|
Name |
Accession |
Description |
Interval |
E-value |
| PRK05182 |
PRK05182 |
DNA-directed RNA polymerase subunit alpha; Provisional |
1-310 |
0e+00 |
|
DNA-directed RNA polymerase subunit alpha; Provisional
Pssm-ID: 235359 [Multi-domain] Cd Length: 310 Bit Score: 536.22 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 906303750 1 MLISQRPTLSEETLADNRSKFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTDIILNL 80
Cdd:PRK05182 3 FLKPQKIEVEEESEDDNYGKFVLEPLERGFGTTLGNALRRVLLSSLPGAAVTSVKIDGVLHEFSTIPGVREDVTEIILNL 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 906303750 81 KGLVVSSEEDEPVTMYLRKQGPGAVTAGDIVPPAGVTVHNPDMHIATLNDKGKLEVELVVERGRGYVPAVQNKaSGAEIG 160
Cdd:PRK05182 83 KGLRLKLHGDEPVTLTLSKKGPGEVTAGDIETDGDVEIVNPDLVIATLNEGAKLEMELTVERGRGYVPAEENK-EDAPIG 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 906303750 161 RIPVDSIYSPVLKVTYKVEATRVEQRTDFDKLILDVETKNSISPRDALASAGKTLVELFGLARELNvEAEGIEIGPSPAE 240
Cdd:PRK05182 162 RIPVDAIFSPVKKVNYTVENTRVGQRTDYDKLILEVETDGSITPEEALALAAKILVEQLSVFVDLE-EAEEAEEEVEEEE 240
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 906303750 241 ADHIASFALPIDDLDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIKLHQLGLSLKD 310
Cdd:PRK05182 241 PEFDPILLRPIEELELSVRSYNCLKRAGINTIGDLVQRTEEELLKTRNLGKKSLEEIKEKLAELGLSLGM 310
|
|
| RpoA |
COG0202 |
DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]; DNA-directed RNA ... |
5-316 |
0e+00 |
|
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: 531.17 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 906303750 5 QRPTL--SEETLADNRSKFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTDIILNLKG 82
Cdd:COG0202 4 EKPRKieVEEEISDNYGKFVLEPLERGYGTTLGNALRRVLLSSLPGAAVTSVKIEGVLHEFSTIPGVKEDVTDIILNLKG 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 906303750 83 LVVSSEEDEPVTMYLRKQGPGAVTAGDIVPPAGVTVHNPDMHIATLNDKGKLEVELVVERGRGYVPAVQNKASGAEIGRI 162
Cdd:COG0202 84 LRLKLHSDEPKTLRLEKKGPGEVTAGDIELPSDVEILNPDLVIATLDEDAKLEMELTVEKGRGYVPAEENKKEDLPIGVI 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 906303750 163 PVDSIYSPVLKVTYKVEATRVEQRTDFDKLILDVETKNSISPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEAD 242
Cdd:COG0202 164 PIDAIFSPVRKVNYTVENTRVGQRTDYDKLILEIWTDGSITPEEALAEAAKILIEHLSLFVNLEEEAEEVEEEVEEEEEE 243
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 906303750 243 HIASFALPIDDLDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIKLHQLGLSLKDSPATFD 316
Cdd:COG0202 244 IDPILLRPIEELELSVRSYNCLKRAGINTIGDLVQKTEEELLKIRNFGKKSLEEIKEKLAELGLSLGMDLENWP 317
|
|
| rpoA |
TIGR02027 |
DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type; This family ... |
18-311 |
3.18e-157 |
|
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: 442.48 E-value: 3.18e-157
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 906303750 18 RSKFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTDIILNLKGLVVSSEEDEPVTMYL 97
Cdd:TIGR02027 1 YGKFVLEPLERGFGITLGNALRRVLLSSIPGAAITAVKIDGVLHEFSTIEGVKEDVTEIILNLKQLVVKSEGDGERTMTL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 906303750 98 RKQGPGAVTAGDIV-PPAGVTVHNPDMHIATLNDKGKLEVELVVERGRGYVPAVQNKASGAEIGRIPVDSIYSPVLKVTY 176
Cdd:TIGR02027 81 SKKGPGVVTAGDIKaPPGDVEIVNPDLVIATLTEPADLEIELRVERGRGYVPAEENREEDRPVGVIAVDAIFSPVLKVNY 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 906303750 177 KVEATRVEQRTDFDKLILDVETKNSISPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHI--ASFALPIDDL 254
Cdd:TIGR02027 161 EVENTRVGQRTDYDKLILEIETNGSITPKDAIAEAAKILIEHLEPFVNLDEEIEAFEEEQEEEEEELEdaKLLSIKIEEL 240
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|....*..
gi 906303750 255 DLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIKLHQLGLSLKDS 311
Cdd:TIGR02027 241 DLSVRSYNCLKRAGIHTLGELVSKSEEELLKIKNFGKKSLTEIKEKLAELGLELGMD 297
|
|
| RNAP_alpha_NTD |
cd06928 |
N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; The bacterial alpha ... |
11-219 |
6.87e-116 |
|
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: 334.44 E-value: 6.87e-116
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 906303750 11 EETLADNRSKFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTDIILNLKGLVV-SSEE 89
Cdd:cd06928 3 VENKRENYGRFVIEPLERGQGTTLGNALRRVLLSSLPGAAITAVKIEGVLHEFSTIPGVREDVLEILLNLKEIVFkSDSE 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 906303750 90 DEPVTMYLRKQGPGAVTAGDIVPPAGVTVHNPDMHIATLNDKGKLEVELVVERGRGYVPAVQNKASGAEIGRIPVDSIYS 169
Cdd:cd06928 83 DEPQVLRLKVKGPGVVTAADIELPSGVEIVNPDQYIATLTEDASLEMELRIEKGRGYVPAEENKSEEKPIGFIPIDAIFS 162
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|
gi 906303750 170 PVLKVTYKVEATRVEQRTDFDKLILDVETKNSISPRDALASAGKTLVELF 219
Cdd:cd06928 163 PVRKVNYSVESTRVGQRTDYEKLILEIWTNGSISPEEALAQAAKILINHF 212
|
|
| RPOLD |
smart00662 |
RNA polymerases D; DNA-directed RNA polymerase subunit D and bacterial alpha chain |
19-221 |
3.18e-71 |
|
RNA polymerases D; DNA-directed RNA polymerase subunit D and bacterial alpha chain
Pssm-ID: 214766 [Multi-domain] Cd Length: 224 Bit Score: 221.33 E-value: 3.18e-71
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 906303750 19 SKFVIEPlepgFGYTLGNSLRRTLLSSIPGAAVTSIRIDGvlheftTVPGVKEDVTDIILNLKGLVVSSEEDEP------ 92
Cdd:smart00662 1 AKFVLEP----YGLTLANALRRVLLSSVPGMAVTSVYIEG------NTSGVQDEVLAHRLGLKPLASDPDGDEYqrdcec 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 906303750 93 --------VTMYLRKQGPGAVTAGDIVPPA--GVTVHNPDMHIATLNDKGKLEVELVVERGRGYVPA---VQNKASGAEI 159
Cdd:smart00662 71 eegcekcsVTLTLDVKGPGEVTAGDLKSDSdpDVEIVNPDIPIAKLREGQELELEARAEKGRGYVHAkwsPVSTVEYRYI 150
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 906303750 160 GRIPVDSIYSPVLKVTYKVEATRVEQRTD----------FDKLILDVETKNSISPRDALASAGKTLVELFGL 221
Cdd:smart00662 151 PRIPVDASFSPVDRVAYQVECPRVVQRTDccrecdegeeYDKLIFDVETNGSLKPEEAVLEAAKILKEKLEA 222
|
|
| RNA_pol_L |
pfam01193 |
RNA polymerase Rpb3/Rpb11 dimerization domain; The two eukaryotic subunits Rpb3 and Rpb11 ... |
25-217 |
1.10e-64 |
|
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: 203.41 E-value: 1.10e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 906303750 25 PLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTDIILNLKGLVVSSEEDEPVTMYLRKQGPGA 104
Cdd:pfam01193 1 FLLRGEDHTLGNALRRILLSEVPGVAIDAVKIEGNTSEFSDEPGAHRLGLIPLLNLKELFFKLSSDDDETLELDKEGPGE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 906303750 105 VTAGDIVPPAGVT---VHNPDMHIATLNDKGKLEVELVVERGRGYVPAVQNKASGAEIGRIPVDSIYSPVLKVTYKVEat 181
Cdd:pfam01193 81 VTAGDINTDSDVEvieIINPDLHIATLEEEAALEMELEVVKGRGYVPAEKNKDVDDPIGDIPIDSIFSPVEKVNYVVE-- 158
|
170 180 190
....*....|....*....|....*....|....*.
gi 906303750 182 rveqRTDFDKLILDVETKNSISPRDALASAGKTLVE 217
Cdd:pfam01193 159 ----NTDYDKLIFEVETDGSIPPEEALKEAAKILKE 190
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PRK05182 |
PRK05182 |
DNA-directed RNA polymerase subunit alpha; Provisional |
1-310 |
0e+00 |
|
DNA-directed RNA polymerase subunit alpha; Provisional
Pssm-ID: 235359 [Multi-domain] Cd Length: 310 Bit Score: 536.22 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 906303750 1 MLISQRPTLSEETLADNRSKFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTDIILNL 80
Cdd:PRK05182 3 FLKPQKIEVEEESEDDNYGKFVLEPLERGFGTTLGNALRRVLLSSLPGAAVTSVKIDGVLHEFSTIPGVREDVTEIILNL 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 906303750 81 KGLVVSSEEDEPVTMYLRKQGPGAVTAGDIVPPAGVTVHNPDMHIATLNDKGKLEVELVVERGRGYVPAVQNKaSGAEIG 160
Cdd:PRK05182 83 KGLRLKLHGDEPVTLTLSKKGPGEVTAGDIETDGDVEIVNPDLVIATLNEGAKLEMELTVERGRGYVPAEENK-EDAPIG 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 906303750 161 RIPVDSIYSPVLKVTYKVEATRVEQRTDFDKLILDVETKNSISPRDALASAGKTLVELFGLARELNvEAEGIEIGPSPAE 240
Cdd:PRK05182 162 RIPVDAIFSPVKKVNYTVENTRVGQRTDYDKLILEVETDGSITPEEALALAAKILVEQLSVFVDLE-EAEEAEEEVEEEE 240
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 906303750 241 ADHIASFALPIDDLDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIKLHQLGLSLKD 310
Cdd:PRK05182 241 PEFDPILLRPIEELELSVRSYNCLKRAGINTIGDLVQRTEEELLKTRNLGKKSLEEIKEKLAELGLSLGM 310
|
|
| RpoA |
COG0202 |
DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]; DNA-directed RNA ... |
5-316 |
0e+00 |
|
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: 531.17 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 906303750 5 QRPTL--SEETLADNRSKFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTDIILNLKG 82
Cdd:COG0202 4 EKPRKieVEEEISDNYGKFVLEPLERGYGTTLGNALRRVLLSSLPGAAVTSVKIEGVLHEFSTIPGVKEDVTDIILNLKG 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 906303750 83 LVVSSEEDEPVTMYLRKQGPGAVTAGDIVPPAGVTVHNPDMHIATLNDKGKLEVELVVERGRGYVPAVQNKASGAEIGRI 162
Cdd:COG0202 84 LRLKLHSDEPKTLRLEKKGPGEVTAGDIELPSDVEILNPDLVIATLDEDAKLEMELTVEKGRGYVPAEENKKEDLPIGVI 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 906303750 163 PVDSIYSPVLKVTYKVEATRVEQRTDFDKLILDVETKNSISPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEAD 242
Cdd:COG0202 164 PIDAIFSPVRKVNYTVENTRVGQRTDYDKLILEIWTDGSITPEEALAEAAKILIEHLSLFVNLEEEAEEVEEEVEEEEEE 243
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 906303750 243 HIASFALPIDDLDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIKLHQLGLSLKDSPATFD 316
Cdd:COG0202 244 IDPILLRPIEELELSVRSYNCLKRAGINTIGDLVQKTEEELLKIRNFGKKSLEEIKEKLAELGLSLGMDLENWP 317
|
|
| rpoA |
TIGR02027 |
DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type; This family ... |
18-311 |
3.18e-157 |
|
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: 442.48 E-value: 3.18e-157
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 906303750 18 RSKFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTDIILNLKGLVVSSEEDEPVTMYL 97
Cdd:TIGR02027 1 YGKFVLEPLERGFGITLGNALRRVLLSSIPGAAITAVKIDGVLHEFSTIEGVKEDVTEIILNLKQLVVKSEGDGERTMTL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 906303750 98 RKQGPGAVTAGDIV-PPAGVTVHNPDMHIATLNDKGKLEVELVVERGRGYVPAVQNKASGAEIGRIPVDSIYSPVLKVTY 176
Cdd:TIGR02027 81 SKKGPGVVTAGDIKaPPGDVEIVNPDLVIATLTEPADLEIELRVERGRGYVPAEENREEDRPVGVIAVDAIFSPVLKVNY 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 906303750 177 KVEATRVEQRTDFDKLILDVETKNSISPRDALASAGKTLVELFGLARELNVEAEGIEIGPSPAEADHI--ASFALPIDDL 254
Cdd:TIGR02027 161 EVENTRVGQRTDYDKLILEIETNGSITPKDAIAEAAKILIEHLEPFVNLDEEIEAFEEEQEEEEEELEdaKLLSIKIEEL 240
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|....*..
gi 906303750 255 DLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIKLHQLGLSLKDS 311
Cdd:TIGR02027 241 DLSVRSYNCLKRAGIHTLGELVSKSEEELLKIKNFGKKSLTEIKEKLAELGLELGMD 297
|
|
| RNAP_alpha_NTD |
cd06928 |
N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; The bacterial alpha ... |
11-219 |
6.87e-116 |
|
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: 334.44 E-value: 6.87e-116
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 906303750 11 EETLADNRSKFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTDIILNLKGLVV-SSEE 89
Cdd:cd06928 3 VENKRENYGRFVIEPLERGQGTTLGNALRRVLLSSLPGAAITAVKIEGVLHEFSTIPGVREDVLEILLNLKEIVFkSDSE 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 906303750 90 DEPVTMYLRKQGPGAVTAGDIVPPAGVTVHNPDMHIATLNDKGKLEVELVVERGRGYVPAVQNKASGAEIGRIPVDSIYS 169
Cdd:cd06928 83 DEPQVLRLKVKGPGVVTAADIELPSGVEIVNPDQYIATLTEDASLEMELRIEKGRGYVPAEENKSEEKPIGFIPIDAIFS 162
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|
gi 906303750 170 PVLKVTYKVEATRVEQRTDFDKLILDVETKNSISPRDALASAGKTLVELF 219
Cdd:cd06928 163 PVRKVNYSVESTRVGQRTDYEKLILEIWTNGSISPEEALAQAAKILINHF 212
|
|
| rpoA |
CHL00013 |
RNA polymerase alpha subunit |
19-309 |
1.41e-85 |
|
RNA polymerase alpha subunit
Pssm-ID: 214333 [Multi-domain] Cd Length: 327 Bit Score: 261.44 E-value: 1.41e-85
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 906303750 19 SKFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTDIILNLKGLVVSSEEDEPVTMYLR 98
Cdd:CHL00013 22 GRFILSPLMKGQADTIGIALRRALLGEIEGTCITRAKIEGVPHEYSTIPGIRESVLEILLNLKEIVLKSNLYGPQKASIC 101
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 906303750 99 KQGPGAVTAGDIVPPAGVTVHNPDMHIATLNDKGKLEVELVVERGRGYVPAVQNKasgAEIGRIPVDSIYSPVLKVTYKV 178
Cdd:CHL00013 102 VQGPKYVTAQDIILPPSVEIVDPTQHIATITEPIDLEIELKIEKGRGYRLKTPKN---FQDGSFPIDAVFMPVRNVNYSI 178
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 906303750 179 EaTRVEQRTDFDKLILDVETKNSISPRDALASAGKTLVELFGL---ARELNVEAEGIEIGPSPAEADH------------ 243
Cdd:CHL00013 179 H-SYGNGNEKQEILFLEIWTNGSITPKEALHEASRNLIDLFIPflhAEEENLKLENNENRVTLLFTFHdrltdlkknkke 257
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 906303750 244 IASFALPIDDLDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIKLHQ-LGLSLK 309
Cdd:CHL00013 258 IALKQIFIEQLELSVRAYNCLKRANIHTLLDLLNYSQEDLLKIKNFGQKSAKEVLEALQKrFGIDLP 324
|
|
| RPOLD |
smart00662 |
RNA polymerases D; DNA-directed RNA polymerase subunit D and bacterial alpha chain |
19-221 |
3.18e-71 |
|
RNA polymerases D; DNA-directed RNA polymerase subunit D and bacterial alpha chain
Pssm-ID: 214766 [Multi-domain] Cd Length: 224 Bit Score: 221.33 E-value: 3.18e-71
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 906303750 19 SKFVIEPlepgFGYTLGNSLRRTLLSSIPGAAVTSIRIDGvlheftTVPGVKEDVTDIILNLKGLVVSSEEDEP------ 92
Cdd:smart00662 1 AKFVLEP----YGLTLANALRRVLLSSVPGMAVTSVYIEG------NTSGVQDEVLAHRLGLKPLASDPDGDEYqrdcec 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 906303750 93 --------VTMYLRKQGPGAVTAGDIVPPA--GVTVHNPDMHIATLNDKGKLEVELVVERGRGYVPA---VQNKASGAEI 159
Cdd:smart00662 71 eegcekcsVTLTLDVKGPGEVTAGDLKSDSdpDVEIVNPDIPIAKLREGQELELEARAEKGRGYVHAkwsPVSTVEYRYI 150
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 906303750 160 GRIPVDSIYSPVLKVTYKVEATRVEQRTD----------FDKLILDVETKNSISPRDALASAGKTLVELFGL 221
Cdd:smart00662 151 PRIPVDASFSPVDRVAYQVECPRVVQRTDccrecdegeeYDKLIFDVETNGSLKPEEAVLEAAKILKEKLEA 222
|
|
| RNA_pol_L |
pfam01193 |
RNA polymerase Rpb3/Rpb11 dimerization domain; The two eukaryotic subunits Rpb3 and Rpb11 ... |
25-217 |
1.10e-64 |
|
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: 203.41 E-value: 1.10e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 906303750 25 PLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEFTTVPGVKEDVTDIILNLKGLVVSSEEDEPVTMYLRKQGPGA 104
Cdd:pfam01193 1 FLLRGEDHTLGNALRRILLSEVPGVAIDAVKIEGNTSEFSDEPGAHRLGLIPLLNLKELFFKLSSDDDETLELDKEGPGE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 906303750 105 VTAGDIVPPAGVT---VHNPDMHIATLNDKGKLEVELVVERGRGYVPAVQNKASGAEIGRIPVDSIYSPVLKVTYKVEat 181
Cdd:pfam01193 81 VTAGDINTDSDVEvieIINPDLHIATLEEEAALEMELEVVKGRGYVPAEKNKDVDDPIGDIPIDSIFSPVEKVNYVVE-- 158
|
170 180 190
....*....|....*....|....*....|....*.
gi 906303750 182 rveqRTDFDKLILDVETKNSISPRDALASAGKTLVE 217
Cdd:pfam01193 159 ----NTDYDKLIFEVETDGSIPPEEALKEAAKILKE 190
|
|
| RNA_pol_A_bac |
pfam01000 |
RNA polymerase Rpb3/RpoA insert domain; Members of this family include: alpha subunit from ... |
54-169 |
1.76e-49 |
|
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: 161.65 E-value: 1.76e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 906303750 54 IRIDGVLHEFTTVPGVKEDVTDIILNLKGLVVSSEEDEP--VTMYLRKQGPGAVTAGDIVPPAGVTVHNPDMHIATLNDK 131
Cdd:pfam01000 1 VYINGVAHEFGLIPGVSEDVLEIILNLKELVCKEEGCEEcsVTLTLDVKGPGEVTAGDLESDPDVEIVNPDILIATLRKG 80
|
90 100 110
....*....|....*....|....*....|....*...
gi 906303750 132 GKLEVELVVERGRGYVPAVQNKASGAEiGRIPVDSIYS 169
Cdd:pfam01000 81 QELELEAYAKKGRGYVHAKENKEDEDP-GRIPVDAIFS 117
|
|
| RNA_pol_A_CTD |
pfam03118 |
Bacterial RNA polymerase, alpha chain C terminal domain; The alpha subunit of RNA polymerase ... |
240-302 |
4.02e-27 |
|
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: 101.46 E-value: 4.02e-27
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 906303750 240 EADHIASFALPIDDLDLTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIKLH 302
Cdd:pfam03118 1 EDDELELLSIPIEELDLSVRSYNCLKRAGINTVGELVALSEEDLLKIKNFGRKSLDEIKEKLE 63
|
|
| RNAP_RPB11_RPB3 |
cd00460 |
RPB11 and RPB3 subunits of RNA polymerase; The eukaryotic RPB11 and RPB3 subunits of RNA ... |
166-218 |
7.98e-10 |
|
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: 55.12 E-value: 7.98e-10
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|...
gi 906303750 166 SIYSPVLKVTYKVEATRVEQRTDFDKLILDVETKNSISPRDALASAGKTLVEL 218
Cdd:cd00460 30 LLKSPVEFAAYYVEHPVKLQRTDEDKFILRIETVGSIPPEEALRRAVEILRKK 82
|
|
| RNAP_D |
cd07030 |
D subunit of Archaeal RNA polymerase; The D subunit of archaeal RNA polymerase (RNAP) is ... |
14-217 |
3.94e-09 |
|
D subunit of Archaeal RNA polymerase; The D subunit of archaeal RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is 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. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The D subunit is equivalent to the RPB3 subunit of eukaryotic RNAP II. It 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 assembly of the two largest archaeal RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of the archaeal D/L heterodimer.
Pssm-ID: 132908 [Multi-domain] Cd Length: 259 Bit Score: 56.51 E-value: 3.94e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 906303750 14 LADNRSKFVIEPLEPGFGytlgNSLRRTLLSSIPGAAVTSIRI--------DGVL-HEFTTVPGVKEDVTDIILNLKGLV 84
Cdd:cd07030 8 LDDDRARFVLEGVPPAFA----NAIRRAIISEVPTLAIDDVNIyentsvlfDEMLaHRLGLIPLRTDLDLYKYRSECSCG 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 906303750 85 VSSEEDEPVTMYLRKQGPGAVTAGDIVP--PAGVTVHnPDMHIATLNDKGKLEVELVVERGRG---------------YV 147
Cdd:cd07030 84 GAGCPLCTVTLTLSVEGPGTVYSGDLKSsdPDVKPVY-DNIPIVKLGKGQKLVLEAYARLGRGkehakwqpttacgykYY 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 906303750 148 PAVQNKASGAEIGRIpVDSIYSPVLKVTYK----------------VEATR---VEQRTDFDKLILDVETKNSISPRDAL 208
Cdd:cd07030 163 PVIEIDEDCDGCGKC-VEECPRGVLELEEGkvvvedledcslcklcERACDagaIRVGWDEDRFIFEVESDGSLPPKEIL 241
|
....*....
gi 906303750 209 ASAGKTLVE 217
Cdd:cd07030 242 LEALRILKE 250
|
|
| PRK00783 |
PRK00783 |
DNA-directed RNA polymerase subunit D; Provisional |
14-217 |
2.14e-08 |
|
DNA-directed RNA polymerase subunit D; Provisional
Pssm-ID: 234837 [Multi-domain] Cd Length: 263 Bit Score: 54.51 E-value: 2.14e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 906303750 14 LADNRSKFVIEPLEPGFGytlgNSLRRTLLSSIPGAAVTSIRI--------DGVL-HEFTTVPgVKEDVTDiiLNLKGLV 84
Cdd:PRK00783 8 LDDRSARFVVEGVTPAFA----NAIRRAMIADVPTMAIDDVRFyentsvlfDEILaHRLGLIP-LTTDLDK--YKPPEEC 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 906303750 85 VSSEEDEP---VTMYLRKQGPGAVTAGDIVP--PAGVTVhNPDMHIATLNDKGKLEVELVVERGRG-------------- 145
Cdd:PRK00783 81 TCEGEGCPdctVTLSLEVEGPKTVYSGDLKSsdPDVKPV-DPNIPIVKLKEGQKLVLEAYARLGRGkehakwqpgsacgy 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 906303750 146 -YVP--AVQNKASGAE--IGRIP--VDSIYSPVLKVTYKVEAT------------RVEQRTDFDKLILDVETKNSISPRD 206
Cdd:PRK00783 160 kYYPriEVSEDCDECEkcVEACPrgVLELKEGKLVVTDLLNCSlcklceracpgkAIRVSDDENKFIFTVESDGSLPVEE 239
|
250
....*....|.
gi 906303750 207 ALASAGKTLVE 217
Cdd:PRK00783 240 ILLEALKILKR 250
|
|
| PRK07758 |
PRK07758 |
hypothetical protein; Provisional |
256-309 |
5.02e-03 |
|
hypothetical protein; Provisional
Pssm-ID: 181104 [Multi-domain] Cd Length: 95 Bit Score: 36.05 E-value: 5.02e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....
gi 906303750 256 LTVRSYNCLKREGVHTVGELVARTESDLLDIRNFGQKSIDEVKIKLHQLGLSLK 309
Cdd:PRK07758 42 LSAPARRALEHHGIHTVEELSKYSEKEILKLHGMGPASLPKLRKALEESGLSFK 95
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