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Conserved domains on  [gi|1474890860|pdb|6GMH|Y]
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Chain Y, Transcription elongation factor SPT4

Protein Classification

transcription elongation factor SPT4( domain architecture ID 10168327)

transcription elongation factor SPT4 is a component of the DRB sensitivity-inducing factor complex (DSIF complex), which regulates mRNA processing and transcription elongation by RNA polymerase II

CATH:  3.30.40.210
Gene Ontology:  GO:0008270|GO:0006355|GO:0000993

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Spt4 cd07973
Transcription elongation factor Spt4; Spt4 is a transcription elongation factor. Three ...
 15-112 8.14e-62

Transcription elongation factor Spt4; Spt4 is a transcription elongation factor. Three transcription-elongation factors Spt4, Spt5, and Spt6, are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. Spt4 functions entirely in the context of the Spt4-Spt5 heterodimer and it has been found only as a complex to Spt5 in Yeast and Human. Spt4 is a small protein that has zinc finger at the N-terminus. Spt5 is a large protein that has several interesting structural features of an acidic N-terminus, a single NGN domain, five or six KOW domains, and a set of simple C-termianl repeats. Spt4 binds to Spt5 NGN domain. Unlike Spt5, Spt4 is not essential for viability in yeast, however Spt4 is critical for normal function of the Spt4-Spt5 complex. Spt4 homolog is not found in bacteria.


:

Pssm-ID: 153422  Cd Length: 98  Bit Score: 183.98  E-value: 8.14e-62
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6GMH_Y       15 RHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGIIAMMSPEDSWVSKWQRVSNFKPGVYAVSVT 94
Cdd:cd07973   1 RGLRACLLCSLIKTEDQFERDGCPNCEGYLDMKGNHERVYDCTSPNFEGIIALMDPEKSWVARWQRIDKFVPGIYAISVS 80

                        90
                ....*....|....*...
6GMH_Y       95 GRLPQGIVRELKSRGVAY 112
Cdd:cd07973  81 GRLPEDIVEELESRGIIY 98
 
Name Accession Description Interval E-value
Spt4 cd07973
Transcription elongation factor Spt4; Spt4 is a transcription elongation factor. Three ...
 15-112 8.14e-62

Transcription elongation factor Spt4; Spt4 is a transcription elongation factor. Three transcription-elongation factors Spt4, Spt5, and Spt6, are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. Spt4 functions entirely in the context of the Spt4-Spt5 heterodimer and it has been found only as a complex to Spt5 in Yeast and Human. Spt4 is a small protein that has zinc finger at the N-terminus. Spt5 is a large protein that has several interesting structural features of an acidic N-terminus, a single NGN domain, five or six KOW domains, and a set of simple C-termianl repeats. Spt4 binds to Spt5 NGN domain. Unlike Spt5, Spt4 is not essential for viability in yeast, however Spt4 is critical for normal function of the Spt4-Spt5 complex. Spt4 homolog is not found in bacteria.


Pssm-ID: 153422  Cd Length: 98  Bit Score: 183.98  E-value: 8.14e-62
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6GMH_Y       15 RHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGIIAMMSPEDSWVSKWQRVSNFKPGVYAVSVT 94
Cdd:cd07973   1 RGLRACLLCSLIKTEDQFERDGCPNCEGYLDMKGNHERVYDCTSPNFEGIIALMDPEKSWVARWQRIDKFVPGIYAISVS 80

                        90
                ....*....|....*...
6GMH_Y       95 GRLPQGIVRELKSRGVAY 112
Cdd:cd07973  81 GRLPEDIVEELESRGIIY 98
Spt4 pfam06093
Spt4/RpoE2 zinc finger; This family consists of several eukaryotic transcription elongation ...
 17-94 1.07e-39

Spt4/RpoE2 zinc finger; This family consists of several eukaryotic transcription elongation Spt4 proteins as well as archaebacterial RpoE2. Three transcription-elongation factors Spt4, Spt5, and Spt6 are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. Spt4 and Spt5 are tightly associated in a complex, while the physical association of the Spt4-Spt5 complex with Spt6 is considerably weaker. It has been demonstrated that Spt4, Spt5, and Spt6 play roles in transcription elongation in both yeast and humans including a role in activation by Tat. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. RpoE2 is one of 13 subunits in the archaeal RNA polymerase. These proteins contain a C4-type zinc finger, and the structure has been solved in. The structure reveals that Spt4-Spt5 binding is governed by an acid-dipole interaction between Spt5 and Spt4, and the complex binds to and travels along the elongating RNA polymerase. The Spt4-Spt5 complex is likely to be an ancient, core component of the transcription elongation machinery.


Pssm-ID: 399233  Cd Length: 77  Bit Score: 127.07  E-value: 1.07e-39
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
6GMH_Y         17 LRACLLCSLVKTIDQFEYDGCDNCDaYLQMKGNREMVYDCTSSSFDGIIAMMSPEDSWVSKWQRVSNFKPGVYAVSVT 94
Cdd:pfam06093   1 LRACLLCSLVKTEDQFEDDGCPNCE-FLHMKGDRERVSECTSENFEGLVAILDPEKSWVAKWQRLGKFVPGCYALKVR 77
SPT4 COG5204
Transcription elongation factor SPT4 [Transcription];
18-116 1.52e-36

Transcription elongation factor SPT4 [Transcription];


Pssm-ID: 227530  Cd Length: 112  Bit Score: 120.45  E-value: 1.52e-36
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6GMH_Y       18 RACLLCSLVKTIDQFEYDGCDNCDAyLQMKGNREMVYDCTSSSFDGIIAMMSPEDSWVSKWQRVSNFKPGVYAVSVTGRL 97
Cdd:COG5204  10 RACLGCGIVKTLNGFRKDGCPNCPM-LNMKGGVTNVEECTSPKFEGVVAMLQPTNSWVAKWQRIDEFRKGLYAMVVEGAL 88

                        90
                ....*....|....*....
6GMH_Y       98 PQGIVRELKSRGVAYKSRD 116
Cdd:COG5204  89 SEDVVEDLEQHGRIYYPRT 107
 
Name Accession Description Interval E-value
Spt4 cd07973
Transcription elongation factor Spt4; Spt4 is a transcription elongation factor. Three ...
 15-112 8.14e-62

Transcription elongation factor Spt4; Spt4 is a transcription elongation factor. Three transcription-elongation factors Spt4, Spt5, and Spt6, are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. Spt4 functions entirely in the context of the Spt4-Spt5 heterodimer and it has been found only as a complex to Spt5 in Yeast and Human. Spt4 is a small protein that has zinc finger at the N-terminus. Spt5 is a large protein that has several interesting structural features of an acidic N-terminus, a single NGN domain, five or six KOW domains, and a set of simple C-termianl repeats. Spt4 binds to Spt5 NGN domain. Unlike Spt5, Spt4 is not essential for viability in yeast, however Spt4 is critical for normal function of the Spt4-Spt5 complex. Spt4 homolog is not found in bacteria.


Pssm-ID: 153422  Cd Length: 98  Bit Score: 183.98  E-value: 8.14e-62
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6GMH_Y       15 RHLRACLLCSLVKTIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGIIAMMSPEDSWVSKWQRVSNFKPGVYAVSVT 94
Cdd:cd07973   1 RGLRACLLCSLIKTEDQFERDGCPNCEGYLDMKGNHERVYDCTSPNFEGIIALMDPEKSWVARWQRIDKFVPGIYAISVS 80

                        90
                ....*....|....*...
6GMH_Y       95 GRLPQGIVRELKSRGVAY 112
Cdd:cd07973  81 GRLPEDIVEELESRGIIY 98
Spt4 pfam06093
Spt4/RpoE2 zinc finger; This family consists of several eukaryotic transcription elongation ...
 17-94 1.07e-39

Spt4/RpoE2 zinc finger; This family consists of several eukaryotic transcription elongation Spt4 proteins as well as archaebacterial RpoE2. Three transcription-elongation factors Spt4, Spt5, and Spt6 are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. Spt4 and Spt5 are tightly associated in a complex, while the physical association of the Spt4-Spt5 complex with Spt6 is considerably weaker. It has been demonstrated that Spt4, Spt5, and Spt6 play roles in transcription elongation in both yeast and humans including a role in activation by Tat. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. RpoE2 is one of 13 subunits in the archaeal RNA polymerase. These proteins contain a C4-type zinc finger, and the structure has been solved in. The structure reveals that Spt4-Spt5 binding is governed by an acid-dipole interaction between Spt5 and Spt4, and the complex binds to and travels along the elongating RNA polymerase. The Spt4-Spt5 complex is likely to be an ancient, core component of the transcription elongation machinery.


Pssm-ID: 399233  Cd Length: 77  Bit Score: 127.07  E-value: 1.07e-39
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
6GMH_Y         17 LRACLLCSLVKTIDQFEYDGCDNCDaYLQMKGNREMVYDCTSSSFDGIIAMMSPEDSWVSKWQRVSNFKPGVYAVSVT 94
Cdd:pfam06093   1 LRACLLCSLVKTEDQFEDDGCPNCE-FLHMKGDRERVSECTSENFEGLVAILDPEKSWVAKWQRLGKFVPGCYALKVR 77
SPT4 COG5204
Transcription elongation factor SPT4 [Transcription];
18-116 1.52e-36

Transcription elongation factor SPT4 [Transcription];


Pssm-ID: 227530  Cd Length: 112  Bit Score: 120.45  E-value: 1.52e-36
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6GMH_Y       18 RACLLCSLVKTIDQFEYDGCDNCDAyLQMKGNREMVYDCTSSSFDGIIAMMSPEDSWVSKWQRVSNFKPGVYAVSVTGRL 97
Cdd:COG5204  10 RACLGCGIVKTLNGFRKDGCPNCPM-LNMKGGVTNVEECTSPKFEGVVAMLQPTNSWVAKWQRIDEFRKGLYAMVVEGAL 88

                        90
                ....*....|....*....
6GMH_Y       98 PQGIVRELKSRGVAYKSRD 116
Cdd:COG5204  89 SEDVVEDLEQHGRIYYPRT 107
 
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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