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Conserved domains on  [gi|514960069|ref|WP_016648658|]
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S1 domain-containing RNA-binding protein [Facklamia hominis]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK08582 super family cl35719
RNA-binding protein S1;
1-158 1.07e-58

RNA-binding protein S1;


The actual alignment was detected with superfamily member PRK08582:

Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 179.46  E-value: 1.07e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514960069   1 MSVEVGQKLKGKVTGIKNFGAFVALENKQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISVAEDGKIGLSIRQAKDKP 80
Cdd:PRK08582   1 MSIEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDDGKIGLSIKKAKDRP 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 514960069  81 avdkskmkkfDAQEAKPtRLSKSNFVKDDQNKKEnfpnqnvtgkyaqksndDFDRLMSNFLKDSEDRLASLRRNTEGK 158
Cdd:PRK08582  81 ----------KRQHDRP-RHEDNRGGGNDVAPKE-----------------DFEQKMSRFLKDSEDRLTSIKRNTESK 130
 
Name Accession Description Interval E-value
PRK08582 PRK08582
RNA-binding protein S1;
1-158 1.07e-58

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 179.46  E-value: 1.07e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514960069   1 MSVEVGQKLKGKVTGIKNFGAFVALENKQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISVAEDGKIGLSIRQAKDKP 80
Cdd:PRK08582   1 MSIEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDDGKIGLSIKKAKDRP 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 514960069  81 avdkskmkkfDAQEAKPtRLSKSNFVKDDQNKKEnfpnqnvtgkyaqksndDFDRLMSNFLKDSEDRLASLRRNTEGK 158
Cdd:PRK08582  81 ----------KRQHDRP-RHEDNRGGGNDVAPKE-----------------DFEQKMSRFLKDSEDRLTSIKRNTESK 130
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 1-158 4.27e-53

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


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 164.58  E-value: 4.27e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514960069   1 MSVEVGQKLKGKVTGIKNFGAFVALENKQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISVAEDGKIGLSIRQAKDKP 80
Cdd:COG1098    1 MSIEVGDIVEGKVTGITPFGAFVELPEGTTGLVHISEIADGYVKDINDYLKVGDEVKVKVLSIDEDGKISLSIKQAEEKP 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 514960069  81 avdkskmkkfdaqeakptrlsksnfvkddqnKKENFPNQNvtgKYAQKSNDDFDRLMSNFLKDSEDRLASLRRNTEGK 158
Cdd:COG1098   81 -------------------------------KRPPRPRRN---SRPKAGFESFEDKLSKFLKDSDERLSDLKKRTESK 124
S1_dom_CvfD NF040579
CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ...
 3-90 4.79e-38

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: 126.00  E-value: 4.79e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514960069   3 VEVGQKLKGKVTGIKNFGAFVALENKQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISVAED-GKIGLSIRQAKDKPA 81
Cdd:NF040579   1 YKIGDIVEGKVTGIQPYGAFVALDEHTQGLIHISEIKHGYVKDINDFLKVGQEVKVKVLDIDEYtGKISLSLRALEEAPE 80


                 ....*....
gi 514960069  82 VDKSKMKKF 90
Cdd:NF040579  81 KHRKRRKHR 89
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 6-74 2.96e-25

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: 91.96  E-value: 2.96e-25
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 514960069   6 GQKLKGKVTGIKNFGAFVALENKQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISVAEDGKIGLSIR 74
Cdd:cd05692    1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARGRISLSIK 69
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
4-74 2.00e-19

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 77.26  E-value: 2.00e-19
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 514960069     4 EVGQKLKGKVTGIKNFGAFVALENKQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISV-AEDGKIGLSIR 74
Cdd:smart00316   1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVdEEKGRIILSLK 72
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 3-73 3.29e-16

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: 68.85  E-value: 3.29e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 514960069    3 VEVGQKLKGKVTGIKNFGAFVALENKQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISVAED-GKIGLSI 73
Cdd:pfam00575   1 PEKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDrRRIILSI 72
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 5-80 1.24e-13

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: 67.45  E-value: 1.24e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 514960069    5 VGQKLKGKVTGIKNFGAFVALENKQSGLVHISEVS-EDYVQDINDLLSLGDEVTVKVISVAED-GKIGLSIRQAKDKP 80
Cdd:TIGR00717 272 VGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSwVKKNSHPSKVVKKGDEVEVMILDIDPErRRLSLGLKQCKANP 349
 
Name Accession Description Interval E-value
PRK08582 PRK08582
RNA-binding protein S1;
1-158 1.07e-58

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 179.46  E-value: 1.07e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514960069   1 MSVEVGQKLKGKVTGIKNFGAFVALENKQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISVAEDGKIGLSIRQAKDKP 80
Cdd:PRK08582   1 MSIEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDDGKIGLSIKKAKDRP 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 514960069  81 avdkskmkkfDAQEAKPtRLSKSNFVKDDQNKKEnfpnqnvtgkyaqksndDFDRLMSNFLKDSEDRLASLRRNTEGK 158
Cdd:PRK08582  81 ----------KRQHDRP-RHEDNRGGGNDVAPKE-----------------DFEQKMSRFLKDSEDRLTSIKRNTESK 130
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 1-158 4.27e-53

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


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 164.58  E-value: 4.27e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514960069   1 MSVEVGQKLKGKVTGIKNFGAFVALENKQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISVAEDGKIGLSIRQAKDKP 80
Cdd:COG1098    1 MSIEVGDIVEGKVTGITPFGAFVELPEGTTGLVHISEIADGYVKDINDYLKVGDEVKVKVLSIDEDGKISLSIKQAEEKP 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 514960069  81 avdkskmkkfdaqeakptrlsksnfvkddqnKKENFPNQNvtgKYAQKSNDDFDRLMSNFLKDSEDRLASLRRNTEGK 158
Cdd:COG1098   81 -------------------------------KRPPRPRRN---SRPKAGFESFEDKLSKFLKDSDERLSDLKKRTESK 124
S1_dom_CvfD NF040579
CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ...
 3-90 4.79e-38

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: 126.00  E-value: 4.79e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514960069   3 VEVGQKLKGKVTGIKNFGAFVALENKQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISVAED-GKIGLSIRQAKDKPA 81
Cdd:NF040579   1 YKIGDIVEGKVTGIQPYGAFVALDEHTQGLIHISEIKHGYVKDINDFLKVGQEVKVKVLDIDEYtGKISLSLRALEEAPE 80


                 ....*....
gi 514960069  82 VDKSKMKKF 90
Cdd:NF040579  81 KHRKRRKHR 89
PRK08059 PRK08059
general stress protein 13; Validated
 4-97 1.66e-30

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 107.05  E-value: 1.66e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514960069   4 EVGQKLKGKVTGIKNFGAFVALENKQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISVAED-GKIGLSIRQAKDKPAV 82
Cdd:PRK08059   6 EVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEkGKISLSIRATEEAPEA 85

                         90
                 ....*....|....*
gi 514960069  83 DKSKMKKFDAQEAKP 97
Cdd:PRK08059  86 KRKKGKILIPNPSEQ 100
PRK05807 PRK05807
RNA-binding protein S1;
1-158 1.13e-28

RNA-binding protein S1;


Pssm-ID: 235614 [Multi-domain]  Cd Length: 136  Bit Score: 102.90  E-value: 1.13e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514960069   1 MSVEVGQKLKGKVTGIKNFGAFVALENKqSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISVAEDGKIGLSIRQA-KDK 79
Cdd:PRK05807   1 MTLKAGSILEGTVVNITNFGAFVEVEGK-TGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDDNGKISLSIKQAmKQK 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 514960069  80 PAVdksKMKKFDAQEAKPTrlsksnfvkddqnkkenfpnqnvtgkyaqKSNDDFDRLMSNFLKDSEDRLASLRRNTEGK 158
Cdd:PRK05807  80 KSV---KPAEIDWQKEKNK-----------------------------NNNGNFEDRLSKFLKDSEERFQDLKKHQDSK 126
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 6-74 2.96e-25

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: 91.96  E-value: 2.96e-25
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 514960069   6 GQKLKGKVTGIKNFGAFVALENKQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISVAEDGKIGLSIR 74
Cdd:cd05692    1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARGRISLSIK 69
Pnp COG1185
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ...
 3-74 7.87e-25

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


Pssm-ID: 440798 [Multi-domain]  Cd Length: 686  Bit Score: 99.69  E-value: 7.87e-25
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 514960069   3 VEVGQKLKGKVTGIKNFGAFVALENKQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISVAEDGKIGLSIR 74
Cdd:COG1185  614 PEVGEIYEGKVVRIMDFGAFVEILPGKDGLVHISELADERVEKVEDVLKEGDEVKVKVLEIDDQGRIKLSRK 685
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 3-76 1.39e-23

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 95.89  E-value: 1.39e-23
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 514960069   3 VEVGQKLKGKVTGIKNFGAFVALENKQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISVAEDGKIGLSIRQA 76
Cdd:PRK11824 619 PEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEIDKRGRIRLSRKAV 692
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
5-74 4.14e-23

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 88.22  E-value: 4.14e-23
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 514960069   5 VGQKLKGKVTGIKNFGAFVALENKQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISVAE-DGKIGLSIR 74
Cdd:PRK07252   3 IGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEyTGKASLSLR 73
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
4-81 1.90e-21

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 90.08  E-value: 1.90e-21
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 514960069   4 EVGQKLKGKVTGIKNFGAFVALENKQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISV-AEDGKIGLSIRQAKDKPA 81
Cdd:COG2183  640 KPGMILEGTVTNVTDFGAFVDIGVHQDGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEVdLKRKRISLSMKLDDEAGA 718
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 6-73 3.13e-21

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: 81.82  E-value: 3.13e-21
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 514960069   6 GQKLKGKVTGIKNFGAFVALENKQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISVAEDGKIGLSI 73
Cdd:cd04472    1 GKIYEGKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDDRGRISLSR 68
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 5-77 6.13e-20

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: 84.71  E-value: 6.13e-20
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 514960069   5 VGQKLKGKVTGIKNFGAFVALENKQSGLVHISEVSED-YVQDINDLLSLGDEVTVKVISV-AEDGKIGLSIRQAK 77
Cdd:COG0539  274 VGDVVKGKVTRLTDFGAFVELEPGVEGLVHISEMSWTkRVAHPSDVVKVGDEVEVKVLDIdPEERRISLSIKQLA 348
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
4-74 2.00e-19

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 77.26  E-value: 2.00e-19
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 514960069     4 EVGQKLKGKVTGIKNFGAFVALENKQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISV-AEDGKIGLSIR 74
Cdd:smart00316   1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVdEEKGRIILSLK 72
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 2-80 8.66e-19

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: 81.24  E-value: 8.66e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514960069   2 SVEVGQKLKGKVTGIKNFGAFVAL---EnkqsGLVHISEVSEDYVQDINDLLSLGDEVTVKVISV-AEDGKIGLSIRQAK 77
Cdd:COG0539  186 KLEEGDVVEGTVKNITDFGAFVDLggvD----GLLHISEISWGRVKHPSEVLKVGDEVEVKVLKIdREKERISLSLKQLQ 261


                 ...
gi 514960069  78 DKP 80
Cdd:COG0539  262 PDP 264
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 6-72 4.45e-18

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: 73.81  E-value: 4.45e-18
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 514960069   6 GQKLKGKVTGIKNFGAFVALENKQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISVAED-GKIGLS 72
Cdd:cd05685    1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEErGRISLS 68
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 4-80 1.09e-17

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 79.05  E-value: 1.09e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 514960069   4 EVGQKLKGKVTGIKNFGAFVALENKQSGLVHISEVSED-YVQDINDLLSLGDEVTVKVISV-AEDGKIGLSIRQAKDKP 80
Cdd:PRK06299 285 PVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMSWTkKNKHPSKVVSVGQEVEVMVLEIdEEKRRISLGLKQCKENP 363
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
5-81 3.90e-17

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 77.68  E-value: 3.90e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 514960069   5 VGQKLKGKVTGIKNFGAFVALENKQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISV-AEDGKIGLSIRQAKDKPA 81
Cdd:PRK00087 562 VGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVdPEEKRIRLSIKEVEEEPG 639
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 2-80 2.64e-16

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 74.91  E-value: 2.64e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514960069   2 SVEVGQKLKGKVTGIKNFGAFVALeNKQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISVAED-GKIGLSIRQAKDKP 80
Cdd:PRK06676 189 SLKEGDVVEGTVARLTDFGAFVDI-GGVDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWEtERISLSLKDTLPGP 267
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 2-100 2.68e-16

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 75.20  E-value: 2.68e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514960069   2 SVEVGQKLKGKVTGIKNFGAFVALENKQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISV-AEDGKIGLSIRqAKDKp 80
Cdd:PRK06299 457 KHKKGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIdRKNRRISLSIK-ALDE- 534

                         90       100
                 ....*....|....*....|
gi 514960069  81 AVDKSKMKKFDAQEAKPTRL 100
Cdd:PRK06299 535 AEEKEAIAEYNSASDSKTTL 554
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 3-73 3.29e-16

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: 68.85  E-value: 3.29e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 514960069    3 VEVGQKLKGKVTGIKNFGAFVALENKQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISVAED-GKIGLSI 73
Cdd:pfam00575   1 PEKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDrRRIILSI 72
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 6-74 7.20e-16

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: 68.42  E-value: 7.20e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 514960069   6 GQKLKGKVTGIKNFGAFVALEN---KQSGLVHISEVSED-YVQDINDLLSLGDEVTVKVISVaEDGKIGLSIR 74
Cdd:cd05684    1 GKIYKGKVTSIMDFGCFVQLEGlkgRKEGLVHISQLSFEgRVANPSDVVKRGQKVKVKVISI-QNGKISLSMK 72
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 5-96 8.84e-16

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 73.37  E-value: 8.84e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514960069   5 VGQKLKGKVTGIKNFGAFVALENKQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISV-AEDGKIGLSIRQAKDKPAVD 83
Cdd:PRK06676 277 EGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVnEEEKRISLSIKALEEAPAEE 356

                         90
                 ....*....|...
gi 514960069  84 KSKMKKFDAQEAK 96
Cdd:PRK06676 357 EDRREEYRQYELP 369
rpsA PRK13806
30S ribosomal protein S1; Provisional
 3-100 1.12e-15

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 73.22  E-value: 1.12e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514960069   3 VEVGQKLKGKVTGIKNFGAFVALENKQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISVAEDGK-----IGLSIRQAK 77
Cdd:PRK13806 200 VKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKgkglrISLSIKQAG 279

                         90       100
                 ....*....|....*....|....
gi 514960069  78 DKPAVDKS-KMKKFDAQEAKPTRL 100
Cdd:PRK13806 280 GDPWDTVGdRLKAGDKVTGKVVRL 303
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 5-78 3.72e-15

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 71.61  E-value: 3.72e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 514960069   5 VGQKLKGKVTGIKNFGAFVALENKQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISV-AEDGKIGLSIRQAKD 78
Cdd:PRK07899 293 IGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIdLERRRISLSLKQANE 367
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 9-72 4.95e-15

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: 65.86  E-value: 4.95e-15
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 514960069   9 LKGKVTGIKNFGAFVALENKQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISV-AEDGKIGLS 72
Cdd:cd00164    1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVdPEKGRISLS 65
S1_pNO40 cd05686
S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function ...
 4-73 2.22e-14

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: 64.42  E-value: 2.22e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 514960069   4 EVGQKLKGKVTGIKNFGAFVALEN-KQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISVAEDGKIGLSI 73
Cdd:cd05686    2 ALYQIFKGEVASVTEYGAFVKIPGcRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKDKMKLSL 72
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 5-80 9.37e-14

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 67.88  E-value: 9.37e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 514960069   5 VGQKLKGKVTGIKNFGAFVALENKQSGLVHISEVS-EDYVQDINDLLSLGDEVTVKVISV-AEDGKIGLSIRQAKDKP 80
Cdd:PRK06299 373 VGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISwDKKGEEAVELYKKGDEVEAVVLKVdVEKERISLGIKQLEEDP 450
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 5-80 1.24e-13

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: 67.45  E-value: 1.24e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 514960069    5 VGQKLKGKVTGIKNFGAFVALENKQSGLVHISEVS-EDYVQDINDLLSLGDEVTVKVISVAED-GKIGLSIRQAKDKP 80
Cdd:TIGR00717 272 VGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSwVKKNSHPSKVVKKGDEVEVMILDIDPErRRLSLGLKQCKANP 349
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
2-80 2.96e-13

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 66.51  E-value: 2.96e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514960069   2 SVEVGQKLKGKVTGIKNFGAFVALeNKQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISV-AEDGKIGLSIRQAKDKP 80
Cdd:PRK00087 474 SLEEGDVVEGEVKRLTDFGAFVDI-GGVDGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIdKENKKLSLSLKKLLPDP 552
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 3-94 5.89e-13

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 65.21  E-value: 5.89e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514960069   3 VEVGQKLKGKVTGIKNFGAFVALeNKQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISV-AEDGKIGLSIRQAKDKP- 80
Cdd:PRK07400 194 LEVGEVVVGTVRGIKPYGAFIDI-GGVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLdAERGRISLSTKQLEPEPg 272

                         90
                 ....*....|....
gi 514960069  81 AVDKSKMKKFDAQE 94
Cdd:PRK07400 273 DMLKDPQKVFDKAE 286
rpsA PRK13806
30S ribosomal protein S1; Provisional
 4-80 1.53e-12

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 64.36  E-value: 1.53e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514960069   4 EVGQKLKGKVTGIKNFGAFVALENKQSGLVHISEVSedYVQDIN---DLLSLGDEVTVKVISV-AEDGKIGLSIRQAKDK 79
Cdd:PRK13806 291 KAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMS--WTRRVNkpeDVVAPGDAVAVKIKDIdPAKRRISLSLRDAEGD 368


                 .
gi 514960069  80 P 80
Cdd:PRK13806 369 P 369
S1_RecJ_like cd04473
S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of ...
 3-72 1.81e-12

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: 59.54  E-value: 1.81e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514960069   3 VEVGQKLKGKVTGIKNFGAFVALENKQSGLVHISEVSEDYvqdindllSLGDEVTVKVISVAEDGKIGLS 72
Cdd:cd04473   14 LEVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNLLRDY--------EVGDEVIVQVTDIPENGNIDLI 75
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 2-108 4.40e-12

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 62.59  E-value: 4.40e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514960069   2 SVEVGQKLKGKVTGIKNFGAFVALEN-KQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISVAE-DGKIGLSIRQAKDK 79
Cdd:PRK06676  14 EVEVGDVVTGEVLKVEDKQVFVNIEGyKVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDgEGNLLLSKRRLEAE 93

                         90       100       110
                 ....*....|....*....|....*....|..
gi 514960069  80 PAVDKSKmKKFDAQ---EAKPTRLSKSNFVKD 108
Cdd:PRK06676  94 KAWDKLE-EKFEEGevvEVKVTEVVKGGLVVD 124
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 5-74 4.49e-12

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: 62.83  E-value: 4.49e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 514960069    5 VGQKLKGKVTGIKNFGAFVALENKQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISV-AEDGKIGLSIR 74
Cdd:TIGR00717 446 VGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIdKKNRKVSLSVK 516
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 4-75 2.40e-11

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: 56.44  E-value: 2.40e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 514960069   4 EVGQKLKGKVTGIKNFGAFVALE--NKQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISVAED-GKIGLSIRQ 75
Cdd:cd04452    2 EEGELVVVTVKSIADMGAYVSLLeyGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEkGYIDLSKKR 76
S1_RNase_R cd04471
S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, ...
 5-69 2.59e-11

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: 56.64  E-value: 2.59e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 514960069   5 VGQKLKGKVTGIKNFGAFVALENKQ-SGLVHISEVSEDYVQDINDLLSL-----------GDEVTVKVISV-AEDGKI 69
Cdd:cd04471    1 VGEEFDGVISGVTSFGLFVELDNLTvEGLVHVSTLGDDYYEFDEENHALvgertgkvfrlGDKVKVRVVRVdLDRRKI 78
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 5-72 6.92e-11

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: 54.94  E-value: 6.92e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 514960069   5 VGQKLKGKVTGIKNFGAFVALeNKQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISV-AEDGKIGLS 72
Cdd:cd05688    1 EGDVVEGTVKSITDFGAFVDL-GGVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIdKERKRISLG 68
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 4-74 7.94e-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: 55.03  E-value: 7.94e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 514960069   4 EVGQKLKGKVTGIKNFGAFVALEN-KQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISV-AEDGKIGLSIR 74
Cdd:cd05708    1 KVGQKIDGTVRRVEDYGVFIDIDGtNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIdAEKKRISLGLK 73
VacB COG0557
Exoribonuclease R [Transcription];
1-73 1.56e-10

Exoribonuclease R [Transcription];


Pssm-ID: 440323 [Multi-domain]  Cd Length: 711  Bit Score: 58.58  E-value: 1.56e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514960069   1 MSVEVGQKLKGKVTGIKNFGAFVALENKQ-SGLVHISEVSEDYVQ--DINDLL---------SLGDEVTVKVISVA-EDG 67
Cdd:COG0557  618 MKDRVGEEFEGVISGVTSFGLFVELDELGvEGLVHVSSLGDDYYEydERRQALvgertgkryRLGDRVEVRVVRVDlDRR 697


                 ....*.
gi 514960069  68 KIGLSI 73
Cdd:COG0557  698 QIDFEL 703
SUI2 COG1093
Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure ...
 4-78 1.90e-10

Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]; Translation initiation factor 2, alpha subunit (eIF-2alpha) is part of the Pathway/BioSystem: Translation factors


Pssm-ID: 440710 [Multi-domain]  Cd Length: 259  Bit Score: 57.52  E-value: 1.90e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 514960069   4 EVGQKLKGKVTGIKNFGAFVAL---ENKQsGLVHISEVSEDYVQDINDLLSLGDEVTVKVISVAED-GKIGLSIRQAKD 78
Cdd:COG1093    9 EEGELVVGTVKEVKDFGAYVTLdeyEGKE-GFIHISEVASGWIKNIRDYVREGQKVVCKVLRVDPKrGHIDLSLKRVNE 86
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 2-80 2.73e-10

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 57.87  E-value: 2.73e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514960069   2 SVEVGQKLKGKVTGIKNFGAFVAL---EnkqsGLVHISEVSEDYVQDINDLLSLGDEVTVKVISVAED-GKIGLSIRQAK 77
Cdd:PRK06299 198 NLEEGQVVEGVVKNITDYGAFVDLggvD----GLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEkKRVSLGLKQLG 273


                 ...
gi 514960069  78 DKP 80
Cdd:PRK06299 274 EDP 276
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 4-78 2.83e-10

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 57.14  E-value: 2.83e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 514960069   4 EVGQKLKGKVTGIKNFGAFVALE---NKQsGLVHISEVSEDYVQDINDLLSLGDEVTVKVISVAED-GKIGLSIRQAKD 78
Cdd:PRK03987   7 EEGELVVGTVKEVKDFGAFVTLDeypGKE-GFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRkGHIDLSLKRVNE 84
S1_RPS1_repeat_ec1_hs1 cd05687
S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 6-74 3.54e-10

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: 53.30  E-value: 3.54e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514960069   6 GQKLKGKVTGIKNFGAFVALENKQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISVA-EDGKIGLSIR 74
Cdd:cd05687    1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEdEEGNVVLSKR 70
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 6-80 1.51e-09

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 55.44  E-value: 1.51e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 514960069   6 GQKLKGKVTGIKNFGAFVALeNKQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISVAED-GKIGLSIRQAKDKP 80
Cdd:PRK07899 209 GQVRKGVVSSIVNFGAFVDL-GGVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDrERVSLSLKATQEDP 283
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 5-80 1.51e-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: 55.51  E-value: 1.51e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 514960069    5 VGQKLKGKVTGIKNFGAFVALENKQSGLVHISEVS-EDYVQDINDLLSLGDEVTVKVISV-AEDGKIGLSIRQAKDKP 80
Cdd:TIGR00717 359 VGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISwDKDGREADHLYKKGDEIEAVVLAVdKEKKRISLGVKQLTENP 436
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 6-74 5.53e-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: 49.92  E-value: 5.53e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514960069   6 GQKLKGKVTGIKNFGAFVALENKQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISV-AEDGKIGLSIR 74
Cdd:cd05698    1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCdPEQQRLLLSCK 70
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
 13-138 8.71e-09

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 53.36  E-value: 8.71e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514960069  13 VTGIKNFGAFVALENKQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISVAEDGKIGLSIRQAKDKPAVDKSKMKKfDA 92
Cdd:PLN00207 762 IKSIAPYGAFVEIAPGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVNDKGQLRLSRRALLPEANSEKSSQKQ-QG 840

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 514960069  93 QEAKPTRLSKSNFVKDDQNKKENFPNQNVTGKYAQKSNDDFDRLMS 138
Cdd:PLN00207 841 GSTKDKAPQKKYVNTSSRPRRAAQAEKNSAENAAVPKKKDYKRATS 886
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 2-80 1.51e-08

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: 52.81  E-value: 1.51e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514960069    2 SVEVGQKLKGKVTGIKNFGAFVALENKQsGLVHISEVSEDYVQDINDLLSLGDEVTVKVISV-AEDGKIGLSIRQAKDKP 80
Cdd:TIGR00717 184 NLKEGDVVKGVVKNITDFGAFVDLGGVD-GLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFdKEKGRISLSLKQLGEDP 262
S1_RPS1_repeat_ec4 cd05689
S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 6-66 1.59e-08

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: 49.11  E-value: 1.59e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 514960069   6 GQKLKGKVTGIKNFGAFVALENKQSGLVHISEVseDYV-QDIN--DLLSLGDEVTVKVISVAED 66
Cdd:cd05689    4 GTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEM--DWTnKNIHpsKVVSLGDEVEVMVLDIDEE 65
PRK08563 PRK08563
DNA-directed RNA polymerase subunit E'; Provisional
 11-75 1.29e-07

DNA-directed RNA polymerase subunit E'; Provisional


Pssm-ID: 236289 [Multi-domain]  Cd Length: 187  Bit Score: 49.05  E-value: 1.29e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514960069  11 GKVTGIKNFGAFVALeNKQSGLVHISEVSEDYV-----------QDINDLLSLGDEVTVKVISV------AEDGKIGLSI 73
Cdd:PRK08563  87 GEVVEVVEFGAFVRI-GPVDGLLHISQIMDDYIsydpkngrligKESKRVLKVGDVVRARIVAVslkerrPRGSKIGLTM 165


                 ..
gi 514960069  74 RQ 75
Cdd:PRK08563 166 RQ 167
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 6-71 1.93e-07

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: 45.95  E-value: 1.93e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 514960069   6 GQKLKGKVTGIKNFGAFVALENKQSGLVHISEVS-EDYVQDINDLLSLGDEVTVKVISV-AEDGKIGL 71
Cdd:cd05690    1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISwTQRVRHPSEIYKKGQEVEAVVLNIdVERERISL 68
S1_RpoE cd04460
S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 11-76 1.94e-07

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: 46.90  E-value: 1.94e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514960069  11 GKVTGIKNFGAFVALeNKQSGLVHISEVSEDYV-----------QDINDLLSLGDEVTVKVISVA------EDGKIGLSI 73
Cdd:cd04460    5 GEVVEVVDFGAFVRI-GPVDGLLHISQIMDDYIsydpknkrligEETKRVLKVGDVVRARIVAVSlkerrpRESKIGLTM 83


                 ...
gi 514960069  74 RQA 76
Cdd:cd04460   84 RQP 86
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 6-78 2.63e-07

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: 2.63e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 514960069   6 GQKLKGKVTGIKNFGAFVALENKQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISV-AEDGKIGLSIRqAKD 78
Cdd:cd05691    1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVdRKNRKISLSIK-AKE 73
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 5-80 6.64e-07

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 48.17  E-value: 6.64e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514960069   5 VGQKLKGKVTGIKNFGAFVALENKQSGLVHISEVSedYVQDI---NDLLSLGDEVTVKVISV-AEDGKIGLSIRQAKDKP 80
Cdd:PRK12269 578 VNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFS--WVKKTskpSDMVKIGDEVECMILGYdIQAGRVSLGLKQVTANP 655
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
2-84 7.01e-07

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 48.02  E-value: 7.01e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514960069   2 SVEVGQKLKGKVTGIKNFGAFVALENKQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISVA-EDGKIGLSIRQAKDKP 80
Cdd:PRK00087 299 QIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEdEDGYVVLSKKEADREK 378


                 ....
gi 514960069  81 AVDK 84
Cdd:PRK00087 379 AWKE 382
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 2-77 9.14e-07

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: 47.35  E-value: 9.14e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 514960069   2 SVEVGQKLKGKVTGIKNFGAFVALENKQSGLVHISEVSEDyvqDINDLLSLGDEVTVKVISV-AEDGKIGLSIRQAK 77
Cdd:COG0539   15 ELKEGDIVKGTVVSIDDDEVLVDIGYKSEGIIPLSEFSDE---PGELEVKVGDEVEVYVEKVeDGEGEIVLSKKKAD 88
PRK11642 PRK11642
ribonuclease R;
1-129 1.26e-06

ribonuclease R;


Pssm-ID: 236944 [Multi-domain]  Cd Length: 813  Bit Score: 47.04  E-value: 1.26e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514960069   1 MSVEVGQKLKGKVTGIKNFGAFVALENK-QSGLVHISEVSEDYVQDIN-----------DLLSLGDEVTVKVISVAEDG- 67
Cdd:PRK11642 639 MLDQVGNVFKGVISSVTGFGFFVRLDDLfIDGLVHVSSLDNDYYRFDQvgqrligessgQTYRLGDRVEVRVEAVNMDEr 718

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 514960069  68 KIGLSI----RQAKDKPAVDKSKMKKFDAQEAKPTRL---SKSNFVKDDQNKKENFPNQNVTGKYAQKS 129
Cdd:PRK11642 719 KIDFSLisseRAPRNVGKTAREKAKKGDAGKKGGKRRqvgKKVNFEPDSAFRGEKKAKPKAAKKDARKA 787
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 3-73 1.35e-06

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: 44.12  E-value: 1.35e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 514960069   3 VEVGQKLKGKVTGIKNFGAFVALENKQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISV-AEDGKIGLSI 73
Cdd:cd04461   12 LKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVdEEKQRFLLSL 83
S1_Rrp5_repeat_sc10 cd05706
S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 3-74 9.75e-06

S1_Rrp5_repeat_sc10: 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 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240211 [Multi-domain]  Cd Length: 73  Bit Score: 41.47  E-value: 9.75e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 514960069   3 VEVGQKLKGKVTGIKNFGAFVALENKQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISV-AEDGKIGLSIR 74
Cdd:cd05706    1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVdVPNKKIALSLR 73
S1_Rrp5_repeat_hs11_sc8 cd05702
S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 6-66 1.12e-05

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: 41.42  E-value: 1.12e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 514960069   6 GQKLKGKVTGIKNFGAFVALENKQSGLVHISEVSEDYVQDINDLLSL--GDEVTVKVISVAED 66
Cdd:cd05702    1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFkiGQKIKARVIGGHDA 63
S1_Rrp5_repeat_sc11 cd05707
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 6-72 4.02e-05

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: 39.59  E-value: 4.02e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 514960069   6 GQKLKGKVTGIKNFGAFVALENKQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISVAED-GKIGLS 72
Cdd:cd05707    1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDnGRIEMT 68
PRK09521 PRK09521
exosome complex RNA-binding protein Csl4; Provisional
 2-75 1.46e-04

exosome complex RNA-binding protein Csl4; Provisional


Pssm-ID: 236547 [Multi-domain]  Cd Length: 189  Bit Score: 40.34  E-value: 1.46e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514960069   2 SVEVGQKLKGKVTGIKNFGAFVALENKQ----------SGLVHISEVSEDYVQDINDLLSLGDEVTVKVISVAEdgKIGL 71
Cdd:PRK09521  61 LLKKGDIVYGRVVDVKEQRALVRIVSIEgserelatskLAYIHISQVSDGYVESLTDAFKIGDIVRAKVISYTD--PLQL 138


                 ....
gi 514960069  72 SIRQ 75
Cdd:PRK09521 139 STKG 142
rpsA PRK13806
30S ribosomal protein S1; Provisional
 5-97 4.30e-04

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 39.71  E-value: 4.30e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514960069   5 VGQKLKGKVTGIKNFGAFVALENKQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISV-AEDGKIGLSIRQAKDKPAVD 83
Cdd:PRK13806 379 PGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISRAGKPATYEKLKPGDSVTLVVEEIdTAKRKISLAPAGAAGSGADD 458

                         90
                 ....*....|....
gi 514960069  84 KSkMKKFDAQEAKP 97
Cdd:PRK13806 459 DD-WKQFAPKKSAP 471
S1_2 pfam13509
S1 domain; The S1 domain was originally identified as a repeat motif in the ribosomal S1 ...
 5-58 7.31e-04

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: 35.97  E-value: 7.31e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 514960069    5 VGQKLKGKVTGIKNFGAFVALENKQSGLVHISEVSEDyvqdindlLSLGDEVTV 58
Cdd:pfam13509   1 IGKINTLKVIRETDFGYFLDGGEGGEVLLPKREVPEE--------LEIGDEVEV 46
S1_Rrp5_repeat_hs1_sc1 cd05693
S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 5-74 9.19e-04

S1_Rrp5_repeat_hs1_sc1: 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 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240198 [Multi-domain]  Cd Length: 100  Bit Score: 36.81  E-value: 9.19e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514960069   5 VGQKLKGKVTGIKNFGAFVALENKQSGLVHISEVSEDYVQ-------------------DINDLLSLGDEVTVKVISVAE 65
Cdd:cd05693    3 EGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTErleeldeeseeeddeeelpDLEDLFSVGQLVRCKVVSLDK 82

                         90
                 ....*....|...
gi 514960069  66 DG----KIGLSIR 74
Cdd:cd05693   83 SKsgkkRIELSLE 95
S1_Rrp5_repeat_hs14 cd05705
S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 3-63 1.73e-03

S1_Rrp5_repeat_hs14: 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 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240210 [Multi-domain]  Cd Length: 74  Bit Score: 35.45  E-value: 1.73e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 514960069   3 VEVGQKLKGKVTGIKNFGAFVALENKQSGLVHISEVSEDYVQD---INDLLSLGDEVTVKVISV 63
Cdd:cd05705    1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDpslYNKYLPEGKLLTAKVLSV 64
S1_RNase_E cd04453
S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential ...
 10-61 2.99e-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: 35.26  E-value: 2.99e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 514960069  10 KGKVT----GIKnfGAFVALENKQSGLVHISEVSEDY---VQDINDLLSLGDEVTVKVI 61
Cdd:cd04453   12 LGRVKkivpGLQ--AAFVDIGLGKNGFLHLSDILPAYfkkHKKIAKLLKEGQEILVQVV 68
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 2-102 4.02e-03

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 37.00  E-value: 4.02e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514960069   2 SVEVGQKLKGKVTGIKNFGAFVALeNKQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISVAE-DGKIGLSIRQAKDKP 80
Cdd:PRK12269 490 SVHIEDSVSGVVKSFTSFGAFIDL-GGFDGLLHVNDMSWGHVARPREFVKKGQTIELKVIRLDQaEKRINLSLKHFQPDP 568

                         90       100
                 ....*....|....*....|..
gi 514960069  81 AVDKSkmKKFDAQEAKPTRLSK 102
Cdd:PRK12269 569 WLEFE--NKFGVNDVVKGRVTK 588
PTZ00248 PTZ00248
eukaryotic translation initiation factor 2 subunit 1; Provisional
 12-89 4.10e-03

eukaryotic translation initiation factor 2 subunit 1; Provisional


Pssm-ID: 240329 [Multi-domain]  Cd Length: 319  Bit Score: 36.56  E-value: 4.10e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514960069  12 KVTGIKNFGAFVAL--ENKQSGLVHISEVSEDYVQDINDLLSLGDEVTVKVISVAED-GKIGLSIRQ--AKDKPAVDK-- 84
Cdd:PTZ00248  24 KVVRITEMGAYVSLleYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEkGYIDLSKKRvsPEDIEACEEkf 103


                 ....*
gi 514960069  85 SKMKK 89
Cdd:PTZ00248 104 SKSKK 108
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 5-90 9.29e-03

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 35.84  E-value: 9.29e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 514960069   5 VGQKLKGKVTGIKNFGAFVALENKQSGLVHISEVSEDYVQDINDLL---SLGDEVTVKVISV-AEDGKIGLSIRQAKDKp 80
Cdd:PRK12269 752 VGSTVEGEVSSVTDFGIFVRVPGGVEGLVRKQHLVENRDGDPGEALrkyAVGDRVKAVIVDMnVKDRKVAFSVRDYQRK- 830

                         90
                 ....*....|
gi 514960069  81 aVDKSKMKKF 90
Cdd:PRK12269 831 -VQRDELSRY 839
 
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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