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Conserved domains on  [gi|444327470|gb|AGE01044|]
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RpoB, partial [Acinetobacter sp. 1156983]

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;
90-124 1.10e-15

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: 71.67  E-value: 1.10e-15
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 444327470   90 KLATGDELTTGVLKVVKVYLAVKRRIQPGDKMAGR 124
Cdd:PRK00405  855 RIEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGR 889
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 90-124 1.10e-15

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 71.67  E-value: 1.10e-15
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 444327470   90 KLATGDELTTGVLKVVKVYLAVKRRIQPGDKMAGR 124
Cdd:PRK00405  855 RIEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGR 889
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 94-124 2.59e-12

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: 62.37  E-value: 2.59e-12
                           10        20        30
                   ....*....|....*....|....*....|.
gi 444327470    94 GDELTTGVLKVVKVYLAVKRRIQPGDKMAGR 124
Cdd:TIGR02013  816 GDELPPGVNKLVKVYIAQKRKIQVGDKMAGR 846
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 94-124 3.31e-10

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: 56.27  E-value: 3.31e-10
                          10        20        30
                  ....*....|....*....|....*....|.
gi 444327470   94 GDELTTGVLKVVKVYLAVKRRIQPGDKMAGR 124
Cdd:COG0085   750 GDELPPGVNKLVRVYVAQKRKIEVGDKLAGR 780
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 96-124 6.44e-09

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: 52.15  E-value: 6.44e-09
                          10        20
                  ....*....|....*....|....*....
gi 444327470   96 ELTTGVLKVVKVYLAVKRRIQPGDKMAGR 124
Cdd:pfam00562 200 ELPPGGIKMVKVYIRQKRKPEVGDKFASR 228
 
Name Accession Description Interval E-value
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 90-124 1.10e-15

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 71.67  E-value: 1.10e-15
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 444327470   90 KLATGDELTTGVLKVVKVYLAVKRRIQPGDKMAGR 124
Cdd:PRK00405  855 RIEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGR 889
rpoB TIGR02013
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ...
 94-124 2.59e-12

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: 62.37  E-value: 2.59e-12
                           10        20        30
                   ....*....|....*....|....*....|.
gi 444327470    94 GDELTTGVLKVVKVYLAVKRRIQPGDKMAGR 124
Cdd:TIGR02013  816 GDELPPGVNKLVKVYIAQKRKIQVGDKMAGR 846
RpoB COG0085
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ...
 94-124 3.31e-10

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: 56.27  E-value: 3.31e-10
                          10        20        30
                  ....*....|....*....|....*....|.
gi 444327470   94 GDELTTGVLKVVKVYLAVKRRIQPGDKMAGR 124
Cdd:COG0085   750 GDELPPGVNKLVRVYVAQKRKIEVGDKLAGR 780
PRK14844 PRK14844
DNA-directed RNA polymerase subunit beta/beta';
41-125 9.59e-10

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 173305 [Multi-domain]  Cd Length: 2836  Bit Score: 55.01  E-value: 9.59e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444327470   41 EEVLSGLELVDLLEIQPADEAIAERLTQIQVFLKEKSAEIDEKFAEKKRKLATGDELTTGVLKVVKVYLAVKRRIQPGDK 120
Cdd:PRK14844 1007 REKFDSIEREQWWGIGLKNQSISEQVKSLKKDFDEKVSHAIAQFKRKVEKLHEGYDLPQGVSMSVKVFIAVKHSLQPGDK 1086


                  ....*
gi 444327470  121 MAGRQ 125
Cdd:PRK14844 1087 MAGRH 1091
PRK09603 PRK09603
DNA-directed RNA polymerase subunit beta/beta';
30-125 2.41e-09

DNA-directed RNA polymerase subunit beta/beta';


Pssm-ID: 181983 [Multi-domain]  Cd Length: 2890  Bit Score: 53.77  E-value: 2.41e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 444327470   30 GGSTKRGDKLVEEVLSGLELVDLLE-IQPADEAIAERLTQIQVFLKEKSAEIDEKFAEKKRKLATGDELTTGVLKVVKVY 108
Cdd:PRK09603 1002 GKDYKEGDQIPKEEIASINRFTLASlVKKYSKEVQNHYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPNGVIKKVKLY 1081

                          90
                  ....*....|....*..
gi 444327470  109 LAVKRRIQPGDKMAGRQ 125
Cdd:PRK09603 1082 IATKRKLKVGDKMAGRH 1098
RNA_pol_Rpb2_6 pfam00562
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ...
 96-124 6.44e-09

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: 52.15  E-value: 6.44e-09
                          10        20
                  ....*....|....*....|....*....
gi 444327470   96 ELTTGVLKVVKVYLAVKRRIQPGDKMAGR 124
Cdd:pfam00562 200 ELPPGGIKMVKVYIRQKRKPEVGDKFASR 228
rpoB CHL00207
RNA polymerase beta subunit; Provisional
 93-124 2.19e-06

RNA polymerase beta subunit; Provisional


Pssm-ID: 214397 [Multi-domain]  Cd Length: 1077  Bit Score: 45.08  E-value: 2.19e-06
                          10        20        30
                  ....*....|....*....|....*....|..
gi 444327470   93 TGDELTTGVLKVVKVYLAVKRRIQPGDKMAGR 124
Cdd:CHL00207  788 KGDELKFGYYLKIRVFIAQIRKIQVGDKLAGR 819
rpoB CHL00001
RNA polymerase beta subunit
 95-124 1.19e-04

RNA polymerase beta subunit


Pssm-ID: 214330 [Multi-domain]  Cd Length: 1070  Bit Score: 40.27  E-value: 1.19e-04
                          10        20        30
                  ....*....|....*....|....*....|
gi 444327470   95 DELTTGVLKVVKVYLAVKRRIQPGDKMAGR 124
Cdd:CHL00001  794 KGGSSYNPETIHVYILQKREIQVGDKVAGR 823
 
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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