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Conserved domains on  [gi|830872876|gb|AKL90316|]
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RNA polymerase subunit alpha, partial [Streptococcus sp. R-55011]

Protein Classification

DNA-directed RNA polymerase subunit alpha( domain architecture ID 15176902)

DNA-directed RNA polymerase subunit alpha catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
RpoA COG0202
DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]; DNA-directed RNA ...
1-262 1.56e-156

DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]; DNA-directed RNA polymerase, alpha subunit/40 kD subunit is part of the Pathway/BioSystem: RNA polymerase


:

Pssm-ID: 439972 [Multi-domain]  Cd Length: 317  Bit Score: 437.57  E-value: 1.56e-156
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830872876   1 EKPTITKIDE--NKDYGRFVIEPLERGYGTTLGNSLRRVLLASLPGAAITSIKIDGVLHEFDTVPGVREDVMQIILNIKG 78
Cdd:COG0202    4 EKPRKIEVEEeiSDNYGKFVLEPLERGYGTTLGNALRRVLLSSLPGAAVTSVKIEGVLHEFSTIPGVKEDVTDIILNLKG 83
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830872876  79 IAVKSYVEDEKKIELDVVGPAEVTAGDILTDSDIEIVNPDHYLFTIAEGKTFKAILTVNSGRGYVPAEGNKKDDAPVGTL 158
Cdd:COG0202   84 LRLKLHSDEPKTLRLEKKGPGEVTAGDIELPSDVEILNPDLVIATLDEDAKLEMELTVEKGRGYVPAEENKKEDLPIGVI 163
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830872876 159 AVDSIYTPVKKVNYQVEPARVGSNDGFDKLTLEISTNGTIIPEDALGLSARILMEHLGLFTDLTEVAKSADVMKETETAS 238
Cdd:COG0202  164 PIDAIFSPVRKVNYTVENTRVGQRTDYDKLILEIWTDGSITPEEALAEAAKILIEHLSLFVNLEEEAEEVEEEVEEEEEE 243
                        250       260
                 ....*....|....*....|....
gi 830872876 239 DDRMLDRTIEELDLSVRSYNCLKR 262
Cdd:COG0202  244 IDPILLRPIEELELSVRSYNCLKR 267
 
Name Accession Description Interval E-value
RpoA COG0202
DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]; DNA-directed RNA ...
1-262 1.56e-156

DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]; DNA-directed RNA polymerase, alpha subunit/40 kD subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 439972 [Multi-domain]  Cd Length: 317  Bit Score: 437.57  E-value: 1.56e-156
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830872876   1 EKPTITKIDE--NKDYGRFVIEPLERGYGTTLGNSLRRVLLASLPGAAITSIKIDGVLHEFDTVPGVREDVMQIILNIKG 78
Cdd:COG0202    4 EKPRKIEVEEeiSDNYGKFVLEPLERGYGTTLGNALRRVLLSSLPGAAVTSVKIEGVLHEFSTIPGVKEDVTDIILNLKG 83
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830872876  79 IAVKSYVEDEKKIELDVVGPAEVTAGDILTDSDIEIVNPDHYLFTIAEGKTFKAILTVNSGRGYVPAEGNKKDDAPVGTL 158
Cdd:COG0202   84 LRLKLHSDEPKTLRLEKKGPGEVTAGDIELPSDVEILNPDLVIATLDEDAKLEMELTVEKGRGYVPAEENKKEDLPIGVI 163
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830872876 159 AVDSIYTPVKKVNYQVEPARVGSNDGFDKLTLEISTNGTIIPEDALGLSARILMEHLGLFTDLTEVAKSADVMKETETAS 238
Cdd:COG0202  164 PIDAIFSPVRKVNYTVENTRVGQRTDYDKLILEIWTDGSITPEEALAEAAKILIEHLSLFVNLEEEAEEVEEEVEEEEEE 243
                        250       260
                 ....*....|....*....|....
gi 830872876 239 DDRMLDRTIEELDLSVRSYNCLKR 262
Cdd:COG0202  244 IDPILLRPIEELELSVRSYNCLKR 267
PRK05182 PRK05182
DNA-directed RNA polymerase subunit alpha; Provisional
1-262 4.65e-152

DNA-directed RNA polymerase subunit alpha; Provisional


Pssm-ID: 235359 [Multi-domain]  Cd Length: 310  Bit Score: 426.05  E-value: 4.65e-152
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830872876   1 EKPTITKIDENKDYGRFVIEPLERGYGTTLGNSLRRVLLASLPGAAITSIKIDGVLHEFDTVPGVREDVMQIILNIKGIA 80
Cdd:PRK05182   7 QKIEVEEESEDDNYGKFVLEPLERGFGTTLGNALRRVLLSSLPGAAVTSVKIDGVLHEFSTIPGVREDVTEIILNLKGLR 86
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830872876  81 VKSYVEDEKKIELDVVGPAEVTAGDILTDSDIEIVNPDHYLFTIAEGKTFKAILTVNSGRGYVPAEGNKKdDAPVGTLAV 160
Cdd:PRK05182  87 LKLHGDEPVTLTLSKKGPGEVTAGDIETDGDVEIVNPDLVIATLNEGAKLEMELTVERGRGYVPAEENKE-DAPIGRIPV 165
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830872876 161 DSIYTPVKKVNYQVEPARVGSNDGFDKLTLEISTNGTIIPEDALGLSARILMEHLGLFTDLTEvAKSADVMKETETASDD 240
Cdd:PRK05182 166 DAIFSPVKKVNYTVENTRVGQRTDYDKLILEVETDGSITPEEALALAAKILVEQLSVFVDLEE-AEEAEEEVEEEEPEFD 244
                        250       260
                 ....*....|....*....|..
gi 830872876 241 RMLDRTIEELDLSVRSYNCLKR 262
Cdd:PRK05182 245 PILLRPIEELELSVRSYNCLKR 266
rpoA TIGR02027
DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type; This family ...
14-262 3.59e-120

DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type; This family consists of the bacterial (and chloroplast) DNA-directed RNA polymerase alpha subunit, encoded by the rpoA gene. The RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. The amino terminal domain is involved in dimerizing and assembling the other RNA polymerase subunits into a transcriptionally active enzyme. The carboxy-terminal domain contains determinants for interaction with DNA and with transcriptional activator proteins. [Transcription, DNA-dependent RNA polymerase]


Pssm-ID: 273934 [Multi-domain]  Cd Length: 297  Bit Score: 345.02  E-value: 3.59e-120
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830872876   14 YGRFVIEPLERGYGTTLGNSLRRVLLASLPGAAITSIKIDGVLHEFDTVPGVREDVMQIILNIKGIAVKSYVEDEKKIEL 93
Cdd:TIGR02027   1 YGKFVLEPLERGFGITLGNALRRVLLSSIPGAAITAVKIDGVLHEFSTIEGVKEDVTEIILNLKQLVVKSEGDGERTMTL 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830872876   94 DVVGPAEVTAGDI-LTDSDIEIVNPDHYLFTIAEGKTFKAILTVNSGRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNY 172
Cdd:TIGR02027  81 SKKGPGVVTAGDIkAPPGDVEIVNPDLVIATLTEPADLEIELRVERGRGYVPAEENREEDRPVGVIAVDAIFSPVLKVNY 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830872876  173 QVEPARVGSNDGFDKLTLEISTNGTIIPEDALGLSARILMEHLGLFTDLTEVAKSADVMKETET--ASDDRMLDRTIEEL 250
Cdd:TIGR02027 161 EVENTRVGQRTDYDKLILEIETNGSITPKDAIAEAAKILIEHLEPFVNLDEEIEAFEEEQEEEEeeLEDAKLLSIKIEEL 240
                         250
                  ....*....|..
gi 830872876  251 DLSVRSYNCLKR 262
Cdd:TIGR02027 241 DLSVRSYNCLKR 252
RNAP_alpha_NTD cd06928
N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; The bacterial alpha ...
5-218 4.50e-111

N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; The bacterial alpha subunit of RNA polymerase (RNAP) consists of two independently folded domains: an amino-terminal domain (alphaNTD) and a carboxy-terminal domain (alphaCTD). AlphaCTD is not required for RNAP assembly but interacts with transcription activators. AlphaNTD is essential in vivo and in vitro for RNAP assembly and basal transcription. It is similar to the eukaryotic RPB3/AC40/archaeal D subunit, and contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The alphaNTDs of plant plastid RNAP (PEP) are also included in this subfamily. PEP is largely responsible for the transcription of photosynthetic genes and is closely related to the multi-subunit bacterial RNAP, which is a large multi-subunit complex responsible for the synthesis of all bacterial RNAs. The bacterial RNAP core enzyme consists of four subunits (beta', beta, alpha and omega). All residues in the alpha subunit that is involved in dimerization or in the interaction with other subunits are located within alphaNTD.


Pssm-ID: 132904 [Multi-domain]  Cd Length: 215  Bit Score: 318.64  E-value: 4.50e-111
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830872876   5 ITKIDENKDYGRFVIEPLERGYGTTLGNSLRRVLLASLPGAAITSIKIDGVLHEFDTVPGVREDVMQIILNIKGIAVKSY 84
Cdd:cd06928    1 SKVENKRENYGRFVIEPLERGQGTTLGNALRRVLLSSLPGAAITAVKIEGVLHEFSTIPGVREDVLEILLNLKEIVFKSD 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830872876  85 VEDE-KKIELDVVGPAEVTAGDILTDSDIEIVNPDHYLFTIAEGKTFKAILTVNSGRGYVPAEGNKKDDAPVGTLAVDSI 163
Cdd:cd06928   81 SEDEpQVLRLKVKGPGVVTAADIELPSGVEIVNPDQYIATLTEDASLEMELRIEKGRGYVPAEENKSEEKPIGFIPIDAI 160
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 830872876 164 YTPVKKVNYQVEPARVGSNDGFDKLTLEISTNGTIIPEDALGLSARILMEHLGLF 218
Cdd:cd06928  161 FSPVRKVNYSVESTRVGQRTDYEKLILEIWTNGSISPEEALAQAAKILINHFSPF 215
RNA_pol_L pfam01193
RNA polymerase Rpb3/Rpb11 dimerization domain; The two eukaryotic subunits Rpb3 and Rpb11 ...
21-214 1.61e-63

RNA polymerase Rpb3/Rpb11 dimerization domain; The two eukaryotic subunits Rpb3 and Rpb11 dimerize to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerization domain of the alpha subunit/Rpb3 is interrupted by an insert domain (pfam01000). Some of the alpha subunits also contain iron-sulphur binding domains (pfam00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp.


Pssm-ID: 460104 [Multi-domain]  Cd Length: 191  Bit Score: 197.24  E-value: 1.61e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830872876   21 PLERGYGTTLGNSLRRVLLASLPGAAITSIKIDGVLHEFDTVPGVREDVMQIILNIKGIAVKSYVEDEKKIELDVVGPAE 100
Cdd:pfam01193   1 FLLRGEDHTLGNALRRILLSEVPGVAIDAVKIEGNTSEFSDEPGAHRLGLIPLLNLKELFFKLSSDDDETLELDKEGPGE 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830872876  101 VTAGDILTDSD---IEIVNPDHYLFTIAEGKTFKAILTVNSGRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPA 177
Cdd:pfam01193  81 VTAGDINTDSDvevIEIINPDLHIATLEEEAALEMELEVVKGRGYVPAEKNKDVDDPIGDIPIDSIFSPVEKVNYVVENT 160
                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 830872876  178 RvgsndgFDKLTLEISTNGTIIPEDALGLSARILMEH 214
Cdd:pfam01193 161 D------YDKLIFEVETDGSIPPEEALKEAAKILKEK 191
RPOLD smart00662
RNA polymerases D; DNA-directed RNA polymerase subunit D and bacterial alpha chain
15-218 8.97e-61

RNA polymerases D; DNA-directed RNA polymerase subunit D and bacterial alpha chain


Pssm-ID: 214766 [Multi-domain]  Cd Length: 224  Bit Score: 191.29  E-value: 8.97e-61
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830872876    15 GRFVIEPlergYGTTLGNSLRRVLLASLPGAAITSIKIDGvlhefdTVPGVREDVMQIILNIKGIAVKSYVE-------- 86
Cdd:smart00662   1 AKFVLEP----YGLTLANALRRVLLSSVPGMAVTSVYIEG------NTSGVQDEVLAHRLGLKPLASDPDGDeyqrdcec 70
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830872876    87 ------DEKKIELDVVGPAEVTAGDILTDSD--IEIVNPDHYLFTIAEGKTFKAILTVNSGRGYVPAE---GNKKDDAPV 155
Cdd:smart00662  71 eegcekCSVTLTLDVKGPGEVTAGDLKSDSDpdVEIVNPDIPIAKLREGQELELEARAEKGRGYVHAKwspVSTVEYRYI 150
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 830872876   156 GTLAVDSIYTPVKKVNYQVEPARVG----------SNDGFDKLTLEISTNGTIIPEDALGLSARILMEHLGLF 218
Cdd:smart00662 151 PRIPVDASFSPVDRVAYQVECPRVVqrtdccrecdEGEEYDKLIFDVETNGSLKPEEAVLEAAKILKEKLEAF 223
 
Name Accession Description Interval E-value
RpoA COG0202
DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]; DNA-directed RNA ...
1-262 1.56e-156

DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]; DNA-directed RNA polymerase, alpha subunit/40 kD subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 439972 [Multi-domain]  Cd Length: 317  Bit Score: 437.57  E-value: 1.56e-156
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830872876   1 EKPTITKIDE--NKDYGRFVIEPLERGYGTTLGNSLRRVLLASLPGAAITSIKIDGVLHEFDTVPGVREDVMQIILNIKG 78
Cdd:COG0202    4 EKPRKIEVEEeiSDNYGKFVLEPLERGYGTTLGNALRRVLLSSLPGAAVTSVKIEGVLHEFSTIPGVKEDVTDIILNLKG 83
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830872876  79 IAVKSYVEDEKKIELDVVGPAEVTAGDILTDSDIEIVNPDHYLFTIAEGKTFKAILTVNSGRGYVPAEGNKKDDAPVGTL 158
Cdd:COG0202   84 LRLKLHSDEPKTLRLEKKGPGEVTAGDIELPSDVEILNPDLVIATLDEDAKLEMELTVEKGRGYVPAEENKKEDLPIGVI 163
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830872876 159 AVDSIYTPVKKVNYQVEPARVGSNDGFDKLTLEISTNGTIIPEDALGLSARILMEHLGLFTDLTEVAKSADVMKETETAS 238
Cdd:COG0202  164 PIDAIFSPVRKVNYTVENTRVGQRTDYDKLILEIWTDGSITPEEALAEAAKILIEHLSLFVNLEEEAEEVEEEVEEEEEE 243
                        250       260
                 ....*....|....*....|....
gi 830872876 239 DDRMLDRTIEELDLSVRSYNCLKR 262
Cdd:COG0202  244 IDPILLRPIEELELSVRSYNCLKR 267
PRK05182 PRK05182
DNA-directed RNA polymerase subunit alpha; Provisional
1-262 4.65e-152

DNA-directed RNA polymerase subunit alpha; Provisional


Pssm-ID: 235359 [Multi-domain]  Cd Length: 310  Bit Score: 426.05  E-value: 4.65e-152
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830872876   1 EKPTITKIDENKDYGRFVIEPLERGYGTTLGNSLRRVLLASLPGAAITSIKIDGVLHEFDTVPGVREDVMQIILNIKGIA 80
Cdd:PRK05182   7 QKIEVEEESEDDNYGKFVLEPLERGFGTTLGNALRRVLLSSLPGAAVTSVKIDGVLHEFSTIPGVREDVTEIILNLKGLR 86
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830872876  81 VKSYVEDEKKIELDVVGPAEVTAGDILTDSDIEIVNPDHYLFTIAEGKTFKAILTVNSGRGYVPAEGNKKdDAPVGTLAV 160
Cdd:PRK05182  87 LKLHGDEPVTLTLSKKGPGEVTAGDIETDGDVEIVNPDLVIATLNEGAKLEMELTVERGRGYVPAEENKE-DAPIGRIPV 165
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830872876 161 DSIYTPVKKVNYQVEPARVGSNDGFDKLTLEISTNGTIIPEDALGLSARILMEHLGLFTDLTEvAKSADVMKETETASDD 240
Cdd:PRK05182 166 DAIFSPVKKVNYTVENTRVGQRTDYDKLILEVETDGSITPEEALALAAKILVEQLSVFVDLEE-AEEAEEEVEEEEPEFD 244
                        250       260
                 ....*....|....*....|..
gi 830872876 241 RMLDRTIEELDLSVRSYNCLKR 262
Cdd:PRK05182 245 PILLRPIEELELSVRSYNCLKR 266
rpoA TIGR02027
DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type; This family ...
14-262 3.59e-120

DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type; This family consists of the bacterial (and chloroplast) DNA-directed RNA polymerase alpha subunit, encoded by the rpoA gene. The RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. The amino terminal domain is involved in dimerizing and assembling the other RNA polymerase subunits into a transcriptionally active enzyme. The carboxy-terminal domain contains determinants for interaction with DNA and with transcriptional activator proteins. [Transcription, DNA-dependent RNA polymerase]


Pssm-ID: 273934 [Multi-domain]  Cd Length: 297  Bit Score: 345.02  E-value: 3.59e-120
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830872876   14 YGRFVIEPLERGYGTTLGNSLRRVLLASLPGAAITSIKIDGVLHEFDTVPGVREDVMQIILNIKGIAVKSYVEDEKKIEL 93
Cdd:TIGR02027   1 YGKFVLEPLERGFGITLGNALRRVLLSSIPGAAITAVKIDGVLHEFSTIEGVKEDVTEIILNLKQLVVKSEGDGERTMTL 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830872876   94 DVVGPAEVTAGDI-LTDSDIEIVNPDHYLFTIAEGKTFKAILTVNSGRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNY 172
Cdd:TIGR02027  81 SKKGPGVVTAGDIkAPPGDVEIVNPDLVIATLTEPADLEIELRVERGRGYVPAEENREEDRPVGVIAVDAIFSPVLKVNY 160
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830872876  173 QVEPARVGSNDGFDKLTLEISTNGTIIPEDALGLSARILMEHLGLFTDLTEVAKSADVMKETET--ASDDRMLDRTIEEL 250
Cdd:TIGR02027 161 EVENTRVGQRTDYDKLILEIETNGSITPKDAIAEAAKILIEHLEPFVNLDEEIEAFEEEQEEEEeeLEDAKLLSIKIEEL 240
                         250
                  ....*....|..
gi 830872876  251 DLSVRSYNCLKR 262
Cdd:TIGR02027 241 DLSVRSYNCLKR 252
RNAP_alpha_NTD cd06928
N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; The bacterial alpha ...
5-218 4.50e-111

N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; The bacterial alpha subunit of RNA polymerase (RNAP) consists of two independently folded domains: an amino-terminal domain (alphaNTD) and a carboxy-terminal domain (alphaCTD). AlphaCTD is not required for RNAP assembly but interacts with transcription activators. AlphaNTD is essential in vivo and in vitro for RNAP assembly and basal transcription. It is similar to the eukaryotic RPB3/AC40/archaeal D subunit, and contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The alphaNTDs of plant plastid RNAP (PEP) are also included in this subfamily. PEP is largely responsible for the transcription of photosynthetic genes and is closely related to the multi-subunit bacterial RNAP, which is a large multi-subunit complex responsible for the synthesis of all bacterial RNAs. The bacterial RNAP core enzyme consists of four subunits (beta', beta, alpha and omega). All residues in the alpha subunit that is involved in dimerization or in the interaction with other subunits are located within alphaNTD.


Pssm-ID: 132904 [Multi-domain]  Cd Length: 215  Bit Score: 318.64  E-value: 4.50e-111
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830872876   5 ITKIDENKDYGRFVIEPLERGYGTTLGNSLRRVLLASLPGAAITSIKIDGVLHEFDTVPGVREDVMQIILNIKGIAVKSY 84
Cdd:cd06928    1 SKVENKRENYGRFVIEPLERGQGTTLGNALRRVLLSSLPGAAITAVKIEGVLHEFSTIPGVREDVLEILLNLKEIVFKSD 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830872876  85 VEDE-KKIELDVVGPAEVTAGDILTDSDIEIVNPDHYLFTIAEGKTFKAILTVNSGRGYVPAEGNKKDDAPVGTLAVDSI 163
Cdd:cd06928   81 SEDEpQVLRLKVKGPGVVTAADIELPSGVEIVNPDQYIATLTEDASLEMELRIEKGRGYVPAEENKSEEKPIGFIPIDAI 160
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 830872876 164 YTPVKKVNYQVEPARVGSNDGFDKLTLEISTNGTIIPEDALGLSARILMEHLGLF 218
Cdd:cd06928  161 FSPVRKVNYSVESTRVGQRTDYEKLILEIWTNGSISPEEALAQAAKILINHFSPF 215
rpoA CHL00013
RNA polymerase alpha subunit
7-262 6.80e-78

RNA polymerase alpha subunit


Pssm-ID: 214333 [Multi-domain]  Cd Length: 327  Bit Score: 238.32  E-value: 6.80e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830872876   7 KIDENKD-YGRFVIEPLERGYGTTLGNSLRRVLLASLPGAAITSIKIDGVLHEFDTVPGVREDVMQIILNIKGIAVKSYV 85
Cdd:CHL00013  13 RVDSKRLyYGRFILSPLMKGQADTIGIALRRALLGEIEGTCITRAKIEGVPHEYSTIPGIRESVLEILLNLKEIVLKSNL 92
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830872876  86 EDEKKIELDVVGPAEVTAGDILTDSDIEIVNPDHYLFTIAEGKTFKAILTVNSGRGYVPAEGNKKDDapvGTLAVDSIYT 165
Cdd:CHL00013  93 YGPQKASICVQGPKYVTAQDIILPPSVEIVDPTQHIATITEPIDLEIELKIEKGRGYRLKTPKNFQD---GSFPIDAVFM 169
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830872876 166 PVKKVNYQVEPaRVGSNDGFDKLTLEISTNGTIIPEDALGLSARILMEhlgLFTDLTEVAKSADVMKETETASDDRMLDR 245
Cdd:CHL00013 170 PVRNVNYSIHS-YGNGNEKQEILFLEIWTNGSITPKEALHEASRNLID---LFIPFLHAEEENLKLENNENRVTLLFTFH 245
                        250       260       270
                 ....*....|....*....|....*....|....*
gi 830872876 246 T------------------IEELDLSVRSYNCLKR 262
Cdd:CHL00013 246 DrltdlkknkkeialkqifIEQLELSVRAYNCLKR 280
RNA_pol_L pfam01193
RNA polymerase Rpb3/Rpb11 dimerization domain; The two eukaryotic subunits Rpb3 and Rpb11 ...
21-214 1.61e-63

RNA polymerase Rpb3/Rpb11 dimerization domain; The two eukaryotic subunits Rpb3 and Rpb11 dimerize to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerization domain of the alpha subunit/Rpb3 is interrupted by an insert domain (pfam01000). Some of the alpha subunits also contain iron-sulphur binding domains (pfam00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp.


Pssm-ID: 460104 [Multi-domain]  Cd Length: 191  Bit Score: 197.24  E-value: 1.61e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830872876   21 PLERGYGTTLGNSLRRVLLASLPGAAITSIKIDGVLHEFDTVPGVREDVMQIILNIKGIAVKSYVEDEKKIELDVVGPAE 100
Cdd:pfam01193   1 FLLRGEDHTLGNALRRILLSEVPGVAIDAVKIEGNTSEFSDEPGAHRLGLIPLLNLKELFFKLSSDDDETLELDKEGPGE 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830872876  101 VTAGDILTDSD---IEIVNPDHYLFTIAEGKTFKAILTVNSGRGYVPAEGNKKDDAPVGTLAVDSIYTPVKKVNYQVEPA 177
Cdd:pfam01193  81 VTAGDINTDSDvevIEIINPDLHIATLEEEAALEMELEVVKGRGYVPAEKNKDVDDPIGDIPIDSIFSPVEKVNYVVENT 160
                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 830872876  178 RvgsndgFDKLTLEISTNGTIIPEDALGLSARILMEH 214
Cdd:pfam01193 161 D------YDKLIFEVETDGSIPPEEALKEAAKILKEK 191
RPOLD smart00662
RNA polymerases D; DNA-directed RNA polymerase subunit D and bacterial alpha chain
15-218 8.97e-61

RNA polymerases D; DNA-directed RNA polymerase subunit D and bacterial alpha chain


Pssm-ID: 214766 [Multi-domain]  Cd Length: 224  Bit Score: 191.29  E-value: 8.97e-61
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830872876    15 GRFVIEPlergYGTTLGNSLRRVLLASLPGAAITSIKIDGvlhefdTVPGVREDVMQIILNIKGIAVKSYVE-------- 86
Cdd:smart00662   1 AKFVLEP----YGLTLANALRRVLLSSVPGMAVTSVYIEG------NTSGVQDEVLAHRLGLKPLASDPDGDeyqrdcec 70
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830872876    87 ------DEKKIELDVVGPAEVTAGDILTDSD--IEIVNPDHYLFTIAEGKTFKAILTVNSGRGYVPAE---GNKKDDAPV 155
Cdd:smart00662  71 eegcekCSVTLTLDVKGPGEVTAGDLKSDSDpdVEIVNPDIPIAKLREGQELELEARAEKGRGYVHAKwspVSTVEYRYI 150
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 830872876   156 GTLAVDSIYTPVKKVNYQVEPARVG----------SNDGFDKLTLEISTNGTIIPEDALGLSARILMEHLGLF 218
Cdd:smart00662 151 PRIPVDASFSPVDRVAYQVECPRVVqrtdccrecdEGEEYDKLIFDVETNGSLKPEEAVLEAAKILKEKLEAF 223
RNA_pol_A_bac pfam01000
RNA polymerase Rpb3/RpoA insert domain; Members of this family include: alpha subunit from ...
50-165 3.42e-43

RNA polymerase Rpb3/RpoA insert domain; Members of this family include: alpha subunit from eubacteria alpha subunits from chloroplasts Rpb3 subunits from eukaryotes RpoD subunits from archaeal


Pssm-ID: 425983  Cd Length: 117  Bit Score: 142.78  E-value: 3.42e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830872876   50 IKIDGVLHEFDTVPGVREDVMQIILNIKGIAVKSYVEDEK--KIELDVVGPAEVTAGDILTDSDIEIVNPDHYLFTIAEG 127
Cdd:pfam01000   1 VYINGVAHEFGLIPGVSEDVLEIILNLKELVCKEEGCEECsvTLTLDVKGPGEVTAGDLESDPDVEIVNPDILIATLRKG 80
                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 830872876  128 KTFKAILTVNSGRGYVPAEGNKKDDAPvGTLAVDSIYT 165
Cdd:pfam01000  81 QELELEAYAKKGRGYVHAKENKEDEDP-GRIPVDAIFS 117
RNAP_RPB11_RPB3 cd00460
RPB11 and RPB3 subunits of RNA polymerase; The eukaryotic RPB11 and RPB3 subunits of RNA ...
157-218 1.79e-06

RPB11 and RPB3 subunits of RNA polymerase; The eukaryotic RPB11 and RPB3 subunits of RNA polymerase (RNAP), as well as their archaeal (L and D subunits) and bacterial (alpha subunit) counterparts, are involved in the assembly of RNAP, a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the archaeal (D/L subunits) and bacterial (alpha subunit) counterparts.


Pssm-ID: 132901  Cd Length: 86  Bit Score: 45.10  E-value: 1.79e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 830872876 157 TLAVDSIYTPVKKVNYQVEPARVGSNDGFDKLTLEISTNGTIIPEDALGLSARILMEHLGLF 218
Cdd:cd00460   25 SLRRILLKSPVEFAAYYVEHPVKLQRTDEDKFILRIETVGSIPPEEALRRAVEILRKKLEHL 86
RNA_pol_A_CTD pfam03118
Bacterial RNA polymerase, alpha chain C terminal domain; The alpha subunit of RNA polymerase ...
243-262 2.78e-06

Bacterial RNA polymerase, alpha chain C terminal domain; The alpha subunit of RNA polymerase consists of two independently folded domains, referred to as amino-terminal and carboxyl terminal domains. The amino terminal domain is involved in the interaction with the other subunits of the RNA polymerase. The carboxyl-terminal domain interacts with the DNA and activators. The amino acid sequence of the alpha subunit is conserved in prokaryotic and chloroplast RNA polymerases. There are three regions of particularly strong conservation, two in the amino-terminal and one in the carboxyl- terminal.


Pssm-ID: 427148 [Multi-domain]  Cd Length: 63  Bit Score: 43.68  E-value: 2.78e-06
                          10        20
                  ....*....|....*....|
gi 830872876  243 LDRTIEELDLSVRSYNCLKR 262
Cdd:pfam03118   8 LSIPIEELDLSVRSYNCLKR 27
RNAP_RPB11_RPB3 cd00460
RPB11 and RPB3 subunits of RNA polymerase; The eukaryotic RPB11 and RPB3 subunits of RNA ...
5-41 6.64e-03

RPB11 and RPB3 subunits of RNA polymerase; The eukaryotic RPB11 and RPB3 subunits of RNA polymerase (RNAP), as well as their archaeal (L and D subunits) and bacterial (alpha subunit) counterparts, are involved in the assembly of RNAP, a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the archaeal (D/L subunits) and bacterial (alpha subunit) counterparts.


Pssm-ID: 132901  Cd Length: 86  Bit Score: 35.09  E-value: 6.64e-03
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 830872876   5 ITKIDENKDYGRFVIEPlergYGTTLGNSLRRVLLAS 41
Cdd:cd00460    1 VKILEKEKNYVDFVLEN----EDHTLGNSLRRILLKS 33
 
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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