDVLCKELDLGRR 130
PHD_VIN3_plant cd15521
PHD finger found in Arabidopsis thaliana protein Vernalization Insensitive 3 (VIN3) and ...
 172-229 1.52e-26

PHD finger found in Arabidopsis thaliana protein Vernalization Insensitive 3 (VIN3) and similar proteins; The lineage specific VIN3 family of proteins includes VIN3, VIN3-like1 (VIL1, or Vernalization5 (VRN5)), VIN3-like2 (VIL2, or Vernalization5/VIN3-like protein 1 (VEL1)), VIN3-like3 (VIL3 or Vernalization5/VIN3-like protein 2 (VEL2)), and similar proteins. They contain a plant homeodomain (PHD) finger, and collectively repress different sets of members of the Flowering LOCUS C (FLC) gene family during the course of vernalization. Both VIN3 and VIL1 are required for modifying the histone architecture of the MADS box floral repressor FLC in response to prolonged cold exposure in Arabidopsis. VIN3 is required for both Histone H3 Lys 9 (H3K9) and Histone H3 Lys 27 (H3K27) methylation at FLC chromatin, ultimately leading to its repression. It is regulated by the components of Polycomb Response Complex2 (PRC2), which trimethylates histone H3 Lys 27 (H3K27me3). VIL1 appears to play a prominent role in regulating FLC by vernalization. VIL2 acts together with PRC2 to repress the floral repressor MAF5, an FLC clade member, in a photoperiod-dependent manner to accelerate flowering under non-inductive photoperiods.


Pssm-ID: 276996  Cd Length: 64  Bit Score: 102.67  E-value: 1.52e-26
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 15234667 172 KYDDNKDPSLWLTCSSDPPFEGESCGFSCHLECAFNTEKSGLGKDKQSEGCCFYCVSC 229
Cdd:cd15521   7 KFDDNKDPSLWLTCGSEKGFDVESCGLSCHLECALKSEKSGVGKNSIDLDGCFYCVSC 64
FN3 smart00060
Fibronectin type 3 domain; One of three types of internal repeat within the plasma protein, ...
 368-445 9.15e-06

Fibronectin type 3 domain; One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins.


Pssm-ID: 214495 [Multi-domain]  Cd Length: 83  Bit Score: 44.53  E-value: 9.15e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15234667    368 TKIRFEDVNATSLTVVLasnEIPSPPNIVHYSIWHRKVPEKDYPEKSTCTLFIPNTRFVVSGLAPASEYCFKVVSYSG 445
Cdd:smart00060   5 SNLRVTDVTSTSVTLSW---EPPPDDGITGYIVGYRVEYREEGSEWKEVNVTPSSTSYTLTGLKPGTEYEFRVRAVNG 79
fn3 pfam00041
Fibronectin type III domain;
370-445 2.41e-04

Fibronectin type III domain;


Pssm-ID: 394996 [Multi-domain]  Cd Length: 85  Bit Score: 40.48  E-value: 2.41e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15234667   370 IRFEDVNATSLTVvlaSNEIPSPPN--IVHYSIwhRKVPEKDYPEKSTCTLFIPNTRFVVSGLAPASEYCFKVVSYSG 445
Cdd:pfam00041   6 LTVTDVTSTSLTV---SWTPPPDGNgpITGYEV--EYRPKNSGEPWNEITVPGTTTSVTLTGLKPGTEYEVRVQAVNG 78
FN3 cd00063
Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein ...
 368-445 2.54e-04

Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.


Pssm-ID: 238020 [Multi-domain]  Cd Length: 93  Bit Score: 40.56  E-value: 2.54e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15234667 368 TKIRFEDVNATSLTVVLASNEIPSPPnIVHYSIWHRKVPEKDYPEKSTCTlfIPNTRFVVSGLAPASEYCFKVVSYSG 445
Cdd:cd00063   5 TNLRVTDVTSTSVTLSWTPPEDDGGP-ITGYVVEYREKGSGDWKEVEVTP--GSETSYTLTGLKPGTEYEFRVRAVNG 79
 
Name Accession Description Interval E-value
PHD_Oberon pfam07227
PHD - plant homeodomain finger protein; PHD_oberon is a plant homeodomain finger domain of ...
 146-264 7.59e-40

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: 142.87  E-value: 7.59e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15234667   146 CKNLACRAVL----------RQEDSFCRRCSCCICRKYDDNKDPSLWLTCSsDPPFEGESCGFSCHLECAFNTEKSGLGK 215
Cdd:pfam07227   1 CRNIACRSQLpvddcdckicSQEDGFCRRCSCCICHKFDDNKDTCSWIGCS-AVVSEGDSCGHWCHLDCALRDYKTGTVK 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 15234667   216 DKQSEG--CCFYCVSCGKANSLLECWKKQLTIAKETRRVEVLCYRLFLVQK 264
Cdd:pfam07227  80 KGGSGGldGQFYCRACGKTSELLGHVKKVLQTCAEAWRRDVLCKELDLGRR 130
PHD_VIN3_plant cd15521
PHD finger found in Arabidopsis thaliana protein Vernalization Insensitive 3 (VIN3) and ...
 172-229 1.52e-26

PHD finger found in Arabidopsis thaliana protein Vernalization Insensitive 3 (VIN3) and similar proteins; The lineage specific VIN3 family of proteins includes VIN3, VIN3-like1 (VIL1, or Vernalization5 (VRN5)), VIN3-like2 (VIL2, or Vernalization5/VIN3-like protein 1 (VEL1)), VIN3-like3 (VIL3 or Vernalization5/VIN3-like protein 2 (VEL2)), and similar proteins. They contain a plant homeodomain (PHD) finger, and collectively repress different sets of members of the Flowering LOCUS C (FLC) gene family during the course of vernalization. Both VIN3 and VIL1 are required for modifying the histone architecture of the MADS box floral repressor FLC in response to prolonged cold exposure in Arabidopsis. VIN3 is required for both Histone H3 Lys 9 (H3K9) and Histone H3 Lys 27 (H3K27) methylation at FLC chromatin, ultimately leading to its repression. It is regulated by the components of Polycomb Response Complex2 (PRC2), which trimethylates histone H3 Lys 27 (H3K27me3). VIL1 appears to play a prominent role in regulating FLC by vernalization. VIL2 acts together with PRC2 to repress the floral repressor MAF5, an FLC clade member, in a photoperiod-dependent manner to accelerate flowering under non-inductive photoperiods.


Pssm-ID: 276996  Cd Length: 64  Bit Score: 102.67  E-value: 1.52e-26
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 15234667 172 KYDDNKDPSLWLTCSSDPPFEGESCGFSCHLECAFNTEKSGLGKDKQSEGCCFYCVSC 229
Cdd:cd15521   7 KFDDNKDPSLWLTCGSEKGFDVESCGLSCHLECALKSEKSGVGKNSIDLDGCFYCVSC 64
FN3 smart00060
Fibronectin type 3 domain; One of three types of internal repeat within the plasma protein, ...
 368-445 9.15e-06

Fibronectin type 3 domain; One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins.


Pssm-ID: 214495 [Multi-domain]  Cd Length: 83  Bit Score: 44.53  E-value: 9.15e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15234667    368 TKIRFEDVNATSLTVVLasnEIPSPPNIVHYSIWHRKVPEKDYPEKSTCTLFIPNTRFVVSGLAPASEYCFKVVSYSG 445
Cdd:smart00060   5 SNLRVTDVTSTSVTLSW---EPPPDDGITGYIVGYRVEYREEGSEWKEVNVTPSSTSYTLTGLKPGTEYEFRVRAVNG 79
fn3 pfam00041
Fibronectin type III domain;
370-445 2.41e-04

Fibronectin type III domain;


Pssm-ID: 394996 [Multi-domain]  Cd Length: 85  Bit Score: 40.48  E-value: 2.41e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15234667   370 IRFEDVNATSLTVvlaSNEIPSPPN--IVHYSIwhRKVPEKDYPEKSTCTLFIPNTRFVVSGLAPASEYCFKVVSYSG 445
Cdd:pfam00041   6 LTVTDVTSTSLTV---SWTPPPDGNgpITGYEV--EYRPKNSGEPWNEITVPGTTTSVTLTGLKPGTEYEVRVQAVNG 78
FN3 cd00063
Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein ...
 368-445 2.54e-04

Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.


Pssm-ID: 238020 [Multi-domain]  Cd Length: 93  Bit Score: 40.56  E-value: 2.54e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15234667 368 TKIRFEDVNATSLTVVLASNEIPSPPnIVHYSIWHRKVPEKDYPEKSTCTlfIPNTRFVVSGLAPASEYCFKVVSYSG 445
Cdd:cd00063   5 TNLRVTDVTSTSVTLSWTPPEDDGGP-ITGYVVEYREKGSGDWKEVEVTP--GSETSYTLTGLKPGTEYEFRVRAVNG 79
 
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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