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Conserved domains on  [gi|721333767|gb|AIX05354|]
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transcription antitermination factor NusB [Streptococcus agalactiae CNCTC 10/84]

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 Ontology:  GO:0031564|GO:0003723
PubMed:  28452979|11491288
SCOP:  4001076

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
nusB PRK00202
transcription antitermination factor NusB;
8-143 2.34e-54

transcription antitermination factor NusB;


:

Pssm-ID: 234686 [Multi-domain]  Cd Length: 137  Bit Score: 167.28  E-value: 2.34e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 721333767   8 SRRDLRERAFQTLFSLETGGEFIDAAhfaygYDKTVSEDKVLEV-PIFLLNLVNGVVDHKDELDTLISSHLKSgWSLERL 86
Cdd:PRK00202   2 ARRKAREAAVQALYQWELSGNDIAEI-----IEAQLLEEQYDKAdPAYFRSLVRGVVENQAELDELISPYLKD-WTLERL 75

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 721333767  87 TLVDKSLLRLGLYEIKYFDETPDRVALNEIIEIAKKYSDETSAKFVNGLLSQFITNE 143
Cdd:PRK00202  76 DPVERAILRLALYELLFRDDVPYKVVINEAIELAKKFGDEDSHKFVNGVLDKIAKEL 132
 
Name Accession Description Interval E-value
nusB PRK00202
transcription antitermination factor NusB;
8-143 2.34e-54

transcription antitermination factor NusB;


Pssm-ID: 234686 [Multi-domain]  Cd Length: 137  Bit Score: 167.28  E-value: 2.34e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 721333767   8 SRRDLRERAFQTLFSLETGGEFIDAAhfaygYDKTVSEDKVLEV-PIFLLNLVNGVVDHKDELDTLISSHLKSgWSLERL 86
Cdd:PRK00202   2 ARRKAREAAVQALYQWELSGNDIAEI-----IEAQLLEEQYDKAdPAYFRSLVRGVVENQAELDELISPYLKD-WTLERL 75

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 721333767  87 TLVDKSLLRLGLYEIKYFDETPDRVALNEIIEIAKKYSDETSAKFVNGLLSQFITNE 143
Cdd:PRK00202  76 DPVERAILRLALYELLFRDDVPYKVVINEAIELAKKFGDEDSHKFVNGVLDKIAKEL 132
nusB TIGR01951
transcription antitermination factor NusB; A transcription antitermination complex active in ...
 9-142 3.66e-47

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: 148.79  E-value: 3.66e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 721333767    9 RRDLRERAFQTLFSLETGGEFIDAAHFAYGYDKTVSEdkvlEVPIFLLNLVNGVVDHKDELDTLISSHLKsGWSLERLTL 88
Cdd:TIGR01951   1 RRKARELALQALYQWELSGEDVDEIIEEFLEERELDE----EDREYFRELVRGVLENQEEIDELISPHLE-DWTLERLDP 75

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 721333767   89 VDKSLLRLGLYEIKYFDETPDRVALNEIIEIAKKYSDETSAKFVNGLLSQFITN 142
Cdd:TIGR01951  76 VDRAILRLAIYELLYRPDVPYKVVINEAVELAKKFGDEDSHKFVNGVLDKIAKE 129
NusB COG0781
Transcription antitermination protein NusB [Transcription];
14-139 1.38e-41

Transcription antitermination protein NusB [Transcription];


Pssm-ID: 440544 [Multi-domain]  Cd Length: 128  Bit Score: 134.50  E-value: 1.38e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 721333767  14 ERAFQTLFSLETGGEFIDAAHFAYGYDKTVSEdkvlEVPIFLLNLVNGVVDHKDELDTLISSHLKsGWSLERLTLVDKSL 93
Cdd:COG0781    1 ELALQALYQVELSGAYANEILEEFLEDEELSE----ADRAFATELVYGVLRNQEELDALIAPYLK-DWPLERLDPVDRAI 75

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 721333767  94 LRLGLYEIKYFDETPDRVALNEIIEIAKKYSDETSAKFVNGLLSQF 139
Cdd:COG0781   76 LRLAAYELLYLDDVPYKVAINEAVELAKKFGTEDSPKFVNGVLDKI 121
NusB pfam01029
NusB family; The NusB protein is involved in the regulation of rRNA biosynthesis by ...
 10-140 6.16e-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: 120.45  E-value: 6.16e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 721333767   10 RDLRERAFQTLFSLETGGEFIDAAHFAYGYDKTVSEDKVLEVPI--FLLNLVNGVVDHKDELDTLISSHLKsGWSLERLT 87
Cdd:pfam01029   1 RNARELALQALYQVEINGSDEEEKGAYLNEALDKALEGDLSEEDraFATELVYGVLRNLEELDALIEKLLE-NWPLERLS 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 721333767   88 LVDKSLLRLGLYEIKYFDETPDRVALNEIIEIAKKYSDETSAKFVNGLLSQFI 140
Cdd:pfam01029  80 PVDRAILRLGLYELLFLDDVPPHVAINEAVELAKKFGGEKSAKFVNGVLRNVA 132
Terminator_NusB cd00619
Transcription termination factor NusB (N protein-Utilization Substance B). NusB plays a key ...
 9-142 1.80e-35

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: 119.31  E-value: 1.80e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 721333767   9 RRDLRERAFQTLFSLETGGEFIDAAhFAYGYDKTVSEDKVLEvpiFLLNLVNGVVDHKDELDTLISSHLKsGWSLERLTL 88
Cdd:cd00619    1 RRRARELAVQALYAWELAPEILAEV-VSLLELLQYKSKKVLP---FALKLVRGVLENIEEIDELIEKHLR-NWSLDRLAI 75

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 721333767  89 VDKSLLRLGLYEIKYFDETPDRVALNEIIEIAKKYSDETSAKFVNGLLSQFITN 142
Cdd:cd00619   76 VERAILRLAVYELLFLPDVPHPVVINEAIELAKRFGGDDSHKFVNGVLDKIAKD 129
 
Name Accession Description Interval E-value
nusB PRK00202
transcription antitermination factor NusB;
8-143 2.34e-54

transcription antitermination factor NusB;


Pssm-ID: 234686 [Multi-domain]  Cd Length: 137  Bit Score: 167.28  E-value: 2.34e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 721333767   8 SRRDLRERAFQTLFSLETGGEFIDAAhfaygYDKTVSEDKVLEV-PIFLLNLVNGVVDHKDELDTLISSHLKSgWSLERL 86
Cdd:PRK00202   2 ARRKAREAAVQALYQWELSGNDIAEI-----IEAQLLEEQYDKAdPAYFRSLVRGVVENQAELDELISPYLKD-WTLERL 75

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 721333767  87 TLVDKSLLRLGLYEIKYFDETPDRVALNEIIEIAKKYSDETSAKFVNGLLSQFITNE 143
Cdd:PRK00202  76 DPVERAILRLALYELLFRDDVPYKVVINEAIELAKKFGDEDSHKFVNGVLDKIAKEL 132
nusB TIGR01951
transcription antitermination factor NusB; A transcription antitermination complex active in ...
 9-142 3.66e-47

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: 148.79  E-value: 3.66e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 721333767    9 RRDLRERAFQTLFSLETGGEFIDAAHFAYGYDKTVSEdkvlEVPIFLLNLVNGVVDHKDELDTLISSHLKsGWSLERLTL 88
Cdd:TIGR01951   1 RRKARELALQALYQWELSGEDVDEIIEEFLEERELDE----EDREYFRELVRGVLENQEEIDELISPHLE-DWTLERLDP 75

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 721333767   89 VDKSLLRLGLYEIKYFDETPDRVALNEIIEIAKKYSDETSAKFVNGLLSQFITN 142
Cdd:TIGR01951  76 VDRAILRLAIYELLYRPDVPYKVVINEAVELAKKFGDEDSHKFVNGVLDKIAKE 129
NusB COG0781
Transcription antitermination protein NusB [Transcription];
14-139 1.38e-41

Transcription antitermination protein NusB [Transcription];


Pssm-ID: 440544 [Multi-domain]  Cd Length: 128  Bit Score: 134.50  E-value: 1.38e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 721333767  14 ERAFQTLFSLETGGEFIDAAHFAYGYDKTVSEdkvlEVPIFLLNLVNGVVDHKDELDTLISSHLKsGWSLERLTLVDKSL 93
Cdd:COG0781    1 ELALQALYQVELSGAYANEILEEFLEDEELSE----ADRAFATELVYGVLRNQEELDALIAPYLK-DWPLERLDPVDRAI 75

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 721333767  94 LRLGLYEIKYFDETPDRVALNEIIEIAKKYSDETSAKFVNGLLSQF 139
Cdd:COG0781   76 LRLAAYELLYLDDVPYKVAINEAVELAKKFGTEDSPKFVNGVLDKI 121
NusB pfam01029
NusB family; The NusB protein is involved in the regulation of rRNA biosynthesis by ...
 10-140 6.16e-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: 120.45  E-value: 6.16e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 721333767   10 RDLRERAFQTLFSLETGGEFIDAAHFAYGYDKTVSEDKVLEVPI--FLLNLVNGVVDHKDELDTLISSHLKsGWSLERLT 87
Cdd:pfam01029   1 RNARELALQALYQVEINGSDEEEKGAYLNEALDKALEGDLSEEDraFATELVYGVLRNLEELDALIEKLLE-NWPLERLS 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 721333767   88 LVDKSLLRLGLYEIKYFDETPDRVALNEIIEIAKKYSDETSAKFVNGLLSQFI 140
Cdd:pfam01029  80 PVDRAILRLGLYELLFLDDVPPHVAINEAVELAKKFGGEKSAKFVNGVLRNVA 132
Terminator_NusB cd00619
Transcription termination factor NusB (N protein-Utilization Substance B). NusB plays a key ...
 9-142 1.80e-35

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: 119.31  E-value: 1.80e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 721333767   9 RRDLRERAFQTLFSLETGGEFIDAAhFAYGYDKTVSEDKVLEvpiFLLNLVNGVVDHKDELDTLISSHLKsGWSLERLTL 88
Cdd:cd00619    1 RRRARELAVQALYAWELAPEILAEV-VSLLELLQYKSKKVLP---FALKLVRGVLENIEEIDELIEKHLR-NWSLDRLAI 75

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 721333767  89 VDKSLLRLGLYEIKYFDETPDRVALNEIIEIAKKYSDETSAKFVNGLLSQFITN 142
Cdd:cd00619   76 VERAILRLAVYELLFLPDVPHPVVINEAIELAKRFGGDDSHKFVNGVLDKIAKD 129
NusB_Sun cd00447
RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or ...
 13-143 2.82e-28

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: 100.89  E-value: 2.82e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 721333767  13 RERAFQTLFSLETGGEFIDAAHFaygyDKTVSEDKVLEVPIFLLNLVNGVVDHKDELDTLISSHLKsGWSLERLTLVDKS 92
Cdd:cd00447    3 REIAFQALYQVEIRNGISLEAVL----SALEKLQLAKKDRPFALELVYGVLRNLPELDDIISPLLK-KWLLDRLDKVDRA 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 721333767  93 LLRLGLYEIKYF-DETPDRVALNEIIEIAKKYSDETSAKFVNGLLSQFITNE 143
Cdd:cd00447   78 ILRLLLYELYQLlYDVPPPVAINEAVELAKRFGDDDSAKFVNGVLRRIAKES 129
PRK14902 PRK14902
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;
54-144 1.13e-19

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


Pssm-ID: 237857 [Multi-domain]  Cd Length: 444  Bit Score: 83.69  E-value: 1.13e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 721333767  54 FLLNLVNGVVDHKDELDTLISSHLKSGWSLERLTLVdksLLRLGLYEIKYFDETPDRVALNEIIEIAKKYSDETSAKFVN 133
Cdd:PRK14902  43 LLTELVYGTIQRKLTLDYYLAPFIKKRKKLDPWVRN---LLRMSLYQLLYLDKVPDHAAVNEAVEIAKKRGHKGIAKFVN 119

                         90
                 ....*....|.
gi 721333767 134 GLLSQFITNEN 144
Cdd:PRK14902 120 GVLRNILREGL 130
PRK14904 PRK14904
16S rRNA methyltransferase B; Provisional
 13-144 3.11e-16

16S rRNA methyltransferase B; Provisional


Pssm-ID: 237858 [Multi-domain]  Cd Length: 445  Bit Score: 73.94  E-value: 3.11e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 721333767  13 RERAFQTLFSLETGGEFIDAA----HFAYGYDKTvseDKVLEVpifllNLVNGVVDHKDELDTLIS---SHlksgwSLER 85
Cdd:PRK14904   5 RELALQVLQELETGERKSDTLlhrmLERSSLERN---DRALAT-----ELVNGVLRYRLQLDFIISrfyHH-----DLEK 71

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 721333767  86 LTLVDKSLLRLGLYEIKYFDETPDRVALNEIIEIAKKYSDETSAKFVNGLLSQfITNEN 144
Cdd:PRK14904  72 AAPVLKNILRLGVYQLLFLDRVPRWAAVNECVKLARKYKGEHMAKLVNGVLRN-ISPET 129
Methyltransferase_Sun cd00620
N-terminal RNA binding domain of the methyltransferase Sun. The rRNA-specific 5-methylcytidine ...
 54-143 2.29e-12

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: 59.66  E-value: 2.29e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 721333767  54 FLLNLVNGVVDHKDELDTLISSHLKSgwSLERLTLVDKSLLRLGLYEIKYFDeTPDRVALNEIIEIAKKYSDETSAKFVN 133
Cdd:cd00620   40 LATELVYGTLRWLALLDWIINPLLKK--PDVGKDPDVRNLLRLGLYQLLYLD-VPPHAAVDETVEIAKIRKDLGRAGLVN 116

                         90
                 ....*....|
gi 721333767 134 GLLSQFITNE 143
Cdd:cd00620  117 AVLRRFERED 126
PRK14901 PRK14901
16S rRNA methyltransferase B; Provisional
 58-140 3.14e-08

16S rRNA methyltransferase B; Provisional


Pssm-ID: 237856 [Multi-domain]  Cd Length: 434  Bit Score: 51.08  E-value: 3.14e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 721333767  58 LVNGVVDHKDELDTLIS-----SHLKSGWSLERLtlvdkslLRLGLYEIKYFDETPDRVALNEIIEIAKKYSDETSAKFV 132
Cdd:PRK14901  44 LVYGCIRRRRTLDAWIDqlgkkPAHKQPPDLRWL-------LHLGLYQLRYMDRIPASAAVNTTVELAKQNGLGGLAGVV 116


                 ....*...
gi 721333767 133 NGLLSQFI 140
Cdd:PRK14901 117 NGILRQYL 124
PRK14903 PRK14903
16S rRNA methyltransferase B; Provisional
 54-136 4.00e-04

16S rRNA methyltransferase B; Provisional


Pssm-ID: 184896 [Multi-domain]  Cd Length: 431  Bit Score: 39.09  E-value: 4.00e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 721333767  54 FLLNLVNGVVDHKDELDTLISSHLKSgwslERLTLVDKSLLRLGLYEIKYFDETPDRVALNEIIEIAKKysdETSAKFVN 133
Cdd:PRK14903  41 FFKELVWGVVRKEELLDWYINQLLKK----KDIPPAVRVALRMGAYQLLFMNSVPDYAAVSETVKLVKN---ENFKKLVN 113


                 ...
gi 721333767 134 GLL 136
Cdd:PRK14903 114 AVL 116
 
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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