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Conserved domains on  [gi|21361576|ref|NP_057589|]
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zinc finger CCHC domain-containing protein 17 isoform c [Homo sapiens]

Protein Classification

S1 domain-containing protein( domain architecture ID 10145446)

S1 domain-containing protein may bind RNA

Graphical summary

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List of domain hits

 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 ...
 13-86 1.46e-46

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: 149.17  E-value: 1.46e-46
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 21361576  13 PALYTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKnDRIKVSLS 86
Cdd:cd05686   1 PALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMK-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 ...
 13-86 1.46e-46

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: 149.17  E-value: 1.46e-46
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 21361576  13 PALYTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKnDRIKVSLS 86
Cdd:cd05686   1 PALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMK-DKMKLSLS 73
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 18-88 2.00e-15

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: 74.31  E-value: 2.00e-15
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 21361576  18 IFQGEVAMVTDYGAFIKIPGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIkvSLSMK 88
Cdd:COG0539 192 VVEGTVKNITDFGAFVDLGGV--DGLLHISEISWGRVKHPSEVLKVGDEVEVKVLKIDREKERI--SLSLK 258
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 18-90 4.08e-15

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 73.93  E-value: 4.08e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 21361576   18 IFQGEVAMVTDYGAFIKI-PGcrKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGremKNDRIKVSLSMKVV 90
Cdd:PRK11824 624 IYEGKVVRIVDFGAFVEIlPG--KDGLVHISEIADERVEKVEDVLKEGDEVKVKVLE---IDKRGRIRLSRKAV 692
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
17-85 6.56e-10

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 53.76  E-value: 6.56e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 21361576     17 TIFQGEVAMVTDYGAFIKIPGcRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVSL 85
Cdd:smart00316   4 DVVEGTVTEITPGGAFVDLGN-GVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSL 71
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 21-85 1.19e-09

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: 57.82  E-value: 1.19e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 21361576    21 GEVAMVTDYGAFIKIPGCRkqGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVSL 85
Cdd:TIGR00717 193 GVVKNITDFGAFVDLGGVD--GLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSL 255
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 17-87 1.35e-08

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: 50.36  E-value: 1.35e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 21361576    17 TIFQGEVAMVTDYGAFIKIpGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIgrEMKNDRIKVSLSM 87
Cdd:pfam00575   5 DVVEGEVTRVTKGGAFVDL-GNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVL--KVDKDRRRIILSI 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 ...
 13-86 1.46e-46

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: 149.17  E-value: 1.46e-46
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 21361576  13 PALYTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKnDRIKVSLS 86
Cdd:cd05686   1 PALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMK-DKMKLSLS 73
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 16-95 1.77e-17

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: 74.20  E-value: 1.77e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361576  16 YTIFQGEVAMVTDYGAFIKIPGC--RKQGLVHRTHMSS-CRVDKPSEIVDVGDKVWVKLIGreMKNDRIkvSLSMKVVNQ 92
Cdd:cd05684   1 GKIYKGKVTSIMDFGCFVQLEGLkgRKEGLVHISQLSFeGRVANPSDVVKRGQKVKVKVIS--IQNGKI--SLSMKDVDQ 76


                ...
gi 21361576  93 GTG 95
Cdd:cd05684  77 DTG 79
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 18-88 2.00e-15

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: 74.31  E-value: 2.00e-15
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 21361576  18 IFQGEVAMVTDYGAFIKIPGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIkvSLSMK 88
Cdd:COG0539 192 VVEGTVKNITDFGAFVDLGGV--DGLLHISEISWGRVKHPSEVLKVGDEVEVKVLKIDREKERI--SLSLK 258
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 18-90 4.08e-15

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 73.93  E-value: 4.08e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 21361576   18 IFQGEVAMVTDYGAFIKI-PGcrKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGremKNDRIKVSLSMKVV 90
Cdd:PRK11824 624 IYEGKVVRIVDFGAFVEIlPG--KDGLVHISEIADERVEKVEDVLKEGDEVKVKVLE---IDKRGRIRLSRKAV 692
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 17-87 4.39e-15

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: 67.57  E-value: 4.39e-15
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 21361576  17 TIFQGEVAMVTDYGAFIKI-PGcrKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGremKNDRIKVSLSM 87
Cdd:cd04472   2 KIYEGKVVKIKDFGAFVEIlPG--KDGLVHISELSDERVEKVEDVLKVGDEVKVKVIE---VDDRGRISLSR 68
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 21-88 6.82e-14

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 69.90  E-value: 6.82e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 21361576   21 GEVAMVTDYGAFIKIPGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIkvSLSMK 88
Cdd:PRK06676 198 GTVARLTDFGAFVDIGGV--DGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERI--SLSLK 261
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 17-88 1.39e-13

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: 63.84  E-value: 1.39e-13
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 21361576  17 TIFQGEVAMVTDYGAFIKIPGcRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREmknDRIKVSLSMK 88
Cdd:cd05692   2 SVVEGTVTRLKPFGAFVELGG-GISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSID---ARGRISLSIK 69
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 18-88 1.99e-13

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 69.04  E-value: 1.99e-13
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 21361576   18 IFQGEVAMVTDYGAFIKIPGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIgrEMKNDRIKVSLSMK 88
Cdd:PRK06299 204 VVEGVVKNITDYGAFVDLGGV--DGLLHITDISWKRVNHPSEVVNVGDEVKVKVL--KFDKEKKRVSLGLK 270
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 17-88 2.28e-13

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: 68.15  E-value: 2.28e-13
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 21361576  17 TIFQGEVAMVTDYGAFIKI-PGCrkQGLVHRTHMS-SCRVDKPSEIVDVGDKVWVKLIgrEMKNDRIKVSLSMK 88
Cdd:COG0539 276 DVVKGKVTRLTDFGAFVELePGV--EGLVHISEMSwTKRVAHPSDVVKVGDEVEVKVL--DIDPEERRISLSIK 345
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 18-86 3.58e-13

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: 62.65  E-value: 3.58e-13
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 21361576  18 IFQGEVAMVTDYGAFIKIPGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIgrEMKNDRIKVSLS 86
Cdd:cd05688   4 VVEGTVKSITDFGAFVDLGGV--DGLLHISDMSWGRVKHPSEVVNVGDEVEVKVL--KIDKERKRISLG 68
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 17-84 1.46e-12

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: 61.09  E-value: 1.46e-12
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 21361576  17 TIFQGEVAMVTDYGAFIKIpGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVS 84
Cdd:cd05685   2 MVLEGVVTNVTDFGAFVDI-GVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 19-84 3.68e-12

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: 59.70  E-value: 3.68e-12
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 21361576  19 FQGEVAMVTDYGAFIKIPGcRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVS 84
Cdd:cd00164   1 VTGKVVSITKFGVFVELED-GVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
17-88 1.07e-11

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 63.81  E-value: 1.07e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 21361576   17 TIFQGEVAMVTDYGAFIKIPGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIG--REMKndriKVSLSMK 88
Cdd:PRK00087 479 DVVEGEVKRLTDFGAFVDIGGV--DGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDidKENK----KLSLSLK 546
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 17-118 1.95e-11

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 62.97  E-value: 1.95e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361576   17 TIFQGEVAMVTDYGAFIKI-PGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIkvSLSMkvvnqgtg 95
Cdd:PRK06676 279 DVIEGTVKRLTDFGAFVEVlPGV--EGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRI--SLSI-------- 346

                         90       100
                 ....*....|....*....|...
gi 21361576   96 KDLDPNNviiEQEERRRRSFQDY 118
Cdd:PRK06676 347 KALEEAP---AEEEDRREEYRQY 366
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
18-96 5.77e-11

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 61.96  E-value: 5.77e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361576  18 IFQGEVAMVTDYGAFIKIpGCrKQ-GLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIkvSLSMKVVNQGTGK 96
Cdd:COG2183 644 ILEGTVTNVTDFGAFVDI-GV-HQdGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEVDLKRKRI--SLSMKLDDEAGAA 719
rpsA PRK13806
30S ribosomal protein S1; Provisional
 18-88 9.09e-11

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 60.89  E-value: 9.09e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 21361576   18 IFQGEVAMVTDYGAFIKI-PGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKL--IGREMKNDRIKVSLSMK 88
Cdd:PRK13806 205 VVEGTVTRLAPFGAFVELaPGV--EGMVHISELSWSRVQKADEAVSVGDTVRVKVlgIERAKKGKGLRISLSIK 276
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 18-130 1.32e-10

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


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 57.50  E-value: 1.32e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361576  18 IFQGEVAMVTDYGAFIKIPGcRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREmknDRIKVSLSMkvvnqgtgKD 97
Cdd:COG1098   8 IVEGKVTGITPFGAFVELPE-GTTGLVHISEIADGYVKDINDYLKVGDEVKVKVLSID---EDGKISLSI--------KQ 75

                        90       100       110
                ....*....|....*....|....*....|...
gi 21361576  98 LDPNNviiEQEERRRRSFQDYTGQKiTLEAVLN 130
Cdd:COG1098  76 AEEKP---KRPPRPRRNSRPKAGFE-SFEDKLS 104
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 19-88 6.01e-10

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: 54.26  E-value: 6.01e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361576  19 FQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIgrEMKNDRIKVSLSMK 88
Cdd:cd05708   6 IDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVL--KIDAEKKRISLGLK 73
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
17-85 6.56e-10

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 53.76  E-value: 6.56e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 21361576     17 TIFQGEVAMVTDYGAFIKIPGcRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVSL 85
Cdd:smart00316   4 DVVEGTVTEITPGGAFVDLGN-GVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSL 71
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
18-91 8.89e-10

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 58.42  E-value: 8.89e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 21361576   18 IFQGEVAMVTDYGAFIKI-PGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIgrEMKNDRIKVSLSMKVVN 91
Cdd:PRK00087 565 IVLGKVVRIAPFGAFVELePGV--DGLVHISQISWKRIDKPEDVLSEGEEVKAKIL--EVDPEEKRIRLSIKEVE 635
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 21-85 1.19e-09

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: 57.82  E-value: 1.19e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 21361576    21 GEVAMVTDYGAFIKIPGCRkqGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVSL 85
Cdd:TIGR00717 193 GVVKNITDFGAFVDLGGVD--GLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSL 255
rpsA PRK13806
30S ribosomal protein S1; Provisional
 17-88 1.94e-09

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 57.04  E-value: 1.94e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 21361576   17 TIFQGEVAMVTDYGAFIKI-PGCrkQGLVHRTHMS-SCRVDKPSEIVDVGDKVWVKLigREMKNDRIKVSLSMK 88
Cdd:PRK13806 294 DKVTGKVVRLAPFGAFVEIlPGI--EGLVHVSEMSwTRRVNKPEDVVAPGDAVAVKI--KDIDPAKRRISLSLR 363
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 21-88 7.54e-09

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 55.44  E-value: 7.54e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 21361576   21 GEVAMVTDYGAFIKIPGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMknDRIKVSLSMK 88
Cdd:PRK07899 214 GVVSSIVNFGAFVDLGGV--DGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDM--DRERVSLSLK 277
PRK05807 PRK05807
RNA-binding protein S1;
17-117 1.28e-08

RNA-binding protein S1;


Pssm-ID: 235614 [Multi-domain]  Cd Length: 136  Bit Score: 52.06  E-value: 1.28e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361576   17 TIFQGEVAMVTDYGAFIKIPGcrKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREmknDRIKVSLSMKVVNQgTGK 96
Cdd:PRK05807   7 SILEGTVVNITNFGAFVEVEG--KTGLVHISEVADTYVKDIREHLKEQDKVKVKVISID---DNGKISLSIKQAMK-QKK 80

                         90       100
                 ....*....|....*....|...
gi 21361576   97 DLDPNNVIIEQEERRRR--SFQD 117
Cdd:PRK05807  81 SVKPAEIDWQKEKNKNNngNFED 103
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 17-87 1.35e-08

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: 50.36  E-value: 1.35e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 21361576    17 TIFQGEVAMVTDYGAFIKIpGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIgrEMKNDRIKVSLSM 87
Cdd:pfam00575   5 DVVEGEVTRVTKGGAFVDL-GNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVL--KVDKDRRRIILSI 72
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 14-100 4.53e-08

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 53.12  E-value: 4.53e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361576   14 ALYTIFQGEVAMVTDYGAFIKIP-GCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMknDRIKVSLSMKVVNQ 92
Cdd:PRK07899 292 AIGQIVPGKVTKLVPFGAFVRVEeGI--EGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDL--ERRRISLSLKQANE 367

                         90
                 ....*....|.
gi 21361576   93 G---TGKDLDP 100
Cdd:PRK07899 368 GvtpESEDFDP 378
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 17-88 1.82e-07

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 51.32  E-value: 1.82e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 21361576   17 TIFQGEVAMVTDYGAFIKI-PGCrkQGLVHRTHMS-SCRVDKPSEIVDVGDKVWVKLIGREMKNDRIkvSLSMK 88
Cdd:PRK06299 288 SKVKGKVTNITDYGAFVELeEGI--EGLVHVSEMSwTKKNKHPSKVVSVGQEVEVMVLEIDEEKRRI--SLGLK 357
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 17-88 3.54e-07

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 50.55  E-value: 3.54e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 21361576   17 TIFQGEVAMVTDYGAFIKIPGCRKqGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIkvSLSMK 88
Cdd:PRK06299 462 SIVTGTVTEVKDKGAFVELEDGVE-GLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRI--SLSIK 530
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 17-88 4.96e-07

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: 49.73  E-value: 4.96e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 21361576    17 TIFQGEVAMVTDYGAFIKIPGcRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDriKVSLSMK 88
Cdd:TIGR00717 448 SVVKGKVTEIKDFGAFVELPG-GVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNR--KVSLSVK 516
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
 8-88 5.27e-07

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 49.89  E-value: 5.27e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361576    8 TMenLPALYTIFQG-EVAMVTDYGAFIKI-PGcrKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIgrEMkNDRIKVSL 85
Cdd:PLN00207 748 TM--VPTVGDIYRNcEIKSIAPYGAFVEIaPG--REGLCHISELSSNWLAKPEDAFKVGDRIDVKLI--EV-NDKGQLRL 820


                 ...
gi 21361576   86 SMK 88
Cdd:PLN00207 821 SRR 823
PRK08059 PRK08059
general stress protein 13; Validated
 17-88 1.65e-06

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 45.81  E-value: 1.65e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 21361576   17 TIFQGEVAMVTDYGAFIKIPGcRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIkvSLSMK 88
Cdd:PRK08059   9 SVVTGKVTGIQPYGAFVALDE-ETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKI--SLSIR 77
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 21-85 4.05e-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: 47.04  E-value: 4.05e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 21361576    21 GEVAMVTDYGAFIKIpGCRKQGLVHRTHMS-SCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVSL 85
Cdd:TIGR00717 278 GRVTNLTDYGVFVEI-EEGIEGLVHVSEMSwVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGL 342
PRK08582 PRK08582
RNA-binding protein S1;
20-88 5.81e-06

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 44.64  E-value: 5.81e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 21361576   20 QGEVAMVTDYGAFIKIPGcRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREmknDRIKVSLSMK 88
Cdd:PRK08582  10 QGKVTGITNFGAFVELPE-GKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVE---DDGKIGLSIK 74
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 17-88 1.34e-05

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 45.54  E-value: 1.34e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 21361576   17 TIFQGEVAMVTDYGAFIKIPGCrKQGLVHRTHMS-SCRVDKPSEIVDVGDKVWVKLIGREMKNDRIkvSLSMK 88
Cdd:PRK06299 375 DVVEGKVKNITDFGAFVGLEGG-IDGLVHLSDISwDKKGEEAVELYKKGDEVEAVVLKVDVEKERI--SLGIK 444
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 21-109 2.74e-05

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 44.41  E-value: 2.74e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361576   21 GEVAMVTDYGAFIKIPGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIgrEMKNDRIKVSLSMKVVNQGTGKDL-D 99
Cdd:PRK07400 202 GTVRGIKPYGAFIDIGGV--SGLLHISEISHEHIETPHSVFNVNDEMKVMII--DLDAERGRISLSTKQLEPEPGDMLkD 277

                         90
                 ....*....|
gi 21361576  100 PNNVIIEQEE 109
Cdd:PRK07400 278 PQKVFDKAEE 287
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 17-85 3.33e-05

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: 40.94  E-value: 3.33e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361576  17 TIFQGEVAMVTDYGAFIKIPGcRKQGLVHRTHMS-SCRVDKPSEIVDVGDKVWVKLIgrEMKNDRIKVSL 85
Cdd:cd05690   2 TVVSGKIKSITDFGIFVGLDG-GIDGLVHISDISwTQRVRHPSEIYKKGQEVEAVVL--NIDVERERISL 68
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 20-85 4.78e-05

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 43.93  E-value: 4.78e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 21361576   20 QGEVAMVTDYGAFIKIPGcRKQGLVHRTHMSSCRVDKPSEIVD---VGDKVWVKLIGREMKNDRIKVSL 85
Cdd:PRK12269 757 EGEVSSVTDFGIFVRVPG-GVEGLVRKQHLVENRDGDPGEALRkyaVGDRVKAVIVDMNVKDRKVAFSV 824
S1_RPS1_repeat_ec4 cd05689
S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 21-85 6.48e-05

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: 40.25  E-value: 6.48e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 21361576  21 GEVAMVTDYGAFIKI-PGCrkQGLVHRTHMSSCRVD-KPSEIVDVGDKVWVKLIgrEMKNDRIKVSL 85
Cdd:cd05689   9 GKVTNLTDYGCFVELeEGV--EGLVHVSEMDWTNKNiHPSKVVSLGDEVEVMVL--DIDEERRRISL 71
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 10-91 1.13e-04

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 42.78  E-value: 1.13e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361576   10 ENLPALYTIFQGEVAMVTDYGAFIKIPGcRKQGLVHRTHMSSCR-VDKPSEIVDVGDKVWVKLIGREMKNDRIKVSLSMK 88
Cdd:PRK12269 573 ENKFGVNDVVKGRVTKIADFGAFIELAE-GIEGLAHISEFSWVKkTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQV 651


                 ...
gi 21361576   89 VVN 91
Cdd:PRK12269 652 TAN 654
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 21-75 2.38e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 41.78  E-value: 2.38e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 21361576   21 GEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGRE 75
Cdd:PRK06676  23 GEVLKVEDKQVFVNIEGYKVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVE 77
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
18-84 3.88e-04

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 41.09  E-value: 3.88e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 21361576   18 IFQGEVAMVTDYGAFIKIPGcRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVS 84
Cdd:PRK00087 305 IVKGTVVSVNENEVFVDVGY-KSEGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEDEDGYVVLS 370
S1_RpoE cd04460
S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 18-88 5.73e-04

S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.


Pssm-ID: 239907 [Multi-domain]  Cd Length: 99  Bit Score: 38.04  E-value: 5.73e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361576  18 IFQGEVAMVTDYGAFIKI-PgcrKQGLVHRTHMSSCRVD-----------KPSEIVDVGDKVWVKLIGREMKNDRI---K 82
Cdd:cd04460   2 VVEGEVVEVVDFGAFVRIgP---VDGLLHISQIMDDYISydpknkrligeETKRVLKVGDVVRARIVAVSLKERRPresK 78


                ....*.
gi 21361576  83 VSLSMK 88
Cdd:cd04460  79 IGLTMR 84
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 17-85 7.87e-04

S1_RPS1_repeat_ec6: 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 6 (ec6) 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: 240196 [Multi-domain]  Cd Length: 73  Bit Score: 37.25  E-value: 7.87e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 21361576  17 TIFQGEVAMVTDYGAFIKIpGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVSL 85
Cdd:cd05691   2 SIVTGKVTEVDAKGATVKL-GDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSI 69
PRK08563 PRK08563
DNA-directed RNA polymerase subunit E'; Provisional
 13-88 1.51e-03

DNA-directed RNA polymerase subunit E'; Provisional


Pssm-ID: 236289 [Multi-domain]  Cd Length: 187  Bit Score: 38.27  E-value: 1.51e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361576   13 PALYTIFQGEVAMVTDYGAFIKI-PgcrKQGLVHRTHMSSCRVD-----------KPSEIVDVGDKVWVKLIGREMKNDR 80
Cdd:PRK08563  79 PELQEVVEGEVVEVVEFGAFVRIgP---VDGLLHISQIMDDYISydpkngrligkESKRVLKVGDVVRARIVAVSLKERR 155

                         90
                 ....*....|.
gi 21361576   81 I---KVSLSMK 88
Cdd:PRK08563 156 PrgsKIGLTMR 166
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 18-85 1.68e-03

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: 36.41  E-value: 1.68e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 21361576  18 IFQGEVAMVTDYGAFIKIPGcRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVSL 85
Cdd:cd04461  17 VVHGYVRNITPYGVFVEFLG-GLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL 83
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 21-85 3.80e-03

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 38.15  E-value: 3.80e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 21361576   21 GEVAMVTDYGAFIKIPGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVSL 85
Cdd:PRK12269 499 GVVKSFTSFGAFIDLGGF--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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