S1 domain-containing post-transcriptional regulator Ygs; Ygs, as first described in Staphylococcus epidermidis, is a full-length homolog of GSP13 (YugI) from Bacillus subtilis. Each has a single copy of the S1 domain, an RNA-binding domain repeated several times in ribosomal small subunit protein S1, and each has been shown to be induced by stress and improve survival. Ygs was shown in Staphylococcus epidermidis to affect polysaccharide intercellular adhesin biosynthesis, and through it, biofilm formation. More recently, the full-length homolog CvfD was shown to be a post-transcriptional regulator, suggesting all members of this family are.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446990039   2 NNYKIGQHIKVRVTGIQPYGAFVETPNHTEGLIHISEIMDDYVHNLKKFLSEGQIVKAKILSIDDEGKLNLSLKDNDYFK 81
Cdd:NF040578   3 KHYKVGQHIKVKVTGIQPYGAFVETPDNTEGLIHISEVMNDYVHNLKKFLSEGQIVKAKILSIDEEGKLNLSLKDNDYFK 82

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 446990039  82 NYERKKEKQSVLDEIRETEKYGFQTLKERLPIWIKQSKR 120
Cdd:NF040578  83 NYERKKEKRSVLDEIRETEKYGFQTLKERLPVWIKQSKK 121

S1 domain-containing post-transcriptional regulator Ygs; Ygs, as first described in Staphylococcus epidermidis, is a full-length homolog of GSP13 (YugI) from Bacillus subtilis. Each has a single copy of the S1 domain, an RNA-binding domain repeated several times in ribosomal small subunit protein S1, and each has been shown to be induced by stress and improve survival. Ygs was shown in Staphylococcus epidermidis to affect polysaccharide intercellular adhesin biosynthesis, and through it, biofilm formation. More recently, the full-length homolog CvfD was shown to be a post-transcriptional regulator, suggesting all members of this family are.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446990039   2 NNYKIGQHIKVRVTGIQPYGAFVETPNHTEGLIHISEIMDDYVHNLKKFLSEGQIVKAKILSIDDEGKLNLSLKDNDYFK 81
Cdd:NF040578   3 KHYKVGQHIKVKVTGIQPYGAFVETPDNTEGLIHISEVMNDYVHNLKKFLSEGQIVKAKILSIDEEGKLNLSLKDNDYFK 82

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 446990039  82 NYERKKEKQSVLDEIRETEKYGFQTLKERLPIWIKQSKR 120
Cdd:NF040578  83 NYERKKEKRSVLDEIRETEKYGFQTLKERLPVWIKQSKK 121

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446990039   3 NYKIGQHIKVRVTGIQPYGAFVETPNHTEGLIHISEIMDDYVHNLKKFLSEGQIVKAKILSIDDEGKLNLSLKDNDYFKN 82
Cdd:COG1098    2 SIEVGDIVEGKVTGITPFGAFVELPEGTTGLVHISEIADGYVKDINDYLKVGDEVKVKVLSIDEDGKISLSIKQAEEKPK 81

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 446990039  83 YERKKEKQSvldeireTEKYGFQTLKERLPIWIKQSKR 120
Cdd:COG1098   82 RPPRPRRNS-------RPKAGFESFEDKLSKFLKDSDE 112

S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446990039  13 RVTGIQPYGAFVETPNHTEGLIHISEIMDDYVHNLKKFLSEGQIVKAKILSIDDEGKLNLSLK 75
Cdd:cd05692    7 TVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARGRISLSIK 69

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446990039    2 NNYKIGQHIKVRVTGIQPYGAFVETPNHTEGLIHISEI-MDDYVHNLKKFLSEGQIVKAKILSID-DEGKLNLSLKD--N 77
Cdd:TIGR00717 268 KKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMsWVKKNSHPSKVVKKGDEVEVMILDIDpERRRLSLGLKQckA 347

                          90       100
                  ....*....|....*....|....*..
gi 446990039   78 DYFKNYERKKEKQSVLD-EIRETEKYG 103
Cdd:TIGR00717 348 NPWEQFEEKHPVGDRVTgKIKKITDFG 374

S1 domain-containing post-transcriptional regulator Ygs; Ygs, as first described in Staphylococcus epidermidis, is a full-length homolog of GSP13 (YugI) from Bacillus subtilis. Each has a single copy of the S1 domain, an RNA-binding domain repeated several times in ribosomal small subunit protein S1, and each has been shown to be induced by stress and improve survival. Ygs was shown in Staphylococcus epidermidis to affect polysaccharide intercellular adhesin biosynthesis, and through it, biofilm formation. More recently, the full-length homolog CvfD was shown to be a post-transcriptional regulator, suggesting all members of this family are.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446990039   2 NNYKIGQHIKVRVTGIQPYGAFVETPNHTEGLIHISEIMDDYVHNLKKFLSEGQIVKAKILSIDDEGKLNLSLKDNDYFK 81
Cdd:NF040578   3 KHYKVGQHIKVKVTGIQPYGAFVETPDNTEGLIHISEVMNDYVHNLKKFLSEGQIVKAKILSIDEEGKLNLSLKDNDYFK 82

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 446990039  82 NYERKKEKQSVLDEIRETEKYGFQTLKERLPIWIKQSKR 120
Cdd:NF040578  83 NYERKKEKRSVLDEIRETEKYGFQTLKERLPVWIKQSKK 121

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446990039   3 NYKIGQHIKVRVTGIQPYGAFVETPNHTEGLIHISEIMDDYVHNLKKFLSEGQIVKAKILSIDDEGKLNLSLKDNDYFKN 82
Cdd:COG1098    2 SIEVGDIVEGKVTGITPFGAFVELPEGTTGLVHISEIADGYVKDINDYLKVGDEVKVKVLSIDEDGKISLSIKQAEEKPK 81

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 446990039  83 YERKKEKQSvldeireTEKYGFQTLKERLPIWIKQSKR 120
Cdd:COG1098   82 RPPRPRRNS-------RPKAGFESFEDKLSKFLKDSDE 112

S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446990039  13 RVTGIQPYGAFVETPNHTEGLIHISEIMDDYVHNLKKFLSEGQIVKAKILSIDDEGKLNLSLK 75
Cdd:cd05692    7 TVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARGRISLSIK 69

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

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446990039   5 KIGQHIKVRVTGIQPYGAFVETPNHTEGLIHISEIMDDYVHNLKKFLSEGQIVKAKILSIDDEGKLNLSLKD 76
Cdd:COG1185  615 EVGEIYEGKVVRIMDFGAFVEILPGKDGLVHISELADERVEKVEDVLKEGDEVKVKVLEIDDQGRIKLSRKA 686

RNA-binding protein S1;

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446990039   6 IGQHIKVRVTGIQPYGAFVETPNHTEGLIHISEIMDDYVHNLKKFLSEGQIVKAKILSIDDEGKLNLSLK 75
Cdd:PRK08582   5 VGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDDGKIGLSIK 74

Ribosomal protein S1-like RNA-binding domain;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446990039     5 KIGQHIKVRVTGIQPYGAFVETPNHTEGLIHISEIMDDYVHNLKKFLSEGQIVKAKILSIDDE-GKLNLSLK 75
Cdd:smart00316   1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEkGRIILSLK 72

S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446990039  13 RVTGIQPYGAFVETPNHTEGLIHISEIMDDYVHNLKKFLSEGQIVKAKILSIDDEGKLNLS 73
Cdd:cd04472    7 KVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDDRGRISLS 67

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446990039   1 MNNYKIGQHIKVRVTGIQPYGAFVETPNHTEGLIHISEIMDDYVHNLKKFLSEGQIVKAKILSIDDEGK-LNLSLKDNDY 79
Cdd:PRK00087 557 EEKYPVGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKrIRLSIKEVEE 636

                         90
                 ....*....|.
gi 446990039  80 FKNYERKKEKQ 90
Cdd:PRK00087 637 EPGDIEKVELE 647

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446990039    2 NNYKIGQHIKVRVTGIQPYGAFVETPNHTEGLIHISEI-MDDYVHNLKKFLSEGQIVKAKILSID-DEGKLNLSLKD--N 77
Cdd:TIGR00717 268 KKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMsWVKKNSHPSKVVKKGDEVEVMILDIDpERRRLSLGLKQckA 347

                          90       100
                  ....*....|....*....|....*..
gi 446990039   78 DYFKNYERKKEKQSVLD-EIRETEKYG 103
Cdd:TIGR00717 348 NPWEQFEEKHPVGDRVTgKIKKITDFG 374

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446990039   1 MNNYKIGQHIKVRVTGIQPYGAFVETpNHTEGLIHISEIMDDYVHNLKKFLSEGQIVKAKILSIDDE-GKLNLSLKD 76
Cdd:COG0539  184 LEKLEEGDVVEGTVKNITDFGAFVDL-GGVDGLLHISEISWGRVKHPSEVLKVGDEVEVKVLKIDREkERISLSLKQ 259

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446990039   5 KIGQHIKVRVTGIQPYGAFVETPN-HTEGLIHISEIMDDYVHNLKKFLSEGQIVKAKILSIDDE-GKLNLSLK 75
Cdd:cd05708    1 KVGQKIDGTVRRVEDYGVFIDIDGtNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEkKRISLGLK 73

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

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446990039   2 NNYKIGQHIKVRVTGIQPYGAFVETpNHTEGLIHISEIMDDYVHNLKKFLSEGQIVKAKILSIDDE-GKLNLSLK 75
Cdd:PRK00087 473 NSLEEGDVVEGEVKRLTDFGAFVDI-GGVDGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKEnKKLSLSLK 546

S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446990039  13 RVTGIQPYGAFVE---TPNHTEGLIHISEIMDD-YVHNLKKFLSEGQIVKAKILSIDDeGKLNLSLKDND 78
Cdd:cd05684    7 KVTSIMDFGCFVQlegLKGRKEGLVHISQLSFEgRVANPSDVVKRGQKVKVKVISIQN-GKISLSMKDVD 75

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446990039   6 IGQHIKVRVTGIQPYGAFVETPNHT-EGLIHISEIMDDYVH-----------NLKKFLSEGQIVKAKILSID-DEGKLNL 72
Cdd:cd04471    1 VGEEFDGVISGVTSFGLFVELDNLTvEGLVHVSTLGDDYYEfdeenhalvgeRTGKVFRLGDKVKVRVVRVDlDRRKIDF 80

                 ..
gi 446990039  73 SL 74
Cdd:cd04471   81 EL 82

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

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446990039    2 NNYKIGQHIKVRVTGIQPYGAFVETPNHTEGLIHISEIMDDYVHNLKKFLSEGQIVKAKILSID-DEGKLNLSLK 75
Cdd:TIGR00717 442 AKYKVGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDkKNRKVSLSVK 516

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446990039  12 VRVTGIQPYGAFV---ETPNhTEGLIHISEIMDDYVHNLKKFLSEGQIVKAKILSID-DEGKLNLSLKD-NDyfknyERK 86
Cdd:COG1093   16 GTVKEVKDFGAYVtldEYEG-KEGFIHISEVASGWIKNIRDYVREGQKVVCKVLRVDpKRGHIDLSLKRvNE-----HQR 89

                 ...
gi 446990039  87 KEK 89
Cdd:COG1093   90 REK 92

30S ribosomal protein S1; Reviewed

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446990039   6 IGQHIKVRVTGIQPYGAFVETPNHTEGLIHISEIMDDYVHNLKKFLSEGQIVKAKILSID-DEGKLNLSLK 75
Cdd:PRK07899 293 IGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDlERRRISLSLK 363

Exoribonuclease R [Transcription];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446990039   5 KIGQHIKVRVTGIQPYGAFVETPNHT-EGLIHISEIMDDYVH-----------NLKKFLSEGQIVKAKILSID-DEGKLN 71
Cdd:COG0557  621 RVGEEFEGVISGVTSFGLFVELDELGvEGLVHVSSLGDDYYEyderrqalvgeRTGKRYRLGDRVEVRVVRVDlDRRQID 700

                 ...
gi 446990039  72 LSL 74
Cdd:COG0557  701 FEL 703

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.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446990039   7 GQHIKVRVTGIQPYGAFVETPNHTEGLIHISEIMDDYVHNLKKFLSEGQIVKAKILSID-DEGKLNLS 73
Cdd:cd05707    1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDpDNGRIEMT 68

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.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446990039  14 VTGIQPYGAFVETPNHTEGLIHISEIMDDYVHNLKKFLSEGQIVKAKILSIDDE-GKLNLSL 74
Cdd:cd04461   22 VRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEkQRFLLSL 83

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446990039   5 KIGQHIKVRVTGIQPYGAFVETPNHTEGLIHISEIMDDYVHNLKKFLSEGQIVKAKILSID-DEGKLNLSLK 75
Cdd:cd05706    2 KVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDvPNKKIALSLR 73

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446990039   7 GQHIKVRVTGIQPYGAFVETPNHTEGLIHISEIMDDYVHNLKKFLSEGQIVKAKILSIDDEG-KLNLSLK 75
Cdd:cd05691    1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNrKISLSIK 70

DNA-directed RNA polymerase, subunit E'/Rpb7 [Transcription]; DNA-directed RNA polymerase, subunit E'/Rpb7 is part of the Pathway/BioSystem: RNA polymerase

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446990039  14 VTGIQPYGAFVET-PnhTEGLIHISEIMDDYV-----------HNLKKFLSEGQIVKAKILSI 64
Cdd:COG1095   89 VVEVVEFGAFVRIgP--IDGLLHISQIMDDYVdydekngrligKESKRTLKVGDVVRARIVAV 149

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

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446990039    1 MNNYKIGQHIKVRVTGIQPYGAFVETpNHTEGLIHISEIMDDYVHNLKKFLSEGQIVKAKILSID-DEGKLNLSLK 75
Cdd:TIGR00717 182 LENLKEGDVVKGVVKNITDFGAFVDL-GGVDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDkEKGRISLSLK 256

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.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 446990039   4 YKIGQHIKVRVTGIQPYGAFVETPNHTEGLIHISEiMDDYVHNL--KKFLSEGQIVKAKILSIDDE 67
Cdd:cd05689    1 YPEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSE-MDWTNKNIhpSKVVSLGDEVEVMVLDIDEE 65

DNA-directed RNA polymerase subunit E'; Provisional

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446990039  14 VTGIQPYGAFVET-PnhTEGLIHISEIMDDYV-----------HNLKKFLSEGQIVKAKI--LSIDDE 67
Cdd:PRK08563  89 VVEVVEFGAFVRIgP--VDGLLHISQIMDDYIsydpkngrligKESKRVLKVGDVVRARIvaVSLKER 154

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".

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446990039   5 KIGQHIKVRVTGIQPYGAFVETPNHTEGLIHISEI----MDDYVHNLKKFLSEGQIVKAKILSIDDEGKLNLSLKDNDYF 80
Cdd:cd05789    5 EVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVnlprTDEDELNMRSYLDEGDLIVAEVQSVDSDGSVSLHTRSLKYG 84

                 .
gi 446990039  81 K 81
Cdd:cd05789   85 K 85

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

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446990039    3 NYKIGQHIKVRVTGIQPYGAFVETPNHTEGLIHISEIM-DDYVHNLKKFLSEGQIVKAKILSIDDEGK-LNLSLK 75
Cdd:TIGR00717 356 KHPVGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISwDKDGREADHLYKKGDEIEAVVLAVDKEKKrISLGVK 430

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446990039   7 GQHIKVRVTGIQPYGAFVETPNHTEGLIHISEIMDDYVHNLKKFLSEGQIVKAKILSIDD-EGKLNLSLK 75
Cdd:cd05687    1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDeEGNVVLSKR 70

exosome complex RNA-binding protein Csl4; Provisional

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446990039  12 VRVTGIQPYGAFVETPnhTEGLIHISEIMDDYVHNLKKFLSEGQIVKAKILSIDDegKLNLSLKDNDY 79
Cdd:PRK09521  82 VRIVSIEGSERELATS--KLAYIHISQVSDGYVESLTDAFKIGDIVRAKVISYTD--PLQLSTKGKDL 145

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446990039   7 GQHIKVRVTGIQPYGAFVETPNHTEGLI---HISEIMddYVHNLKKFlSEGQIVKAKILSID-DEGKLNLSL 74
Cdd:cd05697    1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVppmHLADVR--LKHPEKKF-KPGLKVKCRVLSVEpERKRLVLTL 69

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446990039   5 KIGQHIKVRVTGIQPYGAFVETPNHTEGLIHISEIMDDYVHN---LKKFLSEGQIVKAKILSIDDEGKL-NLS 73
Cdd:cd05705    2 KEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDpslYNKYLPEGKLLTAKVLSVNSEKNLvELS 74