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Conserved domains on  [gi|1278342979|gb|PIY84962|]
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MAG: RNA-binding protein S1 [Candidatus Omnitrophica bacterium CG_4_10_14_0_8_um_filter_43_18]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 18-117 2.36e-31

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


:

Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 107.96  E-value: 2.36e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278342979  18 IGETVEVEVIKITDFGAFVKFSDNRRGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVSGDGKIDLTLKAAKEETVSAG 97
Cdd:COG1098     5 VGDIVEGKVTGITPFGAFVELPEGTTGLVHISEIADGYVKDINDYLKVGDEVKVKVLSIDEDGKISLSIKQAEEKPKRPP 84

                          90       100
                  ....*....|....*....|....
gi 1278342979  98 PKNKEFRTNV----FEEKFNAYLK 117
Cdd:COG1098    85 RPRRNSRPKAgfesFEDKLSKFLK 108
 
Name Accession Description Interval E-value
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 18-117 2.36e-31

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


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 107.96  E-value: 2.36e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278342979  18 IGETVEVEVIKITDFGAFVKFSDNRRGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVSGDGKIDLTLKAAKEETVSAG 97
Cdd:COG1098     5 VGDIVEGKVTGITPFGAFVELPEGTTGLVHISEIADGYVKDINDYLKVGDEVKVKVLSIDEDGKISLSIKQAEEKPKRPP 84

                          90       100
                  ....*....|....*....|....
gi 1278342979  98 PKNKEFRTNV----FEEKFNAYLK 117
Cdd:COG1098    85 RPRRNSRPKAgfesFEDKLSKFLK 108
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 16-89 1.67e-24

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 96.66  E-value: 1.67e-24
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1278342979  16 PAIGETVEVEVIKITDFGAFVKFSDNRRGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVSGDGKIDLTLKAA 89
Cdd:PRK11824  619 PEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEIDKRGRIRLSRKAV 692
S1_dom_CvfD NF040579
CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ...
 18-106 2.42e-21

CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a family of full-length homologs of RNA-binding proteins from the Firmicutes with a single copy of the S1 domain. Several members of the family have been characterized as general stress proteins, and the most recently characterized, CvfD, was shown to act as a post-transcriptional regulator.


Pssm-ID: 468553 [Multi-domain]  Cd Length: 113  Bit Score: 81.70  E-value: 2.42e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278342979  18 IGETVEVEVIKITDFGAFVKFSDNRRGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQV-SGDGKIDLTLKAAKEETVSA 96
Cdd:NF040579    3 IGDIVEGKVTGIQPYGAFVALDEHTQGLIHISEIKHGYVKDINDFLKVGQEVKVKVLDIdEYTGKISLSLRALEEAPEKH 82

                          90
                  ....*....|
gi 1278342979  97 GPKNKEFRTN 106
Cdd:NF040579   83 RKRRKHRWTN 92
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 19-87 2.61e-19

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: 75.40  E-value: 2.61e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1278342979  19 GETVEVEVIKITDFGAFVKFSDNRRGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVSGDGKIDLTLK 87
Cdd:cd05692     1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARGRISLSIK 69
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
18-87 4.49e-17

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 69.94  E-value: 4.49e-17
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1278342979   18 IGETVEVEVIKITDFGAFVKFSDNRRGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQV-SGDGKIDLTLK 87
Cdd:smart00316   2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVdEEKGRIILSLK 72
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 16-86 1.38e-10

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: 53.06  E-value: 1.38e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1278342979  16 PAIGETVEVEVIKITDFGAFVKFSDNRRGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVSGD-GKIDLTL 86
Cdd:pfam00575   1 PEKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDrRRIILSI 72
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 2-87 6.33e-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: 52.43  E-value: 6.33e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278342979   2 PYQNHKNKKRniilpaIGETVEVEVIKITDFGAFVKFSDNRRGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVS-GDG 80
Cdd:TIGR00717 436 PWEKFAAKYK------VGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDkKNR 509


                  ....*..
gi 1278342979  81 KIDLTLK 87
Cdd:TIGR00717 510 KVSLSVK 516
 
Name Accession Description Interval E-value
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 18-117 2.36e-31

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


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 107.96  E-value: 2.36e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278342979  18 IGETVEVEVIKITDFGAFVKFSDNRRGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVSGDGKIDLTLKAAKEETVSAG 97
Cdd:COG1098     5 VGDIVEGKVTGITPFGAFVELPEGTTGLVHISEIADGYVKDINDYLKVGDEVKVKVLSIDEDGKISLSIKQAEEKPKRPP 84

                          90       100
                  ....*....|....*....|....
gi 1278342979  98 PKNKEFRTNV----FEEKFNAYLK 117
Cdd:COG1098    85 RPRRNSRPKAgfesFEDKLSKFLK 108
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 16-89 1.67e-24

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 96.66  E-value: 1.67e-24
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1278342979  16 PAIGETVEVEVIKITDFGAFVKFSDNRRGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVSGDGKIDLTLKAA 89
Cdd:PRK11824  619 PEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEIDKRGRIRLSRKAV 692
Pnp COG1185
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ...
 16-88 1.06e-23

Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440798 [Multi-domain]  Cd Length: 686  Bit Score: 94.69  E-value: 1.06e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1278342979  16 PAIGETVEVEVIKITDFGAFVKFSDNRRGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVSGDGKIDLTLKA 88
Cdd:COG1185   614 PEVGEIYEGKVVRIMDFGAFVEILPGKDGLVHISELADERVEKVEDVLKEGDEVKVKVLEIDDQGRIKLSRKA 686
PRK08582 PRK08582
RNA-binding protein S1;
18-117 4.03e-22

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 84.70  E-value: 4.03e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278342979  18 IGETVEVEVIKITDFGAFVKFSDNRRGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVSGDGKIDLTLKAAKEETVSAG 97
Cdd:PRK08582    5 VGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDDGKIGLSIKKAKDRPKRQH 84

                          90       100       110
                  ....*....|....*....|....*....|
gi 1278342979  98 PKNKEFRTNV----------FEEKFNAYLK 117
Cdd:PRK08582   85 DRPRHEDNRGggndvapkedFEQKMSRFLK 114
S1_dom_CvfD NF040579
CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ...
 18-106 2.42e-21

CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a family of full-length homologs of RNA-binding proteins from the Firmicutes with a single copy of the S1 domain. Several members of the family have been characterized as general stress proteins, and the most recently characterized, CvfD, was shown to act as a post-transcriptional regulator.


Pssm-ID: 468553 [Multi-domain]  Cd Length: 113  Bit Score: 81.70  E-value: 2.42e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278342979  18 IGETVEVEVIKITDFGAFVKFSDNRRGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQV-SGDGKIDLTLKAAKEETVSA 96
Cdd:NF040579    3 IGDIVEGKVTGIQPYGAFVALDEHTQGLIHISEIKHGYVKDINDFLKVGQEVKVKVLDIdEYTGKISLSLRALEEAPEKH 82

                          90
                  ....*....|
gi 1278342979  97 GPKNKEFRTN 106
Cdd:NF040579   83 RKRRKHRWTN 92
PRK05807 PRK05807
RNA-binding protein S1;
19-118 6.42e-20

RNA-binding protein S1;


Pssm-ID: 235614 [Multi-domain]  Cd Length: 136  Bit Score: 79.02  E-value: 6.42e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278342979  19 GETVEVEVIKITDFGAFVKFsDNRRGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVSGDGKIDLTLKAAKEETVSAGP 98
Cdd:PRK05807    6 GSILEGTVVNITNFGAFVEV-EGKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDDNGKISLSIKQAMKQKKSVKP 84

                          90       100
                  ....*....|....*....|....*..
gi 1278342979  99 K----NKEFRTNV---FEEKFNAYLKN 118
Cdd:PRK05807   85 AeidwQKEKNKNNngnFEDRLSKFLKD 111
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 19-87 2.61e-19

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: 75.40  E-value: 2.61e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1278342979  19 GETVEVEVIKITDFGAFVKFSDNRRGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVSGDGKIDLTLK 87
Cdd:cd05692     1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARGRISLSIK 69
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 19-85 6.31e-18

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: 71.80  E-value: 6.31e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1278342979  19 GETVEVEVIKITDFGAFVKFSDNRRGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVSGDGKIDLT 85
Cdd:cd04472     1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDDRGRISLS 67
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
18-87 4.49e-17

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 69.94  E-value: 4.49e-17
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1278342979   18 IGETVEVEVIKITDFGAFVKFSDNRRGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQV-SGDGKIDLTLK 87
Cdd:smart00316   2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVdEEKGRIILSLK 72
PRK08059 PRK08059
general stress protein 13; Validated
 18-113 6.16e-17

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 70.85  E-value: 6.16e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278342979  18 IGETVEVEVIKITDFGAFVKFSDNRRGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVSGD-GKIDLTLKAAKEETVSA 96
Cdd:PRK08059    7 VGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEkGKISLSIRATEEAPEAK 86

                          90
                  ....*....|....*..
gi 1278342979  97 GPKNKEFRTNVFEEKFN 113
Cdd:PRK08059   87 RKKGKILIPNPSEQGFN 103
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 16-87 5.98e-15

S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to complete the initiation complex, which is competent to begin translation. The IF2a subunit is a major site of control of the translation initiation process, via phosphorylation of a specific serine residue. This alpha subunit is well conserved in eukaryotes and archaea but is not present in bacteria. IF2 is a cold-shock-inducible protein.


Pssm-ID: 239899 [Multi-domain]  Cd Length: 76  Bit Score: 64.53  E-value: 5.98e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1278342979  16 PAIGETVEVEVIKITDFGAFVKFS--DNRRGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVSGD-GKIDLTLK 87
Cdd:cd04452     1 PEEGELVVVTVKSIADMGAYVSLLeyGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEkGYIDLSKK 75
PRK08563 PRK08563
DNA-directed RNA polymerase subunit E'; Provisional
 16-87 4.81e-14

DNA-directed RNA polymerase subunit E'; Provisional


Pssm-ID: 236289 [Multi-domain]  Cd Length: 187  Bit Score: 64.85  E-value: 4.81e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278342979  16 PAIGETVEVEVIKITDFGAFVKFS--DnrrGLIHISQIAEDYV-----------KNVTDHLNIGDKVSARVVQVS----- 77
Cdd:PRK08563   79 PELQEVVEGEVVEVVEFGAFVRIGpvD---GLLHISQIMDDYIsydpkngrligKESKRVLKVGDVVRARIVAVSlkerr 155

                          90
                  ....*....|.
gi 1278342979  78 -GDGKIDLTLK 87
Cdd:PRK08563  156 pRGSKIGLTMR 166
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 17-118 5.05e-14

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 66.73  E-value: 5.05e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278342979  17 AIGETVEVEVIKITDFGAFVKFSDNRRGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVSGDGK-IDLTLKA---AKEE 92
Cdd:PRK06299  459 KKGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRrISLSIKAldeAEEK 538

                          90       100
                  ....*....|....*....|....*.
gi 1278342979  93 TVSAGPKNKEFRTNVFEEKFNAYLKN 118
Cdd:PRK06299  539 EAIAEYNSASDSKTTLGDLLKAALKG 564
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
18-92 1.24e-13

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 65.74  E-value: 1.24e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1278342979  18 IGETVEVEVIKITDFGAFVKFSDNRRGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVSGDGK-IDLTLKAAKEE 92
Cdd:PRK00087  562 VGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKrIRLSIKEVEEE 637
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 15-87 1.78e-13

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 64.46  E-value: 1.78e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1278342979  15 LPAIGETVEVEVIKITDFGAFVKFS--DNRRGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVSGD-GKIDLTLK 87
Cdd:PRK03987    5 WPEEGELVVGTVKEVKDFGAFVTLDeyPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRkGHIDLSLK 80
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 18-90 1.96e-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: 65.07  E-value: 1.96e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1278342979  18 IGETVEVEVIKITDFGAFVKFSDNRRGLIHISQIAED-YVKNVTDHLNIGDKVSARVVQVSGDGK-IDLTLKAAK 90
Cdd:COG0539   274 VGDVVKGKVTRLTDFGAFVELEPGVEGLVHISEMSWTkRVAHPSDVVKVGDEVEVKVLDIDPEERrISLSIKQLA 348
S1_RpoE cd04460
S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 20-87 2.70e-13

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: 60.76  E-value: 2.70e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278342979  20 ETVEVEVIKITDFGAFVKFS--DnrrGLIHISQIAEDYV-----------KNVTDHLNIGDKVSARVVQVS------GDG 80
Cdd:cd04460     1 EVVEGEVVEVVDFGAFVRIGpvD---GLLHISQIMDDYIsydpknkrligEETKRVLKVGDVVRARIVAVSlkerrpRES 77


                  ....*..
gi 1278342979  81 KIDLTLK 87
Cdd:cd04460    78 KIGLTMR 84
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 17-111 9.52e-13

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 62.97  E-value: 9.52e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278342979  17 AIGETVEVEVIKITDFGAFVKFSDNRRGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVSGDGK-IDLTLKAAKEETVS 95
Cdd:PRK06676  276 PEGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKrISLSIKALEEAPAE 355

                          90
                  ....*....|....*.
gi 1278342979  96 AGPKNKEFRTNVFEEK 111
Cdd:PRK06676  356 EEDRREEYRQYELPEE 371
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 22-85 2.08e-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: 57.78  E-value: 2.08e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1278342979  22 VEVEVIKITDFGAFVKFSDNRRGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVS-GDGKIDLT 85
Cdd:cd00164     1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDpEKGRISLS 65
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
29-93 3.14e-12

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 61.58  E-value: 3.14e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1278342979  29 ITDFGAFV----KfSDnrrGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVsgD---GKIDLTLKAAKEET 93
Cdd:COG2183   652 VTDFGAFVdigvH-QD---GLVHISQLSDRFVKDPREVVKVGDIVKVKVLEV--DlkrKRISLSMKLDDEAG 717
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 17-89 4.51e-11

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: 54.64  E-value: 4.51e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1278342979  17 AIGETVEVEVIKITDFGAFVKF-SDNRRGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVSGD-GKIDLTLKAA 89
Cdd:cd05708     1 KVGQKIDGTVRRVEDYGVFIDIdGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEkKRISLGLKAS 75
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 19-85 5.98e-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: 54.16  E-value: 5.98e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1278342979  19 GETVEVEVIKITDFGAFVKFSDNRRGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVS-GDGKIDLT 85
Cdd:cd05685     1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDeERGRISLS 68
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 19-92 6.71e-11

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 57.96  E-value: 6.71e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1278342979  19 GETVEVEVIKITDFGAFVKFS--DnrrGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVSGD-GKIDLTLKAAKEE 92
Cdd:PRK06676  193 GDVVEGTVARLTDFGAFVDIGgvD---GLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWEtERISLSLKDTLPG 266
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
18-92 7.72e-11

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 55.09  E-value: 7.72e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1278342979  18 IGETVEVEVIKITDFGAFVKFSDNRRGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVSG-DGKIDLTLKAAKEE 92
Cdd:PRK07252    3 IGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEyTGKASLSLRTLEEE 78
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 17-103 8.45e-11

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 57.75  E-value: 8.45e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278342979  17 AIGETVEVEVIKITDFGAFVKFSDNRRGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVSGDG-KIDLTLKAAKEetvS 95
Cdd:PRK07899  292 AIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLERrRISLSLKQANE---G 368


                  ....*...
gi 1278342979  96 AGPKNKEF 103
Cdd:PRK07899  369 VTPESEDF 376
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 16-86 1.38e-10

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: 53.06  E-value: 1.38e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1278342979  16 PAIGETVEVEVIKITDFGAFVKFSDNRRGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVSGD-GKIDLTL 86
Cdd:pfam00575   1 PEKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDrRRIILSI 72
S1_pNO40 cd05686
S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function ...
 16-87 3.70e-10

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: 52.10  E-value: 3.70e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1278342979  16 PAIGETVEVEVIKITDFGAFVKFSDNRR-GLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVSGDGKIDLTLK 87
Cdd:cd05686     1 PALYQIFKGEVASVTEYGAFVKIPGCRKqGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKDKMKLSLS 73
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
19-88 1.43e-09

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 54.18  E-value: 1.43e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1278342979  19 GETVEVEVIKITDFGAFVKFsDNRRGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVSGD-GKIDLTLKA 88
Cdd:PRK00087  478 GDVVEGEVKRLTDFGAFVDI-GGVDGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKEnKKLSLSLKK 547
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
 7-102 1.46e-09

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 54.13  E-value: 1.46e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278342979   7 KNKKRNI-ILPAIGETVE-VEVIKITDFGAFVKFSDNRRGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVSGDGKIDL 84
Cdd:PLN00207  741 KAIISSLtMVPTVGDIYRnCEIKSIAPYGAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVNDKGQLRL 820

                          90
                  ....*....|....*...
gi 1278342979  85 TLKAAKEETVSAGPKNKE 102
Cdd:PLN00207  821 SRRALLPEANSEKSSQKQ 838
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 26-87 1.89e-09

S1_Rrp5_repeat_hs6_sc5: 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 H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240203 [Multi-domain]  Cd Length: 70  Bit Score: 50.30  E-value: 1.89e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1278342979  26 VIKITDFGAFVKFSDNRRGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQV-SGDGKIDLTLK 87
Cdd:cd05698     8 IVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCdPEQQRLLLSCK 70
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 26-87 2.03e-09

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: 50.32  E-value: 2.03e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1278342979  26 VIKITDFGAFVKFSDNRR---GLIHISQIAED-YVKNVTDHLNIGDKVSARVVQVSGdGKIDLTLK 87
Cdd:cd05684     8 VTSIMDFGCFVQLEGLKGrkeGLVHISQLSFEgRVANPSDVVKRGQKVKVKVISIQN-GKISLSMK 72
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 18-91 2.27e-09

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: 53.51  E-value: 2.27e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1278342979  18 IGETVEVEVIKITDFGAFVKFS--DnrrGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVSGD-GKIDLTLKAAKE 91
Cdd:COG0539   189 EGDVVEGTVKNITDFGAFVDLGgvD---GLLHISEISWGRVKHPSEVLKVGDEVEVKVLKIDREkERISLSLKQLQP 262
rpsA PRK13806
30S ribosomal protein S1; Provisional
 19-92 4.87e-09

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 52.80  E-value: 4.87e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1278342979  19 GETVEVEVIKITDFGAFVKFSDNRRGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVSGDGK-----IDLTLKAAKEE 92
Cdd:PRK13806  203 GDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKgkglrISLSIKQAGGD 281
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 2-87 6.33e-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: 52.43  E-value: 6.33e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278342979   2 PYQNHKNKKRniilpaIGETVEVEVIKITDFGAFVKFSDNRRGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVS-GDG 80
Cdd:TIGR00717 436 PWEKFAAKYK------VGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDkKNR 509


                  ....*..
gi 1278342979  81 KIDLTLK 87
Cdd:TIGR00717 510 KVSLSVK 516
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 18-84 9.22e-09

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: 48.39  E-value: 9.22e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1278342979  18 IGETVEVEVIKITDFGAFVKFSDnRRGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVSGD-GKIDL 84
Cdd:cd05688     1 EGDVVEGTVKSITDFGAFVDLGG-VDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKErKRISL 67
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 18-87 1.21e-08

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 51.32  E-value: 1.21e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1278342979  18 IGETVEVEVIKITDFGAFVKFSDNRRGLIHISQIA-EDYVKNVTDHLNIGDKVSARVVQVSGDG-KIDLTLK 87
Cdd:PRK06299  373 VGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISwDKKGEEAVELYKKGDEVEAVVLKVDVEKeRISLGIK 444
S1_Rrp5_repeat_hs11_sc8 cd05702
S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 19-74 2.96e-08

S1_Rrp5_repeat_hs11_sc8: 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 H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240207 [Multi-domain]  Cd Length: 70  Bit Score: 47.20  E-value: 2.96e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1278342979  19 GETVEVEVIKITDFGAFVKFSDNRRGLIHISQIAEDYV--KNVTDHLNIGDKVSARVV 74
Cdd:cd05702     1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPdgKNPLSKFKIGQKIKARVI 58
COG1107 COG1107
Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [Replication, ...
 31-99 3.75e-08

Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [Replication, recombination and repair];


Pssm-ID: 440724 [Multi-domain]  Cd Length: 626  Bit Score: 50.22  E-value: 3.75e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1278342979  31 DFGAFVKFSDNRRGLIHISQIAEDYvknvtdhlNIGDKVSARVVQVSGDGKIDL---TLKAAKEETVSAGPK 99
Cdd:COG1107    52 DFGVFVDLNDHVTGLLHRSELDQDW--------EVGDEVFVQVKEVRDNGNVDLgwvSIDSYETVEVEKELP 115
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 19-88 9.41e-08

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: 45.72  E-value: 9.41e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1278342979  19 GETVEVEVIKITDFGAFVKFSDNRRGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVsgDGK---IDLTLKA 88
Cdd:cd05691     1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNV--DRKnrkISLSIKA 71
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 18-87 1.70e-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: 48.19  E-value: 1.70e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1278342979  18 IGETVEVEVIKITDFGAFVKFSDNRRGLIHISQIAEDYVKNVTDHLNI-GDKVSARVVQVSGDGK-IDLTLK 87
Cdd:TIGR00717 359 VGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISWDKDGREADHLYKkGDEIEAVVLAVDKEKKrISLGVK 430
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 19-91 2.02e-07

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 47.85  E-value: 2.02e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1278342979  19 GETVEVEVIKITDFGAFV--KFSDnrrGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVSGD-GKIDLTLKAAKE 91
Cdd:PRK06299  202 GQVVEGVVKNITDYGAFVdlGGVD---GLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEkKRVSLGLKQLGE 274
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 19-86 2.20e-07

S1_Rrp5_repeat_hs5: 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 H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240202 [Multi-domain]  Cd Length: 69  Bit Score: 44.92  E-value: 2.20e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1278342979  19 GETVEVEVIKITDFGAFVKFSDNRRGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVSGD-GKIDLTL 86
Cdd:cd05697     1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPErKRLVLTL 69
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 19-91 2.92e-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: 47.42  E-value: 2.92e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1278342979  19 GETVEVEVIKITDFGAFVKFSDNRRGLIHISQIaeDYVKNV---TDHLNIGDKVSARVVQVSGD-GKIDLTLKAAKE 91
Cdd:TIGR00717 273 GDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEM--SWVKKNshpSKVVKKGDEVEVMILDIDPErRRLSLGLKQCKA 347
rpsA PRK13806
30S ribosomal protein S1; Provisional
 19-89 7.45e-07

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 46.26  E-value: 7.45e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1278342979  19 GETVEVEVIKITDFGAFVKFSDNRRGLIHISQIAedYVKNVT---DHLNIGDKVSARVVQVSGDGK-IDLTLKAA 89
Cdd:PRK13806  293 GDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMS--WTRRVNkpeDVVAPGDAVAVKIKDIDPAKRrISLSLRDA 365
S1_RecJ_like cd04473
S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of ...
 18-84 1.02e-06

S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.


Pssm-ID: 239919 [Multi-domain]  Cd Length: 77  Bit Score: 43.36  E-value: 1.02e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1278342979  18 IGETVEVEVIKITDFGAFVKFSDNRRGLIHISQIAEDYvknvtdhlNIGDKVSARVVQVSGDGKIDL 84
Cdd:cd04473    16 VGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLLRDY--------EVGDEVIVQVTDIPENGNIDL 74
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 18-91 1.27e-06

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


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 45.88  E-value: 1.27e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1278342979  18 IGETVEVEVIKITDFGAFVKFsDNRRGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVSGD-GKIDLTLKAAKE 91
Cdd:TIGR00717 187 EGDVVKGVVKNITDFGAFVDL-GGVDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEkGRISLSLKQLGE 260
S1_RNase_R cd04471
S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, ...
 18-86 5.48e-06

S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.


Pssm-ID: 239917 [Multi-domain]  Cd Length: 83  Bit Score: 41.62  E-value: 5.48e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278342979  18 IGETVEVEVIKITDFGAFVKFSDNR-RGLIHISQIAEDYVKNVTDHL-----------NIGDKVSARVVQVS-GDGKIDL 84
Cdd:cd04471     1 VGEEFDGVISGVTSFGLFVELDNLTvEGLVHVSTLGDDYYEFDEENHalvgertgkvfRLGDKVKVRVVRVDlDRRKIDF 80


                  ..
gi 1278342979  85 TL 86
Cdd:cd04471    81 EL 82
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 26-76 2.23e-05

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: 39.88  E-value: 2.23e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1278342979  26 VIKITDFGAFVKFSDNRRGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQV 76
Cdd:cd04461    22 VRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSV 72
PRK09521 PRK09521
exosome complex RNA-binding protein Csl4; Provisional
 9-87 2.40e-05

exosome complex RNA-binding protein Csl4; Provisional


Pssm-ID: 236547 [Multi-domain]  Cd Length: 189  Bit Score: 41.50  E-value: 2.40e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278342979   9 KKRNIILPAIGETVEVEVIKITDFGAFVKFS---DNRRGL-------IHISQIAEDYVKNVTDHLNIGDKVSARVVQVsG 78
Cdd:PRK09521   55 FKKTPPLLKKGDIVYGRVVDVKEQRALVRIVsieGSERELatsklayIHISQVSDGYVESLTDAFKIGDIVRAKVISY-T 133


                  ....*....
gi 1278342979  79 DGkIDLTLK 87
Cdd:PRK09521  134 DP-LQLSTK 141
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 19-76 2.53e-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: 39.40  E-value: 2.53e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1278342979  19 GETVEVEVIKITDFGAFVKFSDNRRGLIHISQIA-EDYVKNVTDHLNIGDKVSARVVQV 76
Cdd:cd05690     1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISwTQRVRHPSEIYKKGQEVEAVVLNI 59
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 18-91 2.92e-05

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 41.69  E-value: 2.92e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1278342979  18 IGETVEVEVIKITDFGAFVKFSDNRRGLIHISQIaeDYVKNV---TDHLNIGDKVSARVVQVSGDG-KIDLTLKAAKE 91
Cdd:PRK06299  286 VGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEM--SWTKKNkhpSKVVSVGQEVEVMVLEIDEEKrRISLGLKQCKE 361
VacB COG0557
Exoribonuclease R [Transcription];
18-86 3.18e-05

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 41.63  E-value: 3.18e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278342979  18 IGETVEVEVIKITDFGAFVKFSDNR-RGLIHISQIAEDYVknvtdHLN----------------IGDKVSARVVQVSGD- 79
Cdd:COG0557   622 VGEEFEGVISGVTSFGLFVELDELGvEGLVHVSSLGDDYY-----EYDerrqalvgertgkryrLGDRVEVRVVRVDLDr 696


                  ....*..
gi 1278342979  80 GKIDLTL 86
Cdd:COG0557   697 RQIDFEL 703
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 17-98 4.12e-05

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 41.62  E-value: 4.12e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278342979  17 AIGETVEVEVIKITDFGAFVKFSDNRRGLIHISQIAedYVKNV---TDHLNIGDKVSARVVQVS-GDGKIDLTLKaakee 92
Cdd:PRK12269  577 GVNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFS--WVKKTskpSDMVKIGDEVECMILGYDiQAGRVSLGLK----- 649


                  ....*.
gi 1278342979  93 TVSAGP 98
Cdd:PRK12269  650 QVTANP 655
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
12-92 6.66e-05

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 40.70  E-value: 6.66e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278342979  12 NIILPAIGETVEVEVIKITDFGAFVKFSDNRRGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVS-GDGKIDLTLKAAK 90
Cdd:PRK00087  296 LEKQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEdEDGYVVLSKKEAD 375


                  ..
gi 1278342979  91 EE 92
Cdd:PRK00087  376 RE 377
PTZ00248 PTZ00248
eukaryotic translation initiation factor 2 subunit 1; Provisional
 16-113 8.93e-05

eukaryotic translation initiation factor 2 subunit 1; Provisional


Pssm-ID: 240329 [Multi-domain]  Cd Length: 319  Bit Score: 40.42  E-value: 8.93e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278342979  16 PAIGETVEVEVIKITDFGAFVKF--SDNRRGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVSGD-GKIDLTLKAAKEE 92
Cdd:PTZ00248   15 PEEDDLVMVKVVRITEMGAYVSLleYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEkGYIDLSKKRVSPE 94

                          90       100
                  ....*....|....*....|.
gi 1278342979  93 TVSAgpknkefrtnvFEEKFN 113
Cdd:PTZ00248   95 DIEA-----------CEEKFS 104
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 19-92 1.84e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 39.47  E-value: 1.84e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1278342979  19 GETVEVEVIKITDFGAFVKFSDNR-RGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVS-GDGKIDLTLKAAKEE 92
Cdd:PRK06676   18 GDVVTGEVLKVEDKQVFVNIEGYKvEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEdGEGNLLLSKRRLEAE 93
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 18-92 2.90e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 39.01  E-value: 2.90e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1278342979  18 IGETVEVEVIKITDFGAFVKFSdNRRGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVSGD-GKIDLTLKAAKEE 92
Cdd:PRK07400  196 VGEVVVGTVRGIKPYGAFIDIG-GVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAErGRISLSTKQLEPE 270
S1_RPS1_repeat_ec1_hs1 cd05687
S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 19-87 5.73e-04

S1_RPS1_repeat_ec1_hs1: 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 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240192 [Multi-domain]  Cd Length: 70  Bit Score: 35.97  E-value: 5.73e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278342979  19 GETVEVEVIKITDFGAFVKFSDNRRGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVS-GDGKIDLTLK 87
Cdd:cd05687     1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEdEEGNVVLSKR 70
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 17-87 6.92e-04

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 38.15  E-value: 6.92e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1278342979  17 AIGETVEVEVIKITDFGAFVKFSDNRRGLIHISQIAEDYVKNVTDHLN---IGDKVSARVVQVS-GDGKIDLTLK 87
Cdd:PRK12269  751 GVGSTVEGEVSSVTDFGIFVRVPGGVEGLVRKQHLVENRDGDPGEALRkyaVGDRVKAVIVDMNvKDRKVAFSVR 825
S1_Rrp5_repeat_hs4 cd05696
S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 24-86 1.12e-03

S1_Rrp5_repeat_hs4: 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 H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240201 [Multi-domain]  Cd Length: 71  Bit Score: 35.32  E-value: 1.12e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1278342979  24 VEVIKIT----DFGAFVKFSDNRRGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVSG-DGKIDLTL 86
Cdd:cd05696     4 VDSVKVTkvepDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPmDGLLQLSL 71
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 26-92 1.22e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 36.95  E-value: 1.22e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278342979  26 VIKITDFGAFVKFS--DnrrGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVSGD-GKIDLTLKAAKEE 92
Cdd:PRK07899  216 VSSIVNFGAFVDLGgvD---GLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDrERVSLSLKATQED 282
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 19-92 2.01e-03

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: 36.56  E-value: 2.01e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1278342979  19 GETVEVEVIKITDFGAFV---KFSDnrrGLIHISQIAEDyvkNVTDHLNIGDKVSARVVQV-SGDGKIDLTLKAAKEE 92
Cdd:COG0539    19 GDIVKGTVVSIDDDEVLVdigYKSE---GIIPLSEFSDE---PGELEVKVGDEVEVYVEKVeDGEGEIVLSKKKADRE 90
S1_Rrp5_repeat_sc11 cd05707
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 19-85 2.34e-03

S1_Rrp5_repeat_sc11: 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 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240212 [Multi-domain]  Cd Length: 68  Bit Score: 34.19  E-value: 2.34e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1278342979  19 GETVEVEVIKITDFGAFVKFSDNRRGLIHISQIAEDYVKNVTDHLNIGDKVSARVVQVS-GDGKIDLT 85
Cdd:cd05707     1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDpDNGRIEMT 68
S1_2 pfam13509
S1 domain; The S1 domain was originally identified as a repeat motif in the ribosomal S1 ...
 18-69 2.54e-03

S1 domain; The S1 domain was originally identified as a repeat motif in the ribosomal S1 protein. It was later identified in a wide range of proteins. The S1 domain has an OB-fold structure. The S1 domain is involved in nucleic acid binding.


Pssm-ID: 433267 [Multi-domain]  Cd Length: 61  Bit Score: 34.04  E-value: 2.54e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1278342979  18 IGETVEVEVIKITDFGAFVKFSDNRRGLIHISQIAEDyvknvtdhLNIGDKV 69
Cdd:pfam13509   1 IGKINTLKVIRETDFGYFLDGGEGGEVLLPKREVPEE--------LEIGDEV 44
S1_Rrp4 cd05789
S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 16-90 3.38e-03

S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".


Pssm-ID: 240215 [Multi-domain]  Cd Length: 86  Bit Score: 34.06  E-value: 3.38e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1278342979  16 PAIGETVEVEVIKITDFGAFVKFSDNRRGLIHISQIAEDYV----KNVTDHLNIGDKVSARVVQVSGDGKIDLTLKAAK 90
Cdd:cd05789     4 PEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPRTdedeLNMRSYLDEGDLIVAEVQSVDSDGSVSLHTRSLK 82
S1_RNase_E cd04453
S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential ...
 33-76 3.54e-03

S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain that is highly homologous to that of RNase E. RNase G not only shares sequence similarity with RNase E, but also functionally overlaps with RNase E. In Escherichia coli, RNase G is involved in the maturation of the 5' end of the 16S rRNA. RNase G plays a secondary role in mRNA decay.


Pssm-ID: 239900 [Multi-domain]  Cd Length: 88  Bit Score: 34.11  E-value: 3.54e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1278342979  33 GAFVKFSDNRRGLIHISQIAEDY---VKNVTDHLNIGDKVsarVVQV 76
Cdd:cd04453    24 AAFVDIGLGKNGFLHLSDILPAYfkkHKKIAKLLKEGQEI---LVQV 67
PRK11642 PRK11642
ribonuclease R;
18-104 3.83e-03

ribonuclease R;


Pssm-ID: 236944 [Multi-domain]  Cd Length: 813  Bit Score: 35.87  E-value: 3.83e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278342979  18 IGETVEVEVIKITDFGAFVKFSD-NRRGLIHISQIAEDYVK--NVTDHL---------NIGDKVSARVVQVSGDG-KIDL 84
Cdd:PRK11642  643 VGNVFKGVISSVTGFGFFVRLDDlFIDGLVHVSSLDNDYYRfdQVGQRLigessgqtyRLGDRVEVRVEAVNMDErKIDF 722

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1278342979  85 TL-----------KAAKEETVSAGPKNKEFR 104
Cdd:PRK11642  723 SLisseraprnvgKTAREKAKKGDAGKKGGK 753
 
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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