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Conserved domains on  [gi|862669363|ref|NP_001297091|]
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negative elongation factor B [Sus scrofa]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
COBRA1 pfam06209
Cofactor of BRCA1 (COBRA1); This family consists of several cofactor of BRCA1 (COBRA1) like ...
 158-501 0e+00

Cofactor of BRCA1 (COBRA1); This family consists of several cofactor of BRCA1 (COBRA1) like proteins. It is thought that COBRA1 along with BRCA1 is involved in chromatin unfolding. COBRA1 is recruited to the chromosome site by the first BRCT repeat of BRCA1, and is itself sufficient to induce chromatin unfolding. BRCA1 mutations that enhance chromatin unfolding also increase its affinity for, and recruitment of, COBRA1. It is thought that that reorganization of higher levels of chromatin structure is an important regulated step in BRCA1-mediated nuclear functions.


:

Pssm-ID: 461851  Cd Length: 346  Bit Score: 680.65  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 862669363  158 PSLQPVVMCVMKHLPKVPEKKLKLVMADKELYRACAVEVKRQIWQDNQALFGDEVSPLLKQYIVEKENALFSPELSVLHN 237
Cdd:pfam06209   1 KSLRPVVMCVLKHLPKIPDKYLKVLVADKELYRDCATEVKRQIWQDNQALFGDEVSPLLSQYIKEKETILFSHELNLSNN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 862669363  238 FFSPSPKTRRQGEVVQKLTRMVGRNVKLYDMVLQFLRTLFLRTRNVHYCTLRAELLMSLHDLDVGDICSVDPCHKFTWCL 317
Cdd:pfam06209  81 FFSPSPKTRRQGEVVQKLAHMIGKSVKLYDMVLQFLRTLFLRTRNVHYCTLRAELLMALHDLEVQDICSVDPCHKFTWCL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 862669363  318 DACIRERFVDGKRARELQGFLDGVKKGQEQVLGDLSMILCDPFAINTLSLSTVRHLQELVGQEMLPRESPDLLLLLRLLA 397
Cdd:pfam06209 161 DACIREKFVDSKRARELQGFLDGVKRGQEQVLGDLSMILCDPFAINTLALSAIKILQHLINNETLPRDSPDLMLLLRMLA 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 862669363  398 LGQGAWDMIDSQVFKEPKMEVELVTRFLPTLMSFVVDDHTFNVDQKLPAEEKAP--VTYPSTLPESFTKFLQEQRMACEV 475
Cdd:pfam06209 241 LGLSAWDMIDSQVFKEPKLDVELVTKFLPALMSLMVDDQVRNLNQKLPPDEKESaiVEHSGPLPDSFQKFIQENRVACEL 320

                         330       340
                  ....*....|....*....|....*.
gi 862669363  476 GLYYVLHITKQRNKNALLRLLPGLVE 501
Cdd:pfam06209 321 ALYYTLHVTKQKDKNALLRVLPILVS 346
DeaD_C pfam12343
DeaD helicase C-terminal disordered region; This region family is found at the C-terminus of ...
 8-49 1.46e-04

DeaD helicase C-terminal disordered region; This region family is found at the C-terminus of the DeaD helicase, which are involved in various cellular processes such as transcription, translation and DNA recombination. This region contains several repeats which contain an ERRE sequence motif.


:

Pssm-ID: 432492 [Multi-domain]  Cd Length: 61  Bit Score: 39.95  E-value: 1.46e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 862669363    8 GERSSGGpRGPGERAAAGPAATGSAPGERGGDGAPSRVGAGA 49
Cdd:pfam12343  13 GERREGG-RRAPGRSFSGERREGGRSGERRGGRAPRRDDSAA 53
 
Name Accession Description Interval E-value
COBRA1 pfam06209
Cofactor of BRCA1 (COBRA1); This family consists of several cofactor of BRCA1 (COBRA1) like ...
 158-501 0e+00

Cofactor of BRCA1 (COBRA1); This family consists of several cofactor of BRCA1 (COBRA1) like proteins. It is thought that COBRA1 along with BRCA1 is involved in chromatin unfolding. COBRA1 is recruited to the chromosome site by the first BRCT repeat of BRCA1, and is itself sufficient to induce chromatin unfolding. BRCA1 mutations that enhance chromatin unfolding also increase its affinity for, and recruitment of, COBRA1. It is thought that that reorganization of higher levels of chromatin structure is an important regulated step in BRCA1-mediated nuclear functions.


Pssm-ID: 461851  Cd Length: 346  Bit Score: 680.65  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 862669363  158 PSLQPVVMCVMKHLPKVPEKKLKLVMADKELYRACAVEVKRQIWQDNQALFGDEVSPLLKQYIVEKENALFSPELSVLHN 237
Cdd:pfam06209   1 KSLRPVVMCVLKHLPKIPDKYLKVLVADKELYRDCATEVKRQIWQDNQALFGDEVSPLLSQYIKEKETILFSHELNLSNN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 862669363  238 FFSPSPKTRRQGEVVQKLTRMVGRNVKLYDMVLQFLRTLFLRTRNVHYCTLRAELLMSLHDLDVGDICSVDPCHKFTWCL 317
Cdd:pfam06209  81 FFSPSPKTRRQGEVVQKLAHMIGKSVKLYDMVLQFLRTLFLRTRNVHYCTLRAELLMALHDLEVQDICSVDPCHKFTWCL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 862669363  318 DACIRERFVDGKRARELQGFLDGVKKGQEQVLGDLSMILCDPFAINTLSLSTVRHLQELVGQEMLPRESPDLLLLLRLLA 397
Cdd:pfam06209 161 DACIREKFVDSKRARELQGFLDGVKRGQEQVLGDLSMILCDPFAINTLALSAIKILQHLINNETLPRDSPDLMLLLRMLA 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 862669363  398 LGQGAWDMIDSQVFKEPKMEVELVTRFLPTLMSFVVDDHTFNVDQKLPAEEKAP--VTYPSTLPESFTKFLQEQRMACEV 475
Cdd:pfam06209 241 LGLSAWDMIDSQVFKEPKLDVELVTKFLPALMSLMVDDQVRNLNQKLPPDEKESaiVEHSGPLPDSFQKFIQENRVACEL 320

                         330       340
                  ....*....|....*....|....*.
gi 862669363  476 GLYYVLHITKQRNKNALLRLLPGLVE 501
Cdd:pfam06209 321 ALYYTLHVTKQKDKNALLRVLPILVS 346
DeaD_C pfam12343
DeaD helicase C-terminal disordered region; This region family is found at the C-terminus of ...
 8-49 1.46e-04

DeaD helicase C-terminal disordered region; This region family is found at the C-terminus of the DeaD helicase, which are involved in various cellular processes such as transcription, translation and DNA recombination. This region contains several repeats which contain an ERRE sequence motif.


Pssm-ID: 432492 [Multi-domain]  Cd Length: 61  Bit Score: 39.95  E-value: 1.46e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 862669363    8 GERSSGGpRGPGERAAAGPAATGSAPGERGGDGAPSRVGAGA 49
Cdd:pfam12343  13 GERREGG-RRAPGRSFSGERREGGRSGERRGGRAPRRDDSAA 53
 
Name Accession Description Interval E-value
COBRA1 pfam06209
Cofactor of BRCA1 (COBRA1); This family consists of several cofactor of BRCA1 (COBRA1) like ...
 158-501 0e+00

Cofactor of BRCA1 (COBRA1); This family consists of several cofactor of BRCA1 (COBRA1) like proteins. It is thought that COBRA1 along with BRCA1 is involved in chromatin unfolding. COBRA1 is recruited to the chromosome site by the first BRCT repeat of BRCA1, and is itself sufficient to induce chromatin unfolding. BRCA1 mutations that enhance chromatin unfolding also increase its affinity for, and recruitment of, COBRA1. It is thought that that reorganization of higher levels of chromatin structure is an important regulated step in BRCA1-mediated nuclear functions.


Pssm-ID: 461851  Cd Length: 346  Bit Score: 680.65  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 862669363  158 PSLQPVVMCVMKHLPKVPEKKLKLVMADKELYRACAVEVKRQIWQDNQALFGDEVSPLLKQYIVEKENALFSPELSVLHN 237
Cdd:pfam06209   1 KSLRPVVMCVLKHLPKIPDKYLKVLVADKELYRDCATEVKRQIWQDNQALFGDEVSPLLSQYIKEKETILFSHELNLSNN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 862669363  238 FFSPSPKTRRQGEVVQKLTRMVGRNVKLYDMVLQFLRTLFLRTRNVHYCTLRAELLMSLHDLDVGDICSVDPCHKFTWCL 317
Cdd:pfam06209  81 FFSPSPKTRRQGEVVQKLAHMIGKSVKLYDMVLQFLRTLFLRTRNVHYCTLRAELLMALHDLEVQDICSVDPCHKFTWCL 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 862669363  318 DACIRERFVDGKRARELQGFLDGVKKGQEQVLGDLSMILCDPFAINTLSLSTVRHLQELVGQEMLPRESPDLLLLLRLLA 397
Cdd:pfam06209 161 DACIREKFVDSKRARELQGFLDGVKRGQEQVLGDLSMILCDPFAINTLALSAIKILQHLINNETLPRDSPDLMLLLRMLA 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 862669363  398 LGQGAWDMIDSQVFKEPKMEVELVTRFLPTLMSFVVDDHTFNVDQKLPAEEKAP--VTYPSTLPESFTKFLQEQRMACEV 475
Cdd:pfam06209 241 LGLSAWDMIDSQVFKEPKLDVELVTKFLPALMSLMVDDQVRNLNQKLPPDEKESaiVEHSGPLPDSFQKFIQENRVACEL 320

                         330       340
                  ....*....|....*....|....*.
gi 862669363  476 GLYYVLHITKQRNKNALLRLLPGLVE 501
Cdd:pfam06209 321 ALYYTLHVTKQKDKNALLRVLPILVS 346
DeaD_C pfam12343
DeaD helicase C-terminal disordered region; This region family is found at the C-terminus of ...
 8-49 1.46e-04

DeaD helicase C-terminal disordered region; This region family is found at the C-terminus of the DeaD helicase, which are involved in various cellular processes such as transcription, translation and DNA recombination. This region contains several repeats which contain an ERRE sequence motif.


Pssm-ID: 432492 [Multi-domain]  Cd Length: 61  Bit Score: 39.95  E-value: 1.46e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 862669363    8 GERSSGGpRGPGERAAAGPAATGSAPGERGGDGAPSRVGAGA 49
Cdd:pfam12343  13 GERREGG-RRAPGRSFSGERREGGRSGERRGGRAPRRDDSAA 53
Collagen pfam01391
Collagen triple helix repeat (20 copies); Members of this family belong to the collagen ...
 7-42 7.75e-04

Collagen triple helix repeat (20 copies); Members of this family belong to the collagen superfamily. Collagens are generally extracellular structural proteins involved in formation of connective tissue structure. The alignment contains 20 copies of the G-X-Y repeat that forms a triple helix. The first position of the repeat is glycine, the second and third positions can be any residue but are frequently proline and hydroxy-proline. Collagens are post translationally modified by proline hydroxylase to form the hydroxy-proline residues. Defective hydroxylation is the cause of scurvy. Some members of the collagen superfamily are not involved in connective tissue structure but share the same triple helical structure. The family includes bacterial collagen-like triple-helix repeat proteins.


Pssm-ID: 460189 [Multi-domain]  Cd Length: 57  Bit Score: 37.86  E-value: 7.75e-04
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 862669363    7 AGERSSGGPRGP-GERAAAGPAATGSAPGERGGDGAP 42
Cdd:pfam01391  18 PGPPGPPGPPGPpGEPGPPGPPGPPGPPGPPGAPGAP 54
 
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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