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Conserved domains on  [gi|1063720468|ref|NP_001329260|]
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GRAM domain family protein [Arabidopsis thaliana]

Protein Classification

GEM family protein( domain architecture ID 10192383)

GEM (GLABRA2 expression modulator) family GRAM domain-containing protein similar to Arabidopsis thaliana GEM-like protein 5

CATH:  2.30.29.30
PubMed:  11050430
SCOP:  4000903

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PH-GRAM_GEM cd13222
GLABRA 2 expression modulator (GEM) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase ...
 78-187 3.21e-61

GLABRA 2 expression modulator (GEM) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain; GEM interacts with CDT1, a pre-replication complex component that is involved in DNA replication, and with TTG1 (Transparent Testa GLABRA 1), a transcriptional regulator of epidermal cell fate. GEM controls the level of histone H3K9 methylation at the promoters of the GLABRA 2 and CAPRICE (CPC) genes, which are essential for epidermis patterning. GEM also regulates cell division in different root cell types. GEM regulates proliferation-differentiation decisions by integrating DNA replication, cell division and transcriptional controls. The GRAM domain is found in glucosyltransferases, myotubularins and other putative membrane-associated proteins. The GRAM domain is part of a larger motif with a pleckstrin homology (PH) domain fold.


:

Pssm-ID: 270042  Cd Length: 109  Bit Score: 185.62  E-value: 3.21e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063720468  78 VEKLLDSFVCYISTTSGPVTGVIYISNRRIAFCSDYAIRLPSSaGGNGVAAYYKVVMEWEKISSISSSTNVLKPSERYVH 157
Cdd:cd13222     1 EEKLLKTFACYLSTSTGPVAGVLYISTKKIAFCSDRPLSFTSP-SGQTSWSYYKVVIPLEQLKSVNPSTNVEKPAEKYIQ 79

                          90       100       110
                  ....*....|....*....|....*....|
gi 1063720468 158 MVTRDGFEFWFMGFVSYIDAFNCLNKALLN 187
Cdd:cd13222    80 IVTVDGHEFWFMGFVNYDKAFKNLQEALRN 109
 
Name Accession Description Interval E-value
PH-GRAM_GEM cd13222
GLABRA 2 expression modulator (GEM) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase ...
 78-187 3.21e-61

GLABRA 2 expression modulator (GEM) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain; GEM interacts with CDT1, a pre-replication complex component that is involved in DNA replication, and with TTG1 (Transparent Testa GLABRA 1), a transcriptional regulator of epidermal cell fate. GEM controls the level of histone H3K9 methylation at the promoters of the GLABRA 2 and CAPRICE (CPC) genes, which are essential for epidermis patterning. GEM also regulates cell division in different root cell types. GEM regulates proliferation-differentiation decisions by integrating DNA replication, cell division and transcriptional controls. The GRAM domain is found in glucosyltransferases, myotubularins and other putative membrane-associated proteins. The GRAM domain is part of a larger motif with a pleckstrin homology (PH) domain fold.


Pssm-ID: 270042  Cd Length: 109  Bit Score: 185.62  E-value: 3.21e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063720468  78 VEKLLDSFVCYISTTSGPVTGVIYISNRRIAFCSDYAIRLPSSaGGNGVAAYYKVVMEWEKISSISSSTNVLKPSERYVH 157
Cdd:cd13222     1 EEKLLKTFACYLSTSTGPVAGVLYISTKKIAFCSDRPLSFTSP-SGQTSWSYYKVVIPLEQLKSVNPSTNVEKPAEKYIQ 79

                          90       100       110
                  ....*....|....*....|....*....|
gi 1063720468 158 MVTRDGFEFWFMGFVSYIDAFNCLNKALLN 187
Cdd:cd13222    80 IVTVDGHEFWFMGFVNYDKAFKNLQEALRN 109
GRAM pfam02893
GRAM domain; The GRAM domain is found in in glucosyltransferases, myotubularins and other ...
 67-189 1.27e-12

GRAM domain; The GRAM domain is found in in glucosyltransferases, myotubularins and other putative membrane-associated proteins. Note the alignment is lacking the last two beta strands and alpha helix.


Pssm-ID: 397160  Cd Length: 112  Bit Score: 61.61  E-value: 1.27e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063720468  67 RVFQREFGVLAVEKLLDSFVCYISTTSGPVTGVIYISNRRIAFCSDyaIRLPSsaggngvaayYKVVMEWEKISSISSST 146
Cdd:pfam02893   1 ELFRKKFKLPPEERLIASYSCYLNRDGGPVQGRLYLTNYRLCFRSL--PKGWS----------TKVVIPLVDIEEIEKLK 68

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1063720468 147 NVLKPSERYVHMVTRDGFEFWFMGFVSYIDAFnCLNKALLNSR 189
Cdd:pfam02893  69 GGANLFPNGIQVETGSNDKFSFAGFVTRDEAI-EFILALLKNA 110
GRAM smart00568
domain in glucosyltransferases, myotubularins and other putative membrane-associated proteins;
74-146 9.86e-11

domain in glucosyltransferases, myotubularins and other putative membrane-associated proteins;


Pssm-ID: 214725 [Multi-domain]  Cd Length: 60  Bit Score: 54.91  E-value: 9.86e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1063720468   74 GVLAVEKLLDSFVCYISTTsGPVTGVIYISNRRIAFCSDYAIRLpssaggngvaayYKVVMEWEKISSISSST 146
Cdd:smart00568   1 KLPEEEKLIADYSCYLSRT-GPVQGRLYISNYRLCFRSNLPGKL------------TKVVIPLADITRIEKST 60
 
Name Accession Description Interval E-value
PH-GRAM_GEM cd13222
GLABRA 2 expression modulator (GEM) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase ...
 78-187 3.21e-61

GLABRA 2 expression modulator (GEM) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain; GEM interacts with CDT1, a pre-replication complex component that is involved in DNA replication, and with TTG1 (Transparent Testa GLABRA 1), a transcriptional regulator of epidermal cell fate. GEM controls the level of histone H3K9 methylation at the promoters of the GLABRA 2 and CAPRICE (CPC) genes, which are essential for epidermis patterning. GEM also regulates cell division in different root cell types. GEM regulates proliferation-differentiation decisions by integrating DNA replication, cell division and transcriptional controls. The GRAM domain is found in glucosyltransferases, myotubularins and other putative membrane-associated proteins. The GRAM domain is part of a larger motif with a pleckstrin homology (PH) domain fold.


Pssm-ID: 270042  Cd Length: 109  Bit Score: 185.62  E-value: 3.21e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063720468  78 VEKLLDSFVCYISTTSGPVTGVIYISNRRIAFCSDYAIRLPSSaGGNGVAAYYKVVMEWEKISSISSSTNVLKPSERYVH 157
Cdd:cd13222     1 EEKLLKTFACYLSTSTGPVAGVLYISTKKIAFCSDRPLSFTSP-SGQTSWSYYKVVIPLEQLKSVNPSTNVEKPAEKYIQ 79

                          90       100       110
                  ....*....|....*....|....*....|
gi 1063720468 158 MVTRDGFEFWFMGFVSYIDAFNCLNKALLN 187
Cdd:cd13222    80 IVTVDGHEFWFMGFVNYDKAFKNLQEALRN 109
GRAM pfam02893
GRAM domain; The GRAM domain is found in in glucosyltransferases, myotubularins and other ...
 67-189 1.27e-12

GRAM domain; The GRAM domain is found in in glucosyltransferases, myotubularins and other putative membrane-associated proteins. Note the alignment is lacking the last two beta strands and alpha helix.


Pssm-ID: 397160  Cd Length: 112  Bit Score: 61.61  E-value: 1.27e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063720468  67 RVFQREFGVLAVEKLLDSFVCYISTTSGPVTGVIYISNRRIAFCSDyaIRLPSsaggngvaayYKVVMEWEKISSISSST 146
Cdd:pfam02893   1 ELFRKKFKLPPEERLIASYSCYLNRDGGPVQGRLYLTNYRLCFRSL--PKGWS----------TKVVIPLVDIEEIEKLK 68

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1063720468 147 NVLKPSERYVHMVTRDGFEFWFMGFVSYIDAFnCLNKALLNSR 189
Cdd:pfam02893  69 GGANLFPNGIQVETGSNDKFSFAGFVTRDEAI-EFILALLKNA 110
GRAM smart00568
domain in glucosyltransferases, myotubularins and other putative membrane-associated proteins;
74-146 9.86e-11

domain in glucosyltransferases, myotubularins and other putative membrane-associated proteins;


Pssm-ID: 214725 [Multi-domain]  Cd Length: 60  Bit Score: 54.91  E-value: 9.86e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1063720468   74 GVLAVEKLLDSFVCYISTTsGPVTGVIYISNRRIAFCSDYAIRLpssaggngvaayYKVVMEWEKISSISSST 146
Cdd:smart00568   1 KLPEEEKLIADYSCYLSRT-GPVQGRLYISNYRLCFRSNLPGKL------------TKVVIPLADITRIEKST 60
PH-GRAM cd10570
Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins ...
 79-178 9.99e-06

Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain; Myotubularin-related proteins are a subfamily of protein tyrosine phosphatases (PTPs) that dephosphorylate D3-phosphorylated inositol lipids. Mutations in this family cause the human neuromuscular disorders myotubular myopathy and type 4B Charcot-Marie-Tooth syndrome. 6 of the 13 MTMRs (MTMRs 5, 9-13) contain naturally occurring substitutions of residues required for catalysis by PTP family enzymes. Although these proteins are predicted to be enzymatically inactive, they are thought to function as antagonists of endogenous phosphatase activity or interaction modules. Most MTMRs contain a N-terminal PH-GRAM domain, a Rac-induced recruitment domain (RID) domain, a PTP domain (which may be active or inactive), a SET-interaction domain, and a C-terminal coiled-coil region. In addition some members contain DENN domain N-terminal to the PH-GRAM domain and FYVE, PDZ, and PH domains C-terminal to the coiled-coil region. The GRAM domain, found in myotubularins, glucosyltransferases, and other putative membrane-associated proteins, is part of a larger motif with a pleckstrin homology (PH) domain fold.


Pssm-ID: 275393  Cd Length: 94  Bit Score: 42.37  E-value: 9.99e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063720468  79 EKLLDSFVCYISTTSGPVTGVIYISNRRIAFCSDYAirlpssaggngvAAYYKVVMEWEKISSISSSTNVLKPSeRYVHM 158
Cdd:cd10570     2 EKLGVRFCCALRPRKLPLEGTLYLSTYRLIFSSKAD------------GDETKLVIPLVDITDVEKIAGASFLP-SGLII 68

                          90       100
                  ....*....|....*....|
gi 1063720468 159 VTRDgFEFWFMGFVSYIDAF 178
Cdd:cd10570    69 TCKD-FRTIKFSFDSEDEAV 87
bPH_3 pfam14470
Bacterial PH domain; Proteins in this family are distantly related to PH domains.
 79-170 3.72e-03

Bacterial PH domain; Proteins in this family are distantly related to PH domains.


Pssm-ID: 464181  Cd Length: 94  Bit Score: 35.33  E-value: 3.72e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063720468  79 EKLLDSFVCYISTTSGPvtGVIYISNRRIAFCSDYAIRLpssaggngvaaYYKVVMEWEKISSISSSTNVLKPSeryvhm 158
Cdd:pfam14470   5 EEILYATSGQINALDKP--GLIVVTNKRIIFLDKGMFGG-----------MKFIEIPYKKIKSVSFKKGLFGAK------ 65

                          90
                  ....*....|..
gi 1063720468 159 vtrdgFEFWFMG 170
Cdd:pfam14470  66 -----IIIETSG 72
 
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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