NCBI Conserved Domain Search

30S ribosomal protein S1; Reviewed

631-703

2.74e-18

30S ribosomal protein S1; Reviewed

Pssm-ID: 235851 [Multi-domain] Cd Length: 390 Bit Score: 87.62 E-value: 2.74e-18

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1083809137 631 VGEVLKGEVVKIADFGAFVKLNSFtDGMVHISELAPFRVERVSDIIKEGMIVPVKVISIDREKSRIGLSIREA 703
Cdd:PRK06676  192 EGDVVEGTVARLTDFGAFVDIGGV-DGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKDT 263

RNase_PH_archRRP41

cd11366

RRP41 subunit of archaeal exosome; The RRP41 subunit of the archaeal exosome is a member of ...

332-551

3.83e-18

RRP41 subunit of archaeal exosome; The RRP41 subunit of the archaeal exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of dimers). In archaea, the ring is formed by three Rrp41:Rrp42 dimers. The central chamber within the ring contains three phosphorolytic active sites located in an Rrp41 pocket at the interface between Rrp42 and Rrp41. The ring is capped by three copies of Rrp4 and/or Csl4 which contain putative RNA interaction domains. The archaeal exosome degrades single-stranded RNA (ssRNA) in the 3'-5' direction, but also can catalyze the reverse reaction of adding nucleoside diphosphates to the 3'-end of RNA which has been shown to lead to the formation of poly-A-rich tails on RNA.

Pssm-ID: 206771 [Multi-domain] Cd Length: 214 Bit Score: 83.54 E-value: 3.83e-18

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083809137 332 ELRDIYAQAGgvsaVLH---GSGIFYRGGTHVLSVLTlgGPED---RHSIDGMQTKLEKRfmhhYNFPPYSSGETGRAGf 405
Cdd:cd11366     1 ELRPIKIEVG----VLKnadGSAYVEWGNNKIIAAVY--GPREvhpRHLQLPDRAVIRVR----YNMAPFSVDERKRPG- 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083809137 406 TNRREVGHGALAEKALAMVLPpLSEFPYT-IRVVSESMASNGSTSQASICASTLALMDGGVPILAPVAGIAMGLMHEtde 484
Cdd:cd11366    70 PDRREIEISKVIKEALEPAII-LEEFPRTaIDVFVEVLQADAGTRVAGLNAASLALADAGIPMRDLVAACAAGKVDG--- 145

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1083809137 485 kyKILTDIQGPEDHHGDMDFKVAGTRKG--VTAIQLDVKVEGVPIKilgEAMEQAKNARIIILDkIQKE 551
Cdd:cd11366   146 --KIVLDLNKEEDNYGEADMPIAMMPNLgeITLLQLDGDLTPDEFK---QAIELAKKGCKRIYE-LQKE 208

smart00316

Ribosomal protein S1-like RNA-binding domain;

631-701

4.67e-18

Ribosomal protein S1-like RNA-binding domain;

Pssm-ID: 197648 [Multi-domain] Cd Length: 72 Bit Score: 78.80 E-value: 4.67e-18

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1083809137  631 VGEVLKGEVVKIADFGAFVKLNSFTDGMVHISELAPFRVERVSDIIKEGMIVPVKVISIDREKSRIGLSIR 701
Cdd:smart00316   2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72

PRK08059

general stress protein 13; Validated

625-702

7.85e-18

general stress protein 13; Validated

Pssm-ID: 181215 [Multi-domain] Cd Length: 123 Bit Score: 80.09 E-value: 7.85e-18

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1083809137 625 MTHEYTVGEVLKGEVVKIADFGAFVKLNSFTDGMVHISELAPFRVERVSDIIKEGMIVPVKVISIDREKSRIGLSIRE 702
Cdd:PRK08059    1 MMSQYEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRA 78

rpsA

30S ribosomal protein S1; Reviewed

624-704

2.73e-17

30S ribosomal protein S1; Reviewed

Pssm-ID: 235851 [Multi-domain] Cd Length: 390 Bit Score: 84.54 E-value: 2.73e-17

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083809137 624 EMTHEYTVGEVLKGEVVKIADFGAFVKLNSFTDGMVHISELAPFRVERVSDIIKEGMIVPVKVISIDREKSRIGLSIREA 703
Cdd:PRK06676  270 GVEEKLPEGDVIEGTVKRLTDFGAFVEVLPGVEGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISLSIKAL 349


                  .
gi 1083809137 704 D 704
Cdd:PRK06676  350 E 350

S1_DHX8_helicase

cd05684

S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...

632-704

4.00e-17

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: 76.51 E-value: 4.00e-17

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1083809137 632 GEVLKGEVVKIADFGAFVKLNSF---TDGMVHISELAPFRVER-VSDIIKEGMIVPVKVISIDREKsrIGLSIREAD 704
Cdd:cd05684     1 GKIYKGKVTSIMDFGCFVQLEGLkgrKEGLVHISQLSFEGRVAnPSDVVKRGQKVKVKVISIQNGK--ISLSMKDVD 75

S1_dom_CvfD

NF040579

CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator; CvfD, Ygs, and GSP13 form a ...

629-705

4.51e-17

Pssm-ID: 468553 [Multi-domain] Cd Length: 113 Bit Score: 77.47 E-value: 4.51e-17

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1083809137 629 YTVGEVLKGEVVKIADFGAFVKLNSFTDGMVHISELAPFRVERVSDIIKEGMIVPVKVISIDREKSRIGLSIREADK 705
Cdd:NF040579    1 YKIGDIVEGKVTGIQPYGAFVALDEHTQGLIHISEIKHGYVKDINDFLKVGQEVKVKVLDIDEYTGKISLSLRALEE 77

PRK00087

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

631-702

1.02e-16

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

Pssm-ID: 234623 [Multi-domain] Cd Length: 647 Bit Score: 84.23 E-value: 1.02e-16

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1083809137 631 VGEVLKGEVVKIADFGAFVKLNSFtDGMVHISELAPFRVERVSDIIKEGMIVPVKVISIDREKSRIGLSIRE 702
Cdd:PRK00087  477 EGDVVEGEVKRLTDFGAFVDIGGV-DGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKK 547

S1_IF2_alpha

cd04452

S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...

631-701

1.24e-16

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: 74.93 E-value: 1.24e-16

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1083809137 631 VGEVLKGEVVKIADFGAFVKLNSFTD--GMVHISELAPFRVERVSDIIKEGMIVPVKVISIDREKSRIGLSIR 701
Cdd:cd04452     3 EGELVVVTVKSIADMGAYVSLLEYGNieGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKK 75

S1_Tex

cd05685

S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...

632-699

1.91e-16

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: 74.19 E-value: 1.91e-16

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1083809137 632 GEVLKGEVVKIADFGAFVKLNSFTDGMVHISELAPFRVERVSDIIKEGMIVPVKVISIDREKSRIGLS 699
Cdd:cd05685     1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68

S1_RPS1_repeat_ec3

cd05688

S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...

631-699

4.43e-16

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: 73.05 E-value: 4.43e-16

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1083809137 631 VGEVLKGEVVKIADFGAFVKLNSFtDGMVHISELAPFRVERVSDIIKEGMIVPVKVISIDREKSRIGLS 699
Cdd:cd05688     1 EGDVVEGTVKSITDFGAFVDLGGV-DGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68

RNase_PH

cd11358

RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that ...

333-541

9.36e-16

RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that catalyze the 3' to 5' processing and decay of RNA substrates. Evolutionarily related members can be fond in prokaryotes, archaea, and eukaryotes. Bacterial ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain and is involved in mRNA degradation in a 3'-5' direction. Archaeal exosomes contain two individually encoded RNase PH-like 3'-5' exoribonucleases and are required for 3' processing of the 5.8S rRNA. The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits, but it is not a phosphorolytic enzyme per se; it directly associates with Rrp44 and Rrp6, which are hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. All members of the RNase PH-like family form ring structures by oligomerization of six domains or subunits, except for a total of 3 subunits with tandem repeats in the case of PNPase, with a central channel through which the RNA substrate must pass to gain access to the phosphorolytic active sites.

Pssm-ID: 206766 [Multi-domain] Cd Length: 218 Bit Score: 76.98 E-value: 9.36e-16

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083809137 333 LRDIYAQAGGVSAVlHGSGIFYRGGTHVLSVLTLGGPEDrhsiDGMQTKLEKRFMHHYNFPPYSSGETgRAGFTNRREVG 412
Cdd:cd11358     1 FRPVEIETGVLNQA-DGSALVKLGNTKVICAVTGPIVEP----DKLERPDKGTLYVNVEISPGAVGER-RQGPPGDEEME 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083809137 413 HGALAEKAL-AMVLPPLS--EFPYTIRVVSESMASNGSTSQASICASTLALMDGGVP-------------ILAPVAGIAM 476
Cdd:cd11358    75 ISRLLERTIeASVILDKStrKPSWVLYVDIQVLSRDGGLLDACWNAAIAALKDAGIPrvfvderspplllMKDLIVAVSV 154

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1083809137 477 GLmhetDEKYKILTDIQGPEDHHGDMDFKVAGTRKG-VTAIQLDVKVEGVPIKILgEAMEQAKNAR 541
Cdd:cd11358   155 GG----ISDGVLLLDPTGEEEELADSTLTVAVDKSGkLCLLSKVGGGSLDTEEIK-ECLELAKKRS 215

PRK05807

RNA-binding protein S1;

631-705

1.10e-15

RNA-binding protein S1;

Pssm-ID: 235614 [Multi-domain] Cd Length: 136 Bit Score: 74.40 E-value: 1.10e-15

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1083809137 631 VGEVLKGEVVKIADFGAFVKLNSFTdGMVHISELAPFRVERVSDIIKEGMIVPVKVISIDrEKSRIGLSIREADK 705
Cdd:PRK05807    5 AGSILEGTVVNITNFGAFVEVEGKT-GLVHISEVADTYVKDIREHLKEQDKVKVKVISID-DNGKISLSIKQAMK 77

S1_RPS1_repeat_hs4

cd05692

S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...

632-701

1.62e-15

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: 71.55 E-value: 1.62e-15

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083809137 632 GEVLKGEVVKIADFGAFVKLNSFTDGMVHISELAPFRVERVSDIIKEGMIVPVKVISIDREKsRIGLSIR 701
Cdd:cd05692     1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARG-RISLSIK 69

Tex

COG2183

Transcriptional accessory protein Tex/SPT6 [Transcription];

631-705

3.14e-15

Transcriptional accessory protein Tex/SPT6 [Transcription];

Pssm-ID: 441786 [Multi-domain] Cd Length: 719 Bit Score: 79.68 E-value: 3.14e-15

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1083809137 631 VGEVLKGEVVKIADFGAFVKLNSFTDGMVHISELAPFRVERVSDIIKEGMIVPVKVISIDREKSRIGLSIREADK 705
Cdd:COG2183   641 PGMILEGTVTNVTDFGAFVDIGVHQDGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEVDLKRKRISLSMKLDDE 715

rpsA

30S ribosomal protein S1; Reviewed

616-700

3.41e-15

30S ribosomal protein S1; Reviewed

Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 79.05 E-value: 3.41e-15

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083809137 616 EKAKSIVLEMTHEytvGEVLKGEVVKIADFGAFVKLNSfTDGMVHISELAPFRVERVSDIIKEGMIVPVKVISIDREKSR 695
Cdd:PRK06299  189 AEEREELLENLEE---GQVVEGVVKNITDYGAFVDLGG-VDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKEKKR 264


                  ....*
gi 1083809137 696 IGLSI 700
Cdd:PRK06299  265 VSLGL 269

rpsA

30S ribosomal protein S1; Reviewed

628-705

6.50e-15

30S ribosomal protein S1; Reviewed

Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 78.28 E-value: 6.50e-15

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1083809137 628 EYTVGEVLKGEVVKIADFGAFVKLNSFTDGMVHISELAPFRVERVSDIIKEGMIVPVKVISIDREKSRIGLSIREADK 705
Cdd:PRK06299  457 KHKKGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIKALDE 534

rpsA

PRK13806

30S ribosomal protein S1; Provisional

631-703

1.08e-14

30S ribosomal protein S1; Provisional

Pssm-ID: 237516 [Multi-domain] Cd Length: 491 Bit Score: 77.07 E-value: 1.08e-14

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1083809137 631 VGEVLKGEVVKIADFGAFVKLNSFTDGMVHISELAPFRVERVSDIIKEGMIVPVKVISIDREKS----RIGLSIREA 703
Cdd:PRK13806  202 EGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKgkglRISLSIKQA 278

PRK08582

RNA-binding protein S1;

631-703

2.18e-14

RNA-binding protein S1;

Pssm-ID: 236305 [Multi-domain] Cd Length: 139 Bit Score: 70.45 E-value: 2.18e-14

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1083809137 631 VGEVLKGEVVKIADFGAFVKLNSFTDGMVHISELAPFRVERVSDIIKEGMIVPVKVISIDREkSRIGLSIREA 703
Cdd:PRK08582    5 VGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDD-GKIGLSIKKA 76

S1_like

cd00164

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...

635-699

2.49e-14

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: 68.18 E-value: 2.49e-14

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1083809137 635 LKGEVVKIADFGAFVKLNSFTDGMVHISELAPFRVERVSDIIKEGMIVPVKVISIDREKSRIGLS 699
Cdd:cd00164     1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65

rpsA

PRK13806

30S ribosomal protein S1; Provisional

629-703

2.68e-14

30S ribosomal protein S1; Provisional

Pssm-ID: 237516 [Multi-domain] Cd Length: 491 Bit Score: 75.92 E-value: 2.68e-14

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1083809137 629 YTVGEVLKGEVVKIADFGAFVKLNSFTDGMVHISELA-PFRVERVSDIIKEGMIVPVKVISIDREKSRIGLSIREA 703
Cdd:PRK13806  290 LKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSwTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRDA 365

pfam00575

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...

631-700

3.05e-14

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: 68.08 E-value: 3.05e-14

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083809137 631 VGEVLKGEVVKIADFGAFVKLNSFTDGMVHISELAPFRVERVSDIIKEGMIVPVKVISIDREKSRIGLSI 700
Cdd:pfam00575   3 KGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72

RNase_PH

cd11358

RNase PH-like 3'-5' exoribonucleases; RNase PH-like 3'-5' exoribonucleases are enzymes that ...

17-174

6.28e-14

Pssm-ID: 206766 [Multi-domain] Cd Length: 218 Bit Score: 71.59 E-value: 6.28e-14

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083809137  17 AIFTDLAEQAHGSVMLKYGETIVLATVC---MSKDKQNGLGFFNLTVDYVEKFYATGKilgsrfmRREGKPSEDAILASR 93
Cdd:cd11358     5 EIETGVLNQADGSALVKLGNTKVICAVTgpiVEPDKLERPDKGTLYVNVEISPGAVGE-------RRQGPPGDEEMEISR 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083809137  94 VIDRTLRPLF--DQSIRH---AVQVIVTVISVDDNdPVILAVNAASLALAVSNIPW-------------NGPIGCVRIGK 155
Cdd:cd11358    78 LLERTIEASVilDKSTRKpswVLYVDIQVLSRDGG-LLDACWNAAIAALKDAGIPRvfvderspplllmKDLIVAVSVGG 156

                         170
                  ....*....|....*....
gi 1083809137 156 YNDENLKINLakLRDEDSL 174
Cdd:cd11358   157 ISDGVLLLDP--TGEEEEL 173

rpsA

PRK07899

30S ribosomal protein S1; Reviewed

626-704

7.78e-14

30S ribosomal protein S1; Reviewed

Pssm-ID: 236126 [Multi-domain] Cd Length: 486 Bit Score: 74.31 E-value: 7.78e-14

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1083809137 626 THeyTVGEVLKGEVVKIADFGAFVKLNSFTDGMVHISELAPFRVERVSDIIKEGMIVPVKVISIDREKSRIGLSIREAD 704
Cdd:PRK07899  290 TH--AIGQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLERRRISLSLKQAN 366

rpsA

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...

615-702

9.14e-14

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: 74.39 E-value: 9.14e-14

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083809137 615 AEKAKSIVLEMTHEytvGEVLKGEVVKIADFGAFVKLNSFtDGMVHISELAPFRVERVSDIIKEGMIVPVKVISIDREKS 694
Cdd:TIGR00717 174 RSQAREELLENLKE---GDVVKGVVKNITDFGAFVDLGGV-DGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKG 249


                  ....*...
gi 1083809137 695 RIGLSIRE 702
Cdd:TIGR00717 250 RISLSLKQ 257

RNase_PH_RRP41

cd11370

RRP41 subunit of eukaryotic exosome; The RRP41 subunit of eukaryotic exosome is a member of ...

324-553

1.25e-13

RRP41 subunit of eukaryotic exosome; The RRP41 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts.

Pssm-ID: 206775 [Multi-domain] Cd Length: 226 Bit Score: 70.65 E-value: 1.25e-13

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083809137 324 RADGRGMDELRDIYAQAGgVSAVLHGSGIFYRGGTHVLSVLTlgGP-EDRHSIDGMQTKLEKRFmhHYNFPPYSSGETGR 402
Cdd:cd11370     3 RLDGRRPNELRRIRCRIG-VFSSADGSAYLEQGNTKVLAAVY--GPhEPRNRSQALHDRAVVNC--EYSMATFSTGERKR 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083809137 403 AGFTNRREVGHGALAEKALAMVLppLSE-FPYT-IRVVSESMASNGSTSQASICASTLALMDGGVPILAPVAGIAMGLMH 480
Cdd:cd11370    78 RGKGDRRSTELSLAIRQTFEAVI--LTHlYPRSqIDIYVQVLQADGGLLAACINAATLALIDAGIPMKDYVCACSAGYLD 155

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1083809137 481 ETdekykILTDIQGPEDHHGDMDFKVA--GTRKGVTAIQLDVKvegVPIKILGEAMEQAKNARIIILDKIQKEIK 553
Cdd:cd11370   156 ST-----PLLDLNYLEESGDLPDLTVAvlPKSDKVVLLQMESR---LHLDRLEKVLELAIEGCKVIREIMDEVVR 222

PRK03987

translation initiation factor IF-2 subunit alpha; Validated

631-701

6.86e-13

translation initiation factor IF-2 subunit alpha; Validated

Pssm-ID: 235188 [Multi-domain] Cd Length: 262 Bit Score: 69.47 E-value: 6.86e-13

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1083809137 631 VGEVLKGEVVKIADFGAFVKLNSFTD--GMVHISELAPFRVERVSDIIKEGMIVPVKVISIDREKSRIGLSIR 701
Cdd:PRK03987    8 EGELVVGTVKEVKDFGAFVTLDEYPGkeGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLK 80

SUI2

COG1093

Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure ...

631-701

1.87e-12

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: 67.92 E-value: 1.87e-12

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1083809137 631 VGEVLKGEVVKIADFGAFVKLNSFTD--GMVHISELAPFRVERVSDIIKEGMIVPVKVISIDREKSRIGLSIR 701
Cdd:COG1093    10 EGELVVGTVKEVKDFGAYVTLDEYEGkeGFIHISEVASGWIKNIRDYVREGQKVVCKVLRVDPKRGHIDLSLK 82

rpsA

30S ribosomal protein S1; Reviewed

628-701

4.78e-12

30S ribosomal protein S1; Reviewed

Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 69.04 E-value: 4.78e-12

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1083809137 628 EYTVGEVLKGEVVKIADFGAFVKLNSFTDGMVHISELAPFRVER-VSDIIKEGMIVPVKVISIDREKSRIGLSIR 701
Cdd:PRK06299  283 KYPVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMSWTKKNKhPSKVVSVGQEVEVMVLEIDEEKRRISLGLK 357

rpsA

30S ribosomal protein S1; Reviewed

624-701

5.54e-12

30S ribosomal protein S1; Reviewed

Pssm-ID: 235775 [Multi-domain] Cd Length: 565 Bit Score: 69.04 E-value: 5.54e-12

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1083809137 624 EMTHEYTVGEVLKGEVVKIADFGAFVKLNSFTDGMVHISELAPFR-VERVSDIIKEGMIVPVKVISIDREKSRIGLSIR 701
Cdd:PRK06299  366 EFAEKYPVGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISWDKkGEEAVELYKKGDEVEAVVLKVDVEKERISLGIK 444

KH-I_PNPase

cd02393

type I K homology (KH) RNA-binding domain found in polyribonucleotide nucleotidyltransferase ...

562-628

9.43e-12

type I K homology (KH) RNA-binding domain found in polyribonucleotide nucleotidyltransferase (PNPase) and similar proteins; PNPase, also called polynucleotide phosphorylase, is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. It catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction. It is also involved, along with RNase II, in tRNA processing. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. The model corresponds to the KH domain.

Pssm-ID: 411803 [Multi-domain] Cd Length: 70 Bit Score: 60.95 E-value: 9.43e-12

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1083809137 562 NAPKILIIKINTDMIGMVIGGGGKTIKEIKEKTGAEITIEDDGTVYFTGK-GDGAEKAKSIVLEMTHE 628
Cdd:cd02393     1 YAPRITTIKIPPDKIGDVIGPGGKTIRAIIEETGAKIDIEDDGTVTIFATdKESAEAAKAMIEDIVAE 68

S1_pNO40

cd05686

S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function ...

633-700

1.22e-11

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: 60.57 E-value: 1.22e-11

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1083809137 633 EVLKGEVVKIADFGAFVKLNSF-TDGMVHISELAPFRVERVSDIIKEGMIVPVKVISIDrEKSRIGLSI 700
Cdd:cd05686     5 QIFKGEVASVTEYGAFVKIPGCrKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGRE-MKDKMKLSL 72

S1_RPS1_repeat_ec5

cd05690

S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...

632-698

2.92e-11

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: 59.43 E-value: 2.92e-11

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1083809137 632 GEVLKGEVVKIADFGAFVKLNSFTDGMVHISELA-PFRVERVSDIIKEGMIVPVKVISIDREKSRIGL 698
Cdd:cd05690     1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISwTQRVRHPSEIYKKGQEVEAVVLNIDVERERISL 68

S1_Rrp5_repeat_sc12

cd05708

S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...

630-707

3.27e-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: 59.65 E-value: 3.27e-11

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1083809137 630 TVGEVLKGEVVKIADFGAFVKL-NSFTDGMVHISELAPFRVERVSDIIKEGMIVPVKVISIDREKSRIGLSIREAdkYF 707
Cdd:cd05708     1 KVGQKIDGTVRRVEDYGVFIDIdGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKAS--YF 77

rpsA

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...

624-701

3.38e-11

Pssm-ID: 273232 [Multi-domain] Cd Length: 516 Bit Score: 66.30 E-value: 3.38e-11

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1083809137 624 EMTHEYTVGEVLKGEVVKIADFGAFVKLNSFTDGMVHISELAPFRVERVSDIIKEGMIVPVKVISIDREKSRIGLSIR 701
Cdd:TIGR00717 439 KFAAKYKVGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 516

rpsA

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...

623-703

9.51e-11

Pssm-ID: 273232 [Multi-domain] Cd Length: 516 Bit Score: 64.76 E-value: 9.51e-11

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083809137 623 LEMTHEYTVGEVLKGEVVKIADFGAFVKLNSFTDGMVHISELA-PFRVERVSDIIKEGMIVPVKVISIDREKSRIGLSIR 701
Cdd:TIGR00717 264 EAIEKKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSwVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLK 343


                  ..
gi 1083809137 702 EA 703
Cdd:TIGR00717 344 QC 345

PRK07252

S1 RNA-binding domain-containing protein;

631-708

2.08e-09

S1 RNA-binding domain-containing protein;

Pssm-ID: 180908 [Multi-domain] Cd Length: 120 Bit Score: 55.86 E-value: 2.08e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083809137 631 VGEVLKGEVVKIADFGAFVKLNSFTDGMVHISELAPFRVERVSDIIKEGMIVPVKVISIDREKSRIGLSIR--EADKYFF 708
Cdd:PRK07252    3 IGDKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLRtlEEEKQHF 82

rpsA

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...

629-702

3.77e-09

Pssm-ID: 273232 [Multi-domain] Cd Length: 516 Bit Score: 59.75 E-value: 3.77e-09

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1083809137 629 YTVGEVLKGEVVKIADFGAFVKLNSFTDGMVHISELAPFRVERVSDIIKE-GMIVPVKVISIDREKSRIGLSIRE 702
Cdd:TIGR00717 357 HPVGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISWDKDGREADHLYKkGDEIEAVVLAVDKEKKRISLGVKQ 431

S1_RPS1_repeat_ec6

cd05691

S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...

632-701

6.11e-09

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: 53.04 E-value: 6.11e-09

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083809137 632 GEVLKGEVVKIADFGAFVKLNSFTDGMVHISELAPFRVERVSDIIKEGMIVPVKVISIDREKSRIGLSIR 701
Cdd:cd05691     1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIK 70

rpsA

PRK07899

30S ribosomal protein S1; Reviewed

632-701

6.13e-09

30S ribosomal protein S1; Reviewed

Pssm-ID: 236126 [Multi-domain] Cd Length: 486 Bit Score: 58.90 E-value: 6.13e-09

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083809137 632 GEVLKGEVVKIADFGAFVKLNSfTDGMVHISELAPFRVERVSDIIKEGMIVPVKVISIDREKSRIGLSIR 701
Cdd:PRK07899  209 GQVRKGVVSSIVNFGAFVDLGG-VDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLSLK 277

PRK12269

bifunctional cytidylate kinase/ribosomal protein S1; Provisional

623-702

1.46e-08

bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Pssm-ID: 105491 [Multi-domain] Cd Length: 863 Bit Score: 58.18 E-value: 1.46e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083809137 623 LEMTHEYTVGEVLKGEVVKIADFGAFVKLNSFTDGMVHISELAPF-RVERVSDIIKEGMIVPVKVISIDREKSRIGLSIR 701
Cdd:PRK12269  570 LEFENKFGVNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFSWVkKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLK 649


                  .
gi 1083809137 702 E 702
Cdd:PRK12269  650 Q 650

S1_RpoE

cd04460

S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...

633-703

1.75e-08

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: 52.67 E-value: 1.75e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083809137 633 EVLKGEVVKIADFGAFVKLNSFtDGMVHISELAPFRV-----------ERVSDIIKEGMIVPVKVISIDR-----EKSRI 696
Cdd:cd04460     1 EVVEGEVVEVVDFGAFVRIGPV-DGLLHISQIMDDYIsydpknkrligEETKRVLKVGDVVRARIVAVSLkerrpRESKI 79


                  ....*..
gi 1083809137 697 GLSIREA 703
Cdd:cd04460    80 GLTMRQP 86

rpsA

30S ribosomal protein S1; Reviewed

623-704

8.59e-08

30S ribosomal protein S1; Reviewed

Pssm-ID: 235851 [Multi-domain] Cd Length: 390 Bit Score: 54.88 E-value: 8.59e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083809137 623 LEMTHEYTVGEVLKGEVVKIADFGAFVKL-NSFTDGMVHISELAPFRVERVSDIIKEGMIVPVKVISIDREKSRIGLSIR 701
Cdd:PRK06676    9 LNSVKEVEVGDVVTGEVLKVEDKQVFVNIeGYKVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNLLLSKR 88


                  ...
gi 1083809137 702 EAD 704
Cdd:PRK06676   89 RLE 91

RpsA

COG0539

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...

628-705

1.08e-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: 54.28 E-value: 1.08e-07

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1083809137 628 EYTVGEVLKGEVVKIADFGAFVKLNSFTDGMVHISElapFRVERVSDIIKEGMIVPVKVISIDREKSRIGLSIREADK 705
Cdd:COG0539    15 ELKEGDIVKGTVVSIDDDEVLVDIGYKSEGIIPLSE---FSDEPGELEVKVGDEVEVYVEKVEDGEGEIVLSKKKADR 89

S1_RPS1_repeat_ec4

cd05689

S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...

629-698

2.00e-07

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: 48.73 E-value: 2.00e-07

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1083809137 629 YTVGEVLKGEVVKIADFGAFVKLNSFTDGMVHISEL-------APFRVERVSDiikegmIVPVKVISIDREKSRIGL 698
Cdd:cd05689     1 YPEGTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMdwtnkniHPSKVVSLGD------EVEVMVLDIDEERRRISL 71

S1_RPS1_repeat_ec1_hs1

cd05687

S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...

632-701

2.09e-07

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: 48.68 E-value: 2.09e-07

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083809137 632 GEVLKGEVVKIADFGAFVKLNSFTDGMVHISELAPFRVERVSDIIKEGMIVPVKVISIDREKSRIGLSIR 701
Cdd:cd05687     1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR 70

RPB7

COG1095

DNA-directed RNA polymerase, subunit E'/Rpb7 [Transcription]; DNA-directed RNA polymerase, ...

597-701

5.41e-07

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

Pssm-ID: 440712 [Multi-domain] Cd Length: 171 Bit Score: 50.18 E-value: 5.41e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083809137 597 EITIEDDGTVYFtgkGDGAE------KAKSIVLEMtheytvGEVLKGEVVKIADFGAFVKLNSFtDGMVHISELAPFRV- 669
Cdd:COG1095    50 DVKVIGEGKIVP---GDGATyhdvefDALTFKPEL------QEVVEGEVVEVVEFGAFVRIGPI-DGLLHISQIMDDYVd 119

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1083809137 670 ----------ERVSDIIKEGMIVPVKVISID-REK----SRIGLSIR 701
Cdd:COG1095   120 ydekngrligKESKRTLKVGDVVRARIVAVSlNEKsprdSKIGLTMR 166

PRK12269

bifunctional cytidylate kinase/ribosomal protein S1; Provisional

616-701

6.96e-07

bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Pssm-ID: 105491 [Multi-domain] Cd Length: 863 Bit Score: 52.79 E-value: 6.96e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083809137 616 EKAKSIVLEMTHEYTVGEVLKGEVVKIADFGAFVKLNSFtDGMVHISELAPFRVERVSDIIKEGMIVPVKVISIDREKSR 695
Cdd:PRK12269  478 ERARQAREEFFNSVHIEDSVSGVVKSFTSFGAFIDLGGF-DGLLHVNDMSWGHVARPREFVKKGQTIELKVIRLDQAEKR 556


                  ....*.
gi 1083809137 696 IGLSIR 701
Cdd:PRK12269  557 INLSLK 562

PRK08563

DNA-directed RNA polymerase subunit E'; Provisional

631-701

2.34e-06

DNA-directed RNA polymerase subunit E'; Provisional

Pssm-ID: 236289 [Multi-domain] Cd Length: 187 Bit Score: 48.67 E-value: 2.34e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083809137 631 VGEVLKGEVVKIADFGAFVKLNSFtDGMVHISELAPFRV-----------ERVSDIIKEGMIVPVKVISI-----DREKS 694
Cdd:PRK08563   81 LQEVVEGEVVEVVEFGAFVRIGPV-DGLLHISQIMDDYIsydpkngrligKESKRVLKVGDVVRARIVAVslkerRPRGS 159


                  ....*..
gi 1083809137 695 RIGLSIR 701
Cdd:PRK08563  160 KIGLTMR 166

S1_Rrp5_repeat_sc10

cd05706

S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...

630-701

3.32e-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: 45.32 E-value: 3.32e-06

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1083809137 630 TVGEVLKGEVVKIADFGAFVKLNSFTDGMVHISELAPFRVERVSDIIKEGMIVPVKVISIDREKSRIGLSIR 701
Cdd:cd05706     2 KVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSLR 73

PRK00087

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

631-704

6.24e-06

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

Pssm-ID: 234623 [Multi-domain] Cd Length: 647 Bit Score: 49.56 E-value: 6.24e-06

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1083809137 631 VGEVLKGEVVKIADFGAFVKLNSFTDGMVHISELAPFRVERVSDIIKEGMIVPVKVISIDREKSRIGLSIREAD 704
Cdd:PRK00087  302 RGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEDEDGYVVLSKKEAD 375

S1_Rrp5_repeat_hs14

cd05705

S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...

632-699

1.25e-05

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: 43.54 E-value: 1.25e-05

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1083809137 632 GEVLKGEVVKIADFGAFVKLNSFTDGMV---HISELAPFRVERVSDIIKEGMIVPVKVISIDREKSRIGLS 699
Cdd:cd05705     4 GQLLRGYVSSVTKQGVFFRLSSSIVGRVlfqNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS 74

RNase_PH_RRP46

cd11372

RRP46 subunit of eukaryotic exosome; The RRP46 subunit of eukaryotic exosome is a member of ...

333-483

4.15e-05

RRP46 subunit of eukaryotic exosome; The RRP46 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts.

Pssm-ID: 206777 [Multi-domain] Cd Length: 199 Bit Score: 45.25 E-value: 4.15e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083809137 333 LRDIYAQAGGVSAVlHGSGIFYRGGTHVLSVLTlgGPEDRHSIDGMQTK--LEKRFmhhynfppyssgetgragftnRRE 410
Cdd:cd11372     1 LRPLSCELGLLSRA-DGSARFSQGDTSVLAAVY--GPIEVKLRKELPDRatLEVIV---------------------RPK 56

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083809137 411 VGHGALAEKALAM----VLPP---LSEFPYT-IRVVSESMASNGSTSQASICASTLALMDGGVPILAPVAGIAMGLMHET 482
Cdd:cd11372    57 SGLPGVKEKLLELllrsTLEPiilLHLHPRTlISVVLQVLQDDGSLLACAINAACLALLDAGVPMKGLFAAVTCAITEDG 136


                  .
gi 1083809137 483 D 483
Cdd:cd11372   137 E 137

RNase_PH_MTR3

cd11371

MTR3 subunit of eukaryotic exosome; The MTR3 subunit of eukaryotic exosome is a member of the ...

17-143

5.43e-05

MTR3 subunit of eukaryotic exosome; The MTR3 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts.

Pssm-ID: 206776 [Multi-domain] Cd Length: 210 Bit Score: 44.86 E-value: 5.43e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083809137  17 AIF--TDLAEQAHGSVMLKYGETIVLATVCMSKDKQNGLGFFN---LTVDYveKF--YATGKIlgsrfmRREGKPSEDAI 89
Cdd:cd11371     3 PIFlkTGVVSQAKGSAYVELGNTKVICSVYGPRPIPGRTEFSDrgrLNCEV--KFapFATPGR------RRHGQDSEERE 74

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1083809137  90 LASRvIDRTLRP-----LFDQSIrhaVQVIVTVISVDDNDPVIlAVNAASLALAVSNIP 143
Cdd:cd11371    75 LSSL-LHQALEPavrleKYPKSQ---IDVFVTVLESDGSVLAA-AITAASLALADAGIE 128

S1_Rrp5_repeat_hs5

cd05697

S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...

632-698

5.74e-05

S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.

Pssm-ID: 240202 [Multi-domain] Cd Length: 69 Bit Score: 41.45 E-value: 5.74e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1083809137 632 GEVLKGEVVKIADFGAFVKLNSFTDGMVHISELAPFRVERVSDIIKEGMIVPVKVISIDREKSRIGL 698
Cdd:cd05697     1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVL 67

S1_Rrp5_repeat_sc11

cd05707

S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...

632-699

9.32e-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: 41.13 E-value: 9.32e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1083809137 632 GEVLKGEVVKIADFGAFVKLNSFTDGMVHISELAPFRVERVSDIIKEGMIVPVKVISIDREKSRIGLS 699
Cdd:cd05707     1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68

VacB

COG0557

Exoribonuclease R [Transcription];

631-705

1.23e-04

Exoribonuclease R [Transcription];

Pssm-ID: 440323 [Multi-domain] Cd Length: 711 Bit Score: 45.48 E-value: 1.23e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083809137 631 VGEVLKGEVVKIADFGAFVKL-NSFTDGMVHISELAP----FRvERVSDIIKE--------GMIVPVKVISIDREKSRIG 697
Cdd:COG0557   622 VGEEFEGVISGVTSFGLFVELdELGVEGLVHVSSLGDdyyeYD-ERRQALVGErtgkryrlGDRVEVRVVRVDLDRRQID 700


                  ....*...
gi 1083809137 698 LSIREADK 705
Cdd:COG0557   701 FELVEGGS 708

PRK07400

30S ribosomal protein S1; Reviewed

631-702

1.39e-04

30S ribosomal protein S1; Reviewed

Pssm-ID: 180960 [Multi-domain] Cd Length: 318 Bit Score: 44.41 E-value: 1.39e-04

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1083809137 631 VGEVLKGEVVKIADFGAFVKLNSFTdGMVHISELA------PFRVERVSDIIKegmivpVKVISIDREKSRIGLSIRE 702
Cdd:PRK07400  196 VGEVVVGTVRGIKPYGAFIDIGGVS-GLLHISEIShehietPHSVFNVNDEMK------VMIIDLDAERGRISLSTKQ 266

S1_RNase_R

cd04471

S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, ...

631-696

1.63e-04

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: 40.85 E-value: 1.63e-04

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1083809137 631 VGEVLKGEVVKIADFGAFVKL-NSFTDGMVHISELAP-----------FRVERVSDIIKEGMIVPVKVISIDREKSRI 696
Cdd:cd04471     1 VGEEFDGVISGVTSFGLFVELdNLTVEGLVHVSTLGDdyyefdeenhaLVGERTGKVFRLGDKVKVRVVRVDLDRRKI 78

S1_Rrp5_repeat_hs8_sc7

cd04461

S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...

617-700

1.64e-04

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: 40.65 E-value: 1.64e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083809137 617 KAKSIVLEMThEYTVGEVLKGEVVKIADFGAFVKLNSFTDGMVHISELAPFRVERVSDIIKEGMIVPVKVISIDREKSRI 696
Cdd:cd04461     1 KEGTLPTNFS-DLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRF 79


                  ....
gi 1083809137 697 GLSI 700
Cdd:cd04461    80 LLSL 83

S1_RecJ_like

cd04473

S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of ...

630-692

2.67e-04

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: 39.90 E-value: 2.67e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1083809137 630 TVGEVLKGEVVKIADFGAFVKLNSFTDGMVHISELapfrveRVSDIIKEGMIVPVKVISIDRE 692
Cdd:cd04473    15 EVGKLYKGKVNGVAKYGVFVDLNDHVRGLIHRSNL------LRDYEVGDEVIVQVTDIPENGN 71

PTZ00248

eukaryotic translation initiation factor 2 subunit 1; Provisional

638-701

3.74e-04

eukaryotic translation initiation factor 2 subunit 1; Provisional

Pssm-ID: 240329 [Multi-domain] Cd Length: 319 Bit Score: 43.11 E-value: 3.74e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1083809137 638 EVVKIADFGAFVKLNSFTD--GMVHISELAPFRVERVSDIIKEGMIVPVKVISIDREKSRIGLSIR 701
Cdd:PTZ00248   24 KVVRITEMGAYVSLLEYDDieGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYIDLSKK 89

S1_Rrp5_repeat_hs6_sc5

cd05698

S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...

632-701

5.52e-04

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: 38.75 E-value: 5.52e-04

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083809137 632 GEVLKGEVVKIADFGAFVKLNSFTDGMVHISELAPFRVERVSDIIKEGMIVPVKVISIDREKSRIGLSIR 701
Cdd:cd05698     1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70

KH-I_Vigilin_rpt6

cd02394

sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, ...

585-626

8.57e-04

sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the sixth one.

Pssm-ID: 411804 [Multi-domain] Cd Length: 68 Bit Score: 38.32 E-value: 8.57e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1083809137 585 KTIKEIKEKTGAEITIEDDGT----VYFTGKGDGAEKAKSIVLEMT 626
Cdd:cd02394    22 ANIKRIREESGVSIRIPDDEAnsdeIRIEGSPEGVKKAKAEILELV 67

rpoE

TIGR00448

DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form; This family seems to be ...

586-702

1.73e-03

DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form; This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to E.coli rpoE. [Transcription, DNA-dependent RNA polymerase]

Pssm-ID: 129540 [Multi-domain] Cd Length: 179 Bit Score: 40.15 E-value: 1.73e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083809137 586 TIKEIKEkTGAEITIEDDGTVYFtgkgdgaekaksivlEMTHEYTV-----GEVLKGEVVKIADFGAFVKLNSFtDGMVH 660
Cdd:TIGR00448  47 TIYDIED-IGEGKVIPGDGSAYH---------------NVTFRALVfkpelGEIVEGEVIEIVEFGAFVSLGPF-DGLFH 109

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1083809137 661 ISEL----APFRVERVSDIIKE------------GMIVPVKVISIDREKSRIGLSIRE 702
Cdd:TIGR00448 110 VSQVtddyCYYDPKESALIGKEtkkvldegdkvrARIVALSLKDRRPEGSKIGLTMRQ 167

RNase_PH_archRRP41

cd11366

RRP41 subunit of archaeal exosome; The RRP41 subunit of the archaeal exosome is a member of ...

79-170

2.15e-03

Pssm-ID: 206771 [Multi-domain] Cd Length: 214 Bit Score: 40.01 E-value: 2.15e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083809137  79 RREGKPSEDAILASRVIDRTLRP--LFDQSIRHAVQVIVTVISVDDNDPVIlAVNAASLALAVSNIPWNGPIGCVRIGKY 156
Cdd:cd11366    65 RKRPGPDRREIEISKVIKEALEPaiILEEFPRTAIDVFVEVLQADAGTRVA-GLNAASLALADAGIPMRDLVAACAAGKV 143

                          90
                  ....*....|....
gi 1083809137 157 nDENLKINLAKLRD 170
Cdd:cd11366   144 -DGKIVLDLNKEED 156

PRK12269

bifunctional cytidylate kinase/ribosomal protein S1; Provisional

624-702

3.52e-03

bifunctional cytidylate kinase/ribosomal protein S1; Provisional

Pssm-ID: 105491 [Multi-domain] Cd Length: 863 Bit Score: 40.85 E-value: 3.52e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083809137 624 EMTHEYTVGEVLKGEVVKIADFGAFVKLNSFTDGMVHISELAPFRVERVSD-IIKEGMIVPVKVISIDREKSRIGLSIRE 702
Cdd:PRK12269  658 EIEARYPVGARFTRRIVKVTNAGAFIEMEEGIDGFLHVDDLSWVKRTRPADhELEVGKEIECMVIECDPQARRIRLGVKQ 737

PRK03983

exosome complex exonuclease Rrp41; Provisional

79-170

5.05e-03

exosome complex exonuclease Rrp41; Provisional

Pssm-ID: 235187 [Multi-domain] Cd Length: 244 Bit Score: 39.23 E-value: 5.05e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1083809137  79 RREGKPSEDAILASRVIDRTLRP--LFDQSIRHAVQVIVTVISVDDNDPViLAVNAASLALAVSNIPWNGPIGCVRIGKY 156
Cdd:PRK03983   87 RKRPGPDRRSIEISKVIREALEPaiMLELFPRTVIDVFIEVLQADAGTRV-AGITAASLALADAGIPMRDLVAGCAVGKV 165

                          90
                  ....*....|....
gi 1083809137 157 NDEnLKINLAKLRD 170
Cdd:PRK03983  166 DGV-IVLDLNKEED 178

rpsA