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Conserved domains on  [gi|1002247570|ref|XP_015627957|]
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uncharacterized protein [Oryza sativa Japonica Group]

Protein Classification

UpxY family transcription antiterminator( domain architecture ID 10177571)

UpxY family transcription antiterminator is a Specialized Paralog of NusG (NusG SP) that acts specifically in transcriptional antitermination of the operon from which it is encoded; UpxYs are necessary and specific for transcription regulation of the polysaccharide biosynthesis operon

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
NGN_plant cd09890
Plant N-Utilization Substance G (NusG) N-terminal (NGN) domain; The N-Utilization Substance G ...
105-216 5.26e-48

Plant 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. NusG contains a NGN domain at its N-terminus and Kyrpides Ouzounis and Woese (KOW) repeats at its C-terminus in bacteria and archaea. The eukaryotic ortholog, Spt5, is a large protein comprising an acidic N-terminus, an NGN domain, and multiple KOW motifs at its C-terminus. Spt5 forms an Spt4-Spt5 complex that is an essential RNA polymerase II elongation factor. The bacterial infected plants contain bacterial DNA, such as NGN sequences, that can be used to clone the DNA of uncultured organisms.


:

Pssm-ID: 193579  Cd Length: 113  Bit Score: 157.13  E-value: 5.26e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002247570 105 QWWLVRVSMAPGTDYVDLLTKAISRRYPELSFKIYNPSIQVKKRLKNGSISTKSKPLHPGLVFLYCTLNKEVHDFIRDTE 184
Cdd:cd09890     1 QWYMLRVPAGRENQAAEALERALATEFPDREFEVWVPSIPVDRKLKNGSISVKEKPLFPGYVLLRCVLNKEVYDFIRDND 80
                          90       100       110
                  ....*....|....*....|....*....|...
gi 1002247570 185 GCYGFIGATVGSI-KRQIKKPKPIPVEEVESII 216
Cdd:cd09890    81 SVYGFVGSKVGKTgKRQIEIPRPVPVEEIEAIF 113
KOW_NusG cd06091
NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; KOW_NusG motif ...
275-326 1.51e-14

NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; KOW_NusG motif is one of the two domains of N-Utilization Substance G (NusG) a transcription elongation and Rho-termination factor in bacteria and archaea. 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 eukaryotic ortholog of NusG is Spt5 with multiple KOW motifs at its C-terminus.


:

Pssm-ID: 240515 [Multi-domain]  Cd Length: 56  Bit Score: 67.10  E-value: 1.51e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1002247570 275 FTPGASVHVLSGPFEGFTGSLLEVNRKNKKATLQLTLFGKESFVDLDFDQIE 326
Cdd:cd06091     4 FEVGDTVRIISGPFAGFEGKVEEIDEEKGKVKVLVEMFGRETPVELDFDQVE 55
 
Name Accession Description Interval E-value
NGN_plant cd09890
Plant N-Utilization Substance G (NusG) N-terminal (NGN) domain; The N-Utilization Substance G ...
105-216 5.26e-48

Plant 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. NusG contains a NGN domain at its N-terminus and Kyrpides Ouzounis and Woese (KOW) repeats at its C-terminus in bacteria and archaea. The eukaryotic ortholog, Spt5, is a large protein comprising an acidic N-terminus, an NGN domain, and multiple KOW motifs at its C-terminus. Spt5 forms an Spt4-Spt5 complex that is an essential RNA polymerase II elongation factor. The bacterial infected plants contain bacterial DNA, such as NGN sequences, that can be used to clone the DNA of uncultured organisms.


Pssm-ID: 193579  Cd Length: 113  Bit Score: 157.13  E-value: 5.26e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002247570 105 QWWLVRVSMAPGTDYVDLLTKAISRRYPELSFKIYNPSIQVKKRLKNGSISTKSKPLHPGLVFLYCTLNKEVHDFIRDTE 184
Cdd:cd09890     1 QWYMLRVPAGRENQAAEALERALATEFPDREFEVWVPSIPVDRKLKNGSISVKEKPLFPGYVLLRCVLNKEVYDFIRDND 80
                          90       100       110
                  ....*....|....*....|....*....|...
gi 1002247570 185 GCYGFIGATVGSI-KRQIKKPKPIPVEEVESII 216
Cdd:cd09890    81 SVYGFVGSKVGKTgKRQIEIPRPVPVEEIEAIF 113
NusG COG0250
Transcription termination/antitermination protein NusG [Transcription];
136-328 7.41e-23

Transcription termination/antitermination protein NusG [Transcription];


Pssm-ID: 440020 [Multi-domain]  Cd Length: 171  Bit Score: 93.35  E-value: 7.41e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002247570 136 FKIYNPSIQVKKRlKNGSISTKSKPLHPGLVFLYCTLNKEVHDFIRDTEGCYGFIGATvgsikrqiKKPKPIPVEEVESI 215
Cdd:COG0250    31 IEVFVPTEEVVEI-KNGKKKTVERPLFPGYVFVRMDLTDESWYLVRNTPGVTGFVGFG--------GKPAPLPDEEVERI 101
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002247570 216 IR--EEKEEQERVDREFEemenggivesfnkpvedselmlmnkikrqfkkpiskggsnhnaftPGASVHVLSGPFEGFTG 293
Cdd:COG0250   102 LArlEEGEEKPRPKVDFE---------------------------------------------VGDRVRITDGPFAGFEG 136
                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1002247570 294 SLLEVNRKNKKATLQLTLFGKESFVDLDFDQIEAV 328
Cdd:COG0250   137 TVEEVDPEKGRVKVLVSIFGRETPVELDFSQVEKI 171
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
105-218 1.81e-22

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: 90.12  E-value: 1.81e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002247570  105 QWWLVRVSMA-PGTDYVDLLTKAISRRYPELSFKIYNPSIQVKKRlKNGSISTKSKPLHPGLVFLYCTLNKEVHDFIRDT 183
Cdd:smart00738   1 NWYAVRTTSGqEKRVAENLERKAEALGLEDKIVSILVPTEEVKEI-RRGKKKVVERKLFPGYIFVEADLEDEVWTAIRGT 79
                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1002247570  184 EGCYGFIGATvgsikrqiKKPKPIPVEEVESIIRE 218
Cdd:smart00738  80 PGVRGFVGGG--------GKPTPVPDDEIEKILKP 106
KOW_NusG cd06091
NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; KOW_NusG motif ...
275-326 1.51e-14

NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; KOW_NusG motif is one of the two domains of N-Utilization Substance G (NusG) a transcription elongation and Rho-termination factor in bacteria and archaea. 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 eukaryotic ortholog of NusG is Spt5 with multiple KOW motifs at its C-terminus.


Pssm-ID: 240515 [Multi-domain]  Cd Length: 56  Bit Score: 67.10  E-value: 1.51e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1002247570 275 FTPGASVHVLSGPFEGFTGSLLEVNRKNKKATLQLTLFGKESFVDLDFDQIE 326
Cdd:cd06091     4 FEVGDTVRIISGPFAGFEGKVEEIDEEKGKVKVLVEMFGRETPVELDFDQVE 55
nusG TIGR00922
transcription termination/antitermination factor NusG; NusG proteins are transcription factors ...
163-327 2.55e-14

transcription termination/antitermination factor NusG; NusG proteins are transcription factors which are aparrently universal in prokaryotes (archaea and eukaryotes have homologs that may have related functions). The essential components of these factors include an N-terminal RNP-like (ribonucleoprotein) domain and a C-terminal KOW motif (pfam00467) believed to be a nucleic acid binding domain. In E. coli, NusA has been shown to interact with RNA polymerase and termination factor Rho. This model covers a wide variety of bacterial species but excludes mycoplasmas which are covered by a separate model (TIGR01956).The function of all of these NusG proteins is likely to be the same at the level of interaction with RNA and other protein factors to affect termination; however different species may utilize NusG towards different processes and in combination with different suites of affector proteins.In E. coli, NusG promotes rho-dependent termination. It is an essential gene. In Streptomyces virginiae and related species, an additional N-terminal sequence is also present and is suggested to play a role in butyrolactone-mediated autoregulation. In Thermotoga maritima, NusG has a long insert, fails to substitute for E. coli NusG (with or without the long insert), is a large 0.7 % of total cellular protein, and has a general, sequence non-specific DNA and RNA binding activity that blocks ethidium staining, yet permits transcription.Archaeal proteins once termed NusG share the KOW domain but are actually a ribosomal protein corresponding to L24p in bacterial and L26e in eukaryotes (TIGR00405). [Transcription, Transcription factors]


Pssm-ID: 273341 [Multi-domain]  Cd Length: 172  Bit Score: 70.02  E-value: 2.55e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002247570 163 PGLVFLYCTLNKEVHDFIRDTEGCYGFIGATvgsikrqiKKPKPIPV-EEVESIireekeeqervdrefeemenggives 241
Cdd:TIGR00922  58 PGYVLVKMDLTDVSWHLVKNTPGVTGFVGSG--------GKPKALSEdEEVKNI-------------------------- 103
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002247570 242 fnkpvedselmlMNKIKRQFKKPISKggsnhNAFTPGASVHVLSGPFEGFTGSLLEVNRKNKKATLQLTLFGKESFVDLD 321
Cdd:TIGR00922 104 ------------LNALEEGKDKPKPK-----IDFEVGEQVRVNDGPFANFTGTVEEVDYEKSKLKVSVSIFGRETPVELE 166

                  ....*.
gi 1002247570 322 FDQIEA 327
Cdd:TIGR00922 167 FSQVEK 172
NusG pfam02357
Transcription termination factor nusG;
133-216 9.70e-10

Transcription termination factor nusG;


Pssm-ID: 426736 [Multi-domain]  Cd Length: 96  Bit Score: 54.92  E-value: 9.70e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002247570 133 ELSFKIYNPSIQVKkRLKNGSISTKSKPLHPGLVFLYCTLNKEVHDFIRDTEGCYGFIGATvgsikrqiKKPKPIPVEEV 212
Cdd:pfam02357  22 RQGIEVFLPTEEVV-EIRNGKKKVVERPLFPGYVFVRMDMTDETWHLVRSTPGVTGFVGGS--------GKPTPIPDEEV 92

                  ....
gi 1002247570 213 ESII 216
Cdd:pfam02357  93 ERIL 96
 
Name Accession Description Interval E-value
NGN_plant cd09890
Plant N-Utilization Substance G (NusG) N-terminal (NGN) domain; The N-Utilization Substance G ...
105-216 5.26e-48

Plant 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. NusG contains a NGN domain at its N-terminus and Kyrpides Ouzounis and Woese (KOW) repeats at its C-terminus in bacteria and archaea. The eukaryotic ortholog, Spt5, is a large protein comprising an acidic N-terminus, an NGN domain, and multiple KOW motifs at its C-terminus. Spt5 forms an Spt4-Spt5 complex that is an essential RNA polymerase II elongation factor. The bacterial infected plants contain bacterial DNA, such as NGN sequences, that can be used to clone the DNA of uncultured organisms.


Pssm-ID: 193579  Cd Length: 113  Bit Score: 157.13  E-value: 5.26e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002247570 105 QWWLVRVSMAPGTDYVDLLTKAISRRYPELSFKIYNPSIQVKKRLKNGSISTKSKPLHPGLVFLYCTLNKEVHDFIRDTE 184
Cdd:cd09890     1 QWYMLRVPAGRENQAAEALERALATEFPDREFEVWVPSIPVDRKLKNGSISVKEKPLFPGYVLLRCVLNKEVYDFIRDND 80
                          90       100       110
                  ....*....|....*....|....*....|...
gi 1002247570 185 GCYGFIGATVGSI-KRQIKKPKPIPVEEVESII 216
Cdd:cd09890    81 SVYGFVGSKVGKTgKRQIEIPRPVPVEEIEAIF 113
NusG COG0250
Transcription termination/antitermination protein NusG [Transcription];
136-328 7.41e-23

Transcription termination/antitermination protein NusG [Transcription];


Pssm-ID: 440020 [Multi-domain]  Cd Length: 171  Bit Score: 93.35  E-value: 7.41e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002247570 136 FKIYNPSIQVKKRlKNGSISTKSKPLHPGLVFLYCTLNKEVHDFIRDTEGCYGFIGATvgsikrqiKKPKPIPVEEVESI 215
Cdd:COG0250    31 IEVFVPTEEVVEI-KNGKKKTVERPLFPGYVFVRMDLTDESWYLVRNTPGVTGFVGFG--------GKPAPLPDEEVERI 101
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002247570 216 IR--EEKEEQERVDREFEemenggivesfnkpvedselmlmnkikrqfkkpiskggsnhnaftPGASVHVLSGPFEGFTG 293
Cdd:COG0250   102 LArlEEGEEKPRPKVDFE---------------------------------------------VGDRVRITDGPFAGFEG 136
                         170       180       190
                  ....*....|....*....|....*....|....*
gi 1002247570 294 SLLEVNRKNKKATLQLTLFGKESFVDLDFDQIEAV 328
Cdd:COG0250   137 TVEEVDPEKGRVKVLVSIFGRETPVELDFSQVEKI 171
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
105-218 1.81e-22

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: 90.12  E-value: 1.81e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002247570  105 QWWLVRVSMA-PGTDYVDLLTKAISRRYPELSFKIYNPSIQVKKRlKNGSISTKSKPLHPGLVFLYCTLNKEVHDFIRDT 183
Cdd:smart00738   1 NWYAVRTTSGqEKRVAENLERKAEALGLEDKIVSILVPTEEVKEI-RRGKKKVVERKLFPGYIFVEADLEDEVWTAIRGT 79
                           90       100       110
                   ....*....|....*....|....*....|....*
gi 1002247570  184 EGCYGFIGATvgsikrqiKKPKPIPVEEVESIIRE 218
Cdd:smart00738  80 PGVRGFVGGG--------GKPTPVPDDEIEKILKP 106
KOW_NusG cd06091
NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; KOW_NusG motif ...
275-326 1.51e-14

NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; KOW_NusG motif is one of the two domains of N-Utilization Substance G (NusG) a transcription elongation and Rho-termination factor in bacteria and archaea. 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 eukaryotic ortholog of NusG is Spt5 with multiple KOW motifs at its C-terminus.


Pssm-ID: 240515 [Multi-domain]  Cd Length: 56  Bit Score: 67.10  E-value: 1.51e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1002247570 275 FTPGASVHVLSGPFEGFTGSLLEVNRKNKKATLQLTLFGKESFVDLDFDQIE 326
Cdd:cd06091     4 FEVGDTVRIISGPFAGFEGKVEEIDEEKGKVKVLVEMFGRETPVELDFDQVE 55
nusG TIGR00922
transcription termination/antitermination factor NusG; NusG proteins are transcription factors ...
163-327 2.55e-14

transcription termination/antitermination factor NusG; NusG proteins are transcription factors which are aparrently universal in prokaryotes (archaea and eukaryotes have homologs that may have related functions). The essential components of these factors include an N-terminal RNP-like (ribonucleoprotein) domain and a C-terminal KOW motif (pfam00467) believed to be a nucleic acid binding domain. In E. coli, NusA has been shown to interact with RNA polymerase and termination factor Rho. This model covers a wide variety of bacterial species but excludes mycoplasmas which are covered by a separate model (TIGR01956).The function of all of these NusG proteins is likely to be the same at the level of interaction with RNA and other protein factors to affect termination; however different species may utilize NusG towards different processes and in combination with different suites of affector proteins.In E. coli, NusG promotes rho-dependent termination. It is an essential gene. In Streptomyces virginiae and related species, an additional N-terminal sequence is also present and is suggested to play a role in butyrolactone-mediated autoregulation. In Thermotoga maritima, NusG has a long insert, fails to substitute for E. coli NusG (with or without the long insert), is a large 0.7 % of total cellular protein, and has a general, sequence non-specific DNA and RNA binding activity that blocks ethidium staining, yet permits transcription.Archaeal proteins once termed NusG share the KOW domain but are actually a ribosomal protein corresponding to L24p in bacterial and L26e in eukaryotes (TIGR00405). [Transcription, Transcription factors]


Pssm-ID: 273341 [Multi-domain]  Cd Length: 172  Bit Score: 70.02  E-value: 2.55e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002247570 163 PGLVFLYCTLNKEVHDFIRDTEGCYGFIGATvgsikrqiKKPKPIPV-EEVESIireekeeqervdrefeemenggives 241
Cdd:TIGR00922  58 PGYVLVKMDLTDVSWHLVKNTPGVTGFVGSG--------GKPKALSEdEEVKNI-------------------------- 103
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002247570 242 fnkpvedselmlMNKIKRQFKKPISKggsnhNAFTPGASVHVLSGPFEGFTGSLLEVNRKNKKATLQLTLFGKESFVDLD 321
Cdd:TIGR00922 104 ------------LNALEEGKDKPKPK-----IDFEVGEQVRVNDGPFANFTGTVEEVDYEKSKLKVSVSIFGRETPVELE 166

                  ....*.
gi 1002247570 322 FDQIEA 327
Cdd:TIGR00922 167 FSQVEK 172
NusG pfam02357
Transcription termination factor nusG;
133-216 9.70e-10

Transcription termination factor nusG;


Pssm-ID: 426736 [Multi-domain]  Cd Length: 96  Bit Score: 54.92  E-value: 9.70e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002247570 133 ELSFKIYNPSIQVKkRLKNGSISTKSKPLHPGLVFLYCTLNKEVHDFIRDTEGCYGFIGATvgsikrqiKKPKPIPVEEV 212
Cdd:pfam02357  22 RQGIEVFLPTEEVV-EIRNGKKKVVERPLFPGYVFVRMDMTDETWHLVRSTPGVTGFVGGS--------GKPTPIPDEEV 92

                  ....
gi 1002247570 213 ESII 216
Cdd:pfam02357  93 ERIL 96
NusG_myco TIGR01956
NusG family protein; This model represents a family of Mycoplasma proteins orthologous to the ...
157-325 1.69e-08

NusG family protein; This model represents a family of Mycoplasma proteins orthologous to the bacterial transcription termination/antitermination factor NusG. These sequences from Mycoplasma are notably diverged (long branches in a Neighbor-joining phylogenetic tree) from the bacterial species. And although NusA and ribosomal protein S10 (NusE) appear to be present, NusB may be absent in Mycoplasmas calling into question whether these species have a functional Nus system including this family as a member.


Pssm-ID: 273895 [Multi-domain]  Cd Length: 258  Bit Score: 54.58  E-value: 1.69e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002247570 157 KSKPLHPGLVFLYCTLNKEVHDFIRDTEGCYGFIGATVgsikrqiKKPKPIPV---EEVESIIREEKEEQ---------E 224
Cdd:TIGR01956  81 SEKNKYNGYIYIKMIMTEDAWFLIRNTENVTGLVGSSG-------KGAKPIPIsadADKLKMLKGISENTkkrvlvtntA 153
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002247570 225 RVDREFEEMENGGIVESFNKPVEDSELMLMNKIKRQFKKPISKGGSNHNA--FTPGASVHVLSGPFEGFTGSLLEVNRKN 302
Cdd:TIGR01956 154 IVEMEENKFDEKCQYILKHKQVKPEAIAQVSESGEIIDEIVEEFQLVDNLskFRVGNFVKIVDGPFKGIVGKIKKIDQEK 233
                         170       180
                  ....*....|....*....|...
gi 1002247570 303 KKATLQLTLFGKESFVDLDFDQI 325
Cdd:TIGR01956 234 KKAIVEVEILGKSVDVDLNFKHL 256
NGN_Bact_1 cd09891
Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; The ...
149-219 6.80e-08

Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; The N-Utilization Substance G (NusG) protein is involved in transcription elongation and termination in bacteria. NusG is essential in Escherichia coli and associates with RNA polymerase elongation and Rho-termination. Homologs of the NusG gene exist in all bacteria. The NusG N-terminal domain (NGN) is similar in all NusG homologs, but its C-terminal domain and the linker that separates these two domains are different. The domain organization of NusG suggests that the common properties of NusG and its homologs are due to their similar NGN domains.


Pssm-ID: 193580 [Multi-domain]  Cd Length: 107  Bit Score: 49.78  E-value: 6.80e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1002247570 149 LKNGSISTKSKPLHPGLVFLYCTLNKEVHDFIRDTEGCYGFIGATvgsikrqiKKPKPIPVEEVESIIREE 219
Cdd:cd09891    45 VKNGKKKVKERKLFPGYVLVEMDMNDDTWHLVRNTPGVTGFVGSG--------GKPVPLSEEEVERILGQV 107
NGN cd08000
N-Utilization Substance G (NusG) N-terminal (NGN) domain Superfamily; The N-Utilization ...
125-216 2.12e-07

N-Utilization Substance G (NusG) N-terminal (NGN) domain Superfamily; The N-Utilization Substance G (NusG) 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 in bacteria and archaea. 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. Spt5 forms a 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 being involved in RNA polymerase elongation and Rho-termination in bacteria. Orthologs of the NusG gene exist in all bacteria, but its functions and requirements are different. The diverse activities suggest that, after diverging from a common ancestor, NusG proteins became specialized in different bacteria.


Pssm-ID: 193574 [Multi-domain]  Cd Length: 99  Bit Score: 48.47  E-value: 2.12e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002247570 125 KAISRRYPELSFKIYNPSIQVKKRLKnGSISTKSKPLHPGLVFLYCTLNKEVHDFIRDTEGCYGFIGATvgsikrqiKKP 204
Cdd:cd08000    17 KLLEKRFEANDIEAFVPKKEVPERKR-GKIEEVIKPLFPGYVFVETDLSPELYELIREVPGVIGILGNG--------EEP 87
                          90
                  ....*....|..
gi 1002247570 205 KPIPVEEVESII 216
Cdd:cd08000    88 SPVSDEEIEMIL 99
KOW_GPKOW_B cd13153
KOW motif of the "G-patch domain and KOW motifs-containing protein" (GPKOW) repeat B; GPKOW ...
278-325 1.71e-06

KOW motif of the "G-patch domain and KOW motifs-containing protein" (GPKOW) repeat B; GPKOW contains one G-patch domain and two KOW motifs. GPKOW is a nuclear protein that regulated by catalytic (C) subunit of Protein Kinase A (PKA) and bind RNA in vivo. PKA may be involved in regulating multiple steps in post-transcriptional processing of pre-mRNAs. 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. GPKOW is also known as the T54 protein or MOS2 homolog.


Pssm-ID: 240517  Cd Length: 51  Bit Score: 44.47  E-value: 1.71e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1002247570 278 GASVHVLSGPFEGFTGSLLEVNRKNKKATLQLTlfGKESFVDLDFDQI 325
Cdd:cd13153     1 GAYVMVVRGKHRGQVGKLLERDKKKETAVVQLL--DDFSVVTLSYDDI 46
 
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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