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Conserved domains on  [gi|543173116|ref|NP_001269498|]
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zinc finger CCHC domain-containing protein 17 isoform d [Homo sapiens]

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 ...
 15-78 8.06e-38

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: 126.44  E-value: 8.06e-38
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 543173116  15 VAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKnDRIKVSLS 78
Cdd:cd05686   11 VASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMK-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 ...
 15-78 8.06e-38

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: 126.44  E-value: 8.06e-38
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 543173116  15 VAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKnDRIKVSLS 78
Cdd:cd05686   11 VASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMK-DKMKLSLS 73
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 2-82 5.61e-15

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 73.55  E-value: 5.61e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543173116   2 KQLIEDTEKNKVYVAMVT---DYGAFIKI-PGcrKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGremKNDRIKVSL 77
Cdd:PRK11824 613 EGITAEPEVGEIYEGKVVrivDFGAFVEIlPG--KDGLVHISEIADERVEKVEDVLKEGDEVKVKVLE---IDKRGRIRL 687


                 ....*
gi 543173116  78 SMKVV 82
Cdd:PRK11824 688 SRKAV 692
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 2-80 2.86e-14

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: 70.84  E-value: 2.86e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543173116   2 KQLIEDTEKNKVY---VAMVTDYGAFIKIPGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIkvSLS 78
Cdd:COG0539  181 EELLEKLEEGDVVegtVKNITDFGAFVDLGGV--DGLLHISEISWGRVKHPSEVLKVGDEVEVKVLKIDREKERI--SLS 256


                 ..
gi 543173116  79 MK 80
Cdd:COG0539  257 LK 258
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 1-77 8.37e-10

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 58.21  E-value: 8.37e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 543173116    1 MKQLIEDTEKNKVYVAMVTDYGAFIKIPGCRkqGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVSL 77
Cdd:TIGR00717 181 LLENLKEGDVVKGVVKNITDFGAFVDLGGVD--GLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSL 255
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
9-77 4.61e-08

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 48.75  E-value: 4.61e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 543173116     9 EKNKVYVAMVT---DYGAFIKIPGcRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVSL 77
Cdd:smart00316   1 EVGDVVEGTVTeitPGGAFVDLGN-GVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSL 71
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 18-77 1.25e-05

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 41.89  E-value: 1.25e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 543173116   18 VTDYGAFIKIpGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVSL 77
Cdd:pfam00575  14 VTKGGAFVDL-GNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
 
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 ...
 15-78 8.06e-38

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: 126.44  E-value: 8.06e-38
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 543173116  15 VAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKnDRIKVSLS 78
Cdd:cd05686   11 VASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMK-DKMKLSLS 73
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 2-82 5.61e-15

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 73.55  E-value: 5.61e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543173116   2 KQLIEDTEKNKVYVAMVT---DYGAFIKI-PGcrKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGremKNDRIKVSL 77
Cdd:PRK11824 613 EGITAEPEVGEIYEGKVVrivDFGAFVEIlPG--KDGLVHISEIADERVEKVEDVLKEGDEVKVKVLE---IDKRGRIRL 687


                 ....*
gi 543173116  78 SMKVV 82
Cdd:PRK11824 688 SRKAV 692
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 11-87 7.30e-15

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: 67.26  E-value: 7.30e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543173116  11 NKVY---VAMVTDYGAFIKIPGC--RKQGLVHRTHMSS-CRVDKPSEIVDVGDKVWVKLIGreMKNDRIkvSLSMKVVNQ 84
Cdd:cd05684    1 GKIYkgkVTSIMDFGCFVQLEGLkgRKEGLVHISQLSFeGRVANPSDVVKRGQKVKVKVIS--IQNGKI--SLSMKDVDQ 76


                 ...
gi 543173116  85 GTG 87
Cdd:cd05684   77 DTG 79
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 2-80 2.86e-14

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: 70.84  E-value: 2.86e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543173116   2 KQLIEDTEKNKVY---VAMVTDYGAFIKIPGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIkvSLS 78
Cdd:COG0539  181 EELLEKLEEGDVVegtVKNITDFGAFVDLGGV--DGLLHISEISWGRVKHPSEVLKVGDEVEVKVLKIDREKERI--SLS 256


                 ..
gi 543173116  79 MK 80
Cdd:COG0539  257 LK 258
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 11-79 1.03e-12

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: 61.02  E-value: 1.03e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 543173116  11 NKVYVAMVT---DYGAFIKI-PGcrKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGremKNDRIKVSLSM 79
Cdd:cd04472    1 GKIYEGKVVkikDFGAFVEIlPG--KDGLVHISELSDERVEKVEDVLKVGDEVKVKVIE---VDDRGRISLSR 68
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 15-80 1.53e-12

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 66.05  E-value: 1.53e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 543173116  15 VAMVTDYGAFIKIPGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIkvSLSMK 80
Cdd:PRK06676 200 VARLTDFGAFVDIGGV--DGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERI--SLSLK 261
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 3-80 2.88e-12

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 65.19  E-value: 2.88e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 543173116   3 QLIEDTEKNkvyvamVTDYGAFIKIPGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIgrEMKNDRIKVSLSMK 80
Cdd:PRK06299 203 QVVEGVVKN------ITDYGAFVDLGGV--DGLLHITDISWKRVNHPSEVVNVGDEVKVKVL--KFDKEKKRVSLGLK 270
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 1-80 3.59e-12

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: 64.68  E-value: 3.59e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543173116   1 MKQLIED-----TEKNKV------YVAMVTDYGAFIKI-PGCrkQGLVHRTHMS-SCRVDKPSEIVDVGDKVWVKLIgrE 67
Cdd:COG0539  257 LKQLQPDpweniAEKYPVgdvvkgKVTRLTDFGAFVELePGV--EGLVHISEMSwTKRVAHPSDVVKVGDEVEVKVL--D 332

                         90
                 ....*....|...
gi 543173116  68 MKNDRIKVSLSMK 80
Cdd:COG0539  333 IDPEERRISLSIK 345
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 15-78 7.74e-12

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: 58.79  E-value: 7.74e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 543173116  15 VAMVTDYGAFIKIPGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIgrEMKNDRIKVSLS 78
Cdd:cd05688    9 VKSITDFGAFVDLGGV--DGLLHISDMSWGRVKHPSEVVNVGDEVEVKVL--KIDKERKRISLG 68
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 15-80 1.18e-11

S1_RPS1_repeat_hs4: 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 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240197 [Multi-domain]  Cd Length: 69  Bit Score: 58.45  E-value: 1.18e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 543173116  15 VAMVTDYGAFIKIPGcRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREmknDRIKVSLSMK 80
Cdd:cd05692    8 VTRLKPFGAFVELGG-GISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSID---ARGRISLSIK 69
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 12-76 6.64e-11

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.


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 56.23  E-value: 6.64e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 543173116  12 KVYVAMVTDYGAFIKIPGcRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVS 76
Cdd:cd00164    2 TGKVVSITKFGVFVELED-GVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 15-76 1.02e-10

S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.


Pssm-ID: 240190 [Multi-domain]  Cd Length: 68  Bit Score: 55.70  E-value: 1.02e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 543173116  15 VAMVTDYGAFIKIpGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVS 76
Cdd:cd05685    8 VTNVTDFGAFVDI-GVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
18-88 2.51e-10

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 59.65  E-value: 2.51e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 543173116  18 VTDYGAFIKIpGCrKQ-GLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIkvSLSMKVVNQGTGK 88
Cdd:COG2183  652 VTDFGAFVDI-GV-HQdGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEVDLKRKRI--SLSMKLDDEAGAA 719
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 1-77 8.37e-10

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 58.21  E-value: 8.37e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 543173116    1 MKQLIEDTEKNKVYVAMVTDYGAFIKIPGCRkqGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVSL 77
Cdd:TIGR00717 181 LLENLKEGDVVKGVVKNITDFGAFVDLGGVD--GLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSL 255
rpsA PRK13806
30S ribosomal protein S1; Provisional
 15-80 9.15e-10

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 57.81  E-value: 9.15e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 543173116  15 VAMVTDYGAFIKI-PGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKL--IGREMKNDRIKVSLSMK 80
Cdd:PRK13806 210 VTRLAPFGAFVELaPGV--EGMVHISELSWSRVQKADEAVSVGDTVRVKVlgIERAKKGKGLRISLSIK 276
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
2-80 2.18e-09

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 56.88  E-value: 2.18e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543173116   2 KQLIEDTEKNKVY---VAMVTDYGAFIKIPGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIG--REMKndriKVS 76
Cdd:PRK00087 469 EETWNSLEEGDVVegeVKRLTDFGAFVDIGGV--DGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDidKENK----KLS 542


                 ....
gi 543173116  77 LSMK 80
Cdd:PRK00087 543 LSLK 546
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 18-122 4.46e-09

Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function prediction only];


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 52.87  E-value: 4.46e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543173116  18 VTDYGAFIKIPGcRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREmknDRIKVSLSMkvvnqgtgKDLDPNNvii 97
Cdd:COG1098   16 ITPFGAFVELPE-GTTGLVHISEIADGYVKDINDYLKVGDEVKVKVLSID---EDGKISLSI--------KQAEEKP--- 80

                         90       100
                 ....*....|....*....|....*
gi 543173116  98 EQEERRRRSFQDYTGQKiTLEAVLN 122
Cdd:COG1098   81 KRPPRPRRNSRPKAGFE-SFEDKLS 104
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 15-110 6.98e-09

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 55.27  E-value: 6.98e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543173116  15 VAMVTDYGAFIKI-PGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIkvSLSMkvvnqgtgKDLDPN 93
Cdd:PRK06676 285 VKRLTDFGAFVEVlPGV--EGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRI--SLSI--------KALEEA 352

                         90
                 ....*....|....*..
gi 543173116  94 NviiEQEERRRRSFQDY 110
Cdd:PRK06676 353 P---AEEEDRREEYRQY 366
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
2-83 7.04e-09

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 55.34  E-value: 7.04e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543173116   2 KQLIED-----TEKNKV------YVAMVTDYGAFIKI-PGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIgrEMK 69
Cdd:PRK00087 546 KKLLPDpwenvEEKYPVgsivlgKVVRIAPFGAFVELePGV--DGLVHISQISWKRIDKPEDVLSEGEEVKAKIL--EVD 621

                         90
                 ....*....|....
gi 543173116  70 NDRIKVSLSMKVVN 83
Cdd:PRK00087 622 PEEKRIRLSIKEVE 635
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 15-80 8.68e-09

S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240213 [Multi-domain]  Cd Length: 77  Bit Score: 50.79  E-value: 8.68e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 543173116  15 VAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIgrEMKNDRIKVSLSMK 80
Cdd:cd05708   10 VRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVL--KIDAEKKRISLGLK 73
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 15-80 1.82e-08

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 53.89  E-value: 1.82e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 543173116  15 VAMVTDYGAFIKIPGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMknDRIKVSLSMK 80
Cdd:PRK07899 216 VSSIVNFGAFVDLGGV--DGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDM--DRERVSLSLK 277
rpsA PRK13806
30S ribosomal protein S1; Provisional
 15-80 3.73e-08

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 53.19  E-value: 3.73e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 543173116  15 VAMVTDYGAFIKI-PGCrkQGLVHRTHMS-SCRVDKPSEIVDVGDKVWVKLigREMKNDRIKVSLSMK 80
Cdd:PRK13806 300 VVRLAPFGAFVEIlPGI--EGLVHVSEMSwTRRVNKPEDVVAPGDAVAVKI--KDIDPAKRRISLSLR 363
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
9-77 4.61e-08

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 48.75  E-value: 4.61e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 543173116     9 EKNKVYVAMVT---DYGAFIKIPGcRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVSL 77
Cdd:smart00316   1 EVGDVVEGTVTeitPGGAFVDLGN-GVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSL 71
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 1-80 1.92e-07

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 50.93  E-value: 1.92e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543173116   1 MKQLIED-----------TEKNKVYVAMVTDYGAFIKI-PGCrkQGLVHRTHMS-SCRVDKPSEIVDVGDKVWVKLIGRE 67
Cdd:PRK06299 269 LKQLGEDpweaiekkypvGSKVKGKVTNITDYGAFVELeEGI--EGLVHVSEMSwTKKNKHPSKVVSVGQEVEVMVLEID 346

                         90
                 ....*....|...
gi 543173116  68 MKNDRIkvSLSMK 80
Cdd:PRK06299 347 EEKRRI--SLGLK 357
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 15-92 6.33e-07

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 49.27  E-value: 6.33e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543173116  15 VAMVTDYGAFIKIP-GCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMknDRIKVSLSMKVVNQG---TGKDL 90
Cdd:PRK07899 301 VTKLVPFGAFVRVEeGI--EGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDL--ERRRISLSLKQANEGvtpESEDF 376


                 ..
gi 543173116  91 DP 92
Cdd:PRK07899 377 DP 378
PRK05807 PRK05807
RNA-binding protein S1;
15-109 2.88e-06

RNA-binding protein S1;


Pssm-ID: 235614 [Multi-domain]  Cd Length: 136  Bit Score: 45.51  E-value: 2.88e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543173116  15 VAMVTDYGAFIKIPGcrKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREmknDRIKVSLSMKVVNQgTGKDLDPNN 94
Cdd:PRK05807  13 VVNITNFGAFVEVEG--KTGLVHISEVADTYVKDIREHLKEQDKVKVKVISID---DNGKISLSIKQAMK-QKKSVKPAE 86

                         90
                 ....*....|....*..
gi 543173116  95 VIIEQEERRRR--SFQD 109
Cdd:PRK05807  87 IDWQKEKNKNNngNFED 103
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 1-80 6.69e-06

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 46.31  E-value: 6.69e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543173116   1 MKQLIED-----TEKNKV------YVAMVTDYGAFIKIPGCRKqGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMK 69
Cdd:PRK06299 443 IKQLEEDpfeefAKKHKKgsivtgTVTEVKDKGAFVELEDGVE-GLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRK 521

                         90
                 ....*....|.
gi 543173116  70 NDRIkvSLSMK 80
Cdd:PRK06299 522 NRRI--SLSIK 530
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
 15-80 8.37e-06

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 46.43  E-value: 8.37e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 543173116  15 VAMVTDYGAFIKI-PGcrKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIgrEMkNDRIKVSLSMK 80
Cdd:PLN00207 762 IKSIAPYGAFVEIaPG--REGLCHISELSSNWLAKPEDAFKVGDRIDVKLI--EV-NDKGQLRLSRR 823
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 2-80 9.49e-06

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 45.88  E-value: 9.49e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543173116    2 KQLIED-----TEKNKV------YVAMVTDYGAFIKIPGcRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKN 70
Cdd:TIGR00717 430 KQLTENpwekfAAKYKVgsvvkgKVTEIKDFGAFVELPG-GVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKN 508

                          90
                  ....*....|
gi 543173116   71 DriKVSLSMK 80
Cdd:TIGR00717 509 R--KVSLSVK 516
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 18-77 1.25e-05

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 41.89  E-value: 1.25e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 543173116   18 VTDYGAFIKIpGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVSL 77
Cdd:pfam00575  14 VTKGGAFVDL-GNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 1-77 1.74e-05

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 45.11  E-value: 1.74e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543173116    1 MKQLIEDT-----------EKNKVYVAMVTDYGAFIKIpGCRKQGLVHRTHMS-SCRVDKPSEIVDVGDKVWVKLIGREM 68
Cdd:TIGR00717 255 LKQLGEDPweaiekkfpvgDKITGRVTNLTDYGVFVEI-EEGIEGLVHVSEMSwVKKNSHPSKVVKKGDEVEVMILDIDP 333


                  ....*....
gi 543173116   69 KNDRIKVSL 77
Cdd:TIGR00717 334 ERRRLSLGL 342
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 21-101 7.36e-05

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 42.86  E-value: 7.36e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543173116  21 YGAFIKIPGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIgrEMKNDRIKVSLSMKVVNQGTGKDL-DPNNVIIEQ 99
Cdd:PRK07400 210 YGAFIDIGGV--SGLLHISEISHEHIETPHSVFNVNDEMKVMII--DLDAERGRISLSTKQLEPEPGDMLkDPQKVFDKA 285


                 ..
gi 543173116 100 EE 101
Cdd:PRK07400 286 EE 287
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 1-80 1.17e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 42.46  E-value: 1.17e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543173116   1 MKQLIED-----TEKNKV------YVAMVTDYGAFIKIPGCrKQGLVHRTHMS-SCRVDKPSEIVDVGDKVWVKLIGREM 68
Cdd:PRK06299 356 LKQCKENpweefAEKYPVgdvvegKVKNITDFGAFVGLEGG-IDGLVHLSDISwDKKGEEAVELYKKGDEVEAVVLKVDV 434

                         90
                 ....*....|..
gi 543173116  69 KNDRIkvSLSMK 80
Cdd:PRK06299 435 EKERI--SLGIK 444
PRK08059 PRK08059
general stress protein 13; Validated
 15-80 1.35e-04

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 40.42  E-value: 1.35e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 543173116  15 VAMVTDYGAFIKIPGcRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIkvSLSMK 80
Cdd:PRK08059  15 VTGIQPYGAFVALDE-ETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKI--SLSIR 77
PRK08582 PRK08582
RNA-binding protein S1;
5-80 1.97e-04

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 40.40  E-value: 1.97e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 543173116   5 IEDTEKNKVYVAMVTDYGAFIKIPGcRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREmknDRIKVSLSMK 80
Cdd:PRK08582   3 IEVGSKLQGKVTGITNFGAFVELPE-GKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVE---DDGKIGLSIK 74
S1_RPS1_repeat_ec4 cd05689
S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 15-77 5.97e-04

S1_RPS1_repeat_ec4: 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 4 (ec4) 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: 240194 [Multi-domain]  Cd Length: 72  Bit Score: 37.56  E-value: 5.97e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 543173116  15 VAMVTDYGAFIKI-PGCrkQGLVHRTHMSSCRVD-KPSEIVDVGDKVWVKLIgrEMKNDRIKVSL 77
Cdd:cd05689   11 VTNLTDYGCFVELeEGV--EGLVHVSEMDWTNKNiHPSKVVSLGDEVEVMVL--DIDEERRRISL 71
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 18-77 6.09e-04

S1_RPS1_repeat_ec5: 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 5 (ec5) 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: 240195 [Multi-domain]  Cd Length: 69  Bit Score: 37.09  E-value: 6.09e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 543173116  18 VTDYGAFIKIPGcRKQGLVHRTHMS-SCRVDKPSEIVDVGDKVWVKLIgrEMKNDRIKVSL 77
Cdd:cd05690   11 ITDFGIFVGLDG-GIDGLVHISDISwTQRVRHPSEIYKKGQEVEAVVL--NIDVERERISL 68
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 5-77 6.61e-04

S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 239908 [Multi-domain]  Cd Length: 83  Bit Score: 37.57  E-value: 6.61e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 543173116   5 IEDTEKNKV---YVAMVTDYGAFIKIPGcRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVSL 77
Cdd:cd04461    9 FSDLKPGMVvhgYVRNITPYGVFVEFLG-GLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL 83
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 15-77 2.07e-03

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 38.92  E-value: 2.07e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 543173116  15 VAMVTDYGAFIKIPGcRKQGLVHRTHMSSCRVDKPSEIVD---VGDKVWVKLIGREMKNDRIKVSL 77
Cdd:PRK12269 760 VSSVTDFGIFVRVPG-GVEGLVRKQHLVENRDGDPGEALRkyaVGDRVKAVIVDMNVKDRKVAFSV 824
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 15-83 2.99e-03

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 38.54  E-value: 2.99e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 543173116  15 VAMVTDYGAFIKIPGcRKQGLVHRTHMSSCR-VDKPSEIVDVGDKVWVKLIGREMKNDRIKVSLSMKVVN 83
Cdd:PRK12269 586 VTKIADFGAFIELAE-GIEGLAHISEFSWVKkTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQVTAN 654
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 9-67 6.27e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 37.16  E-value: 6.27e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 543173116   9 EKNKVYVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGRE 67
Cdd:PRK06676  19 DVVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVE 77
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 15-77 9.28e-03

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 37.00  E-value: 9.28e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 543173116  15 VAMVTDYGAFIKIPGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVSL 77
Cdd:PRK12269 501 VKSFTSFGAFIDLGGF--DGLLHVNDMSWGHVARPREFVKKGQTIELKVIRLDQAEKRINLSL 561
 
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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