|
Name |
Accession |
Description |
Interval |
E-value |
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
11-394 |
0e+00 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 516.71 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 11 FVSPEAIEKAVKKMNSDglLPKILEEELLTKLKDLQITKKQLNTIVKEVRTRFENALVEPGEAVGIVAAQSIGEPGTQMT 90
Cdd:PRK04309 1 MMSEETLEEKLEDASLE--LPQKLKEELREKLEERKLTEEEVEEIIEEVVREYLRSLVEPGEAVGVVAAQSIGEPGTQMT 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 91 LKTFHFAGVAEFTVTQGLPRLIEIVDARRNPSTPMTEVYLDEEHRHDVEKAKEVARKIELTRIENIASNVSIDLSEMEII 170
Cdd:PRK04309 79 MRTFHYAGVAEINVTLGLPRLIEIVDARKEPSTPMMTIYLKDEYAYDREKAEEVARKIEATTLENLAKDISVDLANMTII 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 171 IEIDLDLMHDKGLDIETVANIIAKGRKIAVRTEGNLIYIDPKLEAIKDLQKLAAKIRLLPIKGLLNIRRTQISKdpEKNE 250
Cdd:PRK04309 159 IELDEEMLEDRGLTVDDVKEAIEKKKGGEVEIEGNTLIISPKEPSYRELRKLAEKIRNIKIKGIKGIKRVIIRK--EGDE 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 251 FMIYTEGTDFVKTLRIPGVDQTRLYTNHTYEIAETLGIEAARNAIIKESMEVLKAQGLDVDLRHITLVADLMTANGDVRQ 330
Cdd:PRK04309 237 YVIYTEGSNLKEVLKVEGVDATRTTTNNIHEIEEVLGIEAARNAIIEEIKNTLEEQGLDVDIRHIMLVADMMTWDGEVRQ 316
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1491308752 331 IGRHGISGEKLSVLARASFEITVKHLLEACLQGESDDLKGITENVIVGQMIPLGTGSIDLLMNP 394
Cdd:PRK04309 317 IGRHGVSGEKASVLARAAFEVTVKHLLDAAVRGEVDELKGVTENIIVGQPIPLGTGDVELTMDP 380
|
|
| RNAP_A'' |
cd06528 |
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ... |
34-394 |
1.29e-170 |
|
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis.
Pssm-ID: 132725 [Multi-domain] Cd Length: 363 Bit Score: 481.36 E-value: 1.29e-170
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 34 LEEELLTKLKDLQITKKQLNTIVKEVRTRFENALVEPGEAVGIVAAQSIGEPGTQMTLKTFHFAGVAEFTVTQGLPRLIE 113
Cdd:cd06528 3 LKEKLEEVLKEHGLTLSEAEEIIKEVLREYLRSLIEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVAEINVTLGLPRLIE 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 114 IVDARRNPSTPMTEVYLDEEHRHDVEKAKEVARKIELTRIENIASNVSIDLSEMEIIIEIDLDLMHDKGLDIETVANII- 192
Cdd:cd06528 83 IVDARKEPSTPTMTIYLEEEYKYDREKAEEVARKIEETTLENLAEDISIDLFNMRITIELDEEMLEDRGITVDDVLKAIe 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 193 -AKGRKIAVRTEGNLIYIDPKLEAIKDLQKLAAKIRLLPIKGLLNIRRTQISKdpEKNEFMIYTEGTDFVKTLRIPGVDQ 271
Cdd:cd06528 163 kLKKGKVGEEGDVTLIVLKAEEPSIKELRKLAEKILNTKIKGIKGIKRVIVRK--EEDEYVIYTEGSNLKAVLKVEGVDP 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 272 TRLYTNHTYEIAETLGIEAARNAIIKESMEVLKAQGLDVDLRHITLVADLMTANGDVRQIGRHGISGEKLSVLARASFEI 351
Cdd:cd06528 241 TRTTTNNIHEIEEVLGIEAARNAIINEIKRTLEEQGLDVDIRHIMLVADIMTYDGEVRQIGRHGIAGEKPSVLARAAFEV 320
|
330 340 350 360
....*....|....*....|....*....|....*....|...
gi 1491308752 352 TVKHLLEACLQGESDDLKGITENVIVGQMIPLGTGSIDLLMNP 394
Cdd:cd06528 321 TVKHLLDAAVRGEVDELRGVIENIIVGQPIPLGTGDVELTMDP 363
|
|
| RNA_pol_rpoA2 |
TIGR02389 |
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ... |
29-392 |
1.49e-156 |
|
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274105 [Multi-domain] Cd Length: 367 Bit Score: 446.04 E-value: 1.49e-156
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 29 LLPKILEEELLTKLKDLQITKK-QLNTIVKEVRTRFENALVEPGEAVGIVAAQSIGEPGTQMTLKTFHFAGVAEFTVTQG 107
Cdd:TIGR02389 1 VLPEKLLKELEETVKKREISDKeELDEIIKRVEEEYLRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELNVTLG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 108 LPRLIEIVDARRNPSTPMTEVYLDEEHRHDVEKAKEVARKIELTRIENIASNVSIDLSEMEIIIEIDLDLMHDKGLDIET 187
Cdd:TIGR02389 81 LPRLIEIVDARKTPSTPSMTIYLEDEYEKDREKAEEVAKKIEATKLEDVAKDISIDLADMTVIIELDEEQLKERGITVDD 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 188 VANIIAK---GRKIAVRTEGNLIYIDPKLEAIKDLQKLAAKIRLLPIKGLLNIRRTQISKdpEKNEFMIYTEGTDFVKTL 264
Cdd:TIGR02389 161 VEKAIKKaklGKVIEIDMDNNTITIKPGNPSLKELRKLKEKIKNLHIKGIKGIKRVVIRK--EGDEYVIYTEGSNLKEVL 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 265 RIPGVDQTRLYTNHTYEIAETLGIEAARNAIIKESMEVLKAQGLDVDLRHITLVADLMTANGDVRQIGRHGISGEKLSVL 344
Cdd:TIGR02389 239 KLEGVDKTRTTTNDIHEIAEVLGIEAARNAIIEEIKRTLEEQGLDVDIRHLMLVADLMTWDGEVRQIGRHGISGEKASVL 318
|
330 340 350 360
....*....|....*....|....*....|....*....|....*...
gi 1491308752 345 ARASFEITVKHLLEACLQGESDDLKGITENVIVGQMIPLGTGSIDLLM 392
Cdd:TIGR02389 319 ARAAFEVTVKHLLDAAIRGEVDELKGVIENIIVGQPIPLGTGDVDLVM 366
|
|
| PRK14897 |
PRK14897 |
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional |
30-394 |
7.61e-141 |
|
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain] Cd Length: 509 Bit Score: 411.12 E-value: 7.61e-141
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 30 LPKILEEELLTKLKDLQITKKQLNTIVKEVRTRFENALVEPGEAVGIVAAQSIGEPGTQMTLKTFHFAGVAEFTVTQGLP 109
Cdd:PRK14897 141 LPPSVIEEIAKAMKKKELSDDEYEEILRRIREEYERARVDPYEAVGIVAAQSIGEPGTQMTMRTFHYAGVAEMNVTLGLP 220
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 110 RLIEIVDARRNPSTPMTEVYLDEEHRHDVEKAKEVARKIELTRIENIAsNVSIDLSEMEIIIEIDLDLMHDKGLDIETVA 189
Cdd:PRK14897 221 RLIEIVDARKKPSTPTMTIYLKKDYREDEEKVREVAKKIENTTLIDVA-DIITDIAEMSVVVELDEEKMKERLIEYDDIL 299
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 190 NIIAKGRKIAVRTEGNLIYIDPKLEAIKDLQKLAAKIRLLPIKGLLNIRRTQISKDPEKNEFMIYTEGTDFVKTLRIPGV 269
Cdd:PRK14897 300 AAISKLTFKTVEIDDGIIRLKPQQPSFKKLYLLAEKVKSLTIKGIKGIKRAIARKENDERRWVIYTQGSNLKDVLEIDEV 379
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 270 DQTRLYTNHTYEIAETLGIEAARNAIIKESMEVLKAQGLDVDLRHITLVADLMTANGDVRQIGRHGISGEKLSVLARASF 349
Cdd:PRK14897 380 DPTRTYTNDIIEIATVLGIEAARNAIIHEAKRTLQEQGLNVDIRHIMLVADMMTFDGSVKAIGRHGISGEKSSVLARAAF 459
|
330 340 350 360
....*....|....*....|....*....|....*....|....*
gi 1491308752 350 EITVKHLLEACLQGESDDLKGITENVIVGQMIPLGTGSIDLLMNP 394
Cdd:PRK14897 460 EITGKHLLRAGILGEVDKLAGVAENIIVGQPITLGTGAVSLVYKG 504
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
87-393 |
1.13e-115 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 357.28 E-value: 1.13e-115
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 87 TQMTLKTFHFAGVAEFTVTQGLPRLIEIVDARRNPSTPMTEVYLDEEHRHDVEKAKEVARKIELTRIENIASNVSIDLSE 166
Cdd:PRK14898 541 THNTMRTFHYAGVAEINVTLGLPRMIEIVDARKEPSTPIMTVHLKGEYATDREKAEEVAKKIESLTLGDVATSIAIDLWT 620
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 167 MEIIIEIDLDLMHDKGLDIETVANIIAKGRKIAVRTEGNLIYIDPKLEAIKDLQKLAAKIRLLPIKGLLNIRRTQISKD- 245
Cdd:PRK14898 621 QSIKVELDEETLADRGLTIESVEEAIEKKLGVKIDRKGTVLYLKPKTPSYKALRKRIPKIKNIVLKGIPGIERVLVKKEe 700
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 246 -PEKNEFMIYTEGTDFVKTLRIPGVDQTRLYTNHTYEIAETLGIEAARNAIIKESMEVLKAQGLDVDLRHITLVADLMTA 324
Cdd:PRK14898 701 hENDEEYVLYTQGSNLREVFKIEGVDTSRTTTNNIIEIQEVLGIEAARNAIINEMMNTLEQQGLEVDIRHLMLVADIMTA 780
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1491308752 325 NGDVRQIGRHGISGEKLSVLARASFEITVKHLLEACLQGESDDLKGITENVIVGQMIPLGTGSIDLLMN 393
Cdd:PRK14898 781 DGEVKPIGRHGVAGEKGSVLARAAFEETVKHLYDAAEHGEVDKLKGVIENVIVGKPIKLGTGCVDLRID 849
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
46-393 |
2.61e-102 |
|
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures.
Pssm-ID: 132720 [Multi-domain] Cd Length: 410 Bit Score: 309.14 E-value: 2.61e-102
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 46 QITKKQLNTIVKEVRTRFENALVEPGEAVGIVAAQSIGEPGTQMTLKTFHFAGVAEFTVTQGLPRLIEIVDARRNPSTPM 125
Cdd:cd02584 2 RLNKEAFDWILGEIETRFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTLGVPRLKEIINVAKNIKTPS 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 126 TEVYLDEEHRHDVEKAKEVARKIELTRIENIASNVSI--------------------------------DLSEMEIIIEI 173
Cdd:cd02584 82 LTVYLEPGFAKDEEKAKKIQSRLEHTTLKDVTAATEIyydpdpqntvieedkefvesyfefpdedveqdRLSPWLLRIEL 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 174 DLDLMHDKGLDIETVANIIAKGRK----------------IAVRTEGNLIYIDPKLEAIKDLQKLAAKIRLLPI-KGLLN 236
Cdd:cd02584 162 DRKKMTDKKLSMEQIAKKIKEEFKddlnvifsddnaeklvIRIRIINDDEEKEEDSEDDVFLKKIESNMLSDMTlKGIEG 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 237 IRRTQISKDPEK------------NEFMIYTEGTDFVKTLRIPGVDQTRLYTNHTYEIAETLGIEAARNAIIKESMEVLK 304
Cdd:cd02584 242 IRKVFIREENKKkvdietgefkkrEEWVLETDGVNLREVLSHPGVDPTRTTSNDIVEIFEVLGIEAARKALLKELRNVIS 321
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 305 AQGLDVDLRHITLVADLMTANGDVRQIGRHGISGEKLSVLARASFEITVKHLLEACLQGESDDLKGITENVIVGQMIPLG 384
Cdd:cd02584 322 FDGSYVNYRHLALLCDVMTQRGHLMAITRHGINRQDTGPLMRCSFEETVDILLEAAAFGETDDLKGVSENIMLGQLAPIG 401
|
....*....
gi 1491308752 385 TGSIDLLMN 393
Cdd:cd02584 402 TGCFDLLLD 410
|
|
| RNAP_III_Rpc1_C |
cd02736 |
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ... |
62-388 |
2.08e-98 |
|
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; Eukaryotic RNA polymerase III (RNAP III) is a large multi-subunit complex responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is also known as C160 in yeast. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Pssm-ID: 132723 [Multi-domain] Cd Length: 300 Bit Score: 295.28 E-value: 2.08e-98
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 62 RFENALVEPGEAVGIVAAQSIGEPGTQMTLKTFHFAGVAEFTVTQGLPRLIEIVDARRNPSTPMTEVYLDEEHrhDVEKA 141
Cdd:cd02736 1 KYMRAKVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKNISTPIITAKLENDR--DEKSA 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 142 KEVARKIELTRIENIASNVSIDLSEMEIIIEIDLDLmhdkgldietvaNIIAKGRKIavrtegnliyidpKLEAIKDLQK 221
Cdd:cd02736 79 RIVKGRIEKTYLGEVASYIEEVYSPDDCYILIKLDK------------KIIEKLQLS-------------KSNLYFLLQS 133
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 222 LAAKIRLLPIKGLLNIRRTQISKDPEKNEFMIYTEGTDFVKTLRIPGVDQTRLYTNHTYEIAETLGIEAARNAIIKESME 301
Cdd:cd02736 134 LKRKLPDVVVSGIPEVKRAVINKDKKKGKYKLLVEGYGLRAVMNTPGVIGTRTTSNHIMEVEKVLGIEAARSTIINEIQY 213
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 302 VLKAQGLDVDLRHITLVADLMTANGDVRQIGRHGISGEKLSVLARASFEITVKHLLEACLQGESDDLKGITENVIVGQMI 381
Cdd:cd02736 214 TMKSHGMSIDPRHIMLLADLMTFKGEVLGITRFGIAKMKESVLMLASFEKTTDHLFNAALHGRKDSIEGVSECIIMGKPM 293
|
....*..
gi 1491308752 382 PLGTGSI 388
Cdd:cd02736 294 PIGTGLF 300
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
8-393 |
1.44e-92 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 303.10 E-value: 1.44e-92
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 8 KKSFVSPEAIEKAVKKMNSDGL--LPKILEEelltKLKDLQITKKQLNTIVKEVRTRFENALVEPGEAVGIVAAQSIGEP 85
Cdd:PRK14977 917 RGKGASKDEIEELAKEYTKTFNanLPKLLAD----AIHGAELKEDELEAICAEGKEGFEKAKVEPGQAIGIISAQSIAEP 992
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 86 GTQMTLKTFHFAGVAEFTVTQGLPRLIEIVDARRNPSTPMTEVYLDEEHRHDVEKAKEVARKIELTRIENIASNVSIDLS 165
Cdd:PRK14977 993 GTQMTLRTFHAAGIKAMDVTHGLERFIELVDARAKPSTPTMDIYLDDECKEDIEKAIEIARNLKELKVRALIADSAIDNA 1072
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 166 EMEIIIEIDLDLMHDKGLDIETVANII---AKGRKIAVRTEGNLIYID--PKLEAIKDLQKLAA---KIRLLPIKGLLNI 237
Cdd:PRK14977 1073 NEIKLIKPDKRALENGCIPMERFAEIEaalAKGKKFEMELEDDLIILDlvEAADRDKPLATLIAirnKILDKPVKGVPDI 1152
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 238 RR---TQISKDPEKnEFMIYTEGTDFVKTLRIPGVDQTRLYTNHTYEIAETLGIEAARNAIIKESMEVLKAQGLDVDLRH 314
Cdd:PRK14977 1153 ERawvELVEKDGRD-EWIIQTSGSNLAAVLEMKCIDIANTITNDCFEIAGTLGIEAARNAIFNELASILEDQGLEVDNRY 1231
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 315 ITLVADLMTANGDVRQIG------RHGISGEKLSVLARASFEITVKHLLEACLQGESDDLKGITENVIVGQMIPLGTGSI 388
Cdd:PRK14977 1232 IMLVADIMCSRGTIEAIGlqaagvRHGFAGEKDSPLAKAAFEITTHTIAHAALGGEIEKIKGILDALIMGQNIPIGSGKV 1311
|
....*
gi 1491308752 389 DLLMN 393
Cdd:PRK14977 1312 DLLMD 1316
|
|
| RNAP_I_Rpa1_C |
cd02735 |
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ... |
62-391 |
7.55e-71 |
|
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA polymerase I (RNAP I) is a multi-subunit protein complex responsible for the synthesis of rRNA precursor. It consists of at least 14 different subunits, and the largest one is homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. Rpa1 is also known as Rpa190 in yeast. Structure studies suggest that different RNAP complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Pssm-ID: 132722 [Multi-domain] Cd Length: 309 Bit Score: 225.15 E-value: 7.55e-71
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 62 RFENALVEPGEAVGIVAAQSIGEPGTQMTLKTFHFAGVAEFTVTQGLPRLIEIV-DARRNPSTPMTEVYL-DEEHRHDVE 139
Cdd:cd02735 1 KYMRSLVEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILmTASKNIKTPSMTLPLkNGKSAERAE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 140 KAK---------EVARKIELTRIENIASNVSIDLSEMEIIIEIDLDLMHDKGLdietVANIIakgrkiavrtegnliyid 210
Cdd:cd02735 81 TLKkrlsrvtlsDVVEKVEVTEILKTIERVFKKLLGKWCEVTIKLPLSSPKLL----LLSIV------------------ 138
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 211 pkleaikdlQKLAAKIRLLPIKGllnIRRTQI--SKDPEKNEFMIYTEGTDFVKTLRIPG-VDQTRLYTNHTYEIAETLG 287
Cdd:cd02735 139 ---------EKLARKAVIREIPG---ITRCFVveEDKGGKTKYLVITEGVNLAALWKFSDiLDVNRIYTNDIHAMLNTYG 206
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 288 IEAARNAIIKESMEVLKAQGLDVDLRHITLVADLMTANGDVRQIGRHGISGEKlSVLARASFEITVKHLLEACLQGESDD 367
Cdd:cd02735 207 IEAARRAIVKEISNVFKVYGIAVDPRHLSLIADYMTFEGGYRPFNRIGMESST-SPLQKMSFETTLAFLKKATLNGDIDN 285
|
330 340
....*....|....*....|....
gi 1491308752 368 LKGITENVIVGQMIPLGTGSIDLL 391
Cdd:cd02735 286 LSSPSSRLVVGKPVNGGTGLFDLL 309
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
13-344 |
1.10e-68 |
|
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound.
Pssm-ID: 398596 [Multi-domain] Cd Length: 516 Bit Score: 225.70 E-value: 1.10e-68
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 13 SPEAIEKAVKKMNSDgLLPKILEEELLTKLKdlqITKKQLNTIVKEVRTRFENALVEPGEAVGIVAAQSIGEPGTQMTLK 92
Cdd:pfam04998 126 SKEAQERATLLFELL-LKSGLESKRVRSELT---CNSKAFVCLLCYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLN 201
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 93 TFHFAGVAEFTVTQGLPRLIEIVDARRNPSTPMTEVYLDEEHRHDVEKAKEVARKIELTRIENIASNVSI---------- 162
Cdd:pfam04998 202 TFHFAGVASKNVTLGVPRLKEIINVSKNIKSPSLTVYLFDEVGRELEKAKKVYGAIEKVTLGSVVESGEIlydpdpfntp 281
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 163 ----------------------------DLSEMEIIIEIDLDLM-----------------HDKGLDI---ETVANIIAK 194
Cdd:pfam04998 282 iisdvkgvvkffdiidevtneeeidpetGLLILVIRLLKILNKSikkvvkseviprsirnkVDEGRDIaigEITAFIIKI 361
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 195 GRKIAVRTEGNLIYIDPKLEAIKDLQKLAAKI-RLLPIKGLLNIRRTQISKDP---EKNEFMIYTEGTDFVKTLRIPG-V 269
Cdd:pfam04998 362 SKKIRQDTGGLRRVDELFMEEDPKLAILVASLlGNITLRGIPGIKRILVNEDDkgkVEPDWVLETEGVNLLRVLLVPGfV 441
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1491308752 270 DQTRLYTNHTYEIAETLGIEAARNAIIKESMEVLKAQGLDVDLRHITLVADLMTANGDVRQIGRHGISGEKLSVL 344
Cdd:pfam04998 442 DAGRILSNDIHEILEILGIEAARNALLNEIRNVYRFQGIYINDRHLELIADQMTRKGYIMAIGRHGINKAELSAL 516
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
71-387 |
4.51e-47 |
|
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the 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. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The region covered by this domain makes up part of the foot and jaw structures. In archaea, some photosynthetic organisms, and some organelles, this domain exists as a separate subunit, while it forms the C-terminal region of the RNAP largest subunit in eukaryotes and bacteria.
Pssm-ID: 132719 [Multi-domain] Cd Length: 158 Bit Score: 158.35 E-value: 4.51e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 71 GEAVGIVAAQSIGEPGTQMTLKTFHFAGVAEFTVTQGLPRLIEIVDARrnpstpmtevyldeehrhdvekakevarkiel 150
Cdd:cd00630 1 GEAVGVLAAQSIGEPGTQMTLRTFHFAGVASMNVTLGLPRLKEILNAA-------------------------------- 48
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 151 trieniasnvsidlsemeiiieidldlmhdkgldietvaniiakgrkiavrtegnliyidpkleaikdlqklaakirllp 230
Cdd:cd00630 --------------------------------------------------------------------------------
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 231 ikgllnirrtqiskdpeknefmiytegtdfvktlripgvdqtrlytnHTYEIAETLGIEAARNAIIKESMEVLKAQGLDV 310
Cdd:cd00630 49 -----------------------------------------------SIHEMLEALGIEAARETIIREIQKVLASQGVSV 81
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1491308752 311 DLRHITLVADLMTANGDVRQIGRHGISGEKLSVLARASFEITVKHLLEACLQGESDDLKGITENVIVGQMIPLGTGS 387
Cdd:cd00630 82 DRRHIELIADVMTYSGGLRGVTRSGFRASKTSPLMRASFEKTTKHLLDAAAAGEKDELEGVSENIILGRPAPLGTGS 158
|
|
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
65-386 |
2.62e-32 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 129.42 E-value: 2.62e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 65 NALVEPGEAVGIVAAQSIGEPGTQMTLKTFHFAGVaefTVTQGLPRLIEIVDARRnPstpmtevyldeehrhdvekaKEV 144
Cdd:PRK00566 873 GKLVNIGEAVGVIAAQSIGEPGTQLTMRTFHTGGV---DITGGLPRVAELFEARK-P--------------------KGP 928
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 145 ArkiELTRIENIASNVSIDLSEMEIIIEIDldlmhdkglDIETVANIIAKGRKIAVR-----------TEGNliyIDPKl 213
Cdd:PRK00566 929 A---IIAEIDGTVSFGKETKGKRRIVITPD---------DGEEREYLIPKGKHLLVQegdhveagdklTDGS---IDPH- 992
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 214 eaikdlqklaakirllpikgllnirrtqiskdpeknefmiytegtdfvktlripgvdqtrlytnhtyEIAETLGIEAARN 293
Cdd:PRK00566 993 -------------------------------------------------------------------DILRVLGVEAVQN 1005
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 294 AIIKESMEVLKAQGLDVDLRHI------------------------TLV--ADLMTANGDVRQIGRHGISGEKL------ 341
Cdd:PRK00566 1006 YLVNEVQKVYRLQGVKINDKHIevivrqmlrkvritdpgdtdflpgELVdrSEFEEENRKLIAEGKEPATGRPVllgitk 1085
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|.
gi 1491308752 342 ------SVLARASFEITVKHLLEACLQGESDDLKGITENVIVGQMIPLGTG 386
Cdd:PRK00566 1086 aslateSFLSAASFQETTRVLTEAAIKGKVDPLRGLKENVIIGRLIPAGTG 1136
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
65-386 |
3.14e-27 |
|
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single DNA-directed RNA polymerase, with required subunits that include alpha, beta, and beta-prime. This model describes the predominant architecture of the beta-prime subunit in most bacteria. This model excludes from among the bacterial mostly sequences from the cyanobacteria, where RpoC is replaced by two tandem genes homologous to it but also encoding an additional domain. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274103 [Multi-domain] Cd Length: 1140 Bit Score: 114.38 E-value: 3.14e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 65 NALVEPGEAVGIVAAQSIGEPGTQMTLKTFHFAGVAEFT--VTQGLPRLIEIVDARrnpsTPmtevyldeehrhdveKAK 142
Cdd:TIGR02386 865 GKLVEIGEAVGVIAAQSIGEPGTQLTMRTFHTGGVAGASgdITQGLPRVKELFEAR----TP---------------KDK 925
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 143 EVARKIELTrienIASNVSIDLSEMEIIIeidldlmhdKGLDIETVANIIAKGRKIAVRTEgnliyidpklEAIKDLQKL 222
Cdd:TIGR02386 926 AVIAEVDGT----VEIIEDIVKNKRVVVI---------KDENDEEKKYTIPFGAQLRVKDG----------DSVSAGDKL 982
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 223 aakirllpikgllnirrTQISKDPeknefmiytegtdfvktlripgvdqtrlytnhtYEIAETLGIEAARNAIIKESMEV 302
Cdd:TIGR02386 983 -----------------TEGSIDP---------------------------------HDLLRIKGIQAVQEYLVKEVQKV 1012
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 303 LKAQGLDVDLRHITLVADLM------TANGDV-----RQIGRH------------------------GISGEKL---SVL 344
Cdd:TIGR02386 1013 YRLQGVEINDKHIEVIVRQMlrkvriTDSGDSnllpgELIDIHefneenrklleqgkkpasaipqllGITKASLnteSFL 1092
|
330 340 350 360
....*....|....*....|....*....|....*....|..
gi 1491308752 345 ARASFEITVKHLLEACLQGESDDLKGITENVIVGQMIPLGTG 386
Cdd:TIGR02386 1093 SAASFQETTKVLTDAAIKGKVDYLLGLKENVIIGNLIPAGTG 1134
|
|
| RNAP_beta'_C |
cd02655 |
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ... |
67-386 |
1.21e-20 |
|
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Bacterial RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. This family also includes the eukaryotic plastid-encoded RNAP beta" subunit. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure with two pincers defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. The C-terminal domain includes a G loop that forms part of the floor of the downstream DNA-binding cavity. The position of the G loop may determine the switch of the bridge helix between flipped-out and normal alpha-helical conformations.
Pssm-ID: 132721 [Multi-domain] Cd Length: 204 Bit Score: 89.12 E-value: 1.21e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 67 LVEPGEAVGIVAAQSIGEPGTQMTLKTFHFAGVAEfTVTQGLPRLIEIVDARRNPSTPMTEVYLdeehrhdveKAKEVAR 146
Cdd:cd02655 2 LVELGEAVGIIAAQSIGEPGTQLTMRTFHTGGVAT-DITQGLPRVEELFEARKINPHDLLRIKF---------LGPEAVQ 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 147 KIELTRIENI--ASNVSIdlsemeiiieidldlmHDKglDIEtvanIIAKG--RKIAVRTEGNLIYIDPKLEAIKDLQKL 222
Cdd:cd02655 72 KYLVEEIQKVyrSQGVNI----------------NDK--HIE----IIVRQmtSKVKIIDPGDSGFLPGELVDLNEFEEE 129
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 223 AAKIRLLPIKgllnirrtQISKDPeknefmiytegtdfvktlRIPGVDQTRLYTNhtyeiaetlgieaarnaiikesmev 302
Cdd:cd02655 130 NKRLLLLGKK--------PAKYEP------------------VLLGITKASLNTE------------------------- 158
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 303 lkaqgldvdlrhitlvadlmtangdvrqigrhgisgeklSVLARASFEITVKHLLEACLQGESDDLKGITENVIVGQMIP 382
Cdd:cd02655 159 ---------------------------------------SFISAASFQETTKVLTEAAIEGKIDWLRGLKENVILGRLIP 199
|
....
gi 1491308752 383 LGTG 386
Cdd:cd02655 200 AGTG 203
|
|
| PRK14906 |
PRK14906 |
DNA-directed RNA polymerase subunit beta'; |
68-386 |
9.64e-19 |
|
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain] Cd Length: 1460 Bit Score: 88.78 E-value: 9.64e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 68 VEPGEAVGIVAAQSIGEPGTQMTLKTFHFAGVAEFTVTQGLPRLIEIVDARRnpstPMTEVYLDEehrhdvekakevark 147
Cdd:PRK14906 971 VNIGTAVGIIAAQSIGEPGTQLTMRTFHSGGVAGDDITQGLPRVAELFEARK----PKGEAVLAE--------------- 1031
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 148 ieltrienIASNVSIDLSEMEIIIEIdldlmHDK-GLDIETVanIIAKGRKIAVRTEGNLIYIDPKLeaikdlqklaaki 226
Cdd:PRK14906 1032 --------ISGTLQITGDKTEKTLTI-----HDQdGNSREYV--VSARVQFMPGVEDGVEVRVGQQI------------- 1083
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 227 rllpIKGLLNIRRTQISKDPEKNEFMIYTEGTDFVKTlriPGVDqtrLYTNHTYEIAETLgieaARNAIIKESMEVLKAQ 306
Cdd:PRK14906 1084 ----TRGSVNPHDLLRLTDPNTTLRYIVSQVQDVYVS---QGVD---INDKHIEVIARQM----LRKVAVTNPGDSDYLP 1149
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 307 GLDVDLRHITLVADLMTANGDVRQIGRH---GISGEKLSV---LARASFEITVKHLLEACLQGESDDLKGITENVIVGQM 380
Cdd:PRK14906 1150 GRQVNRYEFEDTANNLILEGKQPPVGQPlllGITKASLATdswLSAASFQETTKVLTDAAIEGKVDHLAGLKENVIIGKP 1229
|
....*.
gi 1491308752 381 IPLGTG 386
Cdd:PRK14906 1230 IPAGTG 1235
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
15-91 |
1.22e-15 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 79.17 E-value: 1.22e-15
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1491308752 15 EAIEKAVKKMNsdglLPKILEEELLTKL-KDLQITKKQLNTIVKEVRTRFENALVEPGEAVGIVAAQSIGEPGTQMTL 91
Cdd:PRK14898 4 EALREKIEDLD----LPRSLKDELFEKLsKRDGVTEEMVEEIIDEVVSAYLNALVEPYEAVGIVAAQSIGEPGTQMSL 77
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
67-103 |
1.65e-14 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 75.75 E-value: 1.65e-14
10 20 30
....*....|....*....|....*....|....*..
gi 1491308752 67 LVEPGEAVGIVAAQSIGEPGTQMTLKTFHFAGVaeFT 103
Cdd:CHL00117 311 LVELGEAVGIIAGQSIGEPGTQLTLRTFHTGGV--FT 345
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
67-393 |
2.65e-13 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 71.96 E-value: 2.65e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 67 LVEPGEAVGIVAAQSIGEPGTQMTLKTFHFAGVaeftVTQGL--PRLIEIVDAR--------------------RNPSTP 124
Cdd:PRK14844 2329 IVSIGEAVGVIAAQSVGEPGTQLTMRTFHIGGV----MTRGVesSNIIASINAKiklnnsniiidkngnkivisRSCEVV 2404
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 125 MTEVYLDEEHRHDVE-KAKEVARKIELTRIENIASnvSIDLSEMEIIIEIDLDLMHDKGLDIETVANIIAKGRKIAVRT- 202
Cdd:PRK14844 2405 LIDSLGSEKLKHSVPyGAKLYVDEGGSVKIGDKVA--EWDPYTLPIITEKTGTVSYQDLKDGISITEVMDESTGISSKVv 2482
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 203 -----EGNLIYIDPKLEAIKDLQK---LAAKIR---LLPIKGLLNIRRTQ-------ISKDPEKN--------------- 249
Cdd:PRK14844 2483 kdwklYSGGANLRPRIVLLDDNGKvmtLASGVEacyFIPIGAVLNVQDGQkvhagdvITRTPRESvktrditgglprvie 2562
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 250 --------EFMIYTEGTDFV----------KTLRIPGVDQ------------TRLYTNHT----------------YEIA 283
Cdd:PRK14844 2563 lfearrpkEHAIVSEIDGYVafsekdrrgkRSILIKPVDEqispveylvsrsKHVIVNEGdfvrkgdllmdgdpdlHDIL 2642
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 284 ETLGIEAARNAIIKESMEVLKAQGLDVDLRHITLVADLM------TANGDVR----------QIGR-------------- 333
Cdd:PRK14844 2643 RVLGLEALAHYMISEIQQVYRLQGVRIDNKHLEVILKQMlqkveiTDPGDTMylvgesidklEVDRendamsnsgkrpah 2722
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1491308752 334 -----HGI---SGEKLSVLARASFEITVKHLLEACLQGESDDLKGITENVIVGQMIPLGTGsidLLMN 393
Cdd:PRK14844 2723 ylpilQGItraSLETSSFISAASFQETTKVLTEAAFCGKSDPLSGLKENVIVGRLIPAGTG---LIMN 2787
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
65-103 |
1.94e-12 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 69.25 E-value: 1.94e-12
10 20 30
....*....|....*....|....*....|....*....
gi 1491308752 65 NALVEPGEAVGIVAAQSIGEPGTQMTLKTFHFAGVaeFT 103
Cdd:PRK02597 305 NHLVDLGEAVGIIAAQSIGEPGTQLTMRTFHTGGV--FT 341
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
64-100 |
9.35e-11 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 64.17 E-value: 9.35e-11
10 20 30
....*....|....*....|....*....|....*..
gi 1491308752 64 ENALVEPGEAVGIVAAQSIGEPGTQMTLKTFHFAGVA 100
Cdd:PRK09603 2270 EGKMSYPGEAVGVVAAQSIGEPGTQLTLRTFHVGGTA 2306
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
65-99 |
3.03e-10 |
|
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274104 [Multi-domain] Cd Length: 1227 Bit Score: 62.18 E-value: 3.03e-10
10 20 30
....*....|....*....|....*....|....*
gi 1491308752 65 NALVEPGEAVGIVAAQSIGEPGTQMTLKTFHFAGV 99
Cdd:TIGR02388 303 AHLVDLGEAVGIIAAQSIGEPGTQLTMRTFHTGGV 337
|
|
| RNAP_IV_NRPD1_C |
cd02737 |
Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain; Higher plants ... |
269-391 |
3.24e-10 |
|
Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain; Higher plants have five multi-subunit nuclear RNA polymerases: RNAP I, RNAP II and RNAP III, which are essential for viability; plus the two isoforms of the non-essential polymerase RNAP IV (IVa and IVb), which specialize in small RNA-mediated gene silencing pathways. RNAP IVa and/or RNAP IVb might be involved in RNA-directed DNA methylation of endogenous repetitive elements, silencing of transgenes, regulation of flowering-time genes, inducible regulation of adjacent gene pairs, and spreading of mobile silencing signals. NRPD1a is the largest subunit of RNAP IVa, whereas NRPD1b is the largest subunit of RNAP IVb. The full subunit compositions of RNAP IVa and RNAP IVb are not known, nor are their templates or enzymatic products. However, it has been shown that RNAP IVa and, to a lesser extent, RNAP IVb are crucial for several RNA-mediated gene silencing phenomena.
Pssm-ID: 132724 [Multi-domain] Cd Length: 381 Bit Score: 61.28 E-value: 3.24e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 269 VDQTRLYTNHTYEIAETLGIEAARNAIIKESMEVLKAQGLDVDLRHITLVADLMTANGDVrqigrHGISG-------EKL 341
Cdd:cd02737 252 IDWERSMPYSIQQIKSVLGIDAAFEQFVQRLESAVSMTGKSVLREHLLLVADSMTYSGEF-----VGLNAkgykaqrRSL 326
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....
gi 1491308752 342 SVLA---RASFEITVKHLLEACLQGESDDLKGITENVIVGQMIPLGTGS-IDLL 391
Cdd:cd02737 327 KISApftEACFSSPIKCFLKAAKKGASDSLSGVLDACAWGKEAPVGTGSkFEIL 380
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
283-386 |
1.61e-09 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 60.01 E-value: 1.61e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 283 AETLGIEAARNAIIKESMEVLKAQGLDVDLRHITLVADLMTAN------GD----------VRQIGRH------------ 334
Cdd:PRK02597 1081 AALEALQKLQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKvriddgGDttmlpgelieLRQVEQVneamaitggapa 1160
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1491308752 335 -------GISGEKL---SVLARASFEITVKHLLEACLQGESDDLKGITENVIVGQMIPLGTG 386
Cdd:PRK02597 1161 eytpvllGITKASLntdSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTG 1222
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
342-406 |
2.64e-08 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 56.10 E-value: 2.64e-08
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1491308752 342 SVLARASFEITVKHLLEACLQGESDDLKGITENVIVGQMIPLGTGSIDlLMNPMIRE---STPKKEKK 406
Cdd:CHL00117 1272 SFISEASFQETTRVLAKAALRGRIDWLKGLKENVILGGLIPAGTGFKG-LVHRSKQHknkNLEIKKKN 1338
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
66-242 |
3.16e-07 |
|
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA polymerase, beta' subunit/160 kD subunit is part of the Pathway/BioSystem: RNA polymerase
Pssm-ID: 439856 [Multi-domain] Cd Length: 1165 Bit Score: 52.86 E-value: 3.16e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 66 ALVEPGEAVGIVAAQSIGEPGTQMTLKTFHFAGVAEFTVTQ----------------------------GLPRLIEIVDA 117
Cdd:COG0086 873 HLVNIGEAVGVIAAQSIGEPGTQLTMRTFHIGGAASRAAEEssieakaggivrlnnlkvvvneegkgvvVSRNSELVIVD 952
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1491308752 118 RRNPSTPMTEVYLDEEHRHDVEKAKEVARKIE-------LTRIENIASNVSIDLSEMEIIIEIDLDLMHDKGLDIETVAN 190
Cdd:COG0086 953 DGGRREEEYKVPYGGVLVVVGGGVVVGGGIVAewdphtpPIIEEVGGGVVFDDIVEGGVIVEKTDEETGGLSIVVEDDKA 1032
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|..
gi 1491308752 191 IIAKGRKIAVRTEGNLIYIDPKLEAIKDLQKLAAKIRLLPIKGLLNIRRTQI 242
Cdd:COG0086 1033 RRGGGKLLIRALKLLDAVGLSLLLGGTDAAAAGVIIGGLDVVLGDGVAIGVG 1084
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
342-386 |
7.35e-06 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 48.38 E-value: 7.35e-06
10 20 30 40
....*....|....*....|....*....|....*....|....*
gi 1491308752 342 SVLARASFEITVKHLLEACLQGESDDLKGITENVIVGQMIPLGTG 386
Cdd:PRK09603 2828 SIISAASFQETTKVLTEASIAMKKDFLEDLKENVVLGRMIPVGTG 2872
|
|
| |
