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Conserved domains on  [gi|564353069|ref|XP_006239032|]
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zinc finger CCHC domain-containing protein 17 isoform X2 [Rattus norvegicus]

Protein Classification

S1 domain-containing protein( domain architecture ID 237)

S1 domain-containing protein may bind RNA

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
S1_like super family cl09927
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 1-38 5.00e-16

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


The actual alignment was detected with superfamily member cd05686:

Pssm-ID: 471952 [Multi-domain]  Cd Length: 73  Bit Score: 69.43  E-value: 5.00e-16
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 564353069   1 MSSCRVDKPSEIVDVGDKVWVKLIGREMKnDRIKVSLS 38
Cdd:cd05686   37 MSSCRVDDPSEVVDVGEKVWVKVIGREMK-DKMKLSLS 73
 
Name Accession Description Interval E-value
S1_pNO40 cd05686
S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function ...
 1-38 5.00e-16

S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.


Pssm-ID: 240191 [Multi-domain]  Cd Length: 73  Bit Score: 69.43  E-value: 5.00e-16
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 564353069   1 MSSCRVDKPSEIVDVGDKVWVKLIGREMKnDRIKVSLS 38
Cdd:cd05686   37 MSSCRVDDPSEVVDVGEKVWVKVIGREMK-DKMKLSLS 73
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 5-42 2.48e-06

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 46.97  E-value: 2.48e-06
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 564353069   5 RVDKPSEIVDVGDKVWVKLIGremKNDRIKVSLSMKVV 42
Cdd:PRK11824 658 RVEKVEDVLKEGDEVKVKVLE---IDKRGRIRLSRKAV 692
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 5-40 4.44e-06

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 45.81  E-value: 4.44e-06
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 564353069   5 RVDKPSEIVDVGDKVWVKLIGREMKNDRIkvSLSMK 40
Cdd:COG0539  225 RVKHPSEVLKVGDEVEVKVLKIDREKERI--SLSLK 258
 
Name Accession Description Interval E-value
S1_pNO40 cd05686
S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function ...
 1-38 5.00e-16

S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.


Pssm-ID: 240191 [Multi-domain]  Cd Length: 73  Bit Score: 69.43  E-value: 5.00e-16
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 564353069   1 MSSCRVDKPSEIVDVGDKVWVKLIGREMKnDRIKVSLS 38
Cdd:cd05686   37 MSSCRVDDPSEVVDVGEKVWVKVIGREMK-DKMKLSLS 73
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 5-47 3.90e-07

S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.


Pssm-ID: 240189 [Multi-domain]  Cd Length: 79  Bit Score: 46.08  E-value: 3.90e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 564353069   5 RVDKPSEIVDVGDKVWVKLIGreMKNDRIkvSLSMKVVNQGTG 47
Cdd:cd05684   41 RVANPSDVVKRGQKVKVKVIS--IQNGKI--SLSMKDVDQDTG 79
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 5-42 2.48e-06

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 46.97  E-value: 2.48e-06
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 564353069   5 RVDKPSEIVDVGDKVWVKLIGremKNDRIKVSLSMKVV 42
Cdd:PRK11824 658 RVEKVEDVLKEGDEVKVKVLE---IDKRGRIRLSRKAV 692
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 5-40 4.44e-06

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 45.81  E-value: 4.44e-06
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 564353069   5 RVDKPSEIVDVGDKVWVKLIGREMKNDRIkvSLSMK 40
Cdd:COG0539  225 RVKHPSEVLKVGDEVEVKVLKIDREKERI--SLSLK 258
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 5-40 2.12e-05

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 44.10  E-value: 2.12e-05
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 564353069   5 RVDKPSEIVDVGDKVWVKLIGREMKNDRIkvSLSMK 40
Cdd:PRK06676 228 RVEKPSEVVSVGQEVEVKVLSIDWETERI--SLSLK 261
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 5-39 3.87e-05

S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.


Pssm-ID: 239918 [Multi-domain]  Cd Length: 68  Bit Score: 40.22  E-value: 3.87e-05
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 564353069   5 RVDKPSEIVDVGDKVWVKLIGremKNDRIKVSLSM 39
Cdd:cd04472   37 RVEKVEDVLKVGDEVKVKVIE---VDDRGRISLSR 68
rpsA PRK13806
30S ribosomal protein S1; Provisional
 5-40 2.35e-04

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 40.86  E-value: 2.35e-04
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 564353069   5 RVDKPSEIVDVGDKVWVKL--IGREMKNDRIKVSLSMK 40
Cdd:PRK13806 239 RVQKADEAVSVGDTVRVKVlgIERAKKGKGLRISLSIK 276
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 1-38 2.98e-04

S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240193 [Multi-domain]  Cd Length: 68  Bit Score: 37.61  E-value: 2.98e-04
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 564353069   1 MSSCRVDKPSEIVDVGDKVWVKLIgrEMKNDRIKVSLS 38
Cdd:cd05688   33 MSWGRVKHPSEVVNVGDEVEVKVL--KIDKERKRISLG 68
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 1-40 3.17e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 40.53  E-value: 3.17e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 564353069   1 MSSCRVDKPSEIVDVGDKVWVKLIgrEMKNDRIKVSLSMK 40
Cdd:PRK06299 233 ISWKRVNHPSEVVNVGDEVKVKVL--KFDKEKKRVSLGLK 270
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 6-40 3.69e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 40.41  E-value: 3.69e-04
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 564353069   6 VDKPSEIVDVGDKVWVKLIGREMknDRIKVSLSMK 40
Cdd:PRK07899 245 IDHPSEVVEVGQEVTVEVLDVDM--DRERVSLSLK 277
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 5-40 3.75e-04

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 40.03  E-value: 3.75e-04
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 564353069   5 RVDKPSEIVDVGDKVWVKLIgrEMKNDRIKVSLSMK 40
Cdd:COG0539  312 RVAHPSDVVKVGDEVEVKVL--DIDPEERRISLSIK 345
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
1-40 3.14e-03

bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 37.62  E-value: 3.14e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 564353069   1 MSSCRVDKPSEIVDVGDKVWVKLIG--REMKndriKVSLSMK 40
Cdd:PRK00087 509 ISWGRVEKPSDVLKVGDEIKVYILDidKENK----KLSLSLK 546
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 5-70 5.07e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 36.78  E-value: 5.07e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 564353069   5 RVDKPSEIVDVGDKVWVKLIGREMKNDRIkvSLSMkvvnqgtgKDLDPNNviiEQEERRRRSFQDY 70
Cdd:PRK06676 314 HIATPSEVLEEGQEVKVKVLEVNEEEKRI--SLSI--------KALEEAP---AEEEDRREEYRQY 366
 
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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