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Conserved domains on  [gi|612535265|gb|EZR54275|]
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transcription antitermination factor NusB [Staphylococcus aureus VET1896R]

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;
1-129 6.58e-57

transcription antitermination factor NusB;


:

Pssm-ID: 234686 [Multi-domain]  Cd Length: 137  Bit Score: 173.06  E-value: 6.58e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612535265   1 MSRKESRVQAFQTLFQLEMKDSDltINEAISFIKDDN--PDLDFEFIHWLVSGVKDHEPVLDETISPYLKDWTIARLLKT 78
Cdd:PRK00202   1 AARRKAREAAVQALYQWELSGND--IAEIIEAQLLEEqyDKADPAYFRSLVRGVVENQAELDELISPYLKDWTLERLDPV 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 612535265  79 DRIILRMATYEILHS-DTPAKVVMNEAVELTKQFSDDDHYKFINGVLSNIKK 129
Cdd:PRK00202  79 ERAILRLALYELLFRdDVPYKVVINEAIELAKKFGDEDSHKFVNGVLDKIAK 130
 
Name Accession Description Interval E-value
nusB PRK00202
transcription antitermination factor NusB;
1-129 6.58e-57

transcription antitermination factor NusB;


Pssm-ID: 234686 [Multi-domain]  Cd Length: 137  Bit Score: 173.06  E-value: 6.58e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612535265   1 MSRKESRVQAFQTLFQLEMKDSDltINEAISFIKDDN--PDLDFEFIHWLVSGVKDHEPVLDETISPYLKDWTIARLLKT 78
Cdd:PRK00202   1 AARRKAREAAVQALYQWELSGND--IAEIIEAQLLEEqyDKADPAYFRSLVRGVVENQAELDELISPYLKDWTLERLDPV 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 612535265  79 DRIILRMATYEILHS-DTPAKVVMNEAVELTKQFSDDDHYKFINGVLSNIKK 129
Cdd:PRK00202  79 ERAILRLALYELLFRdDVPYKVVINEAIELAKKFGDEDSHKFVNGVLDKIAK 130
nusB TIGR01951
transcription antitermination factor NusB; A transcription antitermination complex active in ...
 3-129 1.78e-49

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: 153.80  E-value: 1.78e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612535265    3 RKESRVQAFQTLFQLEMkdSDLTINEAISFIKDDN--PDLDFEFIHWLVSGVKDHEPVLDETISPYLKDWTIARLLKTDR 80
Cdd:TIGR01951   1 RRKARELALQALYQWEL--SGEDVDEIIEEFLEERelDEEDREYFRELVRGVLENQEEIDELISPHLEDWTLERLDPVDR 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 612535265   81 IILRMATYEILHS-DTPAKVVMNEAVELTKQFSDDDHYKFINGVLSNIKK 129
Cdd:TIGR01951  79 AILRLAIYELLYRpDVPYKVVINEAVELAKKFGDEDSHKFVNGVLDKIAK 128
NusB COG0781
Transcription antitermination protein NusB [Transcription];
10-129 1.13e-44

Transcription antitermination protein NusB [Transcription];


Pssm-ID: 440544 [Multi-domain]  Cd Length: 128  Bit Score: 141.82  E-value: 1.13e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612535265  10 AFQTLFQLEMKDSDltINEAISFIKDDNP--DLDFEFIHWLVSGVKDHEPVLDETISPYLKDWTIARLLKTDRIILRMAT 87
Cdd:COG0781    3 ALQALYQVELSGAY--ANEILEEFLEDEElsEADRAFATELVYGVLRNQEELDALIAPYLKDWPLERLDPVDRAILRLAA 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 612535265  88 YEILH-SDTPAKVVMNEAVELTKQFSDDDHYKFINGVLSNIKK 129
Cdd:COG0781   81 YELLYlDDVPYKVAINEAVELAKKFGTEDSPKFVNGVLDKIAK 123
NusB pfam01029
NusB family; The NusB protein is involved in the regulation of rRNA biosynthesis by ...
 5-129 8.98e-38

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: 124.30  E-value: 8.98e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612535265    5 ESRVQAFQTLFQLEMKDSDLTINEAISFIKDDN------PDLDFEFIHWLVSGVKDHEPVLDETISPYLKDWTIARLLKT 78
Cdd:pfam01029   2 NARELALQALYQVEINGSDEEEKGAYLNEALDKalegdlSEEDRAFATELVYGVLRNLEELDALIEKLLENWPLERLSPV 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 612535265   79 DRIILRMATYEILH-SDTPAKVVMNEAVELTKQFSDDDHYKFINGVLSNIKK 129
Cdd:pfam01029  82 DRAILRLGLYELLFlDDVPPHVAINEAVELAKKFGGEKSAKFVNGVLRNVAR 133
Terminator_NusB cd00619
Transcription termination factor NusB (N protein-Utilization Substance B). NusB plays a key ...
 3-129 3.23e-36

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: 120.46  E-value: 3.23e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612535265   3 RKESRVQAFQTLFQLEMkdSDLTINEAISFIKDDNP--DLDFEFIHWLVSGVKDHEPVLDETISPYLKDWTIARLLKTDR 80
Cdd:cd00619    1 RRRARELAVQALYAWEL--APEILAEVVSLLELLQYksKKVLPFALKLVRGVLENIEEIDELIEKHLRNWSLDRLAIVER 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 612535265  81 IILRMATYEILH-SDTPAKVVMNEAVELTKQFSDDDHYKFINGVLSNIKK 129
Cdd:cd00619   79 AILRLAVYELLFlPDVPHPVVINEAIELAKRFGGDDSHKFVNGVLDKIAK 128
 
Name Accession Description Interval E-value
nusB PRK00202
transcription antitermination factor NusB;
1-129 6.58e-57

transcription antitermination factor NusB;


Pssm-ID: 234686 [Multi-domain]  Cd Length: 137  Bit Score: 173.06  E-value: 6.58e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612535265   1 MSRKESRVQAFQTLFQLEMKDSDltINEAISFIKDDN--PDLDFEFIHWLVSGVKDHEPVLDETISPYLKDWTIARLLKT 78
Cdd:PRK00202   1 AARRKAREAAVQALYQWELSGND--IAEIIEAQLLEEqyDKADPAYFRSLVRGVVENQAELDELISPYLKDWTLERLDPV 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 612535265  79 DRIILRMATYEILHS-DTPAKVVMNEAVELTKQFSDDDHYKFINGVLSNIKK 129
Cdd:PRK00202  79 ERAILRLALYELLFRdDVPYKVVINEAIELAKKFGDEDSHKFVNGVLDKIAK 130
nusB TIGR01951
transcription antitermination factor NusB; A transcription antitermination complex active in ...
 3-129 1.78e-49

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: 153.80  E-value: 1.78e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612535265    3 RKESRVQAFQTLFQLEMkdSDLTINEAISFIKDDN--PDLDFEFIHWLVSGVKDHEPVLDETISPYLKDWTIARLLKTDR 80
Cdd:TIGR01951   1 RRKARELALQALYQWEL--SGEDVDEIIEEFLEERelDEEDREYFRELVRGVLENQEEIDELISPHLEDWTLERLDPVDR 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 612535265   81 IILRMATYEILHS-DTPAKVVMNEAVELTKQFSDDDHYKFINGVLSNIKK 129
Cdd:TIGR01951  79 AILRLAIYELLYRpDVPYKVVINEAVELAKKFGDEDSHKFVNGVLDKIAK 128
NusB COG0781
Transcription antitermination protein NusB [Transcription];
10-129 1.13e-44

Transcription antitermination protein NusB [Transcription];


Pssm-ID: 440544 [Multi-domain]  Cd Length: 128  Bit Score: 141.82  E-value: 1.13e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612535265  10 AFQTLFQLEMKDSDltINEAISFIKDDNP--DLDFEFIHWLVSGVKDHEPVLDETISPYLKDWTIARLLKTDRIILRMAT 87
Cdd:COG0781    3 ALQALYQVELSGAY--ANEILEEFLEDEElsEADRAFATELVYGVLRNQEELDALIAPYLKDWPLERLDPVDRAILRLAA 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 612535265  88 YEILH-SDTPAKVVMNEAVELTKQFSDDDHYKFINGVLSNIKK 129
Cdd:COG0781   81 YELLYlDDVPYKVAINEAVELAKKFGTEDSPKFVNGVLDKIAK 123
NusB pfam01029
NusB family; The NusB protein is involved in the regulation of rRNA biosynthesis by ...
 5-129 8.98e-38

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: 124.30  E-value: 8.98e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612535265    5 ESRVQAFQTLFQLEMKDSDLTINEAISFIKDDN------PDLDFEFIHWLVSGVKDHEPVLDETISPYLKDWTIARLLKT 78
Cdd:pfam01029   2 NARELALQALYQVEINGSDEEEKGAYLNEALDKalegdlSEEDRAFATELVYGVLRNLEELDALIEKLLENWPLERLSPV 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 612535265   79 DRIILRMATYEILH-SDTPAKVVMNEAVELTKQFSDDDHYKFINGVLSNIKK 129
Cdd:pfam01029  82 DRAILRLGLYELLFlDDVPPHVAINEAVELAKKFGGEKSAKFVNGVLRNVAR 133
Terminator_NusB cd00619
Transcription termination factor NusB (N protein-Utilization Substance B). NusB plays a key ...
 3-129 3.23e-36

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: 120.46  E-value: 3.23e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612535265   3 RKESRVQAFQTLFQLEMkdSDLTINEAISFIKDDNP--DLDFEFIHWLVSGVKDHEPVLDETISPYLKDWTIARLLKTDR 80
Cdd:cd00619    1 RRRARELAVQALYAWEL--APEILAEVVSLLELLQYksKKVLPFALKLVRGVLENIEEIDELIEKHLRNWSLDRLAIVER 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 612535265  81 IILRMATYEILH-SDTPAKVVMNEAVELTKQFSDDDHYKFINGVLSNIKK 129
Cdd:cd00619   79 AILRLAVYELLFlPDVPHPVVINEAIELAKRFGGDDSHKFVNGVLDKIAK 128
NusB_Sun cd00447
RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or ...
 7-129 6.68e-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: 109.36  E-value: 6.68e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612535265   7 RVQAFQTLFQLEMKDsDLTINEAISF-IKDDNPDLDFEFIHWLVSGVKDHEPVLDETISPYLKDWTIARLLKTDRIILRM 85
Cdd:cd00447    3 REIAFQALYQVEIRN-GISLEAVLSAlEKLQLAKKDRPFALELVYGVLRNLPELDDIISPLLKKWLLDRLDKVDRAILRL 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 612535265  86 ATYEILH--SDTPAKVVMNEAVELTKQFSDDDHYKFINGVLSNIKK 129
Cdd:cd00447   82 LLYELYQllYDVPPPVAINEAVELAKRFGDDDSAKFVNGVLRRIAK 127
Methyltransferase_Sun cd00620
N-terminal RNA binding domain of the methyltransferase Sun. The rRNA-specific 5-methylcytidine ...
 7-129 2.04e-14

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: 64.67  E-value: 2.04e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612535265   7 RVQAFQTLFQLEMKDSDLTINEAiSFIKDDNPDLDFEFIHWLVSGVKDHEPVLDETISPYLKdwtiARLLKTDRII---L 83
Cdd:cd00620    4 RSTAAEVLRDVLQRGASLNAVLS-ALQKKDKSDRDRGLATELVYGTLRWLALLDWIINPLLK----KPDVGKDPDVrnlL 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 612535265  84 RMATYEILHSDTPAKVVMNEAVELTKQFSDDDHYKFINGVLSNIKK 129
Cdd:cd00620   79 RLGLYQLLYLDVPPHAAVDETVEIAKIRKDLGRAGLVNAVLRRFER 124
PRK14902 PRK14902
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;
4-127 1.01e-13

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


Pssm-ID: 237857 [Multi-domain]  Cd Length: 444  Bit Score: 65.97  E-value: 1.01e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612535265   4 KESRVQAFQTLFQLEMKD--SDLTINEAISfiKDDNPDLDFEFIHWLVSGVKDHEPVLDETISPYLKDwtiARLLKTD-R 80
Cdd:PRK14902   3 MNARELALEVLIKVENNGaySNIALNKVLK--KSELSDKDKALLTELVYGTIQRKLTLDYYLAPFIKK---RKKLDPWvR 77

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 612535265  81 IILRMATYEILHSD-TPAKVVMNEAVELTKQFSDDDHYKFINGVLSNI 127
Cdd:PRK14902  78 NLLRMSLYQLLYLDkVPDHAAVNEAVEIAKKRGHKGIAKFVNGVLRNI 125
PRK14904 PRK14904
16S rRNA methyltransferase B; Provisional
 6-129 9.53e-07

16S rRNA methyltransferase B; Provisional


Pssm-ID: 237858 [Multi-domain]  Cd Length: 445  Bit Score: 46.21  E-value: 9.53e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612535265   6 SRVQAFQTLFQLE--MKDSDLTINEAISFIKDDNPD--LDFEfihwLVSGVKDHEPVLDETISPYLKDwtiaRLLKTD-- 79
Cdd:PRK14904   4 ARELALQVLQELEtgERKSDTLLHRMLERSSLERNDraLATE----LVNGVLRYRLQLDFIISRFYHH----DLEKAApv 75

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 612535265  80 -RIILRMATYEILHSD-TPAKVVMNEAVELTKQFSDDDHYKFINGVLSNIKK 129
Cdd:PRK14904  76 lKNILRLGVYQLLFLDrVPRWAAVNECVKLARKYKGEHMAKLVNGVLRNISP 127
PRK14903 PRK14903
16S rRNA methyltransferase B; Provisional
 26-129 2.73e-05

16S rRNA methyltransferase B; Provisional


Pssm-ID: 184896 [Multi-domain]  Cd Length: 431  Bit Score: 42.17  E-value: 2.73e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 612535265  26 INEAISFIKDDnpdlDFEFIHWLVSGVKDHEPVLDETISPYLKDWTIARLLktdRIILRMATYEILHSD-TPAKVVMNEA 104
Cdd:PRK14903  27 VDSVLSFLDDK----DRRFFKELVWGVVRKEELLDWYINQLLKKKDIPPAV---RVALRMGAYQLLFMNsVPDYAAVSET 99

                         90       100
                 ....*....|....*....|....*
gi 612535265 105 VELTKQfsdDDHYKFINGVLSNIKK 129
Cdd:PRK14903 100 VKLVKN---ENFKKLVNAVLRRLRT 121
 
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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