NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|15599939|ref|NP_253433|]
View 

transcription elongation factor NusA [Pseudomonas aeruginosa PAO1]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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: 668.88  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599939    1 MSKEVLLVVESVSNEKGVPAGVIFEALELALATATKKRFEDEVDLRVEINRHNGSYETFRRWHVVadEDYQDPATEITVE 80
Cdd:PRK09202   1 MNKELLEAIEAVAREKGIDREVVIEALEEALATAYKKKYGPEANIRVEIDRKTGDIEVFRRWEVV--EEVEDPTKEISLE 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599939   81 DVQEQKPGAKVGEVIEEKIESIEFGRIAAQTAKQVIVQKVREAERAQVVDAYREKVGEIISGTVKKVTRDNVIVDLGNnA 160
Cdd:PRK09202  79 EARKIDPDAEVGDYIEEEIESVDFGRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIITGVVKRVERGNIIVDLGR-A 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599939  161 EALLARDQIIPRETFRVGTRVRALLKEIRTENRGPQLVLSRTAPEMLIELFRIEVPEIAEQLIDVMAAARDPGSRAKIAV 240
Cdd:PRK09202 158 EAILPRKEQIPRENFRPGDRVRAYVYEVRKEARGPQIILSRTHPEFLKKLFEQEVPEIADGLIEIKAIARDPGSRAKIAV 237

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599939  241 RSKDKRIDPQGACIGMRGSRVQAVSGEIGGERVDIVLWDDNPAQFVINAMAPAEVAAIIVDEDTHTMDIAVAEDNLAQAI 320
Cdd:PRK09202 238 KSNDPRIDPVGACVGMRGSRIQAISNELGGEKIDIILWSDDPAQFIINALSPAEVSSVVVDEDEHSADVVVPDDQLSLAI 317

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599939  321 GRSGQNVRLASQLTGWTLNVMTEADIQAKQQAETGDILQRFVDELDVDEELAQVLVEEGFTTLEEIAYVPMEEMLSIDGF 400
Cdd:PRK09202 318 GKNGQNVRLASKLTGWKIDIMTEEEASEKRQAEFDAILDLFMEALDIDEEIAQLLVEEGFSSLEELAYVPVEELLEIEGF 397

                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15599939  401 DEDIVNELRSRAKDRLLTKAIATEEKLADaqpaeDLLSLDGMSKELALDLALRGVTTREDLAEQSIDDLLDIDGMDEE 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: 668.88  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599939    1 MSKEVLLVVESVSNEKGVPAGVIFEALELALATATKKRFEDEVDLRVEINRHNGSYETFRRWHVVadEDYQDPATEITVE 80
Cdd:PRK09202   1 MNKELLEAIEAVAREKGIDREVVIEALEEALATAYKKKYGPEANIRVEIDRKTGDIEVFRRWEVV--EEVEDPTKEISLE 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599939   81 DVQEQKPGAKVGEVIEEKIESIEFGRIAAQTAKQVIVQKVREAERAQVVDAYREKVGEIISGTVKKVTRDNVIVDLGNnA 160
Cdd:PRK09202  79 EARKIDPDAEVGDYIEEEIESVDFGRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIITGVVKRVERGNIIVDLGR-A 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599939  161 EALLARDQIIPRETFRVGTRVRALLKEIRTENRGPQLVLSRTAPEMLIELFRIEVPEIAEQLIDVMAAARDPGSRAKIAV 240
Cdd:PRK09202 158 EAILPRKEQIPRENFRPGDRVRAYVYEVRKEARGPQIILSRTHPEFLKKLFEQEVPEIADGLIEIKAIARDPGSRAKIAV 237

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599939  241 RSKDKRIDPQGACIGMRGSRVQAVSGEIGGERVDIVLWDDNPAQFVINAMAPAEVAAIIVDEDTHTMDIAVAEDNLAQAI 320
Cdd:PRK09202 238 KSNDPRIDPVGACVGMRGSRIQAISNELGGEKIDIILWSDDPAQFIINALSPAEVSSVVVDEDEHSADVVVPDDQLSLAI 317

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599939  321 GRSGQNVRLASQLTGWTLNVMTEADIQAKQQAETGDILQRFVDELDVDEELAQVLVEEGFTTLEEIAYVPMEEMLSIDGF 400
Cdd:PRK09202 318 GKNGQNVRLASKLTGWKIDIMTEEEASEKRQAEFDAILDLFMEALDIDEEIAQLLVEEGFSSLEELAYVPVEELLEIEGF 397

                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15599939  401 DEDIVNELRSRAKDRLLTKAIATEEKLADaqpaeDLLSLDGMSKELALDLALRGVTTREDLAEQSIDDLLDIDGMDEE 478
Cdd:PRK09202 398 DEETVEELRERAKEALETEALAQEEKLAD-----DLLSLEGLDRELAFKLAEKGIKTLEDLAEQAVDELIDIEGDEEK 470
NusA COG0195
Transcription antitermination factor NusA, contains S1 and KH domains [Transcription];
1-353 5.67e-145

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


Pssm-ID: 439965 [Multi-domain]  Cd Length: 353  Bit Score: 419.28  E-value: 5.67e-145
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599939   1 MSKEVLLVVESVSNEKGVPAGVIFEALELALATATKKRFEDEVDLRVEINRHNGsyETFRRWHVVADEDYQDPATEITVE 80
Cdd:COG0195   4 MLLELLEALEELEKEKGIDKEILIEALEAALKKAYKKNYGNEVVVRVIIDGDTG--EIRVYVVKEVVEEVEDPREEILLE 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599939  81 DVQEQKPGAKVGEVIEEKIESIEFGRIAAQTAKQVIVQKVREAERaQVVDAYREKVGEIISGTVKKVTRDNVIVDLGNNA 160
Cdd:COG0195  82 AAKEDDPDEEGGDIIEEEVPPDFFGRIAAQAAKQVIQQKRREAER-EIIYEEFKDRGGEIVGGVVQRVERGNVIVDLGKV 160

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599939 161 EALLARDQIIPRETFRVGTRVRALLKEIRTENRGPQLVLSRTAPEMLIELFRIEVPEIAEQLIDVMAAARDPGSRAKIAV 240
Cdd:COG0195 161 EAILPRREQIPGENYRVGDRIRAYVLEVRKETRGPQIILSRTHPEFLKRLFELEVPEIADGIVEIKAIAREPGSRAKIAV 240

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599939 241 RSKDKRIDPQGACIGMRGSRVQAVSGEIGGERVDIVLWDDNPAQFVINAMAPAEVAAIIVDEDTHTMDIAVAEDNLAQAI 320
Cdd:COG0195 241 YSNDPRVDPVGACVGMRGSRVQAVVNELNGEKIDIILWSEDPAQFIANALSPAKVSSVEVDEEEKSADVVVPDDQLSLAI 320

                       330       340       350
                ....*....|....*....|....*....|...
gi 15599939 321 GRSGQNVRLASQLTGWTLNVMTEADIQAKQQAE 353
Cdd:COG0195 321 GKGGQNVRLAAKLTGWKIDIKSESEAEEKREEE 353
NusA TIGR01953
transcription termination factor NusA; This model describes NusA, or N utilization substance ...
 4-345 9.93e-138

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: 400.48  E-value: 9.93e-138
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599939     4 EVLLVVESVSNEKGVPAGVIFEALELALATATKKRFEDEVDLRVEINRHNGSYETFRRWHVVadEDYQDPATEITVEDVQ 83
Cdd:TIGR01953   1 EFLAAIEALAKEKGISIETVIEAIEEALEQAYKKTFGQDENVEVNIDRKTGDINVYRRKEVV--EEVEDPSLEISLEDAR 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599939    84 EQKPGAKVGEVIEEKIESIEFGRIAAQTAKQVIVQKVREAERAQVVDAYREKVGEIISGTVKKVTRD-NVIVDLGNNaEA 162
Cdd:TIGR01953  79 EIDPDVQIGDEVKKEIPPENFGRIAAQTAKQVILQKIREAERERVYDEFSSKEGEIISGTVKRVNRRgNLFVELGKT-EG 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599939   163 LLARDQIIPRETFRVGTRVRALLKEIRTENRGPQLVLSRTAPEMLIELFRIEVPEIAEQLIDVMAAARDPGSRAKIAVRS 242
Cdd:TIGR01953 158 ILPKKEQIPGEKFRIGDRIKAYVYEVRKTAKGPQIILSRTHPEFVKELLKLEVPEIADGIIEIKKIAREPGYRTKIAVES 237

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599939   243 KDKRIDPQGACIGMRGSRVQAVSGEIGGERVDIVLWDDNPAQFVINAMAPAEVAAI-IVDEDTHTMDIAVAEDNLAQAIG 321
Cdd:TIGR01953 238 NDENIDPVGACVGPKGSRIQAISKELNGEKIDIIEYSDDPAEFIANALSPAKVISVeVLDEDKRSAEVVVPDDQLSLAIG 317

                         330       340
                  ....*....|....*....|....
gi 15599939   322 RSGQNVRLASQLTGWTLNVMTEAD 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 7.88e-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: 7.88e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599939     6 LLVVESVSNEKGVPAGVIFEALELALATATKKRFEDEVDLRVEINRHNGSYETFRRWHVVADEDyqDPATEITVEDVQEQ 85
Cdd:pfam08529   2 LEALEELAKEKGIDKEVLIEAIEEALLKAYKKKYGADENVRVEIDRETGDIEVYRRKEVVEEVE--DPDTEISLEEAKKI 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 15599939    86 KPGAKVGEVIEEKIESIEFGRIAAQTAKQVIVQKVREAER 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 1.46e-32

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: 118.79  E-value: 1.46e-32
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15599939 204 PEMLIELFRIEVPEIAEQLIDVMAAARDPGSRAKIAVRSKDKRIDPQGACIGMRGSRVQAVSGEIGGERVDIVLW 278
Cdd:cd02134   2 PEFLKRLFELEVPEIADGIVEIKAIAREPGSRTKVAVASNDPRVDPVGACVGVRGSRIQAIVEELGGEKIDIVLW 76
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
135-201 2.29e-08

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 50.68  E-value: 2.29e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15599939    135 KVGEIISGTVKKVTRDNVIVDLGNNAEALLARDQII------PRETFRVGTRVRALLKEIRTENRgpQLVLSR 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: 668.88  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599939    1 MSKEVLLVVESVSNEKGVPAGVIFEALELALATATKKRFEDEVDLRVEINRHNGSYETFRRWHVVadEDYQDPATEITVE 80
Cdd:PRK09202   1 MNKELLEAIEAVAREKGIDREVVIEALEEALATAYKKKYGPEANIRVEIDRKTGDIEVFRRWEVV--EEVEDPTKEISLE 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599939   81 DVQEQKPGAKVGEVIEEKIESIEFGRIAAQTAKQVIVQKVREAERAQVVDAYREKVGEIISGTVKKVTRDNVIVDLGNnA 160
Cdd:PRK09202  79 EARKIDPDAEVGDYIEEEIESVDFGRIAAQTAKQVIVQKIREAERERVYEEYKDRVGEIITGVVKRVERGNIIVDLGR-A 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599939  161 EALLARDQIIPRETFRVGTRVRALLKEIRTENRGPQLVLSRTAPEMLIELFRIEVPEIAEQLIDVMAAARDPGSRAKIAV 240
Cdd:PRK09202 158 EAILPRKEQIPRENFRPGDRVRAYVYEVRKEARGPQIILSRTHPEFLKKLFEQEVPEIADGLIEIKAIARDPGSRAKIAV 237

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599939  241 RSKDKRIDPQGACIGMRGSRVQAVSGEIGGERVDIVLWDDNPAQFVINAMAPAEVAAIIVDEDTHTMDIAVAEDNLAQAI 320
Cdd:PRK09202 238 KSNDPRIDPVGACVGMRGSRIQAISNELGGEKIDIILWSDDPAQFIINALSPAEVSSVVVDEDEHSADVVVPDDQLSLAI 317

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599939  321 GRSGQNVRLASQLTGWTLNVMTEADIQAKQQAETGDILQRFVDELDVDEELAQVLVEEGFTTLEEIAYVPMEEMLSIDGF 400
Cdd:PRK09202 318 GKNGQNVRLASKLTGWKIDIMTEEEASEKRQAEFDAILDLFMEALDIDEEIAQLLVEEGFSSLEELAYVPVEELLEIEGF 397

                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15599939  401 DEDIVNELRSRAKDRLLTKAIATEEKLADaqpaeDLLSLDGMSKELALDLALRGVTTREDLAEQSIDDLLDIDGMDEE 478
Cdd:PRK09202 398 DEETVEELRERAKEALETEALAQEEKLAD-----DLLSLEGLDRELAFKLAEKGIKTLEDLAEQAVDELIDIEGDEEK 470
NusA COG0195
Transcription antitermination factor NusA, contains S1 and KH domains [Transcription];
1-353 5.67e-145

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


Pssm-ID: 439965 [Multi-domain]  Cd Length: 353  Bit Score: 419.28  E-value: 5.67e-145
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599939   1 MSKEVLLVVESVSNEKGVPAGVIFEALELALATATKKRFEDEVDLRVEINRHNGsyETFRRWHVVADEDYQDPATEITVE 80
Cdd:COG0195   4 MLLELLEALEELEKEKGIDKEILIEALEAALKKAYKKNYGNEVVVRVIIDGDTG--EIRVYVVKEVVEEVEDPREEILLE 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599939  81 DVQEQKPGAKVGEVIEEKIESIEFGRIAAQTAKQVIVQKVREAERaQVVDAYREKVGEIISGTVKKVTRDNVIVDLGNNA 160
Cdd:COG0195  82 AAKEDDPDEEGGDIIEEEVPPDFFGRIAAQAAKQVIQQKRREAER-EIIYEEFKDRGGEIVGGVVQRVERGNVIVDLGKV 160

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599939 161 EALLARDQIIPRETFRVGTRVRALLKEIRTENRGPQLVLSRTAPEMLIELFRIEVPEIAEQLIDVMAAARDPGSRAKIAV 240
Cdd:COG0195 161 EAILPRREQIPGENYRVGDRIRAYVLEVRKETRGPQIILSRTHPEFLKRLFELEVPEIADGIVEIKAIAREPGSRAKIAV 240

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599939 241 RSKDKRIDPQGACIGMRGSRVQAVSGEIGGERVDIVLWDDNPAQFVINAMAPAEVAAIIVDEDTHTMDIAVAEDNLAQAI 320
Cdd:COG0195 241 YSNDPRVDPVGACVGMRGSRVQAVVNELNGEKIDIILWSEDPAQFIANALSPAKVSSVEVDEEEKSADVVVPDDQLSLAI 320

                       330       340       350
                ....*....|....*....|....*....|...
gi 15599939 321 GRSGQNVRLASQLTGWTLNVMTEADIQAKQQAE 353
Cdd:COG0195 321 GKGGQNVRLAAKLTGWKIDIKSESEAEEKREEE 353
NusA TIGR01953
transcription termination factor NusA; This model describes NusA, or N utilization substance ...
 4-345 9.93e-138

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: 400.48  E-value: 9.93e-138
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599939     4 EVLLVVESVSNEKGVPAGVIFEALELALATATKKRFEDEVDLRVEINRHNGSYETFRRWHVVadEDYQDPATEITVEDVQ 83
Cdd:TIGR01953   1 EFLAAIEALAKEKGISIETVIEAIEEALEQAYKKTFGQDENVEVNIDRKTGDINVYRRKEVV--EEVEDPSLEISLEDAR 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599939    84 EQKPGAKVGEVIEEKIESIEFGRIAAQTAKQVIVQKVREAERAQVVDAYREKVGEIISGTVKKVTRD-NVIVDLGNNaEA 162
Cdd:TIGR01953  79 EIDPDVQIGDEVKKEIPPENFGRIAAQTAKQVILQKIREAERERVYDEFSSKEGEIISGTVKRVNRRgNLFVELGKT-EG 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599939   163 LLARDQIIPRETFRVGTRVRALLKEIRTENRGPQLVLSRTAPEMLIELFRIEVPEIAEQLIDVMAAARDPGSRAKIAVRS 242
Cdd:TIGR01953 158 ILPKKEQIPGEKFRIGDRIKAYVYEVRKTAKGPQIILSRTHPEFVKELLKLEVPEIADGIIEIKKIAREPGYRTKIAVES 237

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599939   243 KDKRIDPQGACIGMRGSRVQAVSGEIGGERVDIVLWDDNPAQFVINAMAPAEVAAI-IVDEDTHTMDIAVAEDNLAQAIG 321
Cdd:TIGR01953 238 NDENIDPVGACVGPKGSRIQAISKELNGEKIDIIEYSDDPAEFIANALSPAKVISVeVLDEDKRSAEVVVPDDQLSLAIG 317

                         330       340
                  ....*....|....*....|....
gi 15599939   322 RSGQNVRLASQLTGWTLNVMTEAD 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 7.88e-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: 7.88e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599939     6 LLVVESVSNEKGVPAGVIFEALELALATATKKRFEDEVDLRVEINRHNGSYETFRRWHVVADEDyqDPATEITVEDVQEQ 85
Cdd:pfam08529   2 LEALEELAKEKGIDKEVLIEAIEEALLKAYKKKYGADENVRVEIDRETGDIEVYRRKEVVEEVE--DPDTEISLEEAKKI 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 15599939    86 KPGAKVGEVIEEKIESIEFGRIAAQTAKQVIVQKVREAER 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 1.46e-32

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: 118.79  E-value: 1.46e-32
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15599939 204 PEMLIELFRIEVPEIAEQLIDVMAAARDPGSRAKIAVRSKDKRIDPQGACIGMRGSRVQAVSGEIGGERVDIVLW 278
Cdd:cd02134   2 PEFLKRLFELEVPEIADGIVEIKAIAREPGSRTKVAVASNDPRVDPVGACVGVRGSRIQAIVEELGGEKIDIVLW 76
KH_5 pfam13184
NusA-like KH domain;
232-300 7.77e-27

NusA-like KH domain;


Pssm-ID: 433018 [Multi-domain]  Cd Length: 69  Bit Score: 102.70  E-value: 7.77e-27
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15599939   232 PGSRAKIAVRSKDKRIDPQGACIGMRGSRVQAVSGEIGGERVDIVLWDDNPAQFVINAMAPAEVAAIIV 300
Cdd:pfam13184   1 PGNRAKIAVYSRDERIDPVGACVGKKGSRIQAISRELNGEKIDIVEYSEDLRTFIKNALSPARVLSVNI 69
S1_NusA cd04455
S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like ...
 134-201 4.06e-25

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: 97.90  E-value: 4.06e-25
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15599939 134 EKVGEIISGTVKKVTRDNVIVDLGNnAEALLARDQIIPRETFRVGTRVRALLKEIRTENRGPQLVLSR 201
Cdd:cd04455   1 DREGEIVTGIVKRVDRGNVIVDLGK-VEAILPKKEQIPGESYRPGDRIKAYVLEVRKTSKGPQIILSR 67
KH-II_NusA_rpt2 cd22529
second type II K-homology (KH) RNA-binding domain found in transcription termination ...
 281-341 2.29e-24

second type II K-homology (KH) RNA-binding domain found in transcription termination/antitermination protein NusA and similar proteins; NusA, also called N utilization substance protein A or transcription termination/antitermination L factor, is an essential multifunctional transcription elongation factor that participates in both transcription termination and antitermination. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNA polymerase pausing provides a mechanism for synchronizing transcription and translation. In prokaryotes, the N-terminal RNA polymerase-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, the S1 and two K-homology, KH1 and KH2. The K-homology (KH) domains of NusA belong to the type II KH RNA-binding domain superfamily. This model corresponds to the second KH domain of NusA and similar proteins.


Pssm-ID: 411786 [Multi-domain]  Cd Length: 61  Bit Score: 95.68  E-value: 2.29e-24
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15599939 281 NPAQFVINAMAPAEVAAIIVDEDTHTMDIAVAEDNLAQAIGRSGQNVRLASQLTGWTLNVM 341
Cdd:cd22529   1 DPAEFVANALSPAKVISVEIDEDDKKARVVVPDDQLSLAIGKNGQNVRLASKLTGWKIDIK 61
nusA_Cterm_rpt TIGR01954
transcription termination factor NusA, C-terminal duplication; NusA is a bacterial ...
 442-491 2.27e-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: 64.24  E-value: 2.27e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 15599939   442 MSKELALDLALRGVTTREDLAEQSIDDLLDIDGMDEERAGKLIMAARAHW 491
Cdd:TIGR01954   1 INEEIAQLLVEEGFTTVEDLAYVPIDELLSIEGFDEETAKELINRARNAL 50
nusA_Cterm_rpt TIGR01954
transcription termination factor NusA, C-terminal duplication; NusA is a bacterial ...
 367-416 7.77e-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: 7.77e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 15599939   367 VDEELAQVLVEEGFTTLEEIAYVPMEEMLSIDGFDEDIVNELRSRAKDRL 416
Cdd:TIGR01954   1 INEEIAQLLVEEGFTTVEDLAYVPIDELLSIEGFDEETAKELINRARNAL 50
HHH_5 pfam14520
Helix-hairpin-helix domain;
434-488 3.40e-09

Helix-hairpin-helix domain;


Pssm-ID: 434010 [Multi-domain]  Cd Length: 57  Bit Score: 52.88  E-value: 3.40e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 15599939   434 EDLLSLDGMSKELALDLALRGVTTREDLAEQSIDDLLDIDGMDEERAGKLIMAAR 488
Cdd:pfam14520   2 EELLSISGIGPKTALALLSAGIGTVEDLAEADVDELAEIPGIGEKTAQRIILELR 56
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
135-201 2.29e-08

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 50.68  E-value: 2.29e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15599939    135 KVGEIISGTVKKVTRDNVIVDLGNNAEALLARDQII------PRETFRVGTRVRALLKEIRTENRgpQLVLSR 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 3.74e-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: 52.41  E-value: 3.74e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599939   251 GACIGMRGSRVQAVSGEIGgERVDIVLWDDNPAQFVINAMAPAEVAAIIVDE--DTHTMDIAVAEDNLAQAIGRSGQNVR 328
Cdd:TIGR01952  45 GAAIGKGGENVKRLEELIG-KSIELIEYSENLEEFVANKLAPAEVKNVTVSEfnGKKVAYVEVHPRDKGIAIGKGGKNIE 123


                  ....*..
gi 15599939   329 LASQLTG 335
Cdd:TIGR01952 124 RAKELAK 130
PRK08406 PRK08406
transcription elongation factor NusA-like protein; Validated
 251-333 7.87e-08

transcription elongation factor NusA-like protein; Validated


Pssm-ID: 181413 [Multi-domain]  Cd Length: 140  Bit Score: 51.37  E-value: 7.87e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599939  251 GACIGMRGSRVQAVSgEIGGERVDIVLWDDNPAQFVINAMAPAEVAAIIVDE--DTHTMDIAVAEDNLAQAIGRSGQNVR 328
Cdd:PRK08406  44 GLAIGKGGENVKRLE-EKLGKDIELVEYSDDPEEFIKNIFAPAAVRSVTIKKknGDKVAYVEVAPEDKGIAIGKNGKNIE 122


                 ....*
gi 15599939  329 LASQL 333
Cdd:PRK08406 123 RAKDL 127
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 135-201 1.33e-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: 47.35  E-value: 1.33e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599939 135 KVGEIISGTVKKVTRDNVIVDLGNNAEALLARDQIIPRE---TFRVGTRVRALLkeIRTENRGPQLVLSR 201
Cdd:COG0539  17 KEGDIVKGTVVSIDDDEVLVDIGYKSEGIIPLSEFSDEPgelEVKVGDEVEVYV--EKVEDGEGEIVLSK 84
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 135-197 3.81e-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: 41.89  E-value: 3.81e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15599939   135 KVGEIISGTVKKVTRDNVIVDLGNNAEALLARDQI------IPRETFRVGTRVRALLKEIRTENRGPQL 197
Cdd:pfam00575   2 EKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELsddhveDPDEVIKVGDEVKVKVLKVDKDRRRIIL 70
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 135-201 1.32e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 41.30  E-value: 1.32e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599939  135 KVGEIISGTVKKVTRDNVIVDLGNNAEALLARDQIIPRE---TFRVGTRVRALLKeiRTENRGPQLVLSR 201
Cdd:PRK06299  29 REGSIVKGTVVAIDKDYVLVDVGLKSEGRIPLEEFKNEQgelEVKVGDEVEVYVE--RIEDGFGETVLSR 96
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 2.41e-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: 2.41e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15599939 137 GEIISGTVKKVTRDNVIVDLGNNAEALLARDQII------PRETFRVGTRVRALLkeIRTENRGPQLVLSR 201
Cdd:cd05687   1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSddpienGEDEVKVGDEVEVYV--LRVEDEEGNVVLSK 69
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 135-193 3.96e-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: 36.15  E-value: 3.96e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15599939 135 KVGEIISGTVKKVTRDNVIVDL-GNNAEALLARDQIIP------RETFRVGTRVRALLKEIRTENR 193
Cdd:cd05708   1 KVGQKIDGTVRRVEDYGVFIDIdGTNVSGLCHKSEISDnrvadaSKLFRVGDKVRAKVLKIDAEKK 66
TIGR03491 TIGR03491
RecB family nuclease, putative, TM0106 family; Members of this uncharacterized protein family ...
 369-489 4.03e-03

RecB family nuclease, putative, TM0106 family; Members of this uncharacterized protein family are found broadly but sporadically among bacteria. The N-terminal region is homologous to the Cas4 protein of CRISPR systems, although this protein family shows no signs of association with CRISPR repeats.


Pssm-ID: 274603 [Multi-domain]  Cd Length: 457  Bit Score: 39.62  E-value: 4.03e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15599939   369 EELAQVLVEEGFTTLEEIAYVPMEEMLSIDGFDEDIVNELRSRAKD-----------------RLLTKAIATEEKladaq 431
Cdd:TIGR03491 133 ESFQGVAPKKGLIILRDGNSLKVELIKLLPQLRQDLADFLLTLNADlepevfisrkkctlcswRKDCEAVAKEEG----- 207

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 15599939   432 paeDLLSLDGMSKELALDLALRGVTTREDLAEQSIDDLLDIDGMDEERAGKLIMAARA 489
Cdd:TIGR03491 208 ---HLSLVPGIGPSRYRLLQELGIHTLEDLAAADPNDLEDFGEQGLGVAEQLVQQARA 262
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 135-197 5.04e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 39.38  E-value: 5.04e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15599939  135 KVGEIISGTVKKVTRDNVIVDLGNNAEAL-----LARDQIIPR-ETFRVGTRVRALLKEIRTENRGPQL 197
Cdd:PRK06299 459 KKGSIVTGTVTEVKDKGAFVELEDGVEGLiraseLSRDRVEDAtEVLKVGDEVEAKVINIDRKNRRISL 527
KH-II_NusA_arch_rpt2 cd22531
second type II K-homology (KH) RNA-binding domain found in archaeal probable transcription ...
 282-333 6.59e-03

second type II K-homology (KH) RNA-binding domain found in archaeal probable transcription termination protein NusA and similar proteins; NusA, also called N utilization substance protein A, is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. It participates in both transcription termination and antitermination. NusA homologs consisting of only the two type II K-homology (KH) domains are widely conserved in archaea. Although their function remains unclear, it has been found that Aeropyrum pernix NusA strongly binds to a certain CU-rich sequence near a termination signal. Archaeal NusA may have retained some functions of bacterial NusA, including ssRNA-binding ability. This model corresponds to the second KH domain of NusA mainly found in archaea.


Pssm-ID: 411788 [Multi-domain]  Cd Length: 67  Bit Score: 35.30  E-value: 6.59e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 15599939 282 PAQFVINAMAPAEVAAIIVDE--DTHTMDIAVAEDNLAQAIGRSGQNVRLASQL 333
Cdd:cd22531   1 PEEFIKNIFAPAKVQNVKVKEknGKKVAIVEVPPKDKGIAIGKNGKNIERAKLL 54
COG2251 COG2251
Predicted nuclease, RecB family [General function prediction only];
428-489 8.58e-03

Predicted nuclease, RecB family [General function prediction only];


Pssm-ID: 441852 [Multi-domain]  Cd Length: 508  Bit Score: 38.78  E-value: 8.58e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15599939 428 ADAQPAEDLLSLDGMSKELALDLALRGVTTREDLAEqsIDDLLDIDGMDEERAGKLIMAARA 489
Cdd:COG2251 226 AEAEAEDDLSLVAGVTPSQRAKLQAAGITTIDALAA--ADPPQRVPGLGKQTAARLRAQARL 285
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH