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Conserved domains on  [gi|640456407|ref|WP_024906809|]
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MULTISPECIES: transcription antitermination factor NusB [Enterobacter]

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;
11-139 1.62e-62

transcription antitermination factor NusB;


:

Pssm-ID: 234686 [Multi-domain]  Cd Length: 137  Bit Score: 187.69  E-value: 1.62e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640456407  11 ECAVQALYSWQLSQNDISDVEYQFLSEQDVKDVDVLYFRELLSGVATNSAYLDGLMKPYL-SRLLEELGQVEKAVLRIAL 89
Cdd:PRK00202   8 EAAVQALYQWELSGNDIAEIIEAQLLEEQYDKADPAYFRSLVRGVVENQAELDELISPYLkDWTLERLDPVERAILRLAL 87

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 640456407  90 FELSKRDDVPYKVAINEAIELAKTFGAEDSHKFVNGVLDKAAPAIRPHKK 139
Cdd:PRK00202  88 YELLFRDDVPYKVVINEAIELAKKFGDEDSHKFVNGVLDKIAKELRPAEK 137
 
Name Accession Description Interval E-value
nusB PRK00202
transcription antitermination factor NusB;
11-139 1.62e-62

transcription antitermination factor NusB;


Pssm-ID: 234686 [Multi-domain]  Cd Length: 137  Bit Score: 187.69  E-value: 1.62e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640456407  11 ECAVQALYSWQLSQNDISDVEYQFLSEQDVKDVDVLYFRELLSGVATNSAYLDGLMKPYL-SRLLEELGQVEKAVLRIAL 89
Cdd:PRK00202   8 EAAVQALYQWELSGNDIAEIIEAQLLEEQYDKADPAYFRSLVRGVVENQAELDELISPYLkDWTLERLDPVERAILRLAL 87

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 640456407  90 FELSKRDDVPYKVAINEAIELAKTFGAEDSHKFVNGVLDKAAPAIRPHKK 139
Cdd:PRK00202  88 YELLFRDDVPYKVVINEAIELAKKFGDEDSHKFVNGVLDKIAKELRPAEK 137
nusB TIGR01951
transcription antitermination factor NusB; A transcription antitermination complex active in ...
 11-133 1.39e-55

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: 169.98  E-value: 1.39e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640456407   11 ECAVQALYSWQLSQNDISDVEYQFLSEQDVKDVDVLYFRELLSGVATNSAYLDGLMKPYLS-RLLEELGQVEKAVLRIAL 89
Cdd:TIGR01951   6 ELALQALYQWELSGEDVDEIIEEFLEERELDEEDREYFRELVRGVLENQEEIDELISPHLEdWTLERLDPVDRAILRLAI 85

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 640456407   90 FELSKRDDVPYKVAINEAIELAKTFGAEDSHKFVNGVLDKAAPA 133
Cdd:TIGR01951  86 YELLYRPDVPYKVVINEAVELAKKFGDEDSHKFVNGVLDKIAKE 129
NusB COG0781
Transcription antitermination protein NusB [Transcription];
11-136 2.70e-53

Transcription antitermination protein NusB [Transcription];


Pssm-ID: 440544 [Multi-domain]  Cd Length: 128  Bit Score: 164.16  E-value: 2.70e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640456407  11 ECAVQALYSWQLSQNDISDVEYQFLSEQDVKDVDVLYFRELLSGVATNSAYLDGLMKPYL-SRLLEELGQVEKAVLRIAL 89
Cdd:COG0781    1 ELALQALYQVELSGAYANEILEEFLEDEELSEADRAFATELVYGVLRNQEELDALIAPYLkDWPLERLDPVDRAILRLAA 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 640456407  90 FELSKRDDVPYKVAINEAIELAKTFGAEDSHKFVNGVLDKAAPAIRP 136
Cdd:COG0781   81 YELLYLDDVPYKVAINEAVELAKKFGTEDSPKFVNGVLDKIAKELRA 127
Terminator_NusB cd00619
Transcription termination factor NusB (N protein-Utilization Substance B). NusB plays a key ...
 11-134 3.31e-44

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: 141.26  E-value: 3.31e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640456407  11 ECAVQALYSWQLSQNDISDVEYQFLSEQDVKDVDVLYFRELLSGVATNSAYLDGLMKPYLSRL-LEELGQVEKAVLRIAL 89
Cdd:cd00619    6 ELAVQALYAWELAPEILAEVVSLLELLQYKSKKVLPFALKLVRGVLENIEEIDELIEKHLRNWsLDRLAIVERAILRLAV 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 640456407  90 FELSKRDDVPYKVAINEAIELAKTFGAEDSHKFVNGVLDKAAPAI 134
Cdd:cd00619   86 YELLFLPDVPHPVVINEAIELAKRFGGDDSHKFVNGVLDKIAKDL 130
NusB pfam01029
NusB family; The NusB protein is involved in the regulation of rRNA biosynthesis by ...
 11-131 1.48e-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: 1.48e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640456407   11 ECAVQALYSWQLSQNDISDVEyQFLSEQ-------DVKDVDVLYFRELLSGVATNSAYLDGLMKPYL-SRLLEELGQVEK 82
Cdd:pfam01029   5 ELALQALYQVEINGSDEEEKG-AYLNEAldkalegDLSEEDRAFATELVYGVLRNLEELDALIEKLLeNWPLERLSPVDR 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 640456407   83 AVLRIALFELSKRDDVPYKVAINEAIELAKTFGAEDSHKFVNGVLDKAA 131
Cdd:pfam01029  84 AILRLGLYELLFLDDVPPHVAINEAVELAKKFGGEKSAKFVNGVLRNVA 132
 
Name Accession Description Interval E-value
nusB PRK00202
transcription antitermination factor NusB;
11-139 1.62e-62

transcription antitermination factor NusB;


Pssm-ID: 234686 [Multi-domain]  Cd Length: 137  Bit Score: 187.69  E-value: 1.62e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640456407  11 ECAVQALYSWQLSQNDISDVEYQFLSEQDVKDVDVLYFRELLSGVATNSAYLDGLMKPYL-SRLLEELGQVEKAVLRIAL 89
Cdd:PRK00202   8 EAAVQALYQWELSGNDIAEIIEAQLLEEQYDKADPAYFRSLVRGVVENQAELDELISPYLkDWTLERLDPVERAILRLAL 87

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 640456407  90 FELSKRDDVPYKVAINEAIELAKTFGAEDSHKFVNGVLDKAAPAIRPHKK 139
Cdd:PRK00202  88 YELLFRDDVPYKVVINEAIELAKKFGDEDSHKFVNGVLDKIAKELRPAEK 137
nusB TIGR01951
transcription antitermination factor NusB; A transcription antitermination complex active in ...
 11-133 1.39e-55

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: 169.98  E-value: 1.39e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640456407   11 ECAVQALYSWQLSQNDISDVEYQFLSEQDVKDVDVLYFRELLSGVATNSAYLDGLMKPYLS-RLLEELGQVEKAVLRIAL 89
Cdd:TIGR01951   6 ELALQALYQWELSGEDVDEIIEEFLEERELDEEDREYFRELVRGVLENQEEIDELISPHLEdWTLERLDPVDRAILRLAI 85

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 640456407   90 FELSKRDDVPYKVAINEAIELAKTFGAEDSHKFVNGVLDKAAPA 133
Cdd:TIGR01951  86 YELLYRPDVPYKVVINEAVELAKKFGDEDSHKFVNGVLDKIAKE 129
NusB COG0781
Transcription antitermination protein NusB [Transcription];
11-136 2.70e-53

Transcription antitermination protein NusB [Transcription];


Pssm-ID: 440544 [Multi-domain]  Cd Length: 128  Bit Score: 164.16  E-value: 2.70e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640456407  11 ECAVQALYSWQLSQNDISDVEYQFLSEQDVKDVDVLYFRELLSGVATNSAYLDGLMKPYL-SRLLEELGQVEKAVLRIAL 89
Cdd:COG0781    1 ELALQALYQVELSGAYANEILEEFLEDEELSEADRAFATELVYGVLRNQEELDALIAPYLkDWPLERLDPVDRAILRLAA 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 640456407  90 FELSKRDDVPYKVAINEAIELAKTFGAEDSHKFVNGVLDKAAPAIRP 136
Cdd:COG0781   81 YELLYLDDVPYKVAINEAVELAKKFGTEDSPKFVNGVLDKIAKELRA 127
Terminator_NusB cd00619
Transcription termination factor NusB (N protein-Utilization Substance B). NusB plays a key ...
 11-134 3.31e-44

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: 141.26  E-value: 3.31e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640456407  11 ECAVQALYSWQLSQNDISDVEYQFLSEQDVKDVDVLYFRELLSGVATNSAYLDGLMKPYLSRL-LEELGQVEKAVLRIAL 89
Cdd:cd00619    6 ELAVQALYAWELAPEILAEVVSLLELLQYKSKKVLPFALKLVRGVLENIEEIDELIEKHLRNWsLDRLAIVERAILRLAV 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 640456407  90 FELSKRDDVPYKVAINEAIELAKTFGAEDSHKFVNGVLDKAAPAI 134
Cdd:cd00619   86 YELLFLPDVPHPVVINEAIELAKRFGGDDSHKFVNGVLDKIAKDL 130
NusB pfam01029
NusB family; The NusB protein is involved in the regulation of rRNA biosynthesis by ...
 11-131 1.48e-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: 1.48e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640456407   11 ECAVQALYSWQLSQNDISDVEyQFLSEQ-------DVKDVDVLYFRELLSGVATNSAYLDGLMKPYL-SRLLEELGQVEK 82
Cdd:pfam01029   5 ELALQALYQVEINGSDEEEKG-AYLNEAldkalegDLSEEDRAFATELVYGVLRNLEELDALIEKLLeNWPLERLSPVDR 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 640456407   83 AVLRIALFELSKRDDVPYKVAINEAIELAKTFGAEDSHKFVNGVLDKAA 131
Cdd:pfam01029  84 AILRLGLYELLFLDDVPPHVAINEAVELAKKFGGEKSAKFVNGVLRNVA 132
NusB_Sun cd00447
RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or ...
 11-134 8.61e-33

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: 112.06  E-value: 8.61e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640456407  11 ECAVQALYSWQLSQNDISDVEYQFLSEQDVKDVDVLYFRELLSGVATNSAYLDGLMKPYLSR-LLEELGQVEKAVLRIAL 89
Cdd:cd00447    4 EIAFQALYQVEIRNGISLEAVLSALEKLQLAKKDRPFALELVYGVLRNLPELDDIISPLLKKwLLDRLDKVDRAILRLLL 83

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 640456407  90 FELSK-RDDVPYKVAINEAIELAKTFGAEDSHKFVNGVLDKAAPAI 134
Cdd:cd00447   84 YELYQlLYDVPPPVAINEAVELAKRFGDDDSAKFVNGVLRRIAKES 129
PRK14902 PRK14902
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;
35-127 3.60e-10

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


Pssm-ID: 237857 [Multi-domain]  Cd Length: 444  Bit Score: 56.34  E-value: 3.60e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640456407  35 LSEQDVKDVDVLYFRELLSGVATNSAYLDGlmkpYLSRLLEELGQVEKAV---LRIALFELSKRDDVPYKVAINEAIELA 111
Cdd:PRK14902  31 LKKSELSDKDKALLTELVYGTIQRKLTLDY----YLAPFIKKRKKLDPWVrnlLRMSLYQLLYLDKVPDHAAVNEAVEIA 106

                         90
                 ....*....|....*.
gi 640456407 112 KTFGAEDSHKFVNGVL 127
Cdd:PRK14902 107 KKRGHKGIAKFVNGVL 122
PRK14904 PRK14904
16S rRNA methyltransferase B; Provisional
 34-133 8.58e-08

16S rRNA methyltransferase B; Provisional


Pssm-ID: 237858 [Multi-domain]  Cd Length: 445  Bit Score: 49.67  E-value: 8.58e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640456407  34 FLSEQDVKDVDVLYFRELLSGVATNSAYLDGLMKPYLSRLLEELGQVEKAVLRIALFELSKRDDVPYKVAINEAIELAKT 113
Cdd:PRK14904  29 MLERSSLERNDRALATELVNGVLRYRLQLDFIISRFYHHDLEKAAPVLKNILRLGVYQLLFLDRVPRWAAVNECVKLARK 108

                         90       100
                 ....*....|....*....|
gi 640456407 114 FGAEDSHKFVNGVLDKAAPA 133
Cdd:PRK14904 109 YKGEHMAKLVNGVLRNISPE 128
Methyltransferase_Sun cd00620
N-terminal RNA binding domain of the methyltransferase Sun. The rRNA-specific 5-methylcytidine ...
 35-127 1.60e-07

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: 46.95  E-value: 1.60e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640456407  35 LSEQDVKDVDVLYFRELLSGVATNSAYLDGLMKPYLSRLLEELGQVEKAVLRIALFELsKRDDVPYKVAINEAIELAKTF 114
Cdd:cd00620   28 LQKKDKSDRDRGLATELVYGTLRWLALLDWIINPLLKKPDVGKDPDVRNLLRLGLYQL-LYLDVPPHAAVDETVEIAKIR 106

                         90
                 ....*....|...
gi 640456407 115 GAEDSHKFVNGVL 127
Cdd:cd00620  107 KDLGRAGLVNAVL 119
PRK14903 PRK14903
16S rRNA methyltransferase B; Provisional
 32-136 4.01e-05

16S rRNA methyltransferase B; Provisional


Pssm-ID: 184896 [Multi-domain]  Cd Length: 431  Bit Score: 41.78  E-value: 4.01e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 640456407  32 YQFLSEqdVKDVDVLYFRELLSGVATNSAYLDGLMKPYLSRllEELGQVEKAVLRIALFELSKRDDVPYKVAINEAIELA 111
Cdd:PRK14903  28 DSVLSF--LDDKDRRFFKELVWGVVRKEELLDWYINQLLKK--KDIPPAVRVALRMGAYQLLFMNSVPDYAAVSETVKLV 103

                         90       100
                 ....*....|....*....|....*
gi 640456407 112 KTfgaEDSHKFVNGVLDKAAPAIRP 136
Cdd:PRK14903 104 KN---ENFKKLVNAVLRRLRTVPEP 125
PRK14901 PRK14901
16S rRNA methyltransferase B; Provisional
 69-127 1.09e-04

16S rRNA methyltransferase B; Provisional


Pssm-ID: 237856 [Multi-domain]  Cd Length: 434  Bit Score: 40.68  E-value: 1.09e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 640456407  69 YLSRLLEELGQVEKA--------VLRIALFELSKRDDVPYKVAINEAIELAKTFGAEDSHKFVNGVL 127
Cdd:PRK14901  54 TLDAWIDQLGKKPAHkqppdlrwLLHLGLYQLRYMDRIPASAAVNTTVELAKQNGLGGLAGVVNGIL 120
 
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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