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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1720409447   2 GLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKnDRIKVSLS 46
Cdd:cd05686    30 GLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMK-DKMKLSLS 73

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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1720409447   2 GLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKnDRIKVSLS 46
Cdd:cd05686    30 GLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMK-DKMKLSLS 73

polynucleotide phosphorylase/polyadenylase; Provisional

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1720409447   2 GLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGremKNDRIKVSLSMKVV 50
Cdd:PRK11824  647 GLVHISEIADERVEKVEDVLKEGDEVKVKVLE---IDKRGRIRLSRKAV 692

Ribosomal protein S1-like RNA-binding domain;

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 1720409447    2 GLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVSL 45
Cdd:smart00316  28 GLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSL 71

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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1720409447   2 GLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKnDRIKVSLS 46
Cdd:cd05686    30 GLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMK-DKMKLSLS 73

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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1720409447   2 GLVHRTHMSS-CRVDKPSEIVDVGDKVWVKLIGreMKNDRIkvSLSMKVVNQGTG 55
Cdd:cd05684    29 GLVHISQLSFeGRVANPSDVVKRGQKVKVKVIS--IQNGKI--SLSMKDVDQDTG 79

30S ribosomal protein S1; Reviewed

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1720409447   2 GLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIgrEMKNDRIKVSLSMK 48
Cdd:PRK06299  226 GLLHITDISWKRVNHPSEVVNVGDEVKVKVL--KFDKEKKRVSLGLK 270

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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1720409447   2 GLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGremKNDRIKVSLSM 47
Cdd:cd04472    26 GLVHISELSDERVEKVEDVLKVGDEVKVKVIE---VDDRGRISLSR 68

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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1720409447   2 GLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIgrEMKNDRIKVSLS 46
Cdd:cd05688    26 GLLHISDMSWGRVKHPSEVVNVGDEVEVKVL--KIDKERKRISLG 68

30S ribosomal protein S1; Reviewed

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1720409447   2 GLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMknDRIKVSLSMK 48
Cdd:PRK07899  233 GLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDM--DRERVSLSLK 277

30S ribosomal protein S1; Reviewed

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1720409447   2 GLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMknDRIKVSLSMKVVNQG---TGKDLDP 60
Cdd:PRK07899  319 GLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDL--ERRRISLSLKQANEGvtpESEDFDP 378

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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1720409447   2 GLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREmknDRIKVSLSMK 48
Cdd:cd05692    26 GLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSID---ARGRISLSIK 69

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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1720409447   2 GLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVS 44
Cdd:cd05685    26 GLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68

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]

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1720409447   2 GLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVSL 45
Cdd:TIGR00717 212 GLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSL 255

30S ribosomal protein S1; Provisional

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1720409447   2 GLVHRTHMS-SCRVDKPSEIVDVGDKVWVKLigREMKNDRIKVSLSMK 48
Cdd:PRK13806  318 GLVHVSEMSwTRRVNKPEDVVAPGDAVAVKI--KDIDPAKRRISLSLR 363

30S ribosomal protein S1; Reviewed

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1720409447   1 MGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIkvSLSMK 48
Cdd:PRK06299  485 EGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRI--SLSIK 530

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

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1720409447   2 GLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREmknDRIKVSLSMK 48
Cdd:COG1098    31 GLVHISEIADGYVKDINDYLKVGDEVKVKVLSID---EDGKISLSIK 74