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Conserved domains on  [gi|16128401|ref|NP_414950|]
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transcription antitermination protein NusB [Escherichia coli str. K-12 substr. MG1655]

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 2.67e-61

transcription antitermination factor NusB;


:

Pssm-ID: 234686 [Multi-domain]  Cd Length: 137  Bit Score: 184.61  E-value: 2.67e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128401   11 ECAVQALYSWQLSQNDIADVEYQFLAEQDVKDVDVLYFRELLAGVATNTAYLDGLMKPYL-SRLLEELGQVEKAVLRIAL 89
Cdd:PRK00202   8 EAAVQALYQWELSGNDIAEIIEAQLLEEQYDKADPAYFRSLVRGVVENQAELDELISPYLkDWTLERLDPVERAILRLAL 87

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 16128401   90 YELSKRSDVPYKVAINEAIELAKSFGAEDSHKFVNGVLDKAAPVIRPNKK 139
Cdd:PRK00202  88 YELLFRDDVPYKVVINEAIELAKKFGDEDSHKFVNGVLDKIAKELRPAEK 137
 
Name Accession Description Interval E-value
nusB PRK00202
transcription antitermination factor NusB;
11-139 2.67e-61

transcription antitermination factor NusB;


Pssm-ID: 234686 [Multi-domain]  Cd Length: 137  Bit Score: 184.61  E-value: 2.67e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128401   11 ECAVQALYSWQLSQNDIADVEYQFLAEQDVKDVDVLYFRELLAGVATNTAYLDGLMKPYL-SRLLEELGQVEKAVLRIAL 89
Cdd:PRK00202   8 EAAVQALYQWELSGNDIAEIIEAQLLEEQYDKADPAYFRSLVRGVVENQAELDELISPYLkDWTLERLDPVERAILRLAL 87

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 16128401   90 YELSKRSDVPYKVAINEAIELAKSFGAEDSHKFVNGVLDKAAPVIRPNKK 139
Cdd:PRK00202  88 YELLFRDDVPYKVVINEAIELAKKFGDEDSHKFVNGVLDKIAKELRPAEK 137
nusB TIGR01951
transcription antitermination factor NusB; A transcription antitermination complex active in ...
 11-132 1.76e-54

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: 166.90  E-value: 1.76e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128401    11 ECAVQALYSWQLSQNDIADVEYQFLAEQDVKDVDVLYFRELLAGVATNTAYLDGLMKPYLS-RLLEELGQVEKAVLRIAL 89
Cdd:TIGR01951   6 ELALQALYQWELSGEDVDEIIEEFLEERELDEEDREYFRELVRGVLENQEEIDELISPHLEdWTLERLDPVDRAILRLAI 85

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 16128401    90 YELSKRSDVPYKVAINEAIELAKSFGAEDSHKFVNGVLDKAAP 132
Cdd:TIGR01951  86 YELLYRPDVPYKVVINEAVELAKKFGDEDSHKFVNGVLDKIAK 128
NusB COG0781
Transcription antitermination protein NusB [Transcription];
11-137 4.82e-52

Transcription antitermination protein NusB [Transcription];


Pssm-ID: 440544 [Multi-domain]  Cd Length: 128  Bit Score: 160.70  E-value: 4.82e-52
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128401  11 ECAVQALYSWQLSQNDIADVEYQFLAEQDVKDVDVLYFRELLAGVATNTAYLDGLMKPYL-SRLLEELGQVEKAVLRIAL 89
Cdd:COG0781   1 ELALQALYQVELSGAYANEILEEFLEDEELSEADRAFATELVYGVLRNQEELDALIAPYLkDWPLERLDPVDRAILRLAA 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*...
gi 16128401  90 YELSKRSDVPYKVAINEAIELAKSFGAEDSHKFVNGVLDKAAPVIRPN 137
Cdd:COG0781  81 YELLYLDDVPYKVAINEAVELAKKFGTEDSPKFVNGVLDKIAKELRAE 128
Terminator_NusB cd00619
Transcription termination factor NusB (N protein-Utilization Substance B). NusB plays a key ...
 11-134 2.14e-46

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: 146.66  E-value: 2.14e-46
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128401  11 ECAVQALYSWQLSQNDIADVEYQFLAEQDVKDVDVLYFRELLAGVATNTAYLDGLMKPYLSRL-LEELGQVEKAVLRIAL 89
Cdd:cd00619   6 ELAVQALYAWELAPEILAEVVSLLELLQYKSKKVLPFALKLVRGVLENIEEIDELIEKHLRNWsLDRLAIVERAILRLAV 85

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*
gi 16128401  90 YELSKRSDVPYKVAINEAIELAKSFGAEDSHKFVNGVLDKAAPVI 134
Cdd:cd00619  86 YELLFLPDVPHPVVINEAIELAKRFGGDDSHKFVNGVLDKIAKDL 130
NusB pfam01029
NusB family; The NusB protein is involved in the regulation of rRNA biosynthesis by ...
 11-131 1.40e-35

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: 119.29  E-value: 1.40e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128401    11 ECAVQALYSWQLSQNDiADVEYQFLAEQ-------DVKDVDVLYFRELLAGVATNTAYLDGLMKPYL-SRLLEELGQVEK 82
Cdd:pfam01029   5 ELALQALYQVEINGSD-EEEKGAYLNEAldkalegDLSEEDRAFATELVYGVLRNLEELDALIEKLLeNWPLERLSPVDR 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 16128401    83 AVLRIALYELSKRSDVPYKVAINEAIELAKSFGAEDSHKFVNGVLDKAA 131
Cdd:pfam01029  84 AILRLGLYELLFLDDVPPHVAINEAVELAKKFGGEKSAKFVNGVLRNVA 132
 
Name Accession Description Interval E-value
nusB PRK00202
transcription antitermination factor NusB;
11-139 2.67e-61

transcription antitermination factor NusB;


Pssm-ID: 234686 [Multi-domain]  Cd Length: 137  Bit Score: 184.61  E-value: 2.67e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128401   11 ECAVQALYSWQLSQNDIADVEYQFLAEQDVKDVDVLYFRELLAGVATNTAYLDGLMKPYL-SRLLEELGQVEKAVLRIAL 89
Cdd:PRK00202   8 EAAVQALYQWELSGNDIAEIIEAQLLEEQYDKADPAYFRSLVRGVVENQAELDELISPYLkDWTLERLDPVERAILRLAL 87

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 16128401   90 YELSKRSDVPYKVAINEAIELAKSFGAEDSHKFVNGVLDKAAPVIRPNKK 139
Cdd:PRK00202  88 YELLFRDDVPYKVVINEAIELAKKFGDEDSHKFVNGVLDKIAKELRPAEK 137
nusB TIGR01951
transcription antitermination factor NusB; A transcription antitermination complex active in ...
 11-132 1.76e-54

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: 166.90  E-value: 1.76e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128401    11 ECAVQALYSWQLSQNDIADVEYQFLAEQDVKDVDVLYFRELLAGVATNTAYLDGLMKPYLS-RLLEELGQVEKAVLRIAL 89
Cdd:TIGR01951   6 ELALQALYQWELSGEDVDEIIEEFLEERELDEEDREYFRELVRGVLENQEEIDELISPHLEdWTLERLDPVDRAILRLAI 85

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 16128401    90 YELSKRSDVPYKVAINEAIELAKSFGAEDSHKFVNGVLDKAAP 132
Cdd:TIGR01951  86 YELLYRPDVPYKVVINEAVELAKKFGDEDSHKFVNGVLDKIAK 128
NusB COG0781
Transcription antitermination protein NusB [Transcription];
11-137 4.82e-52

Transcription antitermination protein NusB [Transcription];


Pssm-ID: 440544 [Multi-domain]  Cd Length: 128  Bit Score: 160.70  E-value: 4.82e-52
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128401  11 ECAVQALYSWQLSQNDIADVEYQFLAEQDVKDVDVLYFRELLAGVATNTAYLDGLMKPYL-SRLLEELGQVEKAVLRIAL 89
Cdd:COG0781   1 ELALQALYQVELSGAYANEILEEFLEDEELSEADRAFATELVYGVLRNQEELDALIAPYLkDWPLERLDPVDRAILRLAA 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*...
gi 16128401  90 YELSKRSDVPYKVAINEAIELAKSFGAEDSHKFVNGVLDKAAPVIRPN 137
Cdd:COG0781  81 YELLYLDDVPYKVAINEAVELAKKFGTEDSPKFVNGVLDKIAKELRAE 128
Terminator_NusB cd00619
Transcription termination factor NusB (N protein-Utilization Substance B). NusB plays a key ...
 11-134 2.14e-46

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: 146.66  E-value: 2.14e-46
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128401  11 ECAVQALYSWQLSQNDIADVEYQFLAEQDVKDVDVLYFRELLAGVATNTAYLDGLMKPYLSRL-LEELGQVEKAVLRIAL 89
Cdd:cd00619   6 ELAVQALYAWELAPEILAEVVSLLELLQYKSKKVLPFALKLVRGVLENIEEIDELIEKHLRNWsLDRLAIVERAILRLAV 85

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*
gi 16128401  90 YELSKRSDVPYKVAINEAIELAKSFGAEDSHKFVNGVLDKAAPVI 134
Cdd:cd00619  86 YELLFLPDVPHPVVINEAIELAKRFGGDDSHKFVNGVLDKIAKDL 130
NusB pfam01029
NusB family; The NusB protein is involved in the regulation of rRNA biosynthesis by ...
 11-131 1.40e-35

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: 119.29  E-value: 1.40e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128401    11 ECAVQALYSWQLSQNDiADVEYQFLAEQ-------DVKDVDVLYFRELLAGVATNTAYLDGLMKPYL-SRLLEELGQVEK 82
Cdd:pfam01029   5 ELALQALYQVEINGSD-EEEKGAYLNEAldkalegDLSEEDRAFATELVYGVLRNLEELDALIEKLLeNWPLERLSPVDR 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 16128401    83 AVLRIALYELSKRSDVPYKVAINEAIELAKSFGAEDSHKFVNGVLDKAA 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 3.03e-34

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: 115.91  E-value: 3.03e-34
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128401  11 ECAVQALYSWQLSQNDIADVEYQFLAEQDVKDVDVLYFRELLAGVATNTAYLDGLMKPYLSR-LLEELGQVEKAVLRIAL 89
Cdd:cd00447   4 EIAFQALYQVEIRNGISLEAVLSALEKLQLAKKDRPFALELVYGVLRNLPELDDIISPLLKKwLLDRLDKVDRAILRLLL 83

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*.
gi 16128401  90 YELSK-RSDVPYKVAINEAIELAKSFGAEDSHKFVNGVLDKAAPVI 134
Cdd:cd00447  84 YELYQlLYDVPPPVAINEAVELAKRFGDDDSAKFVNGVLRRIAKES 129
PRK14902 PRK14902
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;
35-127 3.79e-09

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


Pssm-ID: 237857 [Multi-domain]  Cd Length: 444  Bit Score: 53.26  E-value: 3.79e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128401   35 LAEQDVKDVDVLYFRELLAGVATNTAYLDGlmkpYLSRLLEELGQVEKAV---LRIALYELSKRSDVPYKVAINEAIELA 111
Cdd:PRK14902  31 LKKSELSDKDKALLTELVYGTIQRKLTLDY----YLAPFIKKRKKLDPWVrnlLRMSLYQLLYLDKVPDHAAVNEAVEIA 106

                         90
                 ....*....|....*.
gi 16128401  112 KSFGAEDSHKFVNGVL 127
Cdd:PRK14902 107 KKRGHKGIAKFVNGVL 122
Methyltransferase_Sun cd00620
N-terminal RNA binding domain of the methyltransferase Sun. The rRNA-specific 5-methylcytidine ...
 38-127 5.23e-08

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: 48.11  E-value: 5.23e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128401  38 QDVKDVDVLYFRELLAGVATNTAYLDGLMKPYLSRLLEELGQVEKAVLRIALYELsKRSDVPYKVAINEAIELAKSFGAE 117
Cdd:cd00620  31 KDKSDRDRGLATELVYGTLRWLALLDWIINPLLKKPDVGKDPDVRNLLRLGLYQL-LYLDVPPHAAVDETVEIAKIRKDL 109

                        90
                ....*....|
gi 16128401 118 DSHKFVNGVL 127
Cdd:cd00620 110 GRAGLVNAVL 119
PRK14904 PRK14904
16S rRNA methyltransferase B; Provisional
 49-132 1.60e-07

16S rRNA methyltransferase B; Provisional


Pssm-ID: 237858 [Multi-domain]  Cd Length: 445  Bit Score: 48.90  E-value: 1.60e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128401   49 RELLAGVATNTAYLDGLMKPYLSRLLEELGQVEKAVLRIALYELSKRSDVPYKVAINEAIELAKSFGAEDSHKFVNGVLD 128
Cdd:PRK14904  44 TELVNGVLRYRLQLDFIISRFYHHDLEKAAPVLKNILRLGVYQLLFLDRVPRWAAVNECVKLARKYKGEHMAKLVNGVLR 123


                 ....
gi 16128401  129 KAAP 132
Cdd:PRK14904 124 NISP 127
PRK14903 PRK14903
16S rRNA methyltransferase B; Provisional
 40-136 5.95e-06

16S rRNA methyltransferase B; Provisional


Pssm-ID: 184896 [Multi-domain]  Cd Length: 431  Bit Score: 44.09  E-value: 5.95e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16128401   40 VKDVDVLYFRELLAGVATNTAYLDGLMKPYLSRllEELGQVEKAVLRIALYELSKRSDVPYKVAINEAIELAKSfgaEDS 119
Cdd:PRK14903  34 LDDKDRRFFKELVWGVVRKEELLDWYINQLLKK--KDIPPAVRVALRMGAYQLLFMNSVPDYAAVSETVKLVKN---ENF 108

                         90
                 ....*....|....*..
gi 16128401  120 HKFVNGVLDKAAPVIRP 136
Cdd:PRK14903 109 KKLVNAVLRRLRTVPEP 125
PRK14901 PRK14901
16S rRNA methyltransferase B; Provisional
 69-127 1.80e-04

16S rRNA methyltransferase B; Provisional


Pssm-ID: 237856 [Multi-domain]  Cd Length: 434  Bit Score: 39.91  E-value: 1.80e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 16128401   69 YLSRLLEELGQVEKA--------VLRIALYELSKRSDVPYKVAINEAIELAKSFGAEDSHKFVNGVL 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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