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Conserved domains on  [gi|966915965|ref|XP_014988648|]
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nucleolar protein of 40 kDa isoform X3 [Macaca mulatta]

Protein Classification

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 ...
 45-108 6.28e-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: 127.98  E-value: 6.28e-38
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 966915965  45 VAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKnDRIKVSLS 108
Cdd:cd05686   11 VASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMK-DKMKLSLS 73
rpsA super family cl35504
30S ribosomal protein S1; Reviewed
 9-140 4.75e-11

30S ribosomal protein S1; Reviewed


The actual alignment was detected with superfamily member PRK06676:

Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 62.20  E-value: 4.75e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966915965   9 SLSLKATprlcsLKLPFsaEGADSKgWEAGPRMPALVAMVTDYGAFIKI-PGCrkQGLVHRTHMSSCRVDKPSEIVDVGD 87
Cdd:PRK06676 257 SLSLKDT-----LPGPW--EGVEEK-LPEGDVIEGTVKRLTDFGAFVEVlPGV--EGLVHISQISHKHIATPSEVLEEGQ 326

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 966915965  88 KVWVKLIGREMKNDRIkvSLSMkvvnqgtgKDLDPNNviiEQEERRRRSFQDY 140
Cdd:PRK06676 327 EVKVKVLEVNEEEKRI--SLSI--------KALEEAP---AEEEDRREEYRQY 366
 
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 ...
 45-108 6.28e-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: 127.98  E-value: 6.28e-38
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 966915965  45 VAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKnDRIKVSLS 108
Cdd:cd05686   11 VASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMK-DKMKLSLS 73
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 48-110 3.74e-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: 71.23  E-value: 3.74e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 966915965  48 VTDYGAFIKIPGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIkvSLSMK 110
Cdd:COG0539  200 ITDFGAFVDLGGV--DGLLHISEISWGRVKHPSEVLKVGDEVEVKVLKIDREKERI--SLSLK 258
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 48-112 4.62e-13

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 68.54  E-value: 4.62e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 966915965  48 VTDYGAFIKI-PGcrKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGremKNDRIKVSLSMKVV 112
Cdd:PRK11824 632 IVDFGAFVEIlPG--KDGLVHISEIADERVEKVEDVLKEGDEVKVKVLE---IDKRGRIRLSRKAV 692
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 9-140 4.75e-11

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 62.20  E-value: 4.75e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966915965   9 SLSLKATprlcsLKLPFsaEGADSKgWEAGPRMPALVAMVTDYGAFIKI-PGCrkQGLVHRTHMSSCRVDKPSEIVDVGD 87
Cdd:PRK06676 257 SLSLKDT-----LPGPW--EGVEEK-LPEGDVIEGTVKRLTDFGAFVEVlPGV--EGLVHISQISHKHIATPSEVLEEGQ 326

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 966915965  88 KVWVKLIGREMKNDRIkvSLSMkvvnqgtgKDLDPNNviiEQEERRRRSFQDY 140
Cdd:PRK06676 327 EVKVKVLEVNEEEKRI--SLSI--------KALEEAP---AEEEDRREEYRQY 366
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 36-107 1.07e-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: 58.21  E-value: 1.07e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 966915965   36 EAGPRMPALVAMVTDYGAFIKIPGCRkqGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVSL 107
Cdd:TIGR00717 186 KEGDVVKGVVKNITDFGAFVDLGGVD--GLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSL 255
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
48-107 1.01e-08

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 50.68  E-value: 1.01e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 966915965    48 VTDYGAFIKIPGcRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVSL 107
Cdd:smart00316  13 ITPGGAFVDLGN-GVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSL 71
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 36-109 2.92e-07

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: 46.90  E-value: 2.92e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 966915965   36 EAGPRMPALVAMVTDYGAFIKIpGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIgrEMKNDRIKVSLSM 109
Cdd:pfam00575   2 EKGDVVEGEVTRVTKGGAFVDL-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 ...
 45-108 6.28e-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: 127.98  E-value: 6.28e-38
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 966915965  45 VAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKnDRIKVSLS 108
Cdd:cd05686   11 VASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMK-DKMKLSLS 73
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 45-117 3.43e-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: 68.80  E-value: 3.43e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 966915965  45 VAMVTDYGAFIKIPGC--RKQGLVHRTHMSS-CRVDKPSEIVDVGDKVWVKLIGreMKNDRIkvSLSMKVVNQGTG 117
Cdd:cd05684    8 VTSIMDFGCFVQLEGLkgRKEGLVHISQLSFeGRVANPSDVVKRGQKVKVKVIS--IQNGKI--SLSMKDVDQDTG 79
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 48-110 3.74e-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: 71.23  E-value: 3.74e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 966915965  48 VTDYGAFIKIPGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIkvSLSMK 110
Cdd:COG0539  200 ITDFGAFVDLGGV--DGLLHISEISWGRVKHPSEVLKVGDEVEVKVLKIDREKERI--SLSLK 258
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 48-112 4.62e-13

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 68.54  E-value: 4.62e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 966915965  48 VTDYGAFIKI-PGcrKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGremKNDRIKVSLSMKVV 112
Cdd:PRK11824 632 IVDFGAFVEIlPG--KDGLVHISEIADERVEKVEDVLKEGDEVKVKVLE---IDKRGRIRLSRKAV 692
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 45-110 5.52e-13

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 67.98  E-value: 5.52e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 966915965  45 VAMVTDYGAFIKIPGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIkvSLSMK 110
Cdd:PRK06676 200 VARLTDFGAFVDIGGV--DGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERI--SLSLK 261
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 45-109 8.83e-13

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: 61.79  E-value: 8.83e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 966915965  45 VAMVTDYGAFIKI-PGcrKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGremKNDRIKVSLSM 109
Cdd:cd04472    8 VVKIKDFGAFVEIlPG--KDGLVHISELSDERVEKVEDVLKVGDEVKVKVIE---VDDRGRISLSR 68
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 48-110 1.77e-12

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 66.73  E-value: 1.77e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 966915965  48 VTDYGAFIKIPGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIgrEMKNDRIKVSLSMK 110
Cdd:PRK06299 212 ITDYGAFVDLGGV--DGLLHITDISWKRVNHPSEVVNVGDEVKVKVL--KFDKEKKRVSLGLK 270
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 45-108 3.37e-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: 60.34  E-value: 3.37e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 966915965  45 VAMVTDYGAFIKIPGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIgrEMKNDRIKVSLS 108
Cdd:cd05688    9 VKSITDFGAFVDLGGV--DGLLHISDMSWGRVKHPSEVVNVGDEVEVKVL--KIDKERKRISLG 68
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 9-110 4.65e-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: 65.07  E-value: 4.65e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966915965   9 SLSLKATprlcsLKLPFsaEGADSKgWEAGPRMPALVAMVTDYGAFIKI-PGCrkQGLVHRTHMS-SCRVDKPSEIVDVG 86
Cdd:COG0539  254 SLSLKQL-----QPDPW--ENIAEK-YPVGDVVKGKVTRLTDFGAFVELePGV--EGLVHISEMSwTKRVAHPSDVVKVG 323

                         90       100
                 ....*....|....*....|....
gi 966915965  87 DKVWVKLIgrEMKNDRIKVSLSMK 110
Cdd:COG0539  324 DEVEVKVL--DIDPEERRISLSIK 345
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 45-110 4.75e-12

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: 59.99  E-value: 4.75e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 966915965  45 VAMVTDYGAFIKIPGcRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREmknDRIKVSLSMK 110
Cdd:cd05692    8 VTRLKPFGAFVELGG-GISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSID---ARGRISLSIK 69
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 45-106 3.29e-11

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: 57.63  E-value: 3.29e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 966915965  45 VAMVTDYGAFIKIpGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVS 106
Cdd:cd05685    8 VTNVTDFGAFVDI-GVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 45-106 3.86e-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: 57.39  E-value: 3.86e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 966915965  45 VAMVTDYGAFIKIPGcRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVS 106
Cdd:cd00164    5 VVSITKFGVFVELED-GVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 9-140 4.75e-11

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 62.20  E-value: 4.75e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966915965   9 SLSLKATprlcsLKLPFsaEGADSKgWEAGPRMPALVAMVTDYGAFIKI-PGCrkQGLVHRTHMSSCRVDKPSEIVDVGD 87
Cdd:PRK06676 257 SLSLKDT-----LPGPW--EGVEEK-LPEGDVIEGTVKRLTDFGAFVEVlPGV--EGLVHISQISHKHIATPSEVLEEGQ 326

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 966915965  88 KVWVKLIGREMKNDRIkvSLSMkvvnqgtgKDLDPNNviiEQEERRRRSFQDY 140
Cdd:PRK06676 327 EVKVKVLEVNEEEKRI--SLSI--------KALEEAP---AEEEDRREEYRQY 366
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
48-118 3.79e-10

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 59.65  E-value: 3.79e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 966915965  48 VTDYGAFIKIpGCrKQ-GLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIkvSLSMKVVNQGTGK 118
Cdd:COG2183  652 VTDFGAFVDI-GV-HQdGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEVDLKRKRI--SLSMKLDDEAGAA 719
rpsA PRK13806
30S ribosomal protein S1; Provisional
 38-110 4.50e-10

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 59.35  E-value: 4.50e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 966915965  38 GPRMPALVAMVTDYGAFIKI-PGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKL--IGREMKNDRIKVSLSMK 110
Cdd:PRK13806 203 GDVVEGTVTRLAPFGAFVELaPGV--EGMVHISELSWSRVQKADEAVSVGDTVRVKVlgIERAKKGKGLRISLSIK 276
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 36-110 6.02e-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: 6.02e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 966915965  36 EAGPRMPALVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIgrEMKNDRIKVSLSMK 110
Cdd:cd05708    1 KVGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVL--KIDAEKKRISLGLK 73
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 48-152 6.56e-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: 55.57  E-value: 6.56e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966915965  48 VTDYGAFIKIPGcRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREmknDRIKVSLSMkvvnqgtgKDLDPNNvii 127
Cdd:COG1098   16 ITPFGAFVELPE-GTTGLVHISEIADGYVKDINDYLKVGDEVKVKVLSID---EDGKISLSI--------KQAEEKP--- 80

                         90       100
                 ....*....|....*....|....*
gi 966915965 128 EQEERRRRSFQDYTGQKiTLEAVLN 152
Cdd:COG1098   81 KRPPRPRRNSRPKAGFE-SFEDKLS 104
rpsA PRK13806
30S ribosomal protein S1; Provisional
 10-110 8.43e-10

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 58.58  E-value: 8.43e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966915965  10 LSLKATPRLCSLKLPFSAEGADSKGW-------EAGPRMPALVAMVTDYGAFIKI-PGCrkQGLVHRTHMS-SCRVDKPS 80
Cdd:PRK13806 258 LGIERAKKGKGLRISLSIKQAGGDPWdtvgdrlKAGDKVTGKVVRLAPFGAFVEIlPGI--EGLVHVSEMSwTRRVNKPE 335

                         90       100       110
                 ....*....|....*....|....*....|
gi 966915965  81 EIVDVGDKVWVKLigREMKNDRIKVSLSMK 110
Cdd:PRK13806 336 DVVAPGDAVAVKI--KDIDPAKRRISLSLR 363
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 36-107 1.07e-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: 58.21  E-value: 1.07e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 966915965   36 EAGPRMPALVAMVTDYGAFIKIPGCRkqGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVSL 107
Cdd:TIGR00717 186 KEGDVVKGVVKNITDFGAFVDLGGVD--GLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSL 255
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
45-110 1.15e-09

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: 1.15e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 966915965  45 VAMVTDYGAFIKIPGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIG--REMKndriKVSLSMK 110
Cdd:PRK00087 485 VKRLTDFGAFVDIGGV--DGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDidKENK----KLSLSLK 546
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
45-131 6.63e-09

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 56.11  E-value: 6.63e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966915965  45 VAMVTDYGAFIKI-PGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVSLsmkvvnqgtgKDLDPN 123
Cdd:PRK00087 570 VVRIAPFGAFVELePGV--DGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSI----------KEVEEE 637


                 ....*...
gi 966915965 124 NVIIEQEE 131
Cdd:PRK00087 638 PGDIEKVE 645
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
48-107 1.01e-08

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 50.68  E-value: 1.01e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 966915965    48 VTDYGAFIKIPGcRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVSL 107
Cdd:smart00316  13 ITPGGAFVDLGN-GVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSL 71
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 42-110 2.38e-08

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 54.28  E-value: 2.38e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 966915965  42 PALVAMVTDYGAFIKIPGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMknDRIKVSLSMK 110
Cdd:PRK07899 213 KGVVSSIVNFGAFVDLGGV--DGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDM--DRERVSLSLK 277
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 9-122 3.79e-08

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 53.51  E-value: 3.79e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966915965   9 SLSLKAT---PrlcslklpfsaegadskgWEAGPR-------MPALVAMVTDYGAFIKIP-GCrkQGLVHRTHMSSCRVD 77
Cdd:PRK07899 273 SLSLKATqedP------------------WQQFARthaigqiVPGKVTKLVPFGAFVRVEeGI--EGLVHISELAERHVE 332

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 966915965  78 KPSEIVDVGDKVWVKLIGREMknDRIKVSLSMKVVNQG---TGKDLDP 122
Cdd:PRK07899 333 VPEQVVQVGDEVFVKVIDIDL--ERRRISLSLKQANEGvtpESEDFDP 378
PRK05807 PRK05807
RNA-binding protein S1;
36-139 9.42e-08

RNA-binding protein S1;


Pssm-ID: 235614 [Multi-domain]  Cd Length: 136  Bit Score: 49.74  E-value: 9.42e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966915965  36 EAGPRMPALVAMVTDYGAFIKIPGcrKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREmknDRIKVSLSMKVVNQg 115
Cdd:PRK05807   4 KAGSILEGTVVNITNFGAFVEVEG--KTGLVHISEVADTYVKDIREHLKEQDKVKVKVISID---DNGKISLSIKQAMK- 77

                         90       100
                 ....*....|....*....|....*.
gi 966915965 116 TGKDLDPNNVIIEQEERRRR--SFQD 139
Cdd:PRK05807  78 QKKSVKPAEIDWQKEKNKNNngNFED 103
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 36-109 2.92e-07

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: 46.90  E-value: 2.92e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 966915965   36 EAGPRMPALVAMVTDYGAFIKIpGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIgrEMKNDRIKVSLSM 109
Cdd:pfam00575   2 EKGDVVEGEVTRVTKGGAFVDL-GNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVL--KVDKDRRRIILSI 72
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 9-110 1.24e-06

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 49.01  E-value: 1.24e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966915965   9 SLSLKATprlcslklpfsaeGADSkgWEA-------GPRMPALVAMVTDYGAFIKI-PGCrkQGLVHRTHMS-SCRVDKP 79
Cdd:PRK06299 266 SLGLKQL-------------GEDP--WEAiekkypvGSKVKGKVTNITDYGAFVELeEGI--EGLVHVSEMSwTKKNKHP 328

                         90       100       110
                 ....*....|....*....|....*....|.
gi 966915965  80 SEIVDVGDKVWVKLIGREMKNDRIkvSLSMK 110
Cdd:PRK06299 329 SKVVSVGQEVEVMVLEIDEEKRRI--SLGLK 357
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 9-107 3.48e-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: 47.81  E-value: 3.48e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966915965    9 SLSLKATprlcslklpfsaegaDSKGWEA-------GPRMPALVAMVTDYGAFIKIpGCRKQGLVHRTHMS-SCRVDKPS 80
Cdd:TIGR00717 252 SLSLKQL---------------GEDPWEAiekkfpvGDKITGRVTNLTDYGVFVEI-EEGIEGLVHVSEMSwVKKNSHPS 315

                          90       100
                  ....*....|....*....|....*..
gi 966915965   81 EIVDVGDKVWVKLIGREMKNDRIKVSL 107
Cdd:TIGR00717 316 KVVKKGDEVEVMILDIDPERRRLSLGL 342
PRK08582 PRK08582
RNA-binding protein S1;
36-110 1.12e-05

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 43.87  E-value: 1.12e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 966915965  36 EAGPRMPALVAMVTDYGAFIKIPGcRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREmknDRIKVSLSMK 110
Cdd:PRK08582   4 EVGSKLQGKVTGITNFGAFVELPE-GKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVE---DDGKIGLSIK 74
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
 45-110 1.46e-05

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 46.04  E-value: 1.46e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 966915965  45 VAMVTDYGAFIKI-PGcrKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIgrEMkNDRIKVSLSMK 110
Cdd:PLN00207 762 IKSIAPYGAFVEIaPG--REGLCHISELSSNWLAKPEDAFKVGDRIDVKLI--EV-NDKGQLRLSRR 823
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 45-110 1.51e-05

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 45.93  E-value: 1.51e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 966915965  45 VAMVTDYGAFIKIPGCRKqGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIkvSLSMK 110
Cdd:PRK06299 468 VTEVKDKGAFVELEDGVE-GLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRI--SLSIK 530
S1_RPS1_repeat_ec4 cd05689
S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 35-107 2.60e-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: 41.41  E-value: 2.60e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 966915965  35 WEAGPRMPALVAMVTDYGAFIKI-PGCrkQGLVHRTHMSSCRVD-KPSEIVDVGDKVWVKLIgrEMKNDRIKVSL 107
Cdd:cd05689    1 YPEGTRLFGKVTNLTDYGCFVELeEGV--EGLVHVSEMDWTNKNiHPSKVVSLGDEVEVMVL--DIDEERRRISL 71
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 43-110 2.73e-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: 2.73e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 966915965   43 ALVAMVTDYGAFIKIPGcRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDriKVSLSMK 110
Cdd:TIGR00717 452 GKVTEIKDFGAFVELPG-GVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNR--KVSLSVK 516
PRK08059 PRK08059
general stress protein 13; Validated
 45-110 4.91e-05

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 41.96  E-value: 4.91e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 966915965  45 VAMVTDYGAFIKIPGcRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIkvSLSMK 110
Cdd:PRK08059  15 VTGIQPYGAFVALDE-ETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKI--SLSIR 77
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 34-131 7.48e-05

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 43.25  E-value: 7.48e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966915965  34 GWEAGPRMPALVAMVTDYGAFIKIPGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIgrEMKNDRIKVSLSMKVVN 113
Cdd:PRK07400 193 RLEVGEVVVGTVRGIKPYGAFIDIGGV--SGLLHISEISHEHIETPHSVFNVNDEMKVMII--DLDAERGRISLSTKQLE 268

                         90
                 ....*....|....*....
gi 966915965 114 QGTGKDL-DPNNVIIEQEE 131
Cdd:PRK07400 269 PEPGDMLkDPQKVFDKAEE 287
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 38-107 1.46e-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: 39.01  E-value: 1.46e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 966915965  38 GPRMPALVAMVTDYGAFIKIPGcRKQGLVHRTHMS-SCRVDKPSEIVDVGDKVWVKLIgrEMKNDRIKVSL 107
Cdd:cd05690    1 GTVVSGKIKSITDFGIFVGLDG-GIDGLVHISDISwTQRVRHPSEIYKKGQEVEAVVL--NIDVERERISL 68
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 45-110 7.29e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 40.53  E-value: 7.29e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 966915965  45 VAMVTDYGAFIKIPGCrKQGLVHRTHMS-SCRVDKPSEIVDVGDKVWVKLIGREMKNDRIkvSLSMK 110
Cdd:PRK06299 381 VKNITDFGAFVGLEGG-IDGLVHLSDISwDKKGEEAVELYKKGDEVEAVVLKVDVEKERI--SLGIK 444
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 32-107 1.71e-03

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 39.70  E-value: 1.71e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 966915965  32 SKGWEAGPRMPALVAMVTDYGAFIKIPGcRKQGLVHRTHMSSCRVDKPSEIVD---VGDKVWVKLIGREMKNDRIKVSL 107
Cdd:PRK12269 747 ANAYGVGSTVEGEVSSVTDFGIFVRVPG-GVEGLVRKQHLVENRDGDPGEALRkyaVGDRVKAVIVDMNVKDRKVAFSV 824
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 25-97 3.22e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 38.32  E-value: 3.22e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 966915965  25 FSAEGADSKGWEAGPRMPALVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGRE 97
Cdd:PRK06676   5 FEESLNSVKEVEVGDVVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVE 77
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 41-107 3.46e-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: 35.64  E-value: 3.46e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 966915965  41 MPALVAMVTDYGAFIKIPGcRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVSL 107
Cdd:cd04461   18 VHGYVRNITPYGVFVEFLG-GLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL 83
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 45-113 3.91e-03

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 38.54  E-value: 3.91e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966915965  45 VAMVTDYGAFIKIPGcRKQGLVHRTHMSSCR-VDKPSEIVDVGDKVWVKLIGREMKNDRIKVSLSMKVVN 113
Cdd:PRK12269 586 VTKIADFGAFIELAE-GIEGLAHISEFSWVKkTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQVTAN 654
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
48-106 7.80e-03

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 37.23  E-value: 7.80e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 966915965  48 VTDYGAFIKIPGcRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVS 106
Cdd:PRK00087 313 VNENEVFVDVGY-KSEGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEDEDGYVVLS 370
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 43-107 8.92e-03

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 37.38  E-value: 8.92e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 966915965  43 ALVAMVTDYGAFIKIPGCrkQGLVHRTHMSSCRVDKPSEIVDVGDKVWVKLIGREMKNDRIKVSL 107
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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