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Conserved domains on  [gi|1356005533|ref|WP_105188119|]
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MULTISPECIES: transcription antitermination factor NusB [unclassified Pseudoalteromonas]

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;
4-136 4.08e-65

transcription antitermination factor NusB;


:

Pssm-ID: 234686 [Multi-domain]  Cd Length: 137  Bit Score: 194.24  E-value: 4.08e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1356005533   4 AARRKARVLALQAVYSWQMSGNAIADIEQNMLIENDVSKVDVEYFKDLARGVAVNFKQLDTILAPHLT-RPYEDIDMVEK 82
Cdd:PRK00202    1 AARRKAREAAVQALYQWELSGNDIAEIIEAQLLEEQYDKADPAYFRSLVRGVVENQAELDELISPYLKdWTLERLDPVER 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1356005533  83 AILRLSAYELKFREDVPYKVAINEGIELAKTFGADDSHKFVNGVLDKAVKELRS 136
Cdd:PRK00202   81 AILRLALYELLFRDDVPYKVVINEAIELAKKFGDEDSHKFVNGVLDKIAKELRP 134
 
Name Accession Description Interval E-value
nusB PRK00202
transcription antitermination factor NusB;
4-136 4.08e-65

transcription antitermination factor NusB;


Pssm-ID: 234686 [Multi-domain]  Cd Length: 137  Bit Score: 194.24  E-value: 4.08e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1356005533   4 AARRKARVLALQAVYSWQMSGNAIADIEQNMLIENDVSKVDVEYFKDLARGVAVNFKQLDTILAPHLT-RPYEDIDMVEK 82
Cdd:PRK00202    1 AARRKAREAAVQALYQWELSGNDIAEIIEAQLLEEQYDKADPAYFRSLVRGVVENQAELDELISPYLKdWTLERLDPVER 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1356005533  83 AILRLSAYELKFREDVPYKVAINEGIELAKTFGADDSHKFVNGVLDKAVKELRS 136
Cdd:PRK00202   81 AILRLALYELLFRDDVPYKVVINEAIELAKKFGDEDSHKFVNGVLDKIAKELRP 134
nusB TIGR01951
transcription antitermination factor NusB; A transcription antitermination complex active in ...
 6-133 2.47e-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: 171.52  E-value: 2.47e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1356005533   6 RRKARVLALQAVYSWQMSGNAIADIEQNMLIENDVSKVDVEYFKDLARGVAVNFKQLDTILAPHL-TRPYEDIDMVEKAI 84
Cdd:TIGR01951   1 RRKARELALQALYQWELSGEDVDEIIEEFLEERELDEEDREYFRELVRGVLENQEEIDELISPHLeDWTLERLDPVDRAI 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1356005533  85 LRLSAYELKFREDVPYKVAINEGIELAKTFGADDSHKFVNGVLDKAVKE 133
Cdd:TIGR01951  81 LRLAIYELLYRPDVPYKVVINEAVELAKKFGDEDSHKFVNGVLDKIAKE 129
NusB COG0781
Transcription antitermination protein NusB [Transcription];
12-136 7.44e-53

Transcription antitermination protein NusB [Transcription];


Pssm-ID: 440544 [Multi-domain]  Cd Length: 128  Bit Score: 162.62  E-value: 7.44e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1356005533  12 LALQAVYSWQMSGNAIADIEQNMLIENDVSKVDVEYFKDLARGVAVNFKQLDTILAPHLT-RPYEDIDMVEKAILRLSAY 90
Cdd:COG0781     2 LALQALYQVELSGAYANEILEEFLEDEELSEADRAFATELVYGVLRNQEELDALIAPYLKdWPLERLDPVDRAILRLAAY 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1356005533  91 ELKFREDVPYKVAINEGIELAKTFGADDSHKFVNGVLDKAVKELRS 136
Cdd:COG0781    82 ELLYLDDVPYKVAINEAVELAKKFGTEDSPKFVNGVLDKIAKELRA 127
Terminator_NusB cd00619
Transcription termination factor NusB (N protein-Utilization Substance B). NusB plays a key ...
 6-134 4.65e-43

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: 138.18  E-value: 4.65e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1356005533   6 RRKARVLALQAVYSWQMSGNAIADIEQNMLIENDVSKVDVEYFKDLARGVAVNFKQLDTILAPHLTRPYED-IDMVEKAI 84
Cdd:cd00619     1 RRRARELAVQALYAWELAPEILAEVVSLLELLQYKSKKVLPFALKLVRGVLENIEEIDELIEKHLRNWSLDrLAIVERAI 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1356005533  85 LRLSAYELKFREDVPYKVAINEGIELAKTFGADDSHKFVNGVLDKAVKEL 134
Cdd:cd00619    81 LRLAVYELLFLPDVPHPVVINEAIELAKRFGGDDSHKFVNGVLDKIAKDL 130
NusB pfam01029
NusB family; The NusB protein is involved in the regulation of rRNA biosynthesis by ...
 7-132 1.35e-39

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: 129.31  E-value: 1.35e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1356005533   7 RKARVLALQAVYSWQMSGN------AIADIEQNMLIENDVSKVDVEYFKDLARGVAVNFKQLDTILAPHLT-RPYEDIDM 79
Cdd:pfam01029   1 RNARELALQALYQVEINGSdeeekgAYLNEALDKALEGDLSEEDRAFATELVYGVLRNLEELDALIEKLLEnWPLERLSP 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1356005533  80 VEKAILRLSAYELKFREDVPYKVAINEGIELAKTFGADDSHKFVNGVLDKAVK 132
Cdd:pfam01029  81 VDRAILRLGLYELLFLDDVPPHVAINEAVELAKKFGGEKSAKFVNGVLRNVAR 133
 
Name Accession Description Interval E-value
nusB PRK00202
transcription antitermination factor NusB;
4-136 4.08e-65

transcription antitermination factor NusB;


Pssm-ID: 234686 [Multi-domain]  Cd Length: 137  Bit Score: 194.24  E-value: 4.08e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1356005533   4 AARRKARVLALQAVYSWQMSGNAIADIEQNMLIENDVSKVDVEYFKDLARGVAVNFKQLDTILAPHLT-RPYEDIDMVEK 82
Cdd:PRK00202    1 AARRKAREAAVQALYQWELSGNDIAEIIEAQLLEEQYDKADPAYFRSLVRGVVENQAELDELISPYLKdWTLERLDPVER 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1356005533  83 AILRLSAYELKFREDVPYKVAINEGIELAKTFGADDSHKFVNGVLDKAVKELRS 136
Cdd:PRK00202   81 AILRLALYELLFRDDVPYKVVINEAIELAKKFGDEDSHKFVNGVLDKIAKELRP 134
nusB TIGR01951
transcription antitermination factor NusB; A transcription antitermination complex active in ...
 6-133 2.47e-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: 171.52  E-value: 2.47e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1356005533   6 RRKARVLALQAVYSWQMSGNAIADIEQNMLIENDVSKVDVEYFKDLARGVAVNFKQLDTILAPHL-TRPYEDIDMVEKAI 84
Cdd:TIGR01951   1 RRKARELALQALYQWELSGEDVDEIIEEFLEERELDEEDREYFRELVRGVLENQEEIDELISPHLeDWTLERLDPVDRAI 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1356005533  85 LRLSAYELKFREDVPYKVAINEGIELAKTFGADDSHKFVNGVLDKAVKE 133
Cdd:TIGR01951  81 LRLAIYELLYRPDVPYKVVINEAVELAKKFGDEDSHKFVNGVLDKIAKE 129
NusB COG0781
Transcription antitermination protein NusB [Transcription];
12-136 7.44e-53

Transcription antitermination protein NusB [Transcription];


Pssm-ID: 440544 [Multi-domain]  Cd Length: 128  Bit Score: 162.62  E-value: 7.44e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1356005533  12 LALQAVYSWQMSGNAIADIEQNMLIENDVSKVDVEYFKDLARGVAVNFKQLDTILAPHLT-RPYEDIDMVEKAILRLSAY 90
Cdd:COG0781     2 LALQALYQVELSGAYANEILEEFLEDEELSEADRAFATELVYGVLRNQEELDALIAPYLKdWPLERLDPVDRAILRLAAY 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1356005533  91 ELKFREDVPYKVAINEGIELAKTFGADDSHKFVNGVLDKAVKELRS 136
Cdd:COG0781    82 ELLYLDDVPYKVAINEAVELAKKFGTEDSPKFVNGVLDKIAKELRA 127
Terminator_NusB cd00619
Transcription termination factor NusB (N protein-Utilization Substance B). NusB plays a key ...
 6-134 4.65e-43

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: 138.18  E-value: 4.65e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1356005533   6 RRKARVLALQAVYSWQMSGNAIADIEQNMLIENDVSKVDVEYFKDLARGVAVNFKQLDTILAPHLTRPYED-IDMVEKAI 84
Cdd:cd00619     1 RRRARELAVQALYAWELAPEILAEVVSLLELLQYKSKKVLPFALKLVRGVLENIEEIDELIEKHLRNWSLDrLAIVERAI 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1356005533  85 LRLSAYELKFREDVPYKVAINEGIELAKTFGADDSHKFVNGVLDKAVKEL 134
Cdd:cd00619    81 LRLAVYELLFLPDVPHPVVINEAIELAKRFGGDDSHKFVNGVLDKIAKDL 130
NusB pfam01029
NusB family; The NusB protein is involved in the regulation of rRNA biosynthesis by ...
 7-132 1.35e-39

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: 129.31  E-value: 1.35e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1356005533   7 RKARVLALQAVYSWQMSGN------AIADIEQNMLIENDVSKVDVEYFKDLARGVAVNFKQLDTILAPHLT-RPYEDIDM 79
Cdd:pfam01029   1 RNARELALQALYQVEINGSdeeekgAYLNEALDKALEGDLSEEDRAFATELVYGVLRNLEELDALIEKLLEnWPLERLSP 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1356005533  80 VEKAILRLSAYELKFREDVPYKVAINEGIELAKTFGADDSHKFVNGVLDKAVK 132
Cdd:pfam01029  81 VDRAILRLGLYELLFLDDVPPHVAINEAVELAKKFGGEKSAKFVNGVLRNVAR 133
NusB_Sun cd00447
RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or ...
 8-133 2.17e-31

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: 108.59  E-value: 2.17e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1356005533   8 KARVLALQAVYSWQMSGNAIADIEQNMLIENDVSKVDVEYFKDLARGVAVNFKQLDTILAPHLTRPYED-IDMVEKAILR 86
Cdd:cd00447     1 SAREIAFQALYQVEIRNGISLEAVLSALEKLQLAKKDRPFALELVYGVLRNLPELDDIISPLLKKWLLDrLDKVDRAILR 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1356005533  87 LSAYELKFRE-DVPYKVAINEGIELAKTFGADDSHKFVNGVLDKAVKE 133
Cdd:cd00447    81 LLLYELYQLLyDVPPPVAINEAVELAKRFGDDDSAKFVNGVLRRIAKE 128
PRK14902 PRK14902
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;
8-127 3.99e-14

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


Pssm-ID: 237857 [Multi-domain]  Cd Length: 444  Bit Score: 67.51  E-value: 3.99e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1356005533   8 KARVLALQAVYswqmsgnaiaDIEQN----------MLIENDVSKVDVEYFKDLARGVAVNFKQLDTILAPHLTRPyEDI 77
Cdd:PRK14902    4 NARELALEVLI----------KVENNgaysnialnkVLKKSELSDKDKALLTELVYGTIQRKLTLDYYLAPFIKKR-KKL 72

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1356005533  78 DMVEKAILRLSAYELKFREDVPYKVAINEGIELAKTFGADDSHKFVNGVL 127
Cdd:PRK14902   73 DPWVRNLLRMSLYQLLYLDKVPDHAAVNEAVEIAKKRGHKGIAKFVNGVL 122
PRK14904 PRK14904
16S rRNA methyltransferase B; Provisional
 8-136 6.39e-12

16S rRNA methyltransferase B; Provisional


Pssm-ID: 237858 [Multi-domain]  Cd Length: 445  Bit Score: 61.23  E-value: 6.39e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1356005533   8 KARVLALQAVYSWQmSGNAIAD-IEQNMLIENDVSKVDVEYFKDLARGVAVNFKQLDTILAPHLTRPYEDIDMVEKAILR 86
Cdd:PRK14904    3 TARELALQVLQELE-TGERKSDtLLHRMLERSSLERNDRALATELVNGVLRYRLQLDFIISRFYHHDLEKAAPVLKNILR 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1356005533  87 LSAYELKFREDVPYKVAINEGIELAKTFGADDSHKFVNGVLDKAVKELRS 136
Cdd:PRK14904   82 LGVYQLLFLDRVPRWAAVNECVKLARKYKGEHMAKLVNGVLRNISPETIS 131
Methyltransferase_Sun cd00620
N-terminal RNA binding domain of the methyltransferase Sun. The rRNA-specific 5-methylcytidine ...
 21-133 1.56e-11

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: 57.35  E-value: 1.56e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1356005533  21 QMSGNAIADIEQN---------MLIENDVSKVDVEYFKDLARGVAVNFKQLDTILAPHLTRPYEDIDMVEKAILRLSAYE 91
Cdd:cd00620     5 STAAEVLRDVLQRgaslnavlsALQKKDKSDRDRGLATELVYGTLRWLALLDWIINPLLKKPDVGKDPDVRNLLRLGLYQ 84

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1356005533  92 LKFReDVPYKVAINEGIELAKTFGADDSHKFVNGVLDKAVKE 133
Cdd:cd00620    85 LLYL-DVPPHAAVDETVEIAKIRKDLGRAGLVNAVLRRFERE 125
PRK14903 PRK14903
16S rRNA methyltransferase B; Provisional
 44-132 9.09e-05

16S rRNA methyltransferase B; Provisional


Pssm-ID: 184896 [Multi-domain]  Cd Length: 431  Bit Score: 40.63  E-value: 9.09e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1356005533  44 DVEYFKDLARGVAVNFKQLDTILAPHLTRPyeDIDMVEKAILRLSAYELKFREDVPYKVAINEGIELAKTfgaDDSHKFV 123
Cdd:PRK14903   38 DRRFFKELVWGVVRKEELLDWYINQLLKKK--DIPPAVRVALRMGAYQLLFMNSVPDYAAVSETVKLVKN---ENFKKLV 112


                  ....*....
gi 1356005533 124 NGVLDKAVK 132
Cdd:PRK14903  113 NAVLRRLRT 121
PRK14901 PRK14901
16S rRNA methyltransferase B; Provisional
 84-127 3.03e-04

16S rRNA methyltransferase B; Provisional


Pssm-ID: 237856 [Multi-domain]  Cd Length: 434  Bit Score: 39.14  E-value: 3.03e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1356005533  84 ILRLSAYELKFREDVPYKVAINEGIELAKTFGADDSHKFVNGVL 127
Cdd:PRK14901   77 LLHLGLYQLRYMDRIPASAAVNTTVELAKQNGLGGLAGVVNGIL 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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