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Conserved domains on  [gi|1821114785|gb|QIK55856|]
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transcription antitermination factor NusB [Dysgonomonas sp. HDW5B]

Protein Classification

transcription antitermination protein NusB( domain architecture ID 10002503)

N utilization substance protein B (NusB) is a lambda and rRNA transcription antitermination protein which also plays a role in ribosomal RNA biogenesis

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
NusB COG0781
Transcription antitermination protein NusB [Transcription];
181-302 1.26e-25

Transcription antitermination protein NusB [Transcription];


:

Pssm-ID: 440544 [Multi-domain]  Cd Length: 128  Bit Score: 98.68  E-value: 1.26e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1821114785 181 FVIKTIKKLDTEKGPNQALLPMF-----KDEEDRQFAIKLLRETMFNVKMARELINKYAKNWESERIAFMDMIIMQTAVS 255
Cdd:COG0781     2 LALQALYQVELSGAYANEILEEFledeeLSEADRAFATELVYGVLRNQEELDALIAPYLKDWPLERLDPVDRAILRLAAY 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1821114785 256 ELLAFPSVPINVTMNEYINIAKSYSTHKSSSFINGILDSVVTELKSE 302
Cdd:COG0781    82 ELLYLDDVPYKVAINEAVELAKKFGTEDSPKFVNGVLDKIAKELRAE 128
 
Name Accession Description Interval E-value
NusB COG0781
Transcription antitermination protein NusB [Transcription];
181-302 1.26e-25

Transcription antitermination protein NusB [Transcription];


Pssm-ID: 440544 [Multi-domain]  Cd Length: 128  Bit Score: 98.68  E-value: 1.26e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1821114785 181 FVIKTIKKLDTEKGPNQALLPMF-----KDEEDRQFAIKLLRETMFNVKMARELINKYAKNWESERIAFMDMIIMQTAVS 255
Cdd:COG0781     2 LALQALYQVELSGAYANEILEEFledeeLSEADRAFATELVYGVLRNQEELDALIAPYLKDWPLERLDPVDRAILRLAAY 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1821114785 256 ELLAFPSVPINVTMNEYINIAKSYSTHKSSSFINGILDSVVTELKSE 302
Cdd:COG0781    82 ELLYLDDVPYKVAINEAVELAKKFGTEDSPKFVNGVLDKIAKELRAE 128
nusB TIGR01951
transcription antitermination factor NusB; A transcription antitermination complex active in ...
 205-298 9.85e-25

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: 96.41  E-value: 9.85e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1821114785 205 DEEDRQFAIKLLRETMFNVKMARELINKYAKNWESERIAFMDMIIMQTAVSELLAFPSVPINVTMNEYINIAKSYSTHKS 284
Cdd:TIGR01951  36 DEEDREYFRELVRGVLENQEEIDELISPHLEDWTLERLDPVDRAILRLAIYELLYRPDVPYKVVINEAVELAKKFGDEDS 115

                          90
                  ....*....|....
gi 1821114785 285 SSFINGILDSVVTE 298
Cdd:TIGR01951 116 HKFVNGVLDKIAKE 129
nusB PRK00202
transcription antitermination factor NusB;
205-304 3.83e-21

transcription antitermination factor NusB;


Pssm-ID: 234686 [Multi-domain]  Cd Length: 137  Bit Score: 87.16  E-value: 3.83e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1821114785 205 DEEDRQFAIKLLRETMFNVKMARELINKYAKNWESERIAFMDMIIMQTAVSELLAFPSVPINVTMNEYINIAKSYSTHKS 284
Cdd:PRK00202   38 DKADPAYFRSLVRGVVENQAELDELISPYLKDWTLERLDPVERAILRLALYELLFRDDVPYKVVINEAIELAKKFGDEDS 117

                          90       100
                  ....*....|....*....|
gi 1821114785 285 SSFINGILDSVVTELKSENK 304
Cdd:PRK00202  118 HKFVNGVLDKIAKELRPAEK 137
NusB pfam01029
NusB family; The NusB protein is involved in the regulation of rRNA biosynthesis by ...
 205-296 7.46e-19

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: 80.77  E-value: 7.46e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1821114785 205 DEEDRQFAIKLLRETMFNVKMARELINKYAKNWESERIAFMDMIIMQTAVSELLAFPSVPINVTMNEYINIAKSYSTHKS 284
Cdd:pfam01029  41 SEEDRAFATELVYGVLRNLEELDALIEKLLENWPLERLSPVDRAILRLGLYELLFLDDVPPHVAINEAVELAKKFGGEKS 120

                          90
                  ....*....|..
gi 1821114785 285 SSFINGILDSVV 296
Cdd:pfam01029 121 AKFVNGVLRNVA 132
Terminator_NusB cd00619
Transcription termination factor NusB (N protein-Utilization Substance B). NusB plays a key ...
 198-299 1.00e-18

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: 80.40  E-value: 1.00e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1821114785 198 ALLPMFKDEEDRQFAIKLLRETMFNVKMARELINKYAKNWESERIAFMDMIIMQTAVSELLAFPSVPINVTMNEYINIAK 277
Cdd:cd00619    29 LELLQYKSKKVLPFALKLVRGVLENIEEIDELIEKHLRNWSLDRLAIVERAILRLAVYELLFLPDVPHPVVINEAIELAK 108

                          90       100
                  ....*....|....*....|..
gi 1821114785 278 SYSTHKSSSFINGILDSVVTEL 299
Cdd:cd00619   109 RFGGDDSHKFVNGVLDKIAKDL 130
 
Name Accession Description Interval E-value
NusB COG0781
Transcription antitermination protein NusB [Transcription];
181-302 1.26e-25

Transcription antitermination protein NusB [Transcription];


Pssm-ID: 440544 [Multi-domain]  Cd Length: 128  Bit Score: 98.68  E-value: 1.26e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1821114785 181 FVIKTIKKLDTEKGPNQALLPMF-----KDEEDRQFAIKLLRETMFNVKMARELINKYAKNWESERIAFMDMIIMQTAVS 255
Cdd:COG0781     2 LALQALYQVELSGAYANEILEEFledeeLSEADRAFATELVYGVLRNQEELDALIAPYLKDWPLERLDPVDRAILRLAAY 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1821114785 256 ELLAFPSVPINVTMNEYINIAKSYSTHKSSSFINGILDSVVTELKSE 302
Cdd:COG0781    82 ELLYLDDVPYKVAINEAVELAKKFGTEDSPKFVNGVLDKIAKELRAE 128
nusB TIGR01951
transcription antitermination factor NusB; A transcription antitermination complex active in ...
 205-298 9.85e-25

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: 96.41  E-value: 9.85e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1821114785 205 DEEDRQFAIKLLRETMFNVKMARELINKYAKNWESERIAFMDMIIMQTAVSELLAFPSVPINVTMNEYINIAKSYSTHKS 284
Cdd:TIGR01951  36 DEEDREYFRELVRGVLENQEEIDELISPHLEDWTLERLDPVDRAILRLAIYELLYRPDVPYKVVINEAVELAKKFGDEDS 115

                          90
                  ....*....|....
gi 1821114785 285 SSFINGILDSVVTE 298
Cdd:TIGR01951 116 HKFVNGVLDKIAKE 129
nusB PRK00202
transcription antitermination factor NusB;
205-304 3.83e-21

transcription antitermination factor NusB;


Pssm-ID: 234686 [Multi-domain]  Cd Length: 137  Bit Score: 87.16  E-value: 3.83e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1821114785 205 DEEDRQFAIKLLRETMFNVKMARELINKYAKNWESERIAFMDMIIMQTAVSELLAFPSVPINVTMNEYINIAKSYSTHKS 284
Cdd:PRK00202   38 DKADPAYFRSLVRGVVENQAELDELISPYLKDWTLERLDPVERAILRLALYELLFRDDVPYKVVINEAIELAKKFGDEDS 117

                          90       100
                  ....*....|....*....|
gi 1821114785 285 SSFINGILDSVVTELKSENK 304
Cdd:PRK00202  118 HKFVNGVLDKIAKELRPAEK 137
NusB pfam01029
NusB family; The NusB protein is involved in the regulation of rRNA biosynthesis by ...
 205-296 7.46e-19

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: 80.77  E-value: 7.46e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1821114785 205 DEEDRQFAIKLLRETMFNVKMARELINKYAKNWESERIAFMDMIIMQTAVSELLAFPSVPINVTMNEYINIAKSYSTHKS 284
Cdd:pfam01029  41 SEEDRAFATELVYGVLRNLEELDALIEKLLENWPLERLSPVDRAILRLGLYELLFLDDVPPHVAINEAVELAKKFGGEKS 120

                          90
                  ....*....|..
gi 1821114785 285 SSFINGILDSVV 296
Cdd:pfam01029 121 AKFVNGVLRNVA 132
Terminator_NusB cd00619
Transcription termination factor NusB (N protein-Utilization Substance B). NusB plays a key ...
 198-299 1.00e-18

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: 80.40  E-value: 1.00e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1821114785 198 ALLPMFKDEEDRQFAIKLLRETMFNVKMARELINKYAKNWESERIAFMDMIIMQTAVSELLAFPSVPINVTMNEYINIAK 277
Cdd:cd00619    29 LELLQYKSKKVLPFALKLVRGVLENIEEIDELIEKHLRNWSLDRLAIVERAILRLAVYELLFLPDVPHPVVINEAIELAK 108

                          90       100
                  ....*....|....*....|..
gi 1821114785 278 SYSTHKSSSFINGILDSVVTEL 299
Cdd:cd00619   109 RFGGDDSHKFVNGVLDKIAKDL 130
NusB_Sun cd00447
RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or ...
 204-298 1.23e-10

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: 58.13  E-value: 1.23e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1821114785 204 KDEEDRQFAIKLLRETMFNVKMARELINKYAKNWESERIAFMDMIIMQTAVSELLAFPS-VPINVTMNEYINIAKSYSTH 282
Cdd:cd00447    33 LAKKDRPFALELVYGVLRNLPELDDIISPLLKKWLLDRLDKVDRAILRLLLYELYQLLYdVPPPVAINEAVELAKRFGDD 112

                          90
                  ....*....|....*.
gi 1821114785 283 KSSSFINGILDSVVTE 298
Cdd:cd00447   113 DSAKFVNGVLRRIAKE 128
 
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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