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Conserved domains on  [gi|2620321557|ref|WP_318655760|]
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transcription termination/antitermination protein NusG [Pseudoclavibacter caeni]

Protein Classification

transcription termination/antitermination protein NusG( domain architecture ID 1007718)

transcription termination/antitermination protein NusG (N-Utilization Substance G) is involved in transcription elongation and termination in bacteria

CATH:  2.30.30.30|3.30.70.940
Gene Ontology:  GO:0006353|GO:0032784|GO:0031564|GO:0006354
SCOP:  4002609

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
NusG COG0250
Transcription termination/antitermination protein NusG [Transcription];
79-278 1.46e-59

Transcription termination/antitermination protein NusG [Transcription];


:

Pssm-ID: 440020 [Multi-domain]  Cd Length: 171  Bit Score: 186.95  E-value: 1.46e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2620321557  79 PGSWYVIHTYAGYEKSVRNSILKRRETqdggddvLEVQVPVETVREVRNGQYKLVKRVRIPGYVLVRMFLNEDSWELVRR 158
Cdd:COG0250     4 EKRWYVVHTYSGYEKKVKENLERRIEG-------IEVFVPTEEVVEIKNGKKKTVERPLFPGYVFVRMDLTDESWYLVRN 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2620321557 159 TPGVTGFVGNAHDPLPLRRKEVFDMLKTTvlqaaqseaekqaqaaagatprggakKAQARPVPVDVDFEIGETITIKEGS 238
Cdd:COG0250    77 TPGVTGFVGFGGKPAPLPDEEVERILARL--------------------------EEGEEKPRPKVDFEVGDRVRITDGP 130

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2620321557 239 FAGLPGTISEINTTSGKLTVLVSLFERETPVELSFDQVTK 278
Cdd:COG0250   131 FAGFEGTVEEVDPEKGRVKVLVSIFGRETPVELDFSQVEK 170
 
Name Accession Description Interval E-value
NusG COG0250
Transcription termination/antitermination protein NusG [Transcription];
79-278 1.46e-59

Transcription termination/antitermination protein NusG [Transcription];


Pssm-ID: 440020 [Multi-domain]  Cd Length: 171  Bit Score: 186.95  E-value: 1.46e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2620321557  79 PGSWYVIHTYAGYEKSVRNSILKRRETqdggddvLEVQVPVETVREVRNGQYKLVKRVRIPGYVLVRMFLNEDSWELVRR 158
Cdd:COG0250     4 EKRWYVVHTYSGYEKKVKENLERRIEG-------IEVFVPTEEVVEIKNGKKKTVERPLFPGYVFVRMDLTDESWYLVRN 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2620321557 159 TPGVTGFVGNAHDPLPLRRKEVFDMLKTTvlqaaqseaekqaqaaagatprggakKAQARPVPVDVDFEIGETITIKEGS 238
Cdd:COG0250    77 TPGVTGFVGFGGKPAPLPDEEVERILARL--------------------------EEGEEKPRPKVDFEVGDRVRITDGP 130

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2620321557 239 FAGLPGTISEINTTSGKLTVLVSLFERETPVELSFDQVTK 278
Cdd:COG0250   131 FAGFEGTVEEVDPEKGRVKVLVSIFGRETPVELDFSQVEK 170
nusG TIGR00922
transcription termination/antitermination factor NusG; NusG proteins are transcription factors ...
 82-278 2.29e-54

transcription termination/antitermination factor NusG; NusG proteins are transcription factors which are aparrently universal in prokaryotes (archaea and eukaryotes have homologs that may have related functions). The essential components of these factors include an N-terminal RNP-like (ribonucleoprotein) domain and a C-terminal KOW motif (pfam00467) believed to be a nucleic acid binding domain. In E. coli, NusA has been shown to interact with RNA polymerase and termination factor Rho. This model covers a wide variety of bacterial species but excludes mycoplasmas which are covered by a separate model (TIGR01956).The function of all of these NusG proteins is likely to be the same at the level of interaction with RNA and other protein factors to affect termination; however different species may utilize NusG towards different processes and in combination with different suites of affector proteins.In E. coli, NusG promotes rho-dependent termination. It is an essential gene. In Streptomyces virginiae and related species, an additional N-terminal sequence is also present and is suggested to play a role in butyrolactone-mediated autoregulation. In Thermotoga maritima, NusG has a long insert, fails to substitute for E. coli NusG (with or without the long insert), is a large 0.7 % of total cellular protein, and has a general, sequence non-specific DNA and RNA binding activity that blocks ethidium staining, yet permits transcription.Archaeal proteins once termed NusG share the KOW domain but are actually a ribosomal protein corresponding to L24p in bacterial and L26e in eukaryotes (TIGR00405). [Transcription, Transcription factors]


Pssm-ID: 273341 [Multi-domain]  Cd Length: 172  Bit Score: 173.64  E-value: 2.29e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2620321557  82 WYVIHTYAGYEKSVRNSILKRRETQDGGDDVLEVQVPVETVREVRNGQYKLVKRVRIPGYVLVRMFLNEDSWELVRRTPG 161
Cdd:TIGR00922   1 WYVVQTYSGYEKKVKQNLEELIELLGMGDYIFEVIVPTEEVVEIKKGKKKVVERKIFPGYVLVKMDLTDVSWHLVKNTPG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2620321557 162 VTGFVGNAHDPLPLRRKEVFDmlktTVLQAAQseaekqaqaaagatprggakKAQARPVPvDVDFEIGETITIKEGSFAG 241
Cdd:TIGR00922  81 VTGFVGSGGKPKALSEDEEVK----NILNALE--------------------EGKDKPKP-KIDFEVGEQVRVNDGPFAN 135

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 2620321557 242 LPGTISEINTTSGKLTVLVSLFERETPVELSFDQVTK 278
Cdd:TIGR00922 136 FTGTVEEVDYEKSKLKVSVSIFGRETPVELEFSQVEK 172
NGN_Bact_1 cd09891
Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; The ...
 82-184 3.33e-43

Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; The N-Utilization Substance G (NusG) protein is involved in transcription elongation and termination in bacteria. NusG is essential in Escherichia coli and associates with RNA polymerase elongation and Rho-termination. Homologs of the NusG gene exist in all bacteria. The NusG N-terminal domain (NGN) is similar in all NusG homologs, but its C-terminal domain and the linker that separates these two domains are different. The domain organization of NusG suggests that the common properties of NusG and its homologs are due to their similar NGN domains.


Pssm-ID: 193580 [Multi-domain]  Cd Length: 107  Bit Score: 143.00  E-value: 3.33e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2620321557  82 WYVIHTYAGYEKSVRNSILKRRETQDGGDDVLEVQVPVETVREVRNGQYKLVKRVRIPGYVLVRMFLNEDSWELVRRTPG 161
Cdd:cd09891     2 WYVVHTYSGYENKVKENLEKRIESEGLEDYIGEVLVPTEEVVEVKNGKKKVKERKLFPGYVLVEMDMNDDTWHLVRNTPG 81

                          90       100
                  ....*....|....*....|...
gi 2620321557 162 VTGFVGNAHDPLPLRRKEVFDML 184
Cdd:cd09891    82 VTGFVGSGGKPVPLSEEEVERIL 104
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
 81-185 4.95e-32

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: 114.01  E-value: 4.95e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2620321557   81 SWYVIHTYAGYEKSVRNSILKRRETQDGGDDVLEVQVPVETVREVRNGQYKLVKRVRIPGYVLVRMFLNEDSWELVRRTP 160
Cdd:smart00738   1 NWYAVRTTSGQEKRVAENLERKAEALGLEDKIVSILVPTEEVKEIRRGKKKVVERKLFPGYIFVEADLEDEVWTAIRGTP 80

                           90       100
                   ....*....|....*....|....*
gi 2620321557  161 GVTGFVGNAHDPLPLRRKEVFDMLK 185
Cdd:smart00738  81 GVRGFVGGGGKPTPVPDDEIEKILK 105
NusG pfam02357
Transcription termination factor nusG;
82-184 9.03e-30

Transcription termination factor nusG;


Pssm-ID: 426736 [Multi-domain]  Cd Length: 96  Bit Score: 108.08  E-value: 9.03e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2620321557  82 WYVIHTYAGYEKSVRNSiLKRREtqdggddvLEVQVPVETVREVRNGQYKLVKRVRIPGYVLVRMFLNEDSWELVRRTPG 161
Cdd:pfam02357   3 WYVLQTYSGKEKKVKEN-LERQG--------IEVFLPTEEVVEIRNGKKKVVERPLFPGYVFVRMDMTDETWHLVRSTPG 73

                          90       100
                  ....*....|....*....|...
gi 2620321557 162 VTGFVGNAHDPLPLRRKEVFDML 184
Cdd:pfam02357  74 VTGFVGGSGKPTPIPDEEVERIL 96
 
Name Accession Description Interval E-value
NusG COG0250
Transcription termination/antitermination protein NusG [Transcription];
79-278 1.46e-59

Transcription termination/antitermination protein NusG [Transcription];


Pssm-ID: 440020 [Multi-domain]  Cd Length: 171  Bit Score: 186.95  E-value: 1.46e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2620321557  79 PGSWYVIHTYAGYEKSVRNSILKRRETqdggddvLEVQVPVETVREVRNGQYKLVKRVRIPGYVLVRMFLNEDSWELVRR 158
Cdd:COG0250     4 EKRWYVVHTYSGYEKKVKENLERRIEG-------IEVFVPTEEVVEIKNGKKKTVERPLFPGYVFVRMDLTDESWYLVRN 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2620321557 159 TPGVTGFVGNAHDPLPLRRKEVFDMLKTTvlqaaqseaekqaqaaagatprggakKAQARPVPVDVDFEIGETITIKEGS 238
Cdd:COG0250    77 TPGVTGFVGFGGKPAPLPDEEVERILARL--------------------------EEGEEKPRPKVDFEVGDRVRITDGP 130

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2620321557 239 FAGLPGTISEINTTSGKLTVLVSLFERETPVELSFDQVTK 278
Cdd:COG0250   131 FAGFEGTVEEVDPEKGRVKVLVSIFGRETPVELDFSQVEK 170
nusG TIGR00922
transcription termination/antitermination factor NusG; NusG proteins are transcription factors ...
 82-278 2.29e-54

transcription termination/antitermination factor NusG; NusG proteins are transcription factors which are aparrently universal in prokaryotes (archaea and eukaryotes have homologs that may have related functions). The essential components of these factors include an N-terminal RNP-like (ribonucleoprotein) domain and a C-terminal KOW motif (pfam00467) believed to be a nucleic acid binding domain. In E. coli, NusA has been shown to interact with RNA polymerase and termination factor Rho. This model covers a wide variety of bacterial species but excludes mycoplasmas which are covered by a separate model (TIGR01956).The function of all of these NusG proteins is likely to be the same at the level of interaction with RNA and other protein factors to affect termination; however different species may utilize NusG towards different processes and in combination with different suites of affector proteins.In E. coli, NusG promotes rho-dependent termination. It is an essential gene. In Streptomyces virginiae and related species, an additional N-terminal sequence is also present and is suggested to play a role in butyrolactone-mediated autoregulation. In Thermotoga maritima, NusG has a long insert, fails to substitute for E. coli NusG (with or without the long insert), is a large 0.7 % of total cellular protein, and has a general, sequence non-specific DNA and RNA binding activity that blocks ethidium staining, yet permits transcription.Archaeal proteins once termed NusG share the KOW domain but are actually a ribosomal protein corresponding to L24p in bacterial and L26e in eukaryotes (TIGR00405). [Transcription, Transcription factors]


Pssm-ID: 273341 [Multi-domain]  Cd Length: 172  Bit Score: 173.64  E-value: 2.29e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2620321557  82 WYVIHTYAGYEKSVRNSILKRRETQDGGDDVLEVQVPVETVREVRNGQYKLVKRVRIPGYVLVRMFLNEDSWELVRRTPG 161
Cdd:TIGR00922   1 WYVVQTYSGYEKKVKQNLEELIELLGMGDYIFEVIVPTEEVVEIKKGKKKVVERKIFPGYVLVKMDLTDVSWHLVKNTPG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2620321557 162 VTGFVGNAHDPLPLRRKEVFDmlktTVLQAAQseaekqaqaaagatprggakKAQARPVPvDVDFEIGETITIKEGSFAG 241
Cdd:TIGR00922  81 VTGFVGSGGKPKALSEDEEVK----NILNALE--------------------EGKDKPKP-KIDFEVGEQVRVNDGPFAN 135

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 2620321557 242 LPGTISEINTTSGKLTVLVSLFERETPVELSFDQVTK 278
Cdd:TIGR00922 136 FTGTVEEVDYEKSKLKVSVSIFGRETPVELEFSQVEK 172
NGN_Bact_1 cd09891
Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; The ...
 82-184 3.33e-43

Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; The N-Utilization Substance G (NusG) protein is involved in transcription elongation and termination in bacteria. NusG is essential in Escherichia coli and associates with RNA polymerase elongation and Rho-termination. Homologs of the NusG gene exist in all bacteria. The NusG N-terminal domain (NGN) is similar in all NusG homologs, but its C-terminal domain and the linker that separates these two domains are different. The domain organization of NusG suggests that the common properties of NusG and its homologs are due to their similar NGN domains.


Pssm-ID: 193580 [Multi-domain]  Cd Length: 107  Bit Score: 143.00  E-value: 3.33e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2620321557  82 WYVIHTYAGYEKSVRNSILKRRETQDGGDDVLEVQVPVETVREVRNGQYKLVKRVRIPGYVLVRMFLNEDSWELVRRTPG 161
Cdd:cd09891     2 WYVVHTYSGYENKVKENLEKRIESEGLEDYIGEVLVPTEEVVEVKNGKKKVKERKLFPGYVLVEMDMNDDTWHLVRNTPG 81

                          90       100
                  ....*....|....*....|...
gi 2620321557 162 VTGFVGNAHDPLPLRRKEVFDML 184
Cdd:cd09891    82 VTGFVGSGGKPVPLSEEEVERIL 104
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
 81-185 4.95e-32

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: 114.01  E-value: 4.95e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2620321557   81 SWYVIHTYAGYEKSVRNSILKRRETQDGGDDVLEVQVPVETVREVRNGQYKLVKRVRIPGYVLVRMFLNEDSWELVRRTP 160
Cdd:smart00738   1 NWYAVRTTSGQEKRVAENLERKAEALGLEDKIVSILVPTEEVKEIRRGKKKVVERKLFPGYIFVEADLEDEVWTAIRGTP 80

                           90       100
                   ....*....|....*....|....*
gi 2620321557  161 GVTGFVGNAHDPLPLRRKEVFDMLK 185
Cdd:smart00738  81 GVRGFVGGGGKPTPVPDDEIEKILK 105
NusG pfam02357
Transcription termination factor nusG;
82-184 9.03e-30

Transcription termination factor nusG;


Pssm-ID: 426736 [Multi-domain]  Cd Length: 96  Bit Score: 108.08  E-value: 9.03e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2620321557  82 WYVIHTYAGYEKSVRNSiLKRREtqdggddvLEVQVPVETVREVRNGQYKLVKRVRIPGYVLVRMFLNEDSWELVRRTPG 161
Cdd:pfam02357   3 WYVLQTYSGKEKKVKEN-LERQG--------IEVFLPTEEVVEIRNGKKKVVERPLFPGYVFVRMDMTDETWHLVRSTPG 73

                          90       100
                  ....*....|....*....|...
gi 2620321557 162 VTGFVGNAHDPLPLRRKEVFDML 184
Cdd:pfam02357  74 VTGFVGGSGKPTPIPDEEVERIL 96
NGN cd08000
N-Utilization Substance G (NusG) N-terminal (NGN) domain Superfamily; The N-Utilization ...
 81-184 1.42e-21

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: 86.60  E-value: 1.42e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2620321557  81 SWYVIHTYAGYEKSVRNSILKRREtqdggDDVLEVQVPVETVREVRNGQYKLVKRVRIPGYVLVRMFLNEDSWELVRRTP 160
Cdd:cd08000     1 NWYVLFVKTGREEKVEKLLEKRFE-----ANDIEAFVPKKEVPERKRGKIEEVIKPLFPGYVFVETDLSPELYELIREVP 75

                          90       100
                  ....*....|....*....|....
gi 2620321557 161 GVTGFVGNAHDPLPLRRKEVFDML 184
Cdd:cd08000    76 GVIGILGNGEEPSPVSDEEIEMIL 99
KOW_NusG cd06091
NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; KOW_NusG motif ...
 223-278 1.20e-19

NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; KOW_NusG motif is one of the two domains of N-Utilization Substance G (NusG) a transcription elongation and Rho-termination factor in bacteria and archaea. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. The eukaryotic ortholog of NusG is Spt5 with multiple KOW motifs at its C-terminus.


Pssm-ID: 240515 [Multi-domain]  Cd Length: 56  Bit Score: 80.19  E-value: 1.20e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2620321557 223 DVDFEIGETITIKEGSFAGLPGTISEINTTSGKLTVLVSLFERETPVELSFDQVTK 278
Cdd:cd06091     1 EVDFEVGDTVRIISGPFAGFEGKVEEIDEEKGKVKVLVEMFGRETPVELDFDQVEK 56
NusG_myco TIGR01956
NusG family protein; This model represents a family of Mycoplasma proteins orthologous to the ...
 82-278 9.75e-13

NusG family protein; This model represents a family of Mycoplasma proteins orthologous to the bacterial transcription termination/antitermination factor NusG. These sequences from Mycoplasma are notably diverged (long branches in a Neighbor-joining phylogenetic tree) from the bacterial species. And although NusA and ribosomal protein S10 (NusE) appear to be present, NusB may be absent in Mycoplasmas calling into question whether these species have a functional Nus system including this family as a member.


Pssm-ID: 273895 [Multi-domain]  Cd Length: 258  Bit Score: 66.52  E-value: 9.75e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2620321557  82 WYVIHTYAGYEKSVRNSILKRRETQDGGDDVLEVQV----------------------------PVETVREVRNGQYKLV 133
Cdd:TIGR01956   2 WYIATTINGNEDEVIENIKAKVRALGLENYISDFKIlkereieekvfepkngqaprsmkntattKWETLDETKYKKTKIS 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2620321557 134 KRVRIPGYVLVRMFLNEDSWELVRRTPGVTGFVGNAHD---PLPL-RRKEVFDMLKTTVLQAAQ---------------- 193
Cdd:TIGR01956  82 EKNKYNGYIYIKMIMTEDAWFLIRNTENVTGLVGSSGKgakPIPIsADADKLKMLKGISENTKKrvlvtntaivemeenk 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2620321557 194 -SEAEKQAQAAAGATPRGGAKKAQARPVPVDV-----------DFEIGETITIKEGSFAGLPGTISEINTTSGKLTVLVS 261
Cdd:TIGR01956 162 fDEKCQYILKHKQVKPEAIAQVSESGEIIDEIveefqlvdnlsKFRVGNFVKIVDGPFKGIVGKIKKIDQEKKKAIVEVE 241

                         250
                  ....*....|....*..
gi 2620321557 262 LFERETPVELSFDQVTK 278
Cdd:TIGR01956 242 ILGKSVDVDLNFKHLKL 258
NGN_Bact_2 cd09889
Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 2; The ...
 81-180 1.01e-10

Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 2; The N-Utilization Substance G (NusG) protein is involved in transcription elongation and termination. NusG is essential in Escherichia coli and associates with RNA polymerase elongation and Rho-termination. 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 domain (NGN) is quite similar in all NusG orthologs, but its C-terminal domain and the linker that separates 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: 193578 [Multi-domain]  Cd Length: 100  Bit Score: 57.33  E-value: 1.01e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2620321557  81 SWYVIHTYAGYEKSVRNSIlkrrETQDGGDDVLEVQVPVETVREVRNGQYKLVKRVRIPGYVLVRMFLNEDSWELVRRTP 160
Cdd:cd09889     1 MWYVVQVRTGREKAVLELL----EKLVGPDVLQECFIPQYERKKRSQGVWRERKYTLFPGYVFVVTDDIDELYYELKRVP 76

                          90       100
                  ....*....|....*....|
gi 2620321557 161 GVTGFVGNAHDPLPLRRKEV 180
Cdd:cd09889    77 GFTRLLGNDGSFFPLTPEEA 96
NGN_SP_TaA cd09893
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), TaA; ...
 81-180 1.30e-09

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: 54.24  E-value: 1.30e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2620321557  81 SWYVIHTYAGYEKSVRNSILKRRetqdggddvLEVQVPVETVREVRNGQYKLVKRVRIPGYVLVRMFLNEDSWELVrRTP 160
Cdd:cd09893     1 SWYALYTRSRHEKKVADRLAKKG---------IESFLPLYEVLSRWKDRKKKIKVPLFPGYLFVRFQLDPERLRIL-KTP 70

                          90       100
                  ....*....|....*....|
gi 2620321557 161 GVTGFVGNAHDPLPLRRKEV 180
Cdd:cd09893    71 GVVRIVGNSGGPIPIPDEEI 90
RfaH TIGR01955
transcription elongation factor/antiterminator RfaH; This model represents the transcription ...
 82-277 1.52e-09

transcription elongation factor/antiterminator RfaH; This model represents the transcription elongation factor/antiterminator, RfaH. This protein is most closely related to the transcriptional termination/antitermination protein NusG (TIGR00922) and contains the KOW motif (pfam00467). This protein appears to be limited to the gamma proteobacteria. In E. coli, this gene appears to control the expression of haemolysin, sex factor and lipopolysaccharide genes. [Transcription, Transcription factors]


Pssm-ID: 131010 [Multi-domain]  Cd Length: 159  Bit Score: 55.55  E-value: 1.52e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2620321557  82 WYVIHTYAGYEKSVRNSIlkrrETQDggddvLEVQVPVETVREVRNGQYKLVKRVRIPGYVLVRMFLNEDSWELVRRTPG 161
Cdd:TIGR01955   1 WYLLYCKPRQEQRAQEHL----ERQA-----VECYLPMITVEKIVRGKRQAVSEPLFPNYLFIEFDPEVDSWTTIRSTRG 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2620321557 162 VTGFVGNAHDPLPLrRKEVFDMLKTTVLQAAQSeaekqaqaaagatprggakkaqarpvPVDVDFEIGETITIKEGSFAG 241
Cdd:TIGR01955  72 VSRFVRFGGHPAPV-PDDLIHQLRQYEPKDSVP--------------------------PATTLPYKGDKVRITDGAFAG 124

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 2620321557 242 LPGTISEINTTSgKLTVLVSLFERETPVELSFDQVT 277
Cdd:TIGR01955 125 FEAIFLEPDGEK-RSMLLLNMIGKQIKVSVPNTSVE 159
NGN_SP cd09886
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP); The ...
 81-185 4.10e-09

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: 52.76  E-value: 4.10e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2620321557  81 SWYVIHTYAGYEKSVRNSILKRRetqdggddvLEVQVPVETVREVRNGQyKLVKRVRI-PGYVLVRM-FLNEDSWELVRR 158
Cdd:cd09886     1 SWYALRTNPGCEQRAEEALEARG---------VEAFLPMLTEERKRRRK-KFDVERPLfPGYVFARLdRSKGQDTSTIRA 70

                          90       100
                  ....*....|....*....|....*..
gi 2620321557 159 TPGVTGFVGNAHDPLPLRRKEVFDMLK 185
Cdd:cd09886    71 CDGVLGVVGFDGRPAPVPEQEMRDLRK 97
NGN_SP_RfaH cd09892
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), RfaH; ...
 81-176 1.18e-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: 48.71  E-value: 1.18e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2620321557  81 SWYVIHTYAGYEK-SVRNsiLKRretQDggddvLEVQVPVETVREVRNGQYKLVKRVRIPGYVLVRMFLNEDSWELVRRT 159
Cdd:cd09892     1 AWYLLYTKPRQEErAAEN--LER---QG-----FEVFLPMIRVEKRRRGKRTVVTEPLFPGYLFVRLDPEVQNWRPIRST 70

                          90
                  ....*....|....*..
gi 2620321557 160 PGVTGFVGNAHDPLPLR 176
Cdd:cd09892    71 RGVSRLVRFGGEPAPVP 87
NGN_plant cd09890
Plant N-Utilization Substance G (NusG) N-terminal (NGN) domain; The N-Utilization Substance G ...
 82-167 3.39e-07

Plant N-Utilization Substance G (NusG) N-terminal (NGN) domain; The N-Utilization Substance G (NusG) protein and its eukaryotic homolog, Spt5, are involved in transcription elongation and termination. NusG contains a 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 comprising an acidic N-terminus, an NGN domain, and multiple KOW motifs at its C-terminus. Spt5 forms an Spt4-Spt5 complex that is an essential RNA polymerase II elongation factor. The bacterial infected plants contain bacterial DNA, such as NGN sequences, that can be used to clone the DNA of uncultured organisms.


Pssm-ID: 193579  Cd Length: 113  Bit Score: 47.73  E-value: 3.39e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2620321557  82 WYVIHTYAGYEKSVRnSILKRRETQDGGDDVLEVQVP-VETVREVRNGQYKlVKRVRI-PGYVLVRMFLNEDSWELVRRT 159
Cdd:cd09890     2 WYMLRVPAGRENQAA-EALERALATEFPDREFEVWVPsIPVDRKLKNGSIS-VKEKPLfPGYVLLRCVLNKEVYDFIRDN 79


                  ....*...
gi 2620321557 160 PGVTGFVG 167
Cdd:cd09890    80 DSVYGFVG 87
NGN_SP_UpxY cd09895
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), UpxY; ...
 82-166 2.44e-05

N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), UpxY; The N-Utilization Substance G (NusG) proteins are involved in transcription elongation and termination. NusG is essential in Escherichia coli and is associated with RNA polymerase elongation and Rho-termination. 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 (lipopolysaccharide) biosynthesis genes. NusG SP family members are operon-specific transcriptional antitermination factors. UpxY proteins, UpxY proteins, where the x is replaced by the letter designation of the specific polysaccharide (UpaY to UphY), are a family of NusG SP factors that act specifically in transcriptional antitermination of operons from which they are encoded. UpxYs are necessary and specific for transcription regulation of the polysaccharide biosynthesis operon. Orthologs of the NusG gene exist in all bacteria, but their functions and requirements are different. The NusG N-terminal (NGN) domain 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: 193584 [Multi-domain]  Cd Length: 95  Bit Score: 42.18  E-value: 2.44e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2620321557  82 WYVIHTYAGYEKSVrnsilKRRETQDGgddvLEVQVPVETVREVRNGQYKLVKRVRIPGYVLVRMFLNEDSweLVRRTPG 161
Cdd:cd09895     2 WYALYTFPRREKKV-----AEYLEKKG----IECFLPMQYEVRQWSGRKKRVEVPLFPNLVFVHITREELD--EVLETPG 70


                  ....*
gi 2620321557 162 VTGFV 166
Cdd:cd09895    71 VVRFV 75
NGN_SP_AnfA1 cd09894
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), AnFA1; ...
 82-176 5.85e-04

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: 38.42  E-value: 5.85e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2620321557  82 WYVIHTYAGYEKSVRNSILkrretqdgGDDVlEVQVPVET--VREVRNGQYKLVKRVRIPGYVLVRMFLNEDSWELVRRT 159
Cdd:cd09894     3 WYLLRCKSGKIQSVIFSLE--------RLGV-EVFCPMIRtrRKRTDCKSYREKIEPLFPGYLFVRFDPEVVHTSKITLA 73

                          90
                  ....*....|....*..
gi 2620321557 160 PGVTGFVGNAHDPLPLR 176
Cdd:cd09894    74 SGVSGFVRFGGEPCPVP 90
 
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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