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Conserved domains on  [gi|50957104|gb|AAT91050|]
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recombination activating protein 1, partial [Andrias japonicus]

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

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 ...
1-503 0e+00

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: 899.41  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50957104     1 RTVKATTGRQIFQPLHALRTAEKALLPGYHPFEWKPPLKNVSASTEVGIINGLSGLVQSVDDYPVDTISKRFRYDVALVS 80
Cdd:pfam12940 106 RTVKATSGRQIFQPLHTLRAAEKALLPGFHHFEWQPALKNVSPSCDVGIIDGLSGWSPSVDDQPADTITRRFRYDVALVA 185
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50957104    81 TLKDMEEEILEGLKTQELDDY-LSGSFTVVVKESCDGMGDVSEKHGCGPPVPEKAVRFSFTVMTIAV---PHNGDNVRIF 156
Cdd:pfam12940 186 ALKDLEEDILEGLKEQGLDDSaCTEGFSVMIKECCDGMGDVSEKHGGGPAVPEKAVRFSFTIMSVSIladDEEGEEVAIF 265
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50957104   157 EESKPNSELCCKPLCLMLADESDHETLTAILSPLIAEREAMKGSELMLEVGGILRTFKFVFRGTGYDEKLVREVEGLEAS 236
Cdd:pfam12940 266 HELKPNSELCCKPLCLMFADESDHETLTAILAPIMAEREAMKESRLILSIGGLLRSFRFHFRGTGYDEKLVRDMEGLEAS 345
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50957104   237 GSVYICTLCDSTRLEASQNIVLHSITRSHTENLERYEMWRSNKHHESADELRDRVKGVSAKPFIETLPSIDALHCDIGNA 316
Cdd:pfam12940 346 GSTYICTLCDSSRAEASKNKVLHAITRSHEENLERYEIWRTNPFSESADDLRDRVKGISAKPFLETQACIDALHCDIGNA 425
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50957104   317 AEFYKIFQLEIGEVFKNPDASKEERKRWQSTLDKHLRKKMNLKPIMRMNGNFARKLMAKETVDAVCELVRTEERQVALRE 396
Cdd:pfam12940 426 TEFYKIFQDEIGEVHKKANPSKEERKRWQAALDKQLRKKMKLKPVMRMNGNFARKLMTQEAVDAVCELVPSEERQEALRE 505
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50957104   397 LMDLYLKMKPVWRSSCPAKECPELLCQYSFNSQRFAELLSTKFKYRYEGKITNYFHKTLAHVPEIIERDGSIGAWASEGN 476
Cdd:pfam12940 506 LMHLYLQMKPVWRATCPAKECPDLLCRYSFNSQRFADLLSTTFKYRYDGKITNYLHKTLAHVPEIIERDGSIGAWASEGN 585
                         490       500
                  ....*....|....*....|....*..
gi 50957104   477 ESGNKLFRRFRKMNARQSKFYEMEDVL 503
Cdd:pfam12940 586 ESANKLFRRFRKMNARQSKSFELEDIL 612
 
Name Accession Description Interval E-value
RAG1 pfam12940
Recombination-activation protein 1 (RAG1), recombinase; This family is one of the two ...
1-503 0e+00

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: 899.41  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50957104     1 RTVKATTGRQIFQPLHALRTAEKALLPGYHPFEWKPPLKNVSASTEVGIINGLSGLVQSVDDYPVDTISKRFRYDVALVS 80
Cdd:pfam12940 106 RTVKATSGRQIFQPLHTLRAAEKALLPGFHHFEWQPALKNVSPSCDVGIIDGLSGWSPSVDDQPADTITRRFRYDVALVA 185
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50957104    81 TLKDMEEEILEGLKTQELDDY-LSGSFTVVVKESCDGMGDVSEKHGCGPPVPEKAVRFSFTVMTIAV---PHNGDNVRIF 156
Cdd:pfam12940 186 ALKDLEEDILEGLKEQGLDDSaCTEGFSVMIKECCDGMGDVSEKHGGGPAVPEKAVRFSFTIMSVSIladDEEGEEVAIF 265
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50957104   157 EESKPNSELCCKPLCLMLADESDHETLTAILSPLIAEREAMKGSELMLEVGGILRTFKFVFRGTGYDEKLVREVEGLEAS 236
Cdd:pfam12940 266 HELKPNSELCCKPLCLMFADESDHETLTAILAPIMAEREAMKESRLILSIGGLLRSFRFHFRGTGYDEKLVRDMEGLEAS 345
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50957104   237 GSVYICTLCDSTRLEASQNIVLHSITRSHTENLERYEMWRSNKHHESADELRDRVKGVSAKPFIETLPSIDALHCDIGNA 316
Cdd:pfam12940 346 GSTYICTLCDSSRAEASKNKVLHAITRSHEENLERYEIWRTNPFSESADDLRDRVKGISAKPFLETQACIDALHCDIGNA 425
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50957104   317 AEFYKIFQLEIGEVFKNPDASKEERKRWQSTLDKHLRKKMNLKPIMRMNGNFARKLMAKETVDAVCELVRTEERQVALRE 396
Cdd:pfam12940 426 TEFYKIFQDEIGEVHKKANPSKEERKRWQAALDKQLRKKMKLKPVMRMNGNFARKLMTQEAVDAVCELVPSEERQEALRE 505
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50957104   397 LMDLYLKMKPVWRSSCPAKECPELLCQYSFNSQRFAELLSTKFKYRYEGKITNYFHKTLAHVPEIIERDGSIGAWASEGN 476
Cdd:pfam12940 506 LMHLYLQMKPVWRATCPAKECPDLLCRYSFNSQRFADLLSTTFKYRYDGKITNYLHKTLAHVPEIIERDGSIGAWASEGN 585
                         490       500
                  ....*....|....*....|....*..
gi 50957104   477 ESGNKLFRRFRKMNARQSKFYEMEDVL 503
Cdd:pfam12940 586 ESANKLFRRFRKMNARQSKSFELEDIL 612
 
Name Accession Description Interval E-value
RAG1 pfam12940
Recombination-activation protein 1 (RAG1), recombinase; This family is one of the two ...
1-503 0e+00

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: 899.41  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50957104     1 RTVKATTGRQIFQPLHALRTAEKALLPGYHPFEWKPPLKNVSASTEVGIINGLSGLVQSVDDYPVDTISKRFRYDVALVS 80
Cdd:pfam12940 106 RTVKATSGRQIFQPLHTLRAAEKALLPGFHHFEWQPALKNVSPSCDVGIIDGLSGWSPSVDDQPADTITRRFRYDVALVA 185
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50957104    81 TLKDMEEEILEGLKTQELDDY-LSGSFTVVVKESCDGMGDVSEKHGCGPPVPEKAVRFSFTVMTIAV---PHNGDNVRIF 156
Cdd:pfam12940 186 ALKDLEEDILEGLKEQGLDDSaCTEGFSVMIKECCDGMGDVSEKHGGGPAVPEKAVRFSFTIMSVSIladDEEGEEVAIF 265
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50957104   157 EESKPNSELCCKPLCLMLADESDHETLTAILSPLIAEREAMKGSELMLEVGGILRTFKFVFRGTGYDEKLVREVEGLEAS 236
Cdd:pfam12940 266 HELKPNSELCCKPLCLMFADESDHETLTAILAPIMAEREAMKESRLILSIGGLLRSFRFHFRGTGYDEKLVRDMEGLEAS 345
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50957104   237 GSVYICTLCDSTRLEASQNIVLHSITRSHTENLERYEMWRSNKHHESADELRDRVKGVSAKPFIETLPSIDALHCDIGNA 316
Cdd:pfam12940 346 GSTYICTLCDSSRAEASKNKVLHAITRSHEENLERYEIWRTNPFSESADDLRDRVKGISAKPFLETQACIDALHCDIGNA 425
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50957104   317 AEFYKIFQLEIGEVFKNPDASKEERKRWQSTLDKHLRKKMNLKPIMRMNGNFARKLMAKETVDAVCELVRTEERQVALRE 396
Cdd:pfam12940 426 TEFYKIFQDEIGEVHKKANPSKEERKRWQAALDKQLRKKMKLKPVMRMNGNFARKLMTQEAVDAVCELVPSEERQEALRE 505
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 50957104   397 LMDLYLKMKPVWRSSCPAKECPELLCQYSFNSQRFAELLSTKFKYRYEGKITNYFHKTLAHVPEIIERDGSIGAWASEGN 476
Cdd:pfam12940 506 LMHLYLQMKPVWRATCPAKECPDLLCRYSFNSQRFADLLSTTFKYRYDGKITNYLHKTLAHVPEIIERDGSIGAWASEGN 585
                         490       500
                  ....*....|....*....|....*..
gi 50957104   477 ESGNKLFRRFRKMNARQSKFYEMEDVL 503
Cdd:pfam12940 586 ESANKLFRRFRKMNARQSKSFELEDIL 612
 
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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