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Conserved domains on  [gi|1394757859|ref|XP_025070076|]
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DNA-directed RNA polymerase II subunit RPB9 isoform X4 [Alligator sinensis]

Protein Classification

zinc ribbon domain-containing protein( domain architecture ID 10652820)

zinc ribbon domain-containing protein is likely to be DNA-binding

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RPOL9 smart00661
RNA polymerase subunit 9;
1-46 1.18e-13

RNA polymerase subunit 9;


:

Pssm-ID: 197822  Cd Length: 52  Bit Score: 60.09  E-value: 1.18e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1394757859    1 MLYPKEDKENRilLYACRNCDYQQEADNSCIYVNKITHEVDELTQI 46
Cdd:smart00661   9 MLYPREGKEKR--RFVCRKCGYEEPAEQKYVYKEKLKHSKDELTVI 52
Zn-ribbon super family cl02609
C-terminal zinc ribbon domain of RNA polymerase intrinsic transcript cleavage subunit; The ...
 52-66 4.68e-04

C-terminal zinc ribbon domain of RNA polymerase intrinsic transcript cleavage subunit; The homologous C-terminal zinc ribbon domains of subunits A12.2, Rpb9, and C11 in RNA Polymerases (Pol) I, II, and III, respectively are required for intrinsic transcript cleavage. TFS is a related archaeal protein that is involved in RNA cleavage by archaeal polymerase. These proteins have two zinc-binding beta-ribbon domains, N-terminal zinc ribbon (N-ribbon) and C-terminal zinc ribbon (C-ribbon). Transcription Factor IIS (TFIIS) domain III is homologous to the C-ribbon domain that stimulates the weak cleavage activity of Rpb9 for Pol II.


The actual alignment was detected with superfamily member cd10508:

Pssm-ID: 445850  Cd Length: 49  Bit Score: 35.31  E-value: 4.68e-04
                          10
                  ....*....|....*
gi 1394757859  52 QDPTLPRTEDHPCQK 66
Cdd:cd10508     1 QDPTLPRTEDHPCPK 15
 
Name Accession Description Interval E-value
RPOL9 smart00661
RNA polymerase subunit 9;
1-46 1.18e-13

RNA polymerase subunit 9;


Pssm-ID: 197822  Cd Length: 52  Bit Score: 60.09  E-value: 1.18e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1394757859    1 MLYPKEDKENRilLYACRNCDYQQEADNSCIYVNKITHEVDELTQI 46
Cdd:smart00661   9 MLYPREGKEKR--RFVCRKCGYEEPAEQKYVYKEKLKHSKDELTVI 52
RNA_POL_M_15KD pfam02150
RNA polymerases M/15 Kd subunit;
1-27 7.93e-05

RNA polymerases M/15 Kd subunit;


Pssm-ID: 280336  Cd Length: 36  Bit Score: 37.07  E-value: 7.93e-05
                          10        20
                  ....*....|....*....|....*..
gi 1394757859   1 MLYPKEDKENRIllYACRNCDYQQEAD 27
Cdd:pfam02150  10 LLLPTEDKLGSN--FECRQCGYEEPAD 34
Zn-ribbon_RPB9 cd10508
C-terminal zinc ribbon domain of RPB9 subunit of RNA polymerase II; The C-terminal zinc ribbon ...
 52-66 4.68e-04

C-terminal zinc ribbon domain of RPB9 subunit of RNA polymerase II; The C-terminal zinc ribbon domain (C-ribbon) of subunit B9 (Zn-ribbon_RPB9) in RNA polymerase (Pol) II is involved in intrinsic transcript cleavage. Eukaryote genomes are transcribed by three nuclear RNA polymerases (Pol I, II and III) that share some subunits. RPB9 have strong homology to RPA12 of Pol I and RPC11 of Pol III subunits but its intrinsic cleavage activity is weaker for Pol II. Zn-ribbon_RPB9 is homologous to Pol II elongation factor TFIIS domain III. The very weak cleavage activity of Pol II is stimulated by TFIIS. RPB9 has two zinc-binding domains separated by a flexible linker.


Pssm-ID: 259793  Cd Length: 49  Bit Score: 35.31  E-value: 4.68e-04
                          10
                  ....*....|....*
gi 1394757859  52 QDPTLPRTEDHPCQK 66
Cdd:cd10508     1 QDPTLPRTEDHPCPK 15
 
Name Accession Description Interval E-value
RPOL9 smart00661
RNA polymerase subunit 9;
1-46 1.18e-13

RNA polymerase subunit 9;


Pssm-ID: 197822  Cd Length: 52  Bit Score: 60.09  E-value: 1.18e-13
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 1394757859    1 MLYPKEDKENRilLYACRNCDYQQEADNSCIYVNKITHEVDELTQI 46
Cdd:smart00661   9 MLYPREGKEKR--RFVCRKCGYEEPAEQKYVYKEKLKHSKDELTVI 52
RNA_POL_M_15KD pfam02150
RNA polymerases M/15 Kd subunit;
1-27 7.93e-05

RNA polymerases M/15 Kd subunit;


Pssm-ID: 280336  Cd Length: 36  Bit Score: 37.07  E-value: 7.93e-05
                          10        20
                  ....*....|....*....|....*..
gi 1394757859   1 MLYPKEDKENRIllYACRNCDYQQEAD 27
Cdd:pfam02150  10 LLLPTEDKLGSN--FECRQCGYEEPAD 34
Zn-ribbon_RPB9 cd10508
C-terminal zinc ribbon domain of RPB9 subunit of RNA polymerase II; The C-terminal zinc ribbon ...
 52-66 4.68e-04

C-terminal zinc ribbon domain of RPB9 subunit of RNA polymerase II; The C-terminal zinc ribbon domain (C-ribbon) of subunit B9 (Zn-ribbon_RPB9) in RNA polymerase (Pol) II is involved in intrinsic transcript cleavage. Eukaryote genomes are transcribed by three nuclear RNA polymerases (Pol I, II and III) that share some subunits. RPB9 have strong homology to RPA12 of Pol I and RPC11 of Pol III subunits but its intrinsic cleavage activity is weaker for Pol II. Zn-ribbon_RPB9 is homologous to Pol II elongation factor TFIIS domain III. The very weak cleavage activity of Pol II is stimulated by TFIIS. RPB9 has two zinc-binding domains separated by a flexible linker.


Pssm-ID: 259793  Cd Length: 49  Bit Score: 35.31  E-value: 4.68e-04
                          10
                  ....*....|....*
gi 1394757859  52 QDPTLPRTEDHPCQK 66
Cdd:cd10508     1 QDPTLPRTEDHPCPK 15
 
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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