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Conserved domains on  [gi|1491308750|gb|RLI72454|]
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MAG: NusA-like transcription termination signal-binding factor [Candidatus Gerdarchaeota archaeon]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK08406 super family cl30325
transcription elongation factor NusA-like protein; Validated
 1-130 7.98e-42

transcription elongation factor NusA-like protein; Validated


The actual alignment was detected with superfamily member PRK08406:

Pssm-ID: 181413 [Multi-domain]  Cd Length: 140  Bit Score: 134.96  E-value: 7.98e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308750   1 MNIFVNITKVSPKDCIIDRkmDRIIFVVKRGSIGTAIGKQGINVKKLKSALAKDIEIIEDDDSPEVFIKNALVPATVEKV 80
Cdd:PRK08406   13 IALFESITGATVKDCIIDD--DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYSDDPEEFIKNIFAPAAVRSV 90

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1491308750  81 VVVRRKNKPDlAFVTIKQGQRGLAIGKDGRNIERARLLAKRHFDIENVIL 130
Cdd:PRK08406   91 TIKKKNGDKV-AYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDIDDIIL 139
 
Name Accession Description Interval E-value
PRK08406 PRK08406
transcription elongation factor NusA-like protein; Validated
 1-130 7.98e-42

transcription elongation factor NusA-like protein; Validated


Pssm-ID: 181413 [Multi-domain]  Cd Length: 140  Bit Score: 134.96  E-value: 7.98e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308750   1 MNIFVNITKVSPKDCIIDRkmDRIIFVVKRGSIGTAIGKQGINVKKLKSALAKDIEIIEDDDSPEVFIKNALVPATVEKV 80
Cdd:PRK08406   13 IALFESITGATVKDCIIDD--DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYSDDPEEFIKNIFAPAAVRSV 90

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1491308750  81 VVVRRKNKPDlAFVTIKQGQRGLAIGKDGRNIERARLLAKRHFDIENVIL 130
Cdd:PRK08406   91 TIKKKNGDKV-AYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDIDDIIL 139
nusA_arch TIGR01952
NusA family KH domain protein, archaeal; This model represents a family of archaeal proteins ...
 1-130 1.01e-34

NusA family KH domain protein, archaeal; This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.


Pssm-ID: 273892  Cd Length: 141  Bit Score: 117.13  E-value: 1.01e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308750   1 MNIFVNITKVSPKDCIIDRKmDRIIFVVKRGSIGTAIGKQGINVKKLKSALAKDIEIIEDDDSPEVFIKNALVPATVEKV 80
Cdd:TIGR01952  13 IALFEDMTGATVVDCLIDDR-NRVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYSENLEEFVANKLAPAEVKNV 91

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1491308750  81 VVVRRKNKpDLAFVTIKQGQRGLAIGKDGRNIERARLLAKRHFDIENVIL 130
Cdd:TIGR01952  92 TVSEFNGK-KVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDIDDVVV 140
KH-II_NusA_arch_rpt1 cd22530
first type II K-homology (KH) RNA-binding domain found in archaeal probable transcription ...
 1-59 3.91e-19

first type II K-homology (KH) RNA-binding domain found in archaeal probable transcription termination protein NusA and similar proteins; NusA, also called N utilization substance protein A, is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. It participates in both transcription termination and antitermination. NusA homologs consisting of only the two type II K-homology (KH) domains are widely conserved in archaea. Although their function remains unclear, it has been found that Aeropyrum pernix NusA strongly binds to a certain CU-rich sequence near a termination signal. Archaeal NusA may have retained some functions of bacterial NusA, including ssRNA-binding ability. This model corresponds to the first KH domain of NusA found mainly in archaea.


Pssm-ID: 411787 [Multi-domain]  Cd Length: 69  Bit Score: 75.35  E-value: 3.91e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1491308750   1 MNIFVNITKVSPKDCIIDRKMDRIIFVVKRGSIGTAIGKQGINVKKLKSALAKDIEIIE 59
Cdd:cd22530    11 ISLFESITGATARDCLIDDENNRVIFVVKKGEMGLAIGKGGSNVKRLEEILGKNIEVVE 69
KH_2 pfam07650
KH domain;
3-69 2.25e-09

KH domain;


Pssm-ID: 429574 [Multi-domain]  Cd Length: 78  Bit Score: 50.63  E-value: 2.25e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1491308750   3 IFVNITKVSPKDCIIDRKMDRIIFVVKRGSIGTAIGKQGINVKKLKSALAKDIEIIEDddsPEVFIK 69
Cdd:pfam07650   6 LAVELKFAGVSKVEIERTPNAVIVVIRASQPGIVIGKGGSRIKKIGKELRKDIEKLLG---KKVYLN 69
NusA COG0195
Transcription antitermination factor NusA, contains S1 and KH domains [Transcription];
55-120 1.07e-03

Transcription antitermination factor NusA, contains S1 and KH domains [Transcription];


Pssm-ID: 439965 [Multi-domain]  Cd Length: 353  Bit Score: 37.54  E-value: 1.07e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1491308750  55 IEIIEDDDSPEVFIKNALVPATVEKVVVVRRKNKpdlAFVTIKQGQRGLAIGKDGRNierARLLAK 120
Cdd:COG0195   273 IDIILWSEDPAQFIANALSPAKVSSVEVDEEEKS---ADVVVPDDQLSLAIGKGGQN---VRLAAK 332
 
Name Accession Description Interval E-value
PRK08406 PRK08406
transcription elongation factor NusA-like protein; Validated
 1-130 7.98e-42

transcription elongation factor NusA-like protein; Validated


Pssm-ID: 181413 [Multi-domain]  Cd Length: 140  Bit Score: 134.96  E-value: 7.98e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308750   1 MNIFVNITKVSPKDCIIDRkmDRIIFVVKRGSIGTAIGKQGINVKKLKSALAKDIEIIEDDDSPEVFIKNALVPATVEKV 80
Cdd:PRK08406   13 IALFESITGATVKDCIIDD--DRIIFVVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEYSDDPEEFIKNIFAPAAVRSV 90

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1491308750  81 VVVRRKNKPDlAFVTIKQGQRGLAIGKDGRNIERARLLAKRHFDIENVIL 130
Cdd:PRK08406   91 TIKKKNGDKV-AYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDIDDIIL 139
nusA_arch TIGR01952
NusA family KH domain protein, archaeal; This model represents a family of archaeal proteins ...
 1-130 1.01e-34

NusA family KH domain protein, archaeal; This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.


Pssm-ID: 273892  Cd Length: 141  Bit Score: 117.13  E-value: 1.01e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308750   1 MNIFVNITKVSPKDCIIDRKmDRIIFVVKRGSIGTAIGKQGINVKKLKSALAKDIEIIEDDDSPEVFIKNALVPATVEKV 80
Cdd:TIGR01952  13 IALFEDMTGATVVDCLIDDR-NRVVFVVKEGEMGAAIGKGGENVKRLEELIGKSIELIEYSENLEEFVANKLAPAEVKNV 91

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1491308750  81 VVVRRKNKpDLAFVTIKQGQRGLAIGKDGRNIERARLLAKRHFDIENVIL 130
Cdd:TIGR01952  92 TVSEFNGK-KVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDIDDVVV 140
KH-II_NusA_arch_rpt1 cd22530
first type II K-homology (KH) RNA-binding domain found in archaeal probable transcription ...
 1-59 3.91e-19

first type II K-homology (KH) RNA-binding domain found in archaeal probable transcription termination protein NusA and similar proteins; NusA, also called N utilization substance protein A, is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. It participates in both transcription termination and antitermination. NusA homologs consisting of only the two type II K-homology (KH) domains are widely conserved in archaea. Although their function remains unclear, it has been found that Aeropyrum pernix NusA strongly binds to a certain CU-rich sequence near a termination signal. Archaeal NusA may have retained some functions of bacterial NusA, including ssRNA-binding ability. This model corresponds to the first KH domain of NusA found mainly in archaea.


Pssm-ID: 411787 [Multi-domain]  Cd Length: 69  Bit Score: 75.35  E-value: 3.91e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1491308750   1 MNIFVNITKVSPKDCIIDRKMDRIIFVVKRGSIGTAIGKQGINVKKLKSALAKDIEIIE 59
Cdd:cd22530    11 ISLFESITGATARDCLIDDENNRVIFVVKKGEMGLAIGKGGSNVKRLEEILGKNIEVVE 69
KH-II_NusA_arch_rpt2 cd22531
second type II K-homology (KH) RNA-binding domain found in archaeal probable transcription ...
 64-130 7.37e-13

second type II K-homology (KH) RNA-binding domain found in archaeal probable transcription termination protein NusA and similar proteins; NusA, also called N utilization substance protein A, is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. It participates in both transcription termination and antitermination. NusA homologs consisting of only the two type II K-homology (KH) domains are widely conserved in archaea. Although their function remains unclear, it has been found that Aeropyrum pernix NusA strongly binds to a certain CU-rich sequence near a termination signal. Archaeal NusA may have retained some functions of bacterial NusA, including ssRNA-binding ability. This model corresponds to the second KH domain of NusA mainly found in archaea.


Pssm-ID: 411788 [Multi-domain]  Cd Length: 67  Bit Score: 59.18  E-value: 7.37e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1491308750  64 PEVFIKNALVPATVEKVVVVRRKNKPDlAFVTIKQGQRGLAIGKDGRNIERARLLAKRHFDIENVIL 130
Cdd:cd22531     1 PEEFIKNIFAPAKVQNVKVKEKNGKKV-AIVEVPPKDKGIAIGKNGKNIERAKLLAKRHFDIDDVVI 66
KH_2 pfam07650
KH domain;
3-69 2.25e-09

KH domain;


Pssm-ID: 429574 [Multi-domain]  Cd Length: 78  Bit Score: 50.63  E-value: 2.25e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1491308750   3 IFVNITKVSPKDCIIDRKMDRIIFVVKRGSIGTAIGKQGINVKKLKSALAKDIEIIEDddsPEVFIK 69
Cdd:pfam07650   6 LAVELKFAGVSKVEIERTPNAVIVVIRASQPGIVIGKGGSRIKKIGKELRKDIEKLLG---KKVYLN 69
NusA COG0195
Transcription antitermination factor NusA, contains S1 and KH domains [Transcription];
55-120 1.07e-03

Transcription antitermination factor NusA, contains S1 and KH domains [Transcription];


Pssm-ID: 439965 [Multi-domain]  Cd Length: 353  Bit Score: 37.54  E-value: 1.07e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1491308750  55 IEIIEDDDSPEVFIKNALVPATVEKVVVVRRKNKpdlAFVTIKQGQRGLAIGKDGRNierARLLAK 120
Cdd:COG0195   273 IDIILWSEDPAQFIANALSPAKVSSVEVDEEEKS---ADVVVPDDQLSLAIGKGGQN---VRLAAK 332
KH_5 pfam13184
NusA-like KH domain;
22-75 1.37e-03

NusA-like KH domain;


Pssm-ID: 433018 [Multi-domain]  Cd Length: 69  Bit Score: 34.90  E-value: 1.37e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308750  22 DRIIFVVKRGS-----IGTAIGKQGINVKKLKSALA-KDIEIIEDDDSPEVFIKNALVPA 75
Cdd:pfam13184   3 NRAKIAVYSRDeridpVGACVGKKGSRIQAISRELNgEKIDIVEYSEDLRTFIKNALSPA 62
KH-II_NusA_rpt2 cd22529
second type II K-homology (KH) RNA-binding domain found in transcription termination ...
 64-126 8.02e-03

second type II K-homology (KH) RNA-binding domain found in transcription termination/antitermination protein NusA and similar proteins; NusA, also called N utilization substance protein A or transcription termination/antitermination L factor, is an essential multifunctional transcription elongation factor that participates in both transcription termination and antitermination. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNA polymerase pausing provides a mechanism for synchronizing transcription and translation. In prokaryotes, the N-terminal RNA polymerase-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, the S1 and two K-homology, KH1 and KH2. The K-homology (KH) domains of NusA belong to the type II KH RNA-binding domain superfamily. This model corresponds to the second KH domain of NusA and similar proteins.


Pssm-ID: 411786 [Multi-domain]  Cd Length: 61  Bit Score: 32.89  E-value: 8.02e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1491308750  64 PEVFIKNALVPATVEKVVVVRRKNKpdlAFVTIKQGQRGLAIGKDGRNIERARLLAKRHFDIE 126
Cdd:cd22529     2 PAEFVANALSPAKVISVEIDEDDKK---ARVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIK 61
nusA PRK09202
transcription elongation factor NusA; Validated
 33-120 8.49e-03

transcription elongation factor NusA; Validated


Pssm-ID: 236410 [Multi-domain]  Cd Length: 470  Bit Score: 34.85  E-value: 8.49e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308750  33 IGTAIGKQGINVKKLKSALAKD-IEIIEDDDSPEVFIKNALVPATVEKVVVVRRKNKpdlAFVTIKQGQRGLAIGKDGRN 111
Cdd:PRK09202  247 VGACVGMRGSRIQAISNELGGEkIDIILWSDDPAQFIINALSPAEVSSVVVDEDEHS---ADVVVPDDQLSLAIGKNGQN 323


                  ....*....
gi 1491308750 112 IeraRLLAK 120
Cdd:PRK09202  324 V---RLASK 329
 
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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