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Conserved domains on  [gi|1808214898|gb|KAF2138712|]
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hypothetical protein K452DRAFT_255494 [Aplosporella prunicola CBS 121167]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1321-1395 4.61e-31

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: 117.43  E-value: 4.61e-31
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1808214898 1321 QVVTGKVRKVEDFGVFIVVDNSsNVSGLCHRSEIADQKVEDVRKLYEEGDAVKAIVLKIDQEKRRVNFGLKASYF 1395
Cdd:cd05708      4 QKIDGTVRRVEDYGVFIDIDGT-NVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKASYF 77
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 649-718 2.58e-30

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: 115.02  E-value: 2.58e-30
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  649 GKQAPGTIIKILRAGAIVQFYGDLKAFLPVSEMSEAYIQDPSEHFRIGQTVTVHTINVDAESDKMTVSCK 718
Cdd:cd05698      1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
S1_Rrp5_repeat_hs11_sc8 cd05702
S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 943-1015 2.08e-28

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: 109.22  E-value: 2.08e-28
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1808214898  943 GKLTTARITHVKDTQLNVHLADNLQGRVDVSEIFDSWENIKDrkhPLRQFKAKQNVPVRVIGIHDARNHRFLP 1015
Cdd:cd05702      1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKN---PLSKFKIGQKIKARVIGGHDAKTHRFLP 70
S1_Rrp5_repeat_hs12_sc9 cd05703
S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 1050-1122 4.67e-28

S1_Rrp5_repeat_hs12_sc9: 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 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


:

Pssm-ID: 240208 [Multi-domain]  Cd Length: 73  Bit Score: 108.43  E-value: 4.67e-28
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1808214898 1050 GSSHIAFVNNISDNCVWVNLSPNVRGRIDLMDLSDDVSLLNNVQGNFPVGSAIKVRVKNVDASNNRLDLTATS 1122
Cdd:cd05703      1 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSARG 73
S1_Rrp5_repeat_hs1_sc1 cd05693
S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 154-262 7.73e-28

S1_Rrp5_repeat_hs1_sc1: 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 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


:

Pssm-ID: 240198 [Multi-domain]  Cd Length: 100  Bit Score: 108.84  E-value: 7.73e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  154 LAPGSMVLGQITQITSKDIALSLPNNLVGFVPLTAVSDQYNERIEALLgedkeSENEEEESSEDDLELKNIFSLGQYLRA 233
Cdd:cd05693      1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELD-----EESEEEDDEEELPDLEDLFSVGQLVRC 75

                           90       100
                   ....*....|....*....|....*....
gi 1808214898  234 TVTSVGDDSKTsqksKKRIELSVNPKDAN 262
Cdd:cd05693     76 KVVSLDKSKSG----KKRIELSLEPELVN 100
rpsA super family cl36730
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 1043-1391 1.59e-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]


The actual alignment was detected with superfamily member TIGR00717:

Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 115.99  E-value: 1.59e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1043 SMDKLTIGSSHIAFVNNISDNCVWVNLSpNVRGRIDLMDLSddVSLLNNVQGNFPVGSAIKVRVKNVDASNNRLDLTATS 1122
Cdd:TIGR00717  181 LLENLKEGDVVKGVVKNITDFGAFVDLG-GVDGLLHITDMS--WKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLKQ 257

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1123 AAASKPTKIQD-LSAGQILPGRVTKVTERHIMVQLSETVSAPVTLTEFSDDYSQANPT-VHKKHDVVRVCILDVDAPNKK 1200
Cdd:TIGR00717  258 LGEDPWEAIEKkFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSWVKKNSHPSkVVKKGDEVEVMILDIDPERRR 337

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1201 LVLSL-----RPSKVLSSSLPVkdpqianirqlkvNDVVRGFVKNVSEKGLFVSLSSNVTAFVRISDLSdsFIKDWRSA- 1274
Cdd:TIGR00717  338 LSLGLkqckaNPWEQFEEKHPV-------------GDRVTGKIKKITDFGAFVELEGGIDGLIHLSDIS--WDKDGREAd 402

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1275 --FEVDQLVTGKIVAVDPllNHVQISLKASMLDKDyvPPTTFNDL-KPRQVVTGKVRKVEDFGVFIVVDNSsnVSGLCHR 1351
Cdd:TIGR00717  403 hlYKKGDEIEAVVLAVDK--EKKRISLGVKQLTEN--PWEKFAAKyKVGSVVKGKVTEIKDFGAFVELPGG--VEGLIRN 476

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|
gi 1808214898 1352 SEIADQKVEDVRKLYEEGDAVKAIVLKIDQEKRRVNFGLK 1391
Cdd:TIGR00717  477 SELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 516
rpsA super family cl36730
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 479-808 2.27e-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]


The actual alignment was detected with superfamily member TIGR00717:

Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 115.60  E-value: 2.27e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  479 GLFMDVGvkGVPGFAHISRLSDKKIDFLSEstgAYKLDSTHRARVVGYNPIDGLYIISLEPKVlEQPFLRV-DDVKVGQV 557
Cdd:TIGR00717  202 GAFVDLG--GVDGLLHITDMSWKRVKHPSE---YVKVGQEVKVKVIKFDKEKGRISLSLKQLG-EDPWEAIeKKFPVGDK 275

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  558 VKGKVEKvlITAKGqgaVVVNLAEGISGLASEAHIA-DVHLQHPEKKFKEGMAVTARVLSTDSEKRQIRLTLKKTLVNSe 636
Cdd:TIGR00717  276 ITGRVTN--LTDYG---VFVEIEEGIEGLVHVSEMSwVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQCKANP- 349

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  637 apvWSKYEDVV-LGKQAPGTIIKILRAGAIVQFYGDLKAFLPVSEMS-EAYIQDPSEHFRIGQTVTVHTINVDAESDKMT 714
Cdd:TIGR00717  350 ---WEQFEEKHpVGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISwDKDGREADHLYKKGDEIEAVVLAVDKEKKRIS 426

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  715 VSCK----DPTTRGAAMTeaydllKVGSVVKGSVSEKSEKTITVELEGsGIKGIIRIGQLtdgSEKKDQSSMKRIRVGQT 790
Cdd:TIGR00717  427 LGVKqlteNPWEKFAAKY------KVGSVVKGKVTEIKDFGAFVELPG-GVEGLIRNSEL---SENRDEDKTDEIKVGDE 496

                          330
                   ....*....|....*....
gi 1808214898  791 LEDLVV-LSKSDKKPLLTL 808
Cdd:TIGR00717  497 VEAKVVdIDKKNRKVSLSV 515
S1_like super family cl09927
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 819-901 3.21e-22

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.


The actual alignment was detected with superfamily member cd04461:

Pssm-ID: 471952 [Multi-domain]  Cd Length: 83  Bit Score: 92.27  E-value: 3.21e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  819 KAGSLVAKYEDLREGQPVNGFVRHIDGQRVFVEFAGGLVGLLLKSQMPEEMANTAEFGLRADQSISAKVLATDNQQRRFL 898
Cdd:cd04461      1 KEGTLPTNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFL 80


                   ...
gi 1808214898  899 VTM 901
Cdd:cd04461     81 LSL 83
PRK00087 super family cl35061
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
269-644 7.77e-17

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


The actual alignment was detected with superfamily member PRK00087:

Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 86.54  E-value: 7.77e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  269 DLVVNSMVQASVVSVEDHGLVMDLGladGAIKGFMGAKEV---GYTVDHSKVEKGAVFLCMITGLSSNGKIVKLSAdyQK 345
Cdd:PRK00087   299 QIRRGDIVKGTVVSVNENEVFVDVG---YKSEGVIPLRELtldEISSLKESVKVGDEIEVKVLKLEDEDGYVVLSK--KE 373

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  346 VGNVKKTNYLTEAptidvLLPGTAVEMLVTEVTITGL---AGQVMGLVDAT-ADIIHAgagesqKDItNRYKtGSKIRGR 421
Cdd:PRK00087   374 ADREKAWKELEEA-----FENGEPVKGKVKEVVKGGLlvdYGGVRAFLPAShVELGYV------EDL-SEYK-GQELEVK 440

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  422 IIcTFPEGERRKLgisvldhVLS----LTNRQSAESKAPLDILPISAFVEeAKVTKVEStLGLFMDVGvkGVPGFAHISR 497
Cdd:PRK00087   441 II-EFNRKRRKKV-------VLSrkaiLEEEKEKKKEETWNSLEEGDVVE-GEVKRLTD-FGAFVDIG--GVDGLLHVSE 508

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  498 LSDKKIDFLSEstgAYKLDSTHRARVVGYNPIDGLYIISLEpKVLEQPFLRVDD-VKVGQVVKGKVEKVLitakGQGAVV 576
Cdd:PRK00087   509 ISWGRVEKPSD---VLKVGDEIKVYILDIDKENKKLSLSLK-KLLPDPWENVEEkYPVGSIVLGKVVRIA----PFGAFV 580

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1808214898  577 vNLAEGISGLASEAHIADVHLQHPEKKFKEGMAVTARVLSTDSEKRQIRLTLKKTLVNSEAPVWSKYE 644
Cdd:PRK00087   581 -ELEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEVEEEPGDIEKVELE 647
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1509-1709 8.57e-08

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


:

Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 55.51  E-value: 8.57e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1509 RTGDLDIAgpqsVADFERLLLGQPNNSALWMQYMAFQIGLNEVQKAKDIAERALKtinirEEEEKMNIWTALLNLEIEQG 1588
Cdd:COG2956     88 KAGLLDRA----EELLEKLLELDPDDAEALRLLAEIYEQEGDWEKAIEVLERLLK-----LGPENAHAYCELAELYLEQG 158

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1589 NEEKVDEVFKRACQYcDPE--EMHNKLITIYTSTGRHEKADSLFQTMTKnksITPNPSFWMNYATFLMTTLNDPSRARQL 1666
Cdd:COG2956    159 DYDEAIEALEKALKL-DPDcaRALLLLAELYLEQGDYEEAIAALERALE---QDPDYLPALPRLAELYEKLGDPEEALEL 234

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|...
gi 1808214898 1667 LPRATQSVPahlhrQLTSKFAALEFQSPNGDAERGRTIFEGLL 1709
Cdd:COG2956    235 LRKALELDP-----SDDLLLALADLLERKEGLEAALALLERQL 272
 
Name Accession Description Interval E-value
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1321-1395 4.61e-31

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: 117.43  E-value: 4.61e-31
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1808214898 1321 QVVTGKVRKVEDFGVFIVVDNSsNVSGLCHRSEIADQKVEDVRKLYEEGDAVKAIVLKIDQEKRRVNFGLKASYF 1395
Cdd:cd05708      4 QKIDGTVRRVEDYGVFIDIDGT-NVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKASYF 77
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 649-718 2.58e-30

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: 115.02  E-value: 2.58e-30
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  649 GKQAPGTIIKILRAGAIVQFYGDLKAFLPVSEMSEAYIQDPSEHFRIGQTVTVHTINVDAESDKMTVSCK 718
Cdd:cd05698      1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
S1_Rrp5_repeat_hs11_sc8 cd05702
S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 943-1015 2.08e-28

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: 109.22  E-value: 2.08e-28
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1808214898  943 GKLTTARITHVKDTQLNVHLADNLQGRVDVSEIFDSWENIKDrkhPLRQFKAKQNVPVRVIGIHDARNHRFLP 1015
Cdd:cd05702      1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKN---PLSKFKIGQKIKARVIGGHDAKTHRFLP 70
S1_Rrp5_repeat_hs12_sc9 cd05703
S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 1050-1122 4.67e-28

S1_Rrp5_repeat_hs12_sc9: 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 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240208 [Multi-domain]  Cd Length: 73  Bit Score: 108.43  E-value: 4.67e-28
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1808214898 1050 GSSHIAFVNNISDNCVWVNLSPNVRGRIDLMDLSDDVSLLNNVQGNFPVGSAIKVRVKNVDASNNRLDLTATS 1122
Cdd:cd05703      1 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSARG 73
S1_Rrp5_repeat_hs1_sc1 cd05693
S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 154-262 7.73e-28

S1_Rrp5_repeat_hs1_sc1: 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 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240198 [Multi-domain]  Cd Length: 100  Bit Score: 108.84  E-value: 7.73e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  154 LAPGSMVLGQITQITSKDIALSLPNNLVGFVPLTAVSDQYNERIEALLgedkeSENEEEESSEDDLELKNIFSLGQYLRA 233
Cdd:cd05693      1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELD-----EESEEEDDEEELPDLEDLFSVGQLVRC 75

                           90       100
                   ....*....|....*....|....*....
gi 1808214898  234 TVTSVGDDSKTsqksKKRIELSVNPKDAN 262
Cdd:cd05693     76 KVVSLDKSKSG----KKRIELSLEPELVN 100
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 1043-1391 1.59e-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: 115.99  E-value: 1.59e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1043 SMDKLTIGSSHIAFVNNISDNCVWVNLSpNVRGRIDLMDLSddVSLLNNVQGNFPVGSAIKVRVKNVDASNNRLDLTATS 1122
Cdd:TIGR00717  181 LLENLKEGDVVKGVVKNITDFGAFVDLG-GVDGLLHITDMS--WKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLKQ 257

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1123 AAASKPTKIQD-LSAGQILPGRVTKVTERHIMVQLSETVSAPVTLTEFSDDYSQANPT-VHKKHDVVRVCILDVDAPNKK 1200
Cdd:TIGR00717  258 LGEDPWEAIEKkFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSWVKKNSHPSkVVKKGDEVEVMILDIDPERRR 337

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1201 LVLSL-----RPSKVLSSSLPVkdpqianirqlkvNDVVRGFVKNVSEKGLFVSLSSNVTAFVRISDLSdsFIKDWRSA- 1274
Cdd:TIGR00717  338 LSLGLkqckaNPWEQFEEKHPV-------------GDRVTGKIKKITDFGAFVELEGGIDGLIHLSDIS--WDKDGREAd 402

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1275 --FEVDQLVTGKIVAVDPllNHVQISLKASMLDKDyvPPTTFNDL-KPRQVVTGKVRKVEDFGVFIVVDNSsnVSGLCHR 1351
Cdd:TIGR00717  403 hlYKKGDEIEAVVLAVDK--EKKRISLGVKQLTEN--PWEKFAAKyKVGSVVKGKVTEIKDFGAFVELPGG--VEGLIRN 476

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|
gi 1808214898 1352 SEIADQKVEDVRKLYEEGDAVKAIVLKIDQEKRRVNFGLK 1391
Cdd:TIGR00717  477 SELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 516
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 1098-1392 1.97e-26

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 116.42  E-value: 1.97e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1098 VGSAIKVRVKNVDASNNRLDLTATSAAASKPTKIQD-LSAGQILPGRVTKVTERHIMVQLSETVSAPVTLTEFSDDYSQA 1176
Cdd:PRK06299   247 VGDEVKVKVLKFDKEKKRVSLGLKQLGEDPWEAIEKkYPVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMSWTKKNK 326

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1177 NPT-VHKKHDVVRVCILDVDAPNKKLVLSLRPSKVlssslpvkDPQIANIRQLKVNDVVRGFVKNVSEKGLFVSLSSNVT 1255
Cdd:PRK06299   327 HPSkVVSVGQEVEVMVLEIDEEKRRISLGLKQCKE--------NPWEEFAEKYPVGDVVEGKVKNITDFGAFVGLEGGID 398

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1256 AFVRISDLS-DSFIKDWRSAFEVDQLVTGKIVAVDPllNHVQISLKASMLDKDyvPPTTF-NDLKPRQVVTGKVRKVEDF 1333
Cdd:PRK06299   399 GLVHLSDISwDKKGEEAVELYKKGDEVEAVVLKVDV--EKERISLGIKQLEED--PFEEFaKKHKKGSIVTGTVTEVKDK 474

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1808214898 1334 GVFIVVDNssNVSGLCHRSEIADQKVEDVRKLYEEGDAVKAIVLKIDQEKRRVNFGLKA 1392
Cdd:PRK06299   475 GAFVELED--GVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIKA 531
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 479-808 2.27e-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: 115.60  E-value: 2.27e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  479 GLFMDVGvkGVPGFAHISRLSDKKIDFLSEstgAYKLDSTHRARVVGYNPIDGLYIISLEPKVlEQPFLRV-DDVKVGQV 557
Cdd:TIGR00717  202 GAFVDLG--GVDGLLHITDMSWKRVKHPSE---YVKVGQEVKVKVIKFDKEKGRISLSLKQLG-EDPWEAIeKKFPVGDK 275

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  558 VKGKVEKvlITAKGqgaVVVNLAEGISGLASEAHIA-DVHLQHPEKKFKEGMAVTARVLSTDSEKRQIRLTLKKTLVNSe 636
Cdd:TIGR00717  276 ITGRVTN--LTDYG---VFVEIEEGIEGLVHVSEMSwVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQCKANP- 349

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  637 apvWSKYEDVV-LGKQAPGTIIKILRAGAIVQFYGDLKAFLPVSEMS-EAYIQDPSEHFRIGQTVTVHTINVDAESDKMT 714
Cdd:TIGR00717  350 ---WEQFEEKHpVGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISwDKDGREADHLYKKGDEIEAVVLAVDKEKKRIS 426

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  715 VSCK----DPTTRGAAMTeaydllKVGSVVKGSVSEKSEKTITVELEGsGIKGIIRIGQLtdgSEKKDQSSMKRIRVGQT 790
Cdd:TIGR00717  427 LGVKqlteNPWEKFAAKY------KVGSVVKGKVTEIKDFGAFVELPG-GVEGLIRNSEL---SENRDEDKTDEIKVGDE 496

                          330
                   ....*....|....*....
gi 1808214898  791 LEDLVV-LSKSDKKPLLTL 808
Cdd:TIGR00717  497 VEAKVVdIDKKNRKVSLSV 515
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 1060-1392 2.63e-26

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: 112.45  E-value: 2.63e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1060 ISDNCVWVNLSPNVRGRIDLMDLSDDvsllnNVQGNFPVGSAIKVRVKNVDASNNRLDLTATSAAASKP-TKIQD-LSAG 1137
Cdd:COG0539     29 IDDDEVLVDIGYKSEGIIPLSEFSDE-----PGELEVKVGDEVEVYVEKVEDGEGEIVLSKKKADREKAwEELEEaFENG 103

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1138 QILPGRVTKVTERHIMVQLsETVSA--PVTL--TEFSDDYSqanPTVHKKhdvVRVCILDVDAPNKKLVLSLRpsKVLSS 1213
Cdd:COG0539    104 EPVEGKVKGVVKGGLIVDI-GGVRAflPASQvdVRPVRDLD---EYVGKT---LEFKIIKLDRKRNNVVVSRR--AVLEE 174

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1214 slpvkdpQIANIRQ-----LKVNDVVRGFVKNVSEKGLFVSLSSnVTAFVRISDLSDSFIKDWRSAFEVDQLVTGKIVAV 1288
Cdd:COG0539    175 -------EREEKREellekLEEGDVVEGTVKNITDFGAFVDLGG-VDGLLHISEISWGRVKHPSEVLKVGDEVEVKVLKI 246

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1289 DPLLNHVQISLKAsmLDKDyvPPTTF-NDLKPRQVVTGKVRKVEDFGVFIVVDNssNVSGLCHRSEIA-DQKVEDVRKLY 1366
Cdd:COG0539    247 DREKERISLSLKQ--LQPD--PWENIaEKYPVGDVVKGKVTRLTDFGAFVELEP--GVEGLVHISEMSwTKRVAHPSDVV 320

                          330       340
                   ....*....|....*....|....*.
gi 1808214898 1367 EEGDAVKAIVLKIDQEKRRVNFGLKA 1392
Cdd:COG0539    321 KVGDEVEVKVLDIDPEERRISLSIKQ 346
S1_Rrp5_repeat_sc11 cd05707
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1231-1298 4.00e-26

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


Pssm-ID: 240212 [Multi-domain]  Cd Length: 68  Bit Score: 102.76  E-value: 4.00e-26
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1808214898 1231 NDVVRGFVKNVSEKGLFVSLSSNVTAFVRISDLSDSFIKDWRSAFEVDQLVTGKIVAVDPLLNHVQIS 1298
Cdd:cd05707      1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 479-811 4.81e-26

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 115.26  E-value: 4.81e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  479 GLFMDVGvkGVPGFAHISRLSDKKIDFLSEstgAYKLDSTHRARVVGYNPIDGLyiISLEPKVLEQ-PFLRVDD-VKVGQ 556
Cdd:PRK06299   216 GAFVDLG--GVDGLLHITDISWKRVNHPSE---VVNVGDEVKVKVLKFDKEKKR--VSLGLKQLGEdPWEAIEKkYPVGS 288

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  557 VVKGKVekVLITAKGqgaVVVNLAEGISGLaseAHIADV----HLQHPEKKFKEGMAVTARVLSTDSEKRQIRLTLKKTL 632
Cdd:PRK06299   289 KVKGKV--TNITDYG---AFVELEEGIEGL---VHVSEMswtkKNKHPSKVVSVGQEVEVMVLEIDEEKRRISLGLKQCK 360

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  633 VNseaPvWSKYEDvvlgKQAPGTIIK-----ILRAGAIVQFYGDLKAFLPVSEMS-EAYIQDPSEHFRIGQTVTVHTINV 706
Cdd:PRK06299   361 EN---P-WEEFAE----KYPVGDVVEgkvknITDFGAFVGLEGGIDGLVHLSDISwDKKGEEAVELYKKGDEVEAVVLKV 432

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  707 DAESDKMTVSCK----DPTTRGAAMteaydlLKVGSVVKGSVSEKSEKTITVELEGsGIKGIIRIGQLTDGSEKKDQSSM 782
Cdd:PRK06299   433 DVEKERISLGIKqleeDPFEEFAKK------HKKGSIVTGTVTEVKDKGAFVELED-GVEGLIRASELSRDRVEDATEVL 505

                          330       340       350
                   ....*....|....*....|....*....|
gi 1808214898  783 KrirVGQTLEDLVV-LSKSDKKPLLTLTNK 811
Cdd:PRK06299   506 K---VGDEVEAKVInIDRKNRRISLSIKAL 532
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 819-901 3.21e-22

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: 92.27  E-value: 3.21e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  819 KAGSLVAKYEDLREGQPVNGFVRHIDGQRVFVEFAGGLVGLLLKSQMPEEMANTAEFGLRADQSISAKVLATDNQQRRFL 898
Cdd:cd04461      1 KEGTLPTNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFL 80


                   ...
gi 1808214898  899 VTM 901
Cdd:cd04461     81 LSL 83
S1_Rrp5_repeat_hs4 cd05696
S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 463-537 4.79e-22

S1_Rrp5_repeat_hs4: 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 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240201 [Multi-domain]  Cd Length: 71  Bit Score: 91.17  E-value: 4.79e-22
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1808214898  463 SAFVEEAKVTKVESTLGLFMDVGVkGVPGFAHISRLSDKKIDFlseSTGAYKLDSTHRARVVGYNPIDGLYIISL 537
Cdd:cd05696      1 GAVVDSVKVTKVEPDLGAVFELKD-GLLGFVHISHLSDDKVPS---DTGPFKAGTTHKARIIGYSPMDGLLQLSL 71
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 654-1300 2.20e-18

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: 90.95  E-value: 2.20e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  654 GTIIKILRAGAIVQFYGDLKAFLPVSEmseayIQDPSEHFRIGQTVTVHtinVDAESDKM--TVSCKDPTTRGAAMTEAY 731
Cdd:TIGR00717   24 GTVVAINKDTVFVDVGLKSEGRIPKEE-----FLDAPLEIQVGDEVEVY---LDRVEDRFgeTVLSREKAQRHELWIKLE 95

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  732 DLLKVGSVVKGSVSEKSEKTITVELEGsgikgiirIGQLTDGSekkdQSSMKRIR-----VGQTLEDLVVlsKSDKKPLL 806
Cdd:TIGR00717   96 KAYEEGSIVEGKIVGKVKGGFIVDLNG--------VEAFLPGS----QVDVKPIKdldslIGKTLKFKII--KLDQKRNN 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  807 TLTNKPTLLQAAKAGSLVAKYEDLREGQPVNGFVRHIDGQRVFVEfAGGLVGLLLKSQM-------PEEMANtaeFGlra 879
Cdd:TIGR00717  162 IVVSRRAYLEEERSQAREELLENLKEGDVVKGVVKNITDFGAFVD-LGGVDGLLHITDMswkrvkhPSEYVK---VG--- 234

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  880 dQSISAKVLATDNQQRRFLVTMKDDQEvtsktataassksaakdetllNPVDEQLtsiSDLTFGKLTTARITHVKDTQLN 959
Cdd:TIGR00717  235 -QEVKVKVIKFDKEKGRISLSLKQLGE---------------------DPWEAIE---KKFPVGDKITGRVTNLTDYGVF 289

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  960 VHLADNLQGRVDVSEIfdSWEniKDRKHPLRQFKAKQNVPVRVIGIhDARNHRFLPISHRTGKTP--VFEltakavnltk 1037
Cdd:TIGR00717  290 VEIEEGIEGLVHVSEM--SWV--KKNSHPSKVVKKGDEVEVMILDI-DPERRRLSLGLKQCKANPweQFE---------- 354

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1038 dsdllsmDKLTIGSSHIAFVNNISDNCVWVNLSPNVRGRIDLMDLSDDvsllnnvqgnfpvgsaikvrvknvdasnnrld 1117
Cdd:TIGR00717  355 -------EKHPVGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISWD-------------------------------- 395

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1118 ltatsaaasKPTKIQDLSagqilpgrvtkvterhimvqlsetvsapvtltefsddysqanptvHKKHDVVRVCILDVDAP 1197
Cdd:TIGR00717  396 ---------KDGREADHL---------------------------------------------YKKGDEIEAVVLAVDKE 421

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1198 NKKLVLSLrpsKVLssslpVKDP--QIANIRqlKVNDVVRGFVKNVSEKGLFVSLSSNVTAFVRISDLSDSFIKDWRSAF 1275
Cdd:TIGR00717  422 KKRISLGV---KQL-----TENPweKFAAKY--KVGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEI 491

                          650       660
                   ....*....|....*....|....*
gi 1808214898 1276 EVDQLVTGKIVAVDPLLNHVQISLK 1300
Cdd:TIGR00717  492 KVGDEVEAKVVDIDKKNRKVSLSVK 516
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
269-644 7.77e-17

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 86.54  E-value: 7.77e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  269 DLVVNSMVQASVVSVEDHGLVMDLGladGAIKGFMGAKEV---GYTVDHSKVEKGAVFLCMITGLSSNGKIVKLSAdyQK 345
Cdd:PRK00087   299 QIRRGDIVKGTVVSVNENEVFVDVG---YKSEGVIPLRELtldEISSLKESVKVGDEIEVKVLKLEDEDGYVVLSK--KE 373

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  346 VGNVKKTNYLTEAptidvLLPGTAVEMLVTEVTITGL---AGQVMGLVDAT-ADIIHAgagesqKDItNRYKtGSKIRGR 421
Cdd:PRK00087   374 ADREKAWKELEEA-----FENGEPVKGKVKEVVKGGLlvdYGGVRAFLPAShVELGYV------EDL-SEYK-GQELEVK 440

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  422 IIcTFPEGERRKLgisvldhVLS----LTNRQSAESKAPLDILPISAFVEeAKVTKVEStLGLFMDVGvkGVPGFAHISR 497
Cdd:PRK00087   441 II-EFNRKRRKKV-------VLSrkaiLEEEKEKKKEETWNSLEEGDVVE-GEVKRLTD-FGAFVDIG--GVDGLLHVSE 508

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  498 LSDKKIDFLSEstgAYKLDSTHRARVVGYNPIDGLYIISLEpKVLEQPFLRVDD-VKVGQVVKGKVEKVLitakGQGAVV 576
Cdd:PRK00087   509 ISWGRVEKPSD---VLKVGDEIKVYILDIDKENKKLSLSLK-KLLPDPWENVEEkYPVGSIVLGKVVRIA----PFGAFV 580

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1808214898  577 vNLAEGISGLASEAHIADVHLQHPEKKFKEGMAVTARVLSTDSEKRQIRLTLKKTLVNSEAPVWSKYE 644
Cdd:PRK00087   581 -ELEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEVEEEPGDIEKVELE 647
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 479-719 1.02e-15

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


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 80.86  E-value: 1.02e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  479 GLFMDVGvkGVPGFAHISRLSDKKIdflsESTGAYKlDSTHRARVVGYNPIDGLYIIS----LEPKVLEQPFLRVDDVKV 554
Cdd:COG0539    117 GLIVDIG--GVRAFLPASQVDVRPV----RDLDEYV-GKTLEFKIIKLDRKRNNVVVSrravLEEEREEKREELLEKLEE 189

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  555 GQVVKGKVEKvlITAKGqgaVVVNLaEGISGLAseaHIADV---HLQHPEKKFKEGMAVTARVLSTDSEKRQIRLTLKKT 631
Cdd:COG0539    190 GDVVEGTVKN--ITDFG---AFVDL-GGVDGLL---HISEIswgRVKHPSEVLKVGDEVEVKVLKIDREKERISLSLKQL 260

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  632 LVNseaPvW----SKYE--DVVlgkqaPGTIIKILRAGAIVQFYGDLKAFLPVSEMS-EAYIQDPSEHFRIGQTVTVHTI 704
Cdd:COG0539    261 QPD---P-WeniaEKYPvgDVV-----KGKVTRLTDFGAFVELEPGVEGLVHISEMSwTKRVAHPSDVVKVGDEVEVKVL 331

                          250
                   ....*....|....*
gi 1808214898  705 NVDAESDKMTVSCKD 719
Cdd:COG0539    332 DIDPEERRISLSIKQ 346
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1318-1391 1.28e-15

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 73.02  E-value: 1.28e-15
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1808214898  1318 KPRQVVTGKVRKVEDFGVFIVVDNssNVSGLCHRSEIADQKVEDVRKLYEEGDAVKAIVLKIDQEKRRVNFGLK 1391
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGN--GVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1229-1300 1.52e-14

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 69.94  E-value: 1.52e-14
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1808214898  1229 KVNDVVRGFVKNVSEKGLFVSLSSNVTAFVRISDLSDSFIKDWRSAFEVDQLVTGKIVAVDPLLNHVQISLK 1300
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 268-631 1.68e-13

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


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 73.93  E-value: 1.68e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  268 SDLVVNSMVQASVVSVEDHGLVMDLGL-ADGAIKgfmgAKEVGYTVDHSKVEKGAVFLCMITGLSSNGKIVKLSadYQKV 346
Cdd:COG0539     14 KELKEGDIVKGTVVSIDDDEVLVDIGYkSEGIIP----LSEFSDEPGELEVKVGDEVEVYVEKVEDGEGEIVLS--KKKA 87

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  347 GNVKKTNYLTEAptidvLLPGTAVEMLVTEVTITGLAGQVMGlVDAtadIIHAgageSQKDI-----TNRYKtGSKIRGR 421
Cdd:COG0539     88 DREKAWEELEEA-----FENGEPVEGKVKGVVKGGLIVDIGG-VRA---FLPA----SQVDVrpvrdLDEYV-GKTLEFK 153

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  422 IIctfpE--GERRKLgisvldhVLS---LTNRQSAESKAPL-------DILpisafveEAKVTKVEStLGLFMDVGvkGV 489
Cdd:COG0539    154 II----KldRKRNNV-------VVSrraVLEEEREEKREELlekleegDVV-------EGTVKNITD-FGAFVDLG--GV 212

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  490 PGFAHISRLSDKKIDFLSEstgAYKLDSTHRARVVGYNPIDGLyiISLEPKVLEQ-PFLRVDD-VKVGQVVKGKVEKvlI 567
Cdd:COG0539    213 DGLLHISEISWGRVKHPSE---VLKVGDEVEVKVLKIDREKER--ISLSLKQLQPdPWENIAEkYPVGDVVKGKVTR--L 285

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1808214898  568 TAKGqgaVVVNLAEGISGLAseaHI----ADVHLQHPEKKFKEGMAVTARVLSTDSEKRQIRLTLKKT 631
Cdd:COG0539    286 TDFG---AFVELEPGVEGLV---HIsemsWTKRVAHPSDVVKVGDEVEVKVLDIDPEERRISLSIKQL 347
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
553-629 6.15e-13

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 65.32  E-value: 6.15e-13
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1808214898   553 KVGQVVKGKVEKvlITAKGqgaVVVNLAEGISGLASEAHIADVHLQHPEKKFKEGMAVTARVLSTDSEKRQIRLTLK 629
Cdd:smart00316    1 EVGDVVEGTVTE--ITPGG---AFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 654-1206 1.12e-12

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 72.89  E-value: 1.12e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  654 GTIIKILRAGAIVqfygD--LK--AFLPVSEmseayIQDPSEH--FRIGQTVTVHtinVDAESDKM--TVSCKDPTTRGA 725
Cdd:PRK06299    36 GTVVAIDKDYVLV----DvgLKseGRIPLEE-----FKNEQGEleVKVGDEVEVY---VERIEDGFgeTVLSREKAKRLE 103

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  726 AMTEAYDLLKVGSVVKGSVSEKSEKTITVELEGsgIKGIIrigqltDGSekkdQSSMKRIR-----VGQTLEDLVVlsKS 800
Cdd:PRK06299   104 AWDKLEKAFENGEIVEGVINGKVKGGFTVDLNG--VEAFL------PGS----QVDVRPVRdtdplEGKELEFKVI--KL 169

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  801 DKKplltlTN-----KPTLLQAAKAG---SLVAKYEdlrEGQPVNGFVRHIDGQRVFVEfAGGLVGLLLKSQM------- 865
Cdd:PRK06299   170 DKK-----RNnivvsRRAVLEEERAEereELLENLE---EGQVVEGVVKNITDYGAFVD-LGGVDGLLHITDIswkrvnh 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  866 PEEMantaefgLRADQSISAKVLATDNQQRRFLVTMKDDQEvtsktataassksaakdetllNPVDEqltsISD-LTFGK 944
Cdd:PRK06299   241 PSEV-------VNVGDEVKVKVLKFDKEKKRVSLGLKQLGE---------------------DPWEA----IEKkYPVGS 288

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  945 LTTARITHVKDTQLNVHLADNLQGRVDVSEIfdSWenIKDRKHPLRQFKAKQNVPVRVIGIhDARNHRflpIShrtgktp 1024
Cdd:PRK06299   289 KVKGKVTNITDYGAFVELEEGIEGLVHVSEM--SW--TKKNKHPSKVVSVGQEVEVMVLEI-DEEKRR---IS------- 353

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1025 vfeltakavnltkdsdlLSMDKLT------------IGSSHIAFVNNISDNCVWVNLSPNVRGRIDLMDLSDDVSLLNNV 1092
Cdd:PRK06299   354 -----------------LGLKQCKenpweefaekypVGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISWDKKGEEAV 416

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1093 QgNFPVGSAIKVRVKNVDASNNRLDLTATSAAASKPTK-IQDLSAGQILPGRVTKVTERHIMVQLSETVSAPVTLTEFSD 1171
Cdd:PRK06299   417 E-LYKKGDEVEAVVLKVDVEKERISLGIKQLEEDPFEEfAKKHKKGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSR 495

                          570       580       590
                   ....*....|....*....|....*....|....*
gi 1808214898 1172 DYSQANPTVHKKHDVVRVCILDVDAPNKKLVLSLR 1206
Cdd:PRK06299   496 DRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIK 530
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
654-718 1.41e-11

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 61.47  E-value: 1.41e-11
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1808214898   654 GTIIKILRAGAIVQFYGDLKAFLPVSEMSEAYIQDPSEHFRIGQTVTVHTINVDAESDKMTVSCK 718
Cdd:smart00316    8 GTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1_Rrp5_repeat_hs2_sc2 cd05694
S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 269-346 5.30e-11

S1_Rrp5_repeat_hs2_sc2: 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 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240199 [Multi-domain]  Cd Length: 74  Bit Score: 59.96  E-value: 5.30e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1808214898  269 DLVVNSMVQASVVSVEDHGLVMDLGLAdgAIKGFMGAKEVGytvDHSKVEKGAVFLCMITGLSSNGKIVKLSADYQKV 346
Cdd:cd05694      1 DLVEGMVLSGCVSSVEDHGYILDIGIP--GTTGFLPKKDAG---NFSKLKVGQLLLCVVEKVKDDGRVVSLSADPSKV 73
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 1321-1384 1.01e-10

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


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 60.96  E-value: 1.01e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1808214898 1321 QVVTGKVRKVEDFGVFIVVDNssNVSGLCHRSEIADQKVEDVRKLYEEGDAVKAIVLKIDQEKR 1384
Cdd:COG1098      7 DIVEGKVTGITPFGAFVELPE--GTTGLVHISEIADGYVKDINDYLKVGDEVKVKVLSIDEDGK 68
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 1321-1390 7.25e-10

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: 56.91  E-value: 7.25e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1321 QVVTGKVRKVEDFGVFIVVDNssNVSGLCHRSEIADQKVEDVRKLYEEGDAVKAIVLKIDQEKRRVNFGL 1390
Cdd:pfam00575    5 DVVEGEVTRVTKGGAFVDLGN--GVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1509-1709 8.57e-08

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 55.51  E-value: 8.57e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1509 RTGDLDIAgpqsVADFERLLLGQPNNSALWMQYMAFQIGLNEVQKAKDIAERALKtinirEEEEKMNIWTALLNLEIEQG 1588
Cdd:COG2956     88 KAGLLDRA----EELLEKLLELDPDDAEALRLLAEIYEQEGDWEKAIEVLERLLK-----LGPENAHAYCELAELYLEQG 158

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1589 NEEKVDEVFKRACQYcDPE--EMHNKLITIYTSTGRHEKADSLFQTMTKnksITPNPSFWMNYATFLMTTLNDPSRARQL 1666
Cdd:COG2956    159 DYDEAIEALEKALKL-DPDcaRALLLLAELYLEQGDYEEAIAALERALE---QDPDYLPALPRLAELYEKLGDPEEALEL 234

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|...
gi 1808214898 1667 LPRATQSVPahlhrQLTSKFAALEFQSPNGDAERGRTIFEGLL 1709
Cdd:COG2956    235 LRKALELDP-----SDDLLLALADLLERKEGLEAALALLERQL 272
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 654-717 8.23e-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: 48.05  E-value: 8.23e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1808214898  654 GTIIKILRAGAIVQFYGDLKAFLPVSEMSEAYIQDPSEHFRIGQTVTVHTINVDAESDKMTVSC 717
Cdd:pfam00575    9 GEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1049-1119 1.25e-06

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 47.60  E-value: 1.25e-06
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1808214898  1049 IGSSHIAFVNNISDNCVWVNLSPNVRGRIDLMDLSDDvsLLNNVQGNFPVGSAIKVRVKNVDASNNRLDLT 1119
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDK--RVKDPEEVLKVGDEVKVKVLSVDEEKGRIILS 70
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
831-902 1.89e-06

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 47.21  E-value: 1.89e-06
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1808214898   831 REGQPVNGFVRHIDGQRVFVEFAGGLVGLLLKSQMPEEMANTAEFGLRADQSISAKVLATDNQQRRFLVTMK 902
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 1136-1205 1.23e-05

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: 44.59  E-value: 1.23e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1136 AGQILPGRVTKVTERHIMVQLSETVSAPVTLTEFSDDYSQANPTVHKKHDVVRVCILDVDAPNKKLVLSL 1205
Cdd:pfam00575    3 KGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 654-719 1.70e-05

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 48.28  E-value: 1.70e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1808214898  654 GTIIKILRAGAIVQF--YGDLKAFLPVSEMSEAYIQDPSEHFRIGQTVTVHTINVDAESDKMTVSCKD 719
Cdd:PRK03987    14 GTVKEVKDFGAFVTLdeYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLKR 81
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 552-628 2.94e-05

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: 43.82  E-value: 2.94e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1808214898  552 VKVGQVVKGKVekvliTAKGQGAVVVNLAEGISGLASEAHIADVHLQHPEKKFKEGMAVTARVLSTDSEKRQIRLTL 628
Cdd:pfam00575    1 PEKGDVVEGEV-----TRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
 
Name Accession Description Interval E-value
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1321-1395 4.61e-31

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: 117.43  E-value: 4.61e-31
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1808214898 1321 QVVTGKVRKVEDFGVFIVVDNSsNVSGLCHRSEIADQKVEDVRKLYEEGDAVKAIVLKIDQEKRRVNFGLKASYF 1395
Cdd:cd05708      4 QKIDGTVRRVEDYGVFIDIDGT-NVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKASYF 77
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 649-718 2.58e-30

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: 115.02  E-value: 2.58e-30
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  649 GKQAPGTIIKILRAGAIVQFYGDLKAFLPVSEMSEAYIQDPSEHFRIGQTVTVHTINVDAESDKMTVSCK 718
Cdd:cd05698      1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
S1_Rrp5_repeat_hs11_sc8 cd05702
S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 943-1015 2.08e-28

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: 109.22  E-value: 2.08e-28
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1808214898  943 GKLTTARITHVKDTQLNVHLADNLQGRVDVSEIFDSWENIKDrkhPLRQFKAKQNVPVRVIGIHDARNHRFLP 1015
Cdd:cd05702      1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKN---PLSKFKIGQKIKARVIGGHDAKTHRFLP 70
S1_Rrp5_repeat_hs12_sc9 cd05703
S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 1050-1122 4.67e-28

S1_Rrp5_repeat_hs12_sc9: 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 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240208 [Multi-domain]  Cd Length: 73  Bit Score: 108.43  E-value: 4.67e-28
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1808214898 1050 GSSHIAFVNNISDNCVWVNLSPNVRGRIDLMDLSDDVSLLNNVQGNFPVGSAIKVRVKNVDASNNRLDLTATS 1122
Cdd:cd05703      1 GQEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSARG 73
S1_Rrp5_repeat_hs1_sc1 cd05693
S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 154-262 7.73e-28

S1_Rrp5_repeat_hs1_sc1: 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 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240198 [Multi-domain]  Cd Length: 100  Bit Score: 108.84  E-value: 7.73e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  154 LAPGSMVLGQITQITSKDIALSLPNNLVGFVPLTAVSDQYNERIEALLgedkeSENEEEESSEDDLELKNIFSLGQYLRA 233
Cdd:cd05693      1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELD-----EESEEEDDEEELPDLEDLFSVGQLVRC 75

                           90       100
                   ....*....|....*....|....*....
gi 1808214898  234 TVTSVGDDSKTsqksKKRIELSVNPKDAN 262
Cdd:cd05693     76 KVVSLDKSKSG----KKRIELSLEPELVN 100
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 1043-1391 1.59e-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: 115.99  E-value: 1.59e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1043 SMDKLTIGSSHIAFVNNISDNCVWVNLSpNVRGRIDLMDLSddVSLLNNVQGNFPVGSAIKVRVKNVDASNNRLDLTATS 1122
Cdd:TIGR00717  181 LLENLKEGDVVKGVVKNITDFGAFVDLG-GVDGLLHITDMS--WKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLKQ 257

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1123 AAASKPTKIQD-LSAGQILPGRVTKVTERHIMVQLSETVSAPVTLTEFSDDYSQANPT-VHKKHDVVRVCILDVDAPNKK 1200
Cdd:TIGR00717  258 LGEDPWEAIEKkFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSWVKKNSHPSkVVKKGDEVEVMILDIDPERRR 337

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1201 LVLSL-----RPSKVLSSSLPVkdpqianirqlkvNDVVRGFVKNVSEKGLFVSLSSNVTAFVRISDLSdsFIKDWRSA- 1274
Cdd:TIGR00717  338 LSLGLkqckaNPWEQFEEKHPV-------------GDRVTGKIKKITDFGAFVELEGGIDGLIHLSDIS--WDKDGREAd 402

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1275 --FEVDQLVTGKIVAVDPllNHVQISLKASMLDKDyvPPTTFNDL-KPRQVVTGKVRKVEDFGVFIVVDNSsnVSGLCHR 1351
Cdd:TIGR00717  403 hlYKKGDEIEAVVLAVDK--EKKRISLGVKQLTEN--PWEKFAAKyKVGSVVKGKVTEIKDFGAFVELPGG--VEGLIRN 476

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|
gi 1808214898 1352 SEIADQKVEDVRKLYEEGDAVKAIVLKIDQEKRRVNFGLK 1391
Cdd:TIGR00717  477 SELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 516
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 1098-1392 1.97e-26

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 116.42  E-value: 1.97e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1098 VGSAIKVRVKNVDASNNRLDLTATSAAASKPTKIQD-LSAGQILPGRVTKVTERHIMVQLSETVSAPVTLTEFSDDYSQA 1176
Cdd:PRK06299   247 VGDEVKVKVLKFDKEKKRVSLGLKQLGEDPWEAIEKkYPVGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMSWTKKNK 326

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1177 NPT-VHKKHDVVRVCILDVDAPNKKLVLSLRPSKVlssslpvkDPQIANIRQLKVNDVVRGFVKNVSEKGLFVSLSSNVT 1255
Cdd:PRK06299   327 HPSkVVSVGQEVEVMVLEIDEEKRRISLGLKQCKE--------NPWEEFAEKYPVGDVVEGKVKNITDFGAFVGLEGGID 398

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1256 AFVRISDLS-DSFIKDWRSAFEVDQLVTGKIVAVDPllNHVQISLKASMLDKDyvPPTTF-NDLKPRQVVTGKVRKVEDF 1333
Cdd:PRK06299   399 GLVHLSDISwDKKGEEAVELYKKGDEVEAVVLKVDV--EKERISLGIKQLEED--PFEEFaKKHKKGSIVTGTVTEVKDK 474

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1808214898 1334 GVFIVVDNssNVSGLCHRSEIADQKVEDVRKLYEEGDAVKAIVLKIDQEKRRVNFGLKA 1392
Cdd:PRK06299   475 GAFVELED--GVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIKA 531
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 479-808 2.27e-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: 115.60  E-value: 2.27e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  479 GLFMDVGvkGVPGFAHISRLSDKKIDFLSEstgAYKLDSTHRARVVGYNPIDGLYIISLEPKVlEQPFLRV-DDVKVGQV 557
Cdd:TIGR00717  202 GAFVDLG--GVDGLLHITDMSWKRVKHPSE---YVKVGQEVKVKVIKFDKEKGRISLSLKQLG-EDPWEAIeKKFPVGDK 275

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  558 VKGKVEKvlITAKGqgaVVVNLAEGISGLASEAHIA-DVHLQHPEKKFKEGMAVTARVLSTDSEKRQIRLTLKKTLVNSe 636
Cdd:TIGR00717  276 ITGRVTN--LTDYG---VFVEIEEGIEGLVHVSEMSwVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQCKANP- 349

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  637 apvWSKYEDVV-LGKQAPGTIIKILRAGAIVQFYGDLKAFLPVSEMS-EAYIQDPSEHFRIGQTVTVHTINVDAESDKMT 714
Cdd:TIGR00717  350 ---WEQFEEKHpVGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISwDKDGREADHLYKKGDEIEAVVLAVDKEKKRIS 426

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  715 VSCK----DPTTRGAAMTeaydllKVGSVVKGSVSEKSEKTITVELEGsGIKGIIRIGQLtdgSEKKDQSSMKRIRVGQT 790
Cdd:TIGR00717  427 LGVKqlteNPWEKFAAKY------KVGSVVKGKVTEIKDFGAFVELPG-GVEGLIRNSEL---SENRDEDKTDEIKVGDE 496

                          330
                   ....*....|....*....
gi 1808214898  791 LEDLVV-LSKSDKKPLLTL 808
Cdd:TIGR00717  497 VEAKVVdIDKKNRKVSLSV 515
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 1060-1392 2.63e-26

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: 112.45  E-value: 2.63e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1060 ISDNCVWVNLSPNVRGRIDLMDLSDDvsllnNVQGNFPVGSAIKVRVKNVDASNNRLDLTATSAAASKP-TKIQD-LSAG 1137
Cdd:COG0539     29 IDDDEVLVDIGYKSEGIIPLSEFSDE-----PGELEVKVGDEVEVYVEKVEDGEGEIVLSKKKADREKAwEELEEaFENG 103

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1138 QILPGRVTKVTERHIMVQLsETVSA--PVTL--TEFSDDYSqanPTVHKKhdvVRVCILDVDAPNKKLVLSLRpsKVLSS 1213
Cdd:COG0539    104 EPVEGKVKGVVKGGLIVDI-GGVRAflPASQvdVRPVRDLD---EYVGKT---LEFKIIKLDRKRNNVVVSRR--AVLEE 174

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1214 slpvkdpQIANIRQ-----LKVNDVVRGFVKNVSEKGLFVSLSSnVTAFVRISDLSDSFIKDWRSAFEVDQLVTGKIVAV 1288
Cdd:COG0539    175 -------EREEKREellekLEEGDVVEGTVKNITDFGAFVDLGG-VDGLLHISEISWGRVKHPSEVLKVGDEVEVKVLKI 246

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1289 DPLLNHVQISLKAsmLDKDyvPPTTF-NDLKPRQVVTGKVRKVEDFGVFIVVDNssNVSGLCHRSEIA-DQKVEDVRKLY 1366
Cdd:COG0539    247 DREKERISLSLKQ--LQPD--PWENIaEKYPVGDVVKGKVTRLTDFGAFVELEP--GVEGLVHISEMSwTKRVAHPSDVV 320

                          330       340
                   ....*....|....*....|....*.
gi 1808214898 1367 EEGDAVKAIVLKIDQEKRRVNFGLKA 1392
Cdd:COG0539    321 KVGDEVEVKVLDIDPEERRISLSIKQ 346
S1_Rrp5_repeat_sc11 cd05707
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1231-1298 4.00e-26

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


Pssm-ID: 240212 [Multi-domain]  Cd Length: 68  Bit Score: 102.76  E-value: 4.00e-26
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1808214898 1231 NDVVRGFVKNVSEKGLFVSLSSNVTAFVRISDLSDSFIKDWRSAFEVDQLVTGKIVAVDPLLNHVQIS 1298
Cdd:cd05707      1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 479-811 4.81e-26

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 115.26  E-value: 4.81e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  479 GLFMDVGvkGVPGFAHISRLSDKKIDFLSEstgAYKLDSTHRARVVGYNPIDGLyiISLEPKVLEQ-PFLRVDD-VKVGQ 556
Cdd:PRK06299   216 GAFVDLG--GVDGLLHITDISWKRVNHPSE---VVNVGDEVKVKVLKFDKEKKR--VSLGLKQLGEdPWEAIEKkYPVGS 288

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  557 VVKGKVekVLITAKGqgaVVVNLAEGISGLaseAHIADV----HLQHPEKKFKEGMAVTARVLSTDSEKRQIRLTLKKTL 632
Cdd:PRK06299   289 KVKGKV--TNITDYG---AFVELEEGIEGL---VHVSEMswtkKNKHPSKVVSVGQEVEVMVLEIDEEKRRISLGLKQCK 360

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  633 VNseaPvWSKYEDvvlgKQAPGTIIK-----ILRAGAIVQFYGDLKAFLPVSEMS-EAYIQDPSEHFRIGQTVTVHTINV 706
Cdd:PRK06299   361 EN---P-WEEFAE----KYPVGDVVEgkvknITDFGAFVGLEGGIDGLVHLSDISwDKKGEEAVELYKKGDEVEAVVLKV 432

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  707 DAESDKMTVSCK----DPTTRGAAMteaydlLKVGSVVKGSVSEKSEKTITVELEGsGIKGIIRIGQLTDGSEKKDQSSM 782
Cdd:PRK06299   433 DVEKERISLGIKqleeDPFEEFAKK------HKKGSIVTGTVTEVKDKGAFVELED-GVEGLIRASELSRDRVEDATEVL 505

                          330       340       350
                   ....*....|....*....|....*....|
gi 1808214898  783 KrirVGQTLEDLVV-LSKSDKKPLLTLTNK 811
Cdd:PRK06299   506 K---VGDEVEAKVInIDRKNRRISLSIKAL 532
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 1131-1392 5.26e-26

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: 111.29  E-value: 5.26e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1131 IQDLSAGQILPGRVTKVTERHIMVQL---SETVsapVTLTEFSDDysQANPTVhKKHDVVRVCILDVDAPNKKLVLSLRP 1207
Cdd:COG0539     13 LKELKEGDIVKGTVVSIDDDEVLVDIgykSEGI---IPLSEFSDE--PGELEV-KVGDEVEVYVEKVEDGEGEIVLSKKK 86

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1208 SKVLSSSLPVKDpqianirQLKVNDVVRGFVKNVSEKGLFVSLSsNVTAFVRISDLSDSFIKDWrSAFeVDQLVTGKIVA 1287
Cdd:COG0539     87 ADREKAWEELEE-------AFENGEPVEGKVKGVVKGGLIVDIG-GVRAFLPASQVDVRPVRDL-DEY-VGKTLEFKIIK 156

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1288 VDPLLNHVQISLKA-------SMLDKdyvpptTFNDLKPRQVVTGKVRKVEDFGVFIVVDNssnVSGLCHRSEIADQKVE 1360
Cdd:COG0539    157 LDRKRNNVVVSRRAvleeereEKREE------LLEKLEEGDVVEGTVKNITDFGAFVDLGG---VDGLLHISEISWGRVK 227

                          250       260       270
                   ....*....|....*....|....*....|..
gi 1808214898 1361 DVRKLYEEGDAVKAIVLKIDQEKRRVNFGLKA 1392
Cdd:COG0539    228 HPSEVLKVGDEVEVKVLKIDREKERISLSLKQ 259
S1_Rrp5_repeat_sc10 cd05706
S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1134-1206 8.52e-26

S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240211 [Multi-domain]  Cd Length: 73  Bit Score: 101.95  E-value: 8.52e-26
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1808214898 1134 LSAGQILPGRVTKVTERHIMVQLSETVSAPVTLTEFSDDYSQANPTVHKKHDVVRVCILDVDAPNKKLVLSLR 1206
Cdd:cd05706      1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSLR 73
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 1102-1391 1.83e-23

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: 106.74  E-value: 1.83e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1102 IKVRVKNVDASNNRLDLTATSAAASKPTKIQDLSAGQILPGRVTKVTERHIMVQLSeTVSAPVTLTEFSDDYSQANPTVH 1181
Cdd:TIGR00717  153 IKLDQKRNNIVVSRRAYLEEERSQAREELLENLKEGDVVKGVVKNITDFGAFVDLG-GVDGLLHITDMSWKRVKHPSEYV 231

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1182 KKHDVVRVCILDVDAPNKKLVLSLRPSKvlssslpvKDPQIANIRQLKVNDVVRGFVKNVSEKGLFVSLSSNVTAFVRIS 1261
Cdd:TIGR00717  232 KVGQEVKVKVIKFDKEKGRISLSLKQLG--------EDPWEAIEKKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVS 303

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1262 DLS-DSFIKDWRSAFEVDQLVTGKIVAVDPLLNHVQISLKASMLDkdyvPPTTFNDLKPR-QVVTGKVRKVEDFGVFIVV 1339
Cdd:TIGR00717  304 EMSwVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLKQCKAN----PWEQFEEKHPVgDRVTGKIKKITDFGAFVEL 379

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|...
gi 1808214898 1340 DNssNVSGLCHRSEIA-DQKVEDVRKLYEEGDAVKAIVLKIDQEKRRVNFGLK 1391
Cdd:TIGR00717  380 EG--GIDGLIHLSDISwDKDGREADHLYKKGDEIEAVVLAVDKEKKRISLGVK 430
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 819-901 3.21e-22

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: 92.27  E-value: 3.21e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  819 KAGSLVAKYEDLREGQPVNGFVRHIDGQRVFVEFAGGLVGLLLKSQMPEEMANTAEFGLRADQSISAKVLATDNQQRRFL 898
Cdd:cd04461      1 KEGTLPTNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFL 80


                   ...
gi 1808214898  899 VTM 901
Cdd:cd04461     81 LSL 83
S1_Rrp5_repeat_hs4 cd05696
S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 463-537 4.79e-22

S1_Rrp5_repeat_hs4: 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 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240201 [Multi-domain]  Cd Length: 71  Bit Score: 91.17  E-value: 4.79e-22
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1808214898  463 SAFVEEAKVTKVESTLGLFMDVGVkGVPGFAHISRLSDKKIDFlseSTGAYKLDSTHRARVVGYNPIDGLYIISL 537
Cdd:cd05696      1 GAVVDSVKVTKVEPDLGAVFELKD-GLLGFVHISHLSDDKVPS---DTGPFKAGTTHKARIIGYSPMDGLLQLSL 71
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 1186-1391 5.67e-22

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: 102.12  E-value: 5.67e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1186 VVRVCILDVDAPNKKLVLSLRpsKVLSSSLPVKDPQIANirQLKVNDVVRGFVKNVSEKGLFVSLSSnVTAFVRISDLSD 1265
Cdd:TIGR00717  147 TLKFKIIKLDQKRNNIVVSRR--AYLEEERSQAREELLE--NLKEGDVVKGVVKNITDFGAFVDLGG-VDGLLHITDMSW 221

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1266 SFIKDWRSAFEVDQLVTGKIVAVDPLLNHVQISLKAsmLDKDyvPPTTF-NDLKPRQVVTGKVRKVEDFGVFIVVDNssN 1344
Cdd:TIGR00717  222 KRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLKQ--LGED--PWEAIeKKFPVGDKITGRVTNLTDYGVFVEIEE--G 295

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*...
gi 1808214898 1345 VSGLCHRSEIA-DQKVEDVRKLYEEGDAVKAIVLKIDQEKRRVNFGLK 1391
Cdd:TIGR00717  296 IEGLVHVSEMSwVKKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLK 343
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 555-628 2.38e-21

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: 89.22  E-value: 2.38e-21
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1808214898  555 GQVVKGKVEKVliTAKGqgaVVVNLAEGISGLASEAHIADVHLQHPEKKFKEGMAVTARVLSTDSEKRQIRLTL 628
Cdd:cd05697      1 GQVVKGTIRKL--RPSG---IFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL 69
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 1130-1392 2.51e-21

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 98.41  E-value: 2.51e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1130 KIQDLSAGQILPGRVTKVTERHIMVQLSET-VSAPVTLTEFSDDYSQ-ANPTVhKKHDVVRVCILDVDAPNKKLVLSLRP 1207
Cdd:PRK06676    11 SVKEVEVGDVVTGEVLKVEDKQVFVNIEGYkVEGVIPISELSNDHIEdINDVV-KVGDELEVYVLKVEDGEGNLLLSKRR 89

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1208 ---SKVLSsslpvkdpQIAniRQLKVNDVVRGFVKNVSEKGLFVSLSsNVTAFVRISDLSDSFIKDWrSAFeVDQLVTGK 1284
Cdd:PRK06676    90 leaEKAWD--------KLE--EKFEEGEVVEVKVTEVVKGGLVVDVE-GVRGFIPASLISTRFVEDF-SDF-KGKTLEVK 156

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1285 IVAVDPLLNHVQISLKAsMLDKDYVP--PTTFNDLKPRQVVTGKVRKVEDFGVFIVVdnsSNVSGLCHRSEIADQKVEDV 1362
Cdd:PRK06676   157 IIELDPEKNRVILSRRA-VVEEERAAkkEELLSSLKEGDVVEGTVARLTDFGAFVDI---GGVDGLVHISELSHERVEKP 232

                          250       260       270
                   ....*....|....*....|....*....|
gi 1808214898 1363 RKLYEEGDAVKAIVLKIDQEKRRVNFGLKA 1392
Cdd:PRK06676   233 SEVVSVGQEVEVKVLSIDWETERISLSLKD 262
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 553-902 3.15e-21

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 100.24  E-value: 3.15e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  553 KVGQVVKGKVEKvlITAKGqgaVVVNLAeGISGLAseaHIADV---HLQHPEKKFKEGMAVTARVLSTDSEKRQIRLTLK 629
Cdd:PRK06299   200 EEGQVVEGVVKN--ITDYG---AFVDLG-GVDGLL---HITDIswkRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLK 270

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  630 KTLVNSEAPVWSKYEdvvLGKQAPGTIIKILRAGAIVQFYGDLKAFLPVSEMS-EAYIQDPSEHFRIGQTVTVHTINVDA 708
Cdd:PRK06299   271 QLGEDPWEAIEKKYP---VGSKVKGKVTNITDYGAFVELEEGIEGLVHVSEMSwTKKNKHPSKVVSVGQEVEVMVLEIDE 347

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  709 ESDKMTVSCK----DPTTrgaAMTEAYdllKVGSVVKGSVsekseKTIT-----VELEGsGIKGIIRIgqlTDGS-EKKD 778
Cdd:PRK06299   348 EKRRISLGLKqckeNPWE---EFAEKY---PVGDVVEGKV-----KNITdfgafVGLEG-GIDGLVHL---SDISwDKKG 412

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  779 QSSMKRIRVGQTLEdLVVLSKSDKKPLLTLTNKptLLQAAKAGSLVAKYedlREGQPVNGFVRHIDGQRVFVEFAGGLVG 858
Cdd:PRK06299   413 EEAVELYKKGDEVE-AVVLKVDVEKERISLGIK--QLEEDPFEEFAKKH---KKGSIVTGTVTEVKDKGAFVELEDGVEG 486

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....
gi 1808214898  859 LLLKSQMPEEMANTAEFGLRADQSISAKVLATDNQQRRFLVTMK 902
Cdd:PRK06299   487 LIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIK 530
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 654-1300 2.20e-18

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: 90.95  E-value: 2.20e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  654 GTIIKILRAGAIVQFYGDLKAFLPVSEmseayIQDPSEHFRIGQTVTVHtinVDAESDKM--TVSCKDPTTRGAAMTEAY 731
Cdd:TIGR00717   24 GTVVAINKDTVFVDVGLKSEGRIPKEE-----FLDAPLEIQVGDEVEVY---LDRVEDRFgeTVLSREKAQRHELWIKLE 95

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  732 DLLKVGSVVKGSVSEKSEKTITVELEGsgikgiirIGQLTDGSekkdQSSMKRIR-----VGQTLEDLVVlsKSDKKPLL 806
Cdd:TIGR00717   96 KAYEEGSIVEGKIVGKVKGGFIVDLNG--------VEAFLPGS----QVDVKPIKdldslIGKTLKFKII--KLDQKRNN 161

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  807 TLTNKPTLLQAAKAGSLVAKYEDLREGQPVNGFVRHIDGQRVFVEfAGGLVGLLLKSQM-------PEEMANtaeFGlra 879
Cdd:TIGR00717  162 IVVSRRAYLEEERSQAREELLENLKEGDVVKGVVKNITDFGAFVD-LGGVDGLLHITDMswkrvkhPSEYVK---VG--- 234

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  880 dQSISAKVLATDNQQRRFLVTMKDDQEvtsktataassksaakdetllNPVDEQLtsiSDLTFGKLTTARITHVKDTQLN 959
Cdd:TIGR00717  235 -QEVKVKVIKFDKEKGRISLSLKQLGE---------------------DPWEAIE---KKFPVGDKITGRVTNLTDYGVF 289

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  960 VHLADNLQGRVDVSEIfdSWEniKDRKHPLRQFKAKQNVPVRVIGIhDARNHRFLPISHRTGKTP--VFEltakavnltk 1037
Cdd:TIGR00717  290 VEIEEGIEGLVHVSEM--SWV--KKNSHPSKVVKKGDEVEVMILDI-DPERRRLSLGLKQCKANPweQFE---------- 354

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1038 dsdllsmDKLTIGSSHIAFVNNISDNCVWVNLSPNVRGRIDLMDLSDDvsllnnvqgnfpvgsaikvrvknvdasnnrld 1117
Cdd:TIGR00717  355 -------EKHPVGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISWD-------------------------------- 395

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1118 ltatsaaasKPTKIQDLSagqilpgrvtkvterhimvqlsetvsapvtltefsddysqanptvHKKHDVVRVCILDVDAP 1197
Cdd:TIGR00717  396 ---------KDGREADHL---------------------------------------------YKKGDEIEAVVLAVDKE 421

                          570       580       590       600       610       620       630       640
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1198 NKKLVLSLrpsKVLssslpVKDP--QIANIRqlKVNDVVRGFVKNVSEKGLFVSLSSNVTAFVRISDLSDSFIKDWRSAF 1275
Cdd:TIGR00717  422 KKRISLGV---KQL-----TENPweKFAAKY--KVGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDEDKTDEI 491

                          650       660
                   ....*....|....*....|....*
gi 1808214898 1276 EVDQLVTGKIVAVDPLLNHVQISLK 1300
Cdd:TIGR00717  492 KVGDEVEAKVVDIDKKNRKVSLSVK 516
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 470-718 1.18e-17

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 88.68  E-value: 1.18e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  470 KVTKVEStLGLFMDVGvKGVPGFAHISRLS-DKKI----DFLSESTGAY----KLDSTHRaRvvgynpidglyiISLEPK 540
Cdd:PRK06299   293 KVTNITD-YGAFVELE-EGIEGLVHVSEMSwTKKNkhpsKVVSVGQEVEvmvlEIDEEKR-R------------ISLGLK 357

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  541 -VLEQPFLRVDD-VKVGQVVKGKVEKvlITAKGqgaVVVNLAEGISGLaseahiadVHLQ---------HPEKKFKEGMA 609
Cdd:PRK06299   358 qCKENPWEEFAEkYPVGDVVEGKVKN--ITDFG---AFVGLEGGIDGL--------VHLSdiswdkkgeEAVELYKKGDE 424

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  610 VTARVLSTDSEKRQIRLTLKKTlvnSEAPvWSKYEDVV-LGKQAPGTIIKILRAGAIVQFYGDLKAFLPVSEMSEAYIQD 688
Cdd:PRK06299   425 VEAVVLKVDVEKERISLGIKQL---EEDP-FEEFAKKHkKGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSRDRVED 500

                          250       260       270
                   ....*....|....*....|....*....|
gi 1808214898  689 PSEHFRIGQTVTVHTINVDAESDKMTVSCK 718
Cdd:PRK06299   501 ATEVLKVGDEVEAKVINIDRKNRRISLSIK 530
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 1041-1392 2.50e-17

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 86.08  E-value: 2.50e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1041 LLSMDKLTIGSSHIAFVNNISDNCVWVNLS-PNVRGRIDLMDLSDDVSllNNVQGNFPVGSAIKVRV--KNVDASNNRLD 1117
Cdd:PRK06676     9 LNSVKEVEVGDVVTGEVLKVEDKQVFVNIEgYKVEGVIPISELSNDHI--EDINDVVKVGDELEVYVlkVEDGEGNLLLS 86

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1118 LTATSAAASKPTKIQDLSAGQILPGRVTKVTERHIMVQLSET---VSAPVTLTEFSDDYSQAnptvhkKHDVVRVCILDV 1194
Cdd:PRK06676    87 KRRLEAEKAWDKLEEKFEEGEVVEVKVTEVVKGGLVVDVEGVrgfIPASLISTRFVEDFSDF------KGKTLEVKIIEL 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1195 DAPNKKLVLSLRpsKVLSSSLPVKDPQIANirQLKVNDVVRGFVKNVSEKGLFVSLSSnVTAFVRISDLSDSFIKDWRSA 1274
Cdd:PRK06676   161 DPEKNRVILSRR--AVVEEERAAKKEELLS--SLKEGDVVEGTVARLTDFGAFVDIGG-VDGLVHISELSHERVEKPSEV 235

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1275 FEVDQLVTGKIVAVDPLLNHVQISLKASMLDkdyvPPTTF-NDLKPRQVVTGKVRKVEDFGVFIVVDnsSNVSGLCHRSE 1353
Cdd:PRK06676   236 VSVGQEVEVKVLSIDWETERISLSLKDTLPG----PWEGVeEKLPEGDVIEGTVKRLTDFGAFVEVL--PGVEGLVHISQ 309

                          330       340       350
                   ....*....|....*....|....*....|....*....
gi 1808214898 1354 IADQKVEDVRKLYEEGDAVKAIVLKIDQEKRRVNFGLKA 1392
Cdd:PRK06676   310 ISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISLSIKA 348
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
1131-1392 3.26e-17

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 87.69  E-value: 3.26e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1131 IQDLSAGQILPGRVTKVTERHIMVQLSETVSAPVTLTEFSDDYSQANPTVHKKHDVVRVCILDVDAPNKKLVLSLRpsKV 1210
Cdd:PRK00087   297 EKQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKESVKVGDEIEVKVLKLEDEDGYVVLSKK--EA 374

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1211 lssslpvkDPQIA--NIRQLKVN-DVVRGFVKNVSEKGLFVSLSsNVTAFVRISDLSDSFIKDwRSAFeVDQLVTGKIVA 1287
Cdd:PRK00087   375 --------DREKAwkELEEAFENgEPVKGKVKEVVKGGLLVDYG-GVRAFLPASHVELGYVED-LSEY-KGQELEVKIIE 443

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1288 VDP------------LLNHVQISLKAsmldkdyvppTTFNDLKPRQVVTGKVRKVEDFGVFIVVDNssnVSGLCHRSEIA 1355
Cdd:PRK00087   444 FNRkrrkkvvlsrkaILEEEKEKKKE----------ETWNSLEEGDVVEGEVKRLTDFGAFVDIGG---VDGLLHVSEIS 510

                          250       260       270
                   ....*....|....*....|....*....|....*..
gi 1808214898 1356 DQKVEDVRKLYEEGDAVKAIVLKIDQEKRRVNFGLKA 1392
Cdd:PRK00087   511 WGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKK 547
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
482-734 3.61e-17

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 87.69  E-value: 3.61e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  482 MDVGVKGVPGFAHISRLSDKKIDFLSEstgaYKlDSTHRARVVGYNPIDGLYIISLEPKVLEQPFLRVDD-----VKVGQ 556
Cdd:PRK00087   405 LLVDYGGVRAFLPASHVELGYVEDLSE----YK-GQELEVKIIEFNRKRRKKVVLSRKAILEEEKEKKKEetwnsLEEGD 479

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  557 VVKGKVEKvlITAKGqgaVVVNLaEGISGLAseaHIADV---HLQHPEKKFKEGMAVTARVLSTDSEKRQIRLTLKKTLV 633
Cdd:PRK00087   480 VVEGEVKR--LTDFG---AFVDI-GGVDGLL---HVSEIswgRVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKKLLP 550

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  634 NSEAPVWSKYE--DVVLGKqapgtIIKILRAGAIVQFYGDLKAFLPVSEMSEAYIQDPSEHFRIGQTVTVHTINVDAESD 711
Cdd:PRK00087   551 DPWENVEEKYPvgSIVLGK-----VVRIAPFGAFVELEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEK 625

                          250       260
                   ....*....|....*....|...
gi 1808214898  712 KMTVSCKDpTTRGAAMTEAYDLL 734
Cdd:PRK00087   626 RIRLSIKE-VEEEPGDIEKVELE 647
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 1130-1392 5.44e-17

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 86.76  E-value: 5.44e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1130 KIQDLSAGQILPGRVTKVTERHIMVQLSETVSAPVTLTEFSDDysQANPTVhKKHDVVRVCILDVDAPNKKLVLSLRPSK 1209
Cdd:PRK06299    24 KESETREGSIVKGTVVAIDKDYVLVDVGLKSEGRIPLEEFKNE--QGELEV-KVGDEVEVYVERIEDGFGETVLSREKAK 100

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1210 VLSSslpvkdpQIANIRQLKVNDVVRGFVKNvSEKGLFVSLSSNVTAFVRISDLSDSFIKDwrsafeVDQLVtGK----- 1284
Cdd:PRK06299   101 RLEA-------WDKLEKAFENGEIVEGVING-KVKGGFTVDLNGVEAFLPGSQVDVRPVRD------TDPLE-GKelefk 165

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1285 IVAVDPLLNHVQISLKAsMLDKDYVP--PTTFNDLKPRQVVTGKVRKVEDFGVFI---VVDnssnvsGLCHRSEIADQKV 1359
Cdd:PRK06299   166 VIKLDKKRNNIVVSRRA-VLEEERAEerEELLENLEEGQVVEGVVKNITDYGAFVdlgGVD------GLLHITDISWKRV 238

                          250       260       270
                   ....*....|....*....|....*....|...
gi 1808214898 1360 EDVRKLYEEGDAVKAIVLKIDQEKRRVNFGLKA 1392
Cdd:PRK06299   239 NHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQ 271
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
269-644 7.77e-17

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 86.54  E-value: 7.77e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  269 DLVVNSMVQASVVSVEDHGLVMDLGladGAIKGFMGAKEV---GYTVDHSKVEKGAVFLCMITGLSSNGKIVKLSAdyQK 345
Cdd:PRK00087   299 QIRRGDIVKGTVVSVNENEVFVDVG---YKSEGVIPLRELtldEISSLKESVKVGDEIEVKVLKLEDEDGYVVLSK--KE 373

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  346 VGNVKKTNYLTEAptidvLLPGTAVEMLVTEVTITGL---AGQVMGLVDAT-ADIIHAgagesqKDItNRYKtGSKIRGR 421
Cdd:PRK00087   374 ADREKAWKELEEA-----FENGEPVKGKVKEVVKGGLlvdYGGVRAFLPAShVELGYV------EDL-SEYK-GQELEVK 440

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  422 IIcTFPEGERRKLgisvldhVLS----LTNRQSAESKAPLDILPISAFVEeAKVTKVEStLGLFMDVGvkGVPGFAHISR 497
Cdd:PRK00087   441 II-EFNRKRRKKV-------VLSrkaiLEEEKEKKKEETWNSLEEGDVVE-GEVKRLTD-FGAFVDIG--GVDGLLHVSE 508

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  498 LSDKKIDFLSEstgAYKLDSTHRARVVGYNPIDGLYIISLEpKVLEQPFLRVDD-VKVGQVVKGKVEKVLitakGQGAVV 576
Cdd:PRK00087   509 ISWGRVEKPSD---VLKVGDEIKVYILDIDKENKKLSLSLK-KLLPDPWENVEEkYPVGSIVLGKVVRIA----PFGAFV 580

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1808214898  577 vNLAEGISGLASEAHIADVHLQHPEKKFKEGMAVTARVLSTDSEKRQIRLTLKKTLVNSEAPVWSKYE 644
Cdd:PRK00087   581 -ELEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEVEEEPGDIEKVELE 647
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 293-718 3.95e-16

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: 83.63  E-value: 3.95e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  293 GLADGAIKGfmgakevGYTVDHSKVE----------KGAVFLCMITGLSSNGKIVKLSADYQKVgNVKKTNYLTE----- 357
Cdd:TIGR00717  106 GKIVGKVKG-------GFIVDLNGVEaflpgsqvdvKPIKDLDSLIGKTLKFKIIKLDQKRNNI-VVSRRAYLEEersqa 177

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  358 -APTIDVLLPGTAVEMLVTEVTITGL---AGQVMGLVDATaDIIHAGAgesqKDITNRYKTGSKIRGRIIcTFPEGERRk 433
Cdd:TIGR00717  178 rEELLENLKEGDVVKGVVKNITDFGAfvdLGGVDGLLHIT-DMSWKRV----KHPSEYVKVGQEVKVKVI-KFDKEKGR- 250

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  434 lgISvldhvLSLTNRQSAESKAPLDILPISAFVEeAKVTKVEStLGLFMDVGvKGVPGFAHISRLS-DKKIdflSESTGA 512
Cdd:TIGR00717  251 --IS-----LSLKQLGEDPWEAIEKKFPVGDKIT-GRVTNLTD-YGVFVEIE-EGIEGLVHVSEMSwVKKN---SHPSKV 317

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  513 YKLDSTHRARVVGYNPIDGLYIISLEpKVLEQPFLRVDDV-KVGQVVKGKVEKvlITAKGqgaVVVNLAEGISGLASEAH 591
Cdd:TIGR00717  318 VKKGDEVEVMILDIDPERRRLSLGLK-QCKANPWEQFEEKhPVGDRVTGKIKK--ITDFG---AFVELEGGIDGLIHLSD 391

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  592 IA-DVHLQHPEKKFKEGMAVTARVLSTDSEKRQIRLTLKKTLVNSeapvWSKYEDVV-LGKQAPGTIIKILRAGAIVQFY 669
Cdd:TIGR00717  392 ISwDKDGREADHLYKKGDEIEAVVLAVDKEKKRISLGVKQLTENP----WEKFAAKYkVGSVVKGKVTEIKDFGAFVELP 467

                          410       420       430       440
                   ....*....|....*....|....*....|....*....|....*....
gi 1808214898  670 GDLKAFLPVSEMSEAYIQDPSEHFRIGQTVTVHTINVDAESDKMTVSCK 718
Cdd:TIGR00717  468 GGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 516
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 542-906 6.79e-16

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 81.85  E-value: 6.79e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  542 LEQPFLRVDDVKVGQVVKGKVEKVlitakGQGAVVVNLA-EGISGLASEAHIADVHLQHPEKKFKEGMAVTARVLSTDSE 620
Cdd:PRK06676     5 FEESLNSVKEVEVGDVVTGEVLKV-----EDKQVFVNIEgYKVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDG 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  621 KRQIRLTLKKtlVNSEApVWSKYEDVVL-GKQAPGTIIKILRAGAIVQFYGdLKAFLPVSEMSEAYIQDPSEHfrIGQTV 699
Cdd:PRK06676    80 EGNLLLSKRR--LEAEK-AWDKLEEKFEeGEVVEVKVTEVVKGGLVVDVEG-VRGFIPASLISTRFVEDFSDF--KGKTL 153

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  700 TVHTINVDAESDKMTVSCKD--PTTRGAAMTEAYDLLKVGSVVKGSVSEksektIT-----VELegSGIKGIIRIGQLTD 772
Cdd:PRK06676   154 EVKIIELDPEKNRVILSRRAvvEEERAAKKEELLSSLKEGDVVEGTVAR-----LTdfgafVDI--GGVDGLVHISELSH 226

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  773 GSEKKDQSSMKrirVGQTLEdLVVLSKSDKKPLLTLTNKPTLlqaAKAGSLVAkyEDLREGQPVNGFVRHIDGQRVFVEF 852
Cdd:PRK06676   227 ERVEKPSEVVS---VGQEVE-VKVLSIDWETERISLSLKDTL---PGPWEGVE--EKLPEGDVIEGTVKRLTDFGAFVEV 297

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1808214898  853 AGGLVGLLLKSQMPEEMANTAEFGLRADQSISAKVLATDNQQRRFLVTMKDDQE 906
Cdd:PRK06676   298 LPGVEGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISLSIKALEE 351
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 479-719 1.02e-15

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


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 80.86  E-value: 1.02e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  479 GLFMDVGvkGVPGFAHISRLSDKKIdflsESTGAYKlDSTHRARVVGYNPIDGLYIIS----LEPKVLEQPFLRVDDVKV 554
Cdd:COG0539    117 GLIVDIG--GVRAFLPASQVDVRPV----RDLDEYV-GKTLEFKIIKLDRKRNNVVVSrravLEEEREEKREELLEKLEE 189

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  555 GQVVKGKVEKvlITAKGqgaVVVNLaEGISGLAseaHIADV---HLQHPEKKFKEGMAVTARVLSTDSEKRQIRLTLKKT 631
Cdd:COG0539    190 GDVVEGTVKN--ITDFG---AFVDL-GGVDGLL---HISEIswgRVKHPSEVLKVGDEVEVKVLKIDREKERISLSLKQL 260

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  632 LVNseaPvW----SKYE--DVVlgkqaPGTIIKILRAGAIVQFYGDLKAFLPVSEMS-EAYIQDPSEHFRIGQTVTVHTI 704
Cdd:COG0539    261 QPD---P-WeniaEKYPvgDVV-----KGKVTRLTDFGAFVELEPGVEGLVHISEMSwTKRVAHPSDVVKVGDEVEVKVL 331

                          250
                   ....*....|....*
gi 1808214898  705 NVDAESDKMTVSCKD 719
Cdd:COG0539    332 DIDPEERRISLSIKQ 346
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1318-1391 1.28e-15

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 73.02  E-value: 1.28e-15
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1808214898  1318 KPRQVVTGKVRKVEDFGVFIVVDNssNVSGLCHRSEIADQKVEDVRKLYEEGDAVKAIVLKIDQEKRRVNFGLK 1391
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGN--GVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
1037-1391 1.39e-15

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 82.30  E-value: 1.39e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1037 KDSDLLSMDKLTIGSSHIAFVNNISDNCVWVNLSPNVRGRIDLMDLSDDVSllNNVQGNFPVGSAIKVRVKNVDASNNRL 1116
Cdd:PRK00087   290 LEYMNELEKQIRRGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEI--SSLKESVKVGDEIEVKVLKLEDEDGYV 367

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1117 DLTATSAAASKPTKIQD--LSAGQILPGRVTKVTERHIMVQLsETVSA--PVTLTE--FSDDYSQAnptvhkKHDVVRVC 1190
Cdd:PRK00087   368 VLSKKEADREKAWKELEeaFENGEPVKGKVKEVVKGGLLVDY-GGVRAflPASHVElgYVEDLSEY------KGQELEVK 440

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1191 ILDVDAPNKKLVlslrpskVLSSSLPVKDPQIANIRQ----LKVNDVVRGFVKNVSEKGLFVSLSSnVTAFVRISDLSDS 1266
Cdd:PRK00087   441 IIEFNRKRRKKV-------VLSRKAILEEEKEKKKEEtwnsLEEGDVVEGEVKRLTDFGAFVDIGG-VDGLLHVSEISWG 512

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1267 FIKDWRSAFEVDQLVTGKIVAVDPLLNHVQISLKASMLDK-DYVPpttfNDLKPRQVVTGKVRKVEDFGVFivVDNSSNV 1345
Cdd:PRK00087   513 RVEKPSDVLKVGDEIKVYILDIDKENKKLSLSLKKLLPDPwENVE----EKYPVGSIVLGKVVRIAPFGAF--VELEPGV 586

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....*.
gi 1808214898 1346 SGLCHRSEIADQKVEDVRKLYEEGDAVKAIVLKIDQEKRRVNFGLK 1391
Cdd:PRK00087   587 DGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIK 632
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 1137-1392 1.30e-14

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


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 79.01  E-value: 1.30e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1137 GQILPGRVTKVTERHIMVQLSETVSAPVTLTEFSDDysqanPTVHKKHDVVRVCILDVDAPNKKLVLSLRPSKVLSSSLP 1216
Cdd:TIGR00717   19 GSIVKGTVVAINKDTVFVDVGLKSEGRIPKEEFLDA-----PLEIQVGDEVEVYLDRVEDRFGETVLSREKAQRHELWIK 93

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1217 VKDpqianiRQLKVNDVVRGFVKNVseKGLFVSLSSNVTAFVRISDLSDSFIKDWRSAfeVDQLVTGKIVAVDPLLNHVQ 1296
Cdd:TIGR00717   94 LEK------AYEEGSIVEGKIVGKV--KGGFIVDLNGVEAFLPGSQVDVKPIKDLDSL--IGKTLKFKIIKLDQKRNNIV 163

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1297 ISLKASMLDKDYVP-PTTFNDLKPRQVVTGKVRKVEDFGVFIVVDNssnVSGLCHRSEIADQKVEDVRKLYEEGDAVKAI 1375
Cdd:TIGR00717  164 VSRRAYLEEERSQArEELLENLKEGDVVKGVVKNITDFGAFVDLGG---VDGLLHITDMSWKRVKHPSEYVKVGQEVKVK 240

                          250
                   ....*....|....*..
gi 1808214898 1376 VLKIDQEKRRVNFGLKA 1392
Cdd:TIGR00717  241 VIKFDKEKGRISLSLKQ 257
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1229-1300 1.52e-14

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 69.94  E-value: 1.52e-14
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1808214898  1229 KVNDVVRGFVKNVSEKGLFVSLSSNVTAFVRISDLSDSFIKDWRSAFEVDQLVTGKIVAVDPLLNHVQISLK 1300
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 555-1005 1.88e-14

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


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 78.24  E-value: 1.88e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  555 GQVVKGKvekvlITAKGQGAVVVNLaEGISGLASEAHI------ADVHLQHPEKKFKegmavtarVLSTDSEKRQIRLTL 628
Cdd:TIGR00717  101 GSIVEGK-----IVGKVKGGFIVDL-NGVEAFLPGSQVdvkpikDLDSLIGKTLKFK--------IIKLDQKRNNIVVSR 166

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  629 KKTL-VNSEAPVWSKYEDVVLGKQAPGTIIKILRAGAIVQFyGDLKAFLPVSEMSEAYIQDPSEHFRIGQTVTVHTINVD 707
Cdd:TIGR00717  167 RAYLeEERSQAREELLENLKEGDVVKGVVKNITDFGAFVDL-GGVDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFD 245

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  708 AESDKMTVSCKDptTRGAAMTEAYDLLKVGSVVKGSVSEKSEKTITVELEgSGIKGIIRIGQLTdgSEKKDQSSMKRIRV 787
Cdd:TIGR00717  246 KEKGRISLSLKQ--LGEDPWEAIEKKFPVGDKITGRVTNLTDYGVFVEIE-EGIEGLVHVSEMS--WVKKNSHPSKVVKK 320

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  788 GQTLEdLVVLSKSDKKPLLTLTnkptlLQAAKAGSLVAKYEDLREGQPVNGFVRHIDGQRVFVEFAGGLVGLLLKSQMPE 867
Cdd:TIGR00717  321 GDEVE-VMILDIDPERRRLSLG-----LKQCKANPWEQFEEKHPVGDRVTGKIKKITDFGAFVELEGGIDGLIHLSDISW 394

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  868 EMANT-AEFGLRADQSISAKVLATDNQQRRFLVTMKDDQEvtsktataassksaakdetllNPVDEqltsISDL-TFGKL 945
Cdd:TIGR00717  395 DKDGReADHLYKKGDEIEAVVLAVDKEKKRISLGVKQLTE---------------------NPWEK----FAAKyKVGSV 449

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  946 TTARITHVKDTQLNVHLADNLQGRVDVSEIfdSWENIKDRKhplRQFKAKQNVPVRVIGI 1005
Cdd:TIGR00717  450 VKGKVTEIKDFGAFVELPGGVEGLIRNSEL--SENRDEDKT---DEIKVGDEVEAKVVDI 504
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 549-896 5.41e-14

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


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 75.47  E-value: 5.41e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  549 VDDVKVGQVVKGKVEKVlitakGQGAVVVNLaegisGLASEAHI--ADVHLQHPEKKFKEGMAVTARVLSTDSEKRQIRL 626
Cdd:COG0539     13 LKELKEGDIVKGTVVSI-----DDDEVLVDI-----GYKSEGIIplSEFSDEPGELEVKVGDEVEVYVEKVEDGEGEIVL 82

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  627 TLKKTLvnsEAPVWSKYEDvVLGKQAP--GTIIKILRAGAIVQFYGdLKAFLPVSEMSEAYIQDPSEHfrIGQTVTVHTI 704
Cdd:COG0539     83 SKKKAD---REKAWEELEE-AFENGEPveGKVKGVVKGGLIVDIGG-VRAFLPASQVDVRPVRDLDEY--VGKTLEFKII 155

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  705 NVDAESDKMTVSCKDP--TTRGAAMTEAYDLLKVGSVVKGSVsekseKTIT-----VELEgsGIKGIIRIGQLtdgsekk 777
Cdd:COG0539    156 KLDRKRNNVVVSRRAVleEEREEKREELLEKLEEGDVVEGTV-----KNITdfgafVDLG--GVDGLLHISEI------- 221

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  778 dqsSMKRIR-------VGQTLEdLVVLSKsDKKplltlTNKPTL-LQAAKAG---SLVAKYEdlrEGQPVNGFVRHI-D- 844
Cdd:COG0539    222 ---SWGRVKhpsevlkVGDEVE-VKVLKI-DRE-----KERISLsLKQLQPDpweNIAEKYP---VGDVVKGKVTRLtDf 288

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  845 GqrVFVEFAGGLVGLLLKSQM--------PEEMantaefgLRADQSISAKVLATDNQQRR 896
Cdd:COG0539    289 G--AFVELEPGVEGLVHISEMswtkrvahPSDV-------VKVGDEVEVKVLDIDPEERR 339
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 1191-1391 7.65e-14

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 76.24  E-value: 7.65e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1191 ILDVDAPNKKLVLSLRP------SKVLSSSLpvkdpqianiRQLKVNDVVRGFVKNVSEKGLFVSLSSnVTAFVRISDLS 1264
Cdd:PRK07899   173 IIELDKNRNNVVLSRRAwleqtqSEVRSEFL----------NQLQKGQVRKGVVSSIVNFGAFVDLGG-VDGLVHVSELS 241

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1265 DSFIKDWRSAFEVDQLVTGKIVAVDPLLNHVQISLKASMLDkdyvPPTTF-NDLKPRQVVTGKVRKVEDFGVFIVVDNss 1343
Cdd:PRK07899   242 WKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLSLKATQED----PWQQFaRTHAIGQIVPGKVTKLVPFGAFVRVEE-- 315

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*...
gi 1808214898 1344 NVSGLCHRSEIADQKVEDVRKLYEEGDAVKAIVLKIDQEKRRVNFGLK 1391
Cdd:PRK07899   316 GIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLERRRISLSLK 363
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 268-631 1.68e-13

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


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 73.93  E-value: 1.68e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  268 SDLVVNSMVQASVVSVEDHGLVMDLGL-ADGAIKgfmgAKEVGYTVDHSKVEKGAVFLCMITGLSSNGKIVKLSadYQKV 346
Cdd:COG0539     14 KELKEGDIVKGTVVSIDDDEVLVDIGYkSEGIIP----LSEFSDEPGELEVKVGDEVEVYVEKVEDGEGEIVLS--KKKA 87

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  347 GNVKKTNYLTEAptidvLLPGTAVEMLVTEVTITGLAGQVMGlVDAtadIIHAgageSQKDI-----TNRYKtGSKIRGR 421
Cdd:COG0539     88 DREKAWEELEEA-----FENGEPVEGKVKGVVKGGLIVDIGG-VRA---FLPA----SQVDVrpvrdLDEYV-GKTLEFK 153

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  422 IIctfpE--GERRKLgisvldhVLS---LTNRQSAESKAPL-------DILpisafveEAKVTKVEStLGLFMDVGvkGV 489
Cdd:COG0539    154 II----KldRKRNNV-------VVSrraVLEEEREEKREELlekleegDVV-------EGTVKNITD-FGAFVDLG--GV 212

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  490 PGFAHISRLSDKKIDFLSEstgAYKLDSTHRARVVGYNPIDGLyiISLEPKVLEQ-PFLRVDD-VKVGQVVKGKVEKvlI 567
Cdd:COG0539    213 DGLLHISEISWGRVKHPSE---VLKVGDEVEVKVLKIDREKER--ISLSLKQLQPdPWENIAEkYPVGDVVKGKVTR--L 285

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1808214898  568 TAKGqgaVVVNLAEGISGLAseaHI----ADVHLQHPEKKFKEGMAVTARVLSTDSEKRQIRLTLKKT 631
Cdd:COG0539    286 TDFG---AFVELEPGVEGLV---HIsemsWTKRVAHPSDVVKVGDEVEVKVLDIDPEERRISLSIKQL 347
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 1222-1290 3.35e-13

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: 66.46  E-value: 3.35e-13
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1808214898 1222 IANIRQLKVNDVVRGFVKNVSEKGLFVSLSSNVTAFVRISDLSDSFIKDWRSAFEVDQLVTGKIVAVDP 1290
Cdd:cd04461      6 PTNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDE 74
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 468-719 3.38e-13

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 73.37  E-value: 3.38e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  468 EAKVTKVESTlGLFMDVGvkGVPGFAHISRLSDKKIDFLSESTGaykldSTHRARVVGYNPIDGLYIIS----LEPKVLE 543
Cdd:PRK06676   110 EVKVTEVVKG-GLVVDVE--GVRGFIPASLISTRFVEDFSDFKG-----KTLEVKIIELDPEKNRVILSrravVEEERAA 181

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  544 QPFLRVDDVKVGQVVKGKVEKvlITAKGqgaVVVNLAeGISGLAseaHIADV---HLQHPEKKFKEGMAVTARVLSTDSE 620
Cdd:PRK06676   182 KKEELLSSLKEGDVVEGTVAR--LTDFG---AFVDIG-GVDGLV---HISELsheRVEKPSEVVSVGQEVEVKVLSIDWE 252

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  621 KRQIRLTLKKTLVNseaPvWskyeDVVLGKQAPGTII-----KILRAGAIVQFYGDLKAFLPVSEMSEAYIQDPSEHFRI 695
Cdd:PRK06676   253 TERISLSLKDTLPG---P-W----EGVEEKLPEGDVIegtvkRLTDFGAFVEVLPGVEGLVHISQISHKHIATPSEVLEE 324

                          250       260
                   ....*....|....*....|....
gi 1808214898  696 GQTVTVHTINVDAESDKMTVSCKD 719
Cdd:PRK06676   325 GQEVKVKVLEVNEEEKRISLSIKA 348
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 641-716 4.85e-13

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: 66.07  E-value: 4.85e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1808214898  641 SKYEDVVLGKQAPGTIIKILRAGAIVQFYGDLKAFLPVSEMSEAYIQDPSEHFRIGQTVTVHTINVDAESDKMTVS 716
Cdd:cd04461      7 TNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLS 82
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
553-629 6.15e-13

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 65.32  E-value: 6.15e-13
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1808214898   553 KVGQVVKGKVEKvlITAKGqgaVVVNLAEGISGLASEAHIADVHLQHPEKKFKEGMAVTARVLSTDSEKRQIRLTLK 629
Cdd:smart00316    1 EVGDVVEGTVTE--ITPGG---AFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
538-906 1.02e-12

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


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 73.06  E-value: 1.02e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  538 EPKVLEQPFLRVDDVKVGQVVKGKVEKVlitakGQGAVVVNL---AEGISGLaSEAHIADVhlQHPEKKFKEGMAVTARV 614
Cdd:PRK00087   286 ENEQLEYMNELEKQIRRGDIVKGTVVSV-----NENEVFVDVgykSEGVIPL-RELTLDEI--SSLKESVKVGDEIEVKV 357

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  615 LSTDSEKRQIRLTLKKtlVNSEApVWSKYEDVVLGKQA-PGTIIKILRAGAIVQfYGDLKAFLPVSEMSEAYIQDPSEHf 693
Cdd:PRK00087   358 LKLEDEDGYVVLSKKE--ADREK-AWKELEEAFENGEPvKGKVKEVVKGGLLVD-YGGVRAFLPASHVELGYVEDLSEY- 432

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  694 rIGQTVTVHTINVDAESDKMTV-SCKD--PTTRGAAMTEAYDLLKVGSVVKGSVsekseKTIT-----VELEgsGIKGII 765
Cdd:PRK00087   433 -KGQELEVKIIEFNRKRRKKVVlSRKAilEEEKEKKKEETWNSLEEGDVVEGEV-----KRLTdfgafVDIG--GVDGLL 504

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  766 RIGQLTDGSEKKDQSSMKrirVGQTLEDLVV-LSKSDKKPLLT---LTNKPtLLQAAKagslvaKYedlREGQPVNGFVR 841
Cdd:PRK00087   505 HVSEISWGRVEKPSDVLK---VGDEIKVYILdIDKENKKLSLSlkkLLPDP-WENVEE------KY---PVGSIVLGKVV 571

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1808214898  842 HIDGQRVFVEFAGGLVGLLLKSQMPEEMANTAEFGLRADQSISAKVLATDNQQRRFLVTMKDDQE 906
Cdd:PRK00087   572 RIAPFGAFVELEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEVEE 636
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 654-1206 1.12e-12

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 72.89  E-value: 1.12e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  654 GTIIKILRAGAIVqfygD--LK--AFLPVSEmseayIQDPSEH--FRIGQTVTVHtinVDAESDKM--TVSCKDPTTRGA 725
Cdd:PRK06299    36 GTVVAIDKDYVLV----DvgLKseGRIPLEE-----FKNEQGEleVKVGDEVEVY---VERIEDGFgeTVLSREKAKRLE 103

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  726 AMTEAYDLLKVGSVVKGSVSEKSEKTITVELEGsgIKGIIrigqltDGSekkdQSSMKRIR-----VGQTLEDLVVlsKS 800
Cdd:PRK06299   104 AWDKLEKAFENGEIVEGVINGKVKGGFTVDLNG--VEAFL------PGS----QVDVRPVRdtdplEGKELEFKVI--KL 169

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  801 DKKplltlTN-----KPTLLQAAKAG---SLVAKYEdlrEGQPVNGFVRHIDGQRVFVEfAGGLVGLLLKSQM------- 865
Cdd:PRK06299   170 DKK-----RNnivvsRRAVLEEERAEereELLENLE---EGQVVEGVVKNITDYGAFVD-LGGVDGLLHITDIswkrvnh 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  866 PEEMantaefgLRADQSISAKVLATDNQQRRFLVTMKDDQEvtsktataassksaakdetllNPVDEqltsISD-LTFGK 944
Cdd:PRK06299   241 PSEV-------VNVGDEVKVKVLKFDKEKKRVSLGLKQLGE---------------------DPWEA----IEKkYPVGS 288

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  945 LTTARITHVKDTQLNVHLADNLQGRVDVSEIfdSWenIKDRKHPLRQFKAKQNVPVRVIGIhDARNHRflpIShrtgktp 1024
Cdd:PRK06299   289 KVKGKVTNITDYGAFVELEEGIEGLVHVSEM--SW--TKKNKHPSKVVSVGQEVEVMVLEI-DEEKRR---IS------- 353

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1025 vfeltakavnltkdsdlLSMDKLT------------IGSSHIAFVNNISDNCVWVNLSPNVRGRIDLMDLSDDVSLLNNV 1092
Cdd:PRK06299   354 -----------------LGLKQCKenpweefaekypVGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISWDKKGEEAV 416

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1093 QgNFPVGSAIKVRVKNVDASNNRLDLTATSAAASKPTK-IQDLSAGQILPGRVTKVTERHIMVQLSETVSAPVTLTEFSD 1171
Cdd:PRK06299   417 E-LYKKGDEVEAVVLKVDVEKERISLGIKQLEEDPFEEfAKKHKKGSIVTGTVTEVKDKGAFVELEDGVEGLIRASELSR 495

                          570       580       590
                   ....*....|....*....|....*....|....*
gi 1808214898 1172 DYSQANPTVHKKHDVVRVCILDVDAPNKKLVLSLR 1206
Cdd:PRK06299   496 DRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIK 530
rpsA PRK13806
30S ribosomal protein S1; Provisional
 1060-1393 1.53e-12

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 72.06  E-value: 1.53e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1060 ISDNCVWVNLSPNVRGRIDLMDLSDDvsllnnvQGNFPVGSAIKVRVKNVDASNNRLDLTATSAAASKPTKIQD-LSAGQ 1138
Cdd:PRK13806    45 ITEDSVFVDTGSKVDGVVDRAELLDA-------DGELTVAVGDEVELYVVSVNGQEIRLSKALSGQGGAAMLEEaYENGV 117

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1139 ILPGRVTKVTERHIMVQ-LSETVSAPVTLTefsDDYSQANPTVHKKHdVVRVCILDVDAPNKKLVLSLRpsKVLSssLPV 1217
Cdd:PRK13806   118 PVEGKVTGTCKGGFNVEvLGRRAFCPVSQI---DLRYVEDPESYVGQ-TFQFLITRVEENGRNIVVSRR--ALLE--REQ 189

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1218 KDPQIANIRQLKVNDVVRGFVKNVSEKGLFVSLSSNVTAFVRISDLSDSFIKDWRSAFEVDQLVTGKIVAVDPLL--NHV 1295
Cdd:PRK13806   190 KEALEAFMETVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKkgKGL 269

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1296 QISLKASMLDKDyvPPTTFND-LKPRQVVTGKVRKVEDFGVFIVVdnSSNVSGLCHRSEIAD----QKVEDVRKLyeeGD 1370
Cdd:PRK13806   270 RISLSIKQAGGD--PWDTVGDrLKAGDKVTGKVVRLAPFGAFVEI--LPGIEGLVHVSEMSWtrrvNKPEDVVAP---GD 342

                          330       340
                   ....*....|....*....|...
gi 1808214898 1371 AVKAIVLKIDQEKRRVNFGLKAS 1393
Cdd:PRK13806   343 AVAVKIKDIDPAKRRISLSLRDA 365
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 1099-1391 2.76e-12

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 72.05  E-value: 2.76e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1099 GSAIKVRVKNVDASNNRLDLTATSAAASKPTKIQD-LSAGQILPGRVTKVTERHIMVQLSETVSAPVTLTEFSDDYSQAN 1177
Cdd:PRK12269   540 GQTIELKVIRLDQAEKRINLSLKHFQPDPWLEFENkFGVNDVVKGRVTKIADFGAFIELAEGIEGLAHISEFSWVKKTSK 619

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1178 PT-VHKKHDVVRVCILDVDAPNKKLVLSLR-----PSKVLSSSLPVKdpqianirqlkvNDVVRGFVKnVSEKGLFVSLS 1251
Cdd:PRK12269   620 PSdMVKIGDEVECMILGYDIQAGRVSLGLKqvtanPWEEIEARYPVG------------ARFTRRIVK-VTNAGAFIEME 686

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1252 SNVTAFVRISDLsdSFIKDWRSA---FEVDQLVTGKIVAVDPLLNHVQISLKaSMLDKdyvPPTTF-NDLKPRQVVTGKV 1327
Cdd:PRK12269   687 EGIDGFLHVDDL--SWVKRTRPAdheLEVGKEIECMVIECDPQARRIRLGVK-QLSDN---PWQVFaNAYGVGSTVEGEV 760

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1808214898 1328 RKVEDFGVFIVVdnSSNVSGLCHRSEIADQKVED----VRKlYEEGDAVKAIVLKIDQEKRRVNFGLK 1391
Cdd:PRK12269   761 SSVTDFGIFVRV--PGGVEGLVRKQHLVENRDGDpgeaLRK-YAVGDRVKAVIVDMNVKDRKVAFSVR 825
rpsA PRK13806
30S ribosomal protein S1; Provisional
 1114-1386 4.30e-12

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 70.52  E-value: 4.30e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1114 NRLDLTATSAAASKPTKIQDLSAGQILPGRVTKVTERHIMVQLSETVSAPVTLTEFSDDYSQANPTVHKKHDVVRVCILD 1193
Cdd:PRK13806   180 SRRALLEREQKEALEAFMETVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLG 259

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1194 VDAPNKKlvlslrpsKVLSSSLPVK----DPQIANIRQLKVNDVVRGFVKNVSEKGLFVSLSSNVTAFVRISDLSDS-FI 1268
Cdd:PRK13806   260 IERAKKG--------KGLRISLSIKqaggDPWDTVGDRLKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSWTrRV 331

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1269 KDWRSAFEVDQLVTGKIVAVDPLLNHVQISLKASMLDkdyvpP--TTFNDLKPRQVVTGKVRKVEDFGVFIVVdnSSNVS 1346
Cdd:PRK13806   332 NKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRDAEGD-----PwaDVAERFAPGTTVTGTVEKRAQFGLFVNL--APGVT 404

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|
gi 1808214898 1347 GLCHRSEIADQKVEDVRKLYEEGDAVKAIVLKIDQEKRRV 1386
Cdd:PRK13806   405 GLLPASVISRAGKPATYEKLKPGDSVTLVVEEIDTAKRKI 444
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 1321-1389 4.37e-12

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: 63.03  E-value: 4.37e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1808214898 1321 QVVTGKVRKVEDFGVFIvvdNSSNVSGLCHRSEIADQKVEDVRKLYEEGDAVKAIVLKIDQEKRRVNFG 1389
Cdd:cd05688      3 DVVEGTVKSITDFGAFV---DLGGVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 1323-1386 9.17e-12

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


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 62.01  E-value: 9.17e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1808214898 1323 VTGKVRKVEDFGVFivVDNSSNVSGLCHRSEIADQKVEDVRKLYEEGDAVKAIVLKIDQEKRRV 1386
Cdd:cd00164      1 VTGKVVSITKFGVF--VELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRI 62
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 1321-1388 1.09e-11

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: 61.87  E-value: 1.09e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1808214898 1321 QVVTGKVRKVEDFGVFivVDNSSNVSGLCHRSEIADQKVEDVRKLYEEGDAVKAIVLKIDQEKRRVNF 1388
Cdd:cd05685      2 MVLEGVVTNVTDFGAF--VDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISL 67
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
654-718 1.41e-11

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 61.47  E-value: 1.41e-11
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1808214898   654 GTIIKILRAGAIVQFYGDLKAFLPVSEMSEAYIQDPSEHFRIGQTVTVHTINVDAESDKMTVSCK 718
Cdd:smart00316    8 GTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
rpsA PRK13806
30S ribosomal protein S1; Provisional
 466-719 1.90e-11

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 68.60  E-value: 1.90e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  466 VEEAKVTKVeSTLGLFMDVgVKGVPGFAHISRLSDKKIDFLSEstgAYKLDSTHRARVVGYNPID--GLYIISLEPK-VL 542
Cdd:PRK13806   205 VVEGTVTRL-APFGAFVEL-APGVEGMVHISELSWSRVQKADE---AVSVGDTVRVKVLGIERAKkgKGLRISLSIKqAG 279

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  543 EQPFLRV-DDVKVGQVVKGKVekVLITAKGqgaVVVNLAEGISGLA--SE-AHIADVHlqHPEKKFKEGMAVTARVLSTD 618
Cdd:PRK13806   280 GDPWDTVgDRLKAGDKVTGKV--VRLAPFG---AFVEILPGIEGLVhvSEmSWTRRVN--KPEDVVAPGDAVAVKIKDID 352

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  619 SEKRQIRLTLKktlvNSEAPVWSKYED-VVLGKQAPGTIIKILRAGAIVQFYGDLKAFLPVSEMSEAYIQDPSEHFRIGQ 697
Cdd:PRK13806   353 PAKRRISLSLR----DAEGDPWADVAErFAPGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISRAGKPATYEKLKPGD 428

                          250       260
                   ....*....|....*....|..
gi 1808214898  698 TVTVHTINVDAESDKMTVSCKD 719
Cdd:PRK13806   429 SVTLVVEEIDTAKRKISLAPAG 450
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 461-658 2.19e-11

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 68.65  E-value: 2.19e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  461 PISAFVEEAKV-TKVEST------LGLFMDVGvKGVPGFAHISRLS-DKKIDFLSEStgaYKLDSTHRARVVGYNPIDGL 532
Cdd:PRK06299   363 PWEEFAEKYPVgDVVEGKvknitdFGAFVGLE-GGIDGLVHLSDISwDKKGEEAVEL---YKKGDEVEAVVLKVDVEKER 438

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  533 yiISLEPKVLEQ-PFLR-VDDVKVGQVVKGKVEKvlITAKGqgaVVVNLAEGISGLASEAHIADVHLQHPEKKFKEGMAV 610
Cdd:PRK06299   439 --ISLGIKQLEEdPFEEfAKKHKKGSIVTGTVTE--VKDKG---AFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEV 511

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*...
gi 1808214898  611 TARVLSTDSEKRQIRLTLKKTLVNSEAPVWSKYEDVVLGKQAPGTIIK 658
Cdd:PRK06299   512 EAKVINIDRKNRRISLSIKALDEAEEKEAIAEYNSASDSKTTLGDLLK 559
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 1311-1386 2.47e-11

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: 61.45  E-value: 2.47e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1808214898 1311 PTTFNDLKPRQVVTGKVRKVEDFGVFivVDNSSNVSGLCHRSEIADQKVEDVRKLYEEGDAVKAIVLKIDQEKRRV 1386
Cdd:cd04461      6 PTNFSDLKPGMVVHGYVRNITPYGVF--VEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRF 79
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 1322-1389 3.37e-11

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


Pssm-ID: 240195 [Multi-domain]  Cd Length: 69  Bit Score: 60.59  E-value: 3.37e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1808214898 1322 VVTGKVRKVEDFGVFIVVDNSsnVSGLCHRSEIA-DQKVEDVRKLYEEGDAVKAIVLKIDQEKRRVNFG 1389
Cdd:cd05690      3 VVSGKIKSITDFGIFVGLDGG--IDGLVHISDISwTQRVRHPSEIYKKGQEVEAVVLNIDVERERISLG 69
S1_Rrp5_repeat_hs2_sc2 cd05694
S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 269-346 5.30e-11

S1_Rrp5_repeat_hs2_sc2: 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 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240199 [Multi-domain]  Cd Length: 74  Bit Score: 59.96  E-value: 5.30e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1808214898  269 DLVVNSMVQASVVSVEDHGLVMDLGLAdgAIKGFMGAKEVGytvDHSKVEKGAVFLCMITGLSSNGKIVKLSADYQKV 346
Cdd:cd05694      1 DLVEGMVLSGCVSSVEDHGYILDIGIP--GTTGFLPKKDAG---NFSKLKVGQLLLCVVEKVKDDGRVVSLSADPSKV 73
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 1321-1392 7.73e-11

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 67.00  E-value: 7.73e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1808214898 1321 QVVTGKVRKVEDFGVFIVVdnSSNVSGLCHRSEIADQKVEDVRKLYEEGDAVKAIVLKIDqEKRRVNFGLKA 1392
Cdd:PRK11824   623 EIYEGKVVRIVDFGAFVEI--LPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEID-KRGRIRLSRKA 691
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 468-772 8.57e-11

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 66.05  E-value: 8.57e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  468 EAKVTKVESTlGLFMDVGVKGVPGFAHISRLSDKKIDFLSEstgAYKLDSTHRARVVGYNPIDGLYIISL----EPKVLE 543
Cdd:PRK06676    22 TGEVLKVEDK-QVFVNIEGYKVEGVIPISELSNDHIEDIND---VVKVGDELEVYVLKVEDGEGNLLLSKrrleAEKAWD 97

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  544 QpflRVDDVKVGQVVKGKVEKVLitakgQGAVVVNLaEGISGLASEAHIADVHLQHPEKkFKeGMAVTARVLSTDSEKRQ 623
Cdd:PRK06676    98 K---LEEKFEEGEVVEVKVTEVV-----KGGLVVDV-EGVRGFIPASLISTRFVEDFSD-FK-GKTLEVKIIELDPEKNR 166

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  624 IRLTlKKTLVNSEA-----PVWSKYE--DVVlgkqaPGTIIKILRAGAIVQFyGDLKAFLPVSEMSEAYIQDPSEHFRIG 696
Cdd:PRK06676   167 VILS-RRAVVEEERaakkeELLSSLKegDVV-----EGTVARLTDFGAFVDI-GGVDGLVHISELSHERVEKPSEVVSVG 239

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  697 QTVTVHTINVDAESDKMTVSCKDptTRGAAMTEAYDLLKVGSVVKGSVsekseKTIT-----VELEgSGIKGIIRIGQLT 771
Cdd:PRK06676   240 QEVEVKVLSIDWETERISLSLKD--TLPGPWEGVEEKLPEGDVIEGTV-----KRLTdfgafVEVL-PGVEGLVHISQIS 311


                   .
gi 1808214898  772 D 772
Cdd:PRK06676   312 H 312
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 1321-1384 1.01e-10

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


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 60.96  E-value: 1.01e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1808214898 1321 QVVTGKVRKVEDFGVFIVVDNssNVSGLCHRSEIADQKVEDVRKLYEEGDAVKAIVLKIDQEKR 1384
Cdd:COG1098      7 DIVEGKVTGITPFGAFVELPE--GTTGLVHISEIADGYVKDINDYLKVGDEVKVKVLSIDEDGK 68
PRK08059 PRK08059
general stress protein 13; Validated
 1321-1392 1.20e-10

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 60.83  E-value: 1.20e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1808214898 1321 QVVTGKVRKVEDFGVFIVVDNSSNvsGLCHRSEIADQKVEDVRKLYEEGDAVKAIVLKIDQEKRRVNFGLKA 1392
Cdd:PRK08059     9 SVVTGKVTGIQPYGAFVALDEETQ--GLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRA 78
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 1321-1392 3.80e-10

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: 57.67  E-value: 3.80e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1808214898 1321 QVVTGKVRKVEDFGvfIVVDNSSNVSGLCHRSEIADQKVEDVRKLYEEGDAVKAIVLKIDQEKRRVNFGLKA 1392
Cdd:cd05691      2 SIVTGKVTEVDAKG--ATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIKA 71
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 1322-1384 3.94e-10

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: 57.30  E-value: 3.94e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1808214898 1322 VVTGKVRKVEDFGVFIVVDNSsnVSGLCHRSEIADQKVEDVRKLYEEGDAVKAIVLKIDQEKR 1384
Cdd:cd05692      3 VVEGTVTRLKPFGAFVELGGG--ISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARGR 63
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 540-1119 5.86e-10

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 64.03  E-value: 5.86e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  540 KVLEQPFLRvDDVKVGQVVKGKVekVLITakgQGAVVVNLaegisGLASEAHIA--DVHLQHPEKKFKEGMAVTARVLST 617
Cdd:PRK06299    17 ELFEESLKE-SETREGSIVKGTV--VAID---KDYVLVDV-----GLKSEGRIPleEFKNEQGELEVKVGDEVEVYVERI 85

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  618 DSEKRQIRLTLKKTLVnSEApvWSKYEDVvLGKQAP--GTIIKILRAGAIVQfYGDLKAFLPVSEMSEAYIQDPSEHfrI 695
Cdd:PRK06299    86 EDGFGETVLSREKAKR-LEA--WDKLEKA-FENGEIveGVINGKVKGGFTVD-LNGVEAFLPGSQVDVRPVRDTDPL--E 158

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  696 GQTVTVHTINVDAESDKMTVSCKD--PTTRGAAMTEAYDLLKVGSVVKGSVsekseKTIT-----VELegSGIKGIIRIg 768
Cdd:PRK06299   159 GKELEFKVIKLDKKRNNIVVSRRAvlEEERAEEREELLENLEEGQVVEGVV-----KNITdygafVDL--GGVDGLLHI- 230

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  769 qlTDGSEK--KDQSSMkrIRVGQTLEdLVVLsKSDKKplltlTNKPTL-LQAAKAG---SLVAKYEdlrEGQPVNGFVRH 842
Cdd:PRK06299   231 --TDISWKrvNHPSEV--VNVGDEVK-VKVL-KFDKE-----KKRVSLgLKQLGEDpweAIEKKYP---VGSKVKGKVTN 296

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  843 IDGQRVFVEFAGGLVGLLLKSQM--------PEEMANTAefglradQSISAKVLATDNQQRRFLVTMKDDQEvtsktata 914
Cdd:PRK06299   297 ITDYGAFVELEEGIEGLVHVSEMswtkknkhPSKVVSVG-------QEVEVMVLEIDEEKRRISLGLKQCKE-------- 361

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  915 assksaakdetllNPVDEqltsISDlTF--GKLTTARITHVKDTQLNVHLADNLQGRVDVSEIfdSWEniKDRKHPLRQF 992
Cdd:PRK06299   362 -------------NPWEE----FAE-KYpvGDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDI--SWD--KKGEEAVELY 419

                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  993 KAKQNVPVRVIGIhDARNHRflpIShrtgktpvfeLTAKAvnLTKD--SDLLSmdKLTIGSSHIAFVNNISDNCVWVNLS 1070
Cdd:PRK06299   420 KKGDEVEAVVLKV-DVEKER---IS----------LGIKQ--LEEDpfEEFAK--KHKKGSIVTGTVTEVKDKGAFVELE 481

                          570       580       590       600
                   ....*....|....*....|....*....|....*....|....*....
gi 1808214898 1071 PNVRGRIDLMDLSDDVSLLNNvqGNFPVGSAIKVRVKNVDASNNRLDLT 1119
Cdd:PRK06299   482 DGVEGLIRASELSRDRVEDAT--EVLKVGDEVEAKVINIDRKNRRISLS 528
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 1321-1390 7.25e-10

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: 56.91  E-value: 7.25e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1321 QVVTGKVRKVEDFGVFIVVDNssNVSGLCHRSEIADQKVEDVRKLYEEGDAVKAIVLKIDQEKRRVNFGL 1390
Cdd:pfam00575    5 DVVEGEVTRVTKGGAFVDLGN--GVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 1234-1298 1.24e-09

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: 55.85  E-value: 1.24e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1808214898 1234 VRGFVKNVSEKGLFVSLSSNVTAFVRISDLSDSFIKDWRSAFEVDQLVTGKIVAVDPLLNHVQIS 1298
Cdd:cd00164      1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 479-630 1.26e-09

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 62.75  E-value: 1.26e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  479 GLFMDVGvkGVPGFAHISRLSDKKIDFLSESTGAYK------LD-STHRARVvgynpidglyiiSLEPKVLE----QPFL 547
Cdd:PRK07899   223 GAFVDLG--GVDGLVHVSELSWKHIDHPSEVVEVGQevtvevLDvDMDRERV------------SLSLKATQedpwQQFA 288

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  548 RvdDVKVGQVVKGKVEKVLitakgQGAVVVNLAEGISGLASEAHIADVHLQHPEKKFKEGMAVTARVLSTDSEKRQIRLT 627
Cdd:PRK07899   289 R--THAIGQIVPGKVTKLV-----PFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLERRRISLS 361


                   ...
gi 1808214898  628 LKK 630
Cdd:PRK07899   362 LKQ 364
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1137-1206 6.04e-09

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 54.15  E-value: 6.04e-09
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  1137 GQILPGRVTKVTERHIMVQLSETVSAPVTLTEFSDDYSQANPTVHKKHDVVRVCILDVDAPNKKLVLSLR 1206
Cdd:smart00316    3 GDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 1231-1301 2.31e-08

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: 52.66  E-value: 2.31e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1808214898 1231 NDVVRGFVKNVSEKGLFVSLSSNVTAFVRISDLSDSFIKDWRSAFEVDQLVTGKIVAVDPLLNHVQISLKA 1301
Cdd:cd05691      1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIKA 71
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 466-638 2.41e-08

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 58.35  E-value: 2.41e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  466 VEEAKVTKVEStLGLFMDVGvkGVPGFAHISRLSDKKIDFLSEstgAYKLDSTHRARVVGYNPIDGLyiISLEPK-VLEQ 544
Cdd:PRK06676   195 VVEGTVARLTD-FGAFVDIG--GVDGLVHISELSHERVEKPSE---VVSVGQEVEVKVLSIDWETER--ISLSLKdTLPG 266

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  545 PFLRV-DDVKVGQVVKGKVEKvLITAkgqGAVVvNLAEGISGLASEAHIADVHLQHPEKKFKEGMAVTARVLSTDSEKRQ 623
Cdd:PRK06676   267 PWEGVeEKLPEGDVIEGTVKR-LTDF---GAFV-EVLPGVEGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKR 341

                          170
                   ....*....|....*
gi 1808214898  624 IRLTLKKTLVNSEAP 638
Cdd:PRK06676   342 ISLSIKALEEAPAEE 356
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 558-627 5.80e-08

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


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 51.23  E-value: 5.80e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  558 VKGKVEKvlITAKGqgaVVVNLAEGISGLASEAHIADVHLQHPEKKFKEGMAVTARVLSTDSEKRQIRLT 627
Cdd:cd00164      1 VTGKVVS--ITKFG---VFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 1322-1391 6.80e-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: 51.43  E-value: 6.80e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1322 VVTGKVRKVEDFGVFIVVDNSSNVSGLCHRSEIADQKVEDVRKLYEEGDAVKAIVLKIDQEKRRVNFGLK 1391
Cdd:cd04452      6 LVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKK 75
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 1321-1386 7.20e-08

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: 51.08  E-value: 7.20e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1808214898 1321 QVVTGKVRKVEDFGVFIVVdnSSNVSGLCHRSEIADQKVEDVRKLYEEGDAVKAIVLKIDQEKRRV 1386
Cdd:cd05697      2 QVVKGTIRKLRPSGIFVKL--SDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRL 65
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1509-1709 8.57e-08

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 55.51  E-value: 8.57e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1509 RTGDLDIAgpqsVADFERLLLGQPNNSALWMQYMAFQIGLNEVQKAKDIAERALKtinirEEEEKMNIWTALLNLEIEQG 1588
Cdd:COG2956     88 KAGLLDRA----EELLEKLLELDPDDAEALRLLAEIYEQEGDWEKAIEVLERLLK-----LGPENAHAYCELAELYLEQG 158

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1589 NEEKVDEVFKRACQYcDPE--EMHNKLITIYTSTGRHEKADSLFQTMTKnksITPNPSFWMNYATFLMTTLNDPSRARQL 1666
Cdd:COG2956    159 DYDEAIEALEKALKL-DPDcaRALLLLAELYLEQGDYEEAIAALERALE---QDPDYLPALPRLAELYEKLGDPEEALEL 234

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|...
gi 1808214898 1667 LPRATQSVPahlhrQLTSKFAALEFQSPNGDAERGRTIFEGLL 1709
Cdd:COG2956    235 LRKALELDP-----SDDLLLALADLLERKEGLEAALALLERQL 272
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 1321-1384 8.59e-08

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


Pssm-ID: 239918 [Multi-domain]  Cd Length: 68  Bit Score: 50.62  E-value: 8.59e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1808214898 1321 QVVTGKVRKVEDFGVFivVDNSSNVSGLCHRSEIADQKVEDVRKLYEEGDAVKAIVLKIDQEKR 1384
Cdd:cd04472      2 KIYEGKVVKIKDFGAF--VEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDDRGR 63
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 549-628 1.27e-07

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: 50.66  E-value: 1.27e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  549 VDDVKVGQVVKGKVEKvlITAKGqgaVVVNLAEGISGLASEAHIADVHLQHPEKKFKEGMAVTARVLSTDSEKRQIRLTL 628
Cdd:cd04461      9 FSDLKPGMVVHGYVRN--ITPYG---VFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL 83
Tex COG2183
Transcriptional accessory protein Tex/SPT6 [Transcription];
1313-1386 1.37e-07

Transcriptional accessory protein Tex/SPT6 [Transcription];


Pssm-ID: 441786 [Multi-domain]  Cd Length: 719  Bit Score: 56.57  E-value: 1.37e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1808214898 1313 TFNDLKPRQVVTGKVRKVEDFGVFivVDnssnV----SGLCHRSEIADQKVEDVRKLYEEGDAVKAIVLKIDQEKRRV 1386
Cdd:COG2183    635 KIEDLKPGMILEGTVTNVTDFGAF--VD----IgvhqDGLVHISQLSDRFVKDPREVVKVGDIVKVKVLEVDLKRKRI 706
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 654-716 1.52e-07

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: 50.07  E-value: 1.52e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1808214898  654 GTIIKILRAGAIVQFYGDLKAFLPVSEMSEAYIQDPSEHFRIGQTVTVHTINVDAESDKMTVS 716
Cdd:cd00164      3 GKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 583-905 2.44e-07

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 55.87  E-value: 2.44e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  583 ISGLASEAHIADV---HLQHPEKKFKEGMAVTARVLSTDSEKRQIRLTLKktlvNSEAPVWSKYE------DVVLGKqap 653
Cdd:PRK12269   513 LGGFDGLLHVNDMswgHVARPREFVKKGQTIELKVIRLDQAEKRINLSLK----HFQPDPWLEFEnkfgvnDVVKGR--- 585

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  654 gtIIKILRAGAIVQFYGDLKAFLPVSEMSEAY-IQDPSEHFRIGQTVTVHTINVDAESDKMTVSCKDPTTRGAAMTEAYd 732
Cdd:PRK12269   586 --VTKIADFGAFIELAEGIEGLAHISEFSWVKkTSKPSDMVKIGDEVECMILGYDIQAGRVSLGLKQVTANPWEEIEAR- 662

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  733 lLKVGSVVKGSVSEKSEKTITVELEgSGIKGIIRIGQLTdgSEKKDQSSMKRIRVGQTLEDLVVLSKSDKKPLL----TL 808
Cdd:PRK12269   663 -YPVGARFTRRIVKVTNAGAFIEME-EGIDGFLHVDDLS--WVKRTRPADHELEVGKEIECMVIECDPQARRIRlgvkQL 738

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  809 TNKPTLLQAAKAGSlvakyedlreGQPVNGFVRHIDGQRVFVEFAGGLVGLLLKSQMPEEMANTAEFGLR---ADQSISA 885
Cdd:PRK12269   739 SDNPWQVFANAYGV----------GSTVEGEVSSVTDFGIFVRVPGGVEGLVRKQHLVENRDGDPGEALRkyaVGDRVKA 808

                          330       340
                   ....*....|....*....|
gi 1808214898  886 KVLATDNQQRRFLVTMKDDQ 905
Cdd:PRK12269   809 VIVDMNVKDRKVAFSVRDYQ 828
rpsA PRK13806
30S ribosomal protein S1; Provisional
 550-903 2.84e-07

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 55.12  E-value: 2.84e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  550 DDVKVGQVVKGKVekvliTAKGQGAVVVNLAEGISGLASEAHIADVHLQHPekkFKEGMAVTARVLS-TDSEkrqIRLTL 628
Cdd:PRK13806    30 TELRVGDKITGTV-----IAITEDSVFVDTGSKVDGVVDRAELLDADGELT---VAVGDEVELYVVSvNGQE---IRLSK 98

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  629 KKTLVNSEAPVWSKYEDvvlGKQAPGTIIKILRAGAIVQFYGDlKAFLPVSEMSEAYIQDPSEHfrIGQTVTVHTINVDA 708
Cdd:PRK13806    99 ALSGQGGAAMLEEAYEN---GVPVEGKVTGTCKGGFNVEVLGR-RAFCPVSQIDLRYVEDPESY--VGQTFQFLITRVEE 172

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  709 ESDKMTVSCKD--PTTRGAAMTEAYDLLKVGSVVKGSVSEKSEKTITVELEgSGIKGIIRIGQLtdgSEKKDQSSMKRIR 786
Cdd:PRK13806   173 NGRNIVVSRRAllEREQKEALEAFMETVKEGDVVEGTVTRLAPFGAFVELA-PGVEGMVHISEL---SWSRVQKADEAVS 248

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  787 VGQTLEDLVVLSKSDKK---PLLTLTNKptllQA-AKAGSLVAkyEDLREGQPVNGFVRHIDGQRVFVEFAGGLVGLLLK 862
Cdd:PRK13806   249 VGDTVRVKVLGIERAKKgkgLRISLSIK----QAgGDPWDTVG--DRLKAGDKVTGKVVRLAPFGAFVEILPGIEGLVHV 322

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|..
gi 1808214898  863 SQMP-EEMANTAEFGLRADQSISAKVLATDNQQRRFLVTMKD 903
Cdd:PRK13806   323 SEMSwTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRD 364
PRK05807 PRK05807
RNA-binding protein S1;
1317-1397 4.33e-07

RNA-binding protein S1;


Pssm-ID: 235614 [Multi-domain]  Cd Length: 136  Bit Score: 50.90  E-value: 4.33e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1317 LKPRQVVTGKVRKVEDFGVFIVVDNSSnvsGLCHRSEIADQKVEDVRKLYEEGDAVKAIVLKIDqEKRRVNFGLKASYFQ 1396
Cdd:PRK05807     3 LKAGSILEGTVVNITNFGAFVEVEGKT---GLVHISEVADTYVKDIREHLKEQDKVKVKVISID-DNGKISLSIKQAMKQ 78


                   .
gi 1808214898 1397 K 1397
Cdd:PRK05807    79 K 79
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1236-1300 5.24e-07

S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240203 [Multi-domain]  Cd Length: 70  Bit Score: 48.38  E-value: 5.24e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1808214898 1236 GFVKNVSEKGLFVSLSSNVTAFVRISDLSDSFIKDWRSAFEVDQLVTGKIVAVDPLLNHVQISLK 1300
Cdd:cd05698      6 GTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 654-717 8.23e-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: 48.05  E-value: 8.23e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1808214898  654 GTIIKILRAGAIVQFYGDLKAFLPVSEMSEAYIQDPSEHFRIGQTVTVHTINVDAESDKMTVSC 717
Cdd:pfam00575    9 GEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
S1_Rrp5_repeat_hs14 cd05705
S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1228-1298 9.88e-07

S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240210 [Multi-domain]  Cd Length: 74  Bit Score: 47.78  E-value: 9.88e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1808214898 1228 LKVNDVVRGFVKNVSEKGLFVSLSSNVTAFVRISDLSDSFIKDwRSAFEV----DQLVTGKIVAVDPLLNHVQIS 1298
Cdd:cd05705      1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSD-PSLYNKylpeGKLLTAKVLSVNSEKNLVELS 74
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 1323-1391 1.07e-06

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 52.13  E-value: 1.07e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1808214898 1323 VTGKVRKVEDFGVFIVVDNSSNVSGLCHRSEIADQKVEDVRKLYEEGDAVKAIVLKIDQEKRRVNFGLK 1391
Cdd:PRK03987    12 VVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLK 80
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1049-1119 1.25e-06

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 47.60  E-value: 1.25e-06
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1808214898  1049 IGSSHIAFVNNISDNCVWVNLSPNVRGRIDLMDLSDDvsLLNNVQGNFPVGSAIKVRVKNVDASNNRLDLT 1119
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDK--RVKDPEEVLKVGDEVKVKVLSVDEEKGRIILS 70
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1509-1739 1.49e-06

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 51.65  E-value: 1.49e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1509 RTGDLDIAgpqsVADFERLLLGQPNNSALWMQYMAFQIGLNEVQKAKDIAERALKtinirEEEEKMNIWTALLNLEIEQG 1588
Cdd:COG2956     20 LNGQPDKA----IDLLEEALELDPETVEAHLALGNLYRRRGEYDRAIRIHQKLLE-----RDPDRAEALLELAQDYLKAG 90

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1589 NEEKVDEVFKRACQYcDP--EEMHNKLITIYTSTGRHEKADSLFQTMTKNKSitPNPSFWMNYATFLMtTLNDPSRARQL 1666
Cdd:COG2956     91 LLDRAEELLEKLLEL-DPddAEALRLLAEIYEQEGDWEKAIEVLERLLKLGP--ENAHAYCELAELYL-EQGDYDEAIEA 166

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1808214898 1667 LPRATQ----SVPAHLHRqltskfAALEFQspNGDAERGRTIFEGLLSTWPKRWDLWDMFVDLEKARGEMDNVRQLY 1739
Cdd:COG2956    167 LEKALKldpdCARALLLL------AELYLE--QGDYEEAIAALERALEQDPDYLPALPRLAELYEKLGDPEEALELL 235
S1_RPS1_repeat_ec2_hs2 cd04465
S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 654-716 1.78e-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: 47.07  E-value: 1.78e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1808214898  654 GTIIKILRAGAIVQFYGdLKAFLPVSEMSEAYIQDPSEHfrIGQTVTVHTINVDAESDKMTVS 716
Cdd:cd04465      6 GKVTEKVKGGLIVDIEG-VRAFLPASQVDLRPVEDLDEY--VGKELKFKIIEIDRERNNIVLS 65
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
831-902 1.89e-06

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 47.21  E-value: 1.89e-06
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1808214898   831 REGQPVNGFVRHIDGQRVFVEFAGGLVGLLLKSQMPEEMANTAEFGLRADQSISAKVLATDNQQRRFLVTMK 902
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1_DHX8_helicase cd05684
S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH ...
 1321-1383 2.65e-06

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: 46.85  E-value: 2.65e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1808214898 1321 QVVTGKVRKVEDFGVFIVVD-NSSNVSGLCHRSEI-ADQKVEDVRKLYEEGDAVKAIVLKIDQEK 1383
Cdd:cd05684      2 KIYKGKVTSIMDFGCFVQLEgLKGRKEGLVHISQLsFEGRVANPSDVVKRGQKVKVKVISIQNGK 66
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 1135-1392 3.52e-06

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 50.95  E-value: 3.52e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1135 SAGQILPGRVTKVTERHIMVQLSETVSAPVTLTEFSDDYSQANPTVHKKHDVVRVCILDVDAPNKKLVLSLRPSKVLSSs 1214
Cdd:PRK07400    30 KPGDIVNGTVFSLEPRGALIDIGAKTAAFMPIQEMSINRVEGPEEVLQPNETREFFILSDENEDGQLTLSIRRIEYMRA- 108

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1215 lpvkdpqIANIRQLKVND-VVRGFVKNVSEKGlfvslssnvtAFVRISDLSdSFIK----DWRSAFE--VDQLVTGKIVA 1287
Cdd:PRK07400   109 -------WERVRQLQKEDaTVRSEVFATNRGG----------ALVRIEGLR-GFIPgshiSTRKPKEelVGEELPLKFLE 170

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1288 VDPLLNHVQISLKASMLDKdyvpptTFNDLKPRQVVTGKVRKVEDFGVFIVVdnsSNVSGLCHRSEIADQKVEDVRKLYE 1367
Cdd:PRK07400   171 VDEERNRLVLSHRRALVER------KMNRLEVGEVVVGTVRGIKPYGAFIDI---GGVSGLLHISEISHEHIETPHSVFN 241

                          250       260
                   ....*....|....*....|....*
gi 1808214898 1368 EGDAVKAIVLKIDQEKRRVNFGLKA 1392
Cdd:PRK07400   242 VNDEMKVMIIDLDAERGRISLSTKQ 266
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 553-629 4.04e-06

S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240213 [Multi-domain]  Cd Length: 77  Bit Score: 46.17  E-value: 4.04e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1808214898  553 KVGQVVKGKVEKVliTAKGqgaVVVNL-AEGISGLASEAHIADVHLQHPEKKFKEGMAVTARVLSTDSEKRQIRLTLK 629
Cdd:cd05708      1 KVGQKIDGTVRRV--EDYG---VFIDIdGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLK 73
S1_Rrp5_repeat_hs13 cd05704
S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1134-1206 4.54e-06

S1_Rrp5_repeat_hs13: 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 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240209 [Multi-domain]  Cd Length: 72  Bit Score: 45.81  E-value: 4.54e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1808214898 1134 LSAGQILPGRVTKVT-ERHIMVQLSETVSAPVTLTEFSDDYSQANPTVHKKHDVVRVCILdvDAPNKKLVLSLR 1206
Cdd:cd05704      1 LEEGAVTLGMVTKVIpHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCIL--SKKDGKYQLSLR 72
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 555-626 6.58e-06

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: 45.56  E-value: 6.58e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1808214898  555 GQVVKGKVEKvlITAKGqgaVVVNLAEGISGLAseaHIADV----HLQHPEKKFKEGMAVTARVLSTDSEKRQIRL 626
Cdd:cd05690      1 GTVVSGKIKS--ITDFG---IFVGLDGGIDGLV---HISDIswtqRVRHPSEIYKKGQEVEAVVLNIDVERERISL 68
PRK05807 PRK05807
RNA-binding protein S1;
1228-1320 1.03e-05

RNA-binding protein S1;


Pssm-ID: 235614 [Multi-domain]  Cd Length: 136  Bit Score: 47.05  E-value: 1.03e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1228 LKVNDVVRGFVKNVSEKGLFVSLSSNvTAFVRISDLSDSFIKDWRSAFEVDQLVTGKIVAVDPlLNHVQISLKASMLDKD 1307
Cdd:PRK05807     3 LKAGSILEGTVVNITNFGAFVEVEGK-TGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDD-NGKISLSIKQAMKQKK 80

                           90
                   ....*....|...
gi 1808214898 1308 YVPPTTFNDLKPR 1320
Cdd:PRK05807    81 SVKPAEIDWQKEK 93
S1_RPS1_repeat_ec4 cd05689
S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 1323-1389 1.07e-05

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: 44.88  E-value: 1.07e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1808214898 1323 VTGKVRKVEDFGVFIVVDnsSNVSGLCHRSEIaDQKVEDVR--KLYEEGDAVKAIVLKIDQEKRRVNFG 1389
Cdd:cd05689      7 LFGKVTNLTDYGCFVELE--EGVEGLVHVSEM-DWTNKNIHpsKVVSLGDEVEVMVLDIDEERRRISLG 72
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 1136-1205 1.23e-05

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: 44.59  E-value: 1.23e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1136 AGQILPGRVTKVTERHIMVQLSETVSAPVTLTEFSDDYSQANPTVHKKHDVVRVCILDVDAPNKKLVLSL 1205
Cdd:pfam00575    3 KGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
PRK08059 PRK08059
general stress protein 13; Validated
 1227-1301 1.47e-05

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 46.19  E-value: 1.47e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1808214898 1227 QLKVNDVVRGFVKNVSEKGLFVSLSSNVTAFVRISDLSDSFIKDWRSAFEVDQLVTGKIVAVDPLLNHVQISLKA 1301
Cdd:PRK08059     4 QYEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRA 78
S1_Rrp5_repeat_hs12_sc9 cd05703
S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 597-630 1.58e-05

S1_Rrp5_repeat_hs12_sc9: 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 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240208 [Multi-domain]  Cd Length: 73  Bit Score: 44.49  E-value: 1.58e-05
                           10        20        30
                   ....*....|....*....|....*....|....
gi 1808214898  597 LQHPEKKFKEGMAVTARVLSTDSEKRQIRLTLKK 630
Cdd:cd05703     40 LEHPEKKFPIGQALKAKVVGVDKEHKLLRLSARG 73
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 555-629 1.68e-05

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: 44.57  E-value: 1.68e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1808214898  555 GQVVKGKVEKVliTAKGqgaVVVNLAEGISGLASEAHIADVHLQHPEKKFKEGMAVTARVLSTDSEKRQIRLTLK 629
Cdd:cd05691      1 GSIVTGKVTEV--DAKG---ATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIK 70
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 654-719 1.70e-05

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 48.28  E-value: 1.70e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1808214898  654 GTIIKILRAGAIVQF--YGDLKAFLPVSEMSEAYIQDPSEHFRIGQTVTVHTINVDAESDKMTVSCKD 719
Cdd:PRK03987    14 GTVKEVKDFGAFVTLdeYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLKR 81
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 1182-1391 2.23e-05

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 49.33  E-value: 2.23e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1182 KKHDVVRVCILDVDAPNKKLVLSLRPSKvlssslpvKDPQIANIRQLKVNDVVRGFVKNVSEKGLFVSLSSNVTAFVRIS 1261
Cdd:PRK12269   538 KKGQTIELKVIRLDQAEKRINLSLKHFQ--------PDPWLEFENKFGVNDVVKGRVTKIADFGAFIELAEGIEGLAHIS 609

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1262 DLsdSFIKDWRSAFEVDQL---VTGKIVAVDPLLNHVQISLKAsmldkdyVPPTTFNDLKPRQVV----TGKVRKVEDFG 1334
Cdd:PRK12269   610 EF--SWVKKTSKPSDMVKIgdeVECMILGYDIQAGRVSLGLKQ-------VTANPWEEIEARYPVgarfTRRIVKVTNAG 680

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 1808214898 1335 VFIVVDNSsnVSGLCHRSEIA-DQKVEDVRKLYEEGDAVKAIVLKIDQEKRRVNFGLK 1391
Cdd:PRK12269   681 AFIEMEEG--IDGFLHVDDLSwVKRTRPADHELEVGKEIECMVIECDPQARRIRLGVK 736
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 1229-1300 2.32e-05

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


Pssm-ID: 239899 [Multi-domain]  Cd Length: 76  Bit Score: 44.11  E-value: 2.32e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1808214898 1229 KVNDVVRGFVKNVSEKGLFVSLSS--NVTAFVRISDLSDSFIKDWRSAFEVDQLVTGKIVAVDPLLNHVQISLK 1300
Cdd:cd04452      2 EEGELVVVTVKSIADMGAYVSLLEygNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKK 75
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 644-719 2.85e-05

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: 43.73  E-value: 2.85e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1808214898  644 EDVVLGkqapgTIIKILRAGAIVQF--YGDLKAFLPVSEMSEAYIQDPSEHFRIGQTVTVHTINVDAESDKMTVSCKD 719
Cdd:cd04452      4 GELVVV-----TVKSIADMGAYVSLleYGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKKR 76
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 552-628 2.94e-05

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: 43.82  E-value: 2.94e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1808214898  552 VKVGQVVKGKVekvliTAKGQGAVVVNLAEGISGLASEAHIADVHLQHPEKKFKEGMAVTARVLSTDSEKRQIRLTL 628
Cdd:pfam00575    1 PEKGDVVEGEV-----TRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
735-811 3.21e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 43.75  E-value: 3.21e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1808214898   735 KVGSVVKGSVSEKSEKTITVELeGSGIKGIIRIGQLTDGSEKKDQssmKRIRVGQTLEdLVVLSKSDKKPLLTLTNK 811
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDL-GNGVEGLIPISELSDKRVKDPE---EVLKVGDEVK-VKVLSVDEEKGRIILSLK 72
S1_RecJ_like cd04473
S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of ...
 1313-1391 3.61e-05

S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.


Pssm-ID: 239919 [Multi-domain]  Cd Length: 77  Bit Score: 43.75  E-value: 3.61e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1808214898 1313 TFNDLKPRQVVTGKVRKVEDFGVFivVDNSSNVSGLCHRSeiadqkveDVRKLYEEGDAVkaIVlKIDQEKRRVNFGLK 1391
Cdd:cd04473     10 TMEDLEVGKLYKGKVNGVAKYGVF--VDLNDHVRGLIHRS--------NLLRDYEVGDEV--IV-QVTDIPENGNIDLI 75
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 649-772 5.66e-05

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 47.73  E-value: 5.66e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  649 GKQAPGTIIKILRAGAIVQFyGDLKAFLPVSEMSEAYIQDPSEHFRIGQTVTVHTINVDAESDKMTVSCK----DPtTRG 724
Cdd:PRK07899   209 GQVRKGVVSSIVNFGAFVDL-GGVDGLVHVSELSWKHIDHPSEVVEVGQEVTVEVLDVDMDRERVSLSLKatqeDP-WQQ 286

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 1808214898  725 AAMTEAydllkVGSVVKGSVSEKSEKTITVELEgSGIKGIIRIGQLTD 772
Cdd:PRK07899   287 FARTHA-----IGQIVPGKVTKLVPFGAFVRVE-EGIEGLVHISELAE 328
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 654-709 5.91e-05

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: 42.66  E-value: 5.91e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1808214898  654 GTIIKILRAGAIVQFYGDLKAFLPVSEMSEAYIQDPSEHFRIGQTVTVHTINVDAE 709
Cdd:cd05692      6 GTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDAR 61
NrfG COG4235
Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, ...
 1519-1633 6.23e-05

Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443378 [Multi-domain]  Cd Length: 131  Bit Score: 44.61  E-value: 6.23e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1519 QSVADFERLLLGQPNNSALWMQ----YMAfqigLNEVQKAKDIAERALktiniREEEEKMNIWTALLNLEIEQGNEEKVD 1594
Cdd:COG4235      1 EAIARLRQALAANPNDAEGWLLlgraYLR----LGRYDEALAAYEKAL-----RLDPDNADALLDLAEALLAAGDTEEAE 71

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 1808214898 1595 EVFKRACQYcDPEEM--HNKLITIYTSTGRHEKADSLFQTM 1633
Cdd:COG4235     72 ELLERALAL-DPDNPeaLYLLGLAAFQQGDYAEAIAAWQKL 111
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 654-718 6.31e-05

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: 42.64  E-value: 6.31e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1808214898  654 GTIIKILRAGAIVQFYGDLKAFLPVSEMSEAYIQDPSEHFRIGQTVTVHTINVDAESDKMTVSCK 718
Cdd:cd05691      6 GKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIK 70
S1_Rrp5_repeat_sc11 cd05707
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1056-1119 7.46e-05

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


Pssm-ID: 240212 [Multi-domain]  Cd Length: 68  Bit Score: 42.28  E-value: 7.46e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1808214898 1056 FVNNISDNCVWVNLSPNVRGRIDLMDLSDdvSLLNNVQGNFPVGSAIKVRVKNVDASNNRLDLT 1119
Cdd:cd05707      7 FVKNIANNGVFVTLGRGVDARVRVSELSD--SYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 1228-1299 8.24e-05

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: 42.27  E-value: 8.24e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1808214898 1228 LKVNDVVRGFVKNVSEKGLFVSLSSNVTAFVRISDLSDSFIKDWRSAFEVDQLVTGKIVAVDPLLNHVQISL 1299
Cdd:pfam00575    1 PEKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
PRK08582 PRK08582
RNA-binding protein S1;
1323-1382 1.10e-04

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 43.87  E-value: 1.10e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1323 VTGKVRKVEDFGVFivVDNSSNVSGLCHRSEIADQKVEDVRKLYEEGDAVKAIVLKIDQE 1382
Cdd:PRK08582     9 LQGKVTGITNFGAF--VELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDD 66
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
468-537 2.24e-04

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 41.05  E-value: 2.24e-04
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898   468 EAKVTKVESTlGLFMDVGvKGVPGFAHISRLSDKKIDFLSEStgaYKLDSTHRARVVGYNPIDGLYIISL 537
Cdd:smart00316    7 EGTVTEITPG-GAFVDLG-NGVEGLIPISELSDKRVKDPEEV---LKVGDEVKVKVLSVDEEKGRIILSL 71
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 643-902 2.66e-04

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 45.86  E-value: 2.66e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  643 YEDVVLGKQAPGTIIKILRAGAIVQFyGDLKAFLPVSEMSEAYIQDPSEHFRIGQTVTVHTINVDAESDKMTVSCK---- 718
Cdd:PRK12269   488 FNSVHIEDSVSGVVKSFTSFGAFIDL-GGFDGLLHVNDMSWGHVARPREFVKKGQTIELKVIRLDQAEKRINLSLKhfqp 566

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  719 DPttrgaaMTEAYDLLKVGSVVKGSVSEKSEKTITVELeGSGIKGIIRIGQLTDGSEKKDQSSMkrIRVGQTLEdLVVLS 798
Cdd:PRK12269   567 DP------WLEFENKFGVNDVVKGRVTKIADFGAFIEL-AEGIEGLAHISEFSWVKKTSKPSDM--VKIGDEVE-CMILG 636

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  799 KSDKKPLLTLTNKPTLLQAakagslvakYEDLREGQPVNG-FVRHI---DGQRVFVEFAGGLVGLLLKSQMP-EEMANTA 873
Cdd:PRK12269   637 YDIQAGRVSLGLKQVTANP---------WEEIEARYPVGArFTRRIvkvTNAGAFIEMEEGIDGFLHVDDLSwVKRTRPA 707

                          250       260
                   ....*....|....*....|....*....
gi 1808214898  874 EFGLRADQSISAKVLATDNQQRRFLVTMK 902
Cdd:PRK12269   708 DHELEVGKEIECMVIECDPQARRIRLGVK 736
S1_Rrp5_repeat_hs12_sc9 cd05703
S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 1232-1299 2.69e-04

S1_Rrp5_repeat_hs12_sc9: 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 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240208 [Multi-domain]  Cd Length: 73  Bit Score: 41.02  E-value: 2.69e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1232 DVVRGFVKNVSEKGLFVSLSSNVTAFVRISDLSD--SFIKDWRSAFEVDQLVTGKIVAVDPLLNHVQISL 1299
Cdd:cd05703      2 QEVTGFVNNVSKEFVWLTISPDVKGRIPLLDLSDdvSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSA 71
PRK08059 PRK08059
general stress protein 13; Validated
 641-718 2.72e-04

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 42.34  E-value: 2.72e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  641 SKYE--DVVLGKqapgtIIKILRAGAIVQFYGDLKAFLPVSEMSEAYIQDPSEHFRIGQTVTVHTINVDAESDKMTVSCK 718
Cdd:PRK08059     3 SQYEvgSVVTGK-----VTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIR 77
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 1230-1300 2.86e-04

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 44.81  E-value: 2.86e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1808214898 1230 VNDVVRGFVKNVSEKGLFVSLS--SNVTAFVRISDLSDSFIKDWRSAFEVDQLVTGKIVAVDPLLNHVQISLK 1300
Cdd:PRK03987     8 EGELVVGTVKEVKDFGAFVTLDeyPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLK 80
S1_Rrp5_repeat_sc10 cd05706
S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1228-1300 3.26e-04

S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240211 [Multi-domain]  Cd Length: 73  Bit Score: 40.70  E-value: 3.26e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1808214898 1228 LKVNDVVRGFVKNVSEKGLFVSLSSNVTAFVRISDLSDSFIKDWRSAFEVDQLVTGKIVAVDPLLNHVQISLK 1300
Cdd:cd05706      1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSLR 73
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 649-716 3.79e-04

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: 40.30  E-value: 3.79e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1808214898  649 GKQAPGTIIKILRAGAIVQFyGDLKAFLPVSEMSEAYIQDPSEHFRIGQTVTVHTINVDAESDKMTVS 716
Cdd:cd05688      2 GDVVEGTVKSITDFGAFVDL-GGVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68
S1_Rrp5_repeat_sc10 cd05706
S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1047-1120 4.21e-04

S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240211 [Multi-domain]  Cd Length: 73  Bit Score: 40.31  E-value: 4.21e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1808214898 1047 LTIGSSHIAFVNNISDNCVWVNLSPNVRGRIDLMDLSDDVSLLNNVqgNFPVGSAIKVRVKNVDASNNRLDLTA 1120
Cdd:cd05706      1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPY--KFKKNDIVRACVLSVDVPNKKIALSL 72
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 1137-1206 6.33e-04

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: 39.95  E-value: 6.33e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1137 GQILPGRVTKVTERHIMVQLSETVSAPVTLTEFSDDYSQANPTVHKKHDVVRVCILDVDAPNKKLVLSLR 1206
Cdd:cd05691      1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIK 70
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 1509-1631 7.45e-04

Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443813 [Multi-domain]  Cd Length: 139  Bit Score: 41.72  E-value: 7.45e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1509 RTGDLDIAgpqsVADFERLLLGQPNNSALWMQYMAFQIGLNEVQKAKDIAERALKtINIREEEekmnIWTALLNLEIEQG 1588
Cdd:COG4783     16 LAGDYDEA----EALLEKALELDPDNPEAFALLGEILLQLGDLDEAIVLLHEALE-LDPDEPE----ARLNLGLALLKAG 86

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 1808214898 1589 NEEKVDEVFKRACQYcDPE--EMHNKLITIYTSTGRHEKADSLFQ 1631
Cdd:COG4783     87 DYDEALALLEKALKL-DPEhpEAYLRLARAYRALGRPDEAIAALE 130
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 832-902 9.31e-04

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: 39.62  E-value: 9.31e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1808214898  832 EGQPVNGFVRHIDGQRVFVEFAG-GLVGLLLKSQMPEEMANTAEFGLRADQSISAKVLATDNQQRRFLVTMK 902
Cdd:cd05708      2 VGQKIDGTVRRVEDYGVFIDIDGtNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLK 73
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 555-629 1.05e-03

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: 39.19  E-value: 1.05e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1808214898  555 GQVVKGKVEKVlitaKGQGAVVvNLAEGISGLASEAHIADVHLQHPEKKFKEGMAVTARVLSTDSEKRqIRLTLK 629
Cdd:cd05692      1 GSVVEGTVTRL----KPFGAFV-ELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARGR-ISLSIK 69
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 1140-1204 1.23e-03

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: 38.90  E-value: 1.23e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1808214898 1140 LPGRVTKVTERHIMVQLSETVSAPVTLTEFSDDYSQANPTVHKKHDVVRVCILDVDAPNKKLVLS 1204
Cdd:cd00164      1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 836-900 1.30e-03

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: 38.90  E-value: 1.30e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1808214898  836 VNGFVRHIDGQRVFVEFAGGLVGLLLKSQMPEEMANTAEFGLRADQSISAKVLATDNQQRRFLVT 900
Cdd:cd00164      1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
rpsA PRK13806
30S ribosomal protein S1; Provisional
 553-643 1.99e-03

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 42.79  E-value: 1.99e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  553 KVGQVVKGKVEKVLitakgQGAVVVNLAEGISGLASEAHIADVHLQHPEKKFKEGMAVTARVLSTDSEKRQIRLT-LKKT 631
Cdd:PRK13806   378 APGTTVTGTVEKRA-----QFGLFVNLAPGVTGLLPASVISRAGKPATYEKLKPGDSVTLVVEEIDTAKRKISLApAGAA 452

                           90
                   ....*....|..
gi 1808214898  632 LVNSEAPVWSKY 643
Cdd:PRK13806   453 GSGADDDDWKQF 464
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 1053-1119 2.39e-03

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: 38.13  E-value: 2.39e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1808214898 1053 HIAFVNNISDNCVWVNLSPNVRGRIDLMDLSDDVSLlnNVQGNFPVGSAIKVRVKNVDASNNRLDLT 1119
Cdd:cd00164      1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVK--DPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 725-850 2.40e-03

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: 42.34  E-value: 2.40e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  725 AAMTEAYDLLKVGSVVKGSVSEKSEKTITVELeGSGIKGIIRIGQLTDGSEKKDqssmkrIRVGQTLEdLVVLSKSDKKP 804
Cdd:COG0539      7 ELLEESLKELKEGDIVKGTVVSIDDDEVLVDI-GYKSEGIIPLSEFSDEPGELE------VKVGDEVE-VYVEKVEDGEG 78

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1808214898  805 LLTLTNKptLLQAAKA-GSLVAKYEdlrEGQPVNGFVRH---------IDGQRVFV 850
Cdd:COG0539     79 EIVLSKK--KADREKAwEELEEAFE---NGEPVEGKVKGvvkgglivdIGGVRAFL 129
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 676-716 3.13e-03

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: 37.98  E-value: 3.13e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 1808214898  676 LPVSEMSEAYIQDPSEHFRIGQTVTVHTINVDAESDKMTVS 716
Cdd:cd05685     28 IHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 849-902 3.18e-03

S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240203 [Multi-domain]  Cd Length: 70  Bit Score: 37.98  E-value: 3.18e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1808214898  849 FVEFAGGLVGLLLKSQMPEEMANTAEFGLRADQSISAKVLATDNQQRRFLVTMK 902
Cdd:cd05698     17 IVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 1232-1290 3.59e-03

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: 37.65  E-value: 3.59e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1808214898 1232 DVVRGFVKNVSEKGLFVSLSSNVTAFVRISDLSDSFIKDWRSAFEVDQLVTGKIVAVDP 1290
Cdd:cd05692      2 SVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDA 60
S1_Rrp5_repeat_hs11_sc8 cd05702
S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 1055-1106 3.63e-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: 37.57  E-value: 3.63e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1808214898 1055 AFVNNISDNCVWVNLSPNVRGRIDLMDLSDDVSLLNNVQGNFPVGSAIKVRV 1106
Cdd:cd05702      6 AKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARV 57
S1_Rrp5_repeat_hs1_sc1 cd05693
S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1228-1300 3.68e-03

S1_Rrp5_repeat_hs1_sc1: 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 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240198 [Multi-domain]  Cd Length: 100  Bit Score: 38.74  E-value: 3.68e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1228 LKVNDVVRGFVKNVSEKGLFVSLSSNVTAFVRISDLSDSF-------------------IKDWRSAFEVDQLVTGKIVAV 1288
Cdd:cd05693      1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYterleeldeeseeeddeeeLPDLEDLFSVGQLVRCKVVSL 80

                           90
                   ....*....|....*
gi 1808214898 1289 DPLL---NHVQISLK 1300
Cdd:cd05693     81 DKSKsgkKRIELSLE 95
S1_Rrp5_repeat_hs14 cd05705
S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 552-627 3.81e-03

S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240210 [Multi-domain]  Cd Length: 74  Bit Score: 37.76  E-value: 3.81e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1808214898  552 VKVGQVVKGKVEKVlitaKGQGaVVVNLAEGISGLASEAHIADVHLQHP---EKKFKEGMAVTARVLSTDSEKRQIRLT 627
Cdd:cd05705      1 IKEGQLLRGYVSSV----TKQG-VFFRLSSSIVGRVLFQNVTKYFVSDPslyNKYLPEGKLLTAKVLSVNSEKNLVELS 74
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 551-638 3.86e-03

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


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 39.39  E-value: 3.86e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898  551 DVKVGQVVKGKVEKvlITAKGqgaVVVNLAEGISGLA--SE-AH--IADVHlQHpekkFKEGMAVTARVLSTDsEKRQIR 625
Cdd:COG1098      2 SIEVGDIVEGKVTG--ITPFG---AFVELPEGTTGLVhiSEiADgyVKDIN-DY----LKVGDEVKVKVLSID-EDGKIS 70

                           90
                   ....*....|...
gi 1808214898  626 LTLKKTLVNSEAP 638
Cdd:COG1098     71 LSIKQAEEKPKRP 83
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 1314-1396 3.86e-03

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 42.01  E-value: 3.86e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1314 FNDLKPRQVVTGKVRKVEDFGVFIvvdNSSNVSGLCHRSEIADQKVEDVRKLYEEGDAVKAIVLKIDQEKRRVNFGLKas 1393
Cdd:PRK12269   488 FNSVHIEDSVSGVVKSFTSFGAFI---DLGGFDGLLHVNDMSWGHVARPREFVKKGQTIELKVIRLDQAEKRINLSLK-- 562


                   ...
gi 1808214898 1394 YFQ 1396
Cdd:PRK12269   563 HFQ 565
S1_RPS1_repeat_ec1_hs1 cd05687
S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 1137-1206 4.14e-03

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


Pssm-ID: 240192 [Multi-domain]  Cd Length: 70  Bit Score: 37.51  E-value: 4.14e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1137 GQILPGRVTKVTERHIMVQLSETVSAPVTLTEFSDDYSQANPTVHKKHDVVRVCILDVDAPNKKLVLSLR 1206
Cdd:cd05687      1 GDIVKGTVVSVDDDEVLVDIGYKSEGIIPISEFSDDPIENGEDEVKVGDEVEVYVLRVEDEEGNVVLSKR 70
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 1060-1119 4.88e-03

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


Pssm-ID: 240202 [Multi-domain]  Cd Length: 69  Bit Score: 37.22  E-value: 4.88e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1808214898 1060 ISDNCVWVNLSPNVRGRIDLMDLSDdvSLLNNVQGNFPVGSAIKVRVKNVDASNNRLDLT 1119
Cdd:cd05697     11 LRPSGIFVKLSDHIKGLVPPMHLAD--VRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLT 68
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 649-712 5.23e-03

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


Pssm-ID: 240202 [Multi-domain]  Cd Length: 69  Bit Score: 37.22  E-value: 5.23e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1808214898  649 GKQAPGTIIKILRAGAIVQFYGDLKAFLPVSEMSEAYIQDPSEHFRIGQTVTVHTINVDAESDK 712
Cdd:cd05697      1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKR 64
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 654-707 5.96e-03

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 41.57  E-value: 5.96e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1808214898  654 GTIIKILRAGAIVQFYGDLKAFLPVSEMSEAYIQDPSEHFRIGQTVTVHTINVD 707
Cdd:PRK11824   627 GKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEID 680
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 1137-1205 6.18e-03

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


Pssm-ID: 240202 [Multi-domain]  Cd Length: 69  Bit Score: 37.22  E-value: 6.18e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1808214898 1137 GQILPGRVTKVTERHIMVQLSETVSAPVTLTEFSDDYSQaNPTvhKKH---DVVRVCILDVDAPNKKLVLSL 1205
Cdd:cd05697      1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLK-HPE--KKFkpgLKVKCRVLSVEPERKRLVLTL 69
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 1232-1299 6.24e-03

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


Pssm-ID: 240202 [Multi-domain]  Cd Length: 69  Bit Score: 36.83  E-value: 6.24e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1808214898 1232 DVVRGFVKNVSEKGLFVSLSSNVTAFVRISDLSDSFIKDWRSAFEVDQLVTGKIVAVDPLLNHVQISL 1299
Cdd:cd05697      2 QVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL 69
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 1128-1205 6.50e-03

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: 37.57  E-value: 6.50e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1808214898 1128 PTKIQDLSAGQILPGRVTKVTERHIMVQLSETVSAPVTLTEFSDDYsQANPTVH-KKHDVVRVCILDVDAPNKKLVLSL 1205
Cdd:cd04461      6 PTNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEF-VTDPSFGfKKGQSVTAKVTSVDEEKQRFLLSL 83
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 737-792 7.91e-03

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


Pssm-ID: 240196 [Multi-domain]  Cd Length: 73  Bit Score: 36.86  E-value: 7.91e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1808214898  737 GSVVKGSVSEKSEKTITVELeGSGIKGIIRIGQLTDgsEKKDQSSmKRIRVGQTLE 792
Cdd:cd05691      1 GSIVTGKVTEVDAKGATVKL-GDGVEGFLRAAELSR--DRVEDAT-ERFKVGDEVE 52
S1_pNO40 cd05686
S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function ...
 1321-1391 8.82e-03

S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.


Pssm-ID: 240191 [Multi-domain]  Cd Length: 73  Bit Score: 36.69  E-value: 8.82e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1808214898 1321 QVVTGKVRKVEDFGVFIVVDNSSNvSGLCHRSEIADQKVEDVRKLYEEGDAVKAIVLKIdQEKRRVNFGLK 1391
Cdd:cd05686      5 QIFKGEVASVTEYGAFVKIPGCRK-QGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGR-EMKDKMKLSLS 73
 
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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