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Conserved domains on  [gi|124808108|ref|XP_001348232|]
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transcription elongation factor SPT6, putative [Plasmodium falciparum 3D7]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
SH2_Nterm_SPT6_like cd09918
N-terminal Src homology 2 (SH2) domain found in Spt6; N-terminal SH2 domain in Spt6. Spt6 is ...
2558-2654 2.73e-18

N-terminal Src homology 2 (SH2) domain found in Spt6; N-terminal SH2 domain in Spt6. Spt6 is an essential transcription elongation factor and histone chaperone that binds the C-terminal repeat domain (CTD) of RNA polymerase II. Spt6 contains a tandem SH2 domain with a novel structure and CTD-binding mode. The tandem SH2 domain binds to a serine 2-phosphorylated CTD peptide in vitro, whereas its N-terminal SH2 subdomain does not. CTD binding requires a positively charged crevice in the C-terminal SH2 subdomain, which lacks the canonical phospho-binding pocket of SH2 domains. The tandem SH2 domain is apparently required for transcription elongation in vivo as its deletion in cells is lethal in the presence of 6-azauracil. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites.


:

Pssm-ID: 198174  Cd Length: 85  Bit Score: 81.51  E-value: 2.73e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124808108 2558 NHPNFKLWNYQEVYTYLKQNNisIGESIIYPSNE-INKLYVIIKTCDnpfyivkftiyekNVQQHNNITNRNIHQP--IQ 2634
Cdd:cd09918     1 RHPLFKNVNYKQAEAYLKSKD--VGEVVIRPSSKgVDHLTVTWKVAD-------------GVYQHIDIEELNKENPfsLG 65
                          90       100
                  ....*....|....*....|
gi 124808108 2635 QIYLINNEQFKSIDQIVTNF 2654
Cdd:cd09918    66 KELIIGGEEYEDLDEIIARF 85
HHH_5 super family cl22429
Helix-hairpin-helix domain;
2060-2159 1.68e-10

Helix-hairpin-helix domain;


The actual alignment was detected with superfamily member pfam14635:

Pssm-ID: 473956  Cd Length: 104  Bit Score: 60.25  E-value: 1.68e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124808108  2060 LHDLQNYICNYKLQYLFERVMIDVVNKIGCDINflRKQKKKHLENSLNYICGLGLRKREELMKLLHNTN--LNTREDLLT 2137
Cdd:pfam14635    8 FHPLQELLPKEELLKALETAFVDIVNLVGVDVN--EAIANKYEAAILPYIAGLGPRKADHLLKILAANNgrLDNRSQLIT 85
                           90       100
                   ....*....|....*....|..
gi 124808108  2138 lsnnKKFIGKCVYRNCSSFIRI 2159
Cdd:pfam14635   86 ----KCIMGPKVFMNCAGFLII 103
SPT6_acidic pfam14632
Acidic N-terminal SPT6; The N-terminus of SPT6 is highly acidic. The full SPT6 protein is a ...
355-393 5.12e-05

Acidic N-terminal SPT6; The N-terminus of SPT6 is highly acidic. The full SPT6 protein is a transcription regulator, but the exact function of this acidic region is not certain.


:

Pssm-ID: 464226  Cd Length: 89  Bit Score: 44.00  E-value: 5.12e-05
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 124808108   355 ENKSLDDEDLELIAENTGIQVIRNEKdtKHRRLKKIKDS 393
Cdd:pfam14632   53 EDDRLDEDDLDLIEENTGVKRRRSSS--KFKRLKRGHDD 89
 
Name Accession Description Interval E-value
SH2_Nterm_SPT6_like cd09918
N-terminal Src homology 2 (SH2) domain found in Spt6; N-terminal SH2 domain in Spt6. Spt6 is ...
2558-2654 2.73e-18

N-terminal Src homology 2 (SH2) domain found in Spt6; N-terminal SH2 domain in Spt6. Spt6 is an essential transcription elongation factor and histone chaperone that binds the C-terminal repeat domain (CTD) of RNA polymerase II. Spt6 contains a tandem SH2 domain with a novel structure and CTD-binding mode. The tandem SH2 domain binds to a serine 2-phosphorylated CTD peptide in vitro, whereas its N-terminal SH2 subdomain does not. CTD binding requires a positively charged crevice in the C-terminal SH2 subdomain, which lacks the canonical phospho-binding pocket of SH2 domains. The tandem SH2 domain is apparently required for transcription elongation in vivo as its deletion in cells is lethal in the presence of 6-azauracil. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites.


Pssm-ID: 198174  Cd Length: 85  Bit Score: 81.51  E-value: 2.73e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124808108 2558 NHPNFKLWNYQEVYTYLKQNNisIGESIIYPSNE-INKLYVIIKTCDnpfyivkftiyekNVQQHNNITNRNIHQP--IQ 2634
Cdd:cd09918     1 RHPLFKNVNYKQAEAYLKSKD--VGEVVIRPSSKgVDHLTVTWKVAD-------------GVYQHIDIEELNKENPfsLG 65
                          90       100
                  ....*....|....*....|
gi 124808108 2635 QIYLINNEQFKSIDQIVTNF 2654
Cdd:cd09918    66 KELIIGGEEYEDLDEIIARF 85
HHH_7 pfam14635
Helix-hairpin-helix motif;
2060-2159 1.68e-10

Helix-hairpin-helix motif;


Pssm-ID: 291309  Cd Length: 104  Bit Score: 60.25  E-value: 1.68e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124808108  2060 LHDLQNYICNYKLQYLFERVMIDVVNKIGCDINflRKQKKKHLENSLNYICGLGLRKREELMKLLHNTN--LNTREDLLT 2137
Cdd:pfam14635    8 FHPLQELLPKEELLKALETAFVDIVNLVGVDVN--EAIANKYEAAILPYIAGLGPRKADHLLKILAANNgrLDNRSQLIT 85
                           90       100
                   ....*....|....*....|..
gi 124808108  2138 lsnnKKFIGKCVYRNCSSFIRI 2159
Cdd:pfam14635   86 ----KCIMGPKVFMNCAGFLII 103
SH2_2 pfam14633
SH2 domain;
2557-2696 3.22e-06

SH2 domain;


Pssm-ID: 464227 [Multi-domain]  Cd Length: 206  Bit Score: 50.61  E-value: 3.22e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124808108  2557 INHPNFKLWNYQEVYTYLKqnNISIGESIIYPSNE-INKLYVIIKTCDNpfyivkftIYeknvqQHNNITNRNIHQP--I 2633
Cdd:pfam14633   24 IKHPLFHNFNYAQAEEYLA--SQDRGDVVIRPSSKgPDHLTVTWKVADG--------VY-----QHIDVLELDKENEfsL 88
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 124808108  2634 QQIYLINNEQFKSIDQIVTNFCDNLKKNLLELYNHPKCKKrKSFEQVQKELSQEMILKPDNIM 2696
Cdd:pfam14633   89 GKTLRIGGEEYEDLDELIARHVQPMARKVEEMMNHRKFKD-GTKEEVEEWLREEKKANPKRSP 150
SPT6_acidic pfam14632
Acidic N-terminal SPT6; The N-terminus of SPT6 is highly acidic. The full SPT6 protein is a ...
355-393 5.12e-05

Acidic N-terminal SPT6; The N-terminus of SPT6 is highly acidic. The full SPT6 protein is a transcription regulator, but the exact function of this acidic region is not certain.


Pssm-ID: 464226  Cd Length: 89  Bit Score: 44.00  E-value: 5.12e-05
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 124808108   355 ENKSLDDEDLELIAENTGIQVIRNEKdtKHRRLKKIKDS 393
Cdd:pfam14632   53 EDDRLDEDDLDLIEENTGVKRRRSSS--KFKRLKRGHDD 89
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
2077-2227 7.33e-03

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 41.93  E-value: 7.33e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124808108 2077 ERVMIDVVNKIGCDINflrkQKKKHLensLNYICGLG-------LRKREElmkllhNTNLNTREDLLTLSNnkkfIGKCV 2149
Cdd:COG2183   475 DAVVEDCVNAVGVDLN----TASAPL---LSYVSGLNptlakniVAYRDE------NGAFKSRKELLKVPR----LGPKA 537
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 124808108 2150 YRNCSSFIRIiSNGDdfvEALDNTRIHPSNcYDIIYDMLKNTvekknsfmkNKDLYElvnyLIDKKRLIKHIEIKDYA 2227
Cdd:COG2183   538 FEQAAGFLRI-RDGD---NPLDNSAVHPES-YPVVEKILKDL---------GVSVKD----LIGNKELLKKLDPEKYA 597
 
Name Accession Description Interval E-value
SH2_Nterm_SPT6_like cd09918
N-terminal Src homology 2 (SH2) domain found in Spt6; N-terminal SH2 domain in Spt6. Spt6 is ...
2558-2654 2.73e-18

N-terminal Src homology 2 (SH2) domain found in Spt6; N-terminal SH2 domain in Spt6. Spt6 is an essential transcription elongation factor and histone chaperone that binds the C-terminal repeat domain (CTD) of RNA polymerase II. Spt6 contains a tandem SH2 domain with a novel structure and CTD-binding mode. The tandem SH2 domain binds to a serine 2-phosphorylated CTD peptide in vitro, whereas its N-terminal SH2 subdomain does not. CTD binding requires a positively charged crevice in the C-terminal SH2 subdomain, which lacks the canonical phospho-binding pocket of SH2 domains. The tandem SH2 domain is apparently required for transcription elongation in vivo as its deletion in cells is lethal in the presence of 6-azauracil. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites.


Pssm-ID: 198174  Cd Length: 85  Bit Score: 81.51  E-value: 2.73e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124808108 2558 NHPNFKLWNYQEVYTYLKQNNisIGESIIYPSNE-INKLYVIIKTCDnpfyivkftiyekNVQQHNNITNRNIHQP--IQ 2634
Cdd:cd09918     1 RHPLFKNVNYKQAEAYLKSKD--VGEVVIRPSSKgVDHLTVTWKVAD-------------GVYQHIDIEELNKENPfsLG 65
                          90       100
                  ....*....|....*....|
gi 124808108 2635 QIYLINNEQFKSIDQIVTNF 2654
Cdd:cd09918    66 KELIIGGEEYEDLDEIIARF 85
HHH_7 pfam14635
Helix-hairpin-helix motif;
2060-2159 1.68e-10

Helix-hairpin-helix motif;


Pssm-ID: 291309  Cd Length: 104  Bit Score: 60.25  E-value: 1.68e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124808108  2060 LHDLQNYICNYKLQYLFERVMIDVVNKIGCDINflRKQKKKHLENSLNYICGLGLRKREELMKLLHNTN--LNTREDLLT 2137
Cdd:pfam14635    8 FHPLQELLPKEELLKALETAFVDIVNLVGVDVN--EAIANKYEAAILPYIAGLGPRKADHLLKILAANNgrLDNRSQLIT 85
                           90       100
                   ....*....|....*....|..
gi 124808108  2138 lsnnKKFIGKCVYRNCSSFIRI 2159
Cdd:pfam14635   86 ----KCIMGPKVFMNCAGFLII 103
SH2_2 pfam14633
SH2 domain;
2557-2696 3.22e-06

SH2 domain;


Pssm-ID: 464227 [Multi-domain]  Cd Length: 206  Bit Score: 50.61  E-value: 3.22e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124808108  2557 INHPNFKLWNYQEVYTYLKqnNISIGESIIYPSNE-INKLYVIIKTCDNpfyivkftIYeknvqQHNNITNRNIHQP--I 2633
Cdd:pfam14633   24 IKHPLFHNFNYAQAEEYLA--SQDRGDVVIRPSSKgPDHLTVTWKVADG--------VY-----QHIDVLELDKENEfsL 88
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 124808108  2634 QQIYLINNEQFKSIDQIVTNFCDNLKKNLLELYNHPKCKKrKSFEQVQKELSQEMILKPDNIM 2696
Cdd:pfam14633   89 GKTLRIGGEEYEDLDELIARHVQPMARKVEEMMNHRKFKD-GTKEEVEEWLREEKKANPKRSP 150
SPT6_acidic pfam14632
Acidic N-terminal SPT6; The N-terminus of SPT6 is highly acidic. The full SPT6 protein is a ...
355-393 5.12e-05

Acidic N-terminal SPT6; The N-terminus of SPT6 is highly acidic. The full SPT6 protein is a transcription regulator, but the exact function of this acidic region is not certain.


Pssm-ID: 464226  Cd Length: 89  Bit Score: 44.00  E-value: 5.12e-05
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 124808108   355 ENKSLDDEDLELIAENTGIQVIRNEKdtKHRRLKKIKDS 393
Cdd:pfam14632   53 EDDRLDEDDLDLIEENTGVKRRRSSS--KFKRLKRGHDD 89
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
2077-2227 7.33e-03

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 41.93  E-value: 7.33e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124808108 2077 ERVMIDVVNKIGCDINflrkQKKKHLensLNYICGLG-------LRKREElmkllhNTNLNTREDLLTLSNnkkfIGKCV 2149
Cdd:COG2183   475 DAVVEDCVNAVGVDLN----TASAPL---LSYVSGLNptlakniVAYRDE------NGAFKSRKELLKVPR----LGPKA 537
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 124808108 2150 YRNCSSFIRIiSNGDdfvEALDNTRIHPSNcYDIIYDMLKNTvekknsfmkNKDLYElvnyLIDKKRLIKHIEIKDYA 2227
Cdd:COG2183   538 FEQAAGFLRI-RDGD---NPLDNSAVHPES-YPVVEKILKDL---------GVSVKD----LIGNKELLKKLDPEKYA 597
 
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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