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Conserved domains on  [gi|2062562351|gb|QXG07303|]
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RNA polymerase beta subunit, partial [Cronobacter sakazakii]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Ricin_B_lectin super family cl47023
Ricin-type beta-trefoil lectin domain;
1-174 1.59e-145

Ricin-type beta-trefoil lectin domain;


The actual alignment was detected with superfamily member PRK00405:

Pssm-ID: 481363 [Multi-domain]  Cd Length: 1112  Bit Score: 431.06  E-value: 1.59e-145
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2062562351    1 AAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYA 80
Cdd:PRK00405   421 AAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYA 500

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2062562351   81 QTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANTNLTEEGRFADDLVTCRSKGESSLFSADQVDYMDVSTQQ 160
Cdd:PRK00405   501 RVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTARYKGEFVLVPPEEVDYMDVSPKQ 580

                          170
                   ....*....|....
gi 2062562351  161 VVSVGASLIPFLEH 174
Cdd:PRK00405   581 VVSVAASLIPFLEH 594
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 1-174 1.59e-145

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 431.06  E-value: 1.59e-145
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2062562351    1 AAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYA 80
Cdd:PRK00405   421 AAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYA 500

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2062562351   81 QTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANTNLTEEGRFADDLVTCRSKGESSLFSADQVDYMDVSTQQ 160
Cdd:PRK00405   501 RVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTARYKGEFVLVPPEEVDYMDVSPKQ 580

                          170
                   ....*....|....
gi 2062562351  161 VVSVGASLIPFLEH 174
Cdd:PRK00405   581 VVSVAASLIPFLEH 594
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 1-174 4.37e-125

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: 376.70  E-value: 4.37e-125
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2062562351    1 AAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYA 80
Cdd:TIGR02013  376 AAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYA 455

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2062562351   81 QTNEYGFLETPYRKVTDGVV--TDEIHYLSAIEEGNYVIAQANTNLTEEGRFADDLVTCRSKGESSLFSADQVDYMDVST 158
Cdd:TIGR02013  456 RVNEYGFIETPYRKVKDGKVvvTDEIDYLTADEEDNYVIAQANAPLDENGRFVEDLVVARYRGEITLVSPDQVDYMDVSP 535

                          170
                   ....*....|....*.
gi 2062562351  159 QQVVSVGASLIPFLEH 174
Cdd:TIGR02013  536 KQVVSVAASLIPFLEH 551
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-174 8.21e-125

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: 374.45  E-value: 8.21e-125
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2062562351    1 AAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYA 80
Cdd:COG0085    360 AAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLALYA 439

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2062562351   81 QTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANTNLTEEGRFADDLVTCRSKGESSLFSADQVDYMDVSTQQ 160
Cdd:COG0085    440 RVNEYGFIETPYRKVENGKVTDEIEYLTADEEENYYIAQANAPLDEDGNFLEERVLVRYRGEEVLVPPEEVDYMDVSPKQ 519

                          170
                   ....*....|....
gi 2062562351  161 VVSVGASLIPFLEH 174
Cdd:COG0085    520 IVSVATSLIPFLEH 533
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-174 5.21e-54

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: 183.15  E-value: 5.21e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2062562351   1 AAVKEFFGSSQ------------LSQFMDQNNPLSEITHKRRISAlgpGGLTRERAGFEVRDVHPTHYGRVCPIETPEGP 68
Cdd:cd00653   290 SGIKEFLATGNwgskrflmqrsgLSQVLDRLNPLSELSHKRRISS---LGLFRERKGFEVRDLHPSHWGRICPIETPEGE 366

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2062562351  69 NIGLINSLSVYAQTNeyGFLETPYRKVtdgvvtdeihylsaieegnyviaqantnlteegrfaddlvtcrskgesslfsA 148
Cdd:cd00653   367 NCGLVKNLALMARIS--GRIERPYRIV----------------------------------------------------E 392

                         170       180
                  ....*....|....*....|....*.
gi 2062562351 149 DQVDYMDVSTQQVVSVGASLIPFLEH 174
Cdd:cd00653   393 KEVTHIEISPSQILSVAASLIPFPEH 418
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 14-81 1.14e-40

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: 131.49  E-value: 1.14e-40
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2062562351  14 QFMDQNNPLSEITHKRRISAlGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQ 81
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNS-PRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 1-174 1.59e-145

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 431.06  E-value: 1.59e-145
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2062562351    1 AAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYA 80
Cdd:PRK00405   421 AAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYA 500

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2062562351   81 QTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANTNLTEEGRFADDLVTCRSKGESSLFSADQVDYMDVSTQQ 160
Cdd:PRK00405   501 RVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTARYKGEFVLVPPEEVDYMDVSPKQ 580

                          170
                   ....*....|....
gi 2062562351  161 VVSVGASLIPFLEH 174
Cdd:PRK00405   581 VVSVAASLIPFLEH 594
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 1-174 4.37e-125

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: 376.70  E-value: 4.37e-125
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2062562351    1 AAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYA 80
Cdd:TIGR02013  376 AAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYA 455

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2062562351   81 QTNEYGFLETPYRKVTDGVV--TDEIHYLSAIEEGNYVIAQANTNLTEEGRFADDLVTCRSKGESSLFSADQVDYMDVST 158
Cdd:TIGR02013  456 RVNEYGFIETPYRKVKDGKVvvTDEIDYLTADEEDNYVIAQANAPLDENGRFVEDLVVARYRGEITLVSPDQVDYMDVSP 535

                          170
                   ....*....|....*.
gi 2062562351  159 QQVVSVGASLIPFLEH 174
Cdd:TIGR02013  536 KQVVSVAASLIPFLEH 551
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 1-174 8.21e-125

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: 374.45  E-value: 8.21e-125
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2062562351    1 AAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYA 80
Cdd:COG0085    360 AAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLALYA 439

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2062562351   81 QTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANTNLTEEGRFADDLVTCRSKGESSLFSADQVDYMDVSTQQ 160
Cdd:COG0085    440 RVNEYGFIETPYRKVENGKVTDEIEYLTADEEENYYIAQANAPLDEDGNFLEERVLVRYRGEEVLVPPEEVDYMDVSPKQ 519

                          170
                   ....*....|....
gi 2062562351  161 VVSVGASLIPFLEH 174
Cdd:COG0085    520 IVSVATSLIPFLEH 533
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
3-174 5.44e-88

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 281.13  E-value: 5.44e-88
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2062562351    3 VKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQT 82
Cdd:PRK14844   523 LRDFFNSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARI 602

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2062562351   83 NEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANTNLTEEGRFADDLVTCRSKGESSLFSADQVDYMDVSTQQVV 162
Cdd:PRK14844   603 NKYGFIESPYRKVVNRVVTDQIEYLSAIDEGLYYIADTSAKLDENNCFVDDMLYCRYAGSFVMVSSDQVSYIDVSPKQVI 682

                          170
                   ....*....|..
gi 2062562351  163 SVGASLIPFLEH 174
Cdd:PRK14844   683 SVAASLIPFLEN 694
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
1-174 4.66e-80

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 258.31  E-value: 4.66e-80
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2062562351    1 AAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYA 80
Cdd:PRK09603   514 STIMEFFMGGQLSQFMDQTNPLSEVTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFT 593

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2062562351   81 QTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANTNLTEEGRFADDLVTCRSKGESSLFSADQVDYMDVSTQQ 160
Cdd:PRK09603   594 RVNDLGFIEAPYKKVVDGKVVGETIYLTAIQEDSHIIAPASTPIDEEGNILGDLIETRVEGEIVLNEKSKVTLMDLSSSM 673

                          170
                   ....*....|....
gi 2062562351  161 VVSVGASLIPFLEH 174
Cdd:PRK09603   674 LVGVAASLIPFLEH 687
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 1-174 3.03e-73

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 237.68  E-value: 3.03e-73
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2062562351    1 AAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYA 80
Cdd:CHL00207   355 ALIREFFGSSQLSQYMDQTNPLSELTHKRRISILGPGGLDKDRISFAVRDIHPSHYGRICPIETPEGPNCGLIGSLATNA 434

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2062562351   81 QTNEYGFLETPYRKVTDGVV--TDEIHYLSAIEEGNYVIAQANTNLTEEGRFADDLVTCRSKGESSLFSADQVDYMDVST 158
Cdd:CHL00207   435 RINKFGFIETPFYKVINGKVkkFGNPIYLTADSEDLYRIAPNDINLNKNNYFKKNIIPVRYKQEFKTVNPSKVDFIAISP 514

                          170
                   ....*....|....*.
gi 2062562351  159 QQVVSVGASLIPFLEH 174
Cdd:CHL00207   515 IQVFSIAESLIPFLEH 530
rpoB CHL00001
RNA polymerase beta subunit
 4-174 3.11e-71

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 232.10  E-value: 3.11e-71
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2062562351    4 KEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTN 83
Cdd:CHL00001   366 ESFFGSHPLSQFLDQTNPLTEIVHGRKLSSLGPGGLTGRTASFRVRDIHPSHYGRICPIDTSEGINAGLIGSLAIHARIG 445

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2062562351   84 EYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANTNLTEEGRFADDLVTCRSKGESSLFSADQVDYMDVSTQQVVS 163
Cdd:CHL00001   446 HWGSLESPFYEISERSKEERMVYLSPSEDEYYMIAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQIHLRSIFPFQYFS 525

                          170
                   ....*....|.
gi 2062562351  164 VGASLIPFLEH 174
Cdd:CHL00001   526 IGASLIPFLEH 536
RNA_pol_B_RPB2 cd00653
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ...
 1-174 5.21e-54

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: 183.15  E-value: 5.21e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2062562351   1 AAVKEFFGSSQ------------LSQFMDQNNPLSEITHKRRISAlgpGGLTRERAGFEVRDVHPTHYGRVCPIETPEGP 68
Cdd:cd00653   290 SGIKEFLATGNwgskrflmqrsgLSQVLDRLNPLSELSHKRRISS---LGLFRERKGFEVRDLHPSHWGRICPIETPEGE 366

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2062562351  69 NIGLINSLSVYAQTNeyGFLETPYRKVtdgvvtdeihylsaieegnyviaqantnlteegrfaddlvtcrskgesslfsA 148
Cdd:cd00653   367 NCGLVKNLALMARIS--GRIERPYRIV----------------------------------------------------E 392

                         170       180
                  ....*....|....*....|....*.
gi 2062562351 149 DQVDYMDVSTQQVVSVGASLIPFLEH 174
Cdd:cd00653   393 KEVTHIEISPSQILSVAASLIPFPEH 418
RNA_pol_Rpb2_3 pfam04565
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ...
 14-81 1.14e-40

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: 131.49  E-value: 1.14e-40
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2062562351  14 QFMDQNNPLSEITHKRRISAlGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQ 81
Cdd:pfam04565   1 QVLDRTNYLSTLSHLRRVNS-PRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
RNA_pol_Rpb2_45 pfam10385
RNA polymerase beta subunit external 1 domain; RNA polymerases catalyze the DNA-dependent ...
 92-157 7.78e-39

RNA polymerase beta subunit external 1 domain; RNA polymerases catalyze the DNA-dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared with three in eukaryotes (not including mitochondrial or chloroplast polymerases). This domain in prokaryotes spans the gap between domains 4 and 5 of the yeast protein. It is also known as the external 1 region of the polymerase and is bound in association with the external 2 region.


Pssm-ID: 463067 [Multi-domain]  Cd Length: 66  Bit Score: 126.71  E-value: 7.78e-39
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2062562351  92 YRKVTDGVVTDEIHYLSAIEEGNYVIAQANTNLTEEGRFADDLVTCRSKGESSLFSADQVDYMDVS 157
Cdd:pfam10385   1 YRKVEDGKVTDEIVYLTADEEDGYVIAQANAPLDEDGRFVDERVSARYRGEFPLVPPEEVDYMDVS 66
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 13-81 3.75e-21

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 89.63  E-value: 3.75e-21
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2062562351   13 SQFMDQNNPLSEITHKRRIsaLGPggLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQ 81
Cdd:PRK08565   403 SQLLDRTNYLSTLSHLRRV--VSP--LSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQ 467
PRK09606 PRK09606
DNA-directed RNA polymerase subunit B''; Validated
 8-81 1.95e-19

DNA-directed RNA polymerase subunit B''; Validated


Pssm-ID: 236587 [Multi-domain]  Cd Length: 494  Bit Score: 84.23  E-value: 1.95e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2062562351   8 GSSQLSQFMDQNNPLSEITHKRRISAlgPggLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQ 81
Cdd:PRK09606  401 GRTGVSQLLDRTDYMATLSHLRRVVS--P--LSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVE 470
 
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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