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Conserved domains on  [gi|21358129|ref|NP_652610|]
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Spt5 [Drosophila melanogaster]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
NGN_Euk cd09888
Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW ...
 215-302 3.81e-38

Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW domain-containing Transcription Factor 1); The N-Utilization Substance G (NusG) protein and its eukaryotic homolog, Spt5, are involved in transcription elongation and termination. NusG contains an NGN domain at its N-terminus and Kyrpides Ouzounis and Woese (KOW) repeats at its C-terminus. Spt5 forms an Spt4-Spt5 complex that is an essential RNA polymerase II elongation factor. NusG was originally discovered as an N-dependent antitermination enhancing activity in Escherichia coli, and has a variety of functions such as its involvement in RNA polymerase elongation and Rho-termination in bacteria. Orthologs of the NusG gene exist in all bacteria, but their functions and requirements are different. Spt5-like is homologous to the Spt5 proteins present in all eukaryotes, which is unique as it encodes a protein with an additional long carboxy-terminal extension that contains WG/GW motifs. Spt5-like, or KTF1 (KOW domain-containing Transcription Factor 1), is a RNA-directed DNA methylation (RdDM) pathway effector in plants.


:

Pssm-ID: 193577 [Multi-domain]  Cd Length: 86  Bit Score: 137.28  E-value: 3.81e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21358129  215 NLWMVKCRIGEEKATALLLMRKYLTYLNTDDPLQIKSIIAPEGVKGYIYLEAYKQTHVKTCIDNVGNLRMgkWKQEMVPI 294
Cdd:cd09888    1 KLWAVKCKPGKEREIVISLMRKFLDLQRTGNPLGIKSVFARDGLKGYIYIEARKEAHVKDAIEGLRGVYL--NTIKLVPI 78


                 ....*...
gi 21358129  295 KEMTDVLK 302
Cdd:cd09888   79 KEMPDVLS 86
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 812-908 2.05e-29

Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif.


:

Pssm-ID: 215026 [Multi-domain]  Cd Length: 121  Bit Score: 113.39  E-value: 2.05e-29
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21358129     812 GAQTPSYTAAGSKTPLVGSQTP----NWDTDTRTPYGTMTPSHDG--SMTPRHGAWDPTANTTPARNND-FDY-SLEEPS 883
Cdd:smart01104    1 GGRTPAWGASGSKTPAWGSRTPgtaaGGAPTARGGSGSRTPAWGGagSRTPAWGGAGPTGSRTPAWGGAsAWGnKSSEGS 80

                            90       100       110
                    ....*....|....*....|....*....|...
gi 21358129     884 PSP-------GYNPSTPGY-QMTSQFAPQTPGT 908
Cdd:smart01104   81 ASSwaagpggAYGAPTPGYgGTPSAYGPATPGG 113
KOW_Spt5_3 cd06083
KOW domain of Spt5, repeat 3; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 512-562 7.72e-23

KOW domain of Spt5, repeat 3; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases.


:

Pssm-ID: 240507  Cd Length: 51  Bit Score: 92.20  E-value: 7.72e-23
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 21358129  512 YFKTGDHARVLAGRYEGETGLIIRVEPTRVVLVSDLTNHELEVLPRDLQLC 562
Cdd:cd06083    1 HFKVGDHVKVISGRHEGETGLVVKVEDDVVTVFSDLTMRELKVFPRDLQLS 51
KOW_Spt5_5 cd06085
KOW domain of Spt5, repeat 5; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 737-788 6.35e-22

KOW domain of Spt5, repeat 5; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases.


:

Pssm-ID: 240509  Cd Length: 52  Bit Score: 89.85  E-value: 6.35e-22
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 21358129  737 RDREILGKTIKISGGPYKGAVGIVKDATESTARVELHTSCQTISVDRNHIAI 788
Cdd:cd06085    1 GRDPLIGKTVRIRKGPYKGYIGIVKDATGTTARVELHSKNKTITVDRSRLAV 52
KOW_Spt5_2 cd06082
KOW domain of Spt5, repeat 2; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 461-511 1.17e-19

KOW domain of Spt5, repeat 2; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases.


:

Pssm-ID: 240506  Cd Length: 51  Bit Score: 83.32  E-value: 1.17e-19
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 21358129  461 FSMGDNVEVCVGDLENLQAKIVAIDGTMITVMPKHQDLKDPLIFKASELRK 511
Cdd:cd06082    1 FQPGDNVEVIEGELKGLQGKVESVDGDIVTIMPKHEDLKEPLEFPAKELRK 51
KOW_Spt5_4 cd06084
KOW domain of Spt5, repeat 4; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 638-680 8.71e-19

KOW domain of Spt5, repeat 4; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases.


:

Pssm-ID: 240508  Cd Length: 43  Bit Score: 80.64  E-value: 8.71e-19
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 21358129  638 RDVVKVMEGPHAGRSGEIKHLYRSLAFLHCRMYTENGGIFVCK 680
Cdd:cd06084    1 GDTVKVVDGPYKGRQGTVLHIYRGTLFLHSREVTENGGIFVVR 43
KOW_Spt5_6 cd06086
KOW domain of Spt5, repeat 6; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 1020-1075 1.30e-18

KOW domain of Spt5, repeat 6; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases.


:

Pssm-ID: 240510  Cd Length: 58  Bit Score: 80.64  E-value: 1.30e-18
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 21358129 1020 EHLAPVLPCNGDEFKIIYGDDRESVGRVLSKDGDVFVCRIN--EEIKLLPINFLCKMK 1075
Cdd:cd06086    1 EHLEPVPPEKGDRVKVIKGEDRGSTGELISIDGADGIVKMDsdGDIKILPMNFLAKLV 58
KOW_Spt5_1 cd06081
KOW domain of Spt5, repeat 1; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 313-350 4.43e-18

KOW domain of Spt5, repeat 1; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases.


:

Pssm-ID: 240505  Cd Length: 38  Bit Score: 78.28  E-value: 4.43e-18
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 21358129  313 KQWVRLKRGLYKDDIAQVDYVDLAQNQVHLKLLPRIDY 350
Cdd:cd06081    1 GSWVRIKRGIYKGDLAQVDEVDENGNRVVVKLIPRIDY 38
Spt5_N pfam11942
Spt5 transcription elongation factor, acidic N-terminal; This is the very acidic N-terminal ...
 139-209 1.39e-08

Spt5 transcription elongation factor, acidic N-terminal; This is the very acidic N-terminal region of the early transcription elongation factor Spt5. The Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The actual function of this N-terminal domain is not known although it is dispensable for binding to Spt4.


:

Pssm-ID: 463406  Cd Length: 97  Bit Score: 53.42  E-value: 1.39e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 21358129    139 GIVGNEIDELGPTARDIEIRRRGTN----LWDTQKEDEIEEYLRKKYADESiakrhFGDGGEEMSDEITQQTLLP 209
Cdd:pfam11942   28 FIEDDEEDEDEEDGRRDDRRHRELDrrreLEEDEDAEEIAEYLKERYGRSS-----SDAYRGDAEEGVPQRLLLP 97
 
Name Accession Description Interval E-value
NGN_Euk cd09888
Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW ...
 215-302 3.81e-38

Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW domain-containing Transcription Factor 1); The N-Utilization Substance G (NusG) protein and its eukaryotic homolog, Spt5, are involved in transcription elongation and termination. NusG contains an NGN domain at its N-terminus and Kyrpides Ouzounis and Woese (KOW) repeats at its C-terminus. Spt5 forms an Spt4-Spt5 complex that is an essential RNA polymerase II elongation factor. NusG was originally discovered as an N-dependent antitermination enhancing activity in Escherichia coli, and has a variety of functions such as its involvement in RNA polymerase elongation and Rho-termination in bacteria. Orthologs of the NusG gene exist in all bacteria, but their functions and requirements are different. Spt5-like is homologous to the Spt5 proteins present in all eukaryotes, which is unique as it encodes a protein with an additional long carboxy-terminal extension that contains WG/GW motifs. Spt5-like, or KTF1 (KOW domain-containing Transcription Factor 1), is a RNA-directed DNA methylation (RdDM) pathway effector in plants.


Pssm-ID: 193577 [Multi-domain]  Cd Length: 86  Bit Score: 137.28  E-value: 3.81e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21358129  215 NLWMVKCRIGEEKATALLLMRKYLTYLNTDDPLQIKSIIAPEGVKGYIYLEAYKQTHVKTCIDNVGNLRMgkWKQEMVPI 294
Cdd:cd09888    1 KLWAVKCKPGKEREIVISLMRKFLDLQRTGNPLGIKSVFARDGLKGYIYIEARKEAHVKDAIEGLRGVYL--NTIKLVPI 78


                 ....*...
gi 21358129  295 KEMTDVLK 302
Cdd:cd09888   79 KEMPDVLS 86
Spt5-NGN pfam03439
Early transcription elongation factor of RNA pol II, NGN section; Spt5p and prokaryotic NusG ...
 215-301 5.49e-30

Early transcription elongation factor of RNA pol II, NGN section; Spt5p and prokaryotic NusG are shown to contain a novel 'NGN' domain. The combined NGN and KOW motif regions of Spt5 form the binding domain with Spt4. Spt5 complexes with Spt4 as a 1:1 heterodimer snf this Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The Schizosaccharomyces pombe core Spt5-Spt4 complex is a heterodimer bearing a trypsin-resistant Spt4-binding domain within the Spt5 subunit.


Pssm-ID: 397481  Cd Length: 84  Bit Score: 113.83  E-value: 5.49e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21358129    215 NLWMVKCRIGEEKATALLLMRKYLTYLNTDDpLQIKSIIAPEGVKGYIYLEAYKQTHVKTCIDNVGNLRMGkwKQEMVPI 294
Cdd:pfam03439    1 KIWAVKCTPGQEREVALSLMRKILALAKTNN-LGIYSVFAPDGLKGYIYVEADRQAAVKRALEGIPNVRGL--VPGLVPI 77


                   ....*..
gi 21358129    295 KEMTDVL 301
Cdd:pfam03439   78 KEMEHLL 84
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 812-908 2.05e-29

Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif.


Pssm-ID: 215026 [Multi-domain]  Cd Length: 121  Bit Score: 113.39  E-value: 2.05e-29
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21358129     812 GAQTPSYTAAGSKTPLVGSQTP----NWDTDTRTPYGTMTPSHDG--SMTPRHGAWDPTANTTPARNND-FDY-SLEEPS 883
Cdd:smart01104    1 GGRTPAWGASGSKTPAWGSRTPgtaaGGAPTARGGSGSRTPAWGGagSRTPAWGGAGPTGSRTPAWGGAsAWGnKSSEGS 80

                            90       100       110
                    ....*....|....*....|....*....|...
gi 21358129     884 PSP-------GYNPSTPGY-QMTSQFAPQTPGT 908
Cdd:smart01104   81 ASSwaagpggAYGAPTPGYgGTPSAYGPATPGG 113
KOW_Spt5_3 cd06083
KOW domain of Spt5, repeat 3; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 512-562 7.72e-23

KOW domain of Spt5, repeat 3; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases.


Pssm-ID: 240507  Cd Length: 51  Bit Score: 92.20  E-value: 7.72e-23
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 21358129  512 YFKTGDHARVLAGRYEGETGLIIRVEPTRVVLVSDLTNHELEVLPRDLQLC 562
Cdd:cd06083    1 HFKVGDHVKVISGRHEGETGLVVKVEDDVVTVFSDLTMRELKVFPRDLQLS 51
KOW_Spt5_5 cd06085
KOW domain of Spt5, repeat 5; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 737-788 6.35e-22

KOW domain of Spt5, repeat 5; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases.


Pssm-ID: 240509  Cd Length: 52  Bit Score: 89.85  E-value: 6.35e-22
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 21358129  737 RDREILGKTIKISGGPYKGAVGIVKDATESTARVELHTSCQTISVDRNHIAI 788
Cdd:cd06085    1 GRDPLIGKTVRIRKGPYKGYIGIVKDATGTTARVELHSKNKTITVDRSRLAV 52
KOW_Spt5_2 cd06082
KOW domain of Spt5, repeat 2; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 461-511 1.17e-19

KOW domain of Spt5, repeat 2; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases.


Pssm-ID: 240506  Cd Length: 51  Bit Score: 83.32  E-value: 1.17e-19
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 21358129  461 FSMGDNVEVCVGDLENLQAKIVAIDGTMITVMPKHQDLKDPLIFKASELRK 511
Cdd:cd06082    1 FQPGDNVEVIEGELKGLQGKVESVDGDIVTIMPKHEDLKEPLEFPAKELRK 51
KOW_Spt5_4 cd06084
KOW domain of Spt5, repeat 4; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 638-680 8.71e-19

KOW domain of Spt5, repeat 4; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases.


Pssm-ID: 240508  Cd Length: 43  Bit Score: 80.64  E-value: 8.71e-19
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 21358129  638 RDVVKVMEGPHAGRSGEIKHLYRSLAFLHCRMYTENGGIFVCK 680
Cdd:cd06084    1 GDTVKVVDGPYKGRQGTVLHIYRGTLFLHSREVTENGGIFVVR 43
KOW_Spt5_6 cd06086
KOW domain of Spt5, repeat 6; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 1020-1075 1.30e-18

KOW domain of Spt5, repeat 6; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases.


Pssm-ID: 240510  Cd Length: 58  Bit Score: 80.64  E-value: 1.30e-18
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 21358129 1020 EHLAPVLPCNGDEFKIIYGDDRESVGRVLSKDGDVFVCRIN--EEIKLLPINFLCKMK 1075
Cdd:cd06086    1 EHLEPVPPEKGDRVKVIKGEDRGSTGELISIDGADGIVKMDsdGDIKILPMNFLAKLV 58
KOW_Spt5_1 cd06081
KOW domain of Spt5, repeat 1; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 313-350 4.43e-18

KOW domain of Spt5, repeat 1; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases.


Pssm-ID: 240505  Cd Length: 38  Bit Score: 78.28  E-value: 4.43e-18
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 21358129  313 KQWVRLKRGLYKDDIAQVDYVDLAQNQVHLKLLPRIDY 350
Cdd:cd06081    1 GSWVRIKRGIYKGDLAQVDEVDENGNRVVVKLIPRIDY 38
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
 215-303 1.44e-14

In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, this domain may confer affinity for Spt4p.Spt4p


Pssm-ID: 197850 [Multi-domain]  Cd Length: 106  Bit Score: 70.48  E-value: 1.44e-14
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21358129     215 NLWMVKCRIGEEKATALLLMRKYLTYLNTDdplQIKSIIAP-EGVK----------------GYIYLEAYKQTHVKTCID 277
Cdd:smart00738    1 NWYAVRTTSGQEKRVAENLERKAEALGLED---KIVSILVPtEEVKeirrgkkkvverklfpGYIFVEADLEDEVWTAIR 77

                            90       100
                    ....*....|....*....|....*....
gi 21358129     278 NVGNLR---MGKWKQEMVPIKEMTDVLKV 303
Cdd:smart00738   78 GTPGVRgfvGGGGKPTPVPDDEIEKILKP 106
CTD pfam12815
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 802-870 8.38e-13

Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteriztic TPA motif.


Pssm-ID: 372327 [Multi-domain]  Cd Length: 71  Bit Score: 64.39  E-value: 8.38e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 21358129    802 GRTPARTPGYGAQTPSYTAAGSKTPLVG---SQTPNWDTDTRTPYgtmtPSHDGSMTPRH-GAWDptANTTPA 870
Cdd:pfam12815    2 SRTPAYNSAGGSRTPAWGADGSRTPAYGgagGRTPAYNQGGKTPA----WGGAGSRTPAYyGAWG--GSRTPA 68
nusG PRK08559
transcription antitermination protein NusG; Validated
 212-352 1.39e-11

transcription antitermination protein NusG; Validated


Pssm-ID: 181467 [Multi-domain]  Cd Length: 153  Bit Score: 63.73  E-value: 1.39e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21358129   212 KDPNLWMVKCRIGEEKATALLLMRKYLTYlntddPLQIKSIIAPEGVKGYIYLEAYKQTHVKTCIDNVGNLRmGKWKQEm 291
Cdd:PRK08559    4 EMSMIFAVKTTAGQERNVALMLAMRAKKE-----NLPIYAILAPPELKGYVLVEAESKGAVEEAIRGIPHVR-GVVPGE- 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21358129   292 VPIKEMTDVLKVVKEQVGLKVKQWVRLKRGLYKDDIAQVDYVDLAQNQVHLKLL----P-----RIDYTR 352
Cdd:PRK08559   77 ISFEEVEHFLKPKPIVEGIKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELLeaavPipvtvRGDQVR 146
Spt5_N pfam11942
Spt5 transcription elongation factor, acidic N-terminal; This is the very acidic N-terminal ...
 139-209 1.39e-08

Spt5 transcription elongation factor, acidic N-terminal; This is the very acidic N-terminal region of the early transcription elongation factor Spt5. The Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The actual function of this N-terminal domain is not known although it is dispensable for binding to Spt4.


Pssm-ID: 463406  Cd Length: 97  Bit Score: 53.42  E-value: 1.39e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 21358129    139 GIVGNEIDELGPTARDIEIRRRGTN----LWDTQKEDEIEEYLRKKYADESiakrhFGDGGEEMSDEITQQTLLP 209
Cdd:pfam11942   28 FIEDDEEDEDEEDGRRDDRRHRELDrrreLEEDEDAEEIAEYLKERYGRSS-----SDAYRGDAEEGVPQRLLLP 97
KOW_elon_Spt5 TIGR00405
transcription elongation factor Spt5; This protein contains a KOW domain, shared by bacterial ...
 219-345 8.64e-07

transcription elongation factor Spt5; This protein contains a KOW domain, shared by bacterial NusG and the uL24 (previously L24p/L26e) family of ribosomal proteins. The most recent papers and crystal structures make this a transcription elongation factor rather than a ribosomal protein.


Pssm-ID: 129499 [Multi-domain]  Cd Length: 145  Bit Score: 49.50  E-value: 8.64e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21358129    219 VKCRIGEEKATALLLMRKYltylnTDDPLQIKSIIAPEGVKGYIYLEAYKQTHVKTCIDNVGNLRmGKWKQEmVPIKEMT 298
Cdd:TIGR00405    3 VKTSVGQEKNVARLMARKA-----RKSGLEVYSILAPESLKGYILVEAETKIDMRNPIIGVPHVR-GVVEGE-IDFEEIE 75

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 21358129    299 DVLKVVKEQVGLKVKQWVRLKRGLYKDDIAQVDYVDLAQNQVHLKLL 345
Cdd:TIGR00405   76 RFLTPKKIIESIKKGDIVEIISGPFKGERAKVIRVDESKEEVTLELI 122
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 639-667 5.68e-03

KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and NusG.


Pssm-ID: 425698 [Multi-domain]  Cd Length: 32  Bit Score: 35.44  E-value: 5.68e-03
                           10        20
                   ....*....|....*....|....*....
gi 21358129    639 DVVKVMEGPHAGRSGEIKHLYRSLAFLHC 667
Cdd:pfam00467    3 DVVRVIAGPFKGKVGKVVEVDDKKNRVLV 31
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 516-544 6.21e-03

KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and NusG.


Pssm-ID: 425698 [Multi-domain]  Cd Length: 32  Bit Score: 35.44  E-value: 6.21e-03
                           10        20        30
                   ....*....|....*....|....*....|
gi 21358129    516 GDHARVLAGRYEGETGLIIRVEPTRV-VLV 544
Cdd:pfam00467    2 GDVVRVIAGPFKGKVGKVVEVDDKKNrVLV 31
 
Name Accession Description Interval E-value
NGN_Euk cd09888
Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW ...
 215-302 3.81e-38

Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW domain-containing Transcription Factor 1); The N-Utilization Substance G (NusG) protein and its eukaryotic homolog, Spt5, are involved in transcription elongation and termination. NusG contains an NGN domain at its N-terminus and Kyrpides Ouzounis and Woese (KOW) repeats at its C-terminus. Spt5 forms an Spt4-Spt5 complex that is an essential RNA polymerase II elongation factor. NusG was originally discovered as an N-dependent antitermination enhancing activity in Escherichia coli, and has a variety of functions such as its involvement in RNA polymerase elongation and Rho-termination in bacteria. Orthologs of the NusG gene exist in all bacteria, but their functions and requirements are different. Spt5-like is homologous to the Spt5 proteins present in all eukaryotes, which is unique as it encodes a protein with an additional long carboxy-terminal extension that contains WG/GW motifs. Spt5-like, or KTF1 (KOW domain-containing Transcription Factor 1), is a RNA-directed DNA methylation (RdDM) pathway effector in plants.


Pssm-ID: 193577 [Multi-domain]  Cd Length: 86  Bit Score: 137.28  E-value: 3.81e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21358129  215 NLWMVKCRIGEEKATALLLMRKYLTYLNTDDPLQIKSIIAPEGVKGYIYLEAYKQTHVKTCIDNVGNLRMgkWKQEMVPI 294
Cdd:cd09888    1 KLWAVKCKPGKEREIVISLMRKFLDLQRTGNPLGIKSVFARDGLKGYIYIEARKEAHVKDAIEGLRGVYL--NTIKLVPI 78


                 ....*...
gi 21358129  295 KEMTDVLK 302
Cdd:cd09888   79 KEMPDVLS 86
Spt5-NGN pfam03439
Early transcription elongation factor of RNA pol II, NGN section; Spt5p and prokaryotic NusG ...
 215-301 5.49e-30

Early transcription elongation factor of RNA pol II, NGN section; Spt5p and prokaryotic NusG are shown to contain a novel 'NGN' domain. The combined NGN and KOW motif regions of Spt5 form the binding domain with Spt4. Spt5 complexes with Spt4 as a 1:1 heterodimer snf this Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The Schizosaccharomyces pombe core Spt5-Spt4 complex is a heterodimer bearing a trypsin-resistant Spt4-binding domain within the Spt5 subunit.


Pssm-ID: 397481  Cd Length: 84  Bit Score: 113.83  E-value: 5.49e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21358129    215 NLWMVKCRIGEEKATALLLMRKYLTYLNTDDpLQIKSIIAPEGVKGYIYLEAYKQTHVKTCIDNVGNLRMGkwKQEMVPI 294
Cdd:pfam03439    1 KIWAVKCTPGQEREVALSLMRKILALAKTNN-LGIYSVFAPDGLKGYIYVEADRQAAVKRALEGIPNVRGL--VPGLVPI 77


                   ....*..
gi 21358129    295 KEMTDVL 301
Cdd:pfam03439   78 KEMEHLL 84
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 812-908 2.05e-29

Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif.


Pssm-ID: 215026 [Multi-domain]  Cd Length: 121  Bit Score: 113.39  E-value: 2.05e-29
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21358129     812 GAQTPSYTAAGSKTPLVGSQTP----NWDTDTRTPYGTMTPSHDG--SMTPRHGAWDPTANTTPARNND-FDY-SLEEPS 883
Cdd:smart01104    1 GGRTPAWGASGSKTPAWGSRTPgtaaGGAPTARGGSGSRTPAWGGagSRTPAWGGAGPTGSRTPAWGGAsAWGnKSSEGS 80

                            90       100       110
                    ....*....|....*....|....*....|...
gi 21358129     884 PSP-------GYNPSTPGY-QMTSQFAPQTPGT 908
Cdd:smart01104   81 ASSwaagpggAYGAPTPGYgGTPSAYGPATPGG 113
KOW_Spt5_3 cd06083
KOW domain of Spt5, repeat 3; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 512-562 7.72e-23

KOW domain of Spt5, repeat 3; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases.


Pssm-ID: 240507  Cd Length: 51  Bit Score: 92.20  E-value: 7.72e-23
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 21358129  512 YFKTGDHARVLAGRYEGETGLIIRVEPTRVVLVSDLTNHELEVLPRDLQLC 562
Cdd:cd06083    1 HFKVGDHVKVISGRHEGETGLVVKVEDDVVTVFSDLTMRELKVFPRDLQLS 51
KOW_Spt5_5 cd06085
KOW domain of Spt5, repeat 5; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 737-788 6.35e-22

KOW domain of Spt5, repeat 5; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases.


Pssm-ID: 240509  Cd Length: 52  Bit Score: 89.85  E-value: 6.35e-22
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 21358129  737 RDREILGKTIKISGGPYKGAVGIVKDATESTARVELHTSCQTISVDRNHIAI 788
Cdd:cd06085    1 GRDPLIGKTVRIRKGPYKGYIGIVKDATGTTARVELHSKNKTITVDRSRLAV 52
KOW_Spt5_2 cd06082
KOW domain of Spt5, repeat 2; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 461-511 1.17e-19

KOW domain of Spt5, repeat 2; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases.


Pssm-ID: 240506  Cd Length: 51  Bit Score: 83.32  E-value: 1.17e-19
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 21358129  461 FSMGDNVEVCVGDLENLQAKIVAIDGTMITVMPKHQDLKDPLIFKASELRK 511
Cdd:cd06082    1 FQPGDNVEVIEGELKGLQGKVESVDGDIVTIMPKHEDLKEPLEFPAKELRK 51
KOW_Spt5_4 cd06084
KOW domain of Spt5, repeat 4; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 638-680 8.71e-19

KOW domain of Spt5, repeat 4; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases.


Pssm-ID: 240508  Cd Length: 43  Bit Score: 80.64  E-value: 8.71e-19
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 21358129  638 RDVVKVMEGPHAGRSGEIKHLYRSLAFLHCRMYTENGGIFVCK 680
Cdd:cd06084    1 GDTVKVVDGPYKGRQGTVLHIYRGTLFLHSREVTENGGIFVVR 43
KOW_Spt5_6 cd06086
KOW domain of Spt5, repeat 6; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 1020-1075 1.30e-18

KOW domain of Spt5, repeat 6; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases.


Pssm-ID: 240510  Cd Length: 58  Bit Score: 80.64  E-value: 1.30e-18
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 21358129 1020 EHLAPVLPCNGDEFKIIYGDDRESVGRVLSKDGDVFVCRIN--EEIKLLPINFLCKMK 1075
Cdd:cd06086    1 EHLEPVPPEKGDRVKVIKGEDRGSTGELISIDGADGIVKMDsdGDIKILPMNFLAKLV 58
KOW_Spt5_1 cd06081
KOW domain of Spt5, repeat 1; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 313-350 4.43e-18

KOW domain of Spt5, repeat 1; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases.


Pssm-ID: 240505  Cd Length: 38  Bit Score: 78.28  E-value: 4.43e-18
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 21358129  313 KQWVRLKRGLYKDDIAQVDYVDLAQNQVHLKLLPRIDY 350
Cdd:cd06081    1 GSWVRIKRGIYKGDLAQVDEVDENGNRVVVKLIPRIDY 38
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
 215-303 1.44e-14

In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, this domain may confer affinity for Spt4p.Spt4p


Pssm-ID: 197850 [Multi-domain]  Cd Length: 106  Bit Score: 70.48  E-value: 1.44e-14
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21358129     215 NLWMVKCRIGEEKATALLLMRKYLTYLNTDdplQIKSIIAP-EGVK----------------GYIYLEAYKQTHVKTCID 277
Cdd:smart00738    1 NWYAVRTTSGQEKRVAENLERKAEALGLED---KIVSILVPtEEVKeirrgkkkvverklfpGYIFVEADLEDEVWTAIR 77

                            90       100
                    ....*....|....*....|....*....
gi 21358129     278 NVGNLR---MGKWKQEMVPIKEMTDVLKV 303
Cdd:smart00738   78 GTPGVRgfvGGGGKPTPVPDDEIEKILKP 106
CTD pfam12815
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 802-870 8.38e-13

Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteriztic TPA motif.


Pssm-ID: 372327 [Multi-domain]  Cd Length: 71  Bit Score: 64.39  E-value: 8.38e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 21358129    802 GRTPARTPGYGAQTPSYTAAGSKTPLVG---SQTPNWDTDTRTPYgtmtPSHDGSMTPRH-GAWDptANTTPA 870
Cdd:pfam12815    2 SRTPAYNSAGGSRTPAWGADGSRTPAYGgagGRTPAYNQGGKTPA----WGGAGSRTPAYyGAWG--GSRTPA 68
nusG PRK08559
transcription antitermination protein NusG; Validated
 212-352 1.39e-11

transcription antitermination protein NusG; Validated


Pssm-ID: 181467 [Multi-domain]  Cd Length: 153  Bit Score: 63.73  E-value: 1.39e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21358129   212 KDPNLWMVKCRIGEEKATALLLMRKYLTYlntddPLQIKSIIAPEGVKGYIYLEAYKQTHVKTCIDNVGNLRmGKWKQEm 291
Cdd:PRK08559    4 EMSMIFAVKTTAGQERNVALMLAMRAKKE-----NLPIYAILAPPELKGYVLVEAESKGAVEEAIRGIPHVR-GVVPGE- 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21358129   292 VPIKEMTDVLKVVKEQVGLKVKQWVRLKRGLYKDDIAQVDYVDLAQNQVHLKLL----P-----RIDYTR 352
Cdd:PRK08559   77 ISFEEVEHFLKPKPIVEGIKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELLeaavPipvtvRGDQVR 146
Spt5_N pfam11942
Spt5 transcription elongation factor, acidic N-terminal; This is the very acidic N-terminal ...
 139-209 1.39e-08

Spt5 transcription elongation factor, acidic N-terminal; This is the very acidic N-terminal region of the early transcription elongation factor Spt5. The Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The actual function of this N-terminal domain is not known although it is dispensable for binding to Spt4.


Pssm-ID: 463406  Cd Length: 97  Bit Score: 53.42  E-value: 1.39e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 21358129    139 GIVGNEIDELGPTARDIEIRRRGTN----LWDTQKEDEIEEYLRKKYADESiakrhFGDGGEEMSDEITQQTLLP 209
Cdd:pfam11942   28 FIEDDEEDEDEEDGRRDDRRHRELDrrreLEEDEDAEEIAEYLKERYGRSS-----SDAYRGDAEEGVPQRLLLP 97
KOW_elon_Spt5 TIGR00405
transcription elongation factor Spt5; This protein contains a KOW domain, shared by bacterial ...
 219-345 8.64e-07

transcription elongation factor Spt5; This protein contains a KOW domain, shared by bacterial NusG and the uL24 (previously L24p/L26e) family of ribosomal proteins. The most recent papers and crystal structures make this a transcription elongation factor rather than a ribosomal protein.


Pssm-ID: 129499 [Multi-domain]  Cd Length: 145  Bit Score: 49.50  E-value: 8.64e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21358129    219 VKCRIGEEKATALLLMRKYltylnTDDPLQIKSIIAPEGVKGYIYLEAYKQTHVKTCIDNVGNLRmGKWKQEmVPIKEMT 298
Cdd:TIGR00405    3 VKTSVGQEKNVARLMARKA-----RKSGLEVYSILAPESLKGYILVEAETKIDMRNPIIGVPHVR-GVVEGE-IDFEEIE 75

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 21358129    299 DVLKVVKEQVGLKVKQWVRLKRGLYKDDIAQVDYVDLAQNQVHLKLL 345
Cdd:TIGR00405   76 RFLTPKKIIESIKKGDIVEIISGPFKGERAKVIRVDESKEEVTLELI 122
NGN_Arch cd09887
Archaeal N-Utilization Substance G (NusG) N-terminal (NGN) domain; The N-Utilization Substance ...
 216-283 3.50e-06

Archaeal N-Utilization Substance G (NusG) N-terminal (NGN) domain; The N-Utilization Substance G (NusG) protein and its eukaryotic homolog, Spt5, are involved in transcription elongation and termination. Transcription in archaea has a eukaryotic-type transcription apparatus, but contains bacterial-type transcription factors. NusG is one of the few archaeal transcription factors that has orthologs in both bacteria and eukaryotes. Archaeal NusG is similar to bacterial NusG, composed of an NGN domain and a Kyrpides Ouzounis and Woese (KOW) repeat. The eukaryotic ortholog, Spt5, is a large protein composed of an acidic N-terminus, an NGN domain, and multiple KOW motifs at its C-terminus. NusG was originally discovered as a N-dependent antitermination enhancing activity in Escherichia coli and has a variety of functions, such as being involved in RNA polymerase elongation and Rho-termination in bacteria. Archaeal NusG forms a complex with DNA-directed RNA polymerase subunit E (rpoE) that is similar to the Spt5-Spt4 complex in eukaryotes.


Pssm-ID: 193576  Cd Length: 82  Bit Score: 45.99  E-value: 3.50e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 21358129  216 LWMVKCRIGEEKATALLLMRKYltylnTDDPLQIKSIIAPEGVKGYIYLEAYKQTHVKTCIDNVGNLR 283
Cdd:cd09887    2 IYAVKTTAGQERNVADLLAMRA-----EKENLDVYSILVPEELKGYVFVEAEDPDRVEELIRGIPHVR 64
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
 742-1002 2.47e-05

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 48.37  E-value: 2.47e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21358129    742 LGKTikisgGPYKGAVGIVKDATESTARVELHTSCQTISVdrnhiaiVGVTGKEGSVSTygRTP-ARTPGYG-----AQT 815
Cdd:pfam05109  539 LGKT-----SPTSAVTTPTPNATSPTPAVTTPTPNATIPT-------LGKTSPTSAVTT--PTPnATSPTVGetspqANT 604

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21358129    816 PSYTAAG-SKTPLVGSQTPNWDTDTRTPYGTMTPSHDGSMTPRHGAWDPTANTTPARNNDFDYSL-EEPSPSPGYNPS-- 891
Cdd:pfam05109  605 TNHTLGGtSSTPVVTSPPKNATSAVTTGQHNITSSSTSSMSLRPSSISETLSPSTSDNSTSHMPLlTSAHPTGGENITqv 684

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21358129    892 TPGYQMTSQFAPQTPGTLYGSDRSYSPFNPSPSPAPSPYPVGYMNTPSPSTYSPNTPGGIPQSPYNPQTPGASLDSSMGD 971
Cdd:pfam05109  685 TPASTSTHHVSTSSPAPRPGTTSQASGPGNSSTSTKPGEVNVTKGTPPKNATSPQAPSGQKTAVPTVTSTGGKANSTTGG 764

                          250       260       270
                   ....*....|....*....|....*....|.
gi 21358129    972 WCTTDIEVRIHTHDDTDLVGQTGIIRTVSNG 1002
Cdd:pfam05109  765 KHTTGHGARTSTEPTTDYGGDSTTPRTRYNA 795
KOW cd00380
KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known ...
 516-560 2.99e-03

KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. The KOW motif contains an invariants glycine residue and comprises alternating blocks of hydrophilic and hydrophobic residues.


Pssm-ID: 240504  Cd Length: 49  Bit Score: 36.81  E-value: 2.99e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 21358129  516 GDHARVLAGRYEGETGLIIRVEPT----RVVLVSDLTNHELEVLPRDLQ 560
Cdd:cd00380    1 GDVVRVLRGPYKGREGVVVDIDPRfgivTVKGATGSKGAELKVRFDDVD 49
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 639-667 5.68e-03

KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and NusG.


Pssm-ID: 425698 [Multi-domain]  Cd Length: 32  Bit Score: 35.44  E-value: 5.68e-03
                           10        20
                   ....*....|....*....|....*....
gi 21358129    639 DVVKVMEGPHAGRSGEIKHLYRSLAFLHC 667
Cdd:pfam00467    3 DVVRVIAGPFKGKVGKVVEVDDKKNRVLV 31
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 516-544 6.21e-03

KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and NusG.


Pssm-ID: 425698 [Multi-domain]  Cd Length: 32  Bit Score: 35.44  E-value: 6.21e-03
                           10        20        30
                   ....*....|....*....|....*....|
gi 21358129    516 GDHARVLAGRYEGETGLIIRVEPTRV-VLV 544
Cdd:pfam00467    2 GDVVRVIAGPFKGKVGKVVEVDDKKNrVLV 31
 
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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