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Conserved domains on  [gi|1812619237|gb|QID75622|]
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recombination activating protein 1, partial [Rattus rattus rufescens]

Protein Classification

RAG1 domain-containing protein( domain architecture ID 139673)

RAG1 domain-containing protein such as RAG1, the recombination activating protein 1, which is the catalytic component of the RAG complex, a multiprotein complex that mediates the DNA cleavage phase during V(D)J recombination and also acts as an E3 ubiquitin-protein ligase that mediates monoubiquitination of histone H3

Gene Ontology:  GO:0033151|GO:0008270|GO:0043565|GO:0061630
PubMed:  29628308|8861909|19621044

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RAG1 super family cl20149
Recombination-activation protein 1 (RAG1), recombinase; This family is one of the two ...
 1-244 2.60e-143

Recombination-activation protein 1 (RAG1), recombinase; This family is one of the two different components of the RAG1-RAG2 V(D)J recombinase complex. The RAG complex, consisting of two RAG1 and two RAG2 proteins is a multi-protein complex that mediates DNA cleavage during V(D)J (variable-diversity-joining) recombination. RAG1 mediates DNA-binding to the conserved recombination signal sequences (RSS). Many of the proteins in this family are fragments. Solution of the structure of the complex of RAG1 and RAG2 shows that each protein dimerizes with itself and each pair then complexes together to from the RAG1-RAG2 V(D)J recombinase enzyme. The different structural elements in RAG1 for UniProtKB:P15919 are: an N-terminal nonamer-binding domain from residues 391-459; a dimerization and DNA-binding domain from 459-515; an extended pre-RNase H domain from 515-588; the catalytic RNase H domain from 588-719; a ZnC2 domain from 719-791; and ZnH2 domain from 791-962; and a three-helix C-terminal domain from 962-1008.


The actual alignment was detected with superfamily member pfam12940:

Pssm-ID: 315595  Cd Length: 653  Bit Score: 415.60  E-value: 2.60e-143
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1812619237   1 HPFEWQPPLKNVSSRTDVGIIDGLSGLASSVDEYPVDTIAKRFRYDSALVSALMDMEEDILDGMRSQDLDDY-LNGPFTV 79
Cdd:pfam12940 135 HHFEWQPALKNVSPSCDVGIIDGLSGWSPSVDDQPADTITRRFRYDVALVAALKDLEEDILEGLKEQGLDDSaCTEGFSV 214

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1812619237  80 VVKESCDGMGDVSEKHGSGPAVPEKAVRFSFTVMRITI---EHGSQNVKIFEEPKPNSELCCKPLCLMLADESDHETLTA 156
Cdd:pfam12940 215 MIKECCDGMGDVSEKHGGGPAVPEKAVRFSFTIMSVSIladDEEGEEVAIFHELKPNSELCCKPLCLMFADESDHETLTA 294

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1812619237 157 ILSPLIAEREAMKSSELMLEMGGIPRTFKFIFRGTGYDEKLVREVEGLEASGSVYICTLCDATRLEASQNLVFHSITRSH 236
Cdd:pfam12940 295 ILAPIMAEREAMKESRLILSIGGLLRSFRFHFRGTGYDEKLVRDMEGLEASGSTYICTLCDSSRAEASKNKVLHAITRSH 374


                  ....*...
gi 1812619237 237 AENLQRYE 244
Cdd:pfam12940 375 EENLERYE 382
 
Name Accession Description Interval E-value
RAG1 pfam12940
Recombination-activation protein 1 (RAG1), recombinase; This family is one of the two ...
 1-244 2.60e-143

Recombination-activation protein 1 (RAG1), recombinase; This family is one of the two different components of the RAG1-RAG2 V(D)J recombinase complex. The RAG complex, consisting of two RAG1 and two RAG2 proteins is a multi-protein complex that mediates DNA cleavage during V(D)J (variable-diversity-joining) recombination. RAG1 mediates DNA-binding to the conserved recombination signal sequences (RSS). Many of the proteins in this family are fragments. Solution of the structure of the complex of RAG1 and RAG2 shows that each protein dimerizes with itself and each pair then complexes together to from the RAG1-RAG2 V(D)J recombinase enzyme. The different structural elements in RAG1 for UniProtKB:P15919 are: an N-terminal nonamer-binding domain from residues 391-459; a dimerization and DNA-binding domain from 459-515; an extended pre-RNase H domain from 515-588; the catalytic RNase H domain from 588-719; a ZnC2 domain from 719-791; and ZnH2 domain from 791-962; and a three-helix C-terminal domain from 962-1008.


Pssm-ID: 315595  Cd Length: 653  Bit Score: 415.60  E-value: 2.60e-143
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1812619237   1 HPFEWQPPLKNVSSRTDVGIIDGLSGLASSVDEYPVDTIAKRFRYDSALVSALMDMEEDILDGMRSQDLDDY-LNGPFTV 79
Cdd:pfam12940 135 HHFEWQPALKNVSPSCDVGIIDGLSGWSPSVDDQPADTITRRFRYDVALVAALKDLEEDILEGLKEQGLDDSaCTEGFSV 214

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1812619237  80 VVKESCDGMGDVSEKHGSGPAVPEKAVRFSFTVMRITI---EHGSQNVKIFEEPKPNSELCCKPLCLMLADESDHETLTA 156
Cdd:pfam12940 215 MIKECCDGMGDVSEKHGGGPAVPEKAVRFSFTIMSVSIladDEEGEEVAIFHELKPNSELCCKPLCLMFADESDHETLTA 294

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1812619237 157 ILSPLIAEREAMKSSELMLEMGGIPRTFKFIFRGTGYDEKLVREVEGLEASGSVYICTLCDATRLEASQNLVFHSITRSH 236
Cdd:pfam12940 295 ILAPIMAEREAMKESRLILSIGGLLRSFRFHFRGTGYDEKLVRDMEGLEASGSTYICTLCDSSRAEASKNKVLHAITRSH 374


                  ....*...
gi 1812619237 237 AENLQRYE 244
Cdd:pfam12940 375 EENLERYE 382
 
Name Accession Description Interval E-value
RAG1 pfam12940
Recombination-activation protein 1 (RAG1), recombinase; This family is one of the two ...
 1-244 2.60e-143

Recombination-activation protein 1 (RAG1), recombinase; This family is one of the two different components of the RAG1-RAG2 V(D)J recombinase complex. The RAG complex, consisting of two RAG1 and two RAG2 proteins is a multi-protein complex that mediates DNA cleavage during V(D)J (variable-diversity-joining) recombination. RAG1 mediates DNA-binding to the conserved recombination signal sequences (RSS). Many of the proteins in this family are fragments. Solution of the structure of the complex of RAG1 and RAG2 shows that each protein dimerizes with itself and each pair then complexes together to from the RAG1-RAG2 V(D)J recombinase enzyme. The different structural elements in RAG1 for UniProtKB:P15919 are: an N-terminal nonamer-binding domain from residues 391-459; a dimerization and DNA-binding domain from 459-515; an extended pre-RNase H domain from 515-588; the catalytic RNase H domain from 588-719; a ZnC2 domain from 719-791; and ZnH2 domain from 791-962; and a three-helix C-terminal domain from 962-1008.


Pssm-ID: 315595  Cd Length: 653  Bit Score: 415.60  E-value: 2.60e-143
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1812619237   1 HPFEWQPPLKNVSSRTDVGIIDGLSGLASSVDEYPVDTIAKRFRYDSALVSALMDMEEDILDGMRSQDLDDY-LNGPFTV 79
Cdd:pfam12940 135 HHFEWQPALKNVSPSCDVGIIDGLSGWSPSVDDQPADTITRRFRYDVALVAALKDLEEDILEGLKEQGLDDSaCTEGFSV 214

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1812619237  80 VVKESCDGMGDVSEKHGSGPAVPEKAVRFSFTVMRITI---EHGSQNVKIFEEPKPNSELCCKPLCLMLADESDHETLTA 156
Cdd:pfam12940 215 MIKECCDGMGDVSEKHGGGPAVPEKAVRFSFTIMSVSIladDEEGEEVAIFHELKPNSELCCKPLCLMFADESDHETLTA 294

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1812619237 157 ILSPLIAEREAMKSSELMLEMGGIPRTFKFIFRGTGYDEKLVREVEGLEASGSVYICTLCDATRLEASQNLVFHSITRSH 236
Cdd:pfam12940 295 ILAPIMAEREAMKESRLILSIGGLLRSFRFHFRGTGYDEKLVRDMEGLEASGSTYICTLCDSSRAEASKNKVLHAITRSH 374


                  ....*...
gi 1812619237 237 AENLQRYE 244
Cdd:pfam12940 375 EENLERYE 382
 
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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