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Conserved domains on  [gi|334183835|ref|NP_177317|]
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Nucleic acid-binding proteins superfamily [Arabidopsis thaliana]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RpsA super family cl33936
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 154-437 9.91e-35

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


The actual alignment was detected with superfamily member COG0539:

Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 133.25  E-value: 9.91e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183835 154 DPKPGDFVVGVVVSGNENKLDVNIGadmlgtmltkeilplydkeldyllcdLKYDaeeflvngkmGIVkdddegvEIAEF 233
Cdd:COG0539   15 ELKEGDIVKGTVVSIDDDEVLVDIG--------------------------YKSE----------GII-------PLSEF 51

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183835 234 A-RQGRPVVEIGTVVFAEVLGRTL-SGRPLLSSRRYFRRIAWHRVRQIKQLNEPIEVKITEWNTGGLLTRIEGLRAFIP- 310
Cdd:COG0539   52 SdEPGELEVKVGDEVEVYVEKVEDgEGEIVLSKKKADREKAWEELEEAFENGEPVEGKVKGVVKGGLIVDIGGVRAFLPa 131

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183835 311 KQELVKKVNTFTELkenVGRRFLVQITRLNEDKNDLILSEKV--------AWEKLY--LREGTLLEGTVVKILPYGAQVK 380
Cdd:COG0539  132 SQVDVRPVRDLDEY---VGKTLEFKIIKLDRKRNNVVVSRRAvleeereeKREELLekLEEGDVVEGTVKNITDFGAFVD 208

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 334183835 381 LG--DssrsGLLHISNITRRRIGSVSDVLQVDESVKVlVVKSLFPDK--ISLSIADLESEP 437
Cdd:COG0539  209 LGgvD----GLLHISEISWGRVKHPSEVLKVGDEVEV-KVLKIDREKerISLSLKQLQPDP 264
 
Name Accession Description Interval E-value
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 154-437 9.91e-35

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: 133.25  E-value: 9.91e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183835 154 DPKPGDFVVGVVVSGNENKLDVNIGadmlgtmltkeilplydkeldyllcdLKYDaeeflvngkmGIVkdddegvEIAEF 233
Cdd:COG0539   15 ELKEGDIVKGTVVSIDDDEVLVDIG--------------------------YKSE----------GII-------PLSEF 51

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183835 234 A-RQGRPVVEIGTVVFAEVLGRTL-SGRPLLSSRRYFRRIAWHRVRQIKQLNEPIEVKITEWNTGGLLTRIEGLRAFIP- 310
Cdd:COG0539   52 SdEPGELEVKVGDEVEVYVEKVEDgEGEIVLSKKKADREKAWEELEEAFENGEPVEGKVKGVVKGGLIVDIGGVRAFLPa 131

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183835 311 KQELVKKVNTFTELkenVGRRFLVQITRLNEDKNDLILSEKV--------AWEKLY--LREGTLLEGTVVKILPYGAQVK 380
Cdd:COG0539  132 SQVDVRPVRDLDEY---VGKTLEFKIIKLDRKRNNVVVSRRAvleeereeKREELLekLEEGDVVEGTVKNITDFGAFVD 208

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 334183835 381 LG--DssrsGLLHISNITRRRIGSVSDVLQVDESVKVlVVKSLFPDK--ISLSIADLESEP 437
Cdd:COG0539  209 LGgvD----GLLHISEISWGRVKHPSEVLKVGDEVEV-KVLKIDREKerISLSLKQLQPDP 264
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 258-462 2.29e-34

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 131.46  E-value: 2.29e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183835 258 GRPLLSSRR--YFRriAWHRVRQIKQLNEPIEVKITEWNTGGLLTRIEGLRAFIPKQELVKKvntftELKEN-VGRRFLV 334
Cdd:PRK07400  94 GQLTLSIRRieYMR--AWERVRQLQKEDATVRSEVFATNRGGALVRIEGLRGFIPGSHISTR-----KPKEElVGEELPL 166

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183835 335 QITRLNEDKNDLILSEKVAW-EKLY--LREGTLLEGTVVKILPYGAQVKLGdsSRSGLLHISNITRRRIGSVSDVLQVDE 411
Cdd:PRK07400 167 KFLEVDEERNRLVLSHRRALvERKMnrLEVGEVVVGTVRGIKPYGAFIDIG--GVSGLLHISEISHEHIETPHSVFNVND 244

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 334183835 412 SVKVLVVkSLFPDK--ISLSIADLESEPGLFISDREKVFTEAEEMAKKYREKM 462
Cdd:PRK07400 245 EMKVMII-DLDAERgrISLSTKQLEPEPGDMLKDPQKVFDKAEEMAAKYRQML 296
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 258-447 4.24e-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: 84.02  E-value: 4.24e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183835  258 GRPLLSSRRYFRRIAWHRVRQIKQLNEPIEVKITEWNTGGLLTRIEGLRAFIP-KQELVKKVNtftELKENVGRRFLVQI 336
Cdd:TIGR00717  76 GETVLSREKAQRHELWIKLEKAYEEGSIVEGKIVGKVKGGFIVDLNGVEAFLPgSQVDVKPIK---DLDSLIGKTLKFKI 152

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183835  337 TRLNEDKNDLILSEKVAWE----------KLYLREGTLLEGTVVKILPYGAQVKLGdsSRSGLLHISNITRRRIGSVSDV 406
Cdd:TIGR00717 153 IKLDQKRNNIVVSRRAYLEeersqareelLENLKEGDVVKGVVKNITDFGAFVDLG--GVDGLLHITDMSWKRVKHPSEY 230

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 334183835  407 LQVDESVKVLVVKSlfpDK----ISLSIADLESEPGLFISDREKV 447
Cdd:TIGR00717 231 VKVGQEVKVKVIKF---DKekgrISLSLKQLGEDPWEAIEKKFPV 272
S1_RPS1_repeat_ec2_hs2 cd04465
S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 283-351 2.27e-15

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: 70.57  E-value: 2.27e-15
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 334183835 283 NEPIEVKITEWNTGGLLTRIEGLRAFIPKQELVKKVNtfTELKENVGRRFLVQITRLNEDKNDLILSEK 351
Cdd:cd04465    1 GEIVEGKVTEKVKGGLIVDIEGVRAFLPASQVDLRPV--EDLDEYVGKELKFKIIEIDRERNNIVLSRR 67
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
360-430 8.68e-10

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 54.92  E-value: 8.68e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 334183835   360 REGTLLEGTVVKILPYGAQVKLGDSSRsGLLHISNITRRRIGSVSDVLQVDESVKVLVVK-SLFPDKISLSI 430
Cdd:smart00316   1 EVGDVVEGTVTEITPGGAFVDLGNGVE-GLIPISELSDKRVKDPEEVLKVGDEVKVKVLSvDEEKGRIILSL 71
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 359-419 7.89e-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: 46.51  E-value: 7.89e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 334183835  359 LREGTLLEGTVVKILPYGAQVKLGdSSRSGLLHISNITRRRIGSVSDVLQVDESVKVLVVK 419
Cdd:pfam00575   1 PEKGDVVEGEVTRVTKGGAFVDLG-NGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLK 60
 
Name Accession Description Interval E-value
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 154-437 9.91e-35

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: 133.25  E-value: 9.91e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183835 154 DPKPGDFVVGVVVSGNENKLDVNIGadmlgtmltkeilplydkeldyllcdLKYDaeeflvngkmGIVkdddegvEIAEF 233
Cdd:COG0539   15 ELKEGDIVKGTVVSIDDDEVLVDIG--------------------------YKSE----------GII-------PLSEF 51

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183835 234 A-RQGRPVVEIGTVVFAEVLGRTL-SGRPLLSSRRYFRRIAWHRVRQIKQLNEPIEVKITEWNTGGLLTRIEGLRAFIP- 310
Cdd:COG0539   52 SdEPGELEVKVGDEVEVYVEKVEDgEGEIVLSKKKADREKAWEELEEAFENGEPVEGKVKGVVKGGLIVDIGGVRAFLPa 131

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183835 311 KQELVKKVNTFTELkenVGRRFLVQITRLNEDKNDLILSEKV--------AWEKLY--LREGTLLEGTVVKILPYGAQVK 380
Cdd:COG0539  132 SQVDVRPVRDLDEY---VGKTLEFKIIKLDRKRNNVVVSRRAvleeereeKREELLekLEEGDVVEGTVKNITDFGAFVD 208

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 334183835 381 LG--DssrsGLLHISNITRRRIGSVSDVLQVDESVKVlVVKSLFPDK--ISLSIADLESEP 437
Cdd:COG0539  209 LGgvD----GLLHISEISWGRVKHPSEVLKVGDEVEV-KVLKIDREKerISLSLKQLQPDP 264
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 258-462 2.29e-34

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 131.46  E-value: 2.29e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183835 258 GRPLLSSRR--YFRriAWHRVRQIKQLNEPIEVKITEWNTGGLLTRIEGLRAFIPKQELVKKvntftELKEN-VGRRFLV 334
Cdd:PRK07400  94 GQLTLSIRRieYMR--AWERVRQLQKEDATVRSEVFATNRGGALVRIEGLRGFIPGSHISTR-----KPKEElVGEELPL 166

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183835 335 QITRLNEDKNDLILSEKVAW-EKLY--LREGTLLEGTVVKILPYGAQVKLGdsSRSGLLHISNITRRRIGSVSDVLQVDE 411
Cdd:PRK07400 167 KFLEVDEERNRLVLSHRRALvERKMnrLEVGEVVVGTVRGIKPYGAFIDIG--GVSGLLHISEISHEHIETPHSVFNVND 244

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 334183835 412 SVKVLVVkSLFPDK--ISLSIADLESEPGLFISDREKVFTEAEEMAKKYREKM 462
Cdd:PRK07400 245 EMKVMII-DLDAERgrISLSTKQLEPEPGDMLKDPQKVFDKAEEMAAKYRQML 296
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
143-437 1.51e-26

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 113.50  E-value: 1.51e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183835 143 DETDRVSVEYYDPKPGDFVVGVVVSGNENKLDVNIGADMLGtmltkeILPLydKELDyllCDLKYDAEEflvngkmgivk 222
Cdd:PRK00087 288 EQLEYMNELEKQIRRGDIVKGTVVSVNENEVFVDVGYKSEG------VIPL--RELT---LDEISSLKE----------- 345

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183835 223 dddegveiaefarqgrpVVEIGTVVFAEVLGRTLS-GRPLLSSRRYFRRIAWHRVRQIKQLNEPIEVKITEWNTGGLLTR 301
Cdd:PRK00087 346 -----------------SVKVGDEIEVKVLKLEDEdGYVVLSKKEADREKAWKELEEAFENGEPVKGKVKEVVKGGLLVD 408

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183835 302 IEGLRAFIPKQELVKKvntFTE-LKENVGRRFLVQITRLNEDKN-DLILSEKVAWEKLY----------LREGTLLEGTV 369
Cdd:PRK00087 409 YGGVRAFLPASHVELG---YVEdLSEYKGQELEVKIIEFNRKRRkKVVLSRKAILEEEKekkkeetwnsLEEGDVVEGEV 485

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 334183835 370 VKILPYGAQVKLG--DssrsGLLHISNITRRRIGSVSDVLQVDESVKVlVVKSLFPD--KISLSIADLESEP 437
Cdd:PRK00087 486 KRLTDFGAFVDIGgvD----GLLHVSEISWGRVEKPSDVLKVGDEIKV-YILDIDKEnkKLSLSLKKLLPDP 552
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 205-437 3.55e-26

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 109.96  E-value: 3.55e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183835 205 LKYDAEEFLVNGKMGIVkdddEGV-EIAEFARQ----GRPVVEIGTVVFAEVLGRTLS-GRPLLSSRRYFRRIAWHRVRQ 278
Cdd:PRK06676  26 LKVEDKQVFVNIEGYKV----EGViPISELSNDhiedINDVVKVGDELEVYVLKVEDGeGNLLLSKRRLEAEKAWDKLEE 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183835 279 IKQLNEPIEVKITEWNTGGLLTRIEGLRAFIPKQEL-VKKVNTFTELKenvGRRFLVQITRLNEDKNDLILSEKV----- 352
Cdd:PRK06676 102 KFEEGEVVEVKVTEVVKGGLVVDVEGVRGFIPASLIsTRFVEDFSDFK---GKTLEVKIIELDPEKNRVILSRRAvveee 178

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183835 353 -------AWEKlyLREGTLLEGTVVKILPYGAQVKLGdsSRSGLLHISNITRRRIGSVSDVLQVDESVKVlVVKSLFPD- 424
Cdd:PRK06676 179 raakkeeLLSS--LKEGDVVEGTVARLTDFGAFVDIG--GVDGLVHISELSHERVEKPSEVVSVGQEVEV-KVLSIDWEt 253

                        250
                 ....*....|....
gi 334183835 425 -KISLSIADLESEP 437
Cdd:PRK06676 254 eRISLSLKDTLPGP 267
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 149-447 4.79e-24

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 105.25  E-value: 4.79e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183835 149 SVEYYDPKPGDFVVGVVVSGNENKLDVNIGADMLGtmltkeILPLydkeldyllcdlkydaEEFLVNGKMGIVKDDDEgV 228
Cdd:PRK06299  22 SLKESETREGSIVKGTVVAIDKDYVLVDVGLKSEG------RIPL----------------EEFKNEQGELEVKVGDE-V 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183835 229 EIAEFARQGRpvveigtvvfaevlgrtlSGRPLLSSRRYFRRIAWHRVRQIKQLNEPIEVKITEWNTGGLLTRIEGLRAF 308
Cdd:PRK06299  79 EVYVERIEDG------------------FGETVLSREKAKRLEAWDKLEKAFENGEIVEGVINGKVKGGFTVDLNGVEAF 140

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183835 309 IPK-QELVKKVNTFTELkenVGRRFLVQITRLNEDKNDLILSEKVAWEKLY----------LREGTLLEGTVVKILPYGA 377
Cdd:PRK06299 141 LPGsQVDVRPVRDTDPL---EGKELEFKVIKLDKKRNNIVVSRRAVLEEERaeereellenLEEGQVVEGVVKNITDYGA 217

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 334183835 378 QVKLG--DssrsGLLHISNITRRRIGSVSDVLQVDESVKVLVVKslFPD---KISLSIADLESEPGLFISDREKV 447
Cdd:PRK06299 218 FVDLGgvD----GLLHITDISWKRVNHPSEVVNVGDEVKVKVLK--FDKekkRVSLGLKQLGEDPWEAIEKKYPV 286
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 258-447 4.24e-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: 84.02  E-value: 4.24e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183835  258 GRPLLSSRRYFRRIAWHRVRQIKQLNEPIEVKITEWNTGGLLTRIEGLRAFIP-KQELVKKVNtftELKENVGRRFLVQI 336
Cdd:TIGR00717  76 GETVLSREKAQRHELWIKLEKAYEEGSIVEGKIVGKVKGGFIVDLNGVEAFLPgSQVDVKPIK---DLDSLIGKTLKFKI 152

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183835  337 TRLNEDKNDLILSEKVAWE----------KLYLREGTLLEGTVVKILPYGAQVKLGdsSRSGLLHISNITRRRIGSVSDV 406
Cdd:TIGR00717 153 IKLDQKRNNIVVSRRAYLEeersqareelLENLKEGDVVKGVVKNITDFGAFVDLG--GVDGLLHITDMSWKRVKHPSEY 230

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 334183835  407 LQVDESVKVLVVKSlfpDK----ISLSIADLESEPGLFISDREKV 447
Cdd:TIGR00717 231 VKVGQEVKVKVIKF---DKekgrISLSLKQLGEDPWEAIEKKFPV 272
S1_RPS1_repeat_ec2_hs2 cd04465
S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 283-351 2.27e-15

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: 70.57  E-value: 2.27e-15
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 334183835 283 NEPIEVKITEWNTGGLLTRIEGLRAFIPKQELVKKVNtfTELKENVGRRFLVQITRLNEDKNDLILSEK 351
Cdd:cd04465    1 GEIVEGKVTEKVKGGLIVDIEGVRAFLPASQVDLRPV--EDLDEYVGKELKFKIIEIDRERNNIVLSRR 67
rpsA PRK13806
30S ribosomal protein S1; Provisional
 285-447 1.30e-14

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 75.92  E-value: 1.30e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183835 285 PIEVKITEWNTGGLLTRIEGLRAFIPkqelVKKVNT-FTELKEN-VGRRFLVQITRLNEDKNDLILSEKV--------AW 354
Cdd:PRK13806 118 PVEGKVTGTCKGGFNVEVLGRRAFCP----VSQIDLrYVEDPESyVGQTFQFLITRVEENGRNIVVSRRAllereqkeAL 193

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183835 355 EKLY--LREGTLLEGTVVKILPYGAQVKLgDSSRSGLLHISNITRRRIGSVSDVLQVDESVKVLVV-----KSLFPDKIS 427
Cdd:PRK13806 194 EAFMetVKEGDVVEGTVTRLAPFGAFVEL-APGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLgieraKKGKGLRIS 272

                        170       180
                 ....*....|....*....|
gi 334183835 428 LSIADLESEPGLFISDREKV 447
Cdd:PRK13806 273 LSIKQAGGDPWDTVGDRLKA 292
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 362-430 2.30e-14

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: 67.70  E-value: 2.30e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 334183835 362 GTLLEGTVVKILPYGAQVKLGDSSrSGLLHISNITRRRIGSVSDVLQVDESVKVLVVKSLFPDKISLSI 430
Cdd:cd05692    1 GSVVEGTVTRLKPFGAFVELGGGI-SGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARGRISLSI 68
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 359-437 5.01e-14

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


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 68.67  E-value: 5.01e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183835 359 LREGTLLEGTVVKILPYGAQVKLGDSsRSGLLHISNITRRRIGSVSDVLQVDESVKVLVVkSLFPD-KISLSIADLESEP 437
Cdd:COG1098    3 IEVGDIVEGKVTGITPFGAFVELPEG-TTGLVHISEIADGYVKDINDYLKVGDEVKVKVL-SIDEDgKISLSIKQAEEKP 80
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 240-437 5.35e-13

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 70.84  E-value: 5.35e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183835 240 VVEIGTVVFAEVLGRTLS-GRPLLSSRR--YFRriAWHRVRQIKQLNEPIEVKITEWNTGGLLTRIeGLRAFIPKQeLV- 315
Cdd:PRK07899  79 VVEVGDEVEALVLQKEDKeGRLILSKKRaqYER--AWGTIEKIKEKDGVVTGTVIEVVKGGLILDI-GLRGFLPAS-LVe 154

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183835 316 -KKVNtftELKENVGRRFLVQITRLNEDKNDLILSEKVAWEKLY----------LREGTLLEGTVVKILPYGAQVKLGds 384
Cdd:PRK07899 155 mRRVR---DLQPYIGQEIEAKIIELDKNRNNVVLSRRAWLEQTQsevrseflnqLQKGQVRKGVVSSIVNFGAFVDLG-- 229

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 334183835 385 SRSGLLHISNITRRRIGSVSDVLQVDESVKVLVVK-SLFPDKISLSIADLESEP 437
Cdd:PRK07899 230 GVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDvDMDRERVSLSLKATQEDP 283
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 361-434 1.59e-12

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 69.69  E-value: 1.59e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 334183835 361 EGTLLEGTVVKILPYGAQVKLGDSsRSGLLHISNITRRRIGSVSDVLQVDESVKVLVVKslFPD--KISLSIADLE 434
Cdd:PRK11824 621 VGEIYEGKVVRIVDFGAFVEILPG-KDGLVHISEIADERVEKVEDVLKEGDEVKVKVLE--IDKrgRIRLSRKAVL 693
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 362-430 1.50e-11

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: 59.86  E-value: 1.50e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 334183835 362 GTLLEGTVVKILPYGAQVKLGdSSRSGLLHISNITRRRIGSVSDVLQVDESVKVLVVKSLFPDKISLSI 430
Cdd:cd04472    1 GKIYEGKVVKIKDFGAFVEIL-PGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDDRGRISLSR 68
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 362-432 1.63e-11

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: 59.95  E-value: 1.63e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 334183835 362 GTLLEGTVVKILPYGA--QVKLGDSSRSGLLHISNIT-RRRIGSVSDVLQVDESVKVLVVkSLFPDKISLSIAD 432
Cdd:cd05684    1 GKIYKGKVTSIMDFGCfvQLEGLKGRKEGLVHISQLSfEGRVANPSDVVKRGQKVKVKVI-SIQNGKISLSMKD 73
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
360-430 8.68e-10

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 54.92  E-value: 8.68e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 334183835   360 REGTLLEGTVVKILPYGAQVKLGDSSRsGLLHISNITRRRIGSVSDVLQVDESVKVLVVK-SLFPDKISLSI 430
Cdd:smart00316   1 EVGDVVEGTVTEITPGGAFVDLGNGVE-GLIPISELSDKRVKDPEEVLKVGDEVKVKVLSvDEEKGRIILSL 71
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
362-436 1.62e-09

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 55.48  E-value: 1.62e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 334183835 362 GTLLEGTVVKILPYGAQVKLgDSSRSGLLHISNITRRRIGSVSDVLQVDESVKVLVVK-SLFPDKISLSIADLESE 436
Cdd:PRK07252   4 GDKLKGTITGIKPYGAFVAL-ENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDfDEYTGKASLSLRTLEEE 78
PRK08059 PRK08059
general stress protein 13; Validated
 362-464 5.03e-09

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 54.28  E-value: 5.03e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183835 362 GTLLEGTVVKILPYGAQVKLgDSSRSGLLHISNITRRRIGSVSDVLQVDESVKvlvVKSLFPD----KISLSIADLESEP 437
Cdd:PRK08059   8 GSVVTGKVTGIQPYGAFVAL-DEETQGLVHISEITHGFVKDIHDFLSVGDEVK---VKVLSVDeekgKISLSIRATEEAP 83

                         90       100
                 ....*....|....*....|....*..
gi 334183835 438 glfisdrekvftEAEEMAKKYREKMPL 464
Cdd:PRK08059  84 ------------EAKRKKGKILIPNPS 98
rpsA PRK13806
30S ribosomal protein S1; Provisional
 359-484 5.91e-09

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 58.20  E-value: 5.91e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183835 359 LREGTLLEGTVVKILPYGAQVKLGdSSRSGLLHISNIT-RRRIGSVSDVLQVDESVKVlVVKSLFPDK--ISLSIADLES 435
Cdd:PRK13806 290 LKAGDKVTGKVVRLAPFGAFVEIL-PGIEGLVHVSEMSwTRRVNKPEDVVAPGDAVAV-KIKDIDPAKrrISLSLRDAEG 367

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 334183835 436 EPGLFISDREKVFTEAEEMAKKyREKMPLVatspISDRPPITSSFPQGK 484
Cdd:PRK13806 368 DPWADVAERFAPGTTVTGTVEK-RAQFGLF----VNLAPGVTGLLPASV 411
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 361-429 1.73e-08

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: 51.09  E-value: 1.73e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 334183835 361 EGTLLEGTVVKILPYGAQVKLGDSSrsGLLHISNITRRRIGSVSDVLQVDESVKVLVVKsLFPDK--ISLS 429
Cdd:cd05688    1 EGDVVEGTVKSITDFGAFVDLGGVD--GLLHISDMSWGRVKHPSEVVNVGDEVEVKVLK-IDKERkrISLG 68
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 362-429 3.96e-08

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: 49.92  E-value: 3.96e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 334183835 362 GTLLEGTVVKILPYGAQVKLGdSSRSGLLHISNITRRRIGSVSDVLQVDESVKVLVVKSLFP-DKISLS 429
Cdd:cd05685    1 GMVLEGVVTNVTDFGAFVDIG-VKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEErGRISLS 68
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 360-429 9.21e-08

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: 49.12  E-value: 9.21e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 334183835 360 REGTLLEGTVVKILPYGAQVKL---GDssRSGLLHISNITRRRIGSVSDVLQVDESVkVLVVKSLFPDK--ISLS 429
Cdd:cd04452    2 EEGELVVVTVKSIADMGAYVSLleyGN--IEGMILLSELSRRRIRSIRKLVKVGRKE-VVKVIRVDKEKgyIDLS 73
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 361-430 2.16e-07

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: 48.09  E-value: 2.16e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 334183835 361 EGTLLEGTVVKILPYGAQVKLGDSSRSGLLHISNITRRRIGSVSDVLQVDESVKVLVVKS-LFPDKISLSI 430
Cdd:cd05708    2 VGQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIdAEKKRISLGL 72
PRK05807 PRK05807
RNA-binding protein S1;
359-430 3.18e-07

RNA-binding protein S1;


Pssm-ID: 235614 [Multi-domain]  Cd Length: 136  Bit Score: 49.36  E-value: 3.18e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 334183835 359 LREGTLLEGTVVKILPYGAQVKLgdSSRSGLLHISNITRRRIGSVSDVLQVDESVKVLVVKSLFPDKISLSI 430
Cdd:PRK05807   3 LKAGSILEGTVVNITNFGAFVEV--EGKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDDNGKISLSI 72
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 359-419 7.89e-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: 46.51  E-value: 7.89e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 334183835  359 LREGTLLEGTVVKILPYGAQVKLGdSSRSGLLHISNITRRRIGSVSDVLQVDESVKVLVVK 419
Cdd:pfam00575   1 PEKGDVVEGEVTRVTKGGAFVDLG-NGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLK 60
S1_pNO40 cd05686
S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function ...
 363-430 1.09e-06

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: 46.32  E-value: 1.09e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 334183835 363 TLLEGTVVKILPYGAQVKLGDSSRSGLLHISNITRRRIGSVSDVLQVDESVKVLVVKSLFPDKISLSI 430
Cdd:cd05686    5 QIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKDKMKLSL 72
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 262-437 3.90e-06

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: 49.35  E-value: 3.90e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183835  262 LSSRRYF--RRIAwHRVRQIKQLNEPIEVK-----ITEWntgGLLTRIEGLRAFIPKQELV-KKVNTFTELKeNVGRRFL 333
Cdd:TIGR00717 164 VSRRAYLeeERSQ-AREELLENLKEGDVVKgvvknITDF---GAFVDLGGVDGLLHITDMSwKRVKHPSEYV-KVGQEVK 238

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183835  334 VQITRLNEDKNDLILSEKV----AWEKLY--LREGTLLEGTVVKILPYGAQVKLGDSSRsGLLHISNIT-RRRIGSVSDV 406
Cdd:TIGR00717 239 VKVIKFDKEKGRISLSLKQlgedPWEAIEkkFPVGDKITGRVTNLTDYGVFVEIEEGIE-GLVHVSEMSwVKKNSHPSKV 317

                         170       180       190
                  ....*....|....*....|....*....|...
gi 334183835  407 LQVDESVKVLVVKsLFPD--KISLSIADLESEP 437
Cdd:TIGR00717 318 VKKGDEVEVMILD-IDPErrRLSLGLKQCKANP 349
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 365-429 5.00e-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: 43.91  E-value: 5.00e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 334183835 365 LEGTVVKILPYGAQVKLGDSSRsGLLHISNITRRRIGSVSDVLQVDESVKVlVVKSLFPDKISLS 429
Cdd:cd00164    1 VTGKVVSITKFGVFVELEDGVE-GLVHISELSDKFVKDPSEVFKVGDEVEV-KVLEVDPEKGRIS 63
PRK08582 PRK08582
RNA-binding protein S1;
362-430 7.98e-06

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 45.41  E-value: 7.98e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 334183835 362 GTLLEGTVVKILPYGAQVKLGDSSrSGLLHISNITRRRIGSVSDVLQVDESVKVLVVKSLFPDKISLSI 430
Cdd:PRK08582   6 GSKLQGKVTGITNFGAFVELPEGK-TGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDDGKIGLSI 73
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 362-436 1.92e-05

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 47.08  E-value: 1.92e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 334183835 362 GTLLEGTVVKILPYGAQVKLGDSSrSGLLHISNITRRRIGSVSDVLQVDESVKVLVVK-SLFPDKISLSIADLESE 436
Cdd:PRK06299 461 GSIVTGTVTEVKDKGAFVELEDGV-EGLIRASELSRDRVEDATEVLKVGDEVEAKVINiDRKNRRISLSIKALDEA 535
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 283-447 2.77e-04

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: 43.57  E-value: 2.77e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183835  283 NEPIEVKITEWNTGGLLTRI-EGLRAFIPKQEL--VKKVNTFTELKeNVGRRFLVQITRLNEDKNDLILSEKVA----WE 355
Cdd:TIGR00717 273 GDKITGRVTNLTDYGVFVEIeEGIEGLVHVSEMswVKKNSHPSKVV-KKGDEVEVMILDIDPERRRLSLGLKQCkanpWE 351

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334183835  356 KLYLRE--GTLLEGTVVKILPYGAQVKLGDSSrSGLLHISNITRRRIGSVSDVL-QVDESVKVLVVKSLFPDK-ISLSIA 431
Cdd:TIGR00717 352 QFEEKHpvGDRVTGKIKKITDFGAFVELEGGI-DGLIHLSDISWDKDGREADHLyKKGDEIEAVVLAVDKEKKrISLGVK 430

                         170
                  ....*....|....*.
gi 334183835  432 DLESEPGLFISDREKV 447
Cdd:TIGR00717 431 QLTENPWEKFAAKYKV 446
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
359-418 3.69e-04

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 43.09  E-value: 3.69e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 334183835 359 LREGTLLEGTVVKILPYGAQVKLG---DssrsGLLHISNITRRRIGSVSDVLQVDESVKVLVV 418
Cdd:COG2183  639 LKPGMILEGTVTNVTDFGAFVDIGvhqD----GLVHISQLSDRFVKDPREVVKVGDIVKVKVL 697
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 361-418 2.30e-03

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 39.81  E-value: 2.30e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 334183835 361 EGTLLEGTVVKILPYGAQVKLGD-SSRSGLLHISNITRRRIGSVSDVLQVDESV--KVLVV 418
Cdd:PRK03987   8 EGELVVGTVKEVKDFGAFVTLDEyPGKEGFIHISEVASGWVKNIRDHVKEGQKVvcKVIRV 68
 
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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