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Conserved domains on  [gi|186505223|ref|NP_180968|]
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Transcription elongation factor Spt5 [Arabidopsis thaliana]

Protein Classification

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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 ...
170-253 3.69e-35

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: 128.42  E-value: 3.69e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186505223 170 KLWLVKCAIGREREVAVCLMQKIVDR---GSEFKIRSAIALDHLQNYVYIEADMEAHVKEAIKGMRNIYANqKILLVPIK 246
Cdd:cd09888    1 KLWAVKCKPGKEREIVISLMRKFLDLqrtGNPLGIKSVFARDGLKGYIYIEARKEAHVKDAIEGLRGVYLN-TIKLVPIK 79

                 ....*..
gi 186505223 247 EMTAVLS 253
Cdd:cd09888   80 EMPDVLS 86
KOW_Spt5_6 cd06086
KOW domain of Spt5, repeat 6; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
930-987 5.46e-19

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: 81.41  E-value: 5.46e-19
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 186505223 930 NKVSLVCPKKNERVKILGGKYCGSTAKVIGEDGQDGIVKLDESLDIKILKLTILAKLV 987
Cdd:cd06086    1 EHLEPVPPEKGDRVKVIKGEDRGSTGELISIDGADGIVKMDSDGDIKILPMNFLAKLV 58
KOW_Spt5_1 cd06081
KOW domain of Spt5, repeat 1; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
264-301 4.43e-17

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: 75.58  E-value: 4.43e-17
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 186505223 264 DSWVRMKLGIYKGDLAQVVDVDNVRKRVTVKLIPRIDL 301
Cdd:cd06081    1 GSWVRIKRGIYKGDLAQVDEVDENGNRVVVKLIPRIDY 38
KOW_Spt5_3 cd06083
KOW domain of Spt5, repeat 3; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
464-514 1.46e-16

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: 74.48  E-value: 1.46e-16
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 186505223 464 YFEPGNFVKVVSGIHEGGTGMIVKVDQHMLIILSDTTKEHICVFADHVAKS 514
Cdd:cd06083    1 HFKVGDHVKVISGRHEGETGLVVKVEDDVVTVFSDLTMRELKVFPRDLQLS 51
KOW_Spt5_2 cd06082
KOW domain of Spt5, repeat 2; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
413-463 2.84e-14

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: 67.91  E-value: 2.84e-14
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 186505223 413 FMKGDAVIVIKGDLKNLKGWIEKVDEENVLIRSEMKDLPNPIAVNGRELCK 463
Cdd:cd06082    1 FQPGDNVEVIEGELKGLQGKVESVDGDIVTIMPKHEDLKEPLEFPAKELRK 51
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
738-866 8.27e-12

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: 63.31  E-value: 8.27e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186505223   738 TPQYNM-GSQTPMHPSRTPlhpcMTPMRHSGATPIHDGMRTPMRGRAWNpympmspprdnwedGNPGSWGTSPYEAATP- 815
Cdd:smart01104   4 TPAWGAsGSKTPAWGSRTP----GTAAGGAPTARGGSGSRTPAWGGAGS--------------RTPAWGGAGPTGSRTPa 65
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 186505223   816 ---GSDWG--SSTPGRSSYrdAGTPINNANAPSP-MTPSSTSYLPTTPGGQAMTPGT 866
Cdd:smart01104  66 wggASAWGnkSSEGSASSW--AAGPGGAYGAPTPgYGGTPSAYGPATPGGGAMAGSA 120
KOW super family cl00354
KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known ...
682-729 1.09e-11

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.


The actual alignment was detected with superfamily member cd06085:

Pssm-ID: 469738  Cd Length: 52  Bit Score: 60.58  E-value: 1.09e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 186505223 682 DDHLVGTYVKIRLGPFKGYSGRLVEVKDKLVRVELEA--KIVTVERKAIS 729
Cdd:cd06085    2 RDPLIGKTVRIRKGPYKGYIGIVKDATGTTARVELHSknKTITVDRSRLA 51
KOW_Spt5_4 cd06084
KOW domain of Spt5, repeat 4; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
598-634 7.10e-10

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: 55.22  E-value: 7.10e-10
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 186505223 598 IEGPSKGKQGPVVQIYKGVLFIHDRHNLEHTGFICTR 634
Cdd:cd06084    7 VDGPYKGRQGTVLHIYRGTLFLHSREVTENGGIFVVR 43
 
Name Accession Description Interval E-value
NGN_Euk cd09888
Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW ...
170-253 3.69e-35

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: 128.42  E-value: 3.69e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186505223 170 KLWLVKCAIGREREVAVCLMQKIVDR---GSEFKIRSAIALDHLQNYVYIEADMEAHVKEAIKGMRNIYANqKILLVPIK 246
Cdd:cd09888    1 KLWAVKCKPGKEREIVISLMRKFLDLqrtGNPLGIKSVFARDGLKGYIYIEARKEAHVKDAIEGLRGVYLN-TIKLVPIK 79

                 ....*..
gi 186505223 247 EMTAVLS 253
Cdd:cd09888   80 EMPDVLS 86
Spt5-NGN pfam03439
Early transcription elongation factor of RNA pol II, NGN section; Spt5p and prokaryotic NusG ...
170-252 1.39e-28

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: 109.60  E-value: 1.39e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186505223  170 KLWLVKCAIGREREVAVCLMQKIVD--RGSEFKIRSAIALDHLQNYVYIEADMEAHVKEAIKGMRNIYANQKIlLVPIKE 247
Cdd:pfam03439   1 KIWAVKCTPGQEREVALSLMRKILAlaKTNNLGIYSVFAPDGLKGYIYVEADRQAAVKRALEGIPNVRGLVPG-LVPIKE 79

                  ....*
gi 186505223  248 MTAVL 252
Cdd:pfam03439  80 MEHLL 84
KOW_Spt5_6 cd06086
KOW domain of Spt5, repeat 6; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
930-987 5.46e-19

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: 81.41  E-value: 5.46e-19
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 186505223 930 NKVSLVCPKKNERVKILGGKYCGSTAKVIGEDGQDGIVKLDESLDIKILKLTILAKLV 987
Cdd:cd06086    1 EHLEPVPPEKGDRVKVIKGEDRGSTGELISIDGADGIVKMDSDGDIKILPMNFLAKLV 58
KOW_Spt5_1 cd06081
KOW domain of Spt5, repeat 1; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
264-301 4.43e-17

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: 75.58  E-value: 4.43e-17
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 186505223 264 DSWVRMKLGIYKGDLAQVVDVDNVRKRVTVKLIPRIDL 301
Cdd:cd06081    1 GSWVRIKRGIYKGDLAQVDEVDENGNRVVVKLIPRIDY 38
KOW_Spt5_3 cd06083
KOW domain of Spt5, repeat 3; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
464-514 1.46e-16

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: 74.48  E-value: 1.46e-16
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 186505223 464 YFEPGNFVKVVSGIHEGGTGMIVKVDQHMLIILSDTTKEHICVFADHVAKS 514
Cdd:cd06083    1 HFKVGDHVKVISGRHEGETGLVVKVEDDVVTVFSDLTMRELKVFPRDLQLS 51
KOW_Spt5_2 cd06082
KOW domain of Spt5, repeat 2; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
413-463 2.84e-14

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: 67.91  E-value: 2.84e-14
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 186505223 413 FMKGDAVIVIKGDLKNLKGWIEKVDEENVLIRSEMKDLPNPIAVNGRELCK 463
Cdd:cd06082    1 FQPGDNVEVIEGELKGLQGKVESVDGDIVTIMPKHEDLKEPLEFPAKELRK 51
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
170-254 5.71e-13

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: 65.86  E-value: 5.71e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186505223   170 KLWLVKCAIGREREVAVCLMQKIVDRGSEFKIRSAIA-LDHLQ----------------NYVYIEADMEAHVKEAIKGMR 232
Cdd:smart00738   1 NWYAVRTTSGQEKRVAENLERKAEALGLEDKIVSILVpTEEVKeirrgkkkvverklfpGYIFVEADLEDEVWTAIRGTP 80
                           90       100
                   ....*....|....*....|....*.
gi 186505223   233 NIY----ANQKILLVPIKEMTAVLSV 254
Cdd:smart00738  81 GVRgfvgGGGKPTPVPDDEIEKILKP 106
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
738-866 8.27e-12

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: 63.31  E-value: 8.27e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186505223   738 TPQYNM-GSQTPMHPSRTPlhpcMTPMRHSGATPIHDGMRTPMRGRAWNpympmspprdnwedGNPGSWGTSPYEAATP- 815
Cdd:smart01104   4 TPAWGAsGSKTPAWGSRTP----GTAAGGAPTARGGSGSRTPAWGGAGS--------------RTPAWGGAGPTGSRTPa 65
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 186505223   816 ---GSDWG--SSTPGRSSYrdAGTPINNANAPSP-MTPSSTSYLPTTPGGQAMTPGT 866
Cdd:smart01104  66 wggASAWGnkSSEGSASSW--AAGPGGAYGAPTPgYGGTPSAYGPATPGGGAMAGSA 120
KOW_Spt5_5 cd06085
KOW domain of Spt5, repeat 5; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
682-729 1.09e-11

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: 60.58  E-value: 1.09e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 186505223 682 DDHLVGTYVKIRLGPFKGYSGRLVEVKDKLVRVELEA--KIVTVERKAIS 729
Cdd:cd06085    2 RDPLIGKTVRIRKGPYKGYIGIVKDATGTTARVELHSknKTITVDRSRLA 51
nusG PRK08559
transcription antitermination protein NusG; Validated
168-296 2.78e-11

transcription antitermination protein NusG; Validated


Pssm-ID: 181467 [Multi-domain]  Cd Length: 153  Bit Score: 62.58  E-value: 2.78e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186505223 168 DPKLWLVKCAIGREREVAVCLMQKIvdRGSEFKIRSAIALDHLQNYVYIEADMEAHVKEAIKGMRNIyanQKIL--LVPI 245
Cdd:PRK08559   5 MSMIFAVKTTAGQERNVALMLAMRA--KKENLPIYAILAPPELKGYVLVEAESKGAVEEAIRGIPHV---RGVVpgEISF 79
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 186505223 246 KEMTAVLSVESKAIDLSRDSWVRMKLGIYKGDLAQVVDVDNVRKRVTVKLI 296
Cdd:PRK08559  80 EEVEHFLKPKPIVEGIKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELL 130
KOW_Spt5_4 cd06084
KOW domain of Spt5, repeat 4; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
598-634 7.10e-10

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: 55.22  E-value: 7.10e-10
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 186505223 598 IEGPSKGKQGPVVQIYKGVLFIHDRHNLEHTGFICTR 634
Cdd:cd06084    7 VDGPYKGRQGTVLHIYRGTLFLHSREVTENGGIFVVR 43
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
686-717 1.36e-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: 36.98  E-value: 1.36e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 186505223  686 VGTYVKIRLGPFKGYSGRLVEVKDKLVRVELE 717
Cdd:pfam00467   1 KGDVVRVIAGPFKGKVGKVVEVDDKKNRVLVE 32
antiterm_UpxY NF033644
UpxY family transcription antiterminator; The UpxY family of NusG-related transcription ...
686-724 5.47e-03

UpxY family transcription antiterminator; The UpxY family of NusG-related transcription antiterminators was described originally from a paralogous family of eight members from Bacteriodes fragilis, UpaY to UphY, each of which was associated with a distinct capsular polysaccharide biosynthesis locus. There is no UpxY protein per se.


Pssm-ID: 468125 [Multi-domain]  Cd Length: 162  Bit Score: 38.61  E-value: 5.47e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 186505223 686 VGTYVKIRLGPFKGYSGRLVEVKDK---LVRVELEAKIVTVE 724
Cdd:NF033644 115 KGDKVRVIGGPLKGLEGELVRVKGKkrvVVRIPGLGAVATVE 156
 
Name Accession Description Interval E-value
NGN_Euk cd09888
Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW ...
170-253 3.69e-35

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: 128.42  E-value: 3.69e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186505223 170 KLWLVKCAIGREREVAVCLMQKIVDR---GSEFKIRSAIALDHLQNYVYIEADMEAHVKEAIKGMRNIYANqKILLVPIK 246
Cdd:cd09888    1 KLWAVKCKPGKEREIVISLMRKFLDLqrtGNPLGIKSVFARDGLKGYIYIEARKEAHVKDAIEGLRGVYLN-TIKLVPIK 79

                 ....*..
gi 186505223 247 EMTAVLS 253
Cdd:cd09888   80 EMPDVLS 86
Spt5-NGN pfam03439
Early transcription elongation factor of RNA pol II, NGN section; Spt5p and prokaryotic NusG ...
170-252 1.39e-28

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: 109.60  E-value: 1.39e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186505223  170 KLWLVKCAIGREREVAVCLMQKIVD--RGSEFKIRSAIALDHLQNYVYIEADMEAHVKEAIKGMRNIYANQKIlLVPIKE 247
Cdd:pfam03439   1 KIWAVKCTPGQEREVALSLMRKILAlaKTNNLGIYSVFAPDGLKGYIYVEADRQAAVKRALEGIPNVRGLVPG-LVPIKE 79

                  ....*
gi 186505223  248 MTAVL 252
Cdd:pfam03439  80 MEHLL 84
KOW_Spt5_6 cd06086
KOW domain of Spt5, repeat 6; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
930-987 5.46e-19

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: 81.41  E-value: 5.46e-19
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 186505223 930 NKVSLVCPKKNERVKILGGKYCGSTAKVIGEDGQDGIVKLDESLDIKILKLTILAKLV 987
Cdd:cd06086    1 EHLEPVPPEKGDRVKVIKGEDRGSTGELISIDGADGIVKMDSDGDIKILPMNFLAKLV 58
KOW_Spt5_1 cd06081
KOW domain of Spt5, repeat 1; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
264-301 4.43e-17

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: 75.58  E-value: 4.43e-17
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 186505223 264 DSWVRMKLGIYKGDLAQVVDVDNVRKRVTVKLIPRIDL 301
Cdd:cd06081    1 GSWVRIKRGIYKGDLAQVDEVDENGNRVVVKLIPRIDY 38
KOW_Spt5_3 cd06083
KOW domain of Spt5, repeat 3; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
464-514 1.46e-16

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: 74.48  E-value: 1.46e-16
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 186505223 464 YFEPGNFVKVVSGIHEGGTGMIVKVDQHMLIILSDTTKEHICVFADHVAKS 514
Cdd:cd06083    1 HFKVGDHVKVISGRHEGETGLVVKVEDDVVTVFSDLTMRELKVFPRDLQLS 51
KOW_Spt5_2 cd06082
KOW domain of Spt5, repeat 2; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
413-463 2.84e-14

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: 67.91  E-value: 2.84e-14
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 186505223 413 FMKGDAVIVIKGDLKNLKGWIEKVDEENVLIRSEMKDLPNPIAVNGRELCK 463
Cdd:cd06082    1 FQPGDNVEVIEGELKGLQGKVESVDGDIVTIMPKHEDLKEPLEFPAKELRK 51
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
170-254 5.71e-13

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: 65.86  E-value: 5.71e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186505223   170 KLWLVKCAIGREREVAVCLMQKIVDRGSEFKIRSAIA-LDHLQ----------------NYVYIEADMEAHVKEAIKGMR 232
Cdd:smart00738   1 NWYAVRTTSGQEKRVAENLERKAEALGLEDKIVSILVpTEEVKeirrgkkkvverklfpGYIFVEADLEDEVWTAIRGTP 80
                           90       100
                   ....*....|....*....|....*.
gi 186505223   233 NIY----ANQKILLVPIKEMTAVLSV 254
Cdd:smart00738  81 GVRgfvgGGGKPTPVPDDEIEKILKP 106
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
738-866 8.27e-12

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: 63.31  E-value: 8.27e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186505223   738 TPQYNM-GSQTPMHPSRTPlhpcMTPMRHSGATPIHDGMRTPMRGRAWNpympmspprdnwedGNPGSWGTSPYEAATP- 815
Cdd:smart01104   4 TPAWGAsGSKTPAWGSRTP----GTAAGGAPTARGGSGSRTPAWGGAGS--------------RTPAWGGAGPTGSRTPa 65
                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 186505223   816 ---GSDWG--SSTPGRSSYrdAGTPINNANAPSP-MTPSSTSYLPTTPGGQAMTPGT 866
Cdd:smart01104  66 wggASAWGnkSSEGSASSW--AAGPGGAYGAPTPgYGGTPSAYGPATPGGGAMAGSA 120
KOW_Spt5_5 cd06085
KOW domain of Spt5, repeat 5; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
682-729 1.09e-11

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: 60.58  E-value: 1.09e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 186505223 682 DDHLVGTYVKIRLGPFKGYSGRLVEVKDKLVRVELEA--KIVTVERKAIS 729
Cdd:cd06085    2 RDPLIGKTVRIRKGPYKGYIGIVKDATGTTARVELHSknKTITVDRSRLA 51
nusG PRK08559
transcription antitermination protein NusG; Validated
168-296 2.78e-11

transcription antitermination protein NusG; Validated


Pssm-ID: 181467 [Multi-domain]  Cd Length: 153  Bit Score: 62.58  E-value: 2.78e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186505223 168 DPKLWLVKCAIGREREVAVCLMQKIvdRGSEFKIRSAIALDHLQNYVYIEADMEAHVKEAIKGMRNIyanQKIL--LVPI 245
Cdd:PRK08559   5 MSMIFAVKTTAGQERNVALMLAMRA--KKENLPIYAILAPPELKGYVLVEAESKGAVEEAIRGIPHV---RGVVpgEISF 79
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 186505223 246 KEMTAVLSVESKAIDLSRDSWVRMKLGIYKGDLAQVVDVDNVRKRVTVKLI 296
Cdd:PRK08559  80 EEVEHFLKPKPIVEGIKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELL 130
KOW_Spt5_4 cd06084
KOW domain of Spt5, repeat 4; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
598-634 7.10e-10

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: 55.22  E-value: 7.10e-10
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 186505223 598 IEGPSKGKQGPVVQIYKGVLFIHDRHNLEHTGFICTR 634
Cdd:cd06084    7 VDGPYKGRQGTVLHIYRGTLFLHSREVTENGGIFVVR 43
NGN_Arch cd09887
Archaeal N-Utilization Substance G (NusG) N-terminal (NGN) domain; The N-Utilization Substance ...
170-234 3.11e-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: 3.11e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 186505223 170 KLWLVKCAIGREREVAVCLMQKIVDRGSEfkIRSAIALDHLQNYVYIEADMEAHVKEAIKGMRNI 234
Cdd:cd09887    1 RIYAVKTTAGQERNVADLLAMRAEKENLD--VYSILVPEELKGYVFVEAEDPDRVEELIRGIPHV 63
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
686-717 1.36e-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: 36.98  E-value: 1.36e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 186505223  686 VGTYVKIRLGPFKGYSGRLVEVKDKLVRVELE 717
Cdd:pfam00467   1 KGDVVRVIAGPFKGKVGKVVEVDDKKNRVLVE 32
antiterm_UpxY NF033644
UpxY family transcription antiterminator; The UpxY family of NusG-related transcription ...
686-724 5.47e-03

UpxY family transcription antiterminator; The UpxY family of NusG-related transcription antiterminators was described originally from a paralogous family of eight members from Bacteriodes fragilis, UpaY to UphY, each of which was associated with a distinct capsular polysaccharide biosynthesis locus. There is no UpxY protein per se.


Pssm-ID: 468125 [Multi-domain]  Cd Length: 162  Bit Score: 38.61  E-value: 5.47e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 186505223 686 VGTYVKIRLGPFKGYSGRLVEVKDK---LVRVELEAKIVTVE 724
Cdd:NF033644 115 KGDKVRVIGGPLKGLEGELVRVKGKkrvVVRIPGLGAVATVE 156
KOW cd00380
KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known ...
416-462 6.40e-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: 35.66  E-value: 6.40e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 186505223 416 GDAVIVIKGDLKNLKGWIEKVDEEN--VLIRSEMKDLPNPIAVNGRELC 462
Cdd:cd00380    1 GDVVRVLRGPYKGREGVVVDIDPRFgiVTVKGATGSKGAELKVRFDDVD 49
 
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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