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Conserved domains on  [gi|1936509796|ref|NP_113961|]
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DNA-directed RNA polymerase I subunit RPA2 [Rattus norvegicus]

Protein Classification

DNA-directed RNA polymerase I subunit RPA2( domain architecture ID 12904785)

DNA-directed RNA polymerase I subunit RPA2 is the second largest core component of RNA polymerase I which synthesizes ribosomal RNA precursors

CATH:  3.90.1110.10|2.40.270.10|2.40.50.150
EC:  2.7.7.6
Gene Ontology:  GO:0003677|GO:0006360|GO:0046872|GO:0003899
PubMed:  8921381|11839495
SCOP:  4003708

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 38-1133 0e+00

RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation.


:

Pssm-ID: 238353 [Multi-domain]  Cd Length: 866  Bit Score: 1094.15  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796   38 LTRAHVDSFNYAVLEGLSHAVQAIPPFEFAFKDERISLTIVDAAISPPAVPKGtiCKELNIYPAECRGRRSTYRGKLTAD 117
Cdd:cd00653      1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDDDGRLKLKFGDIYLGKPKVEEG--GVTRKLTPNECRLRDLTYSAPLYVD 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  118 ISWAVNGVPK-GIIKQFLGYVPIMVKSKLCNLYNLPPQVLIEHHEEAEEMGGYFIINGIEKVIRMLIMPRRNFPI----A 192
Cdd:cd00653     79 IRLTVNDKGKiKEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIvedsK 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  193 MIRPKWKSRGLGYTQFGVSIHCVREEHS-AVNMNLHYVENgtvmlnfiyrkelfflplgfalkalvsfsdyqifqelikg 271
Cdd:cd00653    159 GKRIYTKTSIPSYSPYRGSWLEVKSDKKkDRIYVRIDLKR---------------------------------------- 198

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  272 keedsffknsvsqmlrivmeegchtQKQVLDYLGERFrvklslpdwypnaeaaeflfnqcicihlksntdkfYLLCLMTR 351
Cdd:cd00653    199 -------------------------QEEALKYIGKRF-----------------------------------EDLIYMIR 218

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  352 KLFALARGECMEDNPDSLVNQEVLTPGQLFLMFLKEKMENWLLSIKIALDKRAQKTNVSinnenLMKIFSMGTELTRPFE 431
Cdd:cd00653    219 KLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDL-----TPQLLINSKPITSGIK 293

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  432 YLLATGNLRSKTGLgfMQDSGLCVVADKLNFIRYLSHFRCVHRGADFAKMRTTTVRKLLPESWGFLCPVHTPDGAPCGLL 511
Cdd:cd00653    294 EFLATGNWGSKRFL--MQRSGLSQVLDRLNPLSELSHKRRISSLGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLV 371

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  512 NHLTAVCEVvtkfvytasipallcglgvtpvdaapcrpysdcypvlldgvmvgwvdkelapevadtlrrfkvlrerrvpp 591
Cdd:cd00653    372 KNLALMARI----------------------------------------------------------------------- 380

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  592 wmevalipmTGkpslypglflfttpcRLVRPVQNLElgkeelvgtmeqlfmniaifedevfgGVSTHQELFPHSLLSVIA 671
Cdd:cd00653    381 ---------SG---------------RIERPYRIVE--------------------------KEVTHIEISPSQILSVAA 410

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  672 NFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQTPQSPLVRPCMYDHYDMDNYPIGTNAIVAVISYTGY 751
Cdd:cd00653    411 SLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGY 490

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  752 DMEDAMIVNKASWERGFAHGSVYKSEFIDLSEKFKQGDDSLVFGVKPGDPRVMQKLDNDGLPFIGAKLEFGDPYYGYLNL 831
Cdd:cd00653    491 NFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITP 570

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  832 NTGEGFV--------------VYYKSKENCVVDNIKVCSNDTGSGKFKCVCVTVRVPRNPTIGDKFASRHGQKGILSRLW 897
Cdd:cd00653    571 KGETESTpifgekardvrdtsLKYPGGEKGIVDDVKIFSRELNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKIL 650

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  898 PAEDMPFTESGMMPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFIFSEENSALEYFGEmlkaAGYNFYGTE 977
Cdd:cd00653    651 PQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGE----AGLNYYGKE 726

                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  978 RLYSGISGMELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDKVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDR 1057
Cdd:cd00653    727 VLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQER 806

                         1050      1060      1070      1080      1090      1100      1110
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1936509796 1058 LFNCSDRSVAHVCVKCGSLLSPllekpppswsamrnrkYNCTVCGRSDSIDTVSVPYVFRYFVAELAAMNIKVKLD 1133
Cdd:cd00653    807 LTIKSDDVVARVCVKCGIILSA----------------NLCRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
RNA_pol_Rpa2_4 pfam06883
RNA polymerase I, Rpa2 specific domain; This domain is found between domain 3 (pfam04565) and ...
 563-621 2.36e-24

RNA polymerase I, Rpa2 specific domain; This domain is found between domain 3 (pfam04565) and domain 5 (pfam04565), but shows no homology to domain 4 of Rpb2. The external domains in multisubunit RNA polymerase (those most distant from the active site) are known to demonstrate more sequence variability.


:

Pssm-ID: 462028  Cd Length: 58  Bit Score: 96.78  E-value: 2.36e-24
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1936509796  563 VGWVDKELAPEVADTLRRFKVLRERRVPPWMEVALIPMTgKPSLYPGLFLFTTPCRLVR 621
Cdd:pfam06883    1 IGYVSPKLAKRIADTLRYLKVEGEHGVPLTLEIGYVPPS-NGGQYPGLYLFTSPARMMR 58
RNA_pol_Rpb2_2 super family cl37712
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ...
 186-375 2.00e-10

RNA polymerase Rpb2, domain 2; 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). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 1 (DRI).


The actual alignment was detected with superfamily member pfam04561:

Pssm-ID: 398318 [Multi-domain]  Cd Length: 185  Bit Score: 61.21  E-value: 2.00e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  186 RRNFPIAMIRPKWKSRGLGYTqfgvsihcvREEHSAVNMnLHYVEN--GTVMLNFIYRKELffLPLGFALKALVSFSDYQ 263
Cdd:pfam04561    1 RSNGIYVEKELDKNGIIATYT---------SSLISNRGS-WLKLEIdgKTLIWSRPSKKRK--IPIVIFLKALGLVSDRE 68

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  264 IFqELIKGKEEDSFFKNSVsqMLRIVMEEGCHTQKQVLDYLGERFRVKLSLPDWYPNAEAA------EFLFNQCI--CIH 335
Cdd:pfam04561   69 IL-DRLCYDFNDPQMLELL--KPELEEAENIYTQEEALDYIGKGFALRRGEEPRLQRAREIlysrdpKYNLNKHLglNEP 145

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|
gi 1936509796  336 LKSNTDKFYLLCLMTRKLFALARGECMEDNPDSLVNQEVL 375
Cdd:pfam04561  146 FENERLKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
 
Name Accession Description Interval E-value
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 38-1133 0e+00

RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation.


Pssm-ID: 238353 [Multi-domain]  Cd Length: 866  Bit Score: 1094.15  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796   38 LTRAHVDSFNYAVLEGLSHAVQAIPPFEFAFKDERISLTIVDAAISPPAVPKGtiCKELNIYPAECRGRRSTYRGKLTAD 117
Cdd:cd00653      1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDDDGRLKLKFGDIYLGKPKVEEG--GVTRKLTPNECRLRDLTYSAPLYVD 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  118 ISWAVNGVPK-GIIKQFLGYVPIMVKSKLCNLYNLPPQVLIEHHEEAEEMGGYFIINGIEKVIRMLIMPRRNFPI----A 192
Cdd:cd00653     79 IRLTVNDKGKiKEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIvedsK 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  193 MIRPKWKSRGLGYTQFGVSIHCVREEHS-AVNMNLHYVENgtvmlnfiyrkelfflplgfalkalvsfsdyqifqelikg 271
Cdd:cd00653    159 GKRIYTKTSIPSYSPYRGSWLEVKSDKKkDRIYVRIDLKR---------------------------------------- 198

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  272 keedsffknsvsqmlrivmeegchtQKQVLDYLGERFrvklslpdwypnaeaaeflfnqcicihlksntdkfYLLCLMTR 351
Cdd:cd00653    199 -------------------------QEEALKYIGKRF-----------------------------------EDLIYMIR 218

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  352 KLFALARGECMEDNPDSLVNQEVLTPGQLFLMFLKEKMENWLLSIKIALDKRAQKTNVSinnenLMKIFSMGTELTRPFE 431
Cdd:cd00653    219 KLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDL-----TPQLLINSKPITSGIK 293

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  432 YLLATGNLRSKTGLgfMQDSGLCVVADKLNFIRYLSHFRCVHRGADFAKMRTTTVRKLLPESWGFLCPVHTPDGAPCGLL 511
Cdd:cd00653    294 EFLATGNWGSKRFL--MQRSGLSQVLDRLNPLSELSHKRRISSLGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLV 371

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  512 NHLTAVCEVvtkfvytasipallcglgvtpvdaapcrpysdcypvlldgvmvgwvdkelapevadtlrrfkvlrerrvpp 591
Cdd:cd00653    372 KNLALMARI----------------------------------------------------------------------- 380

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  592 wmevalipmTGkpslypglflfttpcRLVRPVQNLElgkeelvgtmeqlfmniaifedevfgGVSTHQELFPHSLLSVIA 671
Cdd:cd00653    381 ---------SG---------------RIERPYRIVE--------------------------KEVTHIEISPSQILSVAA 410

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  672 NFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQTPQSPLVRPCMYDHYDMDNYPIGTNAIVAVISYTGY 751
Cdd:cd00653    411 SLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGY 490

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  752 DMEDAMIVNKASWERGFAHGSVYKSEFIDLSEKFKQGDDSLVFGVKPGDPRVMQKLDNDGLPFIGAKLEFGDPYYGYLNL 831
Cdd:cd00653    491 NFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITP 570

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  832 NTGEGFV--------------VYYKSKENCVVDNIKVCSNDTGSGKFKCVCVTVRVPRNPTIGDKFASRHGQKGILSRLW 897
Cdd:cd00653    571 KGETESTpifgekardvrdtsLKYPGGEKGIVDDVKIFSRELNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKIL 650

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  898 PAEDMPFTESGMMPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFIFSEENSALEYFGEmlkaAGYNFYGTE 977
Cdd:cd00653    651 PQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGE----AGLNYYGKE 726

                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  978 RLYSGISGMELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDKVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDR 1057
Cdd:cd00653    727 VLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQER 806

                         1050      1060      1070      1080      1090      1100      1110
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1936509796 1058 LFNCSDRSVAHVCVKCGSLLSPllekpppswsamrnrkYNCTVCGRSDSIDTVSVPYVFRYFVAELAAMNIKVKLD 1133
Cdd:cd00653    807 LTIKSDDVVARVCVKCGIILSA----------------NLCRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 38-1134 0e+00

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 623.90  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796   38 LTRAHVDSFNYAVLEGLSHAVQA-------IPPFEFAFKDERISLTIVDAAISppavpkgticKELNIYPAECRGRRSTY 110
Cdd:PRK08565    14 LVRQHLDSYNDFIERGLQEIVDEfgeikteIPGLKIVLGKIRVGEPEIKEADG----------SERPITPMEARLRNLTY 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  111 RGKLTADISWAVNGVPKGIIKQFLGYVPIMVKSKLCNLYNLPPQVLIEHHEEAEEMGGYFIINGIEKVIRML-------I 183
Cdd:PRK08565    84 AAPLYLTMIPVENGIEYEPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQedlapnrV 163

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  184 MPRRNFPIAMIRPKWK--SRGLGYtqfgvsihcvreeHSAVNMNLHyvENGTVMLNF--IYRKelffLPLGFALKAL--- 256
Cdd:PRK08565   164 LVDKGEAGSSITHTAKviSSRAGY-------------RAQVTVERR--KDGTIYVSFpaVPGK----IPFVILMRALgle 224

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  257 --------VSfSDYQIFQELIKGKEEdsffknsVSQMLRivmeegchTQKQVLDYLGERFRVKLSLPDwypNAEAAEFLF 328
Cdd:PRK08565   225 tdrdivyaVS-LDPEIQQELLPSLEQ-------ASSIAA--------TVEDALDYIGKRVAIGQPREY---RIERAEQIL 285

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  329 NQCICIHLKSNTD----KFYLLCLMTRKLFALARGECMEDNPDSLVNQEVLTPGQLFLMFLKEKMENWLLSIKIALDKRA 404
Cdd:PRK08565   286 DKYLLPHLGTSPEdrikKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSY 365

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  405 QKTNvSINNENLMKifsmGTELTRPFEYLLATGN-LRSKTGLgfmqdSGLCvvaDKLNFIRYLSHFRCV----HRG-ADF 478
Cdd:PRK08565   366 ARGR-KLDLRAIVR----PDIITERIRHALATGNwVGGRTGV-----SQLL---DRTNYLSTLSHLRRVvsplSRGqPHF 432

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  479 AkmrtttVRKLLPESWGFLCPVHTPDGAPCGLLNHLTAVCEVVTKfVYTASIPALLCGLGVTPVDAAPCRPYSDCYPVLL 558
Cdd:PRK08565   433 E------ARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVG-VDEEEVEEILYELGVVPVEEAREEEYISWSRVYL 505

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  559 DGVMVGWVDKelAPEVADTLRRFKvlRERRVPPWMEVALIPMTGKPSLYpglfLFTTPCRLVRPVQNLELGKEELVGTM- 637
Cdd:PRK08565   506 NGRLIGYHPD--GEELAEKIRELR--RSGKISDEVNVAYIETGEINEVY----VNCDSGRVRRPLIVVENGKPKLTREHv 577

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  638 EQLFMNIAIFEDEVFGGV------------------------STHQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGK 693
Cdd:PRK08565   578 EKLKKGELTFDDLVKMGVieyldaeeeenayvaldpedltpeHTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAK 657

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  694 QTMGFPLLTYQDRSDNKLYRLQTPQSPLVRPCMYDHYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWERGFAHGS- 772
Cdd:PRK08565   658 QSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTf 737

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  773 --VYKSEFID----LSEKFKQGDDSlVFGVKPgdPRVMQKLDNDGLPFIGAKLEFGDPYYGYLN----LNTGEGFVVYYK 842
Cdd:PRK08565   738 frTYETEERKypggQEDKIEIPEPN-VRGYRG--EEYYRKLDEDGIVSPEVEVKGGDVLIGKTSpprfLEELEELSLGLQ 814

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  843 SK----------ENCVVDNIKVCSNDTGSgkfKCVCVTVRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMMPD 912
Cdd:PRK08565   815 ERrdtsvtvrhgEKGIVDTVLITESPEGN---KLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPD 891

                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  913 ILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFifseENSALEYFGEMLKAAGYNFYGTERLYSGISGMELEADI 992
Cdd:PRK08565   892 LIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPF----YGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPI 967

                         1050      1060      1070      1080      1090      1100      1110      1120
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  993 FIGVVYYQRLRHMVSDKFQVRTTGARDKVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAHVCVK 1072
Cdd:PRK08565   968 FIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCEL 1047

                         1130      1140      1150      1160      1170      1180
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1936509796 1073 CGSllspllekppPSWSAMRNRKYNCTVCGRSDSIDTVSVPYVFRYFVAELAAMNIKVKLDV 1134
Cdd:PRK08565  1048 CGH----------IAWYDRRKNKYVCPIHGDKGNISPVEVSYAFKLLLQELMSMGISPRLKL 1099
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 670-1029 3.42e-176

RNA polymerase Rpb2, domain 6; 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 represents the hybrid binding domain and the wall domain. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion. This domain is also involved in binding to Rpb1 and Rpb3. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).


Pssm-ID: 459854 [Multi-domain]  Cd Length: 371  Bit Score: 521.32  E-value: 3.42e-176
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  670 IANFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQTPQSPLVRPCMYDHYDMDNYPIGTNAIVAVISYT 749
Cdd:pfam00562    1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  750 GYDMEDAMIVNKASWERGFAHGSVYKSEFIdlsEKFKQGDDSLVFGVKPGDPR-VMQKLDNDGLPFIGAKLEFGDPYYGY 828
Cdd:pfam00562   81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEA---RKTKLGPIEEITRDIPNVSEeALKKLDEDGIVRVGAEVKPGDILVGK 157

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  829 LN-------LNTGEG--------FVVYYKSKENCVVDNIKVCsnDTGSGKFKCVCVTVRVPRNPTIGDKFASRHGQKGIL 893
Cdd:pfam00562  158 VGpteltklLRAIFGekardvkdTSLKVPPGEEGVVDDVIVF--ELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVV 235

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  894 SRLWPAEDMPFTESGMMPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFIFSEENsaLEYFGEMLKAAGYNF 973
Cdd:pfam00562  236 SRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASTE--VEDIGELLEKAGYNY 313

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1936509796  974 YGTERLYSGISGMELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDKVTNQPIGGR 1029
Cdd:pfam00562  314 YGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGR 369
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
 556-1134 2.14e-150

DNA-directed RNA polymerase subunit B; This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.


Pssm-ID: 274713 [Multi-domain]  Cd Length: 599  Bit Score: 462.96  E-value: 2.14e-150
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  556 VLLDGVMVGWVDKelAPEVADTLRrfKVLRERRVPPWMEVALIPMTGKpslypgLFLFTTPCRLVRPVQNLELGKEELVG 635
Cdd:TIGR03670    1 VYLNGRLIGYHDD--PEELVEEVR--KLRRSGKLSQEVNVAYYEETNE------VYINCDAGRIRRPLIVVENGKPKLTR 70

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  636 TM-EQLFMNIAIFEDEVFGGV------------------------STHQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQ 690
Cdd:TIGR03670   71 EHvEKLKEGELTWDDLVKQGVieyldaeeeenayialdpeeltpeHTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGAA 150

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  691 MGKQTMGFPLLTYQDRSDNKLYRLQTPQSPLVRPCMYDHYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWERGFAH 770
Cdd:TIGR03670  151 MAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLAR 230

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  771 GS---VYKSEFID----LSEKFKQGDDSlVFGVKPgdPRVMQKLDNDGLPFIGAKLEFGDPYYG------YLNLNTGEGF 837
Cdd:TIGR03670  231 STffrTYEAEERRypggQEDRFEIPEPD-VRGYRG--EEAYKHLDEDGIVYPEVEVKGGDVLIGktspprFLEELREFGL 307

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  838 V--------VYYKSKENCVVDNIKVCSNDTGSgkfKCVCVTVRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGM 909
Cdd:TIGR03670  308 VterrrdtsVTVRHGEKGIVDKVIITETEEGN---KLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGI 384

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  910 MPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFifSEENsaLEYFGEMLKAAGYNFYGTERLYSGISGMELE 989
Cdd:TIGR03670  385 VPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPF--EGEP--EEELRKELLKLGFKPDGKEVMYDGITGEKLE 460

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  990 ADIFIGVVYYQRLRHMVSDKFQVRTTGARDKVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAHV 1069
Cdd:TIGR03670  461 AEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVYV 540

                          570       580       590       600       610       620
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1936509796 1070 CVKCGSLlspllekpppSWSAMRNRKYNCTVCGRSDSIDTVSVPYVFRYFVAELAAMNIKVKLDV 1134
Cdd:TIGR03670  541 CENCGHI----------AWEDKRKGTAYCPVCGETGDISPVEMSYAFKLLLDELKSLGISPRLEL 595
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 35-1132 6.68e-120

DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA polymerase, beta subunit/140 kD subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 439855 [Multi-domain]  Cd Length: 1001  Bit Score: 394.48  E-value: 6.68e-120
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796   35 LQDLTRAHVDSFNYAVLEGLSHAVQAIPPFE-FAfkdERISLTIVDAAISPPavpkgtickelNIYPAECRGRRSTYRGK 113
Cdd:COG0085     13 LPNLLEIQLDSFNWFLEEGLQEIFDEISPIEdFT---GNLSLEFGDYRLGEP-----------KYTPEECKERDLTYAAP 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  114 LTADISWAVNGVpkGIIKQ---FLGYVPIMVKSklcnlynlppqvliehheeaeemgGYFIINGIEKVIRMLI------- 183
Cdd:COG0085     79 LYVKVRLVNKET--GEIKEqevFMGDFPLMTDS------------------------GTFIINGTERVIVSQLvrspgvy 132

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  184 -------MPRRNFpIAMIRPkwkSRGlGYTQFgvsihcvrEEHSavnmnlhyveNGTVMLNFIYRKELFFLPLgfaLKAL 256
Cdd:COG0085    133 fveeedkSGKDLY-SAKVIP---SRG-AWLEF--------ETDK----------DGTIYVRIDRKRKIPVTVL---LRAL 186

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  257 VSFSDYQIFqELIKGKEEDSFFKNSVsqmlrivMEEGCHTQKQVLDYLGERFRvklslPDWYPNAEAAE-----FLFNQC 331
Cdd:COG0085    187 GLETDEEIL-EAFGDDPIQEYILATL-------EKDNTKTQEEALLEIYRKLR-----PGEPPTIERAEqlldnLFFDPK 253

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  332 -----------------ICIHLKSNTDKFYLLCLMTRKLFALARGECMEDNPDSLVNQEVLTPGQLFLM-F--------- 384
Cdd:COG0085    254 rydlahvgrykinkklgLDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNqFrvglsrmer 333

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  385 -LKEKMENwllsikiaLDKRAQKTNVSINnenlmkifsmgtelTRPFeyllaTGNLRSktglgFMQDSGLCVVADKLNFI 463
Cdd:COG0085    334 vVRERMTT--------QDVEAITPQSLIN--------------IRPV-----VAAIKE-----FFGSSQLSQFMDQTNPL 381

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  464 RYLSHFRCV----------HRgADFAkmrtttVRKLLPESWGFLCPVHTPDGAPCGLLNHLTAVCEVvTKFvytasipal 533
Cdd:COG0085    382 SELTHKRRLsalgpgglsrER-AGFE------VRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARV-NEY--------- 444

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  534 lcGLGVTPvdaapcrpysdcYPVLLDGVM---VGWVDkelapevADTLRRFKVLrerrvppwmeVALIPMTGKpslypGL 610
Cdd:COG0085    445 --GFIETP------------YRKVENGKVtdeIEYLT-------ADEEENYYIA----------QANAPLDED-----GN 488

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  611 FLFTTpcrlvrpVQNLELGKEELVGTmeqlfmniaifeDEVfggvsTHQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQ 690
Cdd:COG0085    489 FLEER-------VLVRYRGEEVLVPP------------EEV-----DYMDVSPKQIVSVATSLIPFLEHDDANRALMGAN 544

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  691 MGKQTMG-----FPLLTY---------QDRSDNklyrlqtpQSPLVR--------------PCMydhyDMDNYPIGTNAI 742
Cdd:COG0085    545 MQRQAVPllrpeAPLLHYplqkfqrsnQGTCIN--------QRPIVRvgdrvekgdvladgPAT----DNGELALGQNLL 612

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  743 VAVISYTGYDMEDAMIVNKASWERGfahgsVYKSEFIDLSE----KFKQGDDSLVFGV-KPGDpRVMQKLDNDGLPFIGA 817
Cdd:COG0085    613 VAFMPWEGYNYEDAIIISERLVKDD-----VLTSIHIEEYEiearDTKLGPEEITRDIpNVSE-EALRNLDEDGIIRIGA 686

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  818 KLEFGD---------------PYYGYLNLNTGEgfvvyyKSK------------ENCVVDNIKVCSNDTGS----GKFKC 866
Cdd:COG0085    687 EVKGGDilvgkvtpkgeteltPEERLLRAIFGE------KARevrdtslrvphgEKGKVIDVKVFSREEGDelppGVNKL 760

                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  867 VCVTVRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMMPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHD 946
Cdd:COG0085    761 VRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVA 840

                         1050      1060      1070      1080      1090      1100      1110      1120
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  947 ATPFI-FSEENsaleyFGEMLKAAGYNFYGTERLYSGISGMELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDKVTNQP 1025
Cdd:COG0085    841 TPVFDgAPEEE-----IRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQP 915

                         1130      1140      1150      1160      1170      1180      1190      1200
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796 1026 IGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAHVCVkcgsllspllekpppswsamrnrkYNCTVCGrsD 1105
Cdd:COG0085    916 LGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSDDVCGRVKV------------------------YEAIVKG--E 969

                         1210      1220
                   ....*....|....*....|....*..
gi 1936509796 1106 SIDTVSVPYVFRYFVAELAAMNIKVKL 1132
Cdd:COG0085    970 NIPEPGIPESFKVLLKELQSLGLDVEV 996
RNA_pol_Rpa2_4 pfam06883
RNA polymerase I, Rpa2 specific domain; This domain is found between domain 3 (pfam04565) and ...
 563-621 2.36e-24

RNA polymerase I, Rpa2 specific domain; This domain is found between domain 3 (pfam04565) and domain 5 (pfam04565), but shows no homology to domain 4 of Rpb2. The external domains in multisubunit RNA polymerase (those most distant from the active site) are known to demonstrate more sequence variability.


Pssm-ID: 462028  Cd Length: 58  Bit Score: 96.78  E-value: 2.36e-24
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1936509796  563 VGWVDKELAPEVADTLRRFKVLRERRVPPWMEVALIPMTgKPSLYPGLFLFTTPCRLVR 621
Cdd:pfam06883    1 IGYVSPKLAKRIADTLRYLKVEGEHGVPLTLEIGYVPPS-NGGQYPGLYLFTSPARMMR 58
RNA_pol_Rpb2_2 pfam04561
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ...
 186-375 2.00e-10

RNA polymerase Rpb2, domain 2; 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). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 1 (DRI).


Pssm-ID: 398318 [Multi-domain]  Cd Length: 185  Bit Score: 61.21  E-value: 2.00e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  186 RRNFPIAMIRPKWKSRGLGYTqfgvsihcvREEHSAVNMnLHYVEN--GTVMLNFIYRKELffLPLGFALKALVSFSDYQ 263
Cdd:pfam04561    1 RSNGIYVEKELDKNGIIATYT---------SSLISNRGS-WLKLEIdgKTLIWSRPSKKRK--IPIVIFLKALGLVSDRE 68

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  264 IFqELIKGKEEDSFFKNSVsqMLRIVMEEGCHTQKQVLDYLGERFRVKLSLPDWYPNAEAA------EFLFNQCI--CIH 335
Cdd:pfam04561   69 IL-DRLCYDFNDPQMLELL--KPELEEAENIYTQEEALDYIGKGFALRRGEEPRLQRAREIlysrdpKYNLNKHLglNEP 145

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|
gi 1936509796  336 LKSNTDKFYLLCLMTRKLFALARGECMEDNPDSLVNQEVL 375
Cdd:pfam04561  146 FENERLKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
 
Name Accession Description Interval E-value
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 38-1133 0e+00

RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation.


Pssm-ID: 238353 [Multi-domain]  Cd Length: 866  Bit Score: 1094.15  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796   38 LTRAHVDSFNYAVLEGLSHAVQAIPPFEFAFKDERISLTIVDAAISPPAVPKGtiCKELNIYPAECRGRRSTYRGKLTAD 117
Cdd:cd00653      1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDDDGRLKLKFGDIYLGKPKVEEG--GVTRKLTPNECRLRDLTYSAPLYVD 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  118 ISWAVNGVPK-GIIKQFLGYVPIMVKSKLCNLYNLPPQVLIEHHEEAEEMGGYFIINGIEKVIRMLIMPRRNFPI----A 192
Cdd:cd00653     79 IRLTVNDKGKiKEQEVFIGEIPIMLRSKLCNLNGLTPEELIKLGECPLDPGGYFIINGTEKVIINQEQRSPNVIIvedsK 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  193 MIRPKWKSRGLGYTQFGVSIHCVREEHS-AVNMNLHYVENgtvmlnfiyrkelfflplgfalkalvsfsdyqifqelikg 271
Cdd:cd00653    159 GKRIYTKTSIPSYSPYRGSWLEVKSDKKkDRIYVRIDLKR---------------------------------------- 198

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  272 keedsffknsvsqmlrivmeegchtQKQVLDYLGERFrvklslpdwypnaeaaeflfnqcicihlksntdkfYLLCLMTR 351
Cdd:cd00653    199 -------------------------QEEALKYIGKRF-----------------------------------EDLIYMIR 218

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  352 KLFALARGECMEDNPDSLVNQEVLTPGQLFLMFLKEKMENWLLSIKIALDKRAQKTNVSinnenLMKIFSMGTELTRPFE 431
Cdd:cd00653    219 KLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDL-----TPQLLINSKPITSGIK 293

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  432 YLLATGNLRSKTGLgfMQDSGLCVVADKLNFIRYLSHFRCVHRGADFAKMRTTTVRKLLPESWGFLCPVHTPDGAPCGLL 511
Cdd:cd00653    294 EFLATGNWGSKRFL--MQRSGLSQVLDRLNPLSELSHKRRISSLGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLV 371

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  512 NHLTAVCEVvtkfvytasipallcglgvtpvdaapcrpysdcypvlldgvmvgwvdkelapevadtlrrfkvlrerrvpp 591
Cdd:cd00653    372 KNLALMARI----------------------------------------------------------------------- 380

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  592 wmevalipmTGkpslypglflfttpcRLVRPVQNLElgkeelvgtmeqlfmniaifedevfgGVSTHQELFPHSLLSVIA 671
Cdd:cd00653    381 ---------SG---------------RIERPYRIVE--------------------------KEVTHIEISPSQILSVAA 410

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  672 NFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQTPQSPLVRPCMYDHYDMDNYPIGTNAIVAVISYTGY 751
Cdd:cd00653    411 SLIPFPEHNQSPRNLYQSNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGY 490

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  752 DMEDAMIVNKASWERGFAHGSVYKSEFIDLSEKFKQGDDSLVFGVKPGDPRVMQKLDNDGLPFIGAKLEFGDPYYGYLNL 831
Cdd:cd00653    491 NFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITP 570

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  832 NTGEGFV--------------VYYKSKENCVVDNIKVCSNDTGSGKFKCVCVTVRVPRNPTIGDKFASRHGQKGILSRLW 897
Cdd:cd00653    571 KGETESTpifgekardvrdtsLKYPGGEKGIVDDVKIFSRELNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKIL 650

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  898 PAEDMPFTESGMMPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFIFSEENSALEYFGEmlkaAGYNFYGTE 977
Cdd:cd00653    651 PQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGE----AGLNYYGKE 726

                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  978 RLYSGISGMELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDKVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDR 1057
Cdd:cd00653    727 VLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQER 806

                         1050      1060      1070      1080      1090      1100      1110
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1936509796 1058 LFNCSDRSVAHVCVKCGSLLSPllekpppswsamrnrkYNCTVCGRSDSIDTVSVPYVFRYFVAELAAMNIKVKLD 1133
Cdd:cd00653    807 LTIKSDDVVARVCVKCGIILSA----------------NLCRLCKKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 38-1134 0e+00

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 623.90  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796   38 LTRAHVDSFNYAVLEGLSHAVQA-------IPPFEFAFKDERISLTIVDAAISppavpkgticKELNIYPAECRGRRSTY 110
Cdd:PRK08565    14 LVRQHLDSYNDFIERGLQEIVDEfgeikteIPGLKIVLGKIRVGEPEIKEADG----------SERPITPMEARLRNLTY 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  111 RGKLTADISWAVNGVPKGIIKQFLGYVPIMVKSKLCNLYNLPPQVLIEHHEEAEEMGGYFIINGIEKVIRML-------I 183
Cdd:PRK08565    84 AAPLYLTMIPVENGIEYEPEEVKIGDLPIMVKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQedlapnrV 163

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  184 MPRRNFPIAMIRPKWK--SRGLGYtqfgvsihcvreeHSAVNMNLHyvENGTVMLNF--IYRKelffLPLGFALKAL--- 256
Cdd:PRK08565   164 LVDKGEAGSSITHTAKviSSRAGY-------------RAQVTVERR--KDGTIYVSFpaVPGK----IPFVILMRALgle 224

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  257 --------VSfSDYQIFQELIKGKEEdsffknsVSQMLRivmeegchTQKQVLDYLGERFRVKLSLPDwypNAEAAEFLF 328
Cdd:PRK08565   225 tdrdivyaVS-LDPEIQQELLPSLEQ-------ASSIAA--------TVEDALDYIGKRVAIGQPREY---RIERAEQIL 285

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  329 NQCICIHLKSNTD----KFYLLCLMTRKLFALARGECMEDNPDSLVNQEVLTPGQLFLMFLKEKMENWLLSIKIALDKRA 404
Cdd:PRK08565   286 DKYLLPHLGTSPEdrikKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSY 365

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  405 QKTNvSINNENLMKifsmGTELTRPFEYLLATGN-LRSKTGLgfmqdSGLCvvaDKLNFIRYLSHFRCV----HRG-ADF 478
Cdd:PRK08565   366 ARGR-KLDLRAIVR----PDIITERIRHALATGNwVGGRTGV-----SQLL---DRTNYLSTLSHLRRVvsplSRGqPHF 432

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  479 AkmrtttVRKLLPESWGFLCPVHTPDGAPCGLLNHLTAVCEVVTKfVYTASIPALLCGLGVTPVDAAPCRPYSDCYPVLL 558
Cdd:PRK08565   433 E------ARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVG-VDEEEVEEILYELGVVPVEEAREEEYISWSRVYL 505

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  559 DGVMVGWVDKelAPEVADTLRRFKvlRERRVPPWMEVALIPMTGKPSLYpglfLFTTPCRLVRPVQNLELGKEELVGTM- 637
Cdd:PRK08565   506 NGRLIGYHPD--GEELAEKIRELR--RSGKISDEVNVAYIETGEINEVY----VNCDSGRVRRPLIVVENGKPKLTREHv 577

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  638 EQLFMNIAIFEDEVFGGV------------------------STHQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQMGK 693
Cdd:PRK08565   578 EKLKKGELTFDDLVKMGVieyldaeeeenayvaldpedltpeHTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAK 657

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  694 QTMGFPLLTYQDRSDNKLYRLQTPQSPLVRPCMYDHYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWERGFAHGS- 772
Cdd:PRK08565   658 QSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTf 737

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  773 --VYKSEFID----LSEKFKQGDDSlVFGVKPgdPRVMQKLDNDGLPFIGAKLEFGDPYYGYLN----LNTGEGFVVYYK 842
Cdd:PRK08565   738 frTYETEERKypggQEDKIEIPEPN-VRGYRG--EEYYRKLDEDGIVSPEVEVKGGDVLIGKTSpprfLEELEELSLGLQ 814

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  843 SK----------ENCVVDNIKVCSNDTGSgkfKCVCVTVRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMMPD 912
Cdd:PRK08565   815 ERrdtsvtvrhgEKGIVDTVLITESPEGN---KLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPD 891

                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  913 ILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFifseENSALEYFGEMLKAAGYNFYGTERLYSGISGMELEADI 992
Cdd:PRK08565   892 LIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPF----YGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPI 967

                         1050      1060      1070      1080      1090      1100      1110      1120
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  993 FIGVVYYQRLRHMVSDKFQVRTTGARDKVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAHVCVK 1072
Cdd:PRK08565   968 FIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDKTTIYVCEL 1047

                         1130      1140      1150      1160      1170      1180
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1936509796 1073 CGSllspllekppPSWSAMRNRKYNCTVCGRSDSIDTVSVPYVFRYFVAELAAMNIKVKLDV 1134
Cdd:PRK08565  1048 CGH----------IAWYDRRKNKYVCPIHGDKGNISPVEVSYAFKLLLQELMSMGISPRLKL 1099
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 670-1029 3.42e-176

RNA polymerase Rpb2, domain 6; 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 represents the hybrid binding domain and the wall domain. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion. This domain is also involved in binding to Rpb1 and Rpb3. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).


Pssm-ID: 459854 [Multi-domain]  Cd Length: 371  Bit Score: 521.32  E-value: 3.42e-176
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  670 IANFIPFSDHNQSPRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQTPQSPLVRPCMYDHYDMDNYPIGTNAIVAVISYT 749
Cdd:pfam00562    1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  750 GYDMEDAMIVNKASWERGFAHGSVYKSEFIdlsEKFKQGDDSLVFGVKPGDPR-VMQKLDNDGLPFIGAKLEFGDPYYGY 828
Cdd:pfam00562   81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEA---RKTKLGPIEEITRDIPNVSEeALKKLDEDGIVRVGAEVKPGDILVGK 157

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  829 LN-------LNTGEG--------FVVYYKSKENCVVDNIKVCsnDTGSGKFKCVCVTVRVPRNPTIGDKFASRHGQKGIL 893
Cdd:pfam00562  158 VGpteltklLRAIFGekardvkdTSLKVPPGEEGVVDDVIVF--ELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVV 235

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  894 SRLWPAEDMPFTESGMMPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFIFSEENsaLEYFGEMLKAAGYNF 973
Cdd:pfam00562  236 SRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASTE--VEDIGELLEKAGYNY 313

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1936509796  974 YGTERLYSGISGMELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDKVTNQPIGGR 1029
Cdd:pfam00562  314 YGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGR 369
rpoB_arch TIGR03670
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ...
 556-1134 2.14e-150

DNA-directed RNA polymerase subunit B; This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.


Pssm-ID: 274713 [Multi-domain]  Cd Length: 599  Bit Score: 462.96  E-value: 2.14e-150
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  556 VLLDGVMVGWVDKelAPEVADTLRrfKVLRERRVPPWMEVALIPMTGKpslypgLFLFTTPCRLVRPVQNLELGKEELVG 635
Cdd:TIGR03670    1 VYLNGRLIGYHDD--PEELVEEVR--KLRRSGKLSQEVNVAYYEETNE------VYINCDAGRIRRPLIVVENGKPKLTR 70

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  636 TM-EQLFMNIAIFEDEVFGGV------------------------STHQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQ 690
Cdd:TIGR03670   71 EHvEKLKEGELTWDDLVKQGVieyldaeeeenayialdpeeltpeHTHLEIDPSAILGIIASTIPYPEHNQSPRNTMGAA 150

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  691 MGKQTMGFPLLTYQDRSDNKLYRLQTPQSPLVRPCMYDHYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKASWERGFAH 770
Cdd:TIGR03670  151 MAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLAR 230

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  771 GS---VYKSEFID----LSEKFKQGDDSlVFGVKPgdPRVMQKLDNDGLPFIGAKLEFGDPYYG------YLNLNTGEGF 837
Cdd:TIGR03670  231 STffrTYEAEERRypggQEDRFEIPEPD-VRGYRG--EEAYKHLDEDGIVYPEVEVKGGDVLIGktspprFLEELREFGL 307

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  838 V--------VYYKSKENCVVDNIKVCSNDTGSgkfKCVCVTVRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGM 909
Cdd:TIGR03670  308 VterrrdtsVTVRHGEKGIVDKVIITETEEGN---KLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGI 384

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  910 MPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFifSEENsaLEYFGEMLKAAGYNFYGTERLYSGISGMELE 989
Cdd:TIGR03670  385 VPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPF--EGEP--EEELRKELLKLGFKPDGKEVMYDGITGEKLE 460

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  990 ADIFIGVVYYQRLRHMVSDKFQVRTTGARDKVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAHV 1069
Cdd:TIGR03670  461 AEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVYV 540

                          570       580       590       600       610       620
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1936509796 1070 CVKCGSLlspllekpppSWSAMRNRKYNCTVCGRSDSIDTVSVPYVFRYFVAELAAMNIKVKLDV 1134
Cdd:TIGR03670  541 CENCGHI----------AWEDKRKGTAYCPVCGETGDISPVEMSYAFKLLLDELKSLGISPRLEL 595
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 555-1134 1.52e-134

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 421.68  E-value: 1.52e-134
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  555 PVLLDGVMVGWVD--KELAPEVadtlrrfkvlRERR----VPPWMEVALIPMTGKpslypgLFLFTTPCRLVRP------ 622
Cdd:PRK07225     6 KVYVNGKLIGTHDdpEELVEEI----------REARrsgeISEEVNVSYKEETNE------VIINTDAGRARRPlivven 69

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  623 ------------VQNLELGKEELV--GTMEQL------FMNIAIFEDEVFGGvSTHQELFPHSLLSVIANFIPFSDHNQS 682
Cdd:PRK07225    70 gepllteehiekLKNGELTFDDLVkqGVIEYLdaeeeeNAYIAVYEEDLTEE-HTHLEIDPSLILGIGAGMIPYPEHNAS 148

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  683 PRNMYQCQMGKQTMGFPLLTYQDRSDNKLYRLQTPQSPLVRPCMYDHYDMDNYPIGTNAIVAVISYTGYDMEDAMIVNKA 762
Cdd:PRK07225   149 PRITMGAGMIKQSLGLPAANYKLRPDTRGHLLHYPQVPLVKTQTQEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKA 228

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  763 SWERGFAhgsvyKSEFIDLSEKFK------QGD-----DSLVFGVKPGDprVMQKLDNDGLPFIGAKLEFGDPYYG---- 827
Cdd:PRK07225   229 SIERGLG-----RSHFFRTYEGEErrypggQEDrfeipDKDVRGYRGEE--AYRHLDEDGLVNPETEVKEGDVLIGktsp 301

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  828 --YLNLNTGEGFV--------VYYKSKENCVVDNIKVCSNDTGSgkfKCVCVTVRVPRNPTIGDKFASRHGQKGILSRLW 897
Cdd:PRK07225   302 prFLEEPDDFGISpekrretsVTMRSGEEGIVDTVILTETEEGS---RLVKVRVRDLRIPELGDKFASRHGQKGVIGLIV 378

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  898 PAEDMPFTESGMMPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHDATPFifSEENSalEYFGEMLKAAGYNFYGTE 977
Cdd:PRK07225   379 PQEDMPFTESGVVPDLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRRVDGTAF--SGEDE--EDLREALEKLGFEHTGKE 454

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  978 RLYSGISGMELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDKVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDR 1057
Cdd:PRK07225   455 VMYDGITGEKIEAEIFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKER 534

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796 1058 LFNCSDRSVAHVCVKCGSLlspllekpppswsAMRNRKYN---CTVCGRSDSIDTVSVPYVFRYFVAELAAMNIKVKLDV 1134
Cdd:PRK07225   535 LLDESDKVEIYVCAKCGMI-------------AIYDKKRNrkyCPICGEETDIYPVEMSYAFKLLLDELKSLGIAPRLEL 601
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 35-1132 6.68e-120

DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA polymerase, beta subunit/140 kD subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 439855 [Multi-domain]  Cd Length: 1001  Bit Score: 394.48  E-value: 6.68e-120
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796   35 LQDLTRAHVDSFNYAVLEGLSHAVQAIPPFE-FAfkdERISLTIVDAAISPPavpkgtickelNIYPAECRGRRSTYRGK 113
Cdd:COG0085     13 LPNLLEIQLDSFNWFLEEGLQEIFDEISPIEdFT---GNLSLEFGDYRLGEP-----------KYTPEECKERDLTYAAP 78

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  114 LTADISWAVNGVpkGIIKQ---FLGYVPIMVKSklcnlynlppqvliehheeaeemgGYFIINGIEKVIRMLI------- 183
Cdd:COG0085     79 LYVKVRLVNKET--GEIKEqevFMGDFPLMTDS------------------------GTFIINGTERVIVSQLvrspgvy 132

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  184 -------MPRRNFpIAMIRPkwkSRGlGYTQFgvsihcvrEEHSavnmnlhyveNGTVMLNFIYRKELFFLPLgfaLKAL 256
Cdd:COG0085    133 fveeedkSGKDLY-SAKVIP---SRG-AWLEF--------ETDK----------DGTIYVRIDRKRKIPVTVL---LRAL 186

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  257 VSFSDYQIFqELIKGKEEDSFFKNSVsqmlrivMEEGCHTQKQVLDYLGERFRvklslPDWYPNAEAAE-----FLFNQC 331
Cdd:COG0085    187 GLETDEEIL-EAFGDDPIQEYILATL-------EKDNTKTQEEALLEIYRKLR-----PGEPPTIERAEqlldnLFFDPK 253

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  332 -----------------ICIHLKSNTDKFYLLCLMTRKLFALARGECMEDNPDSLVNQEVLTPGQLFLM-F--------- 384
Cdd:COG0085    254 rydlahvgrykinkklgLDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNqFrvglsrmer 333

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  385 -LKEKMENwllsikiaLDKRAQKTNVSINnenlmkifsmgtelTRPFeyllaTGNLRSktglgFMQDSGLCVVADKLNFI 463
Cdd:COG0085    334 vVRERMTT--------QDVEAITPQSLIN--------------IRPV-----VAAIKE-----FFGSSQLSQFMDQTNPL 381

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  464 RYLSHFRCV----------HRgADFAkmrtttVRKLLPESWGFLCPVHTPDGAPCGLLNHLTAVCEVvTKFvytasipal 533
Cdd:COG0085    382 SELTHKRRLsalgpgglsrER-AGFE------VRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARV-NEY--------- 444

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  534 lcGLGVTPvdaapcrpysdcYPVLLDGVM---VGWVDkelapevADTLRRFKVLrerrvppwmeVALIPMTGKpslypGL 610
Cdd:COG0085    445 --GFIETP------------YRKVENGKVtdeIEYLT-------ADEEENYYIA----------QANAPLDED-----GN 488

                          650       660       670       680       690       700       710       720
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  611 FLFTTpcrlvrpVQNLELGKEELVGTmeqlfmniaifeDEVfggvsTHQELFPHSLLSVIANFIPFSDHNQSPRNMYQCQ 690
Cdd:COG0085    489 FLEER-------VLVRYRGEEVLVPP------------EEV-----DYMDVSPKQIVSVATSLIPFLEHDDANRALMGAN 544

                          730       740       750       760       770       780       790       800
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  691 MGKQTMG-----FPLLTY---------QDRSDNklyrlqtpQSPLVR--------------PCMydhyDMDNYPIGTNAI 742
Cdd:COG0085    545 MQRQAVPllrpeAPLLHYplqkfqrsnQGTCIN--------QRPIVRvgdrvekgdvladgPAT----DNGELALGQNLL 612

                          810       820       830       840       850       860       870       880
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  743 VAVISYTGYDMEDAMIVNKASWERGfahgsVYKSEFIDLSE----KFKQGDDSLVFGV-KPGDpRVMQKLDNDGLPFIGA 817
Cdd:COG0085    613 VAFMPWEGYNYEDAIIISERLVKDD-----VLTSIHIEEYEiearDTKLGPEEITRDIpNVSE-EALRNLDEDGIIRIGA 686

                          890       900       910       920       930       940       950       960
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  818 KLEFGD---------------PYYGYLNLNTGEgfvvyyKSK------------ENCVVDNIKVCSNDTGS----GKFKC 866
Cdd:COG0085    687 EVKGGDilvgkvtpkgeteltPEERLLRAIFGE------KARevrdtslrvphgEKGKVIDVKVFSREEGDelppGVNKL 760

                          970       980       990      1000      1010      1020      1030      1040
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  867 VCVTVRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMMPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHD 946
Cdd:COG0085    761 VRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVA 840

                         1050      1060      1070      1080      1090      1100      1110      1120
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  947 ATPFI-FSEENsaleyFGEMLKAAGYNFYGTERLYSGISGMELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDKVTNQP 1025
Cdd:COG0085    841 TPVFDgAPEEE-----IRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQP 915

                         1130      1140      1150      1160      1170      1180      1190      1200
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796 1026 IGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAHVCVkcgsllspllekpppswsamrnrkYNCTVCGrsD 1105
Cdd:COG0085    916 LGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSDDVCGRVKV------------------------YEAIVKG--E 969

                         1210      1220
                   ....*....|....*....|....*..
gi 1936509796 1106 SIDTVSVPYVFRYFVAELAAMNIKVKL 1132
Cdd:COG0085    970 NIPEPGIPESFKVLLKELQSLGLDVEV 996
RNA_pol_Rpb2_1 pfam04563
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ...
 38-402 2.55e-71

RNA polymerase beta subunit; 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 forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the protrusion domain. The other lobe (pfam04561) is nested within this domain.


Pssm-ID: 367994 [Multi-domain]  Cd Length: 396  Bit Score: 243.44  E-value: 2.55e-71
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796   38 LTRAHVDSFNYAVLEGLSHAVQAIPPFEFAFK-------DERISLTIVDAAISPPAVPKGTIcKELNIYPAECRGRRSTY 110
Cdd:pfam04563    2 LVRQQLDSFNEFVDNDLQKIIDENALIESEFEiqhpgenGDKLSLKFGQIRLGKPMFDETDG-STREIYPQECRLRNLTY 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  111 RGKLTADISWAVNGVPKGI-IKQFLGYVPIMVKSKLCNLYNLPPQVLIEHHEEAEEMGGYFIINGIEKVIRMLIMPRRNF 189
Cdd:pfam04563   81 SAPLYVDLELSVYNGEDIKpIEVFIGRLPIMLRSNACILSGATESELVKLGECPLDPGGYFIINGSEKVIVAQEHRSRNH 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  190 PIAMIRPKWKSRGLGYTQFGVSIHCVRE-EHSAVNMnLHYVENGTVMLNFIYRKELFflPLGFALKALVSFSDYQIFqEL 268
Cdd:pfam04563  161 PIVFKKADPKKRGSVASVRSSAEISVRPdSTSWVNV-LEYLSNGTIYFKFPYIKKEI--PIVIILRALGFTSDREIF-EL 236

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  269 IKGKEEDSFFKNSVSQMLRIVMEEGCHTQKQVLDYLGERFRVKLSL-PDWYPNAEAAEFLFNQCICIHLK----SNTDKF 343
Cdd:pfam04563  237 ICYDVNDQQLQEELLPSLEEGFKIRIQTQEQALDYIGGRGRAIFRMgRPREPRIKYAEEILQKEVLPHLGtyelDETKKA 316

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1936509796  344 YLLCLMTRKLFALARGECMEDNPDSLVNQEVLTPGQLFLMFLKEKMENWLLSIKIALDK 402
Cdd:pfam04563  317 YFIGYMIRRLLLLALGRREVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQK 375
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 737-1063 3.88e-49

DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit of Bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit. [Transcription, DNA-dependent RNA polymerase]


Pssm-ID: 273928 [Multi-domain]  Cd Length: 1065  Bit Score: 190.26  E-value: 3.88e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  737 IGTNAIVAVISYTGYDMEDAMIVNkaswERGF---AHGSVYKSEFIDLSEKFKQGDDSLVFGVKPGDPRVMQKLDNDGLP 813
Cdd:TIGR02013  673 LGRNVLVAFMPWNGYNYEDAILIS----ERLVkddVFTSIHIEEYEVEARDTKLGPEEITRDIPNVSEEALRNLDENGIV 748

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  814 FIGAKLEFGD---------------PYYGYLNLNTGEgfvvyyKSKEncVVDN--------------IKVCSNDTGS--- 861
Cdd:TIGR02013  749 RIGAEVKAGDilvgkvtpkgeteltPEEKLLRAIFGE------KARD--VRDTslrvppgvegtvidVKVFSREQGDelp 820

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  862 -GKFKCVCVTVRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMMPDILFNPHGFPSRMTIGMLIES---MAGKS 937
Cdd:TIGR02013  821 pGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILEThlgWAGKR 900

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  938 AALHGLCHdATPfIFseENSALEYFGEMLKAAGYNFYGTERLYSGISGMELEADIFIGVVYYQRLRHMVSDKFQVRTTGA 1017
Cdd:TIGR02013  901 LGRKGVPI-ATP-VF--DGASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGP 976

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....*.
gi 1936509796 1018 RDKVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSD 1063
Cdd:TIGR02013  977 YSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1022
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 458-1063 5.75e-44

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 174.12  E-value: 5.75e-44
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  458 DKLNFIRYLSH-FRCVHRGAD-FAKMRTTT-VRKLLPESWGFLCPVHTPDGAPCGLLNHLTaVCEVVTKFvytasipall 534
Cdd:CHL00207   371 DQTNPLSELTHkRRISILGPGgLDKDRISFaVRDIHPSHYGRICPIETPEGPNCGLIGSLA-TNARINKF---------- 439

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  535 cGLGVTPvdaapcrpysdCYPVLldgvmVGWVDKELAPE--VADTLRRFKVLrerrvppwmevalipmtgkpslyPGlfl 612
Cdd:CHL00207   440 -GFIETP-----------FYKVI-----NGKVKKFGNPIylTADSEDLYRIA-----------------------PN--- 476

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  613 fttpcrlvrpvqNLELGKEELVgtmeqLFMNIAIFEDEVFGGVSTHQELF----PHSLLSVIANFIPFSDHNQSPRnmyq 688
Cdd:CHL00207   477 ------------DINLNKNNYF-----KKNIIPVRYKQEFKTVNPSKVDFiaisPIQVFSIAESLIPFLEHNDANR---- 535

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  689 CQMGK--QTMGFPLL---------------------------------------TYQDRSDNKL-YRLQ----------T 716
Cdd:CHL00207   536 ALMGSnmQRQAVPLLypekpivgtgyekqialdsgmtiisltegivvsvsaykiIIQDDNNRYIhYYLQkyqrsnqntcI 615

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  717 PQSPLVRP--------CMYDHYDMDN--YPIGTNAIVAVISYTGYDMEDAMIVNKAswergFAHGSVYKSEFIDLSE--- 783
Cdd:CHL00207   616 NYRPIVWVgekinigqILADGSDIDNseLALGQNVLVAYMPWEGYNFEDAILINKR-----LVYEDLFTSIHIEKYEiel 690

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  784 -KFKQGDDSLVFGVKPGDPRVMQKLDNDGLPFIGAKLEFGD-------PYYGYLNLNTGEGFVVYYKSKENCVVDN---- 851
Cdd:CHL00207   691 rQTKLGSEEITRNIPNVSEYSLKNLDENGIISIGSKVLAGDilvgkitPKGESDQLPEGKLLRAIFGEKAKDVKDTslrm 770

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  852 ----------IKVCSNDTGSGKFKCVCVTVRV----PRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMMPDILFNP 917
Cdd:CHL00207   771 pnggygrvikVEIFSRSKGDELKFGYYLKIRVfiaqIRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNP 850

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  918 HGFPSRMTIGMLIESMAGKSAalHGLCHDATPFIFSEENSALE---YFGEMLKAAG--------YNFY--GTERLYSGIS 984
Cdd:CHL00207   851 LGVPSRMNVGQLFECLLGLAG--DNLNKRFKILPFDEMYGSEYsriLINNKLNQASiknneywlFNSYhpGKMVLRDGRT 928

                          650       660       670       680       690       700       710
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1936509796  985 GMELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDKVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSD 1063
Cdd:CHL00207   929 GYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQRFGEMEVWALEAFGAAYTLKELLTIKSD 1007
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 37-542 6.27e-37

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 146.25  E-value: 6.27e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796   37 DLTRAHVDSFNYAVLEGLSHAVQAIPPFEFAFKD-ERISLtiVDAAISPPAV--PKGTICKelnIYPAECRGRRSTYRGK 113
Cdd:PRK09606    17 RLVRHHIDSYNDFVDNGLQKIIDEQGPIETEIEDgVYVEL--GKIRVGKPVVkeADGSERE---IYPMEARLRNLTYSAP 91

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  114 LTADISWAVNGVPKGIIKQFLGYVPIMVKSKLCNLYNLPPQVLIEHHEEAEEMGGYFIINGIEKVIRML--IMPRR---- 187
Cdd:PRK09606    92 LYLEMSPVEGGEEEEPEEVYIGELPVMVGSKICNLYGLSEEELIEVGEDPLDPGGYFIVNGSERVLMTLedLAPNKilve 171

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  188 -----NFPIAmiRPKWKSRGLGYtqfgvSIHCVREEHSavnmnlhyveNGTVMLNFIY-RKELFFLPLgfaLKALVSFSD 261
Cdd:PRK09606   172 kderyGDRIE--VAKVFSQRRGY-----RALVTVERNR----------DGLLEVSFPSvPGSIPFVIL---MRALGLETD 231

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  262 yqifQELIKGKEEDSFFknsVSQMLRIVMEEGCHTQKQVLDYLGERfrvklSLPDWYPNA--EAAEFLFNQCICIHLKSN 339
Cdd:PRK09606   232 ----EEIVEAVSDDPEI---VKFMLENLEEAEVDTQEEALEYIGKR-----VAPGQTKEYriKRAEYVIDRYLLPHLGVE 299

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  340 TDKFYL----LCLMTRKLFALARGECMEDNPDSLVNQEVLTPGQL--------FLMFLKEkmenwllsIKIALDkRAQKT 407
Cdd:PRK09606   300 PEVRRAkahyLGRMAEACFELALGRREEDDKDHYANKRLKLAGDLmedlfrvaFNRLARD--------VKYQLE-RANMR 370

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  408 NvsinnenlmKIFSMGTE-----LTRPFEYLLATGNLRS-KTGLgfmqdSGLcvvADKLNFIRYLSHFRCV--------- 472
Cdd:PRK09606   371 N---------RELSIKTAvrsdvLTERLEHAMATGNWVGgRTGV-----SQL---LDRTDYMATLSHLRRVvsplsrsqp 433

                          490       500       510       520       530       540       550
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  473 HRGAdfakmrtttvRKLLPESWGFLCPVHTPDGAPCGLLNHLTAVCEVVTKFVYTASIPaLLCGLGVTPV 542
Cdd:PRK09606   434 HFEA----------RDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKE-ILKELGVEPE 492
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 848-1054 6.85e-37

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 151.41  E-value: 6.85e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  848 VVDnIKVCS-----NDTGSGKFKCVCVTVRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMMPDILFNPHGFPS 922
Cdd:PRK00405   847 VID-VKVFTrieqgDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPS 925

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  923 RMTIGMLIES---MAGKsaalhGL-CHDATPfIF---SEENsaleyFGEMLKAAGYNFYGTERLYSGISGMELEADIFIG 995
Cdd:PRK00405   926 RMNIGQILEThlgWAAK-----GLgIKFATP-VFdgaKEEE-----IKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVG 994

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1936509796  996 VVYYQRLRHMVSDKFQVRTTGARDKVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLL 1054
Cdd:PRK00405   995 YMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTL 1053
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 455-519 1.63e-32

RNA polymerase Rpb2, domain 3; 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). Domain 3, s also known as the fork domain and is proximal to catalytic site.


Pssm-ID: 428011 [Multi-domain]  Cd Length: 67  Bit Score: 120.32  E-value: 1.63e-32
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1936509796  455 VVADKLNFIRYLSHFRCVH--RGADFAKMRTTTVRKLLPESWGFLCPVHTPDGAPCGLLNHLTAVCE 519
Cdd:pfam04565    1 QVLDRTNYLSTLSHLRRVNspRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
rpoB CHL00001
RNA polymerase beta subunit
 738-1063 1.18e-31

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 134.26  E-value: 1.18e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  738 GTNAIVAVISYTGYDMEDAMIVNkaswERgFAHGSVYKSEFIdlsEKF-------KQGDDSLVFGVKPGDPRVMQKLDND 810
Cdd:CHL00001   652 GKNVLVAYMPWEGYNFEDAVLIS----ER-LVYEDIYTSFHI---RKYeiqthvtSQGPERITKEIPHLEAHLLRNLDKN 723

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  811 GLPFIGAKLEFGDPYYGYL-------NLNTGEGFVVY-------YKSKENC----------VVDNIKVCSNDTGSGKFKC 866
Cdd:CHL00001   724 GIVMLGSWVETGDILVGKLtpqeaeeSSYAPEGRLLRaifgiqvSTSKETClklpiggrgrVIDVRWIQKKGGSSYNPET 803

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  867 VCVTVRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMMPDILFNPHGFPSRMTIGMLIESMAGKSAALHGLCHD 946
Cdd:CHL00001   804 IHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLAGDLLNRHYR 883

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  947 ATPF--IFSEENSALEYFGEMLKA---AGY------NFYGTERLYSGISGMELEADIFIGVVYYQRLRHMVSDKFQVRTT 1015
Cdd:CHL00001   884 IAPFdeRYEQEASRKLVFSELYEAskqTANpwvfepEYPGKSRLFDGRTGDPFEQPVTIGKAYILKLIHQVDDKIHARSS 963

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....*...
gi 1936509796 1016 GARDKVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRLFNCSD 1063
Cdd:CHL00001   964 GPYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSD 1011
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
861-1063 3.96e-28

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 123.50  E-value: 3.96e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  861 SGKFKCVCVTVRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMMPDILFNPHGFPSRMTIGMLIE---SMAGK- 936
Cdd:PRK09603  1072 NGVIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEmhlGLVGKe 1151

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  937 ----------------------------------------------SAALHGLCHD-------ATPfIFseENSALEYFG 963
Cdd:PRK09603  1152 fgkqiasmledktkdfakelrakmleianainekdpltihalencsDEELLEYAKDwskgvkmAIP-VF--EGISQEKFY 1228

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  964 EMLKAAGYNFYGTERLYSGISGMELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDKVTNQPIGGRNVQGGIRFGEMERD 1043
Cdd:PRK09603  1229 KLFELAKIAMDGKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVW 1308

                          250       260
                   ....*....|....*....|
gi 1936509796 1044 ALLAHGTSFLLHDRLFNCSD 1063
Cdd:PRK09603  1309 ALEAYGAAHTLKEMLTIKSD 1328
RNA_pol_Rpa2_4 pfam06883
RNA polymerase I, Rpa2 specific domain; This domain is found between domain 3 (pfam04565) and ...
 563-621 2.36e-24

RNA polymerase I, Rpa2 specific domain; This domain is found between domain 3 (pfam04565) and domain 5 (pfam04565), but shows no homology to domain 4 of Rpb2. The external domains in multisubunit RNA polymerase (those most distant from the active site) are known to demonstrate more sequence variability.


Pssm-ID: 462028  Cd Length: 58  Bit Score: 96.78  E-value: 2.36e-24
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1936509796  563 VGWVDKELAPEVADTLRRFKVLRERRVPPWMEVALIPMTgKPSLYPGLFLFTTPCRLVR 621
Cdd:pfam06883    1 IGYVSPKLAKRIADTLRYLKVEGEHGVPLTLEIGYVPPS-NGGQYPGLYLFTSPARMMR 58
RNA_pol_Rpb2_7 pfam04560
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ...
 1033-1134 1.84e-22

RNA polymerase Rpb2, domain 7; 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). Rpb2 is the second largest subunit of the RNA polymerase. This domain comprised of the structural domains anchor and clamp. The clamp region (C-terminal) contains a zinc-binding motif. The clamp region is named due to its interaction with the clamp domain found in Rpb1. The domain also contains a region termed "switch 4". The switches within the polymerase are thought to signal different stages of transcription.


Pssm-ID: 461355 [Multi-domain]  Cd Length: 87  Bit Score: 92.65  E-value: 1.84e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796 1033 GGIRFGEMERDALLAHGTSFLLHDRLFNCSDRSVAHVCVKCGsllspllekpppswsAMRNRKYnCTVCGRSDSIDTVSV 1112
Cdd:pfam04560    1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDAYEVDVCGRCG---------------LYAAYNK-CPICKGETDISPGYI 64

                           90       100
                   ....*....|....*....|..
gi 1936509796 1113 PYVFRYFVAELAAMNIKVKLDV 1134
Cdd:pfam04560   65 PESFKLLFQELQSLGIDPRLLL 86
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
858-1063 1.15e-20

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 99.31  E-value: 1.15e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  858 DTGSGKFKCVCVTVRVPRNPTIGDKFASRHGQKGILSRLWPAEDMPFTESGMMPDILFNPHGFPSRMTIGMLIESMAG-- 935
Cdd:PRK14844  1062 DLPQGVSMSVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGwa 1141

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  936 ------------------KSAALHGL------------------------------------------------------ 943
Cdd:PRK14844  1142 ckklgekvgnildeinkiKSAFCKGIrslnddnftkfaaayldnkkienidddeitasvlntpnknalndelnelvenyl 1221

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  944 --CHDATPFIFS---------------------EENSALEY----------------------FGEMLKAAGYNFYGTER 978
Cdd:PRK14844  1222 nsCKSAYSNLRNflievyscgsnvsicnnirdiSDNNLIEFarklrdgipvaapvfegpkdeqIAKLFELAGLDNSGQAV 1301

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  979 LYSGISGMELEADIFIGVVYYQRLRHMVSDKFQVRTTGARDKVTNQPIGGRNVQGGIRFGEMERDALLAHGTSFLLHDRL 1058
Cdd:PRK14844  1302 LYDGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEML 1381


                   ....*
gi 1936509796 1059 FNCSD 1063
Cdd:PRK14844  1382 TVKSD 1386
RNA_pol_Rpb2_2 pfam04561
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ...
 186-375 2.00e-10

RNA polymerase Rpb2, domain 2; 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). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 1 (DRI).


Pssm-ID: 398318 [Multi-domain]  Cd Length: 185  Bit Score: 61.21  E-value: 2.00e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  186 RRNFPIAMIRPKWKSRGLGYTqfgvsihcvREEHSAVNMnLHYVEN--GTVMLNFIYRKELffLPLGFALKALVSFSDYQ 263
Cdd:pfam04561    1 RSNGIYVEKELDKNGIIATYT---------SSLISNRGS-WLKLEIdgKTLIWSRPSKKRK--IPIVIFLKALGLVSDRE 68

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1936509796  264 IFqELIKGKEEDSFFKNSVsqMLRIVMEEGCHTQKQVLDYLGERFRVKLSLPDWYPNAEAA------EFLFNQCI--CIH 335
Cdd:pfam04561   69 IL-DRLCYDFNDPQMLELL--KPELEEAENIYTQEEALDYIGKGFALRRGEEPRLQRAREIlysrdpKYNLNKHLglNEP 145

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|
gi 1936509796  336 LKSNTDKFYLLCLMTRKLFALARGECMEDNPDSLVNQEVL 375
Cdd:pfam04561  146 FENERLKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
 
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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