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Conserved domains on  [gi|557733464|gb|ESS29615|]
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S1 RNA binding domain-containing protein [Toxoplasma gondii VEG]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RpsA super family cl33936
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 33-192 9.48e-30

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


The actual alignment was detected with superfamily member COG0539:

Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 117.07  E-value: 9.48e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464  33 DIHKGVVKKLQSYGAFVkvpDLDK-EGLLHISRISDQRVENVEDVLAVGQEVWVKVLS--QEDGKLRLCMKSVNQH--DG 107
Cdd:COG0539  191 DVVEGTVKNITDFGAFV---DLGGvDGLLHISEISWGRVKHPSEVLKVGDEVEVKVLKidREKERISLSLKQLQPDpwEN 267

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464 108 SEReslrqsfihrgegggvKTPElDSIHQGTVRRIQEFGAFVSI-DGFdrDGLLHISCIS-SQKLDRVDDALAVGDKVWV 185
Cdd:COG0539  268 IAE----------------KYPV-GDVVKGKVTRLTDFGAFVELePGV--EGLVHISEMSwTKRVAHPSDVVKVGDEVEV 328


                 ....*..
gi 557733464 186 KVTKVEE 192
Cdd:COG0539  329 KVLDIDP 335
zf-CCHC_3 pfam13917
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 236-283 3.62e-12

Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.


:

Pssm-ID: 404753  Cd Length: 41  Bit Score: 60.50  E-value: 3.62e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 557733464  236 AIYNIACQRCGGKGHMAHECYNTGGNKYEmleeerpARPEHTAVIQPK 283
Cdd:pfam13917   1 ANASARCQKCLKKGHWTYECKNAGERVYT-------ARPSRTQQLKNP 41
 
Name Accession Description Interval E-value
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 33-192 9.48e-30

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: 117.07  E-value: 9.48e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464  33 DIHKGVVKKLQSYGAFVkvpDLDK-EGLLHISRISDQRVENVEDVLAVGQEVWVKVLS--QEDGKLRLCMKSVNQH--DG 107
Cdd:COG0539  191 DVVEGTVKNITDFGAFV---DLGGvDGLLHISEISWGRVKHPSEVLKVGDEVEVKVLKidREKERISLSLKQLQPDpwEN 267

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464 108 SEReslrqsfihrgegggvKTPElDSIHQGTVRRIQEFGAFVSI-DGFdrDGLLHISCIS-SQKLDRVDDALAVGDKVWV 185
Cdd:COG0539  268 IAE----------------KYPV-GDVVKGKVTRLTDFGAFVELePGV--EGLVHISEMSwTKRVAHPSDVVKVGDEVEV 328


                 ....*..
gi 557733464 186 KVTKVEE 192
Cdd:COG0539  329 KVLDIDP 335
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 33-219 5.03e-27

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 110.35  E-value: 5.03e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464  33 DIHKGVVKKLQSYGAFVKVPDLDkeGLLHISRISDQRVENVEDVLAVGQEVWVKVLS--QEDGKLRLCMKsvnqhdgser 110
Cdd:PRK06676 194 DVVEGTVARLTDFGAFVDIGGVD--GLVHISELSHERVEKPSEVVSVGQEVEVKVLSidWETERISLSLK---------- 261

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464 111 ESLRQSFihrgEGGGVKTPElDSIHQGTVRRIQEFGAFVSI-DGFdrDGLLHISCISSQKLDRVDDALAVGDKVWVKVTK 189
Cdd:PRK06676 262 DTLPGPW----EGVEEKLPE-GDVIEGTVKRLTDFGAFVEVlPGV--EGLVHISQISHKHIATPSEVLEEGQEVKVKVLE 334

                        170       180       190
                 ....*....|....*....|....*....|.
gi 557733464 190 V-EEGGKYGLDMRGISQKDGADNDPNNLSRS 219
Cdd:PRK06676 335 VnEEEKRISLSIKALEEAPAEEEDRREEYRQ 365
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 33-97 3.49e-20

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


Pssm-ID: 239918 [Multi-domain]  Cd Length: 68  Bit Score: 83.36  E-value: 3.49e-20
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 557733464  33 DIHKGVVKKLQSYGAFVKVPDlDKEGLLHISRISDQRVENVEDVLAVGQEVWVKVLS-QEDGKLRL 97
Cdd:cd04472    2 KIYEGKVVKIKDFGAFVEILP-GKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEvDDRGRISL 66
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 17-192 9.11e-15

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: 75.54  E-value: 9.11e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464   17 EASPSEERQNGKPQ--STDIHKGVVKKLQSYGAFVKVPDLDkeGLLHISRISDQRVENVEDVLAVGQEVWVKVLSQEDGK 94
Cdd:TIGR00717 171 EEERSQAREELLENlkEGDVVKGVVKNITDFGAFVDLGGVD--GLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEK 248

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464   95 LRLCMkSVNQHDGSERESLRQSFihrGEGGGVKtpeldsihqGTVRRIQEFGAFVSIdGFDRDGLLHISCIS-SQKLDRV 173
Cdd:TIGR00717 249 GRISL-SLKQLGEDPWEAIEKKF---PVGDKIT---------GRVTNLTDYGVFVEI-EEGIEGLVHVSEMSwVKKNSHP 314

                         170
                  ....*....|....*....
gi 557733464  174 DDALAVGDKVWVKVTKVEE 192
Cdd:TIGR00717 315 SKVVKKGDEVEVMILDIDP 333
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
33-100 4.66e-13

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 63.78  E-value: 4.66e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464    33 DIHKGVVKKLQSYGAFVKVPDlDKEGLLHISRISDQRVENVEDVLAVGQEVWVKVLS--QEDGKLRLCMK 100
Cdd:smart00316   4 DVVEGTVTEITPGGAFVDLGN-GVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSvdEEKGRIILSLK 72
zf-CCHC_3 pfam13917
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 236-283 3.62e-12

Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.


Pssm-ID: 404753  Cd Length: 41  Bit Score: 60.50  E-value: 3.62e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 557733464  236 AIYNIACQRCGGKGHMAHECYNTGGNKYEmleeerpARPEHTAVIQPK 283
Cdd:pfam13917   1 ANASARCQKCLKKGHWTYECKNAGERVYT-------ARPSRTQQLKNP 41
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 29-88 1.35e-08

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: 51.13  E-value: 1.35e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464   29 PQSTDIHKGVVKKLQSYGAFVKVpDLDKEGLLHISRISDQRVENVEDVLAVGQEVWVKVL 88
Cdd:pfam00575   1 PEKGDVVEGEVTRVTKGGAFVDL-GNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVL 59
 
Name Accession Description Interval E-value
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 33-192 9.48e-30

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: 117.07  E-value: 9.48e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464  33 DIHKGVVKKLQSYGAFVkvpDLDK-EGLLHISRISDQRVENVEDVLAVGQEVWVKVLS--QEDGKLRLCMKSVNQH--DG 107
Cdd:COG0539  191 DVVEGTVKNITDFGAFV---DLGGvDGLLHISEISWGRVKHPSEVLKVGDEVEVKVLKidREKERISLSLKQLQPDpwEN 267

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464 108 SEReslrqsfihrgegggvKTPElDSIHQGTVRRIQEFGAFVSI-DGFdrDGLLHISCIS-SQKLDRVDDALAVGDKVWV 185
Cdd:COG0539  268 IAE----------------KYPV-GDVVKGKVTRLTDFGAFVELePGV--EGLVHISEMSwTKRVAHPSDVVKVGDEVEV 328


                 ....*..
gi 557733464 186 KVTKVEE 192
Cdd:COG0539  329 KVLDIDP 335
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 33-219 5.03e-27

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 110.35  E-value: 5.03e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464  33 DIHKGVVKKLQSYGAFVKVPDLDkeGLLHISRISDQRVENVEDVLAVGQEVWVKVLS--QEDGKLRLCMKsvnqhdgser 110
Cdd:PRK06676 194 DVVEGTVARLTDFGAFVDIGGVD--GLVHISELSHERVEKPSEVVSVGQEVEVKVLSidWETERISLSLK---------- 261

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464 111 ESLRQSFihrgEGGGVKTPElDSIHQGTVRRIQEFGAFVSI-DGFdrDGLLHISCISSQKLDRVDDALAVGDKVWVKVTK 189
Cdd:PRK06676 262 DTLPGPW----EGVEEKLPE-GDVIEGTVKRLTDFGAFVEVlPGV--EGLVHISQISHKHIATPSEVLEEGQEVKVKVLE 334

                        170       180       190
                 ....*....|....*....|....*....|.
gi 557733464 190 V-EEGGKYGLDMRGISQKDGADNDPNNLSRS 219
Cdd:PRK06676 335 VnEEEKRISLSIKALEEAPAEEEDRREEYRQ 365
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
33-209 4.09e-26

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 110.04  E-value: 4.09e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464  33 DIHKGVVKKLQSYGAFVKVPDLDkeGLLHISRISDQRVENVEDVLAVGQEVWVKVLS--QEDGKLRLCMKSV--NQHDGS 108
Cdd:PRK00087 479 DVVEGEVKRLTDFGAFVDIGGVD--GLLHVSEISWGRVEKPSDVLKVGDEIKVYILDidKENKKLSLSLKKLlpDPWENV 556

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464 109 EreslrqsfihrgegggVKTPElDSIHQGTVRRIQEFGAFVSI-DGFdrDGLLHISCISSQKLDRVDDALAVGDKVWVKV 187
Cdd:PRK00087 557 E----------------EKYPV-GSIVLGKVVRIAPFGAFVELePGV--DGLVHISQISWKRIDKPEDVLSEGEEVKAKI 617

                        170       180
                 ....*....|....*....|...
gi 557733464 188 TKV-EEGGKYGLDMRGISQKDGA 209
Cdd:PRK00087 618 LEVdPEEKRIRLSIKEVEEEPGD 640
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 33-102 7.74e-22

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 97.04  E-value: 7.74e-22
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 557733464  33 DIHKGVVKKLQSYGAFVKVPDlDKEGLLHISRISDQRVENVEDVLAVGQEVWVKVLSQED-GKLRLCMKSV 102
Cdd:PRK11824 623 EIYEGKVVRIVDFGAFVEILP-GKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEIDKrGRIRLSRKAV 692
Pnp COG1185
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ...
 33-100 9.98e-22

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


Pssm-ID: 440798 [Multi-domain]  Cd Length: 686  Bit Score: 97.00  E-value: 9.98e-22
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 557733464  33 DIHKGVVKKLQSYGAFVKVPDlDKEGLLHISRISDQRVENVEDVLAVGQEVWVKVLSQED-GKLRLCMK 100
Cdd:COG1185  618 EIYEGKVVRIMDFGAFVEILP-GKDGLVHISELADERVEKVEDVLKEGDEVKVKVLEIDDqGRIKLSRK 685
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 17-187 1.50e-21

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 96.00  E-value: 1.50e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464  17 EASPSEERQN--GKPQSTDIHKGVVKKLQSYGAFVKVPDLDkeGLLHISRISDQRVENVEDVLAVGQEVWVKVLS--QED 92
Cdd:PRK06299 185 EEERAEEREEllENLEEGQVVEGVVKNITDYGAFVDLGGVD--GLLHITDISWKRVNHPSEVVNVGDEVKVKVLKfdKEK 262

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464  93 GKLRLCMKSVNQH--DGSEReslrqsfihrgegggvKTPElDSIHQGTVRRIQEFGAFVSIDGfDRDGLLHISCIS-SQK 169
Cdd:PRK06299 263 KRVSLGLKQLGEDpwEAIEK----------------KYPV-GSKVKGKVTNITDYGAFVELEE-GIEGLVHVSEMSwTKK 324

                        170
                 ....*....|....*...
gi 557733464 170 LDRVDDALAVGDKVWVKV 187
Cdd:PRK06299 325 NKHPSKVVSVGQEVEVMV 342
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 126-203 4.22e-21

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 95.12  E-value: 4.22e-21
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 557733464 126 VKTPELDSIHQGTVRRIQEFGAFVSI-DGfdRDGLLHISCISSQKLDRVDDALAVGDKVWVKVTKVEEGGKYGLDMRGI 203
Cdd:PRK11824 616 TAEPEVGEIYEGKVVRIVDFGAFVEIlPG--KDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEIDKRGRIRLSRKAV 692
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 33-190 4.96e-21

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 94.46  E-value: 4.96e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464  33 DIHKGVVKKLQSYGAFVKV-PDLdkEGLLHISRIS-DQRVENVEDVLAVGQEVWVKVLS--QEDGKLRLCMKSVNQHDGS 108
Cdd:PRK06299 288 SKVKGKVTNITDYGAFVELeEGI--EGLVHVSEMSwTKKNKHPSKVVSVGQEVEVMVLEidEEKRRISLGLKQCKENPWE 365

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464 109 ERESlrqsfihrgegggvKTPElDSIHQGTVRRIQEFGAFVSIDGfDRDGLLHISCIS-SQKLDRVDDALAVGDKVWVKV 187
Cdd:PRK06299 366 EFAE--------------KYPV-GDVVEGKVKNITDFGAFVGLEG-GIDGLVHLSDISwDKKGEEAVELYKKGDEVEAVV 429


                 ...
gi 557733464 188 TKV 190
Cdd:PRK06299 430 LKV 432
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 33-97 3.49e-20

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


Pssm-ID: 239918 [Multi-domain]  Cd Length: 68  Bit Score: 83.36  E-value: 3.49e-20
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 557733464  33 DIHKGVVKKLQSYGAFVKVPDlDKEGLLHISRISDQRVENVEDVLAVGQEVWVKVLS-QEDGKLRL 97
Cdd:cd04472    2 KIYEGKVVKIKDFGAFVEILP-GKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEvDDRGRISL 66
Pnp COG1185
Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ...
 126-201 4.22e-20

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


Pssm-ID: 440798 [Multi-domain]  Cd Length: 686  Bit Score: 91.99  E-value: 4.22e-20
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 557733464 126 VKTPELDSIHQGTVRRIQEFGAFVSI-DGfdRDGLLHISCISSQKLDRVDDALAVGDKVWVKVTKVEEGGKYGLDMR 201
Cdd:COG1185  611 TAEPEVGEIYEGKVVRIMDFGAFVEIlPG--KDGLVHISELADERVEKVEDVLKEGDEVKVKVLEIDDQGRIKLSRK 685
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 34-107 3.51e-19

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: 81.13  E-value: 3.51e-19
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 557733464  34 IHKGVVKKLQSYGAFVKVPDLD--KEGLLHISRIS-DQRVENVEDVLAVGQEVWVKVLSQEDGKLRLCMKSVNQHDG 107
Cdd:cd05684    3 IYKGKVTSIMDFGCFVQLEGLKgrKEGLVHISQLSfEGRVANPSDVVKRGQKVKVKVISIQNGKISLSMKDVDQDTG 79
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 33-122 4.91e-19

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


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 82.15  E-value: 4.91e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464  33 DIHKGVVKKLQSYGAFVKVPDlDKEGLLHISRISDQRVENVEDVLAVGQEVWVKVLS-QEDGKLRLCMKSVNQHDGSERE 111
Cdd:COG1098    7 DIVEGKVTGITPFGAFVELPE-GTTGLVHISEIADGYVKDINDYLKVGDEVKVKVLSiDEDGKISLSIKQAEEKPKRPPR 85

                         90
                 ....*....|.
gi 557733464 112 SLRQSFIHRGE 122
Cdd:COG1098   86 PRRNSRPKAGF 96
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 33-192 5.21e-19

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 88.30  E-value: 5.21e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464  33 DIHKGVVKKLQSYGAFVKVPDlDKEGLLHISRIS-DQRVENVEDVLAVGQEVWVKVLS--QEDGKLRLCMKsvnQHDGSE 109
Cdd:PRK06299 375 DVVEGKVKNITDFGAFVGLEG-GIDGLVHLSDISwDKKGEEAVELYKKGDEVEAVVLKvdVEKERISLGIK---QLEEDP 450

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464 110 RESLRQSFihrgegggvktpELDSIHQGTVRRIQEFGAFVSIDGfDRDGLLHISCISSQKLDRVDDALAVGDKVWVKVTK 189
Cdd:PRK06299 451 FEEFAKKH------------KKGSIVTGTVTEVKDKGAFVELED-GVEGLIRASELSRDRVEDATEVLKVGDEVEAKVIN 517


                 ...
gi 557733464 190 VEE 192
Cdd:PRK06299 518 IDR 520
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 134-208 1.10e-18

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: 79.59  E-value: 1.10e-18
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 557733464 134 IHQGTVRRIQEFGAFVSIDGFDR--DGLLHISCISSQ-KLDRVDDALAVGDKVWVKVTKVeEGGKYGLDMRGISQKDG 208
Cdd:cd05684    3 IYKGKVTSIMDFGCFVQLEGLKGrkEGLVHISQLSFEgRVANPSDVVKRGQKVKVKVISI-QNGKISLSMKDVDQDTG 79
S1_pNO40 cd05686
S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function ...
 129-200 2.44e-18

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: 78.68  E-value: 2.44e-18
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 557733464 129 PELDSIHQGTVRRIQEFGAFVSIDGFDRDGLLHISCISSQKLDRVDDALAVGDKVWVKVTKVEEGGKYGLDM 200
Cdd:cd05686    1 PALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKDKMKLSL 72
rpsA PRK13806
30S ribosomal protein S1; Provisional
 15-201 6.42e-18

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 85.16  E-value: 6.42e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464  15 DREASPSEERQNGKPQSTDIHKGVVKKLQSYGAFVK-VPDLdkEGLLHISRISDQRVENVEDVLAVGQEVWVKVLSQEDG 93
Cdd:PRK13806 186 EREQKEALEAFMETVKEGDVVEGTVTRLAPFGAFVElAPGV--EGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERA 263

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464  94 K----LRLCMkSVNQHDGSERESLRQSFihrgegggvktpELDSIHQGTVRRIQEFGAFVSI-DGFdrDGLLHISCIS-S 167
Cdd:PRK13806 264 KkgkgLRISL-SIKQAGGDPWDTVGDRL------------KAGDKVTGKVVRLAPFGAFVEIlPGI--EGLVHVSEMSwT 328

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 557733464 168 QKLDRVDDALAVGDKVWVKVTKVE-EGGKYGLDMR 201
Cdd:PRK13806 329 RRVNKPEDVVAPGDAVAVKIKDIDpAKRRISLSLR 363
S1_pNO40 cd05686
S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function ...
 29-100 1.10e-17

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: 76.75  E-value: 1.10e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 557733464  29 PQSTDIHKGVVKKLQSYGAFVKVPDLDKEGLLHISRISDQRVENVEDVLAVGQEVWVKVLSQE-DGKLRLCMK 100
Cdd:cd05686    1 PALYQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREmKDKMKLSLS 73
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 134-198 2.48e-17

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


Pssm-ID: 239918 [Multi-domain]  Cd Length: 68  Bit Score: 75.66  E-value: 2.48e-17
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 557733464 134 IHQGTVRRIQEFGAFVSIDGfDRDGLLHISCISSQKLDRVDDALAVGDKVWVKVTKVEEGGKYGL 198
Cdd:cd04472    3 IYEGKVVKIKDFGAFVEILP-GKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDDRGRISL 66
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 33-100 1.79e-16

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: 73.09  E-value: 1.79e-16
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 557733464  33 DIHKGVVKKLQSYGAFVKVPDlDKEGLLHISRISDQRVENVEDVLAVGQEVWVKVLS-QEDGKLRLCMK 100
Cdd:cd05692    2 SVVEGTVTRLKPFGAFVELGG-GISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSiDARGRISLSIK 69
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 33-103 1.78e-15

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: 76.62  E-value: 1.78e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 557733464  33 DIHKGVVKKLQSYGAFVKV-PDLdkEGLLHISRIS-DQRVENVEDVLAVGQEVWVKVLS--QEDGKLRLCMKSVN 103
Cdd:COG0539  276 DVVKGKVTRLTDFGAFVELePGV--EGLVHISEMSwTKRVAHPSDVVKVGDEVEVKVLDidPEERRISLSIKQLA 348
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 63-201 6.14e-15

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 75.30  E-value: 6.14e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464  63 SRISDQRVENVEDVlaVGQEVWVKV--LSQEDGKLRLCMKSVNQhdgSERESLRQSFIHRGEGGGVKTpeldsihqGTVR 140
Cdd:PRK06676 135 SLISTRFVEDFSDF--KGKTLEVKIieLDPEKNRVILSRRAVVE---EERAAKKEELLSSLKEGDVVE--------GTVA 201

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 557733464 141 RIQEFGAFVSIDGFdrDGLLHISCISSQKLDRVDDALAVGDKVWVKVTKV-EEGGKYGLDMR 201
Cdd:PRK06676 202 RLTDFGAFVDIGGV--DGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIdWETERISLSLK 261
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 17-204 7.06e-15

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 75.85  E-value: 7.06e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464  17 EASPSEERQN--GKPQSTDIHKGVVKKLQSYGAFVKVPDLDkeGLLHISRISDQRVENVEDVLAVGQEVWVKVLSQEDGK 94
Cdd:PRK07899 192 EQTQSEVRSEflNQLQKGQVRKGVVSSIVNFGAFVDLGGVD--GLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDR 269

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464  95 LR--LCMKSVnqhdgseRESLRQSFIHrgegggvkTPELDSIHQGTVRRIQEFGAFVSI-DGFdrDGLLHISCISSQKLD 171
Cdd:PRK07899 270 ERvsLSLKAT-------QEDPWQQFAR--------THAIGQIVPGKVTKLVPFGAFVRVeEGI--EGLVHISELAERHVE 332

                        170       180       190
                 ....*....|....*....|....*....|...
gi 557733464 172 RVDDALAVGDKVWVKVTKVEeggkygLDMRGIS 204
Cdd:PRK07899 333 VPEQVVQVGDEVFVKVIDID------LERRRIS 359
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 17-192 9.11e-15

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: 75.54  E-value: 9.11e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464   17 EASPSEERQNGKPQ--STDIHKGVVKKLQSYGAFVKVPDLDkeGLLHISRISDQRVENVEDVLAVGQEVWVKVLSQEDGK 94
Cdd:TIGR00717 171 EEERSQAREELLENlkEGDVVKGVVKNITDFGAFVDLGGVD--GLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEK 248

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464   95 LRLCMkSVNQHDGSERESLRQSFihrGEGGGVKtpeldsihqGTVRRIQEFGAFVSIdGFDRDGLLHISCIS-SQKLDRV 173
Cdd:TIGR00717 249 GRISL-SLKQLGEDPWEAIEKKF---PVGDKIT---------GRVTNLTDYGVFVEI-EEGIEGLVHVSEMSwVKKNSHP 314

                         170
                  ....*....|....*....
gi 557733464  174 DDALAVGDKVWVKVTKVEE 192
Cdd:TIGR00717 315 SKVVKKGDEVEVMILDIDP 333
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 36-201 1.94e-14

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


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 73.54  E-value: 1.94e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464  36 KGVVKKlqsyGAFVKVPDLdkEGLLHISRISDQRVENVEDVlaVGQEVWVKV--LSQEDGKLRLCMKSVNQhdgSERESL 113
Cdd:COG0539  111 KGVVKG----GLIVDIGGV--RAFLPASQVDVRPVRDLDEY--VGKTLEFKIikLDRKRNNVVVSRRAVLE---EEREEK 179

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464 114 RQSFIHRGEGGGVKTpeldsihqGTVRRIQEFGAFVSIDGFDrdGLLHISCISSQKLDRVDDALAVGDKVWVKVTKV-EE 192
Cdd:COG0539  180 REELLEKLEEGDVVE--------GTVKNITDFGAFVDLGGVD--GLLHISEISWGRVKHPSEVLKVGDEVEVKVLKIdRE 249


                 ....*....
gi 557733464 193 GGKYGLDMR 201
Cdd:COG0539  250 KERISLSLK 258
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 133-220 3.34e-14

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


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 68.67  E-value: 3.34e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464 133 SIHQGTVRRIQEFGAFVSIDGfDRDGLLHISCISSQKLDRVDDALAVGDKVWVKVTKVEEGGKYGLDMRGISQKDGADND 212
Cdd:COG1098    7 DIVEGKVTGITPFGAFVELPE-GTTGLVHISEIADGYVKDINDYLKVGDEVKVKVLSIDEDGKISLSIKQAEEKPKRPPR 85


                 ....*...
gi 557733464 213 PNNLSRSR 220
Cdd:COG1098   86 PRRNSRPK 93
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
63-192 5.39e-14

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 73.44  E-value: 5.39e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464  63 SRISDQRVENVEDVlaVGQEVWVKVLSQEDGKLRLCMKSVNQHDGSERESLRQSFIhrgegggvKTPELDSIHQGTVRRI 142
Cdd:PRK00087 419 SHVELGYVEDLSEY--KGQELEVKIIEFNRKRRKKVVLSRKAILEEEKEKKKEETW--------NSLEEGDVVEGEVKRL 488

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 557733464 143 QEFGAFVSIDGFDrdGLLHISCISSQKLDRVDDALAVGDKVWVKVTKVEE 192
Cdd:PRK00087 489 TDFGAFVDIGGVD--GLLHVSEISWGRVEKPSDVLKVGDEIKVYILDIDK 536
PRK08059 PRK08059
general stress protein 13; Validated
 33-102 5.67e-14

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 67.76  E-value: 5.67e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 557733464  33 DIHKGVVKKLQSYGAFVKVpDLDKEGLLHISRISDQRVENVEDVLAVGQEVWVKVLS--QEDGKLRLCMKSV 102
Cdd:PRK08059   9 SVVTGKVTGIQPYGAFVAL-DEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSvdEEKGKISLSIRAT 79
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 33-97 2.31e-13

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: 64.57  E-value: 2.31e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 557733464  33 DIHKGVVKKLQSYGAFVKVPDLDkeGLLHISRISDQRVENVEDVLAVGQEVWVKVLS--QEDGKLRL 97
Cdd:cd05688    3 DVVEGTVKSITDFGAFVDLGGVD--GLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKidKERKRISL 67
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 20-196 4.42e-13

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


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 70.15  E-value: 4.42e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464   20 PSEERQNGKPQSTDIhKGVVKKLQSYGAFVKVPDlDKEGLLHISRIS-DQRVENVEDVLAVGQEVWVKVLS--QEDGKLR 96
Cdd:TIGR00717 262 PWEAIEKKFPVGDKI-TGRVTNLTDYGVFVEIEE-GIEGLVHVSEMSwVKKNSHPSKVVKKGDEVEVMILDidPERRRLS 339

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464   97 LCMKSVNQHDGSERESlrqsfihrgegggvKTPELDSIhQGTVRRIQEFGAFVSIDGfDRDGLLHISCISSQKLDRVDDA 176
Cdd:TIGR00717 340 LGLKQCKANPWEQFEE--------------KHPVGDRV-TGKIKKITDFGAFVELEG-GIDGLIHLSDISWDKDGREADH 403

                         170       180
                  ....*....|....*....|.
gi 557733464  177 L-AVGDKVWVKVTKVEEGGKY 196
Cdd:TIGR00717 404 LyKKGDEIEAVVLAVDKEKKR 424
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
33-100 4.66e-13

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 63.78  E-value: 4.66e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464    33 DIHKGVVKKLQSYGAFVKVPDlDKEGLLHISRISDQRVENVEDVLAVGQEVWVKVLS--QEDGKLRLCMK 100
Cdd:smart00316   4 DVVEGTVTEITPGGAFVDLGN-GVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSvdEEKGRIILSLK 72
PRK08582 PRK08582
RNA-binding protein S1;
36-134 5.95e-13

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 65.44  E-value: 5.95e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464  36 KGVVKKLQSYGAFVKVPDlDKEGLLHISRISDQRVENVEDVLAVGQEVWVKVLSQE-DGKLRLCMKSVNQHDGSERESLR 114
Cdd:PRK08582  10 QGKVTGITNFGAFVELPE-GKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEdDGKIGLSIKKAKDRPKRQHDRPR 88

                         90       100
                 ....*....|....*....|
gi 557733464 115 QSFIHRGEGGGVKTPELDSI 134
Cdd:PRK08582  89 HEDNRGGGNDVAPKEDFEQK 108
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 133-201 1.28e-12

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


Pssm-ID: 240197 [Multi-domain]  Cd Length: 69  Bit Score: 62.30  E-value: 1.28e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 557733464 133 SIHQGTVRRIQEFGAFVSIdGFDRDGLLHISCISSQKLDRVDDALAVGDKVWVKVTKVEEGGKYGLDMR 201
Cdd:cd05692    2 SVVEGTVTRLKPFGAFVEL-GGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARGRISLSIK 69
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 35-99 1.68e-12

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 62.01  E-value: 1.68e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 557733464  35 HKGVVKKLQSYGAFVKVPDlDKEGLLHISRISDQRVENVEDVLAVGQEVWVKVLSQEDGKLRLCM 99
Cdd:cd00164    1 VTGKVVSITKFGVFVELED-GVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISL 64
zf-CCHC_3 pfam13917
Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following ...
 236-283 3.62e-12

Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.


Pssm-ID: 404753  Cd Length: 41  Bit Score: 60.50  E-value: 3.62e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 557733464  236 AIYNIACQRCGGKGHMAHECYNTGGNKYEmleeerpARPEHTAVIQPK 283
Cdd:pfam13917   1 ANASARCQKCLKKGHWTYECKNAGERVYT-------ARPSRTQQLKNP 41
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 137-195 3.93e-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: 58.49  E-value: 3.93e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 557733464 137 GTVRRIQEFGAFVSIDGFDRDGLLHISCISSQKLDRVDDALAVGDKVWVKVTKVEEGGK 195
Cdd:cd05708    8 GTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKK 66
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 134-190 5.16e-11

S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240193 [Multi-domain]  Cd Length: 68  Bit Score: 58.02  E-value: 5.16e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 557733464 134 IHQGTVRRIQEFGAFVSIDGFDrdGLLHISCISSQKLDRVDDALAVGDKVWVKVTKV 190
Cdd:cd05688    4 VVEGTVKSITDFGAFVDLGGVD--GLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKI 58
PRK08059 PRK08059
general stress protein 13; Validated
 130-201 7.52e-11

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 58.90  E-value: 7.52e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 557733464 130 ELDSIHQGTVRRIQEFGAFVSIDGfDRDGLLHISCISSQKLDRVDDALAVGDKVWVKVTKV-EEGGKYGLDMR 201
Cdd:PRK08059   6 EVGSVVTGKVTGIQPYGAFVALDE-ETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVdEEKGKISLSIR 77
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 136-199 1.26e-10

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: 56.86  E-value: 1.26e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 557733464 136 QGTVRRIQEFGAFVSIdGFDRDGLLHISCISSQKLDRVDDALAVGDKVWVKVTKV-EEGGKYGLD 199
Cdd:cd05685    5 EGVVTNVTDFGAFVDI-GVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIdEERGRISLS 68
rpsA PRK13806
30S ribosomal protein S1; Provisional
 33-212 4.01e-10

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 61.28  E-value: 4.01e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464  33 DIHKGVVKKLQSYGAFVKV-PDLdkEGLLHISRIS-DQRVENVEDVLAVGQEVWVKVLSQEDGKLRLCMksvnqhdgser 110
Cdd:PRK13806 294 DKVTGKVVRLAPFGAFVEIlPGI--EGLVHVSEMSwTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISL----------- 360

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464 111 eSLRQSfihrgEG----GGVKTPELDSIHQGTVRRIQEFGAFVSID-GFdrDGLLHISCISSQKLDRVDDALAVGDKVWV 185
Cdd:PRK13806 361 -SLRDA-----EGdpwaDVAERFAPGTTVTGTVEKRAQFGLFVNLApGV--TGLLPASVISRAGKPATYEKLKPGDSVTL 432

                        170       180
                 ....*....|....*....|....*...
gi 557733464 186 KVTKV-EEGGKYGLDMRGISQKDGADND 212
Cdd:PRK13806 433 VVEEIdTAKRKISLAPAGAAGSGADDDD 460
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 129-196 4.32e-10

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: 55.67  E-value: 4.32e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 557733464 129 PELDSIHQGTVRRIQEFGAFVSIDGF-DRDGLLHISCISSQKLDRVDDALAVGDKVWVKVTKVEEGGKY 196
Cdd:cd04452    1 PEEGELVVVTVKSIADMGAYVSLLEYgNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGY 69
PRK08582 PRK08582
RNA-binding protein S1;
136-229 1.21e-09

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 56.19  E-value: 1.21e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464 136 QGTVRRIQEFGAFVSIDGfDRDGLLHISCISSQKLDRVDDALAVGDKVWVKVTKVEEGGKYGLDMR-GISQKDGADNDPN 214
Cdd:PRK08582  10 QGKVTGITNFGAFVELPE-GKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDDGKIGLSIKkAKDRPKRQHDRPR 88

                         90
                 ....*....|....*
gi 557733464 215 NLSRSRGTRSGPRKQ 229
Cdd:PRK08582  89 HEDNRGGGNDVAPKE 103
PRK05807 PRK05807
RNA-binding protein S1;
30-111 1.49e-09

RNA-binding protein S1;


Pssm-ID: 235614 [Multi-domain]  Cd Length: 136  Bit Score: 55.91  E-value: 1.49e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464  30 QSTDIHKGVVKKLQSYGAFVKVPDldKEGLLHISRISDQRVENVEDVLAVGQEVWVKVLSQED-GKLRLCMKSVNQHDGS 108
Cdd:PRK05807   4 KAGSILEGTVVNITNFGAFVEVEG--KTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDDnGKISLSIKQAMKQKKS 81


                 ...
gi 557733464 109 ERE 111
Cdd:PRK05807  82 VKP 84
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 36-101 2.06e-09

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: 53.49  E-value: 2.06e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 557733464  36 KGVVKKLQSYGAFVKVPDLDKEGLLHISRISDQRVENVEDVLAVGQEVWVKVLS--QEDGKLRLCMKS 101
Cdd:cd05708    7 DGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKidAEKKRISLGLKA 74
PRK05807 PRK05807
RNA-binding protein S1;
128-201 2.09e-09

RNA-binding protein S1;


Pssm-ID: 235614 [Multi-domain]  Cd Length: 136  Bit Score: 55.52  E-value: 2.09e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 557733464 128 TPELDSIHQGTVRRIQEFGAFVSIDGfdRDGLLHISCISSQKLDRVDDALAVGDKVWVKVTKVEEGGKYGLDMR 201
Cdd:PRK05807   2 TLKAGSILEGTVVNITNFGAFVEVEG--KTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDDNGKISLSIK 73
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
130-196 5.81e-09

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 52.22  E-value: 5.81e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 557733464   130 ELDSIHQGTVRRIQEFGAFVSIDGfDRDGLLHISCISSQKLDRVDDALAVGDKVWVKVTKVEEGGKY 196
Cdd:smart00316   1 EVGDVVEGTVTEITPGGAFVDLGN-GVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGR 66
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 33-115 9.23e-09

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 57.10  E-value: 9.23e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464  33 DIHKGVVKKLQSYGAFVKVPDlDKEGLLHISRISDQRVENVEDVLAVGQEVWVKVLS--QEDGKLRLCMKSVNQHDgsER 110
Cdd:PRK06299 462 SIVTGTVTEVKDKGAFVELED-GVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINidRKNRRISLSIKALDEAE--EK 538


                 ....*
gi 557733464 111 ESLRQ 115
Cdd:PRK06299 539 EAIAE 543
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 37-106 1.15e-08

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 55.60  E-value: 1.15e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 557733464  37 GVVKKLQSYGAFVkvpDLD----KEGLLHISRISDQRVENVEDVLAVGQEVWVKVLS--QEDGKLRLCMKSVNQHD 106
Cdd:PRK03987  14 GTVKEVKDFGAFV---TLDeypgKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRvdPRKGHIDLSLKRVNEHQ 86
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 29-88 1.35e-08

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: 51.13  E-value: 1.35e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464   29 PQSTDIHKGVVKKLQSYGAFVKVpDLDKEGLLHISRISDQRVENVEDVLAVGQEVWVKVL 88
Cdd:pfam00575   1 PEKGDVVEGEVTRVTKGGAFVDL-GNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVL 59
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
136-209 1.42e-08

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 56.57  E-value: 1.42e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 557733464 136 QGTVRRIQEFGAFVSIdGFDRDGLLHISCISSQkldRVDDAL---AVGDKVWVKVTKV-EEGGKYGLDMRGISQKDGA 209
Cdd:COG2183  646 EGTVTNVTDFGAFVDI-GVHQDGLVHISQLSDR---FVKDPRevvKVGDIVKVKVLEVdLKRKRISLSMKLDDEAGAA 719
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
132-201 1.48e-08

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 52.40  E-value: 1.48e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 557733464 132 DSIHqGTVRRIQEFGAFVSIDGfDRDGLLHISCISSQKLDRVDDALAVGDKVWVKVTKVEE-GGKYGLDMR 201
Cdd:PRK07252   5 DKLK-GTITGIKPYGAFVALEN-GTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEyTGKASLSLR 73
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 129-196 1.52e-08

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: 51.13  E-value: 1.52e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 557733464  129 PELDSIHQGTVRRIQEFGAFVSIDGfDRDGLLHISCISSQKLDRVDDALAVGDKVWVKVTKVEEGGKY 196
Cdd:pfam00575   1 PEKGDVVEGEVTRVTKGGAFVDLGN-GVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRR 67
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
 139-233 2.79e-08

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 55.67  E-value: 2.79e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464 139 VRRIQEFGAFVSIDGfDRDGLLHISCISSQKLDRVDDALAVGDKVWVKVTKVEEGGKYGLDMRGISQKDGADNDPNNLSR 218
Cdd:PLN00207 762 IKSIAPYGAFVEIAP-GREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVNDKGQLRLSRRALLPEANSEKSSQKQQG 840

                         90
                 ....*....|....*
gi 557733464 219 SRGTRSGPRKQERIT 233
Cdd:PLN00207 841 GSTKDKAPQKKYVNT 855
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
36-88 6.03e-08

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 50.86  E-value: 6.03e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 557733464  36 KGVVKKLQSYGAFVKVPDLDKeGLLHISRISDQRVENVEDVLAVGQEVWVKVL 88
Cdd:PRK07252   8 KGTITGIKPYGAFVALENGTT-GLIHISEIKTGFIDNIHQLLKVGEEVLVQVV 59
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 135-198 7.18e-08

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: 48.92  E-value: 7.18e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 557733464 135 HQGTVRRIQEFGAFVSIDGfDRDGLLHISCISSQKLDRVDDALAVGDKVWVKVTKVEEGGKYGL 198
Cdd:cd00164    1 VTGKVVSITKFGVFVELED-GVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRIS 63
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
 29-115 1.40e-07

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 53.36  E-value: 1.40e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464  29 PQSTDIHKGV-VKKLQSYGAFVKVPDlDKEGLLHISRISDQRVENVEDVLAVGQEVWVKVLS-QEDGKLRLCMKSVNQHD 106
Cdd:PLN00207 751 PTVGDIYRNCeIKSIAPYGAFVEIAP-GREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEvNDKGQLRLSRRALLPEA 829


                 ....*....
gi 557733464 107 GSERESLRQ 115
Cdd:PLN00207 830 NSEKSSQKQ 838
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 19-100 2.12e-07

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


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 52.81  E-value: 2.12e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464   19 SPSEERQNGKPQSTDIhKGVVKKLQSYGAFVKVPDlDKEGLLHISRISDQRVENVEDVLAVGQEVWVKVLSQE--DGKLR 96
Cdd:TIGR00717 435 NPWEKFAAKYKVGSVV-KGKVTEIKDFGAFVELPG-GVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDkkNRKVS 512


                  ....
gi 557733464   97 LCMK 100
Cdd:TIGR00717 513 LSVK 516
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 29-88 2.37e-07

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: 47.58  E-value: 2.37e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 557733464  29 PQSTDIHKGVVKKLQSYGAFVKVPDL-DKEGLLHISRISDQRVENVEDVLAVGQEVWVKVL 88
Cdd:cd04452    1 PEEGELVVVTVKSIADMGAYVSLLEYgNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVI 61
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 33-204 5.68e-07

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 51.64  E-value: 5.68e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464  33 DIHKGVVKKLQSYGAFVKVPDLDkeGLLHISRISDQRVENVEDVLAVGQEVWVKV--LSQEDGKLRLCMKSVNQHDGSER 110
Cdd:PRK12269 495 DSVSGVVKSFTSFGAFIDLGGFD--GLLHVNDMSWGHVARPREFVKKGQTIELKVirLDQAEKRINLSLKHFQPDPWLEF 572

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464 111 ESlrqSFihrgeggGVktpelDSIHQGTVRRIQEFGAFVSI-DGFdrDGLLHISCIS-SQKLDRVDDALAVGDKVWVKVT 188
Cdd:PRK12269 573 EN---KF-------GV-----NDVVKGRVTKIADFGAFIELaEGI--EGLAHISEFSwVKKTSKPSDMVKIGDEVECMIL 635

                        170
                 ....*....|....*..
gi 557733464 189 KVE-EGGKYGLDMRGIS 204
Cdd:PRK12269 636 GYDiQAGRVSLGLKQVT 652
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 36-97 5.85e-07

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: 46.46  E-value: 5.85e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 557733464  36 KGVVKKLQSYGAFVKVpDLDKEGLLHISRISDQRVENVEDVLAVGQEVWVKVLSQEDGKLRL 97
Cdd:cd05685    5 EGVVTNVTDFGAFVDI-GVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRI 65
PRK08563 PRK08563
DNA-directed RNA polymerase subunit E'; Provisional
 129-201 6.00e-07

DNA-directed RNA polymerase subunit E'; Provisional


Pssm-ID: 236289 [Multi-domain]  Cd Length: 187  Bit Score: 49.44  E-value: 6.00e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464 129 PELDSIHQGTVRRIQEFGAFVSIDGFdrDGLLHISCISSQKL--DRVDDALA---------VGDKVWVKVTKV------E 191
Cdd:PRK08563  79 PELQEVVEGEVVEVVEFGAFVRIGPV--DGLLHISQIMDDYIsyDPKNGRLIgkeskrvlkVGDVVRARIVAVslkerrP 156

                         90
                 ....*....|
gi 557733464 192 EGGKYGLDMR 201
Cdd:PRK08563 157 RGSKIGLTMR 166
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 137-192 9.66e-07

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 50.55  E-value: 9.66e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 557733464 137 GTVRRIQEFGAFVSIDGFDrdGLLHISCISSQKLDRVDDALAVGDKVWVKVTKVEE 192
Cdd:PRK06299 207 GVVKNITDYGAFVDLGGVD--GLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDK 260
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
46-89 1.27e-06

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 50.41  E-value: 1.27e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 557733464  46 GAFVkvpdlD---KE-GLLHISRISDQRVENVEDVLAVGQEVWVKVLS 89
Cdd:COG2183  656 GAFV-----DigvHQdGLVHISQLSDRFVKDPREVVKVGDIVKVKVLE 698
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 46-209 2.45e-06

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 48.64  E-value: 2.45e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464  46 GAFVKVPDLdkEGLLHISRISDQRVEnvEDVlaVGQEVWVKVLSQEDGKLRLCMksvnqhdgSERESLRQSFIHRGEGGG 125
Cdd:PRK07400 133 GALVRIEGL--RGFIPGSHISTRKPK--EEL--VGEELPLKFLEVDEERNRLVL--------SHRRALVERKMNRLEVGE 198

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464 126 VKTpeldsihqGTVRRIQEFGAFVSIDGFDrdGLLHISCISSQKLDRVDDALAVGDKVWVKVTKVE-EGGKYGLDMRGIS 204
Cdd:PRK07400 199 VVV--------GTVRGIKPYGAFIDIGGVS--GLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDaERGRISLSTKQLE 268


                 ....*
gi 557733464 205 QKDGA 209
Cdd:PRK07400 269 PEPGD 273
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 33-89 8.65e-06

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: 43.41  E-value: 8.65e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 557733464  33 DIHKGVVKKLQSYGAFVKVPDlDKEGLLHISRISDQRVENVEDVLAVGQEVWVKVLS 89
Cdd:cd05691    2 SIVTGKVTEVDAKGATVKLGD-GVEGFLRAAELSRDRVEDATERFKVGDEVEAKITN 57
S1_RpoE cd04460
S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 134-201 9.55e-06

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: 43.82  E-value: 9.55e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464 134 IHQGTVRRIQEFGAFVSIDGFdrDGLLHISCISSqklDRVD-DA-------------LAVGDKVWVKVTKV------EEG 193
Cdd:cd04460    2 VVEGEVVEVVDFGAFVRIGPV--DGLLHISQIMD---DYISyDPknkrligeetkrvLKVGDVVRARIVAVslkerrPRE 76


                 ....*...
gi 557733464 194 GKYGLDMR 201
Cdd:cd04460   77 SKIGLTMR 84
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 137-192 1.23e-05

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 46.36  E-value: 1.23e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 557733464 137 GTVRRIQEFGAFVSIDGF-DRDGLLHISCISSQKLDRVDDALAVGDKVWVKVTKVEE 192
Cdd:PRK03987  14 GTVKEVKDFGAFVTLDEYpGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDP 70
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 33-99 2.00e-05

S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240195 [Multi-domain]  Cd Length: 69  Bit Score: 42.10  E-value: 2.00e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 557733464  33 DIHKGVVKKLQSYGAFVKVPDlDKEGLLHISRIS-DQRVENVEDVLAVGQEVWVKVLSQEDGKLRLCM 99
Cdd:cd05690    2 TVVSGKIKSITDFGIFVGLDG-GIDGLVHISDISwTQRVRHPSEIYKKGQEVEAVVLNIDVERERISL 68
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 37-97 4.77e-05

S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 239908 [Multi-domain]  Cd Length: 83  Bit Score: 41.42  E-value: 4.77e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 557733464  37 GVVKKLQSYGAFVKVPD-LdkEGLLHISRISDQRVENVEDVLAVGQEVWVKVLSQEDGKLRL 97
Cdd:cd04461   20 GYVRNITPYGVFVEFLGgL--TGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRF 79
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 126-196 5.40e-05

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 44.87  E-value: 5.40e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 557733464 126 VKTPELDSIHQGTVRRIQEFGAFVSIDGFDRDGLLHISCISSQKLDRVDDALAVGDKVWVKVTKVEEGGKY 196
Cdd:PRK06676  12 VKEVEVGDVVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGN 82
S1_RPS1_repeat_ec1_hs1 cd05687
S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 33-93 5.78e-05

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: 40.98  E-value: 5.78e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 557733464  33 DIHKGVVKKLQSYGAFVKVPdLDKEGLLHISRISDQRVENVEDVLAVGQEVWVKVLSQEDG 93
Cdd:cd05687    2 DIVKGTVVSVDDDEVLVDIG-YKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDE 61
S1_RecJ_like cd04473
S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of ...
 130-195 6.86e-05

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: 40.67  E-value: 6.86e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 557733464 130 ELDSIHQGTVRRIQEFGAFVSIDGFDRdGLLHIScissqkldRVDDALAVGDKVWVKVTKVEEGGK 195
Cdd:cd04473   15 EVGKLYKGKVNGVAKYGVFVDLNDHVR-GLIHRS--------NLLRDYEVGDEVIVQVTDIPENGN 71
COG1107 COG1107
Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [Replication, ...
 130-204 3.05e-04

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


Pssm-ID: 440724 [Multi-domain]  Cd Length: 626  Bit Score: 42.90  E-value: 3.05e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 557733464 130 ELDSIHQGTVRRIQEFGAFVSIDgfDR-DGLLHIScissqkldRVDDALAVGDKVWVKVTKVEEGGKYGLDMRGIS 204
Cdd:COG1107   38 EPGRYYRGTVDGVADFGVFVDLN--DHvTGLLHRS--------ELDQDWEVGDEVFVQVKEVRDNGNVDLGWVSID 103
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 23-107 3.16e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 42.09  E-value: 3.16e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464  23 ERQNGKPQSTDIHKGVVKKLQSYGAFVKVPDLdkEGLLHISRISDQRVENVEDVLAVGQEVWVKV--LSQEDGKLRLCMK 100
Cdd:PRK07400 188 ERKMNRLEVGEVVVGTVRGIKPYGAFIDIGGV--SGLLHISEISHEHIETPHSVFNVNDEMKVMIidLDAERGRISLSTK 265


                 ....*..
gi 557733464 101 SVNQHDG 107
Cdd:PRK07400 266 QLEPEPG 272
CafA COG1530
Ribonuclease G or E [Translation, ribosomal structure and biogenesis];
23-87 3.40e-04

Ribonuclease G or E [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441139 [Multi-domain]  Cd Length: 490  Bit Score: 42.44  E-value: 3.40e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 557733464  23 ERQNGKPQSTDIHKGVVKK----LQSygAFVKVpDLDKEGLLHISRIS----------DQRVENVEDVLAVGQEVWVKV 87
Cdd:COG1530   28 ERPGREQLVGNIYKGKVTRvlpgLQA--AFVDI-GLERHGFLHVKDISpeyfslgkedSGKRPNIQDVLKEGQEVLVQV 103
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 58-195 5.42e-04

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 42.01  E-value: 5.42e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464  58 GLLHISRISDQRVENVEDVLAVGQEVWVKVLSQEdgklrlcmksvNQHDGSERESLRQSFIHRGEGGGVKTPELDSIH-- 135
Cdd:PRK12269 426 AFLPISQSDCQKVDAPESLIGLTSKFYIERISQS-----------KQHRGNDNIVINRRRYLEERARQAREEFFNSVHie 494

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 557733464 136 ---QGTVRRIQEFGAFVSIDGFdrDGLLHISCISSQKLDRVDDALAVGDKVWVKVTKVEEGGK 195
Cdd:PRK12269 495 dsvSGVVKSFTSFGAFIDLGGF--DGLLHVNDMSWGHVARPREFVKKGQTIELKVIRLDQAEK 555
S1_RPS1_repeat_ec1_hs1 cd05687
S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 137-193 9.04e-04

S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240192 [Multi-domain]  Cd Length: 70  Bit Score: 37.51  E-value: 9.04e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 557733464 137 GTVRRIQEFGAFVSIdGFDRDGLLHISCISSQKLDRVDDALAVGDKVWVKVTKVEEG 193
Cdd:cd05687    6 GTVVSVDDDEVLVDI-GYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDE 61
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 37-100 1.22e-03

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: 37.21  E-value: 1.22e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 557733464  37 GVVKKLQSYGAFVKVPDlDKEGLLHISRISDQRVENVEDVLAVGQEVWVKVLS--QEDGKLRLCMK 100
Cdd:cd05698    6 GTIVKVKPNGCIVSFYN-NVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLScdPEQQRLLLSCK 70
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 136-191 1.66e-03

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: 36.70  E-value: 1.66e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 557733464 136 QGTVRRIQEFGAFVSIDGfDRDGLLHISCIS-SQKLDRVDDALAVGDKVWVKVTKVE 191
Cdd:cd05690    5 SGKIKSITDFGIFVGLDG-GIDGLVHISDISwTQRVRHPSEIYKKGQEVEAVVLNID 60
S1_RNase_R cd04471
S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, ...
 37-89 2.45e-03

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: 36.61  E-value: 2.45e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 557733464  37 GVVKKLQSYGAFVKVPDLDKEGLLHISRISDQRVENVEDVLA-----------VGQEVWVKVLS 89
Cdd:cd04471    7 GVISGVTSFGLFVELDNLTVEGLVHVSTLGDDYYEFDEENHAlvgertgkvfrLGDKVKVRVVR 70
S1_RpoE cd04460
S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 37-101 4.10e-03

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: 36.50  E-value: 4.10e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557733464  37 GVVKKLQSYGAFVKVPDLDkeGLLHISRISDQRVENVED-----------VLAVGQEVWVKVLS-------QEDGKLRLC 98
Cdd:cd04460    5 GEVVEVVDFGAFVRIGPVD--GLLHISQIMDDYISYDPKnkrligeetkrVLKVGDVVRARIVAvslkerrPRESKIGLT 82


                 ...
gi 557733464  99 MKS 101
Cdd:cd04460   83 MRQ 85
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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