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Conserved domains on  [gi|490227306|ref|WP_004125657|]
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MULTISPECIES: transcription termination factor NusA [Klebsiella]

Protein Classification

transcription termination/antitermination protein NusA( domain architecture ID 11483611)

transcription termination/antitermination protein NusA binds directly to the core enzyme of the DNA-dependent RNA polymerase and to nascent RNA, and participates in both transcription termination and antitermination

CATH:  2.40.50.140|3.30.1480.10
Gene Symbol:  nusA
Gene Ontology:  GO:0006353|GO:0003723|GO:0031564
PubMed:  11430821|20600118|20696893|9139668
SCOP:  4001909|4001200|4003421

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
nusA PRK09202
transcription elongation factor NusA; Validated
 1-476 0e+00

transcription elongation factor NusA; Validated


:

Pssm-ID: 236410 [Multi-domain]  Cd Length: 470  Bit Score: 698.54  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490227306   1 MNKEILAVVEAVSNEKALPREKIFEALESALATATKKKYEQEIDVRVEIDRKSGDFDTFRRWLVVEEVTQPTREITLEAA 80
Cdd:PRK09202   1 MNKELLEAIEAVAREKGIDREVVIEALEEALATAYKKKYGPEANIRVEIDRKTGDIEVFRRWEVVEEVEDPTKEISLEEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490227306  81 RYEDESMNPGDYVEDQIESVTFDRITTQTAKQVIVQKVREAERAMVVDQFREHEGEIITGVVKKVNRDNITLDLGNnAEA 160
Cdd:PRK09202  81 RKIDPDAEVGDYIEEEIESVDFGRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIITGVVKRVERGNIIVDLGR-AEA 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490227306 161 VILREDMLPRENFRPGDRIRGVLYAVRPEARGAQLFVTRSKPEMLVELFRIEVPEIGEEVLEIKAAARDPGSRAKIAVKT 240
Cdd:PRK09202 160 ILPRKEQIPRENFRPGDRVRAYVYEVRKEARGPQIILSRTHPEFLKKLFEQEVPEIADGLIEIKAIARDPGSRAKIAVKS 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490227306 241 NDKRIDPVGACVGMRGARVQAVSTELGGERIDIVLWDDNPAQFVINAMAPADVASIVVDEDKHTMDIAVEAGNLAQAIGR 320
Cdd:PRK09202 240 NDPRIDPVGACVGMRGSRIQAISNELGGEKIDIILWSDDPAQFIINALSPAEVSSVVVDEDEHSADVVVPDDQLSLAIGK 319

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490227306 321 NGQNVRLASQLSGWELNVMTVDDLQAKHQAEAHAAIDTFTKYLDIDEDFATLLVEEGFATLEELAYVPMKELLEIDGLDE 400
Cdd:PRK09202 320 NGQNVRLASKLTGWKIDIMTEEEASEKRQAEFDAILDLFMEALDIDEEIAQLLVEEGFSSLEELAYVPVEELLEIEGFDE 399

                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490227306 401 ATVEALRERAKNALTTLALAKEESLgdskpADDLLNLEGMDRALAFTLAARGVCTLEDLAEQGIDDLADIEGLTDE 476
Cdd:PRK09202 400 ETVEELRERAKEALETEALAQEEKL-----ADDLLSLEGLDRELAFKLAEKGIKTLEDLAEQAVDELIDIEGDEEK 470
 
Name Accession Description Interval E-value
nusA PRK09202
transcription elongation factor NusA; Validated
 1-476 0e+00

transcription elongation factor NusA; Validated


Pssm-ID: 236410 [Multi-domain]  Cd Length: 470  Bit Score: 698.54  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490227306   1 MNKEILAVVEAVSNEKALPREKIFEALESALATATKKKYEQEIDVRVEIDRKSGDFDTFRRWLVVEEVTQPTREITLEAA 80
Cdd:PRK09202   1 MNKELLEAIEAVAREKGIDREVVIEALEEALATAYKKKYGPEANIRVEIDRKTGDIEVFRRWEVVEEVEDPTKEISLEEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490227306  81 RYEDESMNPGDYVEDQIESVTFDRITTQTAKQVIVQKVREAERAMVVDQFREHEGEIITGVVKKVNRDNITLDLGNnAEA 160
Cdd:PRK09202  81 RKIDPDAEVGDYIEEEIESVDFGRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIITGVVKRVERGNIIVDLGR-AEA 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490227306 161 VILREDMLPRENFRPGDRIRGVLYAVRPEARGAQLFVTRSKPEMLVELFRIEVPEIGEEVLEIKAAARDPGSRAKIAVKT 240
Cdd:PRK09202 160 ILPRKEQIPRENFRPGDRVRAYVYEVRKEARGPQIILSRTHPEFLKKLFEQEVPEIADGLIEIKAIARDPGSRAKIAVKS 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490227306 241 NDKRIDPVGACVGMRGARVQAVSTELGGERIDIVLWDDNPAQFVINAMAPADVASIVVDEDKHTMDIAVEAGNLAQAIGR 320
Cdd:PRK09202 240 NDPRIDPVGACVGMRGSRIQAISNELGGEKIDIILWSDDPAQFIINALSPAEVSSVVVDEDEHSADVVVPDDQLSLAIGK 319

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490227306 321 NGQNVRLASQLSGWELNVMTVDDLQAKHQAEAHAAIDTFTKYLDIDEDFATLLVEEGFATLEELAYVPMKELLEIDGLDE 400
Cdd:PRK09202 320 NGQNVRLASKLTGWKIDIMTEEEASEKRQAEFDAILDLFMEALDIDEEIAQLLVEEGFSSLEELAYVPVEELLEIEGFDE 399

                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490227306 401 ATVEALRERAKNALTTLALAKEESLgdskpADDLLNLEGMDRALAFTLAARGVCTLEDLAEQGIDDLADIEGLTDE 476
Cdd:PRK09202 400 ETVEELRERAKEALETEALAQEEKL-----ADDLLSLEGLDRELAFKLAEKGIKTLEDLAEQAVDELIDIEGDEEK 470
NusA TIGR01953
transcription termination factor NusA; This model describes NusA, or N utilization substance ...
 4-343 8.16e-156

transcription termination factor NusA; This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids. [Transcription, Transcription factors]


Pssm-ID: 273893 [Multi-domain]  Cd Length: 341  Bit Score: 446.32  E-value: 8.16e-156
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490227306    4 EILAVVEAVSNEKALPREKIFEALESALATATKKKYEQEIDVRVEIDRKSGDFDTFRRWLVVEEVTQPTREITLEAARYE 83
Cdd:TIGR01953   1 EFLAAIEALAKEKGISIETVIEAIEEALEQAYKKTFGQDENVEVNIDRKTGDINVYRRKEVVEEVEDPSLEISLEDAREI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490227306   84 DESMNPGDYVEDQIESVTFDRITTQTAKQVIVQKVREAERAMVVDQFREHEGEIITGVVKKVNRDNITL-DLGNNaEAVI 162
Cdd:TIGR01953  81 DPDVQIGDEVKKEIPPENFGRIAAQTAKQVILQKIREAERERVYDEFSSKEGEIISGTVKRVNRRGNLFvELGKT-EGIL 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490227306  163 LREDMLPRENFRPGDRIRGVLYAVRPEARGAQLFVTRSKPEMLVELFRIEVPEIGEEVLEIKAAARDPGSRAKIAVKTND 242
Cdd:TIGR01953 160 PKKEQIPGEKFRIGDRIKAYVYEVRKTAKGPQIILSRTHPEFVKELLKLEVPEIADGIIEIKKIAREPGYRTKIAVESND 239

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490227306  243 KRIDPVGACVGMRGARVQAVSTELGGERIDIVLWDDNPAQFVINAMAPADVASI-VVDEDKHTMDIAVEAGNLAQAIGRN 321
Cdd:TIGR01953 240 ENIDPVGACVGPKGSRIQAISKELNGEKIDIIEYSDDPAEFIANALSPAKVISVeVLDEDKRSAEVVVPDDQLSLAIGKG 319

                         330       340
                  ....*....|....*....|..
gi 490227306  322 GQNVRLASQLSGWELNVMTVDD 343
Cdd:TIGR01953 320 GQNVRLASKLTGWNIDVKTESQ 341
NusA COG0195
Transcription antitermination factor NusA, contains S1 and KH domains [Transcription];
1-351 8.64e-149

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


Pssm-ID: 439965 [Multi-domain]  Cd Length: 353  Bit Score: 428.91  E-value: 8.64e-149
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490227306   1 MNKEILAVVEAVSNEKALPREKIFEALESALATATKKKYEQEIDVRVEIDRKSGDFDTFRRWLVVEEVTQPTREITLEAA 80
Cdd:COG0195    4 MLLELLEALEELEKEKGIDKEILIEALEAALKKAYKKNYGNEVVVRVIIDGDTGEIRVYVVKEVVEEVEDPREEILLEAA 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490227306  81 RYEDESMNPGDYVEDQIESVTFDRITTQTAKQVIVQKVREAERAMVVDQFREHEGEIITGVVKKVNRDNITLDLGNnAEA 160
Cdd:COG0195   84 KEDDPDEEGGDIIEEEVPPDFFGRIAAQAAKQVIQQKRREAEREIIYEEFKDRGGEIVGGVVQRVERGNVIVDLGK-VEA 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490227306 161 VILREDMLPRENFRPGDRIRGVLYAVRPEARGAQLFVTRSKPEMLVELFRIEVPEIGEEVLEIKAAARDPGSRAKIAVKT 240
Cdd:COG0195  163 ILPRREQIPGENYRVGDRIRAYVLEVRKETRGPQIILSRTHPEFLKRLFELEVPEIADGIVEIKAIAREPGSRAKIAVYS 242

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490227306 241 NDKRIDPVGACVGMRGARVQAVSTELGGERIDIVLWDDNPAQFVINAMAPADVASIVVDEDKHTMDIAVEAGNLAQAIGR 320
Cdd:COG0195  243 NDPRVDPVGACVGMRGSRVQAVVNELNGEKIDIILWSEDPAQFIANALSPAKVSSVEVDEEEKSADVVVPDDQLSLAIGK 322

                        330       340       350
                 ....*....|....*....|....*....|.
gi 490227306 321 NGQNVRLASQLSGWELNVMTVDDLQAKHQAE 351
Cdd:COG0195  323 GGQNVRLAAKLTGWKIDIKSESEAEEKREEE 353
NusA_N pfam08529
NusA N-terminal domain; This domain represents the RNA polymerase binding domain of NusA.
 5-123 9.20e-46

NusA N-terminal domain; This domain represents the RNA polymerase binding domain of NusA.


Pssm-ID: 462512 [Multi-domain]  Cd Length: 120  Bit Score: 155.68  E-value: 9.20e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490227306    5 ILAVVEAVSNEKALPREKIFEALESALATATKKKYEQEIDVRVEIDRKSGDFDTFRRWLVVEEVTQPTREITLEAARYED 84
Cdd:pfam08529   1 LLEALEELAKEKGIDKEVLIEAIEEALLKAYKKKYGADENVRVEIDRETGDIEVYRRKEVVEEVEDPDTEISLEEAKKID 80

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 490227306   85 ESMNPGDYVEDQIESVTFDRITTQTAKQVIVQKVREAER 123
Cdd:pfam08529  81 PDAEVGDVVEEEVTPKDFGRIAAQTAKQVIIQKIREAER 119
KH-II_NusA_rpt1 cd02134
first type II K-homology (KH) RNA-binding domain found in transcription termination ...
 202-276 2.56e-38

first 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 (KH), KH1 and KH2. The KH domains of NusA belong to the type II KH RNA-binding domain superfamily. This model corresponds to the first KH domain of NusA and similar proteins.


Pssm-ID: 411779 [Multi-domain]  Cd Length: 76  Bit Score: 134.20  E-value: 2.56e-38
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 490227306 202 PEMLVELFRIEVPEIGEEVLEIKAAARDPGSRAKIAVKTNDKRIDPVGACVGMRGARVQAVSTELGGERIDIVLW 276
Cdd:cd02134    2 PEFLKRLFELEVPEIADGIVEIKAIAREPGSRTKVAVASNDPRVDPVGACVGVRGSRIQAIVEELGGEKIDIVLW 76
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
134-195 2.98e-07

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 47.60  E-value: 2.98e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 490227306   134 EGEIITGVVKKVNRDNITLDLGNNAEAVILREDM------LPRENFRPGDRIRGVLYAVRPEARGAQL 195
Cdd:smart00316   2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELsdkrvkDPEEVLKVGDEVKVKVLSVDEEKGRIIL 69
 
Name Accession Description Interval E-value
nusA PRK09202
transcription elongation factor NusA; Validated
 1-476 0e+00

transcription elongation factor NusA; Validated


Pssm-ID: 236410 [Multi-domain]  Cd Length: 470  Bit Score: 698.54  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490227306   1 MNKEILAVVEAVSNEKALPREKIFEALESALATATKKKYEQEIDVRVEIDRKSGDFDTFRRWLVVEEVTQPTREITLEAA 80
Cdd:PRK09202   1 MNKELLEAIEAVAREKGIDREVVIEALEEALATAYKKKYGPEANIRVEIDRKTGDIEVFRRWEVVEEVEDPTKEISLEEA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490227306  81 RYEDESMNPGDYVEDQIESVTFDRITTQTAKQVIVQKVREAERAMVVDQFREHEGEIITGVVKKVNRDNITLDLGNnAEA 160
Cdd:PRK09202  81 RKIDPDAEVGDYIEEEIESVDFGRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIITGVVKRVERGNIIVDLGR-AEA 159

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490227306 161 VILREDMLPRENFRPGDRIRGVLYAVRPEARGAQLFVTRSKPEMLVELFRIEVPEIGEEVLEIKAAARDPGSRAKIAVKT 240
Cdd:PRK09202 160 ILPRKEQIPRENFRPGDRVRAYVYEVRKEARGPQIILSRTHPEFLKKLFEQEVPEIADGLIEIKAIARDPGSRAKIAVKS 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490227306 241 NDKRIDPVGACVGMRGARVQAVSTELGGERIDIVLWDDNPAQFVINAMAPADVASIVVDEDKHTMDIAVEAGNLAQAIGR 320
Cdd:PRK09202 240 NDPRIDPVGACVGMRGSRIQAISNELGGEKIDIILWSDDPAQFIINALSPAEVSSVVVDEDEHSADVVVPDDQLSLAIGK 319

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490227306 321 NGQNVRLASQLSGWELNVMTVDDLQAKHQAEAHAAIDTFTKYLDIDEDFATLLVEEGFATLEELAYVPMKELLEIDGLDE 400
Cdd:PRK09202 320 NGQNVRLASKLTGWKIDIMTEEEASEKRQAEFDAILDLFMEALDIDEEIAQLLVEEGFSSLEELAYVPVEELLEIEGFDE 399

                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490227306 401 ATVEALRERAKNALTTLALAKEESLgdskpADDLLNLEGMDRALAFTLAARGVCTLEDLAEQGIDDLADIEGLTDE 476
Cdd:PRK09202 400 ETVEELRERAKEALETEALAQEEKL-----ADDLLSLEGLDRELAFKLAEKGIKTLEDLAEQAVDELIDIEGDEEK 470
NusA TIGR01953
transcription termination factor NusA; This model describes NusA, or N utilization substance ...
 4-343 8.16e-156

transcription termination factor NusA; This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids. [Transcription, Transcription factors]


Pssm-ID: 273893 [Multi-domain]  Cd Length: 341  Bit Score: 446.32  E-value: 8.16e-156
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490227306    4 EILAVVEAVSNEKALPREKIFEALESALATATKKKYEQEIDVRVEIDRKSGDFDTFRRWLVVEEVTQPTREITLEAARYE 83
Cdd:TIGR01953   1 EFLAAIEALAKEKGISIETVIEAIEEALEQAYKKTFGQDENVEVNIDRKTGDINVYRRKEVVEEVEDPSLEISLEDAREI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490227306   84 DESMNPGDYVEDQIESVTFDRITTQTAKQVIVQKVREAERAMVVDQFREHEGEIITGVVKKVNRDNITL-DLGNNaEAVI 162
Cdd:TIGR01953  81 DPDVQIGDEVKKEIPPENFGRIAAQTAKQVILQKIREAERERVYDEFSSKEGEIISGTVKRVNRRGNLFvELGKT-EGIL 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490227306  163 LREDMLPRENFRPGDRIRGVLYAVRPEARGAQLFVTRSKPEMLVELFRIEVPEIGEEVLEIKAAARDPGSRAKIAVKTND 242
Cdd:TIGR01953 160 PKKEQIPGEKFRIGDRIKAYVYEVRKTAKGPQIILSRTHPEFVKELLKLEVPEIADGIIEIKKIAREPGYRTKIAVESND 239

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490227306  243 KRIDPVGACVGMRGARVQAVSTELGGERIDIVLWDDNPAQFVINAMAPADVASI-VVDEDKHTMDIAVEAGNLAQAIGRN 321
Cdd:TIGR01953 240 ENIDPVGACVGPKGSRIQAISKELNGEKIDIIEYSDDPAEFIANALSPAKVISVeVLDEDKRSAEVVVPDDQLSLAIGKG 319

                         330       340
                  ....*....|....*....|..
gi 490227306  322 GQNVRLASQLSGWELNVMTVDD 343
Cdd:TIGR01953 320 GQNVRLASKLTGWNIDVKTESQ 341
NusA COG0195
Transcription antitermination factor NusA, contains S1 and KH domains [Transcription];
1-351 8.64e-149

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


Pssm-ID: 439965 [Multi-domain]  Cd Length: 353  Bit Score: 428.91  E-value: 8.64e-149
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490227306   1 MNKEILAVVEAVSNEKALPREKIFEALESALATATKKKYEQEIDVRVEIDRKSGDFDTFRRWLVVEEVTQPTREITLEAA 80
Cdd:COG0195    4 MLLELLEALEELEKEKGIDKEILIEALEAALKKAYKKNYGNEVVVRVIIDGDTGEIRVYVVKEVVEEVEDPREEILLEAA 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490227306  81 RYEDESMNPGDYVEDQIESVTFDRITTQTAKQVIVQKVREAERAMVVDQFREHEGEIITGVVKKVNRDNITLDLGNnAEA 160
Cdd:COG0195   84 KEDDPDEEGGDIIEEEVPPDFFGRIAAQAAKQVIQQKRREAEREIIYEEFKDRGGEIVGGVVQRVERGNVIVDLGK-VEA 162

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490227306 161 VILREDMLPRENFRPGDRIRGVLYAVRPEARGAQLFVTRSKPEMLVELFRIEVPEIGEEVLEIKAAARDPGSRAKIAVKT 240
Cdd:COG0195  163 ILPRREQIPGENYRVGDRIRAYVLEVRKETRGPQIILSRTHPEFLKRLFELEVPEIADGIVEIKAIAREPGSRAKIAVYS 242

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490227306 241 NDKRIDPVGACVGMRGARVQAVSTELGGERIDIVLWDDNPAQFVINAMAPADVASIVVDEDKHTMDIAVEAGNLAQAIGR 320
Cdd:COG0195  243 NDPRVDPVGACVGMRGSRVQAVVNELNGEKIDIILWSEDPAQFIANALSPAKVSSVEVDEEEKSADVVVPDDQLSLAIGK 322

                        330       340       350
                 ....*....|....*....|....*....|.
gi 490227306 321 NGQNVRLASQLSGWELNVMTVDDLQAKHQAE 351
Cdd:COG0195  323 GGQNVRLAAKLTGWKIDIKSESEAEEKREEE 353
NusA_N pfam08529
NusA N-terminal domain; This domain represents the RNA polymerase binding domain of NusA.
 5-123 9.20e-46

NusA N-terminal domain; This domain represents the RNA polymerase binding domain of NusA.


Pssm-ID: 462512 [Multi-domain]  Cd Length: 120  Bit Score: 155.68  E-value: 9.20e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490227306    5 ILAVVEAVSNEKALPREKIFEALESALATATKKKYEQEIDVRVEIDRKSGDFDTFRRWLVVEEVTQPTREITLEAARYED 84
Cdd:pfam08529   1 LLEALEELAKEKGIDKEVLIEAIEEALLKAYKKKYGADENVRVEIDRETGDIEVYRRKEVVEEVEDPDTEISLEEAKKID 80

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 490227306   85 ESMNPGDYVEDQIESVTFDRITTQTAKQVIVQKVREAER 123
Cdd:pfam08529  81 PDAEVGDVVEEEVTPKDFGRIAAQTAKQVIIQKIREAER 119
KH-II_NusA_rpt1 cd02134
first type II K-homology (KH) RNA-binding domain found in transcription termination ...
 202-276 2.56e-38

first 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 (KH), KH1 and KH2. The KH domains of NusA belong to the type II KH RNA-binding domain superfamily. This model corresponds to the first KH domain of NusA and similar proteins.


Pssm-ID: 411779 [Multi-domain]  Cd Length: 76  Bit Score: 134.20  E-value: 2.56e-38
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 490227306 202 PEMLVELFRIEVPEIGEEVLEIKAAARDPGSRAKIAVKTNDKRIDPVGACVGMRGARVQAVSTELGGERIDIVLW 276
Cdd:cd02134    2 PEFLKRLFELEVPEIADGIVEIKAIAREPGSRTKVAVASNDPRVDPVGACVGVRGSRIQAIVEELGGEKIDIVLW 76
KH_5 pfam13184
NusA-like KH domain;
230-298 1.41e-29

NusA-like KH domain;


Pssm-ID: 433018 [Multi-domain]  Cd Length: 69  Bit Score: 110.40  E-value: 1.41e-29
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 490227306  230 PGSRAKIAVKTNDKRIDPVGACVGMRGARVQAVSTELGGERIDIVLWDDNPAQFVINAMAPADVASIVV 298
Cdd:pfam13184   1 PGNRAKIAVYSRDERIDPVGACVGKKGSRIQAISRELNGEKIDIVEYSEDLRTFIKNALSPARVLSVNI 69
S1_NusA cd04455
S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like ...
 132-199 2.49e-24

S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.


Pssm-ID: 239902 [Multi-domain]  Cd Length: 67  Bit Score: 95.97  E-value: 2.49e-24
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 490227306 132 EHEGEIITGVVKKVNRDNITLDLGNnAEAVILREDMLPRENFRPGDRIRGVLYAVRPEARGAQLFVTR 199
Cdd:cd04455    1 DREGEIVTGIVKRVDRGNVIVDLGK-VEAILPKKEQIPGESYRPGDRIKAYVLEVRKTSKGPQIILSR 67
KH-II_NusA_rpt2 cd22529
second type II K-homology (KH) RNA-binding domain found in transcription termination ...
 279-339 2.60e-24

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: 95.68  E-value: 2.60e-24
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 490227306 279 NPAQFVINAMAPADVASIVVDEDKHTMDIAVEAGNLAQAIGRNGQNVRLASQLSGWELNVM 339
Cdd:cd22529    1 DPAEFVANALSPAKVISVEIDEDDKKARVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIK 61
nusA_Cterm_rpt TIGR01954
transcription termination factor NusA, C-terminal duplication; NusA is a bacterial ...
 365-414 1.28e-12

transcription termination factor NusA, C-terminal duplication; NusA is a bacterial transcription termination factor. It is named for its interaction with phage lambda protein N, as part of the N utilization substance. Some members of the NusA family have a long C-terminal extension. This model represents an acidic 50-residue region found in two copies toward the C-terminus of most Proteobacterial NusA proteins, spaced about 26 residues apart. Analogous C-terminal extensions in some other bacterial lineages lack apparent homology but appear similarly acidic. [Transcription, Transcription factors]


Pssm-ID: 273894 [Multi-domain]  Cd Length: 50  Bit Score: 62.32  E-value: 1.28e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 490227306  365 IDEDFATLLVEEGFATLEELAYVPMKELLEIDGLDEATVEALRERAKNAL 414
Cdd:TIGR01954   1 INEEIAQLLVEEGFTTVEDLAYVPIDELLSIEGFDEETAKELINRARNAL 50
nusA_Cterm_rpt TIGR01954
transcription termination factor NusA, C-terminal duplication; NusA is a bacterial ...
 440-489 1.47e-10

transcription termination factor NusA, C-terminal duplication; NusA is a bacterial transcription termination factor. It is named for its interaction with phage lambda protein N, as part of the N utilization substance. Some members of the NusA family have a long C-terminal extension. This model represents an acidic 50-residue region found in two copies toward the C-terminus of most Proteobacterial NusA proteins, spaced about 26 residues apart. Analogous C-terminal extensions in some other bacterial lineages lack apparent homology but appear similarly acidic. [Transcription, Transcription factors]


Pssm-ID: 273894 [Multi-domain]  Cd Length: 50  Bit Score: 56.54  E-value: 1.47e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 490227306  440 MDRALAFTLAARGVCTLEDLAEQGIDDLADIEGLTDEKAGELIMAARNIC 489
Cdd:TIGR01954   1 INEEIAQLLVEEGFTTVEDLAYVPIDELLSIEGFDEETAKELINRARNAL 50
HHH_5 pfam14520
Helix-hairpin-helix domain;
432-487 3.88e-09

Helix-hairpin-helix domain;


Pssm-ID: 434010 [Multi-domain]  Cd Length: 57  Bit Score: 52.49  E-value: 3.88e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 490227306  432 DDLLNLEGMDRALAFTLAARGVCTLEDLAEQGIDDLADIEGLTDEKAGELIMAARN 487
Cdd:pfam14520   2 EELLSISGIGPKTALALLSAGIGTVEDLAEADVDELAEIPGIGEKTAQRIILELRD 57
nusA_arch TIGR01952
NusA family KH domain protein, archaeal; This model represents a family of archaeal proteins ...
 248-333 1.66e-08

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: 53.18  E-value: 1.66e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490227306  248 VGACVGMRGARVQAVsTELGGERIDIVLWDDNPAQFVINAMAPADVASIVVDE--DKHTMDIAVEAGNLAQAIGRNGQNV 325
Cdd:TIGR01952  44 MGAAIGKGGENVKRL-EELIGKSIELIEYSENLEEFVANKLAPAEVKNVTVSEfnGKKVAYVEVHPRDKGIAIGKGGKNI 122


                  ....*...
gi 490227306  326 RLASQLSG 333
Cdd:TIGR01952 123 ERAKELAK 130
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
134-195 2.98e-07

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 47.60  E-value: 2.98e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 490227306   134 EGEIITGVVKKVNRDNITLDLGNNAEAVILREDM------LPRENFRPGDRIRGVLYAVRPEARGAQL 195
Cdd:smart00316   2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELsdkrvkDPEEVLKVGDEVKVKVLSVDEEKGRIIL 69
PRK08406 PRK08406
transcription elongation factor NusA-like protein; Validated
 238-331 7.59e-07

transcription elongation factor NusA-like protein; Validated


Pssm-ID: 181413 [Multi-domain]  Cd Length: 140  Bit Score: 48.29  E-value: 7.59e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490227306 238 VKTNDkridpVGACVGMRGARVQAVsTELGGERIDIVLWDDNPAQFVINAMAPADVASIVVDE--DKHTMDIAVEAGNLA 315
Cdd:PRK08406  38 VKEGD-----MGLAIGKGGENVKRL-EEKLGKDIELVEYSDDPEEFIKNIFAPAAVRSVTIKKknGDKVAYVEVAPEDKG 111

                         90
                 ....*....|....*.
gi 490227306 316 QAIGRNGQNVRLASQL 331
Cdd:PRK08406 112 IAIGKNGKNIERAKDL 127
KH-II_SF cd02409
type II K-homology (KH) RNA-binding domain superfamily; The K-homology (KH) domain binds ...
 281-339 1.41e-04

type II K-homology (KH) RNA-binding domain superfamily; The K-homology (KH) domain binds single-stranded RNA or DNA, and is found in a wide variety of proteins including ribosomal proteins, transcription factors, and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but share a single "minimal KH motif" which is folded into a beta-alpha-alpha-beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include an N-terminal extension while type I KH domains (e.g. hnRNP K) contain a C-terminal extension, connected to the KH motif by variable loops that are different in different KH domains, whether they are type I or type II. KH-II superfamily members contain one or two KH domains, most of which are canonical type II KH domains that have the signature motif GXXG (where X represents any amino acid). The first KH domain found in archaeal cleavage and polyadenylation specificity factors (CPSFs) is a non-canonical type II KH domain that lacks the GXXG motif. Some others have mutated GXXG motifs which may or may not have nucleic acid binding ability.


Pssm-ID: 411780 [Multi-domain]  Cd Length: 67  Bit Score: 40.05  E-value: 1.41e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 490227306 281 AQFVINAMAPA-DVASIVVDE--DKHTMDIAVEAGNLAQAIGRNGQNVRLASQLSG-----WELNVM 339
Cdd:cd02409    1 AEILEKLFPAAvTISDVEVEEtpDGIRVIIAVEEGDPGIVIGKGGQRIRELRKELGklgggVEIDVV 67
PLN03186 PLN03186
DNA repair protein RAD51 homolog; Provisional
 373-411 2.11e-04

DNA repair protein RAD51 homolog; Provisional


Pssm-ID: 178728 [Multi-domain]  Cd Length: 342  Bit Score: 43.57  E-value: 2.11e-04
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 490227306 373 LVEEGFATLEELAYVPMKELLEIDGLDEATVEALRERAK 411
Cdd:PLN03186  44 LKDAGIHTVESLAYAPKKDLLQIKGISEAKVEKILEAAS 82
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 134-195 1.90e-03

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 36.88  E-value: 1.90e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 490227306  134 EGEIITGVVKKVNRDNITLDLGNNAEAVILREDM------LPRENFRPGDRIRGVLYAVRPEARGAQL 195
Cdd:pfam00575   3 KGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELsddhveDPDEVIKVGDEVKVKVLKVDKDRRRIIL 70
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 138-195 2.51e-03

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 36.59  E-value: 2.51e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 490227306 138 ITGVVKKVNRDNITLDLGNNAEAVILREDML------PRENFRPGDRIRGVLYAVRPEARGAQL 195
Cdd:cd00164    1 VTGKVVSITKFGVFVELEDGVEGLVHISELSdkfvkdPSEVFKVGDEVEVKVLEVDPEKGRISL 64
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 133-201 2.97e-03

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 39.64  E-value: 2.97e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 490227306 133 HEGEIITGVVKKVNRDNITLDLGNNAEAVILREDMLPRE---NFRPGDRIRgvLYAVRPEARGAQLFVTRSK 201
Cdd:COG0539   17 KEGDIVKGTVVSIDDDEVLVDIGYKSEGIIPLSEFSDEPgelEVKVGDEVE--VYVEKVEDGEGEIVLSKKK 86
KH-II_NusA_arch_rpt2 cd22531
second type II K-homology (KH) RNA-binding domain found in archaeal probable transcription ...
 280-331 4.42e-03

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: 35.68  E-value: 4.42e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 490227306 280 PAQFVINAMAPADVASIVVDE--DKHTMDIAVEAGNLAQAIGRNGQNVRLASQL 331
Cdd:cd22531    1 PEEFIKNIFAPAKVQNVKVKEknGKKVAIVEVPPKDKGIAIGKNGKNIERAKLL 54
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
120-179 6.70e-03

bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 39.16  E-value: 6.70e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490227306 120 EAERAMVVDQFREHEGEIITGVVKKVNRDNITLDLGNNAEAVILREDMLPRENFRP------GDRI 179
Cdd:PRK00087 288 EQLEYMNELEKQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLkesvkvGDEI 353
 
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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