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Conserved domains on  [gi|540324256|gb|AGV05848|]
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recombination activating protein 2, partial [Myotis cf. formosus MR-2013]

Protein Classification

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 ...
 1-309 0e+00

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: 639.86  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 540324256    1 KGGLESERQQYIIHGGKTPNNELSDKMYVMSVVCKNNKKVTFRCTEKDLVGDVPEARYGHSIDVVYSRGKSMGVVFGGRS 80
Cdd:pfam03089  31 KPSDEGEKEQYLIHGGKTPNNELSDKLYIMSLDSKGNKKVTLRCTEKELVGDVPEARYGHTISVVYSRGKSACVLFGGRS 110

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 540324256   81 YIPSAQRTTEKWNTVADCLPHVFLVDFEFGCSTSYILPELQDGLSFHVSIARNDTIYILGGHSLANNIRPANLYRIRVDL 160
Cdd:pfam03089 111 YMPPGQRTTENWNSVVDCPPQVFLIDLEFGCCTSYTLPELQDGQSFHVSLARNDTVYILGGHSLANNSRPPRLYRLKVDL 190

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 540324256  161 PLGSPAVNCTVLPGGISVSSAILTQTNNDEFVIVGGYQLENQKRMVCNIISFEDNKIEIREMETPDWTPDIKHSKIWFGS 240
Cdd:pfam03089 191 PLGSPAVSCTVLPGGISVSSAIVTQTGSHEFVIVGGYQSESQKRMVCNTVVLEDNKIEIEERETPDWTPDIKHSKTWFGS 270

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 540324256  241 NMGNGTVFLGIPGDNKQAVSETYYFYMLKCAEDDVNEDQKTFTNSQTSTEDPGDSTPFEDSEEFCFSAE 309
Cdd:pfam03089 271 SMGKGAVLLGIPGDNKQLPSDANYFYQLNFGEDEEEEEQPTQTCSQESTEDQGDSTPFEDSEEFYFSRE 339
PHD_SF super family cl22851
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ...
 334-382 4.35e-34

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 pfam13341:

Pssm-ID: 473978  Cd Length: 78  Bit Score: 121.04  E-value: 4.35e-34
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 540324256  334 GYWITCCSTCDVDINTWVPFYSTELNKPAMIYCSHGDGHWVHAQCMDLA 382
Cdd:pfam13341   1 GYWIKCCPTCDVDINTWVPFYSTELNKPAMIFCSRGEGHWVHAQCMDLS 49
 
Name Accession Description Interval E-value
RAG2 pfam03089
Recombination activating protein 2; V-D-J recombination is the combinatorial process by which ...
 1-309 0e+00

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: 639.86  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 540324256    1 KGGLESERQQYIIHGGKTPNNELSDKMYVMSVVCKNNKKVTFRCTEKDLVGDVPEARYGHSIDVVYSRGKSMGVVFGGRS 80
Cdd:pfam03089  31 KPSDEGEKEQYLIHGGKTPNNELSDKLYIMSLDSKGNKKVTLRCTEKELVGDVPEARYGHTISVVYSRGKSACVLFGGRS 110

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 540324256   81 YIPSAQRTTEKWNTVADCLPHVFLVDFEFGCSTSYILPELQDGLSFHVSIARNDTIYILGGHSLANNIRPANLYRIRVDL 160
Cdd:pfam03089 111 YMPPGQRTTENWNSVVDCPPQVFLIDLEFGCCTSYTLPELQDGQSFHVSLARNDTVYILGGHSLANNSRPPRLYRLKVDL 190

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 540324256  161 PLGSPAVNCTVLPGGISVSSAILTQTNNDEFVIVGGYQLENQKRMVCNIISFEDNKIEIREMETPDWTPDIKHSKIWFGS 240
Cdd:pfam03089 191 PLGSPAVSCTVLPGGISVSSAIVTQTGSHEFVIVGGYQSESQKRMVCNTVVLEDNKIEIEERETPDWTPDIKHSKTWFGS 270

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 540324256  241 NMGNGTVFLGIPGDNKQAVSETYYFYMLKCAEDDVNEDQKTFTNSQTSTEDPGDSTPFEDSEEFCFSAE 309
Cdd:pfam03089 271 SMGKGAVLLGIPGDNKQLPSDANYFYQLNFGEDEEEEEQPTQTCSQESTEDQGDSTPFEDSEEFYFSRE 339
RAG2_PHD pfam13341
RAG2 PHD domain; This domain is found at the C-terminus of the RAG2 protein. The structure of ...
 334-382 4.35e-34

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: 121.04  E-value: 4.35e-34
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 540324256  334 GYWITCCSTCDVDINTWVPFYSTELNKPAMIYCSHGDGHWVHAQCMDLA 382
Cdd:pfam13341   1 GYWIKCCPTCDVDINTWVPFYSTELNKPAMIFCSRGEGHWVHAQCMDLS 49
PHD_RAG2 cd15569
PHD finger found in V(D)J recombination-activating protein 2 (RAG-2) and similar proteins; ...
 335-381 1.94e-31

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: 113.85  E-value: 1.94e-31
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 540324256 335 YWITCCSTCDVDINTWVPFYSTELNKPAMIYCSHGDGHWVHAQCMDL 381
Cdd:cd15569    1 YWIKCCPSCDVDINTWVPFYSTELNKPAMIFCSHGGGHWVHAQCMDL 47
 
Name Accession Description Interval E-value
RAG2 pfam03089
Recombination activating protein 2; V-D-J recombination is the combinatorial process by which ...
 1-309 0e+00

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: 639.86  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 540324256    1 KGGLESERQQYIIHGGKTPNNELSDKMYVMSVVCKNNKKVTFRCTEKDLVGDVPEARYGHSIDVVYSRGKSMGVVFGGRS 80
Cdd:pfam03089  31 KPSDEGEKEQYLIHGGKTPNNELSDKLYIMSLDSKGNKKVTLRCTEKELVGDVPEARYGHTISVVYSRGKSACVLFGGRS 110

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 540324256   81 YIPSAQRTTEKWNTVADCLPHVFLVDFEFGCSTSYILPELQDGLSFHVSIARNDTIYILGGHSLANNIRPANLYRIRVDL 160
Cdd:pfam03089 111 YMPPGQRTTENWNSVVDCPPQVFLIDLEFGCCTSYTLPELQDGQSFHVSLARNDTVYILGGHSLANNSRPPRLYRLKVDL 190

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 540324256  161 PLGSPAVNCTVLPGGISVSSAILTQTNNDEFVIVGGYQLENQKRMVCNIISFEDNKIEIREMETPDWTPDIKHSKIWFGS 240
Cdd:pfam03089 191 PLGSPAVSCTVLPGGISVSSAIVTQTGSHEFVIVGGYQSESQKRMVCNTVVLEDNKIEIEERETPDWTPDIKHSKTWFGS 270

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 540324256  241 NMGNGTVFLGIPGDNKQAVSETYYFYMLKCAEDDVNEDQKTFTNSQTSTEDPGDSTPFEDSEEFCFSAE 309
Cdd:pfam03089 271 SMGKGAVLLGIPGDNKQLPSDANYFYQLNFGEDEEEEEQPTQTCSQESTEDQGDSTPFEDSEEFYFSRE 339
RAG2_PHD pfam13341
RAG2 PHD domain; This domain is found at the C-terminus of the RAG2 protein. The structure of ...
 334-382 4.35e-34

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: 121.04  E-value: 4.35e-34
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 540324256  334 GYWITCCSTCDVDINTWVPFYSTELNKPAMIYCSHGDGHWVHAQCMDLA 382
Cdd:pfam13341   1 GYWIKCCPTCDVDINTWVPFYSTELNKPAMIFCSRGEGHWVHAQCMDLS 49
PHD_RAG2 cd15569
PHD finger found in V(D)J recombination-activating protein 2 (RAG-2) and similar proteins; ...
 335-381 1.94e-31

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: 113.85  E-value: 1.94e-31
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 540324256 335 YWITCCSTCDVDINTWVPFYSTELNKPAMIYCSHGDGHWVHAQCMDL 381
Cdd:cd15569    1 YWIKCCPSCDVDINTWVPFYSTELNKPAMIFCSHGGGHWVHAQCMDL 47
 
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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