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Conserved domains on  [gi|1002248589|ref|XP_015628466|]
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30S ribosomal protein S1, chloroplastic [Oryza sativa Japonica Group]

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
 62-358 7.32e-101

30S ribosomal protein S1; Reviewed


The actual alignment was detected with superfamily member PRK07400:

Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 302.10  E-value: 7.32e-101
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589  62 RTAPMEGVSFSPEDLDSAVESTDIDTDIGSLIKGTVFMTTSNGAYVDIQSKSTAFLPLDEACLLDVNHIEEAgIRAGLVE 141
Cdd:PRK07400    4 QNTDADDIGFTHEDFAALLDKYDYHFKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSINRVEGPEEV-LQPNETR 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 142 EFMIIDENPGDETLILSLQAIQQDLAWERCRQLQAEDVVVTGKVIGGNKGGVVALVEGLKGFVPFSQVSSKSTAEELLDK 221
Cdd:PRK07400   83 EFFILSDENEDGQLTLSIRRIEYMRAWERVRQLQKEDATVRSEVFATNRGGALVRIEGLRGFIPGSHISTRKPKEELVGE 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 222 ELPLKFVEVDEEQGRLVLSNRKAMADSQA-QLGIGSVVLGTVESLKPYGAFIDIGGINGLLHVSQISHDRVADISTVLQP 300
Cdd:PRK07400  163 ELPLKFLEVDEERNRLVLSHRRALVERKMnRLEVGEVVVGTVRGIKPYGAFIDIGGVSGLLHISEISHEHIETPHSVFNV 242

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1002248589 301 GDTLKVMILSHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKADEMAQIFRQRI-AQAE 358
Cdd:PRK07400  243 NDEMKVMIIDLDAERGRISLSTKQLEPEPGDMLKDPQKVFDKAEEMAAKYRQMLlAQAE 301
 
Name Accession Description Interval E-value
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 62-358 7.32e-101

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 302.10  E-value: 7.32e-101
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589  62 RTAPMEGVSFSPEDLDSAVESTDIDTDIGSLIKGTVFMTTSNGAYVDIQSKSTAFLPLDEACLLDVNHIEEAgIRAGLVE 141
Cdd:PRK07400    4 QNTDADDIGFTHEDFAALLDKYDYHFKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSINRVEGPEEV-LQPNETR 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 142 EFMIIDENPGDETLILSLQAIQQDLAWERCRQLQAEDVVVTGKVIGGNKGGVVALVEGLKGFVPFSQVSSKSTAEELLDK 221
Cdd:PRK07400   83 EFFILSDENEDGQLTLSIRRIEYMRAWERVRQLQKEDATVRSEVFATNRGGALVRIEGLRGFIPGSHISTRKPKEELVGE 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 222 ELPLKFVEVDEEQGRLVLSNRKAMADSQA-QLGIGSVVLGTVESLKPYGAFIDIGGINGLLHVSQISHDRVADISTVLQP 300
Cdd:PRK07400  163 ELPLKFLEVDEERNRLVLSHRRALVERKMnRLEVGEVVVGTVRGIKPYGAFIDIGGVSGLLHISEISHEHIETPHSVFNV 242

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1002248589 301 GDTLKVMILSHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKADEMAQIFRQRI-AQAE 358
Cdd:PRK07400  243 NDEMKVMIIDLDAERGRISLSTKQLEPEPGDMLKDPQKVFDKAEEMAAKYRQMLlAQAE 301
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 74-329 5.67e-70

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: 223.77  E-value: 5.67e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589  74 EDLDSAVESTDIDTDIGSLIKGTVFMTTSNGAYVDIQSKSTAFLPLDEacLLDVNhiEEAGIRAGLVEEFMIIDENPGDE 153
Cdd:COG0539     3 ESFAELLEESLKELKEGDIVKGTVVSIDDDEVLVDIGYKSEGIIPLSE--FSDEP--GELEVKVGDEVEVYVEKVEDGEG 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 154 TLILSLQAIQQDLAWERCRQLQAEDVVVTGKVIGGNKGGVVALVEGLKGFVPFSQVSSK--STAEELLDKELPLKFVEVD 231
Cdd:COG0539    79 EIVLSKKKADREKAWEELEEAFENGEPVEGKVKGVVKGGLIVDIGGVRAFLPASQVDVRpvRDLDEYVGKTLEFKIIKLD 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 232 EEQGRLVLSNRKAMADSQAQ--------LGIGSVVLGTVESLKPYGAFIDIGGINGLLHVSQISHDRVADISTVLQPGDT 303
Cdd:COG0539   159 RKRNNVVVSRRAVLEEEREEkreellekLEEGDVVEGTVKNITDFGAFVDLGGVDGLLHISEISWGRVKHPSEVLKVGDE 238

                         250       260
                  ....*....|....*....|....*.
gi 1002248589 304 LKVMILSHDRERGRVSLSTKKLEPTP 329
Cdd:COG0539   239 VEVKVLKIDREKERISLSLKQLQPDP 264
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 90-335 3.85e-41

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: 152.20  E-value: 3.85e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589  90 GSLIKGTVFMTTSNGAYVDIQSKSTAFLPLDEacLLDVNHIEEAG--IRAGLVEefmiIDENPGDEtlILSLQAIQQDLA 167
Cdd:TIGR00717  19 GSIVKGTVVAINKDTVFVDVGLKSEGRIPKEE--FLDAPLEIQVGdeVEVYLDR----VEDRFGET--VLSREKAQRHEL 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 168 WERCRQLQAEDVVVTGKVIGGNKGGVVALVEGLKGFVPFSQVSSK--STAEELLDKELPLKFVEVDEEQGRLVLSnRKAM 245
Cdd:TIGR00717  91 WIKLEKAYEEGSIVEGKIVGKVKGGFIVDLNGVEAFLPGSQVDVKpiKDLDSLIGKTLKFKIIKLDQKRNNIVVS-RRAY 169

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 246 ADSQA---------QLGIGSVVLGTVESLKPYGAFIDIGGINGLLHVSQISHDRVADISTVLQPGDTLKVMILSHDRERG 316
Cdd:TIGR00717 170 LEEERsqareelleNLKEGDVVKGVVKNITDFGAFVDLGGVDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKG 249

                         250
                  ....*....|....*....
gi 1002248589 317 RVSLSTKKLEPTPGDMIRN 335
Cdd:TIGR00717 250 RISLSLKQLGEDPWEAIEK 268
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 255-323 2.48e-29

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: 108.53  E-value: 2.48e-29
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 255 GSVVLGTVESLKPYGAFIDIG-GINGLLHVSQISHDRVADISTVLQPGDTLKVMILSHDrERGRVSLSTK 323
Cdd:cd05692     1 GSVVEGTVTRLKPFGAFVELGgGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSID-ARGRISLSIK 69
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
254-323 9.45e-22

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 88.04  E-value: 9.45e-22
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1002248589  254 IGSVVLGTVESLKPYGAFIDIG-GINGLLHVSQISHDRVADISTVLQPGDTLKVMILSHDRERGRVSLSTK 323
Cdd:smart00316   2 VGDVVEGTVTEITPGGAFVDLGnGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 254-322 8.36e-14

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 66.16  E-value: 8.36e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 254 IGSVVLGTVESLKPYGAFIDIG-GINGLLHVSQISHDRVADISTVLQPGDTLKVMILSHDRERGRVSLST 322
Cdd:pfam00575   3 KGDVVEGEVTRVTKGGAFVDLGnGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
 
Name Accession Description Interval E-value
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 62-358 7.32e-101

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 302.10  E-value: 7.32e-101
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589  62 RTAPMEGVSFSPEDLDSAVESTDIDTDIGSLIKGTVFMTTSNGAYVDIQSKSTAFLPLDEACLLDVNHIEEAgIRAGLVE 141
Cdd:PRK07400    4 QNTDADDIGFTHEDFAALLDKYDYHFKPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSINRVEGPEEV-LQPNETR 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 142 EFMIIDENPGDETLILSLQAIQQDLAWERCRQLQAEDVVVTGKVIGGNKGGVVALVEGLKGFVPFSQVSSKSTAEELLDK 221
Cdd:PRK07400   83 EFFILSDENEDGQLTLSIRRIEYMRAWERVRQLQKEDATVRSEVFATNRGGALVRIEGLRGFIPGSHISTRKPKEELVGE 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 222 ELPLKFVEVDEEQGRLVLSNRKAMADSQA-QLGIGSVVLGTVESLKPYGAFIDIGGINGLLHVSQISHDRVADISTVLQP 300
Cdd:PRK07400  163 ELPLKFLEVDEERNRLVLSHRRALVERKMnRLEVGEVVVGTVRGIKPYGAFIDIGGVSGLLHISEISHEHIETPHSVFNV 242

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1002248589 301 GDTLKVMILSHDRERGRVSLSTKKLEPTPGDMIRNPKLVFEKADEMAQIFRQRI-AQAE 358
Cdd:PRK07400  243 NDEMKVMIIDLDAERGRISLSTKQLEPEPGDMLKDPQKVFDKAEEMAAKYRQMLlAQAE 301
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 74-329 5.67e-70

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: 223.77  E-value: 5.67e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589  74 EDLDSAVESTDIDTDIGSLIKGTVFMTTSNGAYVDIQSKSTAFLPLDEacLLDVNhiEEAGIRAGLVEEFMIIDENPGDE 153
Cdd:COG0539     3 ESFAELLEESLKELKEGDIVKGTVVSIDDDEVLVDIGYKSEGIIPLSE--FSDEP--GELEVKVGDEVEVYVEKVEDGEG 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 154 TLILSLQAIQQDLAWERCRQLQAEDVVVTGKVIGGNKGGVVALVEGLKGFVPFSQVSSK--STAEELLDKELPLKFVEVD 231
Cdd:COG0539    79 EIVLSKKKADREKAWEELEEAFENGEPVEGKVKGVVKGGLIVDIGGVRAFLPASQVDVRpvRDLDEYVGKTLEFKIIKLD 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 232 EEQGRLVLSNRKAMADSQAQ--------LGIGSVVLGTVESLKPYGAFIDIGGINGLLHVSQISHDRVADISTVLQPGDT 303
Cdd:COG0539   159 RKRNNVVVSRRAVLEEEREEkreellekLEEGDVVEGTVKNITDFGAFVDLGGVDGLLHISEISWGRVKHPSEVLKVGDE 238

                         250       260
                  ....*....|....*....|....*.
gi 1002248589 304 LKVMILSHDRERGRVSLSTKKLEPTP 329
Cdd:COG0539   239 VEVKVLKIDREKERISLSLKQLQPDP 264
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
78-329 6.44e-54

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 189.00  E-value: 6.44e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589  78 SAVESTDIDTDIGSLIKGTVFMTTSNGAYVDIQSKSTAFLPLDEACLLDVNHIEEAgIRAGLVEEFMIIDENPGDETLIL 157
Cdd:PRK00087  291 EYMNELEKQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKES-VKVGDEIEVKVLKLEDEDGYVVL 369

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 158 SLQAIQQDLAWERCRQLQAEDVVVTGKVIGGNKGGVVALVEGLKGFVPFSQVSsKSTAEEL---LDKELPLKFVEVDEEQ 234
Cdd:PRK00087  370 SKKEADREKAWKELEEAFENGEPVKGKVKEVVKGGLLVDYGGVRAFLPASHVE-LGYVEDLseyKGQELEVKIIEFNRKR 448

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 235 GRLVLSNRKAMADSQAQ---------LGIGSVVLGTVESLKPYGAFIDIGGINGLLHVSQISHDRVADISTVLQPGDTLK 305
Cdd:PRK00087  449 RKKVVLSRKAILEEEKEkkkeetwnsLEEGDVVEGEVKRLTDFGAFVDIGGVDGLLHVSEISWGRVEKPSDVLKVGDEIK 528

                         250       260
                  ....*....|....*....|....
gi 1002248589 306 VMILSHDRERGRVSLSTKKLEPTP 329
Cdd:PRK00087  529 VYILDIDKENKKLSLSLKKLLPDP 552
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 90-333 1.73e-52

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 179.69  E-value: 1.73e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589  90 GSLIKGTVFMTTSNGAYVDIQ-SKSTAFLPLDEaclLDVNHIEEAG--IRAGLVEEFMIIDENPGDETLILSLQAIQQDL 166
Cdd:PRK06676   18 GDVVTGEVLKVEDKQVFVNIEgYKVEGVIPISE---LSNDHIEDINdvVKVGDELEVYVLKVEDGEGNLLLSKRRLEAEK 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 167 AWERCRQLQAEDVVVTGKVIGGNKGGVVALVEGLKGFVPFSQVSSK--STAEELLDKELPLKFVEVDEEQGRLVLSNR-- 242
Cdd:PRK06676   95 AWDKLEEKFEEGEVVEVKVTEVVKGGLVVDVEGVRGFIPASLISTRfvEDFSDFKGKTLEVKIIELDPEKNRVILSRRav 174

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 243 ------KAMADSQAQLGIGSVVLGTVESLKPYGAFIDIGGINGLLHVSQISHDRVADISTVLQPGDTLKVMILSHDRERG 316
Cdd:PRK06676  175 veeeraAKKEELLSSLKEGDVVEGTVARLTDFGAFVDIGGVDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETE 254

                         250
                  ....*....|....*..
gi 1002248589 317 RVSLSTKKLEPTPGDMI 333
Cdd:PRK06676  255 RISLSLKDTLPGPWEGV 271
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 74-329 4.03e-52

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 182.67  E-value: 4.03e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589  74 EDLDSAVEST--DIDTDIGSLIKGTVFMTTSNGAYVDIQSKSTAFLPLDEacLLDVNhiEEAGIRAG-LVEEFMIIDENP 150
Cdd:PRK06299   13 ESFAELFEESlkESETREGSIVKGTVVAIDKDYVLVDVGLKSEGRIPLEE--FKNEQ--GELEVKVGdEVEVYVERIEDG 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 151 GDETlILSLQAIQQDLAWERCRQLQAEDVVVTGKVIGGNKGGVVALVEGLKGFVPFSQVSSKST--AEELLDKELPLKFV 228
Cdd:PRK06299   89 FGET-VLSREKAKRLEAWDKLEKAFENGEIVEGVINGKVKGGFTVDLNGVEAFLPGSQVDVRPVrdTDPLEGKELEFKVI 167

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 229 EVDEEQGRLVLSNRKAMADSQA--------QLGIGSVVLGTVESLKPYGAFIDIGGINGLLHVSQISHDRVADISTVLQP 300
Cdd:PRK06299  168 KLDKKRNNIVVSRRAVLEEERAeereelleNLEEGQVVEGVVKNITDYGAFVDLGGVDGLLHITDISWKRVNHPSEVVNV 247

                         250       260
                  ....*....|....*....|....*....
gi 1002248589 301 GDTLKVMILSHDRERGRVSLSTKKLEPTP 329
Cdd:PRK06299  248 GDEVKVKVLKFDKEKKRVSLGLKQLGEDP 276
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 90-335 3.85e-41

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: 152.20  E-value: 3.85e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589  90 GSLIKGTVFMTTSNGAYVDIQSKSTAFLPLDEacLLDVNHIEEAG--IRAGLVEefmiIDENPGDEtlILSLQAIQQDLA 167
Cdd:TIGR00717  19 GSIVKGTVVAINKDTVFVDVGLKSEGRIPKEE--FLDAPLEIQVGdeVEVYLDR----VEDRFGET--VLSREKAQRHEL 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 168 WERCRQLQAEDVVVTGKVIGGNKGGVVALVEGLKGFVPFSQVSSK--STAEELLDKELPLKFVEVDEEQGRLVLSnRKAM 245
Cdd:TIGR00717  91 WIKLEKAYEEGSIVEGKIVGKVKGGFIVDLNGVEAFLPGSQVDVKpiKDLDSLIGKTLKFKIIKLDQKRNNIVVS-RRAY 169

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 246 ADSQA---------QLGIGSVVLGTVESLKPYGAFIDIGGINGLLHVSQISHDRVADISTVLQPGDTLKVMILSHDRERG 316
Cdd:TIGR00717 170 LEEERsqareelleNLKEGDVVKGVVKNITDFGAFVDLGGVDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKG 249

                         250
                  ....*....|....*....
gi 1002248589 317 RVSLSTKKLEPTPGDMIRN 335
Cdd:TIGR00717 250 RISLSLKQLGEDPWEAIEK 268
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 255-323 2.48e-29

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: 108.53  E-value: 2.48e-29
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 255 GSVVLGTVESLKPYGAFIDIG-GINGLLHVSQISHDRVADISTVLQPGDTLKVMILSHDrERGRVSLSTK 323
Cdd:cd05692     1 GSVVEGTVTRLKPFGAFVELGgGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSID-ARGRISLSIK 69
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 72-323 6.58e-28

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 114.76  E-value: 6.58e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589  72 SPEDLDSAVESTDIDTDIGSLIKGTVFMTTSNGAYVDIQSKSTAFLPLDEACL---LDVNHIEEAGIRaglVEEFMIIDE 148
Cdd:PRK07899   18 SAEDFLAAIDKTIKYFNDGDIVEGTVVKVDRDEVLLDIGYKTEGVIPSRELSIkhdVDPNEVVEVGDE---VEALVLQKE 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 149 NPgDETLILSLQAIQQDLAWERCRQLQAEDVVVTGKVIGGNKGGVVaLVEGLKGFVPFSQVSSKSTA--EELLDKELPLK 226
Cdd:PRK07899   95 DK-EGRLILSKKRAQYERAWGTIEKIKEKDGVVTGTVIEVVKGGLI-LDIGLRGFLPASLVEMRRVRdlQPYIGQEIEAK 172

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 227 FVEVDEEQGRLVLSNRKAMADSQA--------QLGIGSVVLGTVESLKPYGAFIDIGGINGLLHVSQISHDRVADISTVL 298
Cdd:PRK07899  173 IIELDKNRNNVVLSRRAWLEQTQSevrseflnQLQKGQVRKGVVSSIVNFGAFVDLGGVDGLVHVSELSWKHIDHPSEVV 252

                         250       260
                  ....*....|....*....|....*
gi 1002248589 299 QPGDTLKVMILSHDRERGRVSLSTK 323
Cdd:PRK07899  253 EVGQEVTVEVLDVDMDRERVSLSLK 277
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 90-337 4.08e-26

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: 109.82  E-value: 4.08e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589  90 GSLIKGTVFMTTSNGAYVDIQSkSTAFLPLDEAcllDVNHIEEAGIRAGLVEEFMIIDENPGDETLILSLQAIqqdLAWE 169
Cdd:TIGR00717 101 GSIVEGKIVGKVKGGFIVDLNG-VEAFLPGSQV---DVKPIKDLDSLIGKTLKFKIIKLDQKRNNIVVSRRAY---LEEE 173

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 170 RCRQLQA------EDVVVTGKVIGGNKGGVVALVEGLKGFVPFSQVSSKSTA--EELLDK--ELPLKFVEVDEEQGRLVL 239
Cdd:TIGR00717 174 RSQAREEllenlkEGDVVKGVVKNITDFGAFVDLGGVDGLLHITDMSWKRVKhpSEYVKVgqEVKVKVIKFDKEKGRISL 253

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 240 SNRKAMADS----QAQLGIGSVVLGTVESLKPYGAFIDIG-GINGLLHVSQISHDR-VADISTVLQPGDTLKVMILSHDR 313
Cdd:TIGR00717 254 SLKQLGEDPweaiEKKFPVGDKITGRVTNLTDYGVFVEIEeGIEGLVHVSEMSWVKkNSHPSKVVKKGDEVEVMILDIDP 333

                         250       260
                  ....*....|....*....|....*.
gi 1002248589 314 ERGRVSLSTKKLEPTPGDMI--RNPK 337
Cdd:TIGR00717 334 ERRRLSLGLKQCKANPWEQFeeKHPV 359
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 254-321 2.47e-24

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: 95.00  E-value: 2.47e-24
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1002248589 254 IGSVVLGTVESLKPYGAFIDIGGINGLLHVSQISHDRVADISTVLQPGDTLKVMILSHDRERGRVSLS 321
Cdd:cd05688     1 EGDVVEGTVKSITDFGAFVDLGGVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 89-335 9.70e-24

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: 102.89  E-value: 9.70e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589  89 IGSLIKGTVFMTTSNGAYVDIQSKStAFLPLDEACLLDVNHIEEAgIRAGLVEEFMIIDENPGDETLILSLQAIQQDlAW 168
Cdd:TIGR00717 187 EGDVVKGVVKNITDFGAFVDLGGVD-GLLHITDMSWKRVKHPSEY-VKVGQEVKVKVIKFDKEKGRISLSLKQLGED-PW 263

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 169 ERCRQLQAEDVVVTGKVIG-GNKGGVVALVEGLKGFVPFSQVS---SKSTAEELLDK--ELPLKFVEVDEEQGRLVLSNR 242
Cdd:TIGR00717 264 EAIEKKFPVGDKITGRVTNlTDYGVFVEIEEGIEGLVHVSEMSwvkKNSHPSKVVKKgdEVEVMILDIDPERRRLSLGLK 343

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 243 KAMADSQAQLG----IGSVVLGTVESLKPYGAFIDIG-GINGLLHVSQISHDR-VADISTVLQPGDTLKVMILSHDRERG 316
Cdd:TIGR00717 344 QCKANPWEQFEekhpVGDRVTGKIKKITDFGAFVELEgGIDGLIHLSDISWDKdGREADHLYKKGDEIEAVVLAVDKEKK 423

                         250
                  ....*....|....*....
gi 1002248589 317 RVSLSTKKLEPTPGDMIRN 335
Cdd:TIGR00717 424 RISLGVKQLTENPWEKFAA 442
rpsA PRK13806
30S ribosomal protein S1; Provisional
 82-333 2.28e-22

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 98.64  E-value: 2.28e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589  82 STDIDTDI--GSLIKGTVFMTTSNGAYVDIQSKSTAFLplDEACLLDVNHieEAGIRAGLVEEFMIIDENPGDETLILSL 159
Cdd:PRK13806   25 EGERKTELrvGDKITGTVIAITEDSVFVDTGSKVDGVV--DRAELLDADG--ELTVAVGDEVELYVVSVNGQEIRLSKAL 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 160 QAIQQDLAWERCRQlqaEDVVVTGKVIGGNKGGVVALVEGLKGFVPFSQVSSKST--AEELLDKELPLKFVEVdEEQGRL 237
Cdd:PRK13806  101 SGQGGAAMLEEAYE---NGVPVEGKVTGTCKGGFNVEVLGRRAFCPVSQIDLRYVedPESYVGQTFQFLITRV-EENGRN 176

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 238 VLSNRKAMADSQ---------AQLGIGSVVLGTVESLKPYGAFIDIG-GINGLLHVSQISHDRVADISTVLQPGDTLKVM 307
Cdd:PRK13806  177 IVVSRRALLEREqkealeafmETVKEGDVVEGTVTRLAPFGAFVELApGVEGMVHISELSWSRVQKADEAVSVGDTVRVK 256

                         250       260       270
                  ....*....|....*....|....*....|
gi 1002248589 308 ILSHDRERG----RVSLSTKKLEPTPGDMI 333
Cdd:PRK13806  257 VLGIERAKKgkglRISLSIKQAGGDPWDTV 286
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
254-323 9.45e-22

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 88.04  E-value: 9.45e-22
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1002248589  254 IGSVVLGTVESLKPYGAFIDIG-GINGLLHVSQISHDRVADISTVLQPGDTLKVMILSHDRERGRVSLSTK 323
Cdd:smart00316   2 VGDVVEGTVTEITPGGAFVDLGnGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 254-334 3.93e-21

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


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 88.31  E-value: 3.93e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 254 IGSVVLGTVESLKPYGAFIDI-GGINGLLHVSQISHDRVADISTVLQPGDTLKVMILSHDrERGRVSLSTKKLEPTPGDM 332
Cdd:COG1098     5 VGDIVEGKVTGITPFGAFVELpEGTTGLVHISEIADGYVKDINDYLKVGDEVKVKVLSID-EDGKISLSIKQAEEKPKRP 83


                  ..
gi 1002248589 333 IR 334
Cdd:COG1098    84 PR 85
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 90-323 4.59e-20

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: 91.72  E-value: 4.59e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589  90 GSLIKGTVFMTTSNGAYVDIQSKSTAFLPLDEACLLDVNHIEEAGIRAGLVEEFMIIDENPGDETLILSLQAIQQDlAWE 169
Cdd:TIGR00717 273 GDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSWVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQCKAN-PWE 351

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 170 RCRQLQAEDVVVTGKVIG-GNKGGVVALVEGLKGFVPFSQVS---SKSTAEELLDK--ELPLKFVEVDEEQGRLVLSnRK 243
Cdd:TIGR00717 352 QFEEKHPVGDRVTGKIKKiTDFGAFVELEGGIDGLIHLSDISwdkDGREADHLYKKgdEIEAVVLAVDKEKKRISLG-VK 430

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 244 AMADS-----QAQLGIGSVVLGTVESLKPYGAFIDI-GGINGLLHVSQISHDRVADISTVLQPGDTLKVMILSHDRERGR 317
Cdd:TIGR00717 431 QLTENpwekfAAKYKVGSVVKGKVTEIKDFGAFVELpGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRK 510


                  ....*.
gi 1002248589 318 VSLSTK 323
Cdd:TIGR00717 511 VSLSVK 516
S1_RPS1_repeat_ec2_hs2 cd04465
S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 178-242 8.01e-20

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: 82.51  E-value: 8.01e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1002248589 178 DVVVTGKVIGGNKGGVVALVEGLKGFVPFSQVSSKST--AEELLDKELPLKFVEVDEEQGRLVLSNR 242
Cdd:cd04465     1 GEIVEGKVTEKVKGGLIVDIEGVRAFLPASQVDLRPVedLDEYVGKELKFKIIEIDRERNNIVLSRR 67
PRK08059 PRK08059
general stress protein 13; Validated
 250-329 1.17e-19

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 83.94  E-value: 1.17e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 250 AQLGIGSVVLGTVESLKPYGAFIDI-GGINGLLHVSQISHDRVADISTVLQPGDTLKVMILSHDRERGRVSLSTKKLEPT 328
Cdd:PRK08059    3 SQYEVGSVVTGKVTGIQPYGAFVALdEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRATEEA 82


                  .
gi 1002248589 329 P 329
Cdd:PRK08059   83 P 83
rpsA PRK13806
30S ribosomal protein S1; Provisional
 93-329 1.40e-18

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 87.47  E-value: 1.40e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589  93 IKGTVFMTTSNGAYVDIQSKsTAFLPLDEaclLDVNHIEEAGIRAGLVEEFMIIDENPGDETLILSLQAI---QQDLAWE 169
Cdd:PRK13806  119 VEGKVTGTCKGGFNVEVLGR-RAFCPVSQ---IDLRYVEDPESYVGQTFQFLITRVEENGRNIVVSRRALlerEQKEALE 194

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 170 RCRQLQAEDVVVTGKVIG-GNKGGVVALVEGLKGFVPFSQVS-SKS-TAEELLD--KELPLKFVEVDEEQG----RLVLS 240
Cdd:PRK13806  195 AFMETVKEGDVVEGTVTRlAPFGAFVELAPGVEGMVHISELSwSRVqKADEAVSvgDTVRVKVLGIERAKKgkglRISLS 274

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 241 NRKAMAD---SQA-QLGIGSVVLGTVESLKPYGAFIDIG-GINGLLHVSQISH-DRVADISTVLQPGDTLKVMILSHDRE 314
Cdd:PRK13806  275 IKQAGGDpwdTVGdRLKAGDKVTGKVVRLAPFGAFVEILpGIEGLVHVSEMSWtRRVNKPEDVVAPGDAVAVKIKDIDPA 354

                         250
                  ....*....|....*
gi 1002248589 315 RGRVSLSTKKLEPTP 329
Cdd:PRK13806  355 KRRISLSLRDAEGDP 369
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 255-321 7.03e-18

S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.


Pssm-ID: 240190 [Multi-domain]  Cd Length: 68  Bit Score: 77.27  E-value: 7.03e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1002248589 255 GSVVLGTVESLKPYGAFIDIG-GINGLLHVSQISHDRVADISTVLQPGDTLKVMILSHDRERGRVSLS 321
Cdd:cd05685     1 GMVLEGVVTNVTDFGAFVDIGvKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 255-321 2.11e-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: 76.04  E-value: 2.11e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1002248589 255 GSVVLGTVESLKPYGAFIDI-GGINGLLHVSQISHDRVADISTVLQPGDTLKVMILSHDrERGRVSLS 321
Cdd:cd04472     1 GKIYEGKVVKIKDFGAFVEIlPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVD-DRGRISLS 67
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 254-326 4.67e-17

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 83.18  E-value: 4.67e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1002248589 254 IGSVVLGTVESLKPYGAFIDI-GGINGLLHVSQISHDRVADISTVLQPGDTLKVMILSHDrERGRVSLSTKKLE 326
Cdd:PRK11824  621 VGEIYEGKVVRIVDFGAFVEIlPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEID-KRGRIRLSRKAVL 693
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 142-326 2.10e-15

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 77.90  E-value: 2.10e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 142 EFMIIDENPGDETLILSLQAIQQDlAWERCRQLQAEDVVVTGKVIGGNKGGV-VALVEGLKGFVPFSQVSSKSTAEELLD 220
Cdd:PRK06299  339 EVMVLEIDEEKRRISLGLKQCKEN-PWEEFAEKYPVGDVVEGKVKNITDFGAfVGLEGGIDGLVHLSDISWDKKGEEAVE 417

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 221 K-----ELPLKFVEVDEEQGRLVLSnRKAMADS-----QAQLGIGSVVLGTVESLKPYGAFIDIG-GINGLLHVSQISHD 289
Cdd:PRK06299  418 LykkgdEVEAVVLKVDVEKERISLG-IKQLEEDpfeefAKKHKKGSIVTGTVTEVKDKGAFVELEdGVEGLIRASELSRD 496

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1002248589 290 RVADISTVLQPGDTLKVMILSHDRERGRVSLSTKKLE 326
Cdd:PRK06299  497 RVEDATEVLKVGDEVEAKVINIDRKNRRISLSIKALD 533
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 255-323 4.25e-15

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: 69.67  E-value: 4.25e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1002248589 255 GSVVLGTVESLKPYGAFIDIGGIN--GLLHVSQISHDRVADISTVLQPGDTLKVMILSHDRERGRVSLSTK 323
Cdd:cd05708     3 GQKIDGTVRRVEDYGVFIDIDGTNvsGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLK 73
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 258-321 7.07e-15

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


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 68.95  E-value: 7.07e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1002248589 258 VLGTVESLKPYGAFIDIG-GINGLLHVSQISHDRVADISTVLQPGDTLKVMILSHDRERGRVSLS 321
Cdd:cd00164     1 VTGKVVSITKFGVFVELEdGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
PRK05807 PRK05807
RNA-binding protein S1;
252-328 3.36e-14

RNA-binding protein S1;


Pssm-ID: 235614 [Multi-domain]  Cd Length: 136  Bit Score: 69.00  E-value: 3.36e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1002248589 252 LGIGSVVLGTVESLKPYGAFIDIGGINGLLHVSQISHDRVADISTVLQPGDTLKVMILSHDrERGRVSLSTKKLEPT 328
Cdd:PRK05807    3 LKAGSILEGTVVNITNFGAFVEVEGKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISID-DNGKISLSIKQAMKQ 78
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 254-322 8.36e-14

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 66.16  E-value: 8.36e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 254 IGSVVLGTVESLKPYGAFIDIG-GINGLLHVSQISHDRVADISTVLQPGDTLKVMILSHDRERGRVSLST 322
Cdd:pfam00575   3 KGDVVEGEVTRVTKGGAFVDLGnGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 80-333 9.46e-14

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 73.21  E-value: 9.46e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589  80 VESTDIDTDiGSLIKGTVFMTTS--NGAYVDIQSKSTAFLPLDEAcllDVNHIEEAGIRAGLVEEFMI-----IDENPGD 152
Cdd:PRK12269  390 VKLRDAERD-GTPVEGRIVRLTEkkSGFEVDLGAGMMAFLPISQS---DCQKVDAPESLIGLTSKFYIerisqSKQHRGN 465

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 153 ETLILSLQAIQQdlawERCRQLQAE-------DVVVTGKVIGGNKGGVVALVEGLKGFVPFSQVSSKSTAE--ELLDK-- 221
Cdd:PRK12269  466 DNIVINRRRYLE----ERARQAREEffnsvhiEDSVSGVVKSFTSFGAFIDLGGFDGLLHVNDMSWGHVARprEFVKKgq 541

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 222 ELPLKFVEVDEEQGRLVLSNRKAMADS----QAQLGIGSVVLGTVESLKPYGAFIDIG-GINGLLHVSQISH-DRVADIS 295
Cdd:PRK12269  542 TIELKVIRLDQAEKRINLSLKHFQPDPwlefENKFGVNDVVKGRVTKIADFGAFIELAeGIEGLAHISEFSWvKKTSKPS 621

                         250       260       270
                  ....*....|....*....|....*....|....*...
gi 1002248589 296 TVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTPGDMI 333
Cdd:PRK12269  622 DMVKIGDEVECMILGYDIQAGRVSLGLKQVTANPWEEI 659
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
269-330 9.01e-13

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 70.05  E-value: 9.01e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1002248589 269 GAFIDIGgI--NGLLHVSQISHDRVADISTVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTPG 330
Cdd:COG2183   656 GAFVDIG-VhqDGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEVDLKRKRISLSMKLDDEAGA 718
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 30-329 9.90e-13

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 69.74  E-value: 9.90e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589  30 PSALVCGTYALTKEE------RERERMCQLFDEASERCRTApmEGVSFSPEDLDsavESTDIDT-DIGSLIKGTVFMTTS 102
Cdd:PRK12269  260 PDALYVDTSCLTIEEvceriaREAHRRALWGGERSVENQEG--KGTPLVPRQLQ---ERYSFEApEPGSVRMGTVVQVNA 334

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 103 NGAYVDIQSKSTAFLPLDEAclldvnhieEAGIRAGLVEEFMIIDENP-GDEtliLSLQAIQQDLAWERCRQLQAEDVVV 181
Cdd:PRK12269  335 GTVFVDIGGKSEGRVPVEEF---------EAPPKAGDGVRVYVERVTPyGPE---LSKTKADRLGLKVKLRDAERDGTPV 402

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 182 TGKVI---GGNKGGVVALVEGLKGFVPFSQ-----VSSKSTAEELLDKELPLKFVEVDEEQGR--LVLSNRKAMADSQAQ 251
Cdd:PRK12269  403 EGRIVrltEKKSGFEVDLGAGMMAFLPISQsdcqkVDAPESLIGLTSKFYIERISQSKQHRGNdnIVINRRRYLEERARQ 482

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 252 --------LGIGSVVLGTVESLKPYGAFIDIGGINGLLHVSQISHDRVADISTVLQPGDTLKVMILSHDRERGRVSLSTK 323
Cdd:PRK12269  483 areeffnsVHIEDSVSGVVKSFTSFGAFIDLGGFDGLLHVNDMSWGHVARPREFVKKGQTIELKVIRLDQAEKRINLSLK 562


                  ....*.
gi 1002248589 324 KLEPTP 329
Cdd:PRK12269  563 HFQPDP 568
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 255-323 6.58e-12

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: 60.72  E-value: 6.58e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1002248589 255 GSVVLGTVESLKPYGAFIDIGGIN----GLLHVSQISHD-RVADISTVLQPGDTLKVMILShdRERGRVSLSTK 323
Cdd:cd05684     1 GKIYKGKVTSIMDFGCFVQLEGLKgrkeGLVHISQLSFEgRVANPSDVVKRGQKVKVKVIS--IQNGKISLSMK 72
rpsA PRK13806
30S ribosomal protein S1; Provisional
 146-331 1.42e-11

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 65.90  E-value: 1.42e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 146 IDENPGDETLILSLQAIQ-QDLAWERCRQLQAEDVVVTGKVIG-GNKGGVVALVEGLKGFVPFSQVS-----SKSTAEEL 218
Cdd:PRK13806  260 IERAKKGKGLRISLSIKQaGGDPWDTVGDRLKAGDKVTGKVVRlAPFGAFVEILPGIEGLVHVSEMSwtrrvNKPEDVVA 339

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 219 LDKELPLKFVEVDEEQGRLVLSNRKAMADSQA----QLGIGSVVLGTVESLKPYGAFIDIG-GINGLLHVSQISHDRVAD 293
Cdd:PRK13806  340 PGDAVAVKIKDIDPAKRRISLSLRDAEGDPWAdvaeRFAPGTTVTGTVEKRAQFGLFVNLApGVTGLLPASVISRAGKPA 419

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1002248589 294 ISTVLQPGDTLKVMILSHDRERGRVSLSTKKLEPTPGD 331
Cdd:PRK13806  420 TYEKLKPGDSVTLVVEEIDTAKRKISLAPAGAAGSGAD 457
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 254-324 5.83e-11

S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to complete the initiation complex, which is competent to begin translation. The IF2a subunit is a major site of control of the translation initiation process, via phosphorylation of a specific serine residue. This alpha subunit is well conserved in eukaryotes and archaea but is not present in bacteria. IF2 is a cold-shock-inducible protein.


Pssm-ID: 239899 [Multi-domain]  Cd Length: 76  Bit Score: 57.98  E-value: 5.83e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1002248589 254 IGSVVLGTVESLKPYGAFIDI---GGINGLLHVSQISHDRVADISTVLQPGDTLKVMILSHDRERGRVSLSTKK 324
Cdd:cd04452     3 EGELVVVTVKSIADMGAYVSLleyGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKKR 76
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 255-323 3.28e-10

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: 55.69  E-value: 3.28e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 255 GSVVLGTVESLKPYGAFIDI-GGINGLLHVSQISHDRVADISTVLQPGDTLKVMILSHDRERGRVSLSTK 323
Cdd:cd05698     1 GLKTHGTIVKVKPNGCIVSFyNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
254-326 1.76e-09

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 55.09  E-value: 1.76e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1002248589 254 IGSVVLGTVESLKPYGAFIDI-GGINGLLHVSQISHDRVADISTVLQPGDTLKVMILSHDRERGRVSLSTKKLE 326
Cdd:PRK07252    3 IGDKLKGTITGIKPYGAFVALeNGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLRTLE 76
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 255-326 2.52e-09

S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240196 [Multi-domain]  Cd Length: 73  Bit Score: 53.43  E-value: 2.52e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1002248589 255 GSVVLGTVESLKPYGAFIDIG-GINGLLHVSQISHDRVADISTVLQPGDTLKVMILSHDRERGRVSLSTKKLE 326
Cdd:cd05691     1 GSIVTGKVTEVDAKGATVKLGdGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIKAKE 73
S1_RPS1_repeat_ec1_hs1 cd05687
S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 255-321 2.93e-09

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: 52.92  E-value: 2.93e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1002248589 255 GSVVLGTVESLKPYGAFIDIGG-INGLLHVSQISHDRVADISTVLQPGDTLKVMILSHDRERGRVSLS 321
Cdd:cd05687     1 GDIVKGTVVSVDDDEVLVDIGYkSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLS 68
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 255-320 5.68e-09

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: 52.11  E-value: 5.68e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1002248589 255 GSVVLGTVESLKPYGAFIDI-GGINGLLHVSQIS-HDRVADISTVLQPGDTLKVMILSHDRERGRVSL 320
Cdd:cd05690     1 GTVVSGKIKSITDFGIFVGLdGGIDGLVHISDISwTQRVRHPSEIYKKGQEVEAVVLNIDVERERISL 68
RPB7 COG1095
DNA-directed RNA polymerase, subunit E'/Rpb7 [Transcription]; DNA-directed RNA polymerase, ...
 257-334 7.87e-09

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


Pssm-ID: 440712 [Multi-domain]  Cd Length: 171  Bit Score: 54.41  E-value: 7.87e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 257 VVLGTVESLKPYGAFIDIGGINGLLHVSQISHDRVadistvlqpgdtlkvmilSHDRERGR-VSLSTKK-LEptPGDMIR 334
Cdd:COG1095    84 VVEGEVVEVVEFGAFVRIGPIDGLLHISQIMDDYV------------------DYDEKNGRlIGKESKRtLK--VGDVVR 143
PRK08563 PRK08563
DNA-directed RNA polymerase subunit E'; Provisional
 257-331 9.00e-09

DNA-directed RNA polymerase subunit E'; Provisional


Pssm-ID: 236289 [Multi-domain]  Cd Length: 187  Bit Score: 54.83  E-value: 9.00e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 257 VVLGTVESLKPYGAFIDIGGINGLLHVSQISHDRVA-----------DISTVLQPGDTLKVMIlshdrergrVSLSTKkl 325
Cdd:PRK08563   84 VVEGEVVEVVEFGAFVRIGPVDGLLHISQIMDDYISydpkngrligkESKRVLKVGDVVRARI---------VAVSLK-- 152


                  ....*.
gi 1002248589 326 EPTPGD 331
Cdd:PRK08563  153 ERRPRG 158
PRK08582 PRK08582
RNA-binding protein S1;
254-329 1.62e-08

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 53.11  E-value: 1.62e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1002248589 254 IGSVVLGTVESLKPYGAFIDI-GGINGLLHVSQISHDRVADISTVLQPGD--TLKVMILSHDrerGRVSLSTKKLEPTP 329
Cdd:PRK08582    5 VGSKLQGKVTGITNFGAFVELpEGKTGLVHISEVADNYVKDINDHLKVGDevEVKVLNVEDD---GKIGLSIKKAKDRP 80
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
213-326 2.74e-08

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 55.72  E-value: 2.74e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 213 STAEELLdKELPLKFVEVDEEQGRLVLSNRKAMADSQAQLGIGSVVLGTVESLKPYGAFIDIGG-INGLLHVSQISHDRV 291
Cdd:PRK00087  262 STPDWII-EEVIKKMSELDNMEEVEENEQLEYMNELEKQIRRGDIVKGTVVSVNENEVFVDVGYkSEGVIPLRELTLDEI 340

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1002248589 292 ADISTVLQPGDTLKVMILSHDRERGRVSLSTKKLE 326
Cdd:PRK00087  341 SSLKESVKVGDEIEVKVLKLEDEDGYVVLSKKEAD 375
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 180-240 5.05e-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: 49.59  E-value: 5.05e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1002248589 180 VVTGKVIGGNKGGV-VALVEGLKGFVPFSQVSSKSTAEE----LLDKELPLKFVEVDEEQGRLVLS 240
Cdd:pfam00575   6 VVEGEVTRVTKGGAfVDLGNGVEGFIPISELSDDHVEDPdeviKVGDEVKVKVLKVDKDRRRIILS 71
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 255-321 6.92e-08

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: 49.51  E-value: 6.92e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1002248589 255 GSVVLGTVESLKPYGAFIDI-GGINGLLHVSQISHDRVADISTVLQPGDTLKVMILSHDRERGRVSLS 321
Cdd:cd04461    15 GMVVHGYVRNITPYGVFVEFlGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLS 82
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 247-326 1.97e-07

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 52.57  E-value: 1.97e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 247 DSQAQLGIGSVVLGTVESLKPYGAFIDIGG--INGLLHVSQISHDRVADISTVLQPGDTLKVMILSHDRERGRVSLSTKK 324
Cdd:PRK06676   10 NSVKEVEVGDVVTGEVLKVEDKQVFVNIEGykVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNLLLSKRR 89


                  ..
gi 1002248589 325 LE 326
Cdd:PRK06676   90 LE 91
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 89-326 2.06e-07

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 53.18  E-value: 2.06e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589  89 IGSLIKGTVFMTTSNGAYVDIQSKSTAFLPLDEACLLDVNHIEEAGIRAGLVEEFMIIDENPGDETLILSLQAIQQDlAW 168
Cdd:PRK12269  578 VNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFSWVKKTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQVTAN-PW 656

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 169 ERCRQLQAEDVVVTGKVIG-GNKGGVVALVEGLKGFVPFSQVS----SKSTAEEL-LDKELPLKFVEVDEEQGRLVLSnR 242
Cdd:PRK12269  657 EEIEARYPVGARFTRRIVKvTNAGAFIEMEEGIDGFLHVDDLSwvkrTRPADHELeVGKEIECMVIECDPQARRIRLG-V 735

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 243 KAMADSQAQL-----GIGSVVLGTVESLKPYGAFIDI-GGINGLLHVSQISHDRVADISTVLQP---GDTLKVMILSHDR 313
Cdd:PRK12269  736 KQLSDNPWQVfanayGVGSTVEGEVSSVTDFGIFVRVpGGVEGLVRKQHLVENRDGDPGEALRKyavGDRVKAVIVDMNV 815

                         250
                  ....*....|...
gi 1002248589 314 ERGRVSLSTKKLE 326
Cdd:PRK12269  816 KDRKVAFSVRDYQ 828
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
180-242 3.24e-07

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 47.21  E-value: 3.24e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1002248589  180 VVTGKVIGGNKGGV-VALVEGLKGFVPFSQVSSKSTAEE----LLDKELPLKFVEVDEEQGRLVLSNR 242
Cdd:smart00316   5 VVEGTVTEITPGGAfVDLGNGVEGLIPISELSDKRVKDPeevlKVGDEVKVKVLSVDEEKGRIILSLK 72
S1_RPS1_repeat_ec4 cd05689
S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 255-320 3.30e-07

S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240194 [Multi-domain]  Cd Length: 72  Bit Score: 47.19  E-value: 3.30e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1002248589 255 GSVVLGTVESLKPYGAFIDIG-GINGLLHVSQIS-HDRVADISTVLQPGDTLKVMILSHDRERGRVSL 320
Cdd:cd05689     4 GTRLFGKVTNLTDYGCFVELEeGVEGLVHVSEMDwTNKNIHPSKVVSLGDEVEVMVLDIDEERRRISL 71
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 255-324 4.02e-07

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 50.98  E-value: 4.02e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1002248589 255 GSVVLGTVESLKPYGAFIDI---GGINGLLHVSQISHDRVADISTVLQPGDTLKVMILSHDRERGRVSLSTKK 324
Cdd:PRK03987    9 GELVVGTVKEVKDFGAFVTLdeyPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLKR 81
S1_RpoE cd04460
S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 257-327 4.62e-07

S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.


Pssm-ID: 239907 [Multi-domain]  Cd Length: 99  Bit Score: 47.67  E-value: 4.62e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1002248589 257 VVLGTVESLKPYGAFIDIGGINGLLHVSQISHDRVA-DISTVLQPGDTLKVMILSHDRERGR-VSLSTKKLEP 327
Cdd:cd04460     2 VVEGEVVEVVDFGAFVRIGPVDGLLHISQIMDDYISyDPKNKRLIGEETKRVLKVGDVVRARiVAVSLKERRP 74
S1_RPS1_repeat_ec1_hs1 cd05687
S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 90-158 5.97e-07

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


Pssm-ID: 240192 [Multi-domain]  Cd Length: 70  Bit Score: 46.37  E-value: 5.97e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1002248589  90 GSLIKGTVFMTTSNGAYVDIQSKSTAFLPLDEACLLDVNHIEEAgIRAGLVEEFMIIDENPGDETLILS 158
Cdd:cd05687     1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDE-VKVGDEVEVYVLRVEDEEGNVVLS 68
S1_RPS1_repeat_ec2_hs2 cd04465
S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 255-323 3.36e-06

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: 44.37  E-value: 3.36e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1002248589 255 GSVVLGTVESLKPYGAFIDIGGINGLLHVSQISHDRVADISTVLqpGDTLKVMILSHDRERGRVSLSTK 323
Cdd:cd04465     1 GEIVEGKVTEKVKGGLIVDIEGVRAFLPASQVDLRPVEDLDEYV--GKELKFKIIEIDRERNNIVLSRR 67
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
89-159 5.29e-06

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 43.75  E-value: 5.29e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1002248589   89 IGSLIKGTVFMTTSNGAYVDIQSKSTAFLPLDEACLLDVNHIEEAgIRAGLVEEFMIIDENPGDETLILSL 159
Cdd:smart00316   2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEV-LKVGDEVKVKVLSVDEEKGRIILSL 71
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 255-320 4.08e-05

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


Pssm-ID: 240202 [Multi-domain]  Cd Length: 69  Bit Score: 41.45  E-value: 4.08e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1002248589 255 GSVVLGTVESLKPYGAFIDI-GGINGLLHVSQISHDRVADISTVLQPGDTLKVMILSHDRERGRVSL 320
Cdd:cd05697     1 GQVVKGTIRKLRPSGIFVKLsDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVL 67
S1_RNase_E cd04453
S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential ...
 254-308 5.07e-05

S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain that is highly homologous to that of RNase E. RNase G not only shares sequence similarity with RNase E, but also functionally overlaps with RNase E. In Escherichia coli, RNase G is involved in the maturation of the 5' end of the 16S rRNA. RNase G plays a secondary role in mRNA decay.


Pssm-ID: 239900 [Multi-domain]  Cd Length: 88  Bit Score: 41.43  E-value: 5.07e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1002248589 254 IGSVVLGTVESLKP--YGAFIDIG-GINGLLHVSQISH---DRVADISTVLQPGDTLKVMI 308
Cdd:cd04453     7 VGNIYLGRVKKIVPglQAAFVDIGlGKNGFLHLSDILPayfKKHKKIAKLLKEGQEILVQV 67
PLN00207 PLN00207
polyribonucleotide nucleotidyltransferase; Provisional
 262-329 1.17e-04

polyribonucleotide nucleotidyltransferase; Provisional


Pssm-ID: 215104 [Multi-domain]  Cd Length: 891  Bit Score: 44.50  E-value: 1.17e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1002248589 262 VESLKPYGAFIDIG-GINGLLHVSQISHDRVADISTVLQPGDTLKVMILSHDrERGRVSLSTKKLEPTP 329
Cdd:PLN00207  762 IKSIAPYGAFVEIApGREGLCHISELSSNWLAKPEDAFKVGDRIDVKLIEVN-DKGQLRLSRRALLPEA 829
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 181-240 1.60e-04

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: 39.67  E-value: 1.60e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1002248589 181 VTGKVIGGNKGGV-VALVEGLKGFVPFSQVSSKST--AEELLD--KELPLKFVEVDEEQGRLVLS 240
Cdd:cd00164     1 VTGKVVSITKFGVfVELEDGVEGLVHISELSDKFVkdPSEVFKvgDEVEVKVLEVDPEKGRISLS 65
S1_Rrp4 cd05789
S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide ...
 254-323 7.89e-04

S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".


Pssm-ID: 240215 [Multi-domain]  Cd Length: 86  Bit Score: 38.30  E-value: 7.89e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1002248589 254 IGSVVLGTVESLKPYGAFIDIGG-INGLLHVSQISHDRVA----DISTVLQPGD--TLKVMILSHDrerGRVSLSTK 323
Cdd:cd05789     6 VGDVVIGRVTEVGFKRWKVDINSpYDAVLPLSEVNLPRTDedelNMRSYLDEGDliVAEVQSVDSD---GSVSLHTR 79
COG1107 COG1107
Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [Replication, ...
 246-328 1.13e-03

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: 40.98  E-value: 1.13e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002248589 246 ADSQAQLGIGSVVLGTVESLKPYGAFIDIG-GINGLLHVSQISHDrvadistvLQPGDTLKVMILSHdRERGRVSLSTKK 324
Cdd:COG1107    31 GCTPDDLEPGRYYRGTVDGVADFGVFVDLNdHVTGLLHRSELDQD--------WEVGDEVFVQVKEV-RDNGNVDLGWVS 101


                  ....
gi 1002248589 325 LEPT 328
Cdd:COG1107   102 IDSY 105
S1_Rrp5_repeat_hs11_sc8 cd05702
S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 255-309 3.04e-03

S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240207 [Multi-domain]  Cd Length: 70  Bit Score: 36.03  E-value: 3.04e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1002248589 255 GSVVLGTVESLKPYGAFIDIG-GINGLLHVSQIShDRVADIS---TVLQPGDTLKVMIL 309
Cdd:cd05702     1 GDLVKAKVKSVKPTQLNVQLAdNVHGRIHVSEVF-DEWPDGKnplSKFKIGQKIKARVI 58
 
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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