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Conserved domains on  [gi|1215837615|ref|YP_009391535|]
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ribosomal protein S1 (chloroplast) [Platysiphonia delicata]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK07400 super family cl32213
30S ribosomal protein S1; Reviewed
 11-263 6.65e-54

30S ribosomal protein S1; Reviewed


The actual alignment was detected with superfamily member PRK07400:

Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 176.91  E-value: 6.65e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215837615  11 NFVEILQKYNYCLHSGNIVAGVIMFKESSGFLVNIGDNFSGYLPQEE--INKKFIRTERAQ-NQliylTRDFFIVKYNLD 87
Cdd:PRK07400   17 DFAALLDKYDYHFKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEmsINRVEGPEEVLQpNE----TREFFILSDENE 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215837615  88 RRQYILSIKRLEYIRSWKRIKQLEFENCMFYLKINYINKGGLITNLEGLQAFVPKSQIYANDYIKSYRNKKVICKILIIN 167
Cdd:PRK07400   93 DGQLTLSIRRIEYMRAWERVRQLQKEDATVRSEVFATNRGGALVRIEGLRGFIPGSHISTRKPKEELVGEELPLKFLEVD 172

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215837615 168 EHKNQLVLTAKSPLIHLSKHKLRPGEILYGTITKVKTYGLFIKIYKIIALLHISEIGFEYIDNIHKVFCINKLIKIRIIH 247
Cdd:PRK07400  173 EERNRLVLSHRRALVERKMNRLEVGEVVVGTVRGIKPYGAFIDIGGVSGLLHISEISHEHIETPHSVFNVNDEMKVMIID 252

                         250
                  ....*....|....*.
gi 1215837615 248 IDSKQGRISVSKRKIK 263
Cdd:PRK07400  253 LDAERGRISLSTKQLE 268
 
Name Accession Description Interval E-value
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 11-263 6.65e-54

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 176.91  E-value: 6.65e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215837615  11 NFVEILQKYNYCLHSGNIVAGVIMFKESSGFLVNIGDNFSGYLPQEE--INKKFIRTERAQ-NQliylTRDFFIVKYNLD 87
Cdd:PRK07400   17 DFAALLDKYDYHFKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEmsINRVEGPEEVLQpNE----TREFFILSDENE 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215837615  88 RRQYILSIKRLEYIRSWKRIKQLEFENCMFYLKINYINKGGLITNLEGLQAFVPKSQIYANDYIKSYRNKKVICKILIIN 167
Cdd:PRK07400   93 DGQLTLSIRRIEYMRAWERVRQLQKEDATVRSEVFATNRGGALVRIEGLRGFIPGSHISTRKPKEELVGEELPLKFLEVD 172

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215837615 168 EHKNQLVLTAKSPLIHLSKHKLRPGEILYGTITKVKTYGLFIKIYKIIALLHISEIGFEYIDNIHKVFCINKLIKIRIIH 247
Cdd:PRK07400  173 EERNRLVLSHRRALVERKMNRLEVGEVVVGTVRGIKPYGAFIDIGGVSGLLHISEISHEHIETPHSVFNVNDEMKVMIID 252

                         250
                  ....*....|....*.
gi 1215837615 248 IDSKQGRISVSKRKIK 263
Cdd:PRK07400  253 LDAERGRISLSTKQLE 268
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 23-258 3.96e-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: 115.53  E-value: 3.96e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215837615  23 LHSGNIVAGVIMFKESSGFLVNIGDNFSGYLPQEEINKKFIRTERAQNQLIyltrDFFIVKYNLDRRQYILSIKRLEYIR 102
Cdd:COG0539    16 LKEGDIVKGTVVSIDDDEVLVDIGYKSEGIIPLSEFSDEPGELEVKVGDEV----EVYVEKVEDGEGEIVLSKKKADREK 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215837615 103 SWKRIKQLEFENCMFYLKINYINKGGLITNLEGLQAFVPKSQIyANDYIK---SYRNKKVICKILIINEHKNQLVLTAKS 179
Cdd:COG0539    92 AWEELEEAFENGEPVEGKVKGVVKGGLIVDIGGVRAFLPASQV-DVRPVRdldEYVGKTLEFKIIKLDRKRNNVVVSRRA 170

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215837615 180 PL-IHLSKHK------LRPGEILYGTITKVKTYGLFIKIYKIIALLHISEIGFEYIDNIHKVFCINKLIKIRIIHIDSKQ 252
Cdd:COG0539   171 VLeEEREEKReellekLEEGDVVEGTVKNITDFGAFVDLGGVDGLLHISEISWGRVKHPSEVLKVGDEVEVKVLKIDREK 250


                  ....*.
gi 1215837615 253 GRISVS 258
Cdd:COG0539   251 ERISLS 256
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 24-263 2.25e-17

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: 81.32  E-value: 2.25e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215837615  24 HSGNIVAGVIMFKESSGFLVNIGDNFSGYLPQEEINKKFIRTERAQnqliylTRDFFIVKYNLDRRQYILSIKRLEYIRS 103
Cdd:TIGR00717  17 RPGSIVKGTVVAINKDTVFVDVGLKSEGRIPKEEFLDAPLEIQVGD------EVEVYLDRVEDRFGETVLSREKAQRHEL 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215837615 104 WKRIKQLEFENCMFYLKINYINKGGLITNLEGLQAFVPKSQI--YANDYIKSYRNKKVICKILIINEHKNQLVLTAKSPL 181
Cdd:TIGR00717  91 WIKLEKAYEEGSIVEGKIVGKVKGGFIVDLNGVEAFLPGSQVdvKPIKDLDSLIGKTLKFKIIKLDQKRNNIVVSRRAYL 170

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215837615 182 -------IHLSKHKLRPGEILYGTITKVKTYGLFIKIYKIIALLHISEIGFEYIDNIHKVFCINKLIKIRIIHIDSKQGR 254
Cdd:TIGR00717 171 eeersqaREELLENLKEGDVVKGVVKNITDFGAFVDLGGVDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGR 250


                  ....*....
gi 1215837615 255 ISVSKRKIK 263
Cdd:TIGR00717 251 ISLSLKQLG 259
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
190-260 7.15e-11

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 56.84  E-value: 7.15e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1215837615  190 RPGEILYGTITKVKTYGLFIKI-YKIIALLHISEIGFEYIDNIHKVFCINKLIKIRIIHIDSKQGRISVSKR 260
Cdd:smart00316   1 EVGDVVEGTVTEITPGGAFVDLgNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 191-258 1.67e-09

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


Pssm-ID: 240193 [Multi-domain]  Cd Length: 68  Bit Score: 53.02  E-value: 1.67e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1215837615 191 PGEILYGTITKVKTYGLFIKIYKIIALLHISEIGFEYIDNIHKVFCINKLIKIRIIHIDSKQGRISVS 258
Cdd:cd05688     1 EGDVVEGTVKSITDFGAFVDLGGVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 189-259 1.45e-07

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: 47.67  E-value: 1.45e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1215837615 189 LRPGEILYGTITKVKTYGLFIKI-YKIIALLHISEIGFEYIDNIHKVFCINKLIKIRIIHIDSKQGRISVSK 259
Cdd:pfam00575   1 PEKGDVVEGEVTRVTKGGAFVDLgNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
 
Name Accession Description Interval E-value
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 11-263 6.65e-54

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 176.91  E-value: 6.65e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215837615  11 NFVEILQKYNYCLHSGNIVAGVIMFKESSGFLVNIGDNFSGYLPQEE--INKKFIRTERAQ-NQliylTRDFFIVKYNLD 87
Cdd:PRK07400   17 DFAALLDKYDYHFKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEmsINRVEGPEEVLQpNE----TREFFILSDENE 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215837615  88 RRQYILSIKRLEYIRSWKRIKQLEFENCMFYLKINYINKGGLITNLEGLQAFVPKSQIYANDYIKSYRNKKVICKILIIN 167
Cdd:PRK07400   93 DGQLTLSIRRIEYMRAWERVRQLQKEDATVRSEVFATNRGGALVRIEGLRGFIPGSHISTRKPKEELVGEELPLKFLEVD 172

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215837615 168 EHKNQLVLTAKSPLIHLSKHKLRPGEILYGTITKVKTYGLFIKIYKIIALLHISEIGFEYIDNIHKVFCINKLIKIRIIH 247
Cdd:PRK07400  173 EERNRLVLSHRRALVERKMNRLEVGEVVVGTVRGIKPYGAFIDIGGVSGLLHISEISHEHIETPHSVFNVNDEMKVMIID 252

                         250
                  ....*....|....*.
gi 1215837615 248 IDSKQGRISVSKRKIK 263
Cdd:PRK07400  253 LDAERGRISLSTKQLE 268
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 23-258 3.96e-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: 115.53  E-value: 3.96e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215837615  23 LHSGNIVAGVIMFKESSGFLVNIGDNFSGYLPQEEINKKFIRTERAQNQLIyltrDFFIVKYNLDRRQYILSIKRLEYIR 102
Cdd:COG0539    16 LKEGDIVKGTVVSIDDDEVLVDIGYKSEGIIPLSEFSDEPGELEVKVGDEV----EVYVEKVEDGEGEIVLSKKKADREK 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215837615 103 SWKRIKQLEFENCMFYLKINYINKGGLITNLEGLQAFVPKSQIyANDYIK---SYRNKKVICKILIINEHKNQLVLTAKS 179
Cdd:COG0539    92 AWEELEEAFENGEPVEGKVKGVVKGGLIVDIGGVRAFLPASQV-DVRPVRdldEYVGKTLEFKIIKLDRKRNNVVVSRRA 170

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215837615 180 PL-IHLSKHK------LRPGEILYGTITKVKTYGLFIKIYKIIALLHISEIGFEYIDNIHKVFCINKLIKIRIIHIDSKQ 252
Cdd:COG0539   171 VLeEEREEKReellekLEEGDVVEGTVKNITDFGAFVDLGGVDGLLHISEISWGRVKHPSEVLKVGDEVEVKVLKIDREK 250


                  ....*.
gi 1215837615 253 GRISVS 258
Cdd:COG0539   251 ERISLS 256
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 23-258 6.16e-24

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 99.18  E-value: 6.16e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215837615  23 LHSGNIVAGVIMFKESSGFLVNI-GDNFSGYLPQEEINKKFIRTeraQNQLIYL--TRDFFIVKYNLDRRQYILSIKRLE 99
Cdd:PRK06676   15 VEVGDVVTGEVLKVEDKQVFVNIeGYKVEGVIPISELSNDHIED---INDVVKVgdELEVYVLKVEDGEGNLLLSKRRLE 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215837615 100 YIRSWKRIKQLEFENCMFYLKINYINKGGLITNLEGLQAFVPKSQIyANDYI---KSYRNKKVICKILIINEHKNQLVLT 176
Cdd:PRK06676   92 AEKAWDKLEEKFEEGEVVEVKVTEVVKGGLVVDVEGVRGFIPASLI-STRFVedfSDFKGKTLEVKIIELDPEKNRVILS 170

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215837615 177 AKSPL--IHLSKHK-----LRPGEILYGTITKVKTYGLFIKIYKIIALLHISEIGFEYIDNIHKVFCINKLIKIRIIHID 249
Cdd:PRK06676  171 RRAVVeeERAAKKEellssLKEGDVVEGTVARLTDFGAFVDIGGVDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSID 250


                  ....*....
gi 1215837615 250 SKQGRISVS 258
Cdd:PRK06676  251 WETERISLS 259
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
23-262 6.97e-21

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 91.55  E-value: 6.97e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215837615  23 LHSGNIVAGVIMFKESSGFLVNIGDNFSGYLPQEEINKKfiRTERAQNQL-IYLTRDFFIVKYNLDRRQYILSIKRLEYI 101
Cdd:PRK00087  300 IRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLD--EISSLKESVkVGDEIEVKVLKLEDEDGYVVLSKKEADRE 377

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215837615 102 RSWKRIKQLeFEN-CMFYLKINYINKGGLITNLEGLQAFVPKSQI---YANDyIKSYRNKKVICKILIINEHKNQLVLTA 177
Cdd:PRK00087  378 KAWKELEEA-FENgEPVKGKVKEVVKGGLLVDYGGVRAFLPASHVelgYVED-LSEYKGQELEVKIIEFNRKRRKKVVLS 455

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215837615 178 KSPLIHLSKHKLR--------PGEILYGTITKVKTYGLFIKIYKIIALLHISEIGFEYIDNIHKVFCINKLIKIRIIHID 249
Cdd:PRK00087  456 RKAILEEEKEKKKeetwnsleEGDVVEGEVKRLTDFGAFVDIGGVDGLLHVSEISWGRVEKPSDVLKVGDEIKVYILDID 535

                         250
                  ....*....|...
gi 1215837615 250 SKQGRISVSKRKI 262
Cdd:PRK00087  536 KENKKLSLSLKKL 548
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 26-258 1.61e-17

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 81.75  E-value: 1.61e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215837615  26 GNIVAGVIMFKESSGFLVNIGDNFSGYLPQEEInkkfirtERAQNQLIYLTRDF---FIVKYNLDRRQYILSIKRLEYIR 102
Cdd:PRK06299   31 GSIVKGTVVAIDKDYVLVDVGLKSEGRIPLEEF-------KNEQGELEVKVGDEvevYVERIEDGFGETVLSREKAKRLE 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215837615 103 SWKRIKQLEFENCMFYLKINYINKGGLITNLEGLQAFVPKSQIYA---NDYIkSYRNKKVICKILIINEHKNQLVLTAKS 179
Cdd:PRK06299  104 AWDKLEKAFENGEIVEGVINGKVKGGFTVDLNGVEAFLPGSQVDVrpvRDTD-PLEGKELEFKVIKLDKKRNNIVVSRRA 182

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215837615 180 pLIHLSK--------HKLRPGEILYGTITKVKTYGLFIKIYKIIALLHISEIGFEYIDNIHKVFCINKLIKIRIIHIDSK 251
Cdd:PRK06299  183 -VLEEERaeereellENLEEGQVVEGVVKNITDYGAFVDLGGVDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLKFDKE 261


                  ....*..
gi 1215837615 252 QGRISVS 258
Cdd:PRK06299  262 KKRVSLG 268
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 24-263 2.25e-17

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: 81.32  E-value: 2.25e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215837615  24 HSGNIVAGVIMFKESSGFLVNIGDNFSGYLPQEEINKKFIRTERAQnqliylTRDFFIVKYNLDRRQYILSIKRLEYIRS 103
Cdd:TIGR00717  17 RPGSIVKGTVVAINKDTVFVDVGLKSEGRIPKEEFLDAPLEIQVGD------EVEVYLDRVEDRFGETVLSREKAQRHEL 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215837615 104 WKRIKQLEFENCMFYLKINYINKGGLITNLEGLQAFVPKSQI--YANDYIKSYRNKKVICKILIINEHKNQLVLTAKSPL 181
Cdd:TIGR00717  91 WIKLEKAYEEGSIVEGKIVGKVKGGFIVDLNGVEAFLPGSQVdvKPIKDLDSLIGKTLKFKIIKLDQKRNNIVVSRRAYL 170

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215837615 182 -------IHLSKHKLRPGEILYGTITKVKTYGLFIKIYKIIALLHISEIGFEYIDNIHKVFCINKLIKIRIIHIDSKQGR 254
Cdd:TIGR00717 171 eeersqaREELLENLKEGDVVKGVVKNITDFGAFVDLGGVDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGR 250


                  ....*....
gi 1215837615 255 ISVSKRKIK 263
Cdd:TIGR00717 251 ISLSLKQLG 259
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 26-263 4.26e-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: 68.61  E-value: 4.26e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215837615  26 GNIVAGVIMFKESSGFLVNIGdNFSGYLPQEEINKKFIRterAQNQLIYLTRDFFIVKYNLDRRQYILSIKR-LEYIRSW 104
Cdd:TIGR00717 101 GSIVEGKIVGKVKGGFIVDLN-GVEAFLPGSQVDVKPIK---DLDSLIGKTLKFKIIKLDQKRNNIVVSRRAyLEEERSQ 176

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215837615 105 KRIKQLEfencmfYLKINYINKG--------GLITNLEGLQAFVPKSQI------YANDYIKsyRNKKVICKILIINEHK 170
Cdd:TIGR00717 177 AREELLE------NLKEGDVVKGvvknitdfGAFVDLGGVDGLLHITDMswkrvkHPSEYVK--VGQEVKVKVIKFDKEK 248

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215837615 171 NQLVLTAK----SPLIHLSKhKLRPGEILYGTITKVKTYGLFIKIYK-IIALLHISEIGFEYiDNIH--KVFCINKLIKI 243
Cdd:TIGR00717 249 GRISLSLKqlgeDPWEAIEK-KFPVGDKITGRVTNLTDYGVFVEIEEgIEGLVHVSEMSWVK-KNSHpsKVVKKGDEVEV 326

                         250       260
                  ....*....|....*....|
gi 1215837615 244 RIIHIDSKQGRISVSKRKIK 263
Cdd:TIGR00717 327 MILDIDPERRRLSLGLKQCK 346
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 92-258 3.22e-11

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 62.75  E-value: 3.22e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215837615  92 ILSIKRLEYIRSWKRIKQLEFENCMFYLKINYINKGGLITNLeGLQAFVPKSQI---YANDyIKSYRNKKVICKILIINE 168
Cdd:PRK07899  101 ILSKKRAQYERAWGTIEKIKEKDGVVTGTVIEVVKGGLILDI-GLRGFLPASLVemrRVRD-LQPYIGQEIEAKIIELDK 178

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215837615 169 HKNQLVLTAKSPLIHLSK-------HKLRPGEILYGTITKVKTYGLFIKIYKIIALLHISEIGFEYIDNIHKVFCINKLI 241
Cdd:PRK07899  179 NRNNVVLSRRAWLEQTQSevrseflNQLQKGQVRKGVVSSIVNFGAFVDLGGVDGLVHVSELSWKHIDHPSEVVEVGQEV 258

                         170
                  ....*....|....*..
gi 1215837615 242 KIRIIHIDSKQGRISVS 258
Cdd:PRK07899  259 TVEVLDVDMDRERVSLS 275
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
190-260 7.15e-11

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 56.84  E-value: 7.15e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1215837615  190 RPGEILYGTITKVKTYGLFIKI-YKIIALLHISEIGFEYIDNIHKVFCINKLIKIRIIHIDSKQGRISVSKR 260
Cdd:smart00316   1 EVGDVVEGTVTEITPGGAFVDLgNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 188-265 1.40e-10

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


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 57.50  E-value: 1.40e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1215837615 188 KLRPGEILYGTITKVKTYGLFIKIY-KIIALLHISEIGFEYIDNIHKVFCINKLIKIRIIHIDSKqGRISVSKRKIKTK 265
Cdd:COG1098     2 SIEVGDIVEGKVTGITPFGAFVELPeGTTGLVHISEIADGYVKDINDYLKVGDEVKVKVLSIDED-GKISLSIKQAEEK 79
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 191-258 1.67e-09

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


Pssm-ID: 240193 [Multi-domain]  Cd Length: 68  Bit Score: 53.02  E-value: 1.67e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1215837615 191 PGEILYGTITKVKTYGLFIKIYKIIALLHISEIGFEYIDNIHKVFCINKLIKIRIIHIDSKQGRISVS 258
Cdd:cd05688     1 EGDVVEGTVKSITDFGAFVDLGGVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 192-258 4.81e-09

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: 51.90  E-value: 4.81e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1215837615 192 GEILYGTITKVKTYGLFIKIYK-IIALLHISEIGFEYIDNIHKVFCINKLIKIRIIHIDsKQGRISVS 258
Cdd:cd05692     1 GSVVEGTVTRLKPFGAFVELGGgISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSID-ARGRISLS 67
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 158-265 6.11e-09

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 56.33  E-value: 6.11e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215837615 158 KVICKILIINEHKNQLVLTAK----SPLIHLSKhKLRPGEILYGTITKVKTYGLFIKIY-KIIALLHISEIGFEYIDNIH 232
Cdd:PRK06299  424 EVEAVVLKVDVEKERISLGIKqleeDPFEEFAK-KHKKGSIVTGTVTEVKDKGAFVELEdGVEGLIRASELSRDRVEDAT 502

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1215837615 233 KVFCINKLIKIRIIHIDSKQGRISVS-KRKIKTK 265
Cdd:PRK06299  503 EVLKVGDEVEAKVINIDRKNRRISLSiKALDEAE 536
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 192-260 6.31e-09

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 56.21  E-value: 6.31e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215837615 192 GEILYGTITKVKTYGLFIKIY-KIIALLHISEIGFEYIDNIHKVFCINKLIKIRIIHIDsKQGRISVSKR 260
Cdd:PRK11824  622 GEIYEGKVVRIVDFGAFVEILpGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEID-KRGRIRLSRK 690
PRK08059 PRK08059
general stress protein 13; Validated
 192-260 1.21e-08

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 51.97  E-value: 1.21e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215837615 192 GEILYGTITKVKTYGLFIKI-YKIIALLHISEIGFEYIDNIHKVFCINKLIKIRIIHIDSKQGRISVSKR 260
Cdd:PRK08059    8 GSVVTGKVTGIQPYGAFVALdEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIR 77
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
192-260 2.20e-08

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 51.24  E-value: 2.20e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215837615 192 GEILYGTITKVKTYGLFIKIYK-IIALLHISEIGFEYIDNIHKVFCINKLIKIRIIHIDSKQGRISVSKR 260
Cdd:PRK07252    4 GDKLKGTITGIKPYGAFVALENgTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLR 73
S1_RPS1_repeat_ec2_hs2 cd04465
S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 120-178 4.59e-08

S1_RPS1_repeat_ec2_hs2: 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 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 239911 [Multi-domain]  Cd Length: 67  Bit Score: 48.99  E-value: 4.59e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1215837615 120 KINYINKGGLITNLEGLQAFVPKSQI---YANDyIKSYRNKKVICKILIINEHKNQLVLTAK 178
Cdd:cd04465     7 KVTEKVKGGLIVDIEGVRAFLPASQVdlrPVED-LDEYVGKELKFKIIEIDRERNNIVLSRR 67
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 192-259 5.16e-08

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: 48.69  E-value: 5.16e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1215837615 192 GEILYGTITKVKTYGLFIKIY-KIIALLHISEIGFEYIDNIHKVFCINKLIKIRIIHIDsKQGRISVSK 259
Cdd:cd04472     1 GKIYEGKVVKIKDFGAFVEILpGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVD-DRGRISLSR 68
PRK05807 PRK05807
RNA-binding protein S1;
189-265 7.52e-08

RNA-binding protein S1;


Pssm-ID: 235614 [Multi-domain]  Cd Length: 136  Bit Score: 50.13  E-value: 7.52e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1215837615 189 LRPGEILYGTITKVKTYGLFIKIYKIIALLHISEIGFEYIDNIHKVFCINKLIKIRIIHIDSKqGRISVS-KRKIKTK 265
Cdd:PRK05807    3 LKAGSILEGTVVNITNFGAFVEVEGKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDDN-GKISLSiKQAMKQK 79
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 192-260 1.03e-07

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: 47.99  E-value: 1.03e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215837615 192 GEILYGTITKVKTYGLFIKIY-KIIALLHISEIGFEYIDNIHKVFCINKLIKIRIIHIDSKQGRISVSKR 260
Cdd:cd05698     1 GLKTHGTIVKVKPNGCIVSFYnNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 189-259 1.45e-07

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: 47.67  E-value: 1.45e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1215837615 189 LRPGEILYGTITKVKTYGLFIKI-YKIIALLHISEIGFEYIDNIHKVFCINKLIKIRIIHIDSKQGRISVSK 259
Cdd:pfam00575   1 PEKGDVVEGEVTRVTKGGAFVDLgNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 192-258 1.01e-06

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: 45.40  E-value: 1.01e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1215837615 192 GEILYGTITKVKTYGLFIKI--YKIIALLHISEIGFEYIDNIHKVFCINKLIKIRIIHIDSKQGRISVS 258
Cdd:cd05708     3 GQKIDGTVRRVEDYGVFIDIdgTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLG 71
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 192-258 1.31e-06

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: 44.92  E-value: 1.31e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1215837615 192 GEILYGTITKVKTYGLFIKI-YKIIALLHISEIGFEYIDNIHKVFCINKLIKIRIIHIDSKQGRISVS 258
Cdd:cd05685     1 GMVLEGVVTNVTDFGAFVDIgVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 190-261 1.48e-06

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: 44.88  E-value: 1.48e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1215837615 190 RPGEILYGTITKVKTYGLFIKIYK---IIALLHISEIGFEYIDNIHKVFCINKLIKIRIIHIDSKQGRISVSKRK 261
Cdd:cd04452     2 EEGELVVVTVKSIADMGAYVSLLEygnIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKKR 76
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 197-258 2.04e-06

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: 44.29  E-value: 2.04e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1215837615 197 GTITKVKTYGLFIKIYK-IIALLHISEIGFEYIDNIHKVFCINKLIKIRIIHIDSKQGRISVS 258
Cdd:cd00164     3 GKVVSITKFGVFVELEDgVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 188-258 1.39e-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: 42.57  E-value: 1.39e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1215837615 188 KLRPGEILYGTITKVKTYGLFIKI-YKIIALLHISEIGFEYIDNIHKVFCINKLIKIRIIHIDSKQGRISVS 258
Cdd:cd04461    11 DLKPGMVVHGYVRNITPYGVFVEFlGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLS 82
S1_Rrp5_repeat_sc11 cd05707
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 192-258 3.54e-05

S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240212 [Multi-domain]  Cd Length: 68  Bit Score: 40.74  E-value: 3.54e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1215837615 192 GEILYGTITKVKTYGLFIKI-YKIIALLHISEIGFEYIDNIHKVFCINKLIKIRIIHIDSKQGRISVS 258
Cdd:cd05707     1 GDVVRGFVKNIANNGVFVTLgRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
189-263 1.72e-04

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 42.70  E-value: 1.72e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1215837615 189 LRPGEILYGTITKVKTYGLFIKI-YKIIALLHISEIGFEYIDNIHKVFCINKLIKIRIIHIDSKQGRISVSKRKIK 263
Cdd:COG2183   639 LKPGMILEGTVTNVTDFGAFVDIgVHQDGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEVDLKRKRISLSMKLDD 714
PRK08582 PRK08582
RNA-binding protein S1;
192-263 1.96e-04

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 40.40  E-value: 1.96e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1215837615 192 GEILYGTITKVKTYGLFIKIYK-IIALLHISEIGFEYIDNIHKVFCINKLIKIRIIHIDsKQGRISVSKRKIK 263
Cdd:PRK08582    6 GSKLQGKVTGITNFGAFVELPEgKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVE-DDGKIGLSIKKAK 77
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 32-262 2.15e-04

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 42.39  E-value: 2.15e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215837615  32 VIMFKESSGFLVNIGDNFSGYLPqeeINKKFIRTERAQNQLIYLTRDFFIVKYNLDRRQY---ILSIKRLEYIRSWKRIK 108
Cdd:PRK12269  407 VRLTEKKSGFEVDLGAGMMAFLP---ISQSDCQKVDAPESLIGLTSKFYIERISQSKQHRgndNIVINRRRYLEERARQA 483

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215837615 109 QLEFENCMFYLKinyiNKGGLITNLEGLQAFVP----KSQIYAND-----------YIKsyRNKKVICKILIINEHKNQL 173
Cdd:PRK12269  484 REEFFNSVHIED----SVSGVVKSFTSFGAFIDlggfDGLLHVNDmswghvarpreFVK--KGQTIELKVIRLDQAEKRI 557

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215837615 174 VLTAK----SPLIHLsKHKLRPGEILYGTITKVKTYGLFIKIYK-IIALLHISEigFEYIDNIHK---VFCINKLIKIRI 245
Cdd:PRK12269  558 NLSLKhfqpDPWLEF-ENKFGVNDVVKGRVTKIADFGAFIELAEgIEGLAHISE--FSWVKKTSKpsdMVKIGDEVECMI 634

                         250
                  ....*....|....*..
gi 1215837615 246 IHIDSKQGRISVSKRKI 262
Cdd:PRK12269  635 LGYDIQAGRVSLGLKQV 651
rpsA PRK13806
30S ribosomal protein S1; Provisional
 126-261 2.72e-04

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 42.02  E-value: 2.72e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215837615 126 KGGLITNLEGLQAFVPKSQI---YANDyIKSYRNKKVICKILIINEHKNQLVLTAKSPLIHLSKH-------KLRPGEIL 195
Cdd:PRK13806  128 KGGFNVEVLGRRAFCPVSQIdlrYVED-PESYVGQTFQFLITRVEENGRNIVVSRRALLEREQKEaleafmeTVKEGDVV 206

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1215837615 196 YGTITKVKTYGLFIKIYK-IIALLHISEIGFEYIDNIHKVFCINKLIKIRIIHIDSKQG----RISVSKRK 261
Cdd:PRK13806  207 EGTVTRLAPFGAFVELAPgVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKgkglRISLSIKQ 277
S1_RpoE cd04460
S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 193-259 1.86e-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: 36.88  E-value: 1.86e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1215837615 193 EILYGTITKVKTYGLFIKIYKIIALLHISEIGFEYI--DNIHKVFCINK---------LIKIRIIHIDSKQGRISVSK 259
Cdd:cd04460     1 EVVEGEVVEVVDFGAFVRIGPVDGLLHISQIMDDYIsyDPKNKRLIGEEtkrvlkvgdVVRARIVAVSLKERRPRESK 78
PRK08563 PRK08563
DNA-directed RNA polymerase subunit E'; Provisional
 192-259 1.89e-03

DNA-directed RNA polymerase subunit E'; Provisional


Pssm-ID: 236289 [Multi-domain]  Cd Length: 187  Bit Score: 38.27  E-value: 1.89e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1215837615 192 GEILYGTITKVKTYGLFIKIYKIIALLHISEIGFEYID-----------NIHKVFCINKLIKIRIIHIDSKQGRISVSK 259
Cdd:PRK08563   82 QEVVEGEVVEVVEFGAFVRIGPVDGLLHISQIMDDYISydpkngrligkESKRVLKVGDVVRARIVAVSLKERRPRGSK 160
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 191-262 2.18e-03

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 38.65  E-value: 2.18e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1215837615 191 PGEILYGTITKVKTYGLFIKI--Y-KIIALLHISEIGFEYIDNIHKVFCINKLIKIRIIHIDSKQGRISVSKRKI 262
Cdd:PRK03987    8 EGELVVGTVKEVKDFGAFVTLdeYpGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLKRV 82
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 192-265 2.45e-03

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: 35.71  E-value: 2.45e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1215837615 192 GEILYGTITKVKTYGLFIKIYK-IIALLHISEIGFEYIDNIHKVFCINKLIKIRIIHIDSKQGRISVSkrkIKTK 265
Cdd:cd05691     1 GSIVTGKVTEVDAKGATVKLGDgVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLS---IKAK 72
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 192-257 2.74e-03

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


Pssm-ID: 240202 [Multi-domain]  Cd Length: 69  Bit Score: 35.68  E-value: 2.74e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1215837615 192 GEILYGTITKVKTYGLFIKIYK----IIALLHISEIgfeYIDNIHKVFCINKLIKIRIIHIDSKQGRISV 257
Cdd:cd05697     1 GQVVKGTIRKLRPSGIFVKLSDhikgLVPPMHLADV---RLKHPEKKFKPGLKVKCRVLSVEPERKRLVL 67
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
26-96 4.31e-03

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 35.27  E-value: 4.31e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1215837615   26 GNIVAGVIMFKESSGFLVNIGDNFSGYLPQEEINKKFIRTERAQ---NQLIyltrDFFIVKYNLDRRQYILSIK 96
Cdd:smart00316   3 GDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVlkvGDEV----KVKVLSVDEEKGRIILSLK 72
S1_RPS1_repeat_ec2_hs2 cd04465
S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 192-260 5.40e-03

S1_RPS1_repeat_ec2_hs2: 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 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 239911 [Multi-domain]  Cd Length: 67  Bit Score: 34.74  E-value: 5.40e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1215837615 192 GEILYGTITKVKTYGLFIKIYKIIALLHISEIGFEYIDNIHKVfcINKLIKIRIIHIDSKQGRISVSKR 260
Cdd:cd04465     1 GEIVEGKVTEKVKGGLIVDIEGVRAFLPASQVDLRPVEDLDEY--VGKELKFKIIEIDRERNNIVLSRR 67
S1_pNO40 cd05686
S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function ...
 193-258 7.25e-03

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: 34.38  E-value: 7.25e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1215837615 193 EILYGTITKVKTYGLFIKI--YKIIALLHISEIGFEYIDNIHKVFCINKLIKIRIIHIDSKqGRISVS 258
Cdd:cd05686     5 QIFKGEVASVTEYGAFVKIpgCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMK-DKMKLS 71
 
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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