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Conserved domains on  [gi|2242229819|emb|CAH3990113|]
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Transcription antitermination protein RfaH (plasmid) [Enterobacter cloacae]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
NGN super family cl02766
N-Utilization Substance G (NusG) N-terminal (NGN) domain Superfamily; The N-Utilization ...
 19-120 2.31e-25

N-Utilization Substance G (NusG) N-terminal (NGN) domain Superfamily; The N-Utilization Substance G (NusG) and its eukaryotic homolog Spt5 are involved in transcription elongation and termination. NusG contains an NGN domain at its N-terminus and Kyrpides Ouzounis and Woese (KOW) repeats at its C-terminus in bacteria and archaea. The eukaryotic ortholog, Spt5, is a large protein composed of an acidic N-terminus, an NGN domain, and multiple KOW motifs at its C-terminus. Spt5 forms a Spt4-Spt5 complex that is an essential RNA Polymerase II elongation factor. NusG was originally discovered as an N-dependent antitermination enhancing activity in Escherichia coli and has a variety of functions, such as being involved in RNA polymerase elongation and Rho-termination in bacteria. Orthologs of the NusG gene exist in all bacteria, but its functions and requirements are different. The diverse activities suggest that, after diverging from a common ancestor, NusG proteins became specialized in different bacteria.


The actual alignment was detected with superfamily member cd09894:

Pssm-ID: 445911 [Multi-domain]  Cd Length: 99  Bit Score: 93.50  E-value: 2.31e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2242229819  19 QQWYLALYITGgKNRENLFDWLHDRrITPWTPLSLTQIRRADAPHVfRKRISAVFPGYFFLKADFESQKIDMIRAHSAFC 98
Cdd:cd09894     1 KRWYLLRCKSG-KIQSVIFSLERLG-VEVFCPMIRTRRKRTDCKSY-REKIEPLFPGYLFVRFDPEVVHTSKITLASGVS 77

                          90       100
                  ....*....|....*....|..
gi 2242229819  99 DFVKFGSKIAPVNTRVVEALMK 120
Cdd:cd09894    78 GFVRFGGEPCPVPDAVIRALML 99
 
Name Accession Description Interval E-value
NGN_SP_AnfA1 cd09894
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), AnFA1; ...
 19-120 2.31e-25

N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), AnFA1; Regulation of the afp, antifeeding prophage, gene cluster is mediated by AnFA1, a RfaH-like transcriptional antiterminator. RfaH is an operon-specific virulence regulator, thought to arisen from an early duplication of N-Utilization Substance G (NusG). NusG is essential in Escherichia coli and is associated with RNA polymerase elongation and Rho-termination in bacteria. Paralogs of eubacterial NusG, NusG SP (Specialized Paralog of NusG), are more diverse and often found as the first ORF in operons encoding secreted proteins and LPS biosynthesis genes. NusG SP family members are operon-specific transcriptional antitermination factors. Orthologs of the NusG gene exist in all bacteria, but their functions and requirements are different. The NusG N-terminal domain (NGN) is similar in all NusG orthologs, but its C-terminal domain and the linker that separate these two domains are different. The domain organization of NusG and its orthologs suggests that the common properties of NusG and its orthologs and paralogs are due to their similar NGN domains.


Pssm-ID: 193583 [Multi-domain]  Cd Length: 99  Bit Score: 93.50  E-value: 2.31e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2242229819  19 QQWYLALYITGgKNRENLFDWLHDRrITPWTPLSLTQIRRADAPHVfRKRISAVFPGYFFLKADFESQKIDMIRAHSAFC 98
Cdd:cd09894     1 KRWYLLRCKSG-KIQSVIFSLERLG-VEVFCPMIRTRRKRTDCKSY-REKIEPLFPGYLFVRFDPEVVHTSKITLASGVS 77

                          90       100
                  ....*....|....*....|..
gi 2242229819  99 DFVKFGSKIAPVNTRVVEALMK 120
Cdd:cd09894    78 GFVRFGGEPCPVPDAVIRALML 99
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
 20-121 3.22e-10

In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, this domain may confer affinity for Spt4p.Spt4p


Pssm-ID: 197850 [Multi-domain]  Cd Length: 106  Bit Score: 54.69  E-value: 3.22e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2242229819   20 QWYLALYITGgkNRENLFDWLHDRRIT---------PWTPL-SLTQIRRADAPHVFRKrisaVFPGYFFLKADFESQKID 89
Cdd:smart00738   1 NWYAVRTTSG--QEKRVAENLERKAEAlgledkivsILVPTeEVKEIRRGKKKVVERK----LFPGYIFVEADLEDEVWT 74

                           90       100       110
                   ....*....|....*....|....*....|..
gi 2242229819   90 MIRAHSAFCDFVKFGSKIAPVNTRVVEALMKK 121
Cdd:smart00738  75 AIRGTPGVRGFVGGGGKPTPVPDDEIEKILKP 106
NusG COG0250
Transcription termination/antitermination protein NusG [Transcription];
66-136 3.60e-06

Transcription termination/antitermination protein NusG [Transcription];


Pssm-ID: 440020 [Multi-domain]  Cd Length: 171  Bit Score: 44.81  E-value: 3.60e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2242229819  66 RKRIS--AVFPGYFFLKADFESQKIDMIRAHSAFCDFVKFGSKIAPVNTRVVEALMKKYPDPTHHPAARAELE 136
Cdd:COG0250    47 KKKTVerPLFPGYVFVRMDLTDESWYLVRNTPGVTGFVGFGGKPAPLPDEEVERILARLEEGEEKPRPKVDFE 119
rfaH PRK09014
transcription/translation regulatory transformer protein RfaH;
19-129 2.26e-04

transcription/translation regulatory transformer protein RfaH;


Pssm-ID: 181611 [Multi-domain]  Cd Length: 162  Bit Score: 39.87  E-value: 2.26e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2242229819  19 QQWYLaLYItggKNRENLFDWLHDRR--ITPWTPL-SLTQIRRAdaphvfrKRI---SAVFPGYFFLKADFESQKIDMIR 92
Cdd:PRK09014    2 KSWYL-LYC---KRGQLQRAQEHLERqgVECLYPMiTLEKIVRG-------KRTevsEPLFPNYLFVEFDPEVIHTTTIR 70

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2242229819  93 AHSAFCDFVKFGSKIAPVNTRVVEALMKKYPDPTHHP 129
Cdd:PRK09014   71 STRGVSHFVRFGAQPAIVPSDVIYQLSVYKPEKIVDP 107
 
Name Accession Description Interval E-value
NGN_SP_AnfA1 cd09894
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), AnFA1; ...
 19-120 2.31e-25

N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), AnFA1; Regulation of the afp, antifeeding prophage, gene cluster is mediated by AnFA1, a RfaH-like transcriptional antiterminator. RfaH is an operon-specific virulence regulator, thought to arisen from an early duplication of N-Utilization Substance G (NusG). NusG is essential in Escherichia coli and is associated with RNA polymerase elongation and Rho-termination in bacteria. Paralogs of eubacterial NusG, NusG SP (Specialized Paralog of NusG), are more diverse and often found as the first ORF in operons encoding secreted proteins and LPS biosynthesis genes. NusG SP family members are operon-specific transcriptional antitermination factors. Orthologs of the NusG gene exist in all bacteria, but their functions and requirements are different. The NusG N-terminal domain (NGN) is similar in all NusG orthologs, but its C-terminal domain and the linker that separate these two domains are different. The domain organization of NusG and its orthologs suggests that the common properties of NusG and its orthologs and paralogs are due to their similar NGN domains.


Pssm-ID: 193583 [Multi-domain]  Cd Length: 99  Bit Score: 93.50  E-value: 2.31e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2242229819  19 QQWYLALYITGgKNRENLFDWLHDRrITPWTPLSLTQIRRADAPHVfRKRISAVFPGYFFLKADFESQKIDMIRAHSAFC 98
Cdd:cd09894     1 KRWYLLRCKSG-KIQSVIFSLERLG-VEVFCPMIRTRRKRTDCKSY-REKIEPLFPGYLFVRFDPEVVHTSKITLASGVS 77

                          90       100
                  ....*....|....*....|..
gi 2242229819  99 DFVKFGSKIAPVNTRVVEALMK 120
Cdd:cd09894    78 GFVRFGGEPCPVPDAVIRALML 99
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
 20-121 3.22e-10

In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, this domain may confer affinity for Spt4p.Spt4p


Pssm-ID: 197850 [Multi-domain]  Cd Length: 106  Bit Score: 54.69  E-value: 3.22e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2242229819   20 QWYLALYITGgkNRENLFDWLHDRRIT---------PWTPL-SLTQIRRADAPHVFRKrisaVFPGYFFLKADFESQKID 89
Cdd:smart00738   1 NWYAVRTTSG--QEKRVAENLERKAEAlgledkivsILVPTeEVKEIRRGKKKVVERK----LFPGYIFVEADLEDEVWT 74

                           90       100       110
                   ....*....|....*....|....*....|..
gi 2242229819   90 MIRAHSAFCDFVKFGSKIAPVNTRVVEALMKK 121
Cdd:smart00738  75 AIRGTPGVRGFVGGGGKPTPVPDDEIEKILKP 106
NGN_SP_RfaH cd09892
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), RfaH; ...
 51-119 2.99e-07

N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), RfaH; RfaH is an operon-specific virulence regulator, thought to have arisen from an early duplication of N-Utilization Substance G (NusG). Paralogs of eubacterial NusG, NusG SP (Specialized Paralog of NusG), are more diverse and often found as the first ORF in operons encoding secreted proteins and LPS biosynthesis genes. NusG SP family members are operon-specific transcriptional antitermination factors. NusG is essential in Escherichia coli and is associated with RNA polymerase elongation and Rho-termination in bacteria. In contrast, RfaH is a non-essential protein that controls expression of operons containing an ops (operon polarity suppressor) element in their transcribed DNA. RfaH and NusG are different in their response to Rho-dependent terminators and regulatory targets. The NusG N-terminal (NGN) domain is quite similar in all NusG orthologs, but its C-terminal domains and the linker that separate these two domains are different. The domain organization of NusG and its homologs suggest that the common properties of NusG and RfaH are due to their similar NGN domains.


Pssm-ID: 193581 [Multi-domain]  Cd Length: 96  Bit Score: 46.40  E-value: 2.99e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2242229819  51 LSLTQIRRAdaphVFRKRISAVFPGYFFLKADFESQKIDMIRAHSAFCDFVKFGSKIAPVNTRVVEALM 119
Cdd:cd09892    31 IRVEKRRRG----KRTVVTEPLFPGYLFVRLDPEVQNWRPIRSTRGVSRLVRFGGEPAPVPDALIEALR 95
NusG COG0250
Transcription termination/antitermination protein NusG [Transcription];
66-136 3.60e-06

Transcription termination/antitermination protein NusG [Transcription];


Pssm-ID: 440020 [Multi-domain]  Cd Length: 171  Bit Score: 44.81  E-value: 3.60e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2242229819  66 RKRIS--AVFPGYFFLKADFESQKIDMIRAHSAFCDFVKFGSKIAPVNTRVVEALMKKYPDPTHHPAARAELE 136
Cdd:COG0250    47 KKKTVerPLFPGYVFVRMDLTDESWYLVRNTPGVTGFVGFGGKPAPLPDEEVERILARLEEGEEKPRPKVDFE 119
NGN_SP cd09886
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP); The ...
 20-120 7.18e-06

N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP); The N-Utilization Substance G (NusG) protein is involved in transcription elongation and termination. NusG is essential in Escherichia coli and is associated with RNA polymerase elongation and Rho-termination in bacteria. Paralogs of eubacterial NusG, NusG SP (Specialized Paralog of NusG), are more diverse and often found as the first ORF in operons encoding secreted proteins and LPS biosynthesis genes. NusG SP family members are operon-specific transcriptional antitermination factors. The NusG N-terminal (NGN) domain is quite similar in all NusG orthologs, but its C-terminal domains and the linker that separate these two domains are different. The domain organization of NusG and its orthologs suggest that the common properties of NusG and its orthologs and paralogs are due to their similar NGN domains.


Pssm-ID: 193575 [Multi-domain]  Cd Length: 97  Bit Score: 42.74  E-value: 7.18e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2242229819  20 QWYlALYITGGKNREnLFDWLHDRRITPWTP-LSLTQIRRadaphvfRKRISA---VFPGYFFLKADFE-SQKIDMIRAH 94
Cdd:cd09886     1 SWY-ALRTNPGCEQR-AEEALEARGVEAFLPmLTEERKRR-------RKKFDVerpLFPGYVFARLDRSkGQDTSTIRAC 71

                          90       100
                  ....*....|....*....|....*.
gi 2242229819  95 SAFCDFVKFGSKIAPVNTRVVEALMK 120
Cdd:cd09886    72 DGVLGVVGFDGRPAPVPEQEMRDLRK 97
NGN cd08000
N-Utilization Substance G (NusG) N-terminal (NGN) domain Superfamily; The N-Utilization ...
 20-110 2.03e-05

N-Utilization Substance G (NusG) N-terminal (NGN) domain Superfamily; The N-Utilization Substance G (NusG) and its eukaryotic homolog Spt5 are involved in transcription elongation and termination. NusG contains an NGN domain at its N-terminus and Kyrpides Ouzounis and Woese (KOW) repeats at its C-terminus in bacteria and archaea. The eukaryotic ortholog, Spt5, is a large protein composed of an acidic N-terminus, an NGN domain, and multiple KOW motifs at its C-terminus. Spt5 forms a Spt4-Spt5 complex that is an essential RNA Polymerase II elongation factor. NusG was originally discovered as an N-dependent antitermination enhancing activity in Escherichia coli and has a variety of functions, such as being involved in RNA polymerase elongation and Rho-termination in bacteria. Orthologs of the NusG gene exist in all bacteria, but its functions and requirements are different. The diverse activities suggest that, after diverging from a common ancestor, NusG proteins became specialized in different bacteria.


Pssm-ID: 193574 [Multi-domain]  Cd Length: 99  Bit Score: 41.54  E-value: 2.03e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2242229819  20 QWYlALYITGGKNR--ENLFDWLHDRR-ITPWTPLSLTQIRRADaphVFRKRISAVFPGYFFLKADFESQKIDMIRAHSA 96
Cdd:cd08000     1 NWY-VLFVKTGREEkvEKLLEKRFEANdIEAFVPKKEVPERKRG---KIEEVIKPLFPGYVFVETDLSPELYELIREVPG 76

                          90
                  ....*....|....
gi 2242229819  97 FCDFVKFGSKIAPV 110
Cdd:cd08000    77 VIGILGNGEEPSPV 90
rfaH PRK09014
transcription/translation regulatory transformer protein RfaH;
19-129 2.26e-04

transcription/translation regulatory transformer protein RfaH;


Pssm-ID: 181611 [Multi-domain]  Cd Length: 162  Bit Score: 39.87  E-value: 2.26e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2242229819  19 QQWYLaLYItggKNRENLFDWLHDRR--ITPWTPL-SLTQIRRAdaphvfrKRI---SAVFPGYFFLKADFESQKIDMIR 92
Cdd:PRK09014    2 KSWYL-LYC---KRGQLQRAQEHLERqgVECLYPMiTLEKIVRG-------KRTevsEPLFPNYLFVEFDPEVIHTTTIR 70

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2242229819  93 AHSAFCDFVKFGSKIAPVNTRVVEALMKKYPDPTHHP 129
Cdd:PRK09014   71 STRGVSHFVRFGAQPAIVPSDVIYQLSVYKPEKIVDP 107
NGN_SP_TaA cd09893
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), TaA; ...
 20-120 5.99e-03

N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), TaA; The N-Utilization Substance G (NusG) protein is involved in transcription elongation and termination. NusG is essential in Escherichia coli and is associated with RNA polymerase elongation and Rho-termination in bacteria. Paralogs of eubacterial NusG, NusG SP (Specialized Paralog of NusG), are more diverse and often found as the first ORF in operons encoding secreted proteins and LPS biosynthesis genes. NusG SP family members are operon-specific transcriptional antiterminationn factors. TaA is a NusG SP factor that is required for synthesis of a polyketide antibiotic TA in Myxococcus xanthus. Orthologs of the NusG gene exist in all bacteria, but its functions and requirements are different. The NusG N-terminal (NGN) domain is quite similar in all NusG orthologs, but its C-terminal domains and the linker that separate these two domains are different. The domain organization of NusG and its orthologs suggest that the common properties of NusG and its orthologs and paralogs are due to their similar NGN domains.


Pssm-ID: 193582 [Multi-domain]  Cd Length: 95  Bit Score: 34.59  E-value: 5.99e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2242229819  20 QWYlALYiTGGKNRENLFDWLHDRRITPWTPLSLTQIRRADAphvfRKRI-SAVFPGYFFLKADFESQKIDMIRAHSAFc 98
Cdd:cd09893     1 SWY-ALY-TRSRHEKKVADRLAKKGIESFLPLYEVLSRWKDR----KKKIkVPLFPGYLFVRFQLDPERLRILKTPGVV- 73

                          90       100
                  ....*....|....*....|..
gi 2242229819  99 DFVKFGSKIAPVNTRVVEALMK 120
Cdd:cd09893    74 RIVGNSGGPIPIPDEEIASLRI 95
 
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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