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Conserved domains on  [gi|2787127128|ref|WP_370275314|]
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transcription termination factor NusA [Hyphomonas atlantica]

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
 9-481 0e+00

transcription elongation factor NusA; Validated


:

Pssm-ID: 236410 [Multi-domain]  Cd Length: 470  Bit Score: 607.64  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2787127128   9 NRLEILQIAKAVAEEKAIDQTIVIEAMQEAIEKAAKAKYGQEHDIRAKIDATTGEQTLWRVQTVVADdaFEDEAKELRLS 88
Cdd:PRK09202    1 MNKELLEAIEAVAREKGIDREVVIEALEEALATAYKKKYGPEANIRVEIDRKTGDIEVFRRWEVVEE--VEDPTKEISLE 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2787127128  89 EAKKLDETLEAGDELKEELPPFDFGRVAAQTAKQVIMQKVRDAERERQYNEYKDRVGEVISGVVKRVEYGHVIVDLGRAE 168
Cdd:PRK09202   79 EARKIDPDAEVGDYIEEEIESVDFGRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIITGVVKRVERGNIIVDLGRAE 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2787127128 169 GIIRRNDGIPRENFQTNDRVRAYLYKVSRETKGPQIFLSRAAPDFMVRLFAQEVPEVYEGVIEIKACSRDPGSRAKIGVI 248
Cdd:PRK09202  159 AILPRKEQIPRENFRPGDRVRAYVYEVRKEARGPQIILSRTHPEFLKKLFEQEVPEIADGLIEIKAIARDPGSRAKIAVK 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2787127128 249 SNDSSIDPVGAWVGMRGARVQAVVGELSGEKIDIIPWNYDDATFIVNALQPAEVSKVVLDEEERRVEVVVADDQFPLAIG 328
Cdd:PRK09202  239 SNDPRIDPVGACVGMRGSRIQAISNELGGEKIDIILWSDDPAQFIINALSPAEVSSVVVDEDEHSADVVVPDDQLSLAIG 318

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2787127128 329 RRGQNVRLASQLTGWQIDLVTETADSERYQREFQERTDLFMKALDADETLAQLLASEGFETVEEIAYVAPEDFITIEGFD 408
Cdd:PRK09202  319 KNGQNVRLASKLTGWKIDIMTEEEASEKRQAEFDAILDLFMEALDIDEEIAQLLVEEGFSSLEELAYVPVEELLEIEGFD 398

                         410       420       430       440       450       460       470
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2787127128 409 EDVAEELQERAREFLERLAAENDAKRrelgvEDAVMELEGMSPSFAVRLGEEGVQTLDDVAGLVPDDITGWRE 481
Cdd:PRK09202  399 EETVEELRERAKEALETEALAQEEKL-----ADDLLSLEGLDRELAFKLAEKGIKTLEDLAEQAVDELIDIEG 466
 
Name Accession Description Interval E-value
nusA PRK09202
transcription elongation factor NusA; Validated
 9-481 0e+00

transcription elongation factor NusA; Validated


Pssm-ID: 236410 [Multi-domain]  Cd Length: 470  Bit Score: 607.64  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2787127128   9 NRLEILQIAKAVAEEKAIDQTIVIEAMQEAIEKAAKAKYGQEHDIRAKIDATTGEQTLWRVQTVVADdaFEDEAKELRLS 88
Cdd:PRK09202    1 MNKELLEAIEAVAREKGIDREVVIEALEEALATAYKKKYGPEANIRVEIDRKTGDIEVFRRWEVVEE--VEDPTKEISLE 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2787127128  89 EAKKLDETLEAGDELKEELPPFDFGRVAAQTAKQVIMQKVRDAERERQYNEYKDRVGEVISGVVKRVEYGHVIVDLGRAE 168
Cdd:PRK09202   79 EARKIDPDAEVGDYIEEEIESVDFGRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIITGVVKRVERGNIIVDLGRAE 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2787127128 169 GIIRRNDGIPRENFQTNDRVRAYLYKVSRETKGPQIFLSRAAPDFMVRLFAQEVPEVYEGVIEIKACSRDPGSRAKIGVI 248
Cdd:PRK09202  159 AILPRKEQIPRENFRPGDRVRAYVYEVRKEARGPQIILSRTHPEFLKKLFEQEVPEIADGLIEIKAIARDPGSRAKIAVK 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2787127128 249 SNDSSIDPVGAWVGMRGARVQAVVGELSGEKIDIIPWNYDDATFIVNALQPAEVSKVVLDEEERRVEVVVADDQFPLAIG 328
Cdd:PRK09202  239 SNDPRIDPVGACVGMRGSRIQAISNELGGEKIDIILWSDDPAQFIINALSPAEVSSVVVDEDEHSADVVVPDDQLSLAIG 318

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2787127128 329 RRGQNVRLASQLTGWQIDLVTETADSERYQREFQERTDLFMKALDADETLAQLLASEGFETVEEIAYVAPEDFITIEGFD 408
Cdd:PRK09202  319 KNGQNVRLASKLTGWKIDIMTEEEASEKRQAEFDAILDLFMEALDIDEEIAQLLVEEGFSSLEELAYVPVEELLEIEGFD 398

                         410       420       430       440       450       460       470
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2787127128 409 EDVAEELQERAREFLERLAAENDAKRrelgvEDAVMELEGMSPSFAVRLGEEGVQTLDDVAGLVPDDITGWRE 481
Cdd:PRK09202  399 EETVEELRERAKEALETEALAQEEKL-----ADDLLSLEGLDRELAFKLAEKGIKTLEDLAEQAVDELIDIEG 466
NusA COG0195
Transcription antitermination factor NusA, contains S1 and KH domains [Transcription];
7-360 2.98e-150

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


Pssm-ID: 439965 [Multi-domain]  Cd Length: 353  Bit Score: 436.22  E-value: 2.98e-150
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2787127128   7 SANRLEILQIAKAVAEEKAIDQTIVIEAMQEAIEKAAKAKYGQEHDIRAKIDATTGEQTLWRVQTVVADDafEDEAKELR 86
Cdd:COG0195     2 SMMLLELLEALEELEKEKGIDKEILIEALEAALKKAYKKNYGNEVVVRVIIDGDTGEIRVYVVKEVVEEV--EDPREEIL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2787127128  87 LSEAKKLDETLEAGDELKEELPPFDFGRVAAQTAKQVIMQKVRDAERERQYNEYKDRVGEVISGVVKRVEYGHVIVDLGR 166
Cdd:COG0195    80 LEAAKEDDPDEEGGDIIEEEVPPDFFGRIAAQAAKQVIQQKRREAEREIIYEEFKDRGGEIVGGVVQRVERGNVIVDLGK 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2787127128 167 AEGIIRRNDGIPRENFQTNDRVRAYLYKVSRETKGPQIFLSRAAPDFMVRLFAQEVPEVYEGVIEIKACSRDPGSRAKIG 246
Cdd:COG0195   160 VEAILPRREQIPGENYRVGDRIRAYVLEVRKETRGPQIILSRTHPEFLKRLFELEVPEIADGIVEIKAIAREPGSRAKIA 239

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2787127128 247 VISNDSSIDPVGAWVGMRGARVQAVVGELSGEKIDIIPWNYDDATFIVNALQPAEVSKVVLDEEERRVEVVVADDQFPLA 326
Cdd:COG0195   240 VYSNDPRVDPVGACVGMRGSRVQAVVNELNGEKIDIILWSEDPAQFIANALSPAKVSSVEVDEEEKSADVVVPDDQLSLA 319

                         330       340       350
                  ....*....|....*....|....*....|....
gi 2787127128 327 IGRRGQNVRLASQLTGWQIDLVTETADSERYQRE 360
Cdd:COG0195   320 IGKGGQNVRLAAKLTGWKIDIKSESEAEEKREEE 353
NusA TIGR01953
transcription termination factor NusA; This model describes NusA, or N utilization substance ...
 12-350 1.74e-142

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: 415.89  E-value: 1.74e-142
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2787127128  12 EILQIAKAVAEEKAIDQTIVIEAMQEAIEKAAKAKYGQEHDIRAKIDATTGEQTLWRVQTVVadDAFEDEAKELRLSEAK 91
Cdd:TIGR01953   1 EFLAAIEALAKEKGISIETVIEAIEEALEQAYKKTFGQDENVEVNIDRKTGDINVYRRKEVV--EEVEDPSLEISLEDAR 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2787127128  92 KLDETLEAGDELKEELPPFDFGRVAAQTAKQVIMQKVRDAERERQYNEYKDRVGEVISGVVKRVEY-GHVIVDLGRAEGI 170
Cdd:TIGR01953  79 EIDPDVQIGDEVKKEIPPENFGRIAAQTAKQVILQKIREAERERVYDEFSSKEGEIISGTVKRVNRrGNLFVELGKTEGI 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2787127128 171 IRRNDGIPRENFQTNDRVRAYLYKVSRETKGPQIFLSRAAPDFMVRLFAQEVPEVYEGVIEIKACSRDPGSRAKIGVISN 250
Cdd:TIGR01953 159 LPKKEQIPGEKFRIGDRIKAYVYEVRKTAKGPQIILSRTHPEFVKELLKLEVPEIADGIIEIKKIAREPGYRTKIAVESN 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2787127128 251 DSSIDPVGAWVGMRGARVQAVVGELSGEKIDIIPWNYDDATFIVNALQPAEVSKV-VLDEEERRVEVVVADDQFPLAIGR 329
Cdd:TIGR01953 239 DENIDPVGACVGPKGSRIQAISKELNGEKIDIIEYSDDPAEFIANALSPAKVISVeVLDEDKRSAEVVVPDDQLSLAIGK 318

                         330       340
                  ....*....|....*....|.
gi 2787127128 330 RGQNVRLASQLTGWQIDLVTE 350
Cdd:TIGR01953 319 GGQNVRLASKLTGWNIDVKTE 339
NusA_N pfam08529
NusA N-terminal domain; This domain represents the RNA polymerase binding domain of NusA.
 13-134 2.76e-39

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


Pssm-ID: 462512 [Multi-domain]  Cd Length: 120  Bit Score: 139.89  E-value: 2.76e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2787127128  13 ILQIAKAVAEEKAIDQTIVIEAMQEAIEKAAKAKYGQEHDIRAKIDATTGEQTLWRVQTVVADDafEDEAKELRLSEAKK 92
Cdd:pfam08529   1 LLEALEELAKEKGIDKEVLIEAIEEALLKAYKKKYGADENVRVEIDRETGDIEVYRRKEVVEEV--EDPDTEISLEEAKK 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 2787127128  93 LDETLEAGDELKEELPPFDFGRVAAQTAKQVIMQKVRDAERE 134
Cdd:pfam08529  79 IDPDAEVGDVVEEEVTPKDFGRIAAQTAKQVIIQKIREAERE 120
KH-II_NusA_rpt1 cd02134
first type II K-homology (KH) RNA-binding domain found in transcription termination ...
 211-285 9.67e-37

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: 131.12  E-value: 9.67e-37
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2787127128 211 PDFMVRLFAQEVPEVYEGVIEIKACSRDPGSRAKIGVISNDSSIDPVGAWVGMRGARVQAVVGELSGEKIDIIPW 285
Cdd:cd02134     2 PEFLKRLFELEVPEIADGIVEIKAIAREPGSRTKVAVASNDPRVDPVGACVGVRGSRIQAIVEELGGEKIDIVLW 76
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
143-208 2.72e-06

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 45.29  E-value: 2.72e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2787127128  143 RVGEVISGVVKRVEYGHVIVDLG-------RAEGIIRRNDGIPRENFQTNDRVRAYLYKVSRETKgpQIFLSR 208
Cdd:smart00316   1 EVGDVVEGTVTEITPGGAFVDLGngvegliPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKG--RIILSL 71
 
Name Accession Description Interval E-value
nusA PRK09202
transcription elongation factor NusA; Validated
 9-481 0e+00

transcription elongation factor NusA; Validated


Pssm-ID: 236410 [Multi-domain]  Cd Length: 470  Bit Score: 607.64  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2787127128   9 NRLEILQIAKAVAEEKAIDQTIVIEAMQEAIEKAAKAKYGQEHDIRAKIDATTGEQTLWRVQTVVADdaFEDEAKELRLS 88
Cdd:PRK09202    1 MNKELLEAIEAVAREKGIDREVVIEALEEALATAYKKKYGPEANIRVEIDRKTGDIEVFRRWEVVEE--VEDPTKEISLE 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2787127128  89 EAKKLDETLEAGDELKEELPPFDFGRVAAQTAKQVIMQKVRDAERERQYNEYKDRVGEVISGVVKRVEYGHVIVDLGRAE 168
Cdd:PRK09202   79 EARKIDPDAEVGDYIEEEIESVDFGRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIITGVVKRVERGNIIVDLGRAE 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2787127128 169 GIIRRNDGIPRENFQTNDRVRAYLYKVSRETKGPQIFLSRAAPDFMVRLFAQEVPEVYEGVIEIKACSRDPGSRAKIGVI 248
Cdd:PRK09202  159 AILPRKEQIPRENFRPGDRVRAYVYEVRKEARGPQIILSRTHPEFLKKLFEQEVPEIADGLIEIKAIARDPGSRAKIAVK 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2787127128 249 SNDSSIDPVGAWVGMRGARVQAVVGELSGEKIDIIPWNYDDATFIVNALQPAEVSKVVLDEEERRVEVVVADDQFPLAIG 328
Cdd:PRK09202  239 SNDPRIDPVGACVGMRGSRIQAISNELGGEKIDIILWSDDPAQFIINALSPAEVSSVVVDEDEHSADVVVPDDQLSLAIG 318

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2787127128 329 RRGQNVRLASQLTGWQIDLVTETADSERYQREFQERTDLFMKALDADETLAQLLASEGFETVEEIAYVAPEDFITIEGFD 408
Cdd:PRK09202  319 KNGQNVRLASKLTGWKIDIMTEEEASEKRQAEFDAILDLFMEALDIDEEIAQLLVEEGFSSLEELAYVPVEELLEIEGFD 398

                         410       420       430       440       450       460       470
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2787127128 409 EDVAEELQERAREFLERLAAENDAKRrelgvEDAVMELEGMSPSFAVRLGEEGVQTLDDVAGLVPDDITGWRE 481
Cdd:PRK09202  399 EETVEELRERAKEALETEALAQEEKL-----ADDLLSLEGLDRELAFKLAEKGIKTLEDLAEQAVDELIDIEG 466
NusA COG0195
Transcription antitermination factor NusA, contains S1 and KH domains [Transcription];
7-360 2.98e-150

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


Pssm-ID: 439965 [Multi-domain]  Cd Length: 353  Bit Score: 436.22  E-value: 2.98e-150
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2787127128   7 SANRLEILQIAKAVAEEKAIDQTIVIEAMQEAIEKAAKAKYGQEHDIRAKIDATTGEQTLWRVQTVVADDafEDEAKELR 86
Cdd:COG0195     2 SMMLLELLEALEELEKEKGIDKEILIEALEAALKKAYKKNYGNEVVVRVIIDGDTGEIRVYVVKEVVEEV--EDPREEIL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2787127128  87 LSEAKKLDETLEAGDELKEELPPFDFGRVAAQTAKQVIMQKVRDAERERQYNEYKDRVGEVISGVVKRVEYGHVIVDLGR 166
Cdd:COG0195    80 LEAAKEDDPDEEGGDIIEEEVPPDFFGRIAAQAAKQVIQQKRREAEREIIYEEFKDRGGEIVGGVVQRVERGNVIVDLGK 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2787127128 167 AEGIIRRNDGIPRENFQTNDRVRAYLYKVSRETKGPQIFLSRAAPDFMVRLFAQEVPEVYEGVIEIKACSRDPGSRAKIG 246
Cdd:COG0195   160 VEAILPRREQIPGENYRVGDRIRAYVLEVRKETRGPQIILSRTHPEFLKRLFELEVPEIADGIVEIKAIAREPGSRAKIA 239

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2787127128 247 VISNDSSIDPVGAWVGMRGARVQAVVGELSGEKIDIIPWNYDDATFIVNALQPAEVSKVVLDEEERRVEVVVADDQFPLA 326
Cdd:COG0195   240 VYSNDPRVDPVGACVGMRGSRVQAVVNELNGEKIDIILWSEDPAQFIANALSPAKVSSVEVDEEEKSADVVVPDDQLSLA 319

                         330       340       350
                  ....*....|....*....|....*....|....
gi 2787127128 327 IGRRGQNVRLASQLTGWQIDLVTETADSERYQRE 360
Cdd:COG0195   320 IGKGGQNVRLAAKLTGWKIDIKSESEAEEKREEE 353
NusA TIGR01953
transcription termination factor NusA; This model describes NusA, or N utilization substance ...
 12-350 1.74e-142

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: 415.89  E-value: 1.74e-142
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2787127128  12 EILQIAKAVAEEKAIDQTIVIEAMQEAIEKAAKAKYGQEHDIRAKIDATTGEQTLWRVQTVVadDAFEDEAKELRLSEAK 91
Cdd:TIGR01953   1 EFLAAIEALAKEKGISIETVIEAIEEALEQAYKKTFGQDENVEVNIDRKTGDINVYRRKEVV--EEVEDPSLEISLEDAR 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2787127128  92 KLDETLEAGDELKEELPPFDFGRVAAQTAKQVIMQKVRDAERERQYNEYKDRVGEVISGVVKRVEY-GHVIVDLGRAEGI 170
Cdd:TIGR01953  79 EIDPDVQIGDEVKKEIPPENFGRIAAQTAKQVILQKIREAERERVYDEFSSKEGEIISGTVKRVNRrGNLFVELGKTEGI 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2787127128 171 IRRNDGIPRENFQTNDRVRAYLYKVSRETKGPQIFLSRAAPDFMVRLFAQEVPEVYEGVIEIKACSRDPGSRAKIGVISN 250
Cdd:TIGR01953 159 LPKKEQIPGEKFRIGDRIKAYVYEVRKTAKGPQIILSRTHPEFVKELLKLEVPEIADGIIEIKKIAREPGYRTKIAVESN 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2787127128 251 DSSIDPVGAWVGMRGARVQAVVGELSGEKIDIIPWNYDDATFIVNALQPAEVSKV-VLDEEERRVEVVVADDQFPLAIGR 329
Cdd:TIGR01953 239 DENIDPVGACVGPKGSRIQAISKELNGEKIDIIEYSDDPAEFIANALSPAKVISVeVLDEDKRSAEVVVPDDQLSLAIGK 318

                         330       340
                  ....*....|....*....|.
gi 2787127128 330 RGQNVRLASQLTGWQIDLVTE 350
Cdd:TIGR01953 319 GGQNVRLASKLTGWNIDVKTE 339
NusA_N pfam08529
NusA N-terminal domain; This domain represents the RNA polymerase binding domain of NusA.
 13-134 2.76e-39

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


Pssm-ID: 462512 [Multi-domain]  Cd Length: 120  Bit Score: 139.89  E-value: 2.76e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2787127128  13 ILQIAKAVAEEKAIDQTIVIEAMQEAIEKAAKAKYGQEHDIRAKIDATTGEQTLWRVQTVVADDafEDEAKELRLSEAKK 92
Cdd:pfam08529   1 LLEALEELAKEKGIDKEVLIEAIEEALLKAYKKKYGADENVRVEIDRETGDIEVYRRKEVVEEV--EDPDTEISLEEAKK 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 2787127128  93 LDETLEAGDELKEELPPFDFGRVAAQTAKQVIMQKVRDAERE 134
Cdd:pfam08529  79 IDPDAEVGDVVEEEVTPKDFGRIAAQTAKQVIIQKIREAERE 120
KH-II_NusA_rpt1 cd02134
first type II K-homology (KH) RNA-binding domain found in transcription termination ...
 211-285 9.67e-37

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: 131.12  E-value: 9.67e-37
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2787127128 211 PDFMVRLFAQEVPEVYEGVIEIKACSRDPGSRAKIGVISNDSSIDPVGAWVGMRGARVQAVVGELSGEKIDIIPW 285
Cdd:cd02134     2 PEFLKRLFELEVPEIADGIVEIKAIAREPGSRTKVAVASNDPRVDPVGACVGVRGSRIQAIVEELGGEKIDIVLW 76
S1_NusA cd04455
S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like ...
 142-208 4.51e-29

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: 109.45  E-value: 4.51e-29
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2787127128 142 DRVGEVISGVVKRVEYGHVIVDLGRAEGIIRRNDGIPRENFQTNDRVRAYLYKVSRETKGPQIFLSR 208
Cdd:cd04455     1 DREGEIVTGIVKRVDRGNVIVDLGKVEAILPKKEQIPGESYRPGDRIKAYVLEVRKTSKGPQIILSR 67
KH_5 pfam13184
NusA-like KH domain;
239-307 5.86e-24

NusA-like KH domain;


Pssm-ID: 433018 [Multi-domain]  Cd Length: 69  Bit Score: 95.38  E-value: 5.86e-24
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2787127128 239 PGSRAKIGVISNDSSIDPVGAWVGMRGARVQAVVGELSGEKIDIIPWNYDDATFIVNALQPAEVSKVVL 307
Cdd:pfam13184   1 PGNRAKIAVYSRDERIDPVGACVGKKGSRIQAISRELNGEKIDIVEYSEDLRTFIKNALSPARVLSVNI 69
KH-II_NusA_rpt2 cd22529
second type II K-homology (KH) RNA-binding domain found in transcription termination ...
 288-346 1.11e-19

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: 82.97  E-value: 1.11e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2787127128 288 DDATFIVNALQPAEVSKVVLDEEERRVEVVVADDQFPLAIGRRGQNVRLASQLTGWQID 346
Cdd:cd22529     1 DPAEFVANALSPAKVISVEIDEDDKKARVVVPDDQLSLAIGKNGQNVRLASKLTGWKID 59
nusA_Cterm_rpt TIGR01954
transcription termination factor NusA, C-terminal duplication; NusA is a bacterial ...
 375-423 1.17e-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: 59.62  E-value: 1.17e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2787127128 375 DETLAQLLASEGFETVEEIAYVAPEDFITIEGFDEDVAEELQERAREFL 423
Cdd:TIGR01954   2 NEEIAQLLVEEGFTTVEDLAYVPIDELLSIEGFDEETAKELINRARNAL 50
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
143-208 2.72e-06

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 45.29  E-value: 2.72e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2787127128  143 RVGEVISGVVKRVEYGHVIVDLG-------RAEGIIRRNDGIPRENFQTNDRVRAYLYKVSRETKgpQIFLSR 208
Cdd:smart00316   1 EVGDVVEGTVTEITPGGAFVDLGngvegliPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKG--RIILSL 71
HHH_5 pfam14520
Helix-hairpin-helix domain;
378-421 3.71e-04

Helix-hairpin-helix domain;


Pssm-ID: 434010 [Multi-domain]  Cd Length: 57  Bit Score: 38.62  E-value: 3.71e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 2787127128 378 LAQLLASEGFETVEEIAYVAPEDFITIEGFDEDVAEELQERARE 421
Cdd:pfam14520  14 TALALLSAGIGTVEDLAEADVDELAEIPGIGEKTAQRIILELRD 57
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 144-200 1.05e-03

S1_RPS1_repeat_ec3: 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 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240193 [Multi-domain]  Cd Length: 68  Bit Score: 37.61  E-value: 1.05e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2787127128 144 VGEVISGVVKRV-EYGhVIVDLGRAEGIIRRND------GIPRENFQTNDRVRAYLYKVSRETK 200
Cdd:cd05688     1 EGDVVEGTVKSItDFG-AFVDLGGVDGLLHISDmswgrvKHPSEVVNVGDEVEVKVLKIDKERK 63
nusA_arch TIGR01952
NusA family KH domain protein, archaeal; This model represents a family of archaeal proteins ...
 257-347 1.36e-03

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: 39.32  E-value: 1.36e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2787127128 257 VGAWVGMRGARVQAVVgELSGEKIDIIPWNYDDATFIVNALQPAEVSKVVLDEEERRVEV--VVADDQFPLAIGRRGQNV 334
Cdd:TIGR01952  44 MGAAIGKGGENVKRLE-ELIGKSIELIEYSENLEEFVANKLAPAEVKNVTVSEFNGKKVAyvEVHPRDKGIAIGKGGKNI 122

                          90
                  ....*....|...
gi 2787127128 335 RLASQLTGWQIDL 347
Cdd:TIGR01952 123 ERAKELAKRHHDI 135
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 142-208 2.24e-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: 2.24e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2787127128 142 DRVGEVISGVVKRVEYGHVIVDLG-RAEGII------RRNDGIPRENFQTNDRVRAYLYKVSRETKGpqIFLSR 208
Cdd:pfam00575   1 PEKGDVVEGEVTRVTKGGAFVDLGnGVEGFIpiselsDDHVEDPDEVIKVGDEVKVKVLKVDKDRRR--IILSI 72
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 123-207 2.85e-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: 40.03  E-value: 2.85e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2787127128 123 VIMQKVRDAERERQYNEYKdrVGEVISGVVKRV-EYGhVIVDLGRAEGIIRRNDgI-------PRENFQTNDRVRAYLYK 194
Cdd:COG0539   170 AVLEEEREEKREELLEKLE--EGDVVEGTVKNItDFG-AFVDLGGVDGLLHISE-IswgrvkhPSEVLKVGDEVEVKVLK 245

                          90
                  ....*....|...
gi 2787127128 195 VSRETKgpQIFLS 207
Cdd:COG0539   246 IDREKE--RISLS 256
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 143-208 5.35e-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: 39.26  E-value: 5.35e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2787127128 143 RVGEVISGVVKRVEYGHVIVDLG-RAEGIIRRN---DGIPRENFQTNDRVRAYLykVSRETKGPQIFLSR 208
Cdd:COG0539    17 KEGDIVKGTVVSIDDDEVLVDIGyKSEGIIPLSefsDEPGELEVKVGDEVEVYV--EKVEDGEGEIVLSK 84
 
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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