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Conserved domains on  [gi|1207804147|gb|OWJ98662|]
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transcription termination protein NusA [Pseudomonas sp. A46]

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
 1-478 0e+00

transcription elongation factor NusA; Validated


:

Pssm-ID: 236410 [Multi-domain]  Cd Length: 470  Bit Score: 661.18  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207804147   1 MSKEVLLVVESVSNEKGVPAGVIFEALELALATATKKRYEDEVDLRVSINRHNGNYDTFRRWTVVadEDFEDPDIQLTLD 80
Cdd:PRK09202    1 MNKELLEAIEAVAREKGIDREVVIEALEEALATAYKKKYGPEANIRVEIDRKTGDIEVFRRWEVV--EEVEDPTKEISLE 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207804147  81 QAQARDENAKIGDVIEEKIESIEFGRIAAQTAKQVIVQKVREAERAQVVEAYREKLGDIISGTVKKVTRDNVIVDLGNnA 160
Cdd:PRK09202   79 EARKIDPDAEVGDYIEEEIESVDFGRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIITGVVKRVERGNIIVDLGR-A 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207804147 161 EALLAREDIIARETFRVGARVRALLKEIRTENRGPQLILSRTAPQMLIELFRIEVPEIAEELIEVMAASRDPGSRAKIAV 240
Cdd:PRK09202  158 EAILPRKEQIPRENFRPGDRVRAYVYEVRKEARGPQIILSRTHPEFLKKLFEQEVPEIADGLIEIKAIARDPGSRAKIAV 237

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207804147 241 RSKDKRIDPQGACIGMRGSRVQAVSGELGGERVDIVLWDDNPAQFVINAMAPAEVVAIIVDEDAHAMDIAVAEDNLAQAI 320
Cdd:PRK09202  238 KSNDPRIDPVGACVGMRGSRIQAISNELGGEKIDIILWSDDPAQFIINALSPAEVSSVVVDEDEHSADVVVPDDQLSLAI 317

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207804147 321 GRGGQNVRLASQLTGWTLNVMTEADIQAKQQAETGGILRSFVDELEVDEELAQVLVEEGFTSLEEIAYVPMEEMLSIEGF 400
Cdd:PRK09202  318 GKNGQNVRLASKLTGWKIDIMTEEEASEKRQAEFDAILDLFMEALDIDEEIAQLLVEEGFSSLEELAYVPVEELLEIEGF 397

                         410       420       430       440       450       460       470
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1207804147 401 DEDIVNELRARAKDRLLTKAIATEEKLADaqpaeDLLSLEGMDKDLAVELAVRGVINREDLAEQSIDDLLDIDGMDEE 478
Cdd:PRK09202  398 DEETVEELRERAKEALETEALAQEEKLAD-----DLLSLEGLDRELAFKLAEKGIKTLEDLAEQAVDELIDIEGDEEK 470
 
Name Accession Description Interval E-value
nusA PRK09202
transcription elongation factor NusA; Validated
 1-478 0e+00

transcription elongation factor NusA; Validated


Pssm-ID: 236410 [Multi-domain]  Cd Length: 470  Bit Score: 661.18  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207804147   1 MSKEVLLVVESVSNEKGVPAGVIFEALELALATATKKRYEDEVDLRVSINRHNGNYDTFRRWTVVadEDFEDPDIQLTLD 80
Cdd:PRK09202    1 MNKELLEAIEAVAREKGIDREVVIEALEEALATAYKKKYGPEANIRVEIDRKTGDIEVFRRWEVV--EEVEDPTKEISLE 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207804147  81 QAQARDENAKIGDVIEEKIESIEFGRIAAQTAKQVIVQKVREAERAQVVEAYREKLGDIISGTVKKVTRDNVIVDLGNnA 160
Cdd:PRK09202   79 EARKIDPDAEVGDYIEEEIESVDFGRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIITGVVKRVERGNIIVDLGR-A 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207804147 161 EALLAREDIIARETFRVGARVRALLKEIRTENRGPQLILSRTAPQMLIELFRIEVPEIAEELIEVMAASRDPGSRAKIAV 240
Cdd:PRK09202  158 EAILPRKEQIPRENFRPGDRVRAYVYEVRKEARGPQIILSRTHPEFLKKLFEQEVPEIADGLIEIKAIARDPGSRAKIAV 237

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207804147 241 RSKDKRIDPQGACIGMRGSRVQAVSGELGGERVDIVLWDDNPAQFVINAMAPAEVVAIIVDEDAHAMDIAVAEDNLAQAI 320
Cdd:PRK09202  238 KSNDPRIDPVGACVGMRGSRIQAISNELGGEKIDIILWSDDPAQFIINALSPAEVSSVVVDEDEHSADVVVPDDQLSLAI 317

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207804147 321 GRGGQNVRLASQLTGWTLNVMTEADIQAKQQAETGGILRSFVDELEVDEELAQVLVEEGFTSLEEIAYVPMEEMLSIEGF 400
Cdd:PRK09202  318 GKNGQNVRLASKLTGWKIDIMTEEEASEKRQAEFDAILDLFMEALDIDEEIAQLLVEEGFSSLEELAYVPVEELLEIEGF 397

                         410       420       430       440       450       460       470
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1207804147 401 DEDIVNELRARAKDRLLTKAIATEEKLADaqpaeDLLSLEGMDKDLAVELAVRGVINREDLAEQSIDDLLDIDGMDEE 478
Cdd:PRK09202  398 DEETVEELRERAKEALETEALAQEEKLAD-----DLLSLEGLDRELAFKLAEKGIKTLEDLAEQAVDELIDIEGDEEK 470
NusA COG0195
Transcription antitermination factor NusA, contains S1 and KH domains [Transcription];
1-353 1.85e-143

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


Pssm-ID: 439965 [Multi-domain]  Cd Length: 353  Bit Score: 415.42  E-value: 1.85e-143
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207804147   1 MSKEVLLVVESVSNEKGVPAGVIFEALELALATATKKRYEDEVDLRVSINRhngNYDTFRRWTVVADEDFEDPDIQLTLD 80
Cdd:COG0195     4 MLLELLEALEELEKEKGIDKEILIEALEAALKKAYKKNYGNEVVVRVIIDG---DTGEIRVYVVKEVVEEVEDPREEILL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207804147  81 QAQARDENAKIGDVIEEKIESIEFGRIAAQTAKQVIVQKVREAERAQVVEAYREKLGDIISGTVKKVTRDNVIVDLGNNA 160
Cdd:COG0195    81 EAAKEDDPDEEGGDIIEEEVPPDFFGRIAAQAAKQVIQQKRREAEREIIYEEFKDRGGEIVGGVVQRVERGNVIVDLGKV 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207804147 161 EALLAREDIIARETFRVGARVRALLKEIRTENRGPQLILSRTAPQMLIELFRIEVPEIAEELIEVMAASRDPGSRAKIAV 240
Cdd:COG0195   161 EAILPRREQIPGENYRVGDRIRAYVLEVRKETRGPQIILSRTHPEFLKRLFELEVPEIADGIVEIKAIAREPGSRAKIAV 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207804147 241 RSKDKRIDPQGACIGMRGSRVQAVSGELGGERVDIVLWDDNPAQFVINAMAPAEVVAIIVDEDAHAMDIAVAEDNLAQAI 320
Cdd:COG0195   241 YSNDPRVDPVGACVGMRGSRVQAVVNELNGEKIDIILWSEDPAQFIANALSPAKVSSVEVDEEEKSADVVVPDDQLSLAI 320

                         330       340       350
                  ....*....|....*....|....*....|...
gi 1207804147 321 GRGGQNVRLASQLTGWTLNVMTEADIQAKQQAE 353
Cdd:COG0195   321 GKGGQNVRLAAKLTGWKIDIKSESEAEEKREEE 353
NusA TIGR01953
transcription termination factor NusA; This model describes NusA, or N utilization substance ...
 4-345 3.00e-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: 396.63  E-value: 3.00e-136
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207804147   4 EVLLVVESVSNEKGVPAGVIFEALELALATATKKRYEDEVDLRVSINRHNGNYDTFRRWTVVadEDFEDPDIQLTLDQAQ 83
Cdd:TIGR01953   1 EFLAAIEALAKEKGISIETVIEAIEEALEQAYKKTFGQDENVEVNIDRKTGDINVYRRKEVV--EEVEDPSLEISLEDAR 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207804147  84 ARDENAKIGDVIEEKIESIEFGRIAAQTAKQVIVQKVREAERAQVVEAYREKLGDIISGTVKKVTRD-NVIVDLGNNaEA 162
Cdd:TIGR01953  79 EIDPDVQIGDEVKKEIPPENFGRIAAQTAKQVILQKIREAERERVYDEFSSKEGEIISGTVKRVNRRgNLFVELGKT-EG 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207804147 163 LLAREDIIARETFRVGARVRALLKEIRTENRGPQLILSRTAPQMLIELFRIEVPEIAEELIEVMAASRDPGSRAKIAVRS 242
Cdd:TIGR01953 158 ILPKKEQIPGEKFRIGDRIKAYVYEVRKTAKGPQIILSRTHPEFVKELLKLEVPEIADGIIEIKKIAREPGYRTKIAVES 237

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207804147 243 KDKRIDPQGACIGMRGSRVQAVSGELGGERVDIVLWDDNPAQFVINAMAPAEVVAI-IVDEDAHAMDIAVAEDNLAQAIG 321
Cdd:TIGR01953 238 NDENIDPVGACVGPKGSRIQAISKELNGEKIDIIEYSDDPAEFIANALSPAKVISVeVLDEDKRSAEVVVPDDQLSLAIG 317

                         330       340
                  ....*....|....*....|....
gi 1207804147 322 RGGQNVRLASQLTGWTLNVMTEAD 345
Cdd:TIGR01953 318 KGGQNVRLASKLTGWNIDVKTESQ 341
NusA_N pfam08529
NusA N-terminal domain; This domain represents the RNA polymerase binding domain of NusA.
 6-125 8.93e-44

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


Pssm-ID: 462512 [Multi-domain]  Cd Length: 120  Bit Score: 150.29  E-value: 8.93e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207804147   6 LLVVESVSNEKGVPAGVIFEALELALATATKKRYEDEVDLRVSINRHNGNYDTFRRWTVVadEDFEDPDIQLTLDQAQAR 85
Cdd:pfam08529   2 LEALEELAKEKGIDKEVLIEAIEEALLKAYKKKYGADENVRVEIDRETGDIEVYRRKEVV--EEVEDPDTEISLEEAKKI 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1207804147  86 DENAKIGDVIEEKIESIEFGRIAAQTAKQVIVQKVREAER 125
Cdd:pfam08529  80 DPDAEVGDVVEEEVTPKDFGRIAAQTAKQVIIQKIREAER 119
KH-II_NusA_rpt1 cd02134
first type II K-homology (KH) RNA-binding domain found in transcription termination ...
 204-278 2.27e-33

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: 121.10  E-value: 2.27e-33
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1207804147 204 PQMLIELFRIEVPEIAEELIEVMAASRDPGSRAKIAVRSKDKRIDPQGACIGMRGSRVQAVSGELGGERVDIVLW 278
Cdd:cd02134     2 PEFLKRLFELEVPEIADGIVEIKAIAREPGSRTKVAVASNDPRVDPVGACVGVRGSRIQAIVEELGGEKIDIVLW 76
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
135-201 7.05e-08

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 49.52  E-value: 7.05e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1207804147  135 KLGDIISGTVKKVTRDNVIVDLGNNAEALLAREDII------ARETFRVGARVRALLKEIRTENRgpQLILSR 201
Cdd:smart00316   1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSdkrvkdPEEVLKVGDEVKVKVLSVDEEKG--RIILSL 71
 
Name Accession Description Interval E-value
nusA PRK09202
transcription elongation factor NusA; Validated
 1-478 0e+00

transcription elongation factor NusA; Validated


Pssm-ID: 236410 [Multi-domain]  Cd Length: 470  Bit Score: 661.18  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207804147   1 MSKEVLLVVESVSNEKGVPAGVIFEALELALATATKKRYEDEVDLRVSINRHNGNYDTFRRWTVVadEDFEDPDIQLTLD 80
Cdd:PRK09202    1 MNKELLEAIEAVAREKGIDREVVIEALEEALATAYKKKYGPEANIRVEIDRKTGDIEVFRRWEVV--EEVEDPTKEISLE 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207804147  81 QAQARDENAKIGDVIEEKIESIEFGRIAAQTAKQVIVQKVREAERAQVVEAYREKLGDIISGTVKKVTRDNVIVDLGNnA 160
Cdd:PRK09202   79 EARKIDPDAEVGDYIEEEIESVDFGRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIITGVVKRVERGNIIVDLGR-A 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207804147 161 EALLAREDIIARETFRVGARVRALLKEIRTENRGPQLILSRTAPQMLIELFRIEVPEIAEELIEVMAASRDPGSRAKIAV 240
Cdd:PRK09202  158 EAILPRKEQIPRENFRPGDRVRAYVYEVRKEARGPQIILSRTHPEFLKKLFEQEVPEIADGLIEIKAIARDPGSRAKIAV 237

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207804147 241 RSKDKRIDPQGACIGMRGSRVQAVSGELGGERVDIVLWDDNPAQFVINAMAPAEVVAIIVDEDAHAMDIAVAEDNLAQAI 320
Cdd:PRK09202  238 KSNDPRIDPVGACVGMRGSRIQAISNELGGEKIDIILWSDDPAQFIINALSPAEVSSVVVDEDEHSADVVVPDDQLSLAI 317

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207804147 321 GRGGQNVRLASQLTGWTLNVMTEADIQAKQQAETGGILRSFVDELEVDEELAQVLVEEGFTSLEEIAYVPMEEMLSIEGF 400
Cdd:PRK09202  318 GKNGQNVRLASKLTGWKIDIMTEEEASEKRQAEFDAILDLFMEALDIDEEIAQLLVEEGFSSLEELAYVPVEELLEIEGF 397

                         410       420       430       440       450       460       470
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1207804147 401 DEDIVNELRARAKDRLLTKAIATEEKLADaqpaeDLLSLEGMDKDLAVELAVRGVINREDLAEQSIDDLLDIDGMDEE 478
Cdd:PRK09202  398 DEETVEELRERAKEALETEALAQEEKLAD-----DLLSLEGLDRELAFKLAEKGIKTLEDLAEQAVDELIDIEGDEEK 470
NusA COG0195
Transcription antitermination factor NusA, contains S1 and KH domains [Transcription];
1-353 1.85e-143

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


Pssm-ID: 439965 [Multi-domain]  Cd Length: 353  Bit Score: 415.42  E-value: 1.85e-143
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207804147   1 MSKEVLLVVESVSNEKGVPAGVIFEALELALATATKKRYEDEVDLRVSINRhngNYDTFRRWTVVADEDFEDPDIQLTLD 80
Cdd:COG0195     4 MLLELLEALEELEKEKGIDKEILIEALEAALKKAYKKNYGNEVVVRVIIDG---DTGEIRVYVVKEVVEEVEDPREEILL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207804147  81 QAQARDENAKIGDVIEEKIESIEFGRIAAQTAKQVIVQKVREAERAQVVEAYREKLGDIISGTVKKVTRDNVIVDLGNNA 160
Cdd:COG0195    81 EAAKEDDPDEEGGDIIEEEVPPDFFGRIAAQAAKQVIQQKRREAEREIIYEEFKDRGGEIVGGVVQRVERGNVIVDLGKV 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207804147 161 EALLAREDIIARETFRVGARVRALLKEIRTENRGPQLILSRTAPQMLIELFRIEVPEIAEELIEVMAASRDPGSRAKIAV 240
Cdd:COG0195   161 EAILPRREQIPGENYRVGDRIRAYVLEVRKETRGPQIILSRTHPEFLKRLFELEVPEIADGIVEIKAIAREPGSRAKIAV 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207804147 241 RSKDKRIDPQGACIGMRGSRVQAVSGELGGERVDIVLWDDNPAQFVINAMAPAEVVAIIVDEDAHAMDIAVAEDNLAQAI 320
Cdd:COG0195   241 YSNDPRVDPVGACVGMRGSRVQAVVNELNGEKIDIILWSEDPAQFIANALSPAKVSSVEVDEEEKSADVVVPDDQLSLAI 320

                         330       340       350
                  ....*....|....*....|....*....|...
gi 1207804147 321 GRGGQNVRLASQLTGWTLNVMTEADIQAKQQAE 353
Cdd:COG0195   321 GKGGQNVRLAAKLTGWKIDIKSESEAEEKREEE 353
NusA TIGR01953
transcription termination factor NusA; This model describes NusA, or N utilization substance ...
 4-345 3.00e-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: 396.63  E-value: 3.00e-136
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207804147   4 EVLLVVESVSNEKGVPAGVIFEALELALATATKKRYEDEVDLRVSINRHNGNYDTFRRWTVVadEDFEDPDIQLTLDQAQ 83
Cdd:TIGR01953   1 EFLAAIEALAKEKGISIETVIEAIEEALEQAYKKTFGQDENVEVNIDRKTGDINVYRRKEVV--EEVEDPSLEISLEDAR 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207804147  84 ARDENAKIGDVIEEKIESIEFGRIAAQTAKQVIVQKVREAERAQVVEAYREKLGDIISGTVKKVTRD-NVIVDLGNNaEA 162
Cdd:TIGR01953  79 EIDPDVQIGDEVKKEIPPENFGRIAAQTAKQVILQKIREAERERVYDEFSSKEGEIISGTVKRVNRRgNLFVELGKT-EG 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207804147 163 LLAREDIIARETFRVGARVRALLKEIRTENRGPQLILSRTAPQMLIELFRIEVPEIAEELIEVMAASRDPGSRAKIAVRS 242
Cdd:TIGR01953 158 ILPKKEQIPGEKFRIGDRIKAYVYEVRKTAKGPQIILSRTHPEFVKELLKLEVPEIADGIIEIKKIAREPGYRTKIAVES 237

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207804147 243 KDKRIDPQGACIGMRGSRVQAVSGELGGERVDIVLWDDNPAQFVINAMAPAEVVAI-IVDEDAHAMDIAVAEDNLAQAIG 321
Cdd:TIGR01953 238 NDENIDPVGACVGPKGSRIQAISKELNGEKIDIIEYSDDPAEFIANALSPAKVISVeVLDEDKRSAEVVVPDDQLSLAIG 317

                         330       340
                  ....*....|....*....|....
gi 1207804147 322 RGGQNVRLASQLTGWTLNVMTEAD 345
Cdd:TIGR01953 318 KGGQNVRLASKLTGWNIDVKTESQ 341
NusA_N pfam08529
NusA N-terminal domain; This domain represents the RNA polymerase binding domain of NusA.
 6-125 8.93e-44

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


Pssm-ID: 462512 [Multi-domain]  Cd Length: 120  Bit Score: 150.29  E-value: 8.93e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207804147   6 LLVVESVSNEKGVPAGVIFEALELALATATKKRYEDEVDLRVSINRHNGNYDTFRRWTVVadEDFEDPDIQLTLDQAQAR 85
Cdd:pfam08529   2 LEALEELAKEKGIDKEVLIEAIEEALLKAYKKKYGADENVRVEIDRETGDIEVYRRKEVV--EEVEDPDTEISLEEAKKI 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1207804147  86 DENAKIGDVIEEKIESIEFGRIAAQTAKQVIVQKVREAER 125
Cdd:pfam08529  80 DPDAEVGDVVEEEVTPKDFGRIAAQTAKQVIIQKIREAER 119
KH-II_NusA_rpt1 cd02134
first type II K-homology (KH) RNA-binding domain found in transcription termination ...
 204-278 2.27e-33

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: 121.10  E-value: 2.27e-33
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1207804147 204 PQMLIELFRIEVPEIAEELIEVMAASRDPGSRAKIAVRSKDKRIDPQGACIGMRGSRVQAVSGELGGERVDIVLW 278
Cdd:cd02134     2 PEFLKRLFELEVPEIADGIVEIKAIAREPGSRTKVAVASNDPRVDPVGACVGVRGSRIQAIVEELGGEKIDIVLW 76
KH_5 pfam13184
NusA-like KH domain;
232-300 6.96e-27

NusA-like KH domain;


Pssm-ID: 433018 [Multi-domain]  Cd Length: 69  Bit Score: 103.08  E-value: 6.96e-27
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1207804147 232 PGSRAKIAVRSKDKRIDPQGACIGMRGSRVQAVSGELGGERVDIVLWDDNPAQFVINAMAPAEVVAIIV 300
Cdd:pfam13184   1 PGNRAKIAVYSRDERIDPVGACVGKKGSRIQAISRELNGEKIDIVEYSEDLRTFIKNALSPARVLSVNI 69
KH-II_NusA_rpt2 cd22529
second type II K-homology (KH) RNA-binding domain found in transcription termination ...
 281-341 9.91e-25

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: 96.84  E-value: 9.91e-25
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1207804147 281 NPAQFVINAMAPAEVVAIIVDEDAHAMDIAVAEDNLAQAIGRGGQNVRLASQLTGWTLNVM 341
Cdd:cd22529     1 DPAEFVANALSPAKVISVEIDEDDKKARVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIK 61
S1_NusA cd04455
S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like ...
 134-201 4.43e-23

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: 92.12  E-value: 4.43e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1207804147 134 EKLGDIISGTVKKVTRDNVIVDLGNnAEALLAREDIIARETFRVGARVRALLKEIRTENRGPQLILSR 201
Cdd:cd04455     1 DREGEIVTGIVKRVDRGNVIVDLGK-VEAILPKKEQIPGESYRPGDRIKAYVLEVRKTSKGPQIILSR 67
nusA_Cterm_rpt TIGR01954
transcription termination factor NusA, C-terminal duplication; NusA is a bacterial ...
 367-416 9.54e-13

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: 62.70  E-value: 9.54e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1207804147 367 VDEELAQVLVEEGFTSLEEIAYVPMEEMLSIEGFDEDIVNELRARAKDRL 416
Cdd:TIGR01954   1 INEEIAQLLVEEGFTTVEDLAYVPIDELLSIEGFDEETAKELINRARNAL 50
nusA_Cterm_rpt TIGR01954
transcription termination factor NusA, C-terminal duplication; NusA is a bacterial ...
 442-491 3.80e-11

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: 58.08  E-value: 3.80e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1207804147 442 MDKDLAVELAVRGVINREDLAEQSIDDLLDIDGMDEERAGKLIMAARAHW 491
Cdd:TIGR01954   1 INEEIAQLLVEEGFTTVEDLAYVPIDELLSIEGFDEETAKELINRARNAL 50
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
135-201 7.05e-08

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 49.52  E-value: 7.05e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1207804147  135 KLGDIISGTVKKVTRDNVIVDLGNNAEALLAREDII------ARETFRVGARVRALLKEIRTENRgpQLILSR 201
Cdd:smart00316   1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSdkrvkdPEEVLKVGDEVKVKVLSVDEEKG--RIILSL 71
nusA_arch TIGR01952
NusA family KH domain protein, archaeal; This model represents a family of archaeal proteins ...
 251-335 8.64e-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: 51.26  E-value: 8.64e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207804147 251 GACIGMRGSRVQAVSgELGGERVDIVLWDDNPAQFVINAMAPAEV--VAIIVDEDAHAMDIAVAEDNLAQAIGRGGQNVR 328
Cdd:TIGR01952  45 GAAIGKGGENVKRLE-ELIGKSIELIEYSENLEEFVANKLAPAEVknVTVSEFNGKKVAYVEVHPRDKGIAIGKGGKNIE 123


                  ....*..
gi 1207804147 329 LASQLTG 335
Cdd:TIGR01952 124 RAKELAK 130
HHH_5 pfam14520
Helix-hairpin-helix domain;
434-488 8.95e-08

Helix-hairpin-helix domain;


Pssm-ID: 434010 [Multi-domain]  Cd Length: 57  Bit Score: 48.64  E-value: 8.95e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1207804147 434 EDLLSLEGMDKDLAVELAVRGVINREDLAEQSIDDLLDIDGMDEERAGKLIMAAR 488
Cdd:pfam14520   2 EELLSISGIGPKTALALLSAGIGTVEDLAEADVDELAEIPGIGEKTAQRIILELR 56
PRK08406 PRK08406
transcription elongation factor NusA-like protein; Validated
 251-333 1.26e-07

transcription elongation factor NusA-like protein; Validated


Pssm-ID: 181413 [Multi-domain]  Cd Length: 140  Bit Score: 50.60  E-value: 1.26e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207804147 251 GACIGMRGSRVQAVSgELGGERVDIVLWDDNPAQFVINAMAPAEVVAIIV-----DEDAHamdIAVAEDNLAQAIGRGGQ 325
Cdd:PRK08406   44 GLAIGKGGENVKRLE-EKLGKDIELVEYSDDPEEFIKNIFAPAAVRSVTIkkkngDKVAY---VEVAPEDKGIAIGKNGK 119


                  ....*...
gi 1207804147 326 NVRLASQL 333
Cdd:PRK08406  120 NIERAKDL 127
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 135-197 2.73e-05

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: 42.27  E-value: 2.73e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1207804147 135 KLGDIISGTVKKVTRDNVIVDLGNNAEALLAREDIIAR------ETFRVGARVRALLKEIRTENRGPQL 197
Cdd:pfam00575   2 EKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDhvedpdEVIKVGDEVKVKVLKVDKDRRRIIL 70
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 137-201 7.79e-05

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: 44.65  E-value: 7.79e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1207804147 137 GDIISGTVKKVTRDNVIVDLGNNAEALLAREDIIARE---TFRVGARVRALLkeIRTENRGPQLILSR 201
Cdd:COG0539    19 GDIVKGTVVSIDDDEVLVDIGYKSEGIIPLSEFSDEPgelEVKVGDEVEVYV--EKVEDGEGEIVLSK 84
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 135-197 3.42e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 43.23  E-value: 3.42e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1207804147 135 KLGDIISGTVKKVTRDNVIVDLGNNAEALLAREDII------ARETFRVGARVRALLKEIRTENRGPQL 197
Cdd:PRK06299  459 KKGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSrdrvedATEVLKVGDEVEAKVINIDRKNRRISL 527
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 137-205 5.88e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 42.34  E-value: 5.88e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1207804147 137 GDIISGTVKKVTRDNVIVDLGNNAEALL-ARE-----DIIARETFRVGARVRALLkeIRTENRGPQLILSRTAPQ 205
Cdd:PRK07899   36 GDIVEGTVVKVDRDEVLLDIGYKTEGVIpSRElsikhDVDPNEVVEVGDEVEALV--LQKEDKEGRLILSKKRAQ 108
S1_RPS1_repeat_ec1_hs1 cd05687
S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 137-201 2.04e-03

S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240192 [Multi-domain]  Cd Length: 70  Bit Score: 36.74  E-value: 2.04e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1207804147 137 GDIISGTVKKVTRDNVIVDLGNNAEALLAREDII------ARETFRVGARVRALLkeIRTENRGPQLILSR 201
Cdd:cd05687     1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSddpienGEDEVKVGDEVEVYV--LRVEDEEGNVVLSK 69
KH-II_SF cd02409
type II K-homology (KH) RNA-binding domain superfamily; The K-homology (KH) domain binds ...
 283-335 3.12e-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: 36.20  E-value: 3.12e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1207804147 283 AQFVINAMAPA-EVVAIIVDE--DAHAMDIAVAEDNLAQAIGRGGQNVRLASQLTG 335
Cdd:cd02409     1 AEILEKLFPAAvTISDVEVEEtpDGIRVIIAVEEGDPGIVIGKGGQRIRELRKELG 56
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 135-201 4.43e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 39.76  E-value: 4.43e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207804147 135 KLGDIISGTVKKVTRDNVIVDLGNNAEALLAREDIIARE---TFRVGARVRALLKeiRTENRGPQLILSR 201
Cdd:PRK06299   29 REGSIVKGTVVAIDKDYVLVDVGLKSEGRIPLEEFKNEQgelEVKVGDEVEVYVE--RIEDGFGETVLSR 96
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 137-214 7.44e-03

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 38.95  E-value: 7.44e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1207804147 137 GDIISGTVKKVTRDNVIVDLGNNAEALLAREDII-ARETFRVGARVRALLKeiRTENRGPQLILSRTAPQMLIELFRIE 214
Cdd:TIGR00717  19 GSIVKGTVVAINKDTVFVDVGLKSEGRIPKEEFLdAPLEIQVGDEVEVYLD--RVEDRFGETVLSREKAQRHELWIKLE 95
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 135-193 7.88e-03

S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240213 [Multi-domain]  Cd Length: 77  Bit Score: 35.38  E-value: 7.88e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1207804147 135 KLGDIISGTVKKVTRDNVIVDL-GNNAEALLAREDII------ARETFRVGARVRALLKEIRTENR 193
Cdd:cd05708     1 KVGQKIDGTVRRVEDYGVFIDIdGTNVSGLCHKSEISdnrvadASKLFRVGDKVRAKVLKIDAEKK 66
KH-II_NusA_arch_rpt2 cd22531
second type II K-homology (KH) RNA-binding domain found in archaeal probable transcription ...
 282-333 8.52e-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: 34.91  E-value: 8.52e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1207804147 282 PAQFVINAMAPAEVVAIIVDEDAHAMD--IAVAEDNLAQAIGRGGQNVRLASQL 333
Cdd:cd22531     1 PEEFIKNIFAPAKVQNVKVKEKNGKKVaiVEVPPKDKGIAIGKNGKNIERAKLL 54
 
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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