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Conserved domains on  [gi|610505942|emb|CCX28526|]
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beta subunit of RNA polymerase, partial (chloroplast) [Badula decumbens]

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;
1-84 3.85e-64

Ricin-type beta-trefoil lectin domain;


The actual alignment was detected with superfamily member CHL00001:

Pssm-ID: 481363 [Multi-domain]  Cd Length: 1070  Bit Score: 207.83  E-value: 3.85e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 610505942    1 GDAIRIPLVMYQRSNKNTCMHQKPQVQRGRCIKRGQILADGAATVGGELALGKNVVVAYMPWEGYNFEDAVLISERLVYE 80
Cdd:CHL00001  601 GDTLSIPLVMYQRSNKNTCMHQKPQVRRGKCVKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYE 680


                  ....
gi 610505942   81 EIYT 84
Cdd:CHL00001  681 DIYT 684
 
Name Accession Description Interval E-value
rpoB CHL00001
RNA polymerase beta subunit
 1-84 3.85e-64

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 207.83  E-value: 3.85e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 610505942    1 GDAIRIPLVMYQRSNKNTCMHQKPQVQRGRCIKRGQILADGAATVGGELALGKNVVVAYMPWEGYNFEDAVLISERLVYE 80
Cdd:CHL00001  601 GDTLSIPLVMYQRSNKNTCMHQKPQVRRGKCVKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYE 680


                  ....
gi 610505942   81 EIYT 84
Cdd:CHL00001  681 DIYT 684
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 4-84 1.32e-39

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: 138.26  E-value: 1.32e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 610505942     4 IRIPLVMYQRSNKNTCMHQKPQVQRGRCIKRGQILADGAATVGGELALGKNVVVAYMPWEGYNFEDAVLISERLVYEEIY 83
Cdd:TIGR02013  626 DIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRNVLVAFMPWNGYNYEDAILISERLVKDDVF 705


                   .
gi 610505942    84 T 84
Cdd:TIGR02013  706 T 706
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 7-84 1.59e-39

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: 137.93  E-value: 1.59e-39
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 610505942    7 PLVMYQRSNKNTCMHQKPQVQRGRCIKRGQILADGAATVGGELALGKNVVVAYMPWEGYNFEDAVLISERLVYEEIYT 84
Cdd:COG0085   563 PLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLT 640
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 6-84 2.48e-22

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: 87.97  E-value: 2.48e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 610505942    6 IPLVMYQRSNKNT---CMHQKPQVQRGRcIKRGQIladgaatvgGELALGKNVVVAYMPWEGYNFEDAVLISERLVYEEI 82
Cdd:pfam00562  30 YTLNKFYRSDQNTyvlCYPQKPLVKTGA-VEAGGF---------GELPLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGF 99


                  ..
gi 610505942   83 YT 84
Cdd:pfam00562 100 FT 101
 
Name Accession Description Interval E-value
rpoB CHL00001
RNA polymerase beta subunit
 1-84 3.85e-64

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 207.83  E-value: 3.85e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 610505942    1 GDAIRIPLVMYQRSNKNTCMHQKPQVQRGRCIKRGQILADGAATVGGELALGKNVVVAYMPWEGYNFEDAVLISERLVYE 80
Cdd:CHL00001  601 GDTLSIPLVMYQRSNKNTCMHQKPQVRRGKCVKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYE 680


                  ....
gi 610505942   81 EIYT 84
Cdd:CHL00001  681 DIYT 684
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 7-84 1.91e-43

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 149.10  E-value: 1.91e-43
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 610505942    7 PLVMYQRSNKNTCMHQKPQVQRGRCIKRGQILADGAATVGGELALGKNVVVAYMPWEGYNFEDAVLISERLVYEEIYT 84
Cdd:PRK00405  671 NLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELALGQNVLVAFMPWNGYNFEDAILISERLVKEDVFT 748
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 4-84 1.32e-39

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: 138.26  E-value: 1.32e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 610505942     4 IRIPLVMYQRSNKNTCMHQKPQVQRGRCIKRGQILADGAATVGGELALGKNVVVAYMPWEGYNFEDAVLISERLVYEEIY 83
Cdd:TIGR02013  626 DIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRNVLVAFMPWNGYNYEDAILISERLVKDDVF 705


                   .
gi 610505942    84 T 84
Cdd:TIGR02013  706 T 706
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 7-84 1.59e-39

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: 137.93  E-value: 1.59e-39
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 610505942    7 PLVMYQRSNKNTCMHQKPQVQRGRCIKRGQILADGAATVGGELALGKNVVVAYMPWEGYNFEDAVLISERLVYEEIYT 84
Cdd:COG0085   563 PLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLT 640
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 11-84 3.73e-37

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 130.98  E-value: 3.73e-37
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 610505942   11 YQRSNKNTCMHQKPQVQRGRCIKRGQILADGAATVGGELALGKNVVVAYMPWEGYNFEDAVLISERLVYEEIYT 84
Cdd:CHL00207  606 YQRSNQNTCINYRPIVWVGEKINIGQILADGSDIDNSELALGQNVLVAYMPWEGYNFEDAILINKRLVYEDLFT 679
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
13-84 6.64e-28

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 104.62  E-value: 6.64e-28
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 610505942   13 RSNKNTCMHQKPQVQRGRCIKRGQILADGAATVGGELALGKNVVVAYMPWEGYNFEDAVLISERLVYEEIYT 84
Cdd:PRK09603  768 RTNQNTSFNQVPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERITKDDIFT 839
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
8-84 3.24e-27

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 102.78  E-value: 3.24e-27
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 610505942    8 LVMYQRSNKNTCMHQKPQVQRGRCIKRGQILADGAATVGGELALGKNVVVAYMPWEGYNFEDAVLISERLVYEEIYT 84
Cdd:PRK14844  773 LRKFQRSNHNTCINQKPLVCVGDYVKEGDVIADGPAINSGELALGQNLLVAFMSWQGYNFEDSIIISSEVVKKDLFT 849
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 6-84 2.48e-22

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: 87.97  E-value: 2.48e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 610505942    6 IPLVMYQRSNKNT---CMHQKPQVQRGRcIKRGQIladgaatvgGELALGKNVVVAYMPWEGYNFEDAVLISERLVYEEI 82
Cdd:pfam00562  30 YTLNKFYRSDQNTyvlCYPQKPLVKTGA-VEAGGF---------GELPLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGF 99


                  ..
gi 610505942   83 YT 84
Cdd:pfam00562 100 FT 101
PRK08565 PRK08565
DNA-directed RNA polymerase subunit B; Provisional
 52-74 1.93e-04

DNA-directed RNA polymerase subunit B; Provisional


Pssm-ID: 236291 [Multi-domain]  Cd Length: 1103  Bit Score: 38.01  E-value: 1.93e-04
                          10        20
                  ....*....|....*....|...
gi 610505942   52 GKNVVVAYMPWEGYNFEDAVLIS 74
Cdd:PRK08565  702 GQNAVVAVLSYTGYNIEDAIIMN 724
PRK07225 PRK07225
DNA-directed RNA polymerase subunit B'; Validated
 52-75 3.95e-04

DNA-directed RNA polymerase subunit B'; Validated


Pssm-ID: 235972 [Multi-domain]  Cd Length: 605  Bit Score: 37.25  E-value: 3.95e-04
                         10        20
                 ....*....|....*....|....
gi 610505942  52 GKNVVVAYMPWEGYNFEDAVLISE 75
Cdd:PRK07225 204 GQNFVVAVMSYEGYNIEDALIMNK 227
 
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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