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MULTISPECIES: transcription antitermination factor NusB [Rahnella]

Protein Classification

transcription antitermination protein NusB( domain architecture ID 10011308)

transcription antitermination protein NusB (N utilization substance protein B) is a lambda and rRNA transcription antitermination protein which also plays a role in ribosomal RNA biogenesis

CATH:  1.10.940.10
Gene Symbol:  nusB
Gene Ontology:  GO:0031564|GO:0003723|GO:0006353
SCOP:  4001076

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
nusB PRK00202
transcription antitermination factor NusB;
11-137 8.54e-62

transcription antitermination factor NusB;


:

Pssm-ID: 234686 [Multi-domain]  Cd Length: 137  Bit Score: 185.77  E-value: 8.54e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503342002  11 ECAVQALYSWQLSKNDIADVELEFLTEQDVKDVDIAYFRELLAGVANSAEKLDALMAPYL-SRQLDELGQVERAILRLAL 89
Cdd:PRK00202   8 EAAVQALYQWELSGNDIAEIIEAQLLEEQYDKADPAYFRSLVRGVVENQAELDELISPYLkDWTLERLDPVERAILRLAL 87

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 503342002  90 FELSKRQDVPYKVAINEAIELAKTFGAEDSHKFVNGVLDKAGPHIRKK 137
Cdd:PRK00202  88 YELLFRDDVPYKVVINEAIELAKKFGDEDSHKFVNGVLDKIAKELRPA 135
 
Name Accession Description Interval E-value
nusB PRK00202
transcription antitermination factor NusB;
11-137 8.54e-62

transcription antitermination factor NusB;


Pssm-ID: 234686 [Multi-domain]  Cd Length: 137  Bit Score: 185.77  E-value: 8.54e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503342002  11 ECAVQALYSWQLSKNDIADVELEFLTEQDVKDVDIAYFRELLAGVANSAEKLDALMAPYL-SRQLDELGQVERAILRLAL 89
Cdd:PRK00202   8 EAAVQALYQWELSGNDIAEIIEAQLLEEQYDKADPAYFRSLVRGVVENQAELDELISPYLkDWTLERLDPVERAILRLAL 87

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 503342002  90 FELSKRQDVPYKVAINEAIELAKTFGAEDSHKFVNGVLDKAGPHIRKK 137
Cdd:PRK00202  88 YELLFRDDVPYKVVINEAIELAKKFGDEDSHKFVNGVLDKIAKELRPA 135
nusB TIGR01951
transcription antitermination factor NusB; A transcription antitermination complex active in ...
 11-130 9.34e-56

transcription antitermination factor NusB; A transcription antitermination complex active in many bacteria was designated N-utilization substance (Nus) in E. coli because of its interaction with phage lambda protein N. This model represents NusB. Other components are NusA and NusG. NusE is, in fact, ribosomal protein S10. [Transcription, Transcription factors]


Pssm-ID: 273891 [Multi-domain]  Cd Length: 129  Bit Score: 170.36  E-value: 9.34e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503342002   11 ECAVQALYSWQLSKNDIADVELEFLTEQDVKDVDIAYFRELLAGVANSAEKLDALMAPYLS-RQLDELGQVERAILRLAL 89
Cdd:TIGR01951   6 ELALQALYQWELSGEDVDEIIEEFLEERELDEEDREYFRELVRGVLENQEEIDELISPHLEdWTLERLDPVDRAILRLAI 85

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 503342002   90 FELSKRQDVPYKVAINEAIELAKTFGAEDSHKFVNGVLDKA 130
Cdd:TIGR01951  86 YELLYRPDVPYKVVINEAVELAKKFGDEDSHKFVNGVLDKI 126
NusB COG0781
Transcription antitermination protein NusB [Transcription];
11-137 2.48e-53

Transcription antitermination protein NusB [Transcription];


Pssm-ID: 440544 [Multi-domain]  Cd Length: 128  Bit Score: 164.16  E-value: 2.48e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503342002  11 ECAVQALYSWQLSKNDIADVELEFLTEQDVKDVDIAYFRELLAGVANSAEKLDALMAPYL-SRQLDELGQVERAILRLAL 89
Cdd:COG0781    1 ELALQALYQVELSGAYANEILEEFLEDEELSEADRAFATELVYGVLRNQEELDALIAPYLkDWPLERLDPVDRAILRLAA 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 503342002  90 FELSKRQDVPYKVAINEAIELAKTFGAEDSHKFVNGVLDKAGPHIRKK 137
Cdd:COG0781   81 YELLYLDDVPYKVAINEAVELAKKFGTEDSPKFVNGVLDKIAKELRAE 128
Terminator_NusB cd00619
Transcription termination factor NusB (N protein-Utilization Substance B). NusB plays a key ...
 11-134 4.63e-45

Transcription termination factor NusB (N protein-Utilization Substance B). NusB plays a key role in the regulation of ribosomal RNA biosynthesis in eubacteria by modulating the efficiency of transcriptional antitermination. NusB along with other Nus factors (NusA, NusE/S10 and NusG) forms the core complex with the boxA element of the nut site of the rRNA operons. These interactions help RNA polymerase to counteract polarity during transcription of rRNA operons and allow stable antitermination. The transcription antitermination system can be appropriated by some bacteriophages such as lambda, which use the system to switch between the lysogenic and lytic modes of phage propagation.


Pssm-ID: 238342 [Multi-domain]  Cd Length: 130  Bit Score: 143.19  E-value: 4.63e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503342002  11 ECAVQALYSWQLSKNDIADVELEFLTEQDVKDVDIAYFRELLAGVANSAEKLDALMAPYLSR-QLDELGQVERAILRLAL 89
Cdd:cd00619    6 ELAVQALYAWELAPEILAEVVSLLELLQYKSKKVLPFALKLVRGVLENIEEIDELIEKHLRNwSLDRLAIVERAILRLAV 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 503342002  90 FELSKRQDVPYKVAINEAIELAKTFGAEDSHKFVNGVLDKAGPHI 134
Cdd:cd00619   86 YELLFLPDVPHPVVINEAIELAKRFGGDDSHKFVNGVLDKIAKDL 130
NusB pfam01029
NusB family; The NusB protein is involved in the regulation of rRNA biosynthesis by ...
 11-130 1.04e-36

NusB family; The NusB protein is involved in the regulation of rRNA biosynthesis by transcriptional antitermination.


Pssm-ID: 460031 [Multi-domain]  Cd Length: 133  Bit Score: 121.99  E-value: 1.04e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503342002   11 ECAVQALYSWQLSKNDIADVE------LEFLTEQDVKDVDIAYFRELLAGVANSAEKLDALMAPYL-SRQLDELGQVERA 83
Cdd:pfam01029   5 ELALQALYQVEINGSDEEEKGaylneaLDKALEGDLSEEDRAFATELVYGVLRNLEELDALIEKLLeNWPLERLSPVDRA 84

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 503342002   84 ILRLALFELSKRQDVPYKVAINEAIELAKTFGAEDSHKFVNGVLDKA 130
Cdd:pfam01029  85 ILRLGLYELLFLDDVPPHVAINEAVELAKKFGGEKSAKFVNGVLRNV 131
 
Name Accession Description Interval E-value
nusB PRK00202
transcription antitermination factor NusB;
11-137 8.54e-62

transcription antitermination factor NusB;


Pssm-ID: 234686 [Multi-domain]  Cd Length: 137  Bit Score: 185.77  E-value: 8.54e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503342002  11 ECAVQALYSWQLSKNDIADVELEFLTEQDVKDVDIAYFRELLAGVANSAEKLDALMAPYL-SRQLDELGQVERAILRLAL 89
Cdd:PRK00202   8 EAAVQALYQWELSGNDIAEIIEAQLLEEQYDKADPAYFRSLVRGVVENQAELDELISPYLkDWTLERLDPVERAILRLAL 87

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 503342002  90 FELSKRQDVPYKVAINEAIELAKTFGAEDSHKFVNGVLDKAGPHIRKK 137
Cdd:PRK00202  88 YELLFRDDVPYKVVINEAIELAKKFGDEDSHKFVNGVLDKIAKELRPA 135
nusB TIGR01951
transcription antitermination factor NusB; A transcription antitermination complex active in ...
 11-130 9.34e-56

transcription antitermination factor NusB; A transcription antitermination complex active in many bacteria was designated N-utilization substance (Nus) in E. coli because of its interaction with phage lambda protein N. This model represents NusB. Other components are NusA and NusG. NusE is, in fact, ribosomal protein S10. [Transcription, Transcription factors]


Pssm-ID: 273891 [Multi-domain]  Cd Length: 129  Bit Score: 170.36  E-value: 9.34e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503342002   11 ECAVQALYSWQLSKNDIADVELEFLTEQDVKDVDIAYFRELLAGVANSAEKLDALMAPYLS-RQLDELGQVERAILRLAL 89
Cdd:TIGR01951   6 ELALQALYQWELSGEDVDEIIEEFLEERELDEEDREYFRELVRGVLENQEEIDELISPHLEdWTLERLDPVDRAILRLAI 85

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 503342002   90 FELSKRQDVPYKVAINEAIELAKTFGAEDSHKFVNGVLDKA 130
Cdd:TIGR01951  86 YELLYRPDVPYKVVINEAVELAKKFGDEDSHKFVNGVLDKI 126
NusB COG0781
Transcription antitermination protein NusB [Transcription];
11-137 2.48e-53

Transcription antitermination protein NusB [Transcription];


Pssm-ID: 440544 [Multi-domain]  Cd Length: 128  Bit Score: 164.16  E-value: 2.48e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503342002  11 ECAVQALYSWQLSKNDIADVELEFLTEQDVKDVDIAYFRELLAGVANSAEKLDALMAPYL-SRQLDELGQVERAILRLAL 89
Cdd:COG0781    1 ELALQALYQVELSGAYANEILEEFLEDEELSEADRAFATELVYGVLRNQEELDALIAPYLkDWPLERLDPVDRAILRLAA 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 503342002  90 FELSKRQDVPYKVAINEAIELAKTFGAEDSHKFVNGVLDKAGPHIRKK 137
Cdd:COG0781   81 YELLYLDDVPYKVAINEAVELAKKFGTEDSPKFVNGVLDKIAKELRAE 128
Terminator_NusB cd00619
Transcription termination factor NusB (N protein-Utilization Substance B). NusB plays a key ...
 11-134 4.63e-45

Transcription termination factor NusB (N protein-Utilization Substance B). NusB plays a key role in the regulation of ribosomal RNA biosynthesis in eubacteria by modulating the efficiency of transcriptional antitermination. NusB along with other Nus factors (NusA, NusE/S10 and NusG) forms the core complex with the boxA element of the nut site of the rRNA operons. These interactions help RNA polymerase to counteract polarity during transcription of rRNA operons and allow stable antitermination. The transcription antitermination system can be appropriated by some bacteriophages such as lambda, which use the system to switch between the lysogenic and lytic modes of phage propagation.


Pssm-ID: 238342 [Multi-domain]  Cd Length: 130  Bit Score: 143.19  E-value: 4.63e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503342002  11 ECAVQALYSWQLSKNDIADVELEFLTEQDVKDVDIAYFRELLAGVANSAEKLDALMAPYLSR-QLDELGQVERAILRLAL 89
Cdd:cd00619    6 ELAVQALYAWELAPEILAEVVSLLELLQYKSKKVLPFALKLVRGVLENIEEIDELIEKHLRNwSLDRLAIVERAILRLAV 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 503342002  90 FELSKRQDVPYKVAINEAIELAKTFGAEDSHKFVNGVLDKAGPHI 134
Cdd:cd00619   86 YELLFLPDVPHPVVINEAIELAKRFGGDDSHKFVNGVLDKIAKDL 130
NusB pfam01029
NusB family; The NusB protein is involved in the regulation of rRNA biosynthesis by ...
 11-130 1.04e-36

NusB family; The NusB protein is involved in the regulation of rRNA biosynthesis by transcriptional antitermination.


Pssm-ID: 460031 [Multi-domain]  Cd Length: 133  Bit Score: 121.99  E-value: 1.04e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503342002   11 ECAVQALYSWQLSKNDIADVE------LEFLTEQDVKDVDIAYFRELLAGVANSAEKLDALMAPYL-SRQLDELGQVERA 83
Cdd:pfam01029   5 ELALQALYQVEINGSDEEEKGaylneaLDKALEGDLSEEDRAFATELVYGVLRNLEELDALIEKLLeNWPLERLSPVDRA 84

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 503342002   84 ILRLALFELSKRQDVPYKVAINEAIELAKTFGAEDSHKFVNGVLDKA 130
Cdd:pfam01029  85 ILRLGLYELLFLDDVPPHVAINEAVELAKKFGGEKSAKFVNGVLRNV 131
NusB_Sun cd00447
RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or ...
 11-129 7.40e-32

RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins. This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the rRNA-specific 5-methylcytidine transferase (m5C-methyltransferase) Sun. The NusB protein plays a key role in the regulation of ribosomal RNA biosynthesis in eubacteria by modulating the efficiency of transcriptional antitermination. NusB along with other Nus factors (NusA, NusE/S10 and NusG) forms the core complex with the boxA element of the nut site of the rRNA operons. These interactions help RNA polymerase to counteract polarity during transcription of rRNA operons and allow stable antitermination. The transcription antitermination system can be appropriated by some bacteriophages such as lambda, which use the system to switch between the lysogenic and lytic modes of phage propagation. The m5C-methyltransferase Sun shares the N-terminal non-catalytic RNA-binding domain with NusB.


Pssm-ID: 238253 [Multi-domain]  Cd Length: 129  Bit Score: 109.75  E-value: 7.40e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503342002  11 ECAVQALYSWQLSKNDIADVELEFLTEQDVKDVDIAYFRELLAGVANSAEKLDALMAPYLSR-QLDELGQVERAILRLAL 89
Cdd:cd00447    4 EIAFQALYQVEIRNGISLEAVLSALEKLQLAKKDRPFALELVYGVLRNLPELDDIISPLLKKwLLDRLDKVDRAILRLLL 83

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 503342002  90 FELSKRQ-DVPYKVAINEAIELAKTFGAEDSHKFVNGVLDK 129
Cdd:cd00447   84 YELYQLLyDVPPPVAINEAVELAKRFGDDDSAKFVNGVLRR 124
PRK14902 PRK14902
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;
35-127 2.37e-09

16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;


Pssm-ID: 237857 [Multi-domain]  Cd Length: 444  Bit Score: 54.03  E-value: 2.37e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503342002  35 LTEQDVKDVDIAYFRELLAGVANSAEKLDALMAPYLsRQLDELGQVERAILRLALFELSKRQDVPYKVAINEAIELAKTF 114
Cdd:PRK14902  31 LKKSELSDKDKALLTELVYGTIQRKLTLDYYLAPFI-KKRKKLDPWVRNLLRMSLYQLLYLDKVPDHAAVNEAVEIAKKR 109

                         90
                 ....*....|...
gi 503342002 115 GAEDSHKFVNGVL 127
Cdd:PRK14902 110 GHKGIAKFVNGVL 122
Methyltransferase_Sun cd00620
N-terminal RNA binding domain of the methyltransferase Sun. The rRNA-specific 5-methylcytidine ...
 38-127 4.14e-09

N-terminal RNA binding domain of the methyltransferase Sun. The rRNA-specific 5-methylcytidine transferase Sun, also known as RrmB or Fmu shares the RNA-binding non-catalytic domain with the transcription termination factor NusB. The precise biological role of this domain in Sun is unknown, although it is likely to be involved in sequence-specific RNA binding. The C-terminal methyltransferase domain of Sun has been shown to catalyze formation of m5C at position 967 of 16S rRNA in Escherichia coli.


Pssm-ID: 238343 [Multi-domain]  Cd Length: 126  Bit Score: 51.19  E-value: 4.14e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503342002  38 QDVKDVDIAYFRELLAGVANSAEKLDALMAPYLSRQLDELGQVERAILRLALFELsKRQDVPYKVAINEAIELAKTFGAE 117
Cdd:cd00620   31 KDKSDRDRGLATELVYGTLRWLALLDWIINPLLKKPDVGKDPDVRNLLRLGLYQL-LYLDVPPHAAVDETVEIAKIRKDL 109

                         90
                 ....*....|
gi 503342002 118 DSHKFVNGVL 127
Cdd:cd00620  110 GRAGLVNAVL 119
PRK14904 PRK14904
16S rRNA methyltransferase B; Provisional
 33-132 6.33e-09

16S rRNA methyltransferase B; Provisional


Pssm-ID: 237858 [Multi-domain]  Cd Length: 445  Bit Score: 52.75  E-value: 6.33e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503342002  33 EFLTEQDVKDVDIAYFRELLAGVANSAEKLDALMAPYLSRQLDELGQVERAILRLALFELSKRQDVPYKVAINEAIELAK 112
Cdd:PRK14904  28 RMLERSSLERNDRALATELVNGVLRYRLQLDFIISRFYHHDLEKAAPVLKNILRLGVYQLLFLDRVPRWAAVNECVKLAR 107

                         90       100
                 ....*....|....*....|
gi 503342002 113 TFGAEDSHKFVNGVLDKAGP 132
Cdd:PRK14904 108 KYKGEHMAKLVNGVLRNISP 127
PRK14901 PRK14901
16S rRNA methyltransferase B; Provisional
 28-127 4.97e-08

16S rRNA methyltransferase B; Provisional


Pssm-ID: 237856 [Multi-domain]  Cd Length: 434  Bit Score: 50.31  E-value: 4.97e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503342002  28 ADVELE-FLTEQDVKDVDIAYFRELLAGVANSAEKLDALmapylsrqLDELGQVE--------RAILRLALFELSKRQDV 98
Cdd:PRK14901  20 ADVALErVLRKYPLSGADRALVTELVYGCIRRRRTLDAW--------IDQLGKKPahkqppdlRWLLHLGLYQLRYMDRI 91

                         90       100
                 ....*....|....*....|....*....
gi 503342002  99 PYKVAINEAIELAKTFGAEDSHKFVNGVL 127
Cdd:PRK14901  92 PASAAVNTTVELAKQNGLGGLAGVVNGIL 120
PRK14903 PRK14903
16S rRNA methyltransferase B; Provisional
 40-129 3.20e-04

16S rRNA methyltransferase B; Provisional


Pssm-ID: 184896 [Multi-domain]  Cd Length: 431  Bit Score: 39.09  E-value: 3.20e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503342002  40 VKDVDIAYFRELLAGVANSAEKLDALMAPYLSRQldELGQVERAILRLALFELSKRQDVPYKVAINEAIELAKTfgaEDS 119
Cdd:PRK14903  34 LDDKDRRFFKELVWGVVRKEELLDWYINQLLKKK--DIPPAVRVALRMGAYQLLFMNSVPDYAAVSETVKLVKN---ENF 108

                         90
                 ....*....|
gi 503342002 120 HKFVNGVLDK 129
Cdd:PRK14903 109 KKLVNAVLRR 118
PRK10901 PRK10901
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;
38-127 1.22e-03

16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;


Pssm-ID: 236790 [Multi-domain]  Cd Length: 427  Bit Score: 37.48  E-value: 1.22e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503342002  38 QDVKDVDIAYFRELLAGVANSAEKLDALMAPYLSRQLDELGQVERAILRLALFELSKRQdVPYKVAINEAIELAKTFGAE 117
Cdd:PRK10901  31 QKVSDKDRALLQELCYGVLRRLPRLEWLIAQLLAKPLKGKQRIVHALLLVGLYQLLYTR-IPAHAAVDETVEAAKALKRP 109

                         90
                 ....*....|
gi 503342002 118 DSHKFVNGVL 127
Cdd:PRK10901 110 WAKGLVNAVL 119
 
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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