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Conserved domains on  [gi|1819251929|ref|WP_164962291|]
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MULTISPECIES: transcription termination factor NusA [unclassified Rubrivivax]

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: 615.73  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1819251929   1 MNREMLMLVDAISREKTVDRDVVFGAVEAALASATKKLHGGEVDIRVAVDRETGEYETFRRWHVVPNeagLQNADAEVLL 80
Cdd:PRK09202    1 MNKELLEAIEAVAREKGIDREVVIEALEEALATAYKKKYGPEANIRVEIDRKTGDIEVFRRWEVVEE---VEDPTKEISL 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1819251929  81 FEAQEQIADIEVDDYIEESVDSVPIGRIGAQAAKQVILQKIRDAEREQLLNDFLARGDKIFVGTVKRLDKGDIIVESGRV 160
Cdd:PRK09202   78 EEARKIDPDAEVGDYIEEEIESVDFGRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIITGVVKRVERGNIIVDLGRA 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1819251929 161 EGRLKRSEMIPKENLRSGDRVRAFILGVDPTQRGPQIMLSRSAPGFMVELFGQEVPEIEQGLLEIKSCARDPGSRAKIAV 240
Cdd:PRK09202  158 EAILPRKEQIPRENFRPGDRVRAYVYEVRKEARGPQIILSRTHPEFLKKLFEQEVPEIADGLIEIKAIARDPGSRAKIAV 237

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1819251929 241 VSHDRRVDPIGTCVGVRGSRVNGVTTELAGERVDIVLWSEDPAQFVIGALAPANVQSIVVDEERHAMDVVVDEENLAIAI 320
Cdd:PRK09202  238 KSNDPRIDPVGACVGMRGSRIQAISNELGGEKIDIILWSDDPAQFIINALSPAEVSSVVVDEDEHSADVVVPDDQLSLAI 317

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1819251929 321 GRGGQNVRLASELTGWRINIMTAEESQAKQATETESVRKIFVEKLDVDEEVADILIAEGFTSLEEVAYVPLQEMLEIEAF 400
Cdd:PRK09202  318 GKNGQNVRLASKLTGWKIDIMTEEEASEKRQAEFDAILDLFMEALDIDEEIAQLLVEEGFSSLEELAYVPVEELLEIEGF 397

                         410       420       430       440       450       460       470
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1819251929 401 DEDTVQELRTRAKDALLTMeieREEKVEEVSQDLRDLEGLTPELIGKLSDGGVNTRDDLADLAVDELVEMTGVDET 476
Cdd:PRK09202  398 DEETVEELRERAKEALETE---ALAQEEKLADDLLSLEGLDRELAFKLAEKGIKTLEDLAEQAVDELIDIEGDEEK 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: 615.73  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1819251929   1 MNREMLMLVDAISREKTVDRDVVFGAVEAALASATKKLHGGEVDIRVAVDRETGEYETFRRWHVVPNeagLQNADAEVLL 80
Cdd:PRK09202    1 MNKELLEAIEAVAREKGIDREVVIEALEEALATAYKKKYGPEANIRVEIDRKTGDIEVFRRWEVVEE---VEDPTKEISL 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1819251929  81 FEAQEQIADIEVDDYIEESVDSVPIGRIGAQAAKQVILQKIRDAEREQLLNDFLARGDKIFVGTVKRLDKGDIIVESGRV 160
Cdd:PRK09202   78 EEARKIDPDAEVGDYIEEEIESVDFGRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIITGVVKRVERGNIIVDLGRA 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1819251929 161 EGRLKRSEMIPKENLRSGDRVRAFILGVDPTQRGPQIMLSRSAPGFMVELFGQEVPEIEQGLLEIKSCARDPGSRAKIAV 240
Cdd:PRK09202  158 EAILPRKEQIPRENFRPGDRVRAYVYEVRKEARGPQIILSRTHPEFLKKLFEQEVPEIADGLIEIKAIARDPGSRAKIAV 237

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1819251929 241 VSHDRRVDPIGTCVGVRGSRVNGVTTELAGERVDIVLWSEDPAQFVIGALAPANVQSIVVDEERHAMDVVVDEENLAIAI 320
Cdd:PRK09202  238 KSNDPRIDPVGACVGMRGSRIQAISNELGGEKIDIILWSDDPAQFIINALSPAEVSSVVVDEDEHSADVVVPDDQLSLAI 317

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1819251929 321 GRGGQNVRLASELTGWRINIMTAEESQAKQATETESVRKIFVEKLDVDEEVADILIAEGFTSLEEVAYVPLQEMLEIEAF 400
Cdd:PRK09202  318 GKNGQNVRLASKLTGWKIDIMTEEEASEKRQAEFDAILDLFMEALDIDEEIAQLLVEEGFSSLEELAYVPVEELLEIEGF 397

                         410       420       430       440       450       460       470
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1819251929 401 DEDTVQELRTRAKDALLTMeieREEKVEEVSQDLRDLEGLTPELIGKLSDGGVNTRDDLADLAVDELVEMTGVDET 476
Cdd:PRK09202  398 DEETVEELRERAKEALETE---ALAQEEKLADDLLSLEGLDRELAFKLAEKGIKTLEDLAEQAVDELIDIEGDEEK 470
NusA COG0195
Transcription antitermination factor NusA, contains S1 and KH domains [Transcription];
1-353 1.00e-148

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


Pssm-ID: 439965 [Multi-domain]  Cd Length: 353  Bit Score: 428.91  E-value: 1.00e-148
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1819251929   1 MNREMLMLVDAISREKTVDRDVVFGAVEAALASATKKLHGGEVDIRVAVDRETGEYETFRRWHVVPNEAGLQNADAEVLL 80
Cdd:COG0195     1 MSMMLLELLEALEELEKEKGIDKEILIEALEAALKKAYKKNYGNEVVVRVIIDGDTGEIRVYVVKEVVEEVEDPREEILL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1819251929  81 FEAQEQIADIEVDDYIEESVDSVPIGRIGAQAAKQVILQKIRDAEREQLLNDFLARGDKIFVGTVKRLDKGDIIVESGRV 160
Cdd:COG0195    81 EAAKEDDPDEEGGDIIEEEVPPDFFGRIAAQAAKQVIQQKRREAEREIIYEEFKDRGGEIVGGVVQRVERGNVIVDLGKV 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1819251929 161 EGRLKRSEMIPKENLRSGDRVRAFILGVDPTQRGPQIMLSRSAPGFMVELFGQEVPEIEQGLLEIKSCARDPGSRAKIAV 240
Cdd:COG0195   161 EAILPRREQIPGENYRVGDRIRAYVLEVRKETRGPQIILSRTHPEFLKRLFELEVPEIADGIVEIKAIAREPGSRAKIAV 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1819251929 241 VSHDRRVDPIGTCVGVRGSRVNGVTTELAGERVDIVLWSEDPAQFVIGALAPANVQSIVVDEERHAMDVVVDEENLAIAI 320
Cdd:COG0195   241 YSNDPRVDPVGACVGMRGSRVQAVVNELNGEKIDIILWSEDPAQFIANALSPAKVSSVEVDEEEKSADVVVPDDQLSLAI 320

                         330       340       350
                  ....*....|....*....|....*....|...
gi 1819251929 321 GRGGQNVRLASELTGWRINIMTAEESQAKQATE 353
Cdd:COG0195   321 GKGGQNVRLAAKLTGWKIDIKSESEAEEKREEE 353
NusA TIGR01953
transcription termination factor NusA; This model describes NusA, or N utilization substance ...
 4-345 1.46e-136

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: 397.40  E-value: 1.46e-136
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1819251929   4 EMLMLVDAISREKTVDRDVVFGAVEAALASATKKLHGGEVDIRVAVDRETGEYETFRRWHVVPNeagLQNADAEVLLFEA 83
Cdd:TIGR01953   1 EFLAAIEALAKEKGISIETVIEAIEEALEQAYKKTFGQDENVEVNIDRKTGDINVYRRKEVVEE---VEDPSLEISLEDA 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1819251929  84 QEQIADIEVDDYIEESVDSVPIGRIGAQAAKQVILQKIRDAEREQLLNDFLARGDKIFVGTVKRLDK-GDIIVESGRVEG 162
Cdd:TIGR01953  78 REIDPDVQIGDEVKKEIPPENFGRIAAQTAKQVILQKIREAERERVYDEFSSKEGEIISGTVKRVNRrGNLFVELGKTEG 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1819251929 163 RLKRSEMIPKENLRSGDRVRAFILGVDPTQRGPQIMLSRSAPGFMVELFGQEVPEIEQGLLEIKSCARDPGSRAKIAVVS 242
Cdd:TIGR01953 158 ILPKKEQIPGEKFRIGDRIKAYVYEVRKTAKGPQIILSRTHPEFVKELLKLEVPEIADGIIEIKKIAREPGYRTKIAVES 237

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1819251929 243 HDRRVDPIGTCVGVRGSRVNGVTTELAGERVDIVLWSEDPAQFVIGALAPANVQSI-VVDEERHAMDVVVDEENLAIAIG 321
Cdd:TIGR01953 238 NDENIDPVGACVGPKGSRIQAISKELNGEKIDIIEYSDDPAEFIANALSPAKVISVeVLDEDKRSAEVVVPDDQLSLAIG 317

                         330       340
                  ....*....|....*....|....
gi 1819251929 322 RGGQNVRLASELTGWRINIMTAEE 345
Cdd:TIGR01953 318 KGGQNVRLASKLTGWNIDVKTESQ 341
NusA_N pfam08529
NusA N-terminal domain; This domain represents the RNA polymerase binding domain of NusA.
 5-127 1.54e-40

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


Pssm-ID: 462512 [Multi-domain]  Cd Length: 120  Bit Score: 141.81  E-value: 1.54e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1819251929   5 MLMLVDAISREKTVDRDVVFGAVEAALASATKKLHGGEVDIRVAVDRETGEYETFRRWHVVPNEaglQNADAEVLLFEAQ 84
Cdd:pfam08529   1 LLEALEELAKEKGIDKEVLIEAIEEALLKAYKKKYGADENVRVEIDRETGDIEVYRRKEVVEEV---EDPDTEISLEEAK 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1819251929  85 EQIADIEVDDYIEESVDSVPIGRIGAQAAKQVILQKIRDAERE 127
Cdd:pfam08529  78 KIDPDAEVGDVVEEEVTPKDFGRIAAQTAKQVIIQKIREAERE 120
KH-II_NusA_rpt1 cd02134
first type II K-homology (KH) RNA-binding domain found in transcription termination ...
 204-278 1.08e-35

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: 127.26  E-value: 1.08e-35
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1819251929 204 PGFMVELFGQEVPEIEQGLLEIKSCARDPGSRAKIAVVSHDRRVDPIGTCVGVRGSRVNGVTTELAGERVDIVLW 278
Cdd:cd02134     2 PEFLKRLFELEVPEIADGIVEIKAIAREPGSRTKVAVASNDPRVDPVGACVGVRGSRIQAIVEELGGEKIDIVLW 76
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
139-201 6.38e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 41.05  E-value: 6.38e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1819251929  139 KIFVGTVKRLDKGDIIVE-SGRVEGRLKRSEMI------PKENLRSGDRVRAFILGVDPTQRgpQIMLSR 201
Cdd:smart00316   4 DVVEGTVTEITPGGAFVDlGNGVEGLIPISELSdkrvkdPEEVLKVGDEVKVKVLSVDEEKG--RIILSL 71
 
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: 615.73  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1819251929   1 MNREMLMLVDAISREKTVDRDVVFGAVEAALASATKKLHGGEVDIRVAVDRETGEYETFRRWHVVPNeagLQNADAEVLL 80
Cdd:PRK09202    1 MNKELLEAIEAVAREKGIDREVVIEALEEALATAYKKKYGPEANIRVEIDRKTGDIEVFRRWEVVEE---VEDPTKEISL 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1819251929  81 FEAQEQIADIEVDDYIEESVDSVPIGRIGAQAAKQVILQKIRDAEREQLLNDFLARGDKIFVGTVKRLDKGDIIVESGRV 160
Cdd:PRK09202   78 EEARKIDPDAEVGDYIEEEIESVDFGRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIITGVVKRVERGNIIVDLGRA 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1819251929 161 EGRLKRSEMIPKENLRSGDRVRAFILGVDPTQRGPQIMLSRSAPGFMVELFGQEVPEIEQGLLEIKSCARDPGSRAKIAV 240
Cdd:PRK09202  158 EAILPRKEQIPRENFRPGDRVRAYVYEVRKEARGPQIILSRTHPEFLKKLFEQEVPEIADGLIEIKAIARDPGSRAKIAV 237

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1819251929 241 VSHDRRVDPIGTCVGVRGSRVNGVTTELAGERVDIVLWSEDPAQFVIGALAPANVQSIVVDEERHAMDVVVDEENLAIAI 320
Cdd:PRK09202  238 KSNDPRIDPVGACVGMRGSRIQAISNELGGEKIDIILWSDDPAQFIINALSPAEVSSVVVDEDEHSADVVVPDDQLSLAI 317

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1819251929 321 GRGGQNVRLASELTGWRINIMTAEESQAKQATETESVRKIFVEKLDVDEEVADILIAEGFTSLEEVAYVPLQEMLEIEAF 400
Cdd:PRK09202  318 GKNGQNVRLASKLTGWKIDIMTEEEASEKRQAEFDAILDLFMEALDIDEEIAQLLVEEGFSSLEELAYVPVEELLEIEGF 397

                         410       420       430       440       450       460       470
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1819251929 401 DEDTVQELRTRAKDALLTMeieREEKVEEVSQDLRDLEGLTPELIGKLSDGGVNTRDDLADLAVDELVEMTGVDET 476
Cdd:PRK09202  398 DEETVEELRERAKEALETE---ALAQEEKLADDLLSLEGLDRELAFKLAEKGIKTLEDLAEQAVDELIDIEGDEEK 470
NusA COG0195
Transcription antitermination factor NusA, contains S1 and KH domains [Transcription];
1-353 1.00e-148

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


Pssm-ID: 439965 [Multi-domain]  Cd Length: 353  Bit Score: 428.91  E-value: 1.00e-148
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1819251929   1 MNREMLMLVDAISREKTVDRDVVFGAVEAALASATKKLHGGEVDIRVAVDRETGEYETFRRWHVVPNEAGLQNADAEVLL 80
Cdd:COG0195     1 MSMMLLELLEALEELEKEKGIDKEILIEALEAALKKAYKKNYGNEVVVRVIIDGDTGEIRVYVVKEVVEEVEDPREEILL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1819251929  81 FEAQEQIADIEVDDYIEESVDSVPIGRIGAQAAKQVILQKIRDAEREQLLNDFLARGDKIFVGTVKRLDKGDIIVESGRV 160
Cdd:COG0195    81 EAAKEDDPDEEGGDIIEEEVPPDFFGRIAAQAAKQVIQQKRREAEREIIYEEFKDRGGEIVGGVVQRVERGNVIVDLGKV 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1819251929 161 EGRLKRSEMIPKENLRSGDRVRAFILGVDPTQRGPQIMLSRSAPGFMVELFGQEVPEIEQGLLEIKSCARDPGSRAKIAV 240
Cdd:COG0195   161 EAILPRREQIPGENYRVGDRIRAYVLEVRKETRGPQIILSRTHPEFLKRLFELEVPEIADGIVEIKAIAREPGSRAKIAV 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1819251929 241 VSHDRRVDPIGTCVGVRGSRVNGVTTELAGERVDIVLWSEDPAQFVIGALAPANVQSIVVDEERHAMDVVVDEENLAIAI 320
Cdd:COG0195   241 YSNDPRVDPVGACVGMRGSRVQAVVNELNGEKIDIILWSEDPAQFIANALSPAKVSSVEVDEEEKSADVVVPDDQLSLAI 320

                         330       340       350
                  ....*....|....*....|....*....|...
gi 1819251929 321 GRGGQNVRLASELTGWRINIMTAEESQAKQATE 353
Cdd:COG0195   321 GKGGQNVRLAAKLTGWKIDIKSESEAEEKREEE 353
NusA TIGR01953
transcription termination factor NusA; This model describes NusA, or N utilization substance ...
 4-345 1.46e-136

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: 397.40  E-value: 1.46e-136
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1819251929   4 EMLMLVDAISREKTVDRDVVFGAVEAALASATKKLHGGEVDIRVAVDRETGEYETFRRWHVVPNeagLQNADAEVLLFEA 83
Cdd:TIGR01953   1 EFLAAIEALAKEKGISIETVIEAIEEALEQAYKKTFGQDENVEVNIDRKTGDINVYRRKEVVEE---VEDPSLEISLEDA 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1819251929  84 QEQIADIEVDDYIEESVDSVPIGRIGAQAAKQVILQKIRDAEREQLLNDFLARGDKIFVGTVKRLDK-GDIIVESGRVEG 162
Cdd:TIGR01953  78 REIDPDVQIGDEVKKEIPPENFGRIAAQTAKQVILQKIREAERERVYDEFSSKEGEIISGTVKRVNRrGNLFVELGKTEG 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1819251929 163 RLKRSEMIPKENLRSGDRVRAFILGVDPTQRGPQIMLSRSAPGFMVELFGQEVPEIEQGLLEIKSCARDPGSRAKIAVVS 242
Cdd:TIGR01953 158 ILPKKEQIPGEKFRIGDRIKAYVYEVRKTAKGPQIILSRTHPEFVKELLKLEVPEIADGIIEIKKIAREPGYRTKIAVES 237

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1819251929 243 HDRRVDPIGTCVGVRGSRVNGVTTELAGERVDIVLWSEDPAQFVIGALAPANVQSI-VVDEERHAMDVVVDEENLAIAIG 321
Cdd:TIGR01953 238 NDENIDPVGACVGPKGSRIQAISKELNGEKIDIIEYSDDPAEFIANALSPAKVISVeVLDEDKRSAEVVVPDDQLSLAIG 317

                         330       340
                  ....*....|....*....|....
gi 1819251929 322 RGGQNVRLASELTGWRINIMTAEE 345
Cdd:TIGR01953 318 KGGQNVRLASKLTGWNIDVKTESQ 341
NusA_N pfam08529
NusA N-terminal domain; This domain represents the RNA polymerase binding domain of NusA.
 5-127 1.54e-40

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


Pssm-ID: 462512 [Multi-domain]  Cd Length: 120  Bit Score: 141.81  E-value: 1.54e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1819251929   5 MLMLVDAISREKTVDRDVVFGAVEAALASATKKLHGGEVDIRVAVDRETGEYETFRRWHVVPNEaglQNADAEVLLFEAQ 84
Cdd:pfam08529   1 LLEALEELAKEKGIDKEVLIEAIEEALLKAYKKKYGADENVRVEIDRETGDIEVYRRKEVVEEV---EDPDTEISLEEAK 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1819251929  85 EQIADIEVDDYIEESVDSVPIGRIGAQAAKQVILQKIRDAERE 127
Cdd:pfam08529  78 KIDPDAEVGDVVEEEVTPKDFGRIAAQTAKQVIIQKIREAERE 120
KH-II_NusA_rpt1 cd02134
first type II K-homology (KH) RNA-binding domain found in transcription termination ...
 204-278 1.08e-35

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: 127.26  E-value: 1.08e-35
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1819251929 204 PGFMVELFGQEVPEIEQGLLEIKSCARDPGSRAKIAVVSHDRRVDPIGTCVGVRGSRVNGVTTELAGERVDIVLW 278
Cdd:cd02134     2 PEFLKRLFELEVPEIADGIVEIKAIAREPGSRTKVAVASNDPRVDPVGACVGVRGSRIQAIVEELGGEKIDIVLW 76
KH-II_NusA_rpt2 cd22529
second type II K-homology (KH) RNA-binding domain found in transcription termination ...
 281-341 3.98e-27

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: 103.39  E-value: 3.98e-27
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1819251929 281 DPAQFVIGALAPANVQSIVVDEERHAMDVVVDEENLAIAIGRGGQNVRLASELTGWRINIM 341
Cdd:cd22529     1 DPAEFVANALSPAKVISVEIDEDDKKARVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIK 61
KH_5 pfam13184
NusA-like KH domain;
232-300 1.65e-25

NusA-like KH domain;


Pssm-ID: 433018 [Multi-domain]  Cd Length: 69  Bit Score: 99.23  E-value: 1.65e-25
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1819251929 232 PGSRAKIAVVSHDRRVDPIGTCVGVRGSRVNGVTTELAGERVDIVLWSEDPAQFVIGALAPANVQSIVV 300
Cdd:pfam13184   1 PGNRAKIAVYSRDERIDPVGACVGKKGSRIQAISRELNGEKIDIVEYSEDLRTFIKNALSPARVLSVNI 69
S1_NusA cd04455
S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like ...
 135-201 1.80e-21

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: 87.88  E-value: 1.80e-21
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1819251929 135 ARGDKIFVGTVKRLDKGDIIVESGRVEGRLKRSEMIPKENLRSGDRVRAFILGVDPTQRGPQIMLSR 201
Cdd:cd04455     1 DREGEIVTGIVKRVDRGNVIVDLGKVEAILPKKEQIPGESYRPGDRIKAYVLEVRKTSKGPQIILSR 67
nusA_Cterm_rpt TIGR01954
transcription termination factor NusA, C-terminal duplication; NusA is a bacterial ...
 367-416 8.92e-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: 60.01  E-value: 8.92e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1819251929 367 VDEEVADILIAEGFTSLEEVAYVPLQEMLEIEAFDEDTVQELRTRAKDAL 416
Cdd:TIGR01954   1 INEEIAQLLVEEGFTTVEDLAYVPIDELLSIEGFDEETAKELINRARNAL 50
PRK08406 PRK08406
transcription elongation factor NusA-like protein; Validated
 250-333 2.31e-09

transcription elongation factor NusA-like protein; Validated


Pssm-ID: 181413 [Multi-domain]  Cd Length: 140  Bit Score: 55.61  E-value: 2.31e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1819251929 250 IGTCVGVRGSRVNGVTtELAGERVDIVLWSEDPAQFVIGALAPANVQSIVVDEERHAMDVV--VDEENLAIAIGRGGQNV 327
Cdd:PRK08406   43 MGLAIGKGGENVKRLE-EKLGKDIELVEYSDDPEEFIKNIFAPAAVRSVTIKKKNGDKVAYveVAPEDKGIAIGKNGKNI 121


                  ....*.
gi 1819251929 328 RLASEL 333
Cdd:PRK08406  122 ERAKDL 127
nusA_arch TIGR01952
NusA family KH domain protein, archaeal; This model represents a family of archaeal proteins ...
 250-335 3.62e-09

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: 55.11  E-value: 3.62e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1819251929 250 IGTCVGVRGSRVNGVTtELAGERVDIVLWSEDPAQFVIGALAPANVQSIVVDEERHAMDVV--VDEENLAIAIGRGGQNV 327
Cdd:TIGR01952  44 MGAAIGKGGENVKRLE-ELIGKSIELIEYSENLEEFVANKLAPAEVKNVTVSEFNGKKVAYveVHPRDKGIAIGKGGKNI 122


                  ....*...
gi 1819251929 328 RLASELTG 335
Cdd:TIGR01952 123 ERAKELAK 130
HHH_5 pfam14520
Helix-hairpin-helix domain;
431-487 1.53e-08

Helix-hairpin-helix domain;


Pssm-ID: 434010 [Multi-domain]  Cd Length: 57  Bit Score: 50.95  E-value: 1.53e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1819251929 431 SQDLRDLEGLTPELIGKLSDGGVNTRDDLADLAVDELVEMTGVDETQARALIMKARE 487
Cdd:pfam14520   1 FEELLSISGIGPKTALALLSAGIGTVEDLAEADVDELAEIPGIGEKTAQRIILELRD 57
nusA_Cterm_rpt TIGR01954
transcription termination factor NusA, C-terminal duplication; NusA is a bacterial ...
 443-489 1.34e-07

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: 48.07  E-value: 1.34e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1819251929 443 ELIGKLSDGGVNTRDDLADLAVDELVEMTGVDETQARALIMKAREHW 489
Cdd:TIGR01954   4 EIAQLLVEEGFTTVEDLAYVPIDELLSIEGFDEETAKELINRARNAL 50
KH-II_NusA_arch_rpt2 cd22531
second type II K-homology (KH) RNA-binding domain found in archaeal probable transcription ...
 282-333 3.88e-05

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: 41.46  E-value: 3.88e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1819251929 282 PAQFVIGALAPANVQSIVVDEERHAMDVV--VDEENLAIAIGRGGQNVRLASEL 333
Cdd:cd22531     1 PEEFIKNIFAPAKVQNVKVKEKNGKKVAIveVPPKDKGIAIGKNGKNIERAKLL 54
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
139-201 6.38e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 41.05  E-value: 6.38e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1819251929  139 KIFVGTVKRLDKGDIIVE-SGRVEGRLKRSEMI------PKENLRSGDRVRAFILGVDPTQRgpQIMLSR 201
Cdd:smart00316   4 DVVEGTVTEITPGGAFVDlGNGVEGLIPISELSdkrvkdPEEVLKVGDEVKVKVLSVDEEKG--RIILSL 71
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
112-201 4.16e-04

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 43.01  E-value: 4.16e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1819251929 112 AAKQVILQKIRDAEREQLLNDfLARGDkIFVGTVKRLDKGDIIVESGRVEGRLKRSEMI------PKENLRSGDRVRAFI 185
Cdd:PRK00087  454 LSRKAILEEEKEKKKEETWNS-LEEGD-VVEGEVKRLTDFGAFVDIGGVDGLLHVSEISwgrvekPSDVLKVGDEIKVYI 531

                          90
                  ....*....|....*.
gi 1819251929 186 LGVDPTQRgpQIMLSR 201
Cdd:PRK00087  532 LDIDKENK--KLSLSL 545
KH smart00322
K homology RNA-binding domain;
307-375 5.79e-04

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 38.43  E-value: 5.79e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1819251929  307 MDVVVDEENLAIAIGRGGQNVRLASELTGWRINIMTAEesqakqatETESVRKIFVEKLDVDEEVADIL 375
Cdd:smart00322   5 IEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPG--------SEERVVEITGPPENVEKAAELIL 65
KH-II_NusA_arch_rpt1 cd22530
first type II K-homology (KH) RNA-binding domain found in archaeal probable transcription ...
 293-340 2.63e-03

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: 36.44  E-value: 2.63e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1819251929 293 ANVQSIVVDEERHAMDVVVDEENLAIAIGRGGQNVRLASELTGWRINI 340
Cdd:cd22530    20 ATARDCLIDDENNRVIFVVKKGEMGLAIGKGGSNVKRLEEILGKNIEV 67
KH-II_SF cd02409
type II K-homology (KH) RNA-binding domain superfamily; The K-homology (KH) domain binds ...
 283-341 9.74e-03

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: 34.66  E-value: 9.74e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1819251929 283 AQFVIGALAPAN-VQSIVVDEE--RHAMDVVVDEENLAIAIGRGGQNVRLASELTG-----WRINIM 341
Cdd:cd02409     1 AEILEKLFPAAVtISDVEVEETpdGIRVIIAVEEGDPGIVIGKGGQRIRELRKELGklgggVEIDVV 67
 
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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