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Conserved domains on  [gi|1103856371|gb|APD25047|]
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recombination activating protein 2, partial [Ochotona rufescens]

Protein Classification

PHD finger domain-containing protein( domain architecture ID 11976271)

PHD (plant homeodomain) finger domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RAG2 super family cl28748
Recombination activating protein 2; V-D-J recombination is the combinatorial process by which ...
 1-216 5.53e-154

Recombination activating protein 2; V-D-J recombination is the combinatorial process by which the huge range of immunoglobulin and T cell binding specificity is generated from a limited amount of genetic material. This process is synergistically activated by RAG1 and RAG2 in developing lymphocytes. Defects in RAG2 in humans are a cause of severe combined immunodeficiency B cell negative and Omenn syndrome.


The actual alignment was detected with superfamily member pfam03089:

Pssm-ID: 427128  Cd Length: 339  Bit Score: 434.55  E-value: 5.53e-154
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1103856371   1 SVDDCLPHVFLVDFDFGCATSYILPELQDGLSFHVSIARNDTIYILGGHSLANNIRPASLYRIRIDLPLGSPAVNCTVLP 80
Cdd:pfam03089 124 SVVDCPPQVFLIDLEFGCCTSYTLPELQDGQSFHVSLARNDTVYILGGHSLANNSRPPRLYRLKVDLPLGSPAVSCTVLP 203

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1103856371  81 GGISVSSAILCQTGNDEFVIVGGYQLENQKRMVCNMVSLDDNKIEIREMETPDWTPDIKHSKIWFGSDMGNGSIFLGIPG 160
Cdd:pfam03089 204 GGISVSSAIVTQTGSHEFVIVGGYQSESQKRMVCNTVVLEDNKIEIEERETPDWTPDIKHSKTWFGSSMGKGAVLLGIPG 283

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1103856371 161 DNKQAVSEAFYFYMLKCTEDDVNEDQRTFTSTQPSTEDPGDSTPFEDSEEFCFSAE 216
Cdd:pfam03089 284 DNKQLPSDANYFYQLNFGEDEEEEEQPTQTCSQESTEDQGDSTPFEDSEEFYFSRE 339
RAG2_PHD pfam13341
RAG2 PHD domain; This domain is found at the C-terminus of the RAG2 protein. The structure of ...
 241-318 6.90e-53

RAG2 PHD domain; This domain is found at the C-terminus of the RAG2 protein. The structure of this domain has been shown bound to histone H3 trimethylated at lysine 4 (H3K4me3).


:

Pssm-ID: 404256  Cd Length: 78  Bit Score: 168.04  E-value: 6.90e-53
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1103856371 241 GYWITCCPTCDVNINTWVPFYSTELNKPAMIYCSHRDGHWVHAQCMDLAERTLIHLSEGSNKYYCNEHVEIARALQTP 318
Cdd:pfam13341   1 GYWIKCCPTCDVDINTWVPFYSTELNKPAMIFCSRGEGHWVHAQCMDLSESMLIRLSEGNVKYFCNEHVDLARGLQTP 78
 
Name Accession Description Interval E-value
RAG2 pfam03089
Recombination activating protein 2; V-D-J recombination is the combinatorial process by which ...
 1-216 5.53e-154

Recombination activating protein 2; V-D-J recombination is the combinatorial process by which the huge range of immunoglobulin and T cell binding specificity is generated from a limited amount of genetic material. This process is synergistically activated by RAG1 and RAG2 in developing lymphocytes. Defects in RAG2 in humans are a cause of severe combined immunodeficiency B cell negative and Omenn syndrome.


Pssm-ID: 427128  Cd Length: 339  Bit Score: 434.55  E-value: 5.53e-154
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1103856371   1 SVDDCLPHVFLVDFDFGCATSYILPELQDGLSFHVSIARNDTIYILGGHSLANNIRPASLYRIRIDLPLGSPAVNCTVLP 80
Cdd:pfam03089 124 SVVDCPPQVFLIDLEFGCCTSYTLPELQDGQSFHVSLARNDTVYILGGHSLANNSRPPRLYRLKVDLPLGSPAVSCTVLP 203

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1103856371  81 GGISVSSAILCQTGNDEFVIVGGYQLENQKRMVCNMVSLDDNKIEIREMETPDWTPDIKHSKIWFGSDMGNGSIFLGIPG 160
Cdd:pfam03089 204 GGISVSSAIVTQTGSHEFVIVGGYQSESQKRMVCNTVVLEDNKIEIEERETPDWTPDIKHSKTWFGSSMGKGAVLLGIPG 283

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1103856371 161 DNKQAVSEAFYFYMLKCTEDDVNEDQRTFTSTQPSTEDPGDSTPFEDSEEFCFSAE 216
Cdd:pfam03089 284 DNKQLPSDANYFYQLNFGEDEEEEEQPTQTCSQESTEDQGDSTPFEDSEEFYFSRE 339
RAG2_PHD pfam13341
RAG2 PHD domain; This domain is found at the C-terminus of the RAG2 protein. The structure of ...
 241-318 6.90e-53

RAG2 PHD domain; This domain is found at the C-terminus of the RAG2 protein. The structure of this domain has been shown bound to histone H3 trimethylated at lysine 4 (H3K4me3).


Pssm-ID: 404256  Cd Length: 78  Bit Score: 168.04  E-value: 6.90e-53
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1103856371 241 GYWITCCPTCDVNINTWVPFYSTELNKPAMIYCSHRDGHWVHAQCMDLAERTLIHLSEGSNKYYCNEHVEIARALQTP 318
Cdd:pfam13341   1 GYWIKCCPTCDVDINTWVPFYSTELNKPAMIFCSRGEGHWVHAQCMDLSESMLIRLSEGNVKYFCNEHVDLARGLQTP 78
PHD_RAG2 cd15569
PHD finger found in V(D)J recombination-activating protein 2 (RAG-2) and similar proteins; ...
 242-308 2.65e-43

PHD finger found in V(D)J recombination-activating protein 2 (RAG-2) and similar proteins; RAG-2 is an essential component of the lymphoid-specific recombination activating gene RAG1/2 V(D)J recombinase mediating antigen-receptor gene assembly. It contains an acidic hinge region implicated in histone-binding, a non-canonical plant homeodomain (PHD) finger followed by a C-terminal extension of 40 amino acids that is essential for phosphoinositide (PtdIns)-binding. The PHD finger is a chromatin-binding module that specifically recognizes histone H3 trimethylated at lysine 4 (H3K4me3) and influences V(D)J recombination.


Pssm-ID: 277044  Cd Length: 67  Bit Score: 143.13  E-value: 2.65e-43
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1103856371 242 YWITCCPTCDVNINTWVPFYSTELNKPAMIYCSHRDGHWVHAQCMDLAERTLIHLSEGSNKYYCNEH 308
Cdd:cd15569     1 YWIKCCPSCDVDINTWVPFYSTELNKPAMIFCSHGGGHWVHAQCMDLSESMLLQLSQGNNKYFCNEH 67
 
Name Accession Description Interval E-value
RAG2 pfam03089
Recombination activating protein 2; V-D-J recombination is the combinatorial process by which ...
 1-216 5.53e-154

Recombination activating protein 2; V-D-J recombination is the combinatorial process by which the huge range of immunoglobulin and T cell binding specificity is generated from a limited amount of genetic material. This process is synergistically activated by RAG1 and RAG2 in developing lymphocytes. Defects in RAG2 in humans are a cause of severe combined immunodeficiency B cell negative and Omenn syndrome.


Pssm-ID: 427128  Cd Length: 339  Bit Score: 434.55  E-value: 5.53e-154
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1103856371   1 SVDDCLPHVFLVDFDFGCATSYILPELQDGLSFHVSIARNDTIYILGGHSLANNIRPASLYRIRIDLPLGSPAVNCTVLP 80
Cdd:pfam03089 124 SVVDCPPQVFLIDLEFGCCTSYTLPELQDGQSFHVSLARNDTVYILGGHSLANNSRPPRLYRLKVDLPLGSPAVSCTVLP 203

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1103856371  81 GGISVSSAILCQTGNDEFVIVGGYQLENQKRMVCNMVSLDDNKIEIREMETPDWTPDIKHSKIWFGSDMGNGSIFLGIPG 160
Cdd:pfam03089 204 GGISVSSAIVTQTGSHEFVIVGGYQSESQKRMVCNTVVLEDNKIEIEERETPDWTPDIKHSKTWFGSSMGKGAVLLGIPG 283

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1103856371 161 DNKQAVSEAFYFYMLKCTEDDVNEDQRTFTSTQPSTEDPGDSTPFEDSEEFCFSAE 216
Cdd:pfam03089 284 DNKQLPSDANYFYQLNFGEDEEEEEQPTQTCSQESTEDQGDSTPFEDSEEFYFSRE 339
RAG2_PHD pfam13341
RAG2 PHD domain; This domain is found at the C-terminus of the RAG2 protein. The structure of ...
 241-318 6.90e-53

RAG2 PHD domain; This domain is found at the C-terminus of the RAG2 protein. The structure of this domain has been shown bound to histone H3 trimethylated at lysine 4 (H3K4me3).


Pssm-ID: 404256  Cd Length: 78  Bit Score: 168.04  E-value: 6.90e-53
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1103856371 241 GYWITCCPTCDVNINTWVPFYSTELNKPAMIYCSHRDGHWVHAQCMDLAERTLIHLSEGSNKYYCNEHVEIARALQTP 318
Cdd:pfam13341   1 GYWIKCCPTCDVDINTWVPFYSTELNKPAMIFCSRGEGHWVHAQCMDLSESMLIRLSEGNVKYFCNEHVDLARGLQTP 78
PHD_RAG2 cd15569
PHD finger found in V(D)J recombination-activating protein 2 (RAG-2) and similar proteins; ...
 242-308 2.65e-43

PHD finger found in V(D)J recombination-activating protein 2 (RAG-2) and similar proteins; RAG-2 is an essential component of the lymphoid-specific recombination activating gene RAG1/2 V(D)J recombinase mediating antigen-receptor gene assembly. It contains an acidic hinge region implicated in histone-binding, a non-canonical plant homeodomain (PHD) finger followed by a C-terminal extension of 40 amino acids that is essential for phosphoinositide (PtdIns)-binding. The PHD finger is a chromatin-binding module that specifically recognizes histone H3 trimethylated at lysine 4 (H3K4me3) and influences V(D)J recombination.


Pssm-ID: 277044  Cd Length: 67  Bit Score: 143.13  E-value: 2.65e-43
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1103856371 242 YWITCCPTCDVNINTWVPFYSTELNKPAMIYCSHRDGHWVHAQCMDLAERTLIHLSEGSNKYYCNEH 308
Cdd:cd15569     1 YWIKCCPSCDVDINTWVPFYSTELNKPAMIFCSHGGGHWVHAQCMDLSESMLLQLSQGNNKYFCNEH 67
 
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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